Introduction (11 August 2011)

1-1

General Atomic and Molecular Electronic Structure System GAMESS User's Guide Department of Chemistry Iowa State University Ames, IA 50011 literature citations: "General Atomic and Molecular Electronic Structure System" M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery J.Comput.Chem. 14, 1347-1363(1993) doi:10.1002/jcc.540141112 "Advances in electronic structure theory: GAMESS a decade later" M.S.Gordon, M.W.Schmidt Chapter 41, pp 1167-1189, in "Theory and Applications of Computational Chemistry, the first forty years" C.E.Dykstra, G.Frenking, K.S.Kim, G.E.Scuseria, editors Elsevier, Amsterdam, 2005. http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Graphical display of results is possible using MacMolPlt, a back end visualizer, which can be downloaded freely at the web site above. Avogadro, a program for molecule building and input creation can be linked to from the web site above. Both programs run on all common desktop platforms: MAC OS X, Linux, or Windows. Movies showing how to use GAMESS and a simple batch queue GamessQ on desktop platforms, and other information about what GAMESS can do are at Jan Jensen's blog, http://molecularmodelingbasics.blogspot.com

Introduction

1-2

Contents of this manual: Section Section Section Section Section Section 1 2 3 4 5 6 INTRO.DOC INPUT.DOC TESTS.DOC REFS.DOC PROG.DOC IRON.DOC Overview Input Description Input Examples Further Information Programmer's Reference Hardware Specifics

Contents of Section 1: Capabilities ____________________________________________________________ 3 History of GAMESS_____________________________________________________ 7 Distribution Policy _____________________________________________________ 23 Input Philosophy ______________________________________________________ 24 Input Checking________________________________________________________ 28 Program Limitations ___________________________________________________ 29 Restart Capability______________________________________________________ 30

Introduction

1-3

Capabilities
A wide range of quantum chemical computations are possible using GAMESS, which 1. Calculates RHF, UHF, ROHF, GVB, or MCSCF selfconsistent field molecular wavefunctions. 2. Calculates the electron correlation energy correction for these SCF wavefunctions using Density Functional Theory (DFT), Configuration Interaction (CI), Many Body Perturbation Theory (MP2), coupled-cluster (CC) or Equation of Motion CC (EOM-CC) methodologies. (see summary table below). 3. Calculates semi-empirical MNDO, AM1, or PM3 models using RHF, UHF, ROHF, or GVB wavefunctions. 4. Calculates analytic energy gradients for any of the SCF or DFT wavefunctions, closed or open shell MP2, or closed shell reference-based CI. 5. Optimizes molecular geometries using the energy gradient, using internal or Cartesian coordinates. 6. Searches for saddle points (transition states) on the potential energy surface. 7. Computes the energy hessian, and thus normal modes, vibrational frequencies, and IR intensities. Raman activities are a follow-up option. 8. Obtains anharmonic vibrational frequencies and intensities (fundamentals or overtones). 9. Traces the intrinsic reaction path from the saddle point towards products, or back to reactants. 10. Traces gradient extremal curves, which may lead from one stationary point such as a minimum to another, which might be a saddle point. 11. Follows the dynamic reaction coordinate, a classical mechanics trajectory on the potential energy surface. This is also known as "direct dynamics". 12. Computes excited state energies, wavefunctions, and transition dipole moments at various levels:

Introduction a. SCF (e.g. ROHF or MCSCF) b. CIS (RHF plus single excitations) c. much more general CI functions d. time dependent DFT (or TDHF) e. Equation of Motion-Coupled Cluster with analytic gradients for SCF, CIS, TD-DFT and GUGA CI. 13. Searches for the minimum energy crossing point between two intersecting potential energy surfaces. 14. Evaluates relativistic effects, including a. scalar corrections, via infinite order two component, or 2nd or 3rd order Douglas-Kroll transformations. Gradients are available. b. spin-orbit coupling matrix elements and the resulting spin-mixed wavefunctions.

1-4

15. Evaluates the static linear polarizability and the first and second order hyperpolarizabilities for all wavefunctions, by applying finite electric fields. 16. Evaluates both the static and frequency dependent polarizabilities for various non-linear optical processes, by analytic means, for RHF wavefunctions. Nuclear derivatives of the polarizabilities lead to analytic Raman and hyperRaman spectra, also for RHF. Imaginary frequency dependent polarizabilities can also be obtained, again for RHF only. 17. Obtains localized orbitals by the Foster-Boys, Edmiston-Ruedenberg, or Pipek-Mezey methods, with optional SCF or MP2 energy analysis of the LMOs. 18. Calculates the following molecular properties: a. dipole, quadrupole, and octupole moments b. electrostatic potential c. electric field and electric field gradients d. electron density and spin density e. Mulliken and Lowdin population analysis f. virial theorem and energy components g. Stone's distributed multipole analysis 19. Models solvent effects by discrete particles a. effective fragment potentials (EFP) or by a continuum b. polarizable continuum model (PCM) c. surface and simulation of volume polarization for electrostatics (SS(V)PE)

Introduction d. conductor-like screening model (COSMO) e. self-consistent reaction field (SCRF) allowing for EFP and PCM to be combined. 20. Performs all-electron calculations based on the Fragment Molecular Orbital (FMO) method. 21. Models the formation of aperiodic polymers with the Elongation Method. 22. Perform QM/MM style HF, DFT, GVB, MCSCF, MP2 and TDDFT calculations, using the integrated QuanPol program. 23. When combined with the plug-in TINKER molecular mechanics program, performs Surface IMOMM (SIMOMM) or IMOMM QM/MM type simulations. Download from http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html 24. When combined with the plug-in NEO program (Nuclear Electron Orbitals), performs quantum mechanics computations of nuclear structure. NEO's code is included with GAMESS source distributions, see the directory ~/gamess/qmnuc. 25. When combined with the plug-in VB2000 program, performs valence bond calculations. See http://www.scinetec.com/~vb for more information. 26. When combined with the plug-in XMVB program, performs valence bond calculations. Please contact Professor Wei Wu of Xiamen University for more information, weiwu@xmu.edu.cn, and see also http://ctc.xmu.edu.cn/xmvb/index.html.

1-5

27. When combined with the plug-in NBO program, performs Natural Bond Order analyses. This program is available at http://www.chem.wisc.edu/~nbo5, for a modest license fee. Many of these calculations may be performed in parallel!

Introduction A quick summary of the current program capabilities is given below: SCFTYP= RHF ROHF UHF GVB MCSCF -------------SCF energy CDFpEP CDFpEP CD-pEP CD-pEP CDFpEP SCF analytic gradient SCF analytic Hessian MP2 energy MP2 gradient CI energy CI gradient CC energy EOMCC excitations CDFpEP CD-pEP CD-pEP CD-pEP CDFpEP CD-p-- CD-p-- ------ CD-p-- -D-p-CDFpEP CDFpEP CD-pEP ------ CD-pEP CDFpEP -D-pEP CD-pEP ------ -----CDFp-- CD-p-- ------ CD-p-- CD-p-CD---- ------ ------ ------ -----CDFp-- CDF--- ------ ------ -----CD---- ------ ------ ------ ------

1-6

semi-empirical models: DFT energy DFT gradient TD-DFT energy TD-DFT gradient MOPAC energy MOPAC gradient CDFpEP CD-pEP CD-pEP CDFpEP CD-pEP CD-pEP CDFpEP ------ CD-p-CDFpEP ------ -----yes yes yes yes yes yes n/a n/a n/a n/a yes no n/a n/a n/a n/a n/a n/a

C= conventional storage of AO integrals on disk D= direct evaluation of AO integrals whenever needed F= Fragment Molecular Orbital methodology is enabled. "F" pertains to the gas phase; for FMO with PCM or EFP there are further restrictions not specified here. p= parallel execution E= Effective Fragment Potential discrete solvation P= Polarizable Continuum Model continuum solvation Numerical gradients and fully or partly numerical Hessians are available for any energy or gradient in this table.

Introduction

1-7

History of GAMESS
GAMESS was put together from several existing quantum chemistry programs, particularly HONDO, by the staff of the National Resources for Computations in Chemistry. The NRCC project (1 Oct 77 to 30 Sep 81) was funded by NSF and DOE, and was limited to the field of chemistry. The NRCC staff added new capabilities to GAMESS as well. Besides providing public access to the code on the CDC 7600 at the site of the NRCC (the Lawrence Berkeley Laboratory), the NRCC made copies of the program source code (for a VAX) available to users at other sites. The original citation for this program was M. Dupuis, D. Spangler, and J. J. Wendoloski National Resource for Computations in Chemistry Software Catalog, University of California: Berkeley, CA (1980), Program QG01 This manual is a completely rewritten version of the original documentation for GAMESS. Any errors found in this documentation, or the program itself, should not be attributed to the original NRCC authors. The present version of the program has undergone many changes since the NRCC days. This occurred at North Dakota State University from 1982 up to 1992, and now continues at Iowa State University to the present. It would be difficult to overestimate the contributions Michel Dupuis has made to this program, in its original form, and since. This includes the donation of code from HONDO, and numerous suggestions for other improvements. The continued development of this program from 1982 on can be directly attributed to the nurturing environment provided by Professor Mark Gordon, at North Dakota State and then Iowa State University. It is important to also single out Professor Emeritus Klaus Ruedenberg of Iowa State University, whose group is responsible for the determinant technology lying underneath the MCSCF programs in GAMESS. Even when our students and postdocs leave Iowa State, many continue to make contributions to GAMESS. In addition, we have also included many codes developed in

Introduction

1-8

other groups over the years, so that the list of authors of GAMESS is actually much longer than the author list of the 1993 J. Comput. Chem. article. A complete list of authors may be found at the top of every log file from a GAMESS run. Funding of many of the developments in GAMESS from 1982 to the present time was, and is provided by the Air Force Office of Scientific Research. This has always been the backbone of the support for GAMESS. In late 1987, NDSU and IBM reached a Joint Study Agreement. One goal of this JSA was the development of a version of GAMESS that was vectorized for the IBM 3090's Vector Facility, which was accomplished by the fall of 1988. This phase of the JSA led to a program which is also considerably faster in scalar mode as well. The second phase of the JSA, which ended in 1990, was to enhance GAMESS' scientific capabilities. These additions include analytic hessians, ECPs, MP2, spin-orbit coupling and radiative transitions, and so on. Everyone who uses the current version of GAMESS owes thanks to IBM in general, and Michel Dupuis of IBM Kingston in particular, for their sponsorship of GAMESS during this JSA. During the first six months of 1990, Digital awarded a Innovator's Program grant to NDSU. The purpose of this grant was to ensure GAMESS would run on the DECstation, and to develop graphical display programs. As a result, the companion programs MOLPLT, PLTORB, DENDIF, and MEPMAP were modernized for the X-windows environment, and interfaced to GAMESS. These programs now run under the X-windows environments, and many other X-windows environments as well. The ability to visualize the molecular structures, orbitals, and electrostatic potentials is a significant improvement. These graphics programs eventually formed the nucleus of the program MacMolPlt. Parallelization of GAMESS began in 1991, with most of the early work and design strategy done by Theresa Windus. This benefited greatly from the ARPA sponsorship of the Touchstone Delta experimental computer. Message passing used the TCGMSG library of Robert Harrison in the early years, up to 1999. Parallelization of GAMESS has turned into a multi-year process as detailed below. The DoD awarded a CHSSI grant to ISU in 1996 to extend that scalability of existing parallel methods, and more importantly develop new techniques. This brought Graham

Introduction

1-9

Fletcher on board as a postdoc, and led to the introduction of the Distributed Data Interface (DDI) programming model. The first version of DDI, written at ISU, was used from June 1999 to May 2004. Ryan Olson, with help from Alistair Rendell of Australian National University, rewrote DDI entirely in C, adding optimizations for the commonplace SMP nodes, especially System V memory use. Dmitri Fedorov of the National Institute for Advanced Industrial Science and Technology added the concept of subgroups at the same time. This combined new version of DDI has been the message passing support layer for GAMESS since May 2004. The DoE awarded a SciDAC grant to ISU in 2002 to enable additional scientific capabilities in GAMESS, with emphasis on scalable algorithms. To date, this has supported parallelization of the EFP solvent molecule, and new codes for analytic MCSCF Hessians, and open shell MP2 gradients. Some summary of these various grants and initiatives is in order. The 1982 version of GAMESS contained roughly 80,000 lines of FORTRAN code, implementing the present five wavefunction types, and analytic nuclear gradients for each, enabling geometry optimization and transition state search, and numerically differentiated frequencies. The only electron correlation method available was GUGA based CI computation. All computations were in the gas phase. By 2005, GAMESS had grown to roughly 650,000 lines of FORTRAN. Analytic hessian computation is now routine at the SCF levels. Electron correlation is now treated with direct determinant CI codes, and in addition perturbation theory, density functional, or coupled cluster methods (with analytic gradients for some of these) may be used. New AO integral codes, including effective core potentials are used, and direct AO integral computation is possible. Discrete and continuum models for solvated molecules are provided, and there is an associated program for surface chemistry. Additional chemistry runs are provided, such as reaction paths and dynamical trajectories, IR and Raman spectra, anharmonic vibrational corrections, static or frequency dependent polarizabilities, transition moments, and spin-orbit couplings. Scalar relativistic corrections can be applied to any computation. Improvements or complete rewrites have been made for geometry searches, SCF convergers, internal coordinates, ease of use, available basis sets, and so on. The majority of these computations can be run on parallel computers. The rest of this section gives more specific credit

Introduction to the sources of various parts of the program. * * * *

1-10

GAMESS is a synthesis, with many major modifications, of several programs. A large part of the program originate from HONDO 5. For sp basis functions, modified Gaussian76 s,p,L shell code is used. Both the sp rotated axis integrals and the sp gradient packages were modified in 2001 by Jose Maria Sierra of Synstar Computer Services in Madrid, Spain. The sp integral routines were modified in 2003 and in 2004 by Kazuya Ishimura of the Institute for Molecular Science to use McMurchie-Davidson quadratures for the basic axes-1 integrals, after which they are rotated ala Hehre/Pople. For spd functions, the s,p,d,L shell rotated axis code written by Kazuya Ishimura of the Institute for Molecular Science is used. For integral quartets with higher angular momentum, the s,p,d,f,g Electron Repulsion Integral Calculator (ERIC) code written by Graham Fletcher at NASA/Eloret in 2004 is used, provided the total angular momentum of the quartet is no more than 5. Both rotated axis codes, the sp gradient code, and ERIC share a common, fully accurate evaluation of Fm(t) integrals, and have been tested for very small (down to 0.005) and very large (1.0d+11) Gaussian exponents. The Rys polynomial program of Michel Dupuis is used to handle the general integral case: s,p,d,f,g, or L shells. HONDO 1e- and 2e- Rys routines were redimensioned to handle up to g shells by Theresa Windus at North Dakota State University in 1991. Any sp gradient integrals are done with Jose Sierra's modified version of the Gaussian80 code due to Schlegel. The spdfg gradient package consists of Michel Dupuis' Rys Polynomial code, and was adapted into GAMESS by Brett Bode at Iowa State University in 1994. The use of quantum fast multipole methods for avoiding long range integral evaluation in large molecules was programmed by Cheol Choi at Iowa State and at Kyungpook National University, and included in GAMESS in 2001. The ECP code goes back to Louis Kahn, with gradient modifications originally made by K.Kitaura, S.Obara, and K.Morokuma at IMS in Japan. The code was adapted to HONDO by Stevens, Basch, and Krauss, from whence Kiet Nguyen adapted it to GAMESS at NDSU. Modifications for f functions were made by Drora Cohen and Brett Bode. This

Introduction

1-11

code was completely rewritten to use spdfg basis sets, to exploit shell structure during integral evaluation, and to add the capability of analytic second derivatives by Brett Bode at ISU in 1997-1998. Jose Sierra of Synstar removed the last few bugs from this in 2003. The Model Core Potential (MCP) codes originate from the University of Alberta and the University of Kyushu. MCP energy code was interfaced to GAMESS in 2003 by Mariusz Klobukowski (UofA). Many model core potentials, and their associated valence basis sets, were added as a basis library by Mariusz in 2005. Hirotoshi Mori and Eisaku Miyoshi (KyuDai) developed the nuclear gradient code for MCP with the assistance of a JSPS grant, and this code was included in GAMESS in March 2007. The ZFK family of model core potentials for p-block elements was added to GAMESS by Toby Zeng in April 2010. Changes in the manner of entering the basis set, and the atomic coordinates (including Z-matrix forms) are due to Jan Jensen at North Dakota State University. The direct SCF implementation was done at NDSU, guided by a pilot code for the RHF case by Frank Jensen. The UHF code was taught to do high spin ROHF by John Montgomery at United Technologies, who extended DIIS use to ROHF and the one pair GVB case. The GVB code is a heavily modified version of GVBONE. The SCF for Molecular Interactions option was added to GAMESS in 1997 by Antonino Famulari, during a summer visit from the University of Milan. This two fragment code was replaced with a multi-fragment code from Maurizio Sironi of the University of Milan in 2004. The Direct Inversion in the Iterative Subspace (DIIS) convergence procedure was implemented by Brenda Lam (then at the University of Houston) in 1986, for RHF and UHF functions. Additional GVB-DIIS cases were programmed by Galina Chaban at ISU. The approximate second order SCF converger was implemented by Galina Chaban at Iowa State University in 1995, and was provided for RHF, ROHF, GVB, and MCSCF cases. The FULLNR and FOCAS MCSCF convergers were contributed by Michel Dupuis from his HONDO program. A parallel implementation of the FULLNR converger was written by Graham Fletcher at Eloret in 2002. The Jacobi orbital rotation scheme for MCSCF orbital optimization was

Introduction written by Joe Ivanic and Klaus Ruedenberg at Iowa State University in 2001.

1-12

The Ames Laboratory determinant full CI code was written by Joe Ivanic and Klaus Ruedenberg. As befits code written by an Australian living in Iowa, it was interfaced to GAMESS during an extremely cordial visit to Australia National University in January 1998. An update by Joe in October 2000 exploits Abelian point group symmetry. A general CI program based on selected determinants was added by Joe and Klaus in July 2001. After moving from Ames Laboratory at ISU to the Advanced Biomedical Computing Center of the National Cancer Institute-Frederick, Fort Detrick, Joe wrote a determinant based program for second order CI, in 2002. In early 2003, Joe added the Occupation Restricted Multiple Active Space determinant CI program, again written at NCI. The GUGA CI is based on Brooks and Schaefer's unitary group program which was modified to run within GAMESS, using a Davidson eigenvector method written by Steve Elbert. Programming of the GUGA analytic CI gradient was done by Simon Webb in 1996 at Iowa State University. The CIS gradient program was written in 2003 by Simon Webb of the Advanced Biomedical Computing Center of the National Cancer Institute in Frederick. Transition moments were added by Simon and Pooja Arora in June 2005. The sequential MP2 and UMP2 energy code was adapted from HONDO in 1994 by Nikita Matsunaga at ISU. Nikita programmed the RMP open shell energy in 1992. The ZAPT open shell energy was programmed by Rob Bell in 1999. The serial closed shell MP2 gradient code is also from HONDO, and was adapted to GAMESS in 1995 by Simon Webb and Nikita Matsunaga. In 1996, Simon Webb added the frozen core gradient option at ISU. The parallel closed shell MP2 code is a descendant of work for GAMESS-UK by Graham Fletcher, Alistair Rendell, and Paul Sherwood at Daresbury. This was adapted to GAMESS at ISU by Graham Fletcher in 1999. Serial and parallel codes for the spin unrestricted UMP2 gradient were programmed by Christine Aikens at ISU, in 2002. Christine Aikens added a parallel spin-restricted open shell (ZAPT) gradient code in 2005. Programs for parallel closed shell MP2 energy (2006) and gradient (2007) using disk storage were written by Kazuya Ishimura at the Institute for Molecular Science (IMS) in Okazaki. The

Introduction

1-13

parallel Resolution of the Identity MP2 program by Michio Katouda, also from IMS, was added in 2010. Credits for multiconfigurational PT follow. Haruyuki Nakano, then at the University of Tokyo, interfaced his multireference MCQDPT code (based on CSFs) to GAMESS during a 1996 visit to ISU. Parallelization of the Tokyo multireference PT code was done by Hiroaki Umeda at Mie University, and included into GAMESS in 2001. A determinant based equivalent to MRMP/MCQDPT was programmed in 2005 by Joe Ivanic of the National Cancer Institute, this is MRMP=MRPT. In 2008, Haruyuki Nakano of the University of Kyushu contributed a general MCSCF reference quasi-degenerate perturbation theory code, MRMP=GMCPT, which is capable of treating non-CAS references, including those of the ORMAS type. The grid-free DFT energy and gradient code was written by Kurt Glaesemann at Iowa State University, starting from the code of Almlof and Zheng, adding four center overlap integrals, a gradient program, developing the auxiliary basis option, and adding some functionals. This was included in GAMESS in 1999. The grid based DFT program was introduced in 2001 at the University of Tokyo, by Takao Tsuneda, Muneaki Kamiya, Susumu Yanagisawa, and Dmitri Fedorov. The original program is from Nevin Oliphant, Hideo Sekino, and Rod Bartlett at QTP. Many improvements were made to this early program at U. Tokyo: using point group symmetry, switching from coarse to fine grids, functional development, and parallelization. Sarom Sok at ISU added many new functionals in 2007, 2008, and 2009, some with the help of Huub van Dam's density functional repository. Sarom added the Truhlar group's meta-GGA M06 and M08 functionals in 2008 and 2009, using source code from U.Minnesota. Roberto Peverati of the University of Zurich added Grimme's dispersion correction in 2008. Roberto added "wB97" range separated GGA, "B97" style GGA and metaGGA, and B2-PLYP in 2009. Federico Zahariev at ISU included the TPSS family of meta-GGAs in 2008 and 2009. Kiet Nguyen at Wright-Patterson AFB added CAM-B3LYP in 2009. The HPTi project (Jean-Philippe Blaudeau, Shawn Brown, Mike Lasinksi, Nick Romero, Anthony Yau) enabled the use of Lebedev or Standard Grid-1 grids in April 2008, and Janssen's grids in May 2009. The time dependent DFT program originated in the group of Takao Tsuneda at University of Tokyo, and was included into GAMESS in the fall of 2006 by Mahito Chiba at AIST in

Introduction

1-14

Tsukuba. He also included the "long range correction" option (aka "range separation") for both ground and excited states. The analytic TDDFT gradient for singlet excited states from a closed shell reference was added by Mahito Chiba in August 2007. Mahito Chiba, in collaboration with Dmitri Fedorov, also developed FMO functionality in TDDFT energies. The TDDFT energy for UHF ground states was added by Soohaeng Yoo at Iowa State, in February 2008. Tamm/Dancoff approximation coding was done by Federico Zahariev at ISU in 2010. The HPTi project parallelized the closed shell TDDFT energy and gradient programs in April 2008. Sarom Sok and Federico Zahariev have developed higher derivatives for many functionals, allowing them to be used in TDDFT energies and gradients. TD-DFT solvation effects include EFP1 discrete solvation, added to the closed shell TD-DFT excitation energies in 2008 by Soohaeng Yoo, and to its gradient in 2010 by Noriyuki Minezawa at ISU. C-PCM solvent effects on TD-DFT closed shell excitation energies were added by Mahito Chiba in December 2008, with PCM modifications to this gradient by Yali Wang and Hui Li in November 2009. The combined TDDFT/EFP/PCM solvation model was finished in November 2010 by Nandun Thellamurege and Hui Li at U. Nebraska. Incorporation of enough MOPAC version 6 routines to run PM3, AM1, and MNDO calculations from within GAMESS was done by Jan Jensen at North Dakota State University. The numerical force constant computation and normal mode analysis was adapted from Andy Komornicki's GRADSCF program, with decomposition of normal modes in internal coordinates written at NDSU by Jerry Boatz. The code for the analytic computation of RHF Hessians was contributed by Michel Dupuis of IBM from HONDO 7. High and low spin restricted open shell CPHF code was written at NDSU in 1989. The TCSCF CPHF code is the result of a collaboration between NDSU and John Montgomery, then at United Technologies, in 1990. Analytic IR intensities and polarizabilities (during hessian runs) were programmed by Simon Webb at ISU in 1995. Analytic Hessians for MCSCF wavefunctions based on determinants were coded, and enabled for parallel execution, by Tim Dudley at ISU, and included into GAMESS in April 2004, with a souped-up version added in March 2006.

Introduction Code for Raman intensity prediction was written at Tokyo Metropolitan University in April 2000.

1-15

The vibrational SCF and MP2 anharmonic frequency code for fundamental modes and overtones was written by Galina Chaban, Joon Jung, and Benny Gerber at U.California-Irvine and Hebrew University of Jerusalem, and included in GAMESS in 2000. The solver was modified to perform degenerate perturbation theory for more accurate results by Nikita Matsunaga at Long Island University in 2001. Delocalized internal coordinates were implemented by Jim Shoemaker at the Air Force Institute of Technology in 1997, and put online in GAMESS by Cheol Choi at ISU after further improvements in 1998. Most of the geometry search procedures (OPTIMIZE and SADPOINT) were developed by Frank Jensen of the University of Aarhus. These methods are adapted to use GAMESS symmetry, and Cartesian or internal coordinates. Numerical differentiation of the energy to obtain gradients and Hessians which may be used in OPTIMIZE or SADPOINT searches was programmed by Ryan Olson at ISU in 2003. The MEX procedure for searching for minimum energy crossing points between two surfaces was programmed by Jeremy Harvey and Nikita Matsunaga, and finally included into GAMESS in 2006. The non-gradient optimization (so aptly named TRUDGE) was adapted from HONDO 7 by Mariusz Klobukowski at U.Alberta, this may be more interesting for its exponent optimization option. The intrinsic reaction coordinate pathfinder was written at North Dakota State University, and modified later for new integration methods by Kim Baldridge. The Gonzales-Schelegel IRC stepper was incorporated by Shujun Su at Iowa State, based on pilot code from Frank Jensen. The code for the Dynamic Reaction Coordinate was developed by Tetsuya Taketsugu at Ochanomizu U. and U. of Tokyo, and added to GAMESS by him at ISU in 1994. The two algorithms for tracing gradient extremals were programmed by Frank Jensen, now at the University of Aarhus. The program for Monte Carlo generation of trial structures along with a simulated annealing protocol was written by Paul Day at Wright-Patterson Air Force Base.

Introduction

1-16

Modifications to this were made by Pradipta Bandyopadhyay at ISU, and the code was included in 2001. The surface scanning option was implemented by Richard Muller at the University of Southern California. Static polarizabilities for any type of energy value are bases on a code from Henry Kurtz of the University of Memphis. This uses a numerical differentiation based on application of finite electric fields. The program was added in 1992, and was modified by Sanka Ghosh to produce all tensor components in 2005. Henry Kurtz' program for the fully analytic calculation of static and frequency dependent polarizabilities for NLO properties for closed shell systems was included in 1994, based on a MOPAC implementation by Prakashan Korambath at U. Memphis. An extended TDHF package for the analytic computation of static and frequency dependent polarizabilities, and also their nuclear derivatives, plus Raman and hyperRaman spectra prediction was written by Olivier Quinet and Benoit Champagne at the Facultes Universitaires Notre-Dame de la Paix, and coworker Bernard Kirtman at UC-Santa Barbara. Financial support for this was provided by Belgium. This package was added to GAMESS in February 2005. Ivana Adamovic programmed the imaginary frequency polarizability computation for closed shell functions in 2005, at ISU. Edmiston-Ruedenberg energy localization is done with a version of the ALIS program "LOCL", modified at NDSU to run inside GAMESS. Foster-Boys localization is based on a highly modified version of QCPE program 354 by D.Boerth, J.A.Hasmall, and A.Streitweiser. John Montgomery implemented the Pipek/Mezey population localization. The LCD SCF decomposition and the MP2 decomposition were written by Jan Jensen at Iowa State in 1994. Point Determined Charges were implemented by Mark Spackman at the University of New England, Australia. The at Iowa Orbital Peifeng 2009. Morokuma decomposition was implemented by Wei Chen State University, in 1995. The Localized Molecular Energy Decomposition Analysis was implemented by Su and Hui Li at the University of Nebraska in

Introduction

1-17

The radiative transition moment and effective nuclear charge spin-orbit coupling modules were written by Shiro Koseki at North Dakota State University in 1990. The full Breit-Pauli spin-orbit coupling integral package was written by Thomas Furlani. This code was incorporated into GAMESS by Dmitri Fedorov at Iowa State University in 1997, who generalized the spin-orbit coupling matrix element code generously provided by Thomas Furlani (restricted to an active space of two electrons in two orbitals), with assistance from visits to ISU by Thomas Furlani and Shiro Koseki. Dmitri Fedorov has since generalized the full two electron approach to allow for any spins, for more than two spin multiplicities at a time, and a partial treatment of the the two electron terms that runs in time similar to the one electron operator. Space and spin symmetries are exploited to speed up the runs. Dmitri Fedorov programmed the SO-MCQDPT options at the University of Tokyo in 2001. Density matrix calculation for spinorbit coupled states was programmed by Toby Zeng and Mariusz Klobukowski at the University of Alberta, and added to GAMESS in April 2010. Inclusion of relativistic effects by means of the Douglas-Kroll transformation was developed to the third order by Takahito Nakajima and Kimihiko Hirao at the University of Tokyo. It was implemented into GAMESS by Takahito Nakajima and Dmitri Fedorov, including energy, semi-analytic nuclear gradient, and spin-orbit coupling (at the first order, DK1). The program was included with GAMESS in November 2003. Inclusion of relativistic effects by the Relativistic scheme of Elimination of Small Components (RESC) method, was developed by Takahito Nakajima and Kimihiko Hirao at the University of Tokyo. This code was written by Takahito Nakajima and consequently adapted into GAMESS by Dmitri Fedorov, who extended the methodology in March 2000 to the computation of gradients. RESC provides both scalar (spin free) and vector (spin-dependent) relativistic corrections. The Normalized Elimination of Small Components (NESC) was programmed by Dmitri Fedorov at ISU and the University of Tokyo. Special thanks are due to Kenneth Dyall for his assistance in providing check values. Extension of NESC to include gradient computation was also done by Dmitri.

Introduction

1-18

Finally, inclusion of scalar relativstic corrections to an infinite order two-component (IOTC) transformation was added in September 2010, by Maria Barysz of Nicholas Copernicus University. Development of the EFP method began in the group of Walt Stevens at NIST's Center for Advanced Research in Biotechnology (CARB) in 1988. Walt is the originator of this method, and has provided both guidance and some early financial support to ISU for its continued development. Mark Gordon's group's participation began in 1989-90 as discussions during a year Mark spent in the DC area, and became more serious in 1991 with a visit by Jan Jensen to CARB. At this time the method worked for the energy, and gradient with respect to the ab initio nuclei, for one fragment only. Jan has assisted with most aspects of the multi-fragment development since. Paul Day at NDSU and ISU derived and implemented the gradient with respect to fragments, and programmed EFP geometry optimization, from 1992-1994. Wei Chen at ISU debugged many parts of the EFP energy and gradient, developed the code for following IRCs, improved geometry searches, and fitted much more accurate repulsive potentials, from 1995-1996. Simon Webb at ISU programmed the current self-consistency process for the induced dipoles in 1994. The EFP method was sufficiently developed, tested, and described, to be released in September 1996, with an RHF level potential for water. Code for charge penetration was added by Mark Freitag in 2001, and made numerically stabile by Lyuda Slipchenko in 2006. Ivana Adamovic included a DFT level EFP for water in 2002. Parallelization of the EFP codes was done by Heather Netzloff in 2005. The second EFP theory (called EFP2) was begun in 1996 by Jan Jensen, who programmed an analytic formula for the exchange repulsion. Hui Li replaced this with a faster, more accurate code in 2005. Ivana Adamovic programmed a dispersion term for EFP2 in 2005. Hui Li added the charge transfer term for EFP2 in 2005. Two other methods using the EFP model are available. A combination of EFP + PCM energies (an onion-like solution model) was programmed by Pradipta Bandyopadhyay in 2000. The use of EFPs to model biological systems, including a boundary across a covalent bond, was coded at the University of Iowa in 2000, by Jan Jensen, Visvaldas Kairys, and Hui Li.

Introduction

1-19

The SCRF solvent model was implemented by Dave Garmer at CARB, and was adapted to GAMESS by Jan Jensen and Simon Webb at Iowa State University. The COSMO model was developed by Andreas Klamt and Kim Baldridge, starting at the San Diego Supercomputer Center, and later at University of Zurich. It was included into GAMESS by Laura Brovold in March 2000 during a visit to Ames. Subsequent additions were made by Yohann Potier and Roberto Peverati, at the University of Zurich, and included in GAMESS in June 2010. The PCM code originated in the group of Jacopo Tomasi at the University of Pisa. Benedetta Mennucci was instrumental in interfacing the original D-PCM code to GAMESS in 1997, and answering many technical questions about the code, the methodology, and the documentation. In 2000, Benedetta Menucci provided code implementing an improved IEF solver for the PCM surface charges. The changes to implement iterative solution of the PCM equations for large molecules, and to provide an accurate nuclear gradient were carried out by Hui Li and Jan Jensen at the University of Iowa in 2001-2004, along with the parallelization. This included implementation of two new surface tessellation schemes, GEPOL-AS and GEPOL-RT. Hui and Jan also implemented the Conductor-PCM method, and extended the PCM methodology to all types of SCF functions. Hui Li's research group at the University of Nebraska implemented the following improvements: FIXPVA tessellation with smooth switching functions for reliable geometry optimizations (Peifeng Su, 2008), extension of FIXPVA to cavitation, repulsion, and dispersion (2009), heterogenous CPCM (Dejun Si, 2009), closed shell PCM/TDDFT gradients (Yali Wang, 2009), closed shell PCM/MP2 gradients (Dejun Si, 2010), open shell PCM/MP2 gradients (Dejun Si, September 2010), and combined EFP/PCM solvation for all single reference MP2 gradients (Nandun Thellamurege and Dejun Si, November 2010). The SMD modifications to the PCM model are due to Alek Marenich, Junjun Liu, Chang-Guo Zhan, Christopher Cramer, and Don Truhlar at U. Minnesota (November 2010). The Surface and Volume Polarization for Electrostatics continuum solvation model is written by Dan Chipman of Notre Dame University, using several integral routines written by Michel Dupuis for the SVP model included in HONDO. The SVP model was added to GAMESS in June 2005.

Introduction

1-20

The SIMOMM model for surface chemistry is based on the Tinker program of Jay Ponder's group, and is available as a plug-in option. The treatment is QM embedded in a MM background. The coding for this was done by Jim Shoemaker at the Air Force Institute of Technology, and finished by Cheol Ho Choi at ISU. The interface to GAMESS was completed in 1998. The Coupled-Cluster (CC) and Equation of Motion Coupled-Cluster (EOMCC) programs included in GAMESS are due to Piotr Piecuch, Karol Kowalski, Marta Wloch, Jeffrey Gour, and Jesse Lutz of Michigan State University (MSU), and Stanislaw A. Kucharski and Monika Musial of the University of Silesia. In addition to a number of standard CC and EOMCC methods, including the older CCSD, CCSD(T), and EOMCCSD approaches, the CC codes incorporated in GAMESS are capable of performing renormalized (R) and completely renormalized (CR) CCSD[T] and CCSD(T) calculations for the ground state, the ground-state calculations employing the rigorously size extensive completely renormalized noniterative triples CR-CCSD(T)_L = CR-CC(2,3) approach. The combined corrections due to triply and quadruply excited clusters are available in the factorized forms of the CCSD(TQ), renormalized CCSD(TQ), and completely renormalized CCSD(TQ) models. For excited states, completely renormalized EOMCCSD(T) (CR-EOMCCSD(T)) and EOMCR-CC(23) calculations are possible. Electron attachment and detachments (including excitations) are available as IP-EOM and EA-CC methods. The one-body reduced density matrices, dipole moments, transition dipole moments, and oscillator strengths are available at the CCSD and EOMCCSD levels, for RHF. The ground-state CC, R-CC, and CR-CC programs were initially incorporated into GAMESS in May 2002. The excited-state EOMCC and CR-EOMCC programs were incorporated in April 2004. Quadruples corrections and CCSD/EOM-CCSD density matrices were added in June 2005. The CR-CC(2,3) ground-state approach was added in January 2006. Parallel computation of CCSD and CCSD(T) for closed shell references was enabled by Ryan Olson and Jonathan Bentz at Iowa State, in October 2006. Open shell CCSD and CR-CCL based on ROHF reference orbitals was added in May 2007. CR-EOML and IP-EOMCC2/EA-EOMCC2 were included in October 2009, and active triples for IP/EA calculations were finished in September 2010. All of these programs were developed with the support of the US Department of Energy, Office of Basic Energy Sciences, SciDAC Computational Chemistry Program and the Chemical Sciences, Geosciences, and Biosciences Division. Additional support

Introduction

1-21

has been provided by the NSF's ITR program and the Alfred P. Sloan Foundation. The GIAO computation of NMR properties for closed shell molecules was programmed by Mark Freitag at Iowa State University, and included in GAMESS in November 2003. The code for the Fragment Molecular Orbital (FMO) method incorporated and distributed as a part of the standard GAMESS package since May 2004 is being developed at the National Institute of Advanced Industrial Science and Technology (AIST, Japan) by Dmitri Fedorov and Kazuo Kitaura. The FMO method is the successor of the EDA scheme developed by K. Kitaura and K. Morokuma (known in GAMESS as Morokuma-Kitaura decomposition), however, the FMO code was written independently. In GAMESS only the full FMO method is incorporated whereas in the literature one can also find a simplified approach suited for molecular crystals. Since "FMO" is also used to mean "Frontier Molecular Orbitals" and the concept of fragments is also introduced in the EFP method (see above), it is stressed here that the FMO method bears no relation to either of the two methods, that is to say, it is independent of the two, but might be combined with either of them in the future just as EFPs are used in e.g. RHF. The Nuclear Electron Orbital (NEO) plug-in code is developed in the group of Sharon Hammes-Schiffer at Pennsylvania State University, with programming by Simon P. Webb, Tzvetelin Iordanov, Mike Pak, and Chet Swalina. The initial release in 2006 permits HF and MP2 level treatment of nuclear wavefunctions. The elongation method, coded and linked to the standard GAMESS package since April 2006, is a method to mimic the mechanism of the polymerization/copolymerization in experiment. Attacking monomers approach a starting chain, one by one and the electron structure is determined in the interactive region. Thus, one can perform very efficient calculations for the electronic structure of huge random (aperiodic) polymers. The elongation method was first proposed by A. Imamura and Y. Aoki in 1990s. The present code was written by Feng Long Gu, Jacek Korchowiec, Marcin Makowski, and Yuriko Aoki at the Department of Molecular and Material Sciences, Faculty of Engineering Sciences, at Kyushu University. The Divide and Conquer SCF, MP2, and CCSD programs were developed at Waseda University, and were included in GAMESS

Introduction

1-22

in January 2009. The code was written by Masato Kobayashi, Tomoko Akama, and Hiromi Nakai. The quantum chemistry polarizable force field program (QuanPol) was written by Hui Li, Nandun Thellamurege and Dejun Si at the University of Nebraska-Lincoln. These authors finished the initial implementation of QuanPol in August 2011, under an NSF support. Many of the options just mentioned have been programmed to run in parallel, on systems ranging from Linux clusters to high-end parallel systems. The same software interface sits between the quantum chemistry in GAMESS and any such hardware, namely the Distributed Data Interface (DDI). This implements a mechanism for using the memory of the entire system to store the large arrays appearing in quantum chemistry codes. The first version of DDI was due to Graham Fletcher and Mike Schmidt, introduced in 1999. The second version of DDI is due to Ryan Olson of ISU, and Alistair Rendell of the Australian National University, and includes optimizations for SMP systems, along with other improvements for some high end systems. The second version also includes the 'group' scheme, presently used only in FMO jobs. This DDI was introduced into GAMESS in April 2004, with public release in June 2004.

Introduction

1-23

Distribution Policy
To get a copy, please fill out the application form available at http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Persons receiving copies of GAMESS are requested to acknowledge that they will not make copies of GAMESS for use at other sites, or incorporate any portion of GAMESS into any other program, without receiving permission to do so from ISU. If you know anyone who wants a copy of GAMESS, please refer them to the web site above, for the most up to date version available. No large program can ever be guaranteed to be free of bugs, and GAMESS is no exception. If you would like to receive an updated version (fewer bugs, and with new capabilities), simply return to the web site mentioned. You should probably allow a half year or so to pass for enough significant changes to accumulate. The web page always contains a short synopsis of the most recent changes.

Introduction

1-24

Input Philosophy
Input to GAMESS may be in upper or lower case. All input groups begin with a $ sign in column 2, meaning exactly column 2 or else it is not detected, followed by a name identifying that group. There are three types of input groups in GAMESS: 1. A pseudo-namelist, free format, keyword driven group. Almost all input groups fall into this first category. 2. A free format group which does not use keywords. The first line of these will contain only the group name, followed by several lines of positional data usually with no keywords, and a last line containing " $END" only. The only members of this category are $DATA, $ECP, $MCP, $GCILST, $POINTS, $STONE, and the EFP related data $EFRAG, $FRAGNAME, $FRGRPL, and $DAMPGS. 3. Formatted data. This data is NEVER typed by the user, but rather is generated in the correct format by some earlier GAMESS run. Like category 2, the first line contains only the group name, and the last line is a separate $END line. Type 1 groups may have keyword input on the same line as the group name, and the $END may appear anywhere. Because each group has a unique name, the groups may be given in any order desired. In fact, multiple occurrences of category 1 groups are permissible. * * * Most of the groups can be omitted if the program defaults are adequate. An exception is $DATA, which is always required. A typical free format $DATA group is $DATA STO-3G test case for water CNV 2 OXYGEN STO 3 8.0 1.0 -0.758 0.0 0.545

HYDROGEN STO 3

Introduction $END

1-25

Here, position is important. For example, the atom name must be followed by the nuclear charge and then the x,y,z coordinates. Note that missing values will be read as zero, so that the oxygen is placed at the origin. The zero Y coordinate must be given for the hydrogen, so that the final number is taken as Z. The free format scanner code used to read $DATA is adapted from the ALIS program, and is described in the documentation for the graphics programs which accompany GAMESS. Note that the characters ;>! mean something special to the free format scanner, and so use of these characters in $DATA and $ECP should probably be avoided. Because the default type of calculation is a single point (geometry) closed shell SCF, the $DATA group shown is the only input required to do a RHF/STO-3G water calculation. * * * As mentioned, the most common type of input is a namelist-like, keyword driven, free format group. These groups must begin with the $ sign in column 2, but have no further format restrictions. You are not allowed to abbreviate the keywords, or any string value they might expect. They are terminated by a $END string, appearing anywhere. The groups may extend over more than one physical card. In fact, you can give a particular group more than once, as multiple occurrences will be found and processed. We can rewrite the STO-3G water calculation using the keyword groups $CONTRL and $BASIS as $CONTRL SCFTYP=RHF RUNTYP=ENERGY $END $BASIS GBASIS=STO NGAUSS=3 $END $DATA STO-3G TEST CASE FOR WATER Cnv 2 Oxygen Hydrogen $END 8.0 1.0 0.0 -0.758 0.0 0.0 0.0 0.545

Keywords may expect logical, integer, floating point, or string values. Group names and keywords never exceed 6 characters. String values assigned to keywords never

Introduction exceed 8 characters. separate items: Spaces or commas may be used to

1-26

$CONTRL MULT=3 SCFTYP=UHF,TIMLIM=30.0 $END Floating point numbers need not include the decimal, and may be given in exponential form, i.e. TIMLIM=30, TIMLIM=3.E1, and TIMLIM=3.0D+01 are all equivalent. Numerical values follow the FORTRAN variable name convention. All keywords which expect an integer value begin with the letters I-N, and all keywords which expect a floating point value begin with A-H or O-Z. String or logical keywords may begin with any letter. Some keyword variables are actually arrays. Array elements are entered by specifying the desired subscript: $SCF NO(1)=1 NO(2)=1 $END When contiguous array elements are given this may be given in a shorter form: $SCF NO(1)=1,1 $END When just one value is given to the first element of an array, the subscript may be omitted: $SCF NO=1 NO(2)=1 $END Logical variables can be .TRUE. or .FALSE. or .T. or .F. The periods are required. The program rewinds the input file for the namelist group it needs. This order in which the namelist groups are immaterial, and that comment cards may namelist groups. before searching means that the given is be placed between

Furthermore, the input file is read all the way through for each free-form namelist so multiple occurrences will be processed, although only the LAST occurrence of a variable will be accepted. Comment fields within a free-form namelist group are turned on and off by an exclamation point (!). Comments may also be placed after the $END's of free format namelist groups. Usually, comments are placed in between groups, $CONTRL SCFTYP=RHF RUNTYP=GRADIENT $END

Introduction --$CONTRL EXETYP=CHECK $END $DATA molecule goes here...

1-27

The second $CONTRL is not read, because it does not have a blank and a $ in the first two columns. Here a careful user has executed a CHECK job, and is now running the real calculation. The CHECK card is now just a comment line. * * * The final form of input is the fixed format group. These groups must be given IN CAPITAL LETTERS only! This includes the beginning $NAME and closing $END cards, as well as the group contents. The formatted groups are $VEC, $HESS, $GRAD, $DIPDR, and $VIB. Each of these is produced by some earlier GAMESS run, in exactly the correct format for reuse. Thus, the format by which they are read is not documented in section 2 of this manual. * * * Each group is described in the Input Description section. Fixed format groups are indicated as such, and the conditions for which each group is required and/or relevant are stated. There are a number of examples of GAMESS input given in the Input Examples section of this manual.

Introduction

1-28

Input Checking
Because some of the data in the input file may not be processed until well into a lengthy run, a facility to check the validity of the input has been provided. If EXETYP=CHECK is specified in the $CONTRL group, GAMESS will run without doing much real work so that all the input sections can be executed and the data checked for correct syntax and validity to the extent possible. The one-electron integrals are evaluated and the distinct row table is generated. Problems involving insufficient memory can be identified at this stage. To help avoid the inadvertent absence of data, which may result in the inappropriate use of default values, GAMESS will report the absence of any control group it tries to read in CHECK mode. This is of some value in determining which control groups are applicable to a particular problem. The use of EXETYP=CHECK is HIGHLY recommended for the initial execution of a new problem.

Introduction

1-29

Program Limitations
GAMESS can use an arbitrary Gaussian basis of spdfg type for computation of the energy or gradient. Some restrictions apply, for example, analytic hessians are limited to spd basis sets. This program is limited to a total of 2,000 atoms. The total number of symmetry unique basis set shells cannot exceed 5,000, containing no more than 20,000 Gaussian primitives. Each contraction must contain no more than 30 Gaussians. The total number of contracted basis functions, or AOs, cannot exceed 8192. You may use up to 1050 effective fragments, of at most 5 types, containing no more than 2000 multipole/polarizability/other expansion points. In practice, you will probably run out of CPU time or disk storage before you encounter any of these limitations. See Section 5 of this manual for information about changing any of these limits, or minimizing program memory use. Except for these limits, the program is basically dimension limitation free. Memory allocations other than these limits are dynamic, from the storage requested by the input.

Introduction

1-30

Restart Capability
The program checks for CPU time, and will stop if time is running short. Restart data are printed and punched out automatically, so the run can be restarted where it left off. At present all SCF modules will place the current orbitals on the punch file if the maximum number of iterations is reached. These orbitals may be used in conjunction with the GUESS=MOREAD option to restart the iterations where they quit. Also, if the TIMLIM option is used to specify a time limit just slightly less than the job's batch time limit, GAMESS will halt if there is insufficient time to complete another full iteration, and the current orbitals will be punched. When searching for equilibrium geometries or saddle points, if time runs short, or the maximum number of steps is exceeded, the updated hessian matrix is punched for restart. Optimization runs can also be restarted with the direct access file DICTNRY. See $STATPT for details. Force constant matrix runs can be restarted from cards. See the $VIB group for details. The two electron integrals may be reused. The NewtonRaphson formula tape for MCSCF runs can be saved and reused. * * * * The binary file restart options are rarely used, and so may not work well (or at all). Restarts which change the card input (adding a partially converged $VEC, or updating the coordinates in $DATA, etc.) are far more likely to be successful than restarts from the DAF file.

Input Description (12 August 2011) ********************************* * * * Section 2 - Input Description * * * *********************************

2-1

This section of the manual describes the input to GAMESS. The section is written in a reference, rather than tutorial fashion. However, there are frequent reminders that more information can be found on a particular input group, or type of calculation, in the 'Further Information' section of this manual. Numerous complete input files are shown in the 'Input Examples' section. Note that this chapter of the manual can be searched online by means of the "gmshelp" command, if your computer runs Unix. A command such as gmshelp scf will display the $SCF input group. With no arguments, the gmshelp command will show you all of the input group names. Type "<return>" to see the next screen, "b" to back up to the previous screen, and "q" to exit the pager. If gmshelp does not work, ask the person who installed GAMESS to fix the 'gmshelp' script, as it is extremely useful. The order of this section is chosen to approximate the order in which most people prepare their input ($CONTRL, $BASIS/$DATA, $GUESS, and so on). The next few pages contain a list of all possible input groups, grouped in this way. The PDF version of this file contains an index of all group names in alphabetical order.

Input Description name function module:routine -----------------------Molecule, basis set, wavefunction specification: $CONTRL chemical control data INPUTA:START $SYSTEM computer related options INPUTA:START $BASIS basis set INPUTB:BASISS $DATA molecule, geometry, basis set INPUTB:MOLE $ZMAT internal coordinates ZMATRX:ZMATIN $LIBE linear bend coordinates ZMATRX:LIBE $SCF HF-SCF wavefunction control SCFLIB:SCFIN $SCFMI SCF-MI input control data SCFMI :MIINP $DFT density functional theory DFT :DFTINP $TDDFT time-dependent DFT TDDFT :TDDINP $CIS singly excited CI CISGRD:CISINP $CISVEC vectors for CIS CISGRD:CISVRD $MP2 2nd order Moller-Plesset MP2 :MP2INP $RIMP2 resolution of the identity MP2 RIMP2 :RIDRVR $AUXBAS RI-MP2's basis set specifiction RIMP2 :RIDRVR $CCINP coupled cluster input CCSDT :CCINP $EOMINP equation of motion CC EOMCC :EOMINP $MOPAC semi-empirical specification MPCMOL:MOLDAT $GUESS initial orbital selection GUESS :GUESMO $VEC orbitals (formatted) GUESS :READMO $MOFRZ freezes MOs during SCF runs EFPCOV:MFRZIN Note that MCSCF and CI input is listed below. Potential energy surface options: $STATPT $TRUDGE $TRURST $FORCE $CPHF $MASS $HESS $GRAD $DIPDR $VIB $VIB2 $VSCF $VIBSCF $GAMMA $EQGEOM $HLOWT $GLOWT $IRC $DRC geometry search control nongradient optimization restart data for TRUDGE hessian, normal coordinates coupled-Hartree-Fock options isotope selection force constant matrix (formatted) gradient vector (formatted) dipole deriv. matrix (formatted) HESSIAN restart data (formatted) num GRAD/HESS restart (formatted) vibrational anharmonicity VSCF restart data (formatted) 3rd nuclear derivatives equilibrium geometry data hessian data from equilibrium 3rd derivatives at equilibrium intrinsic reaction coordinate dynamic reaction path STATPT:SETSIG TRUDGE:TRUINP TRUDGE:TRUDGX HESS :HESSX CPHF :CPINP VIBANL:RAMS HESS :FCMIN HESS :EGIN HESS :DDMIN HESS :HSSNUM HESS :HSSFUL VSCF :VSCFIN VSCF :VGRID HESS :GAMMXX HESS :FFCARX HESS :FFCARX HESS :FFCARX RXNCRD:IRCX DRC :DRCDRV

2-2 *

Input Description $MEX $CONICL $MD $RDF $GLOBOP $GRADEX $SURF minimum energy crossing point conical intersection search molecular dynamics trajectory radial dist. functions for MD Monte Carlo global optimization gradient extremal path potential surface scan MEXING:MEXINP MDEFP :MDX MDEFP :RDFX GLOBOP:GLOPDR GRADEX:GRXSET SURF :SRFINP

2-3

Interpretation, properties: $LOCAL $TRUNCN $ELMOM $ELPOT $ELDENS $ELFLDG $POINTS $GRID $PDC $RADIAL $MOLGRF $STONE $RAMAN $ALPDR $NMR $MOROKM $LMOEDA $QMEFP $FFCALC $TDHF $TDHFX localized molecular orbitals localized orbital truncations electrostatic moments electrostatic potential electron density electric field/gradient property calculation points property calculation mesh MEP fitting mesh atomic orbital radial data orbital plots distributed multipole analysis Raman intensity alpha polar. der. (formatted) NMR shielding tensors Morokuma energy decomposition LMO-based energy decomposition QM/EFP energy decomposition finite field polarizabilities time dependent HF of NLO props TDHF for NLO, Raman, hyperRaman LOCAL :LMOINP EFPCOV:TRNCIN PRPLIB:INPELM PRPLIB:INPELP PRPLIB:INPELD PRPLIB:INPELF PRPLIB:INPPGS PRPLIB:INPPGS PRPLIB:INPPDC PRPPOP:RADWFN PARLEY:PLTMEM PRPPOP:STNRD RAMAN :RAMANX RAMAN :ADMIN NMR :NMRX MOROKM:MOROIN MOROKM:MMOEDIN EFINP :QMEFPAX FFIELD:FFLDX TDHF :TDHFX TDX:FINDTDHFX

Solvation models: $EFRAG use effective fragment potential $FRAGNAME specifically named fragment pot. $FRGRPL inter-fragment repulsion $EWALD Ewald sums for EFP electrostatics $MAKEFP generate effective fragment pot. $PRTEFP simplified EFP generation $DAMP EFP multipole screening fit $DAMPGS initial guess screening params $PCM polarizable continuum model $PCMGRD PCM gradient control $PCMCAV PCM cavity generation $TESCAV PCM cavity tesselation $NEWCAV PCM escaped charge cavity $IEFPCM PCM integral equation form. data $PCMITR PCM iterative IEF input EFINP :EFINP EFINP :RDSTFR EFINP :RDDFRL EWALD :EWALDX EFINP :EFPX EFINP :PREFIN CHGPEN:CGPINP CHGPEN:CGPINP PCM :PCMINP PCMCV2:PCMGIN PCM :MAKCAV PCMCV2:TESIN PCM :DISREP PCM :IEFDAT PCMIEF:ITIEFIN

Input Description $DISBS $DISREP $SVP $SVPIRF $COSGMS $SCRF PCM dispersion basis set PCM dispersion/repulsion Surface Volume Polarization model reaction field points (formatted) conductor-like screening model self consistent reaction field PCMDIS:ENLBS PCMVCH:MORETS SVPINP:SVPINP SVPINP:SVPIRF COSMO :COSMIN SCRF :ZRFINP

2-4

Integral, and integral modification options: $ECP $MCP $RELWFN $EFIELD $INTGRL $FMM $TRANS effective core potentials model core potentials scalar relativistic integrals external electric field 2e- integrals fast multipole method integral transformation ECPLIB:ECPPAR MCPINP:MMPRED INPUTB:RWFINP PRPLIB:INPEF INT2A :INTIN QMFM :QFMMIN TRANS :TRFIN

Fragment Molecular Orbital method: $FMO $FMOPRP $FMOXYZ $OPTFMO $FMOHYB $FMOBND $FMOENM $FMOEND $OPTRST $GDDI define FMO fragments FMO properties and convergers atomic coordinates for FMO input for special FMO optimizer localized MO for FMO boundaries FMO bond cleavage definition monomer energies for FMO restart dimer energies for FMO restart OPTFMO restart data group DDI definition FMOIO :FMOMIN FMOIO :FMOPIN FMOIO :FMOXYZ FMOGRD:OPTFMO FMOIO :FMOLMO FMOIO :FMOBON FMOIO :EMINOU FMOIO :EDIN FMOGRD:RSTOPT INPUTA:GDDINP

Polymer model: $ELG polymer elongation method ELGLIB:ELGINP

Divide and conquer model: $DANDC $DCCORR $SUBSCF $SUBCOR $MP2RES $CCRES DC SCF input DC correlation method input subsystem definition for SCF subsystem definition for MP2/CC restart data for DC-MP2 restart data for DC-CC DCLIB DCLIB DCLIB DCLIB DCMP2 DCCC :DCINP :DCCRIN :DFLCST :DFLCST :RDMPDC :RDCCDC

quantum mechanics/molecular mechanics model: $FFDATA $FFPDB QuanPol calcualtion for molecules QUANPO:QUANPOL QuanPol calculation for proteins QUANPO:QUANPOL

MCSCF and CI wavefunctions, and their properties:

Input Description $CIINP $DET $CIDET $GEN $CIGEN $ORMAS $CEEIS $CEDATA $GCILST $GMCPT $PDET $ADDDET $REMDET $SODET $DRT $CIDRT $MCSCF $MRMP $DETPT $MCQDPT $CASCI $IVOORB $CISORT $GUGEM $GUGDIA $GUGDM $GUGDM2 $LAGRAN $TRFDM2 $TRANST control over CI calculation determinant full CI for MCSCF determinant full CI determinant general CI for MCSCF determinant general CI determinant multiple active space CI energy extrapolation restart data for CEEIS general MCSCF/CI determinant list general MCSCF/CI determinant list parent determinant list add determinants to reference remove determinants from ref. determinant second order CI GUGA distinct row table for MCSCF GUGA CI (CSF) distinct row table control over MCSCF calculation MRPT selection det. multireference pert. theory CSF multireference pert. theory IVO-CASCI input fine tuning of IVO-CASCI GUGA CI integral sorting GUGA CI Hamiltonian matrix GUGA CI diagonalization GUGA CI 1e- density matrix GUGA CI 2e- density matrix GUGA CI Lagrangian GUGA CI 2e- density backtransform transition moments, spin-orbit GAMESS:WFNCI ALDECI:DETINP ALDECI:DETINP ALGNCI:GCIINP ALGNCI:GCIINP ORMAS :FCINPT CEEIS :CEEISIN CEEIS :RDCEEIS ALGNCI:GCIGEN GMCPT :OSRDDAT GMCPT :OSMKREF GMCPT :OSMKREF GMCPT :OSMKREF FSODCI:SOCINP GUGDRT:ORDORB GUGDRT:ORDORB MCSCF :MCSCF MP2 :MRMPIN DEMRPT:DMRINP MCQDPT:MQREAD IVOCAS:IVODRV IVOCAS:ORBREAD GUGSRT:GUGSRT GUGEM :GUGAEM GUGDGA:GUGADG GUGDM :GUGADM GUGDM2:GUG2DM LAGRAN:CILGRN TRFDM2:TRF2DM TRNSTN:TRNSTX

2-5

* this column is more useful to programmers than to users.

Input Description

$CONTRL

2-6

==========================================================

$CONTRL

group

(note:

only one "oh"!)

This group specifies the type of wavefunction, the type of calculation, use of core potentials, spherical harmonics, coordinate choices, and similar fundamental job options. SCFTYP = RHF = UHF = ROHF = GVB = MCSCF = NONE specifies the self-consistent field wavefunction. You may choose from Restricted Hartree Fock calculation (default) Unrestricted Hartree Fock calculation Restricted open shell Hartree-Fock. (high spin, see GVB for low spin) Generalized valence bond wavefunction, or low spin ROHF. (needs $SCF input) Multiconfigurational SCF wavefunction (this requires $DET or $DRT input) indicates a single point computation, rereading a converged SCF function. This option requires that you select CITYP=ALDET, ORMAS, FSOCI, GENCI, or GUGA, requesting only RUNTYP=ENERGY or TRANSITN, and using GUESS=MOREAD.

The treatment of electron correlation for the above SCF wavefunctions is controlled by the keywords DFTTYP, MPLEVL, CITYP, and CCTYP contained in this group. Obviously, at most only one of these may be chosen in a run. Scalar relativistic effects may be incorporated using RELWFN for any of these wavefunction choices, correlated or not.

Input Description

$CONTRL

2-7

DFTTYP = NONE = XXXXXX

ab initio computation (default) perform density functional theory run, using the functional specified. Many choices for XXXXXX are listed in the $DFT and $TDDFT input groups. no excited states (default) generate time-dependent DFT excitation energies, using the DFTTYP= functional, for RHF or UHF references. Analytic nuclear gradients are available for RHF. See $TDDFT. spin-flip TD-DFT, for either UHF or ROHF references. Nuclear gradients are available for UHF. See $TDDFT. * * * * *

TDDFT

= NONE = EXCITE

= SPNFLP

MPLEVL = = 0 = 2

chooses Moller-Plesset perturbation theory level, after the SCF. See $MP2, or $MRMP for MCSCF. skip the MP computation (default) perform second order energy correction.

MP2 (a.k.a. MBPT(2)) is implemented for RHF, UHF, ROHF, and MCSCF wavefunctions, but not GVB. Gradients are available for RHF, UHF, or ROHF based MP2, but for MCSCF, you must choose numerical derivatives to use any RUNTYP other than ENERGY, TRUDGE, SURFACE, or FFIELD. * * * * * CITYP = = NONE = CIS chooses CI computation after the SCF, for any SCFTYP except UHF. skips the CI. (default) single excitations from a SCFTYP=RHF reference, only. This is for excited states, with analytic nuclear gradients available. See the $CIS input group. spin-flip style CIS, see $CIS input. runs the Ames Laboratory determinant full CI package, requiring $CIDET. runs an Occupation Restricted Multiple Active Space determinant CI. The input

= SFCIS = ALDET = ORMAS

Input Description

$CONTRL is $CIDET and $ORMAS. runs a full second order CI using determinants, see $CIDET and $SODET. runs a determinant CI program that permits arbitrary specification of the determinants, requiring $CIGEN. runs the Unitary Group CI package, which requires $CIDRT input. Analytic gradients are available only for RHF, so for other SCFTYPs, you may choose only RUNTYP=ENERGY, TRUDGE, SURFACE, FFIELD, TRANSITN. * * * * *

2-8

= FSOCI = GENCI = GUGA

CCTYP

chooses a Coupled-Cluster (CC calculation for the ground state and, optionally, Equation of Motion Coupled-Cluster (EOMCC) computation for excited states, both performed after the SCF (RHF or ROHF). See also $CCINP and $EOMINP. Only CCSD and CCSD(T) for RHF can run in parallel. For ROHF, you may choose only CCSD and CR-CCL. = NONE = LCCD = CCD = CCSD = CCSD(T) = R-CC = CR-CC = CR-CCL skips CC computation (default). perform a coupled-cluster calculation using the linearized coupled-cluster method with double excitations. perform a CC calculation using the coupled-cluster method with doubles. perform a CC calculation with both single and double excitations. in addition to CCSD, the non-iterative triples corrections are computed, giving standard CCSD[T] and CCSD(T) energies. in addition to all CCSD(T) calculations, compute the renormalized R-CCSD[T] and R-CCSD(T) energies. in addition to all R-CC calculations, the completely renormalized CR-CCSD[T] and CR-CCSD(T) energies are computed. in addition to a CCSD ground state, the non-iterative triples energy correction defining the rigorously size extensive completely renormalized CR-CC(2,3), also called CR-CCSD(T)_L theory, is computed.

Input Description

$CONTRL

2-9

= CCSD(TQ)

= CR-CC(Q)

Ground state only (zero NSTATE vector) CCTYP=CR-EOM type CR-EOMCCSD(T) energies and CCSD properties are also generated. For further information about accuracy, and A to D CR-CC(2,3) energy types, see REFS.DOC. in addition to all R-CC calculations, non-iterative triple and quadruple corrections are used, to give CCSD(TQ) and various R-CCSD(TQ) energies. in addition to all CR-CC and CCSD(TQ) calculations, the CR-CCSD(TQ) energies are obtained. in addition to a CCSD ground state, excited states are calculated using the equation of motion coupled-cluster method with singles and doubles. in addition to the CCSD and EOM-CCSD, noniterative triples corrections to CCSD ground-state and EOM-CCSD excited-state energies are found, using completely renormalized CR-EOMCCSD(T) approaches. in addition to printing all results that CR-EOM obtains, this solves the lambda equations, and gives triples corrections analogous to ground state CR-CCL.

= EOM-CCSD

= CR-EOM

= CR-EOML

= IP-EOM2 ionization potential, e.g. IP-EOM-CCSD = IP-EOM3A ionization potential, e.g. IP-EOM-CCSDt = EA-EOM2 electron affinity, e.g. EA-EOM-CCSD = EA-EOM3A electron affinity, e.g. EA-EOM-CCSDt For electron affinities, 2 refers to truncation at the 2 particle, 1 hole level, while 3 refers to truncation at 3 particle, 2 hole using selected active orbitals. For ionization potentials, these reverse: 2 means 2 holes, 1 particle, while 3 means 3 holes, 2 particles using only the active orbitals. EA and IP runs produce both ground and excited states of the e- attached or detached systems, and thus obey $CCINP as well as $EOMINP inputs. Any publication describing the results of CC calculations obtained using GAMESS should reference the appropriate papers, which are listed on the output of every run, and in chapter 4 of this manual.

Input Description

$CONTRL

2-10

Analytic gradients are not available, so use CCTYP only for RUNTYP=ENERGY, TRUDGE, SURFACE, or maybe FFIELD, or request numerical derivatives. Generally speaking, the Renormalized energies are obtained at similar cost to the standard values, while Completely Renormalized energies cost twice the time. For usage tips and more information about resources on the various Coupled Cluster methods, see Section 4, 'Further Information'. * * * * * RELWFN = NONE (default) See also the $RELWFN input group. = IOTC infinite-order two-component method of M. Barysz and A.J. Sadlej = DK Douglas-Kroll transformation, available at the 1st, 2nd, or 3rd order. = RESC relativistic elimination of small component, the method of T. Nakajima and K. Hirao, available at 2nd order only. = NESC normalised elimination of small component, the method of K. Dyall, 2nd order only. * * * * * RUNTYP = ENERGY = GRADIENT = HESSIAN specifies the type of computation, for example at a single geometry point: Molecular energy. (default) Molecular energy plus gradient. Molecular energy plus gradient plus second derivatives, including harmonic harmonic vibrational analysis. See the $FORCE and $CPHF input groups. Evaluate up to 3rd nuclear derivatives, by finite differencing of Hessians. See $GAMMA, and also NFFLVL in $CONTRL. multiple geometry options: = OPTIMIZE = TRUDGE Optimize the molecular geometry using analytic energy gradients. See $STATPT. Non-gradient total energy minimization. See $TRUDGE and $TRURST.

= GAMMA

Input Description = SADPOINT = MEX = CONICAL = IRC = VSCF = DRC = MD = GLOBOP = OPTFMO = GRADEXTR = SURFACE

$CONTRL

2-11

Locate saddle point (transition state). See $STATPT. Locate minimum energy crossing point on the intersection seam of two potential energy surfaces. See $MEX. Locate conical intersection point on the intersection seam of two potential energy surfaces. See $CONICL. Follow intrinsic reaction coordinate. See $IRC. anharmonic vibrational corrections. See $VSCF. Follow dynamic reaction coordinate. See $DRC. molecular dynamics trajectory, see $MD. Monte Carlo-type global optimization. See $GLOBOP. genuine FMO geometry optimization using nearly analytic gradient. See $OPTFMO. Trace gradient extremal. See $GRADEX. Scan linear cross sections of the potential energy surface. See $SURF. single geometry property options:

= G3MP2 = PROP

= RAMAN = NACME

= NMR = EDA = QMEFPEA

evaluate heat of formation using the G3(MP2,CCSD(T)) methodology. See test example exam43.inp for more information. Properties will be calculated. A $DATA deck and converged $VEC deck should be input. Optionally, orbital localization can be done. See $ELPOT, etc. computes Raman intensities, see $RAMAN. non-adiabatic coupling matrix element between two or more state averaged MCSCF wavefunctions, of FORS/CAS type. The calculation has no special input group, but must use determinants (SCFTYP=MCSCF, using CISTEP=ALDET). NMR shielding tensors for closed shell molecules by the GIAO method. See $NMR. Perform energy decomposition analysis. Give one of $MOROKM or $LMOEDA inputs. QM/EFP solvent energy analysis, see $QMEFP.

Input Description = TRANSITN = FFIELD = TDHF = TDHFX = MAKEFP = FMO0

$CONTRL

2-12

Compute radiative transition moment or spin-orbit coupling. See $TRANST. applies finite electric fields, most commonly to extract polarizabilities. See $FFCALC. analytic computation of time dependent polarizabilities. See $TDHF. extended TDHF package, including nuclear polarizability derivatives, and Raman and Hyper-Raman spectra. See $TDHFX. creates an effective fragment potential, for SCFTYP=RHF or ROHF only. See $MAKEFP, $DAMP, $DAMPGS, $STONE, ... performs the free state FMO calculation. See $FMO.

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * Note that RUNTYPs which require the nuclear gradient are GRADIENT, HESSIAN, OPTIMIZE, SADPOINT, GLOBOP, IRC, GRADEXTR, DRC, and RAMAN These are efficient with analytic gradients, which are available only for certain CI or MP2 calculations, but no CC calculations, as indicated above. See NUMGRD. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * NUMGRD Flag to allow numerical differentiation of the energy. Each gradient requires the energy be computed twice (forward and backward displacements) along each totally symmetric modes. It is thus recommended only for systems with just a few symmetry unique atoms in $DATA. The default is .FALSE. Actually do the run. (default) Wavefunction and energy will not be evaluated. This lets you speedily check input and memory requirements. See the overview section for details. Note that you must set PARALL=.TRUE. in $SYSTEM to test distributed memory allocations. Massive amounts of output are printed, useful only if you hate trees. Maximum output is generated by the

EXETYP = RUN = CHECK

= DEBUG = routine

Input Description

$CONTRL routine named. Check the source for the routines this applies to. * * * * * * *

2-13

ICHARG = MULT = = 1 = 2,3,...

Molecular charge.

(default=0, neutral)

Multiplicity of the electronic state singlet (default) doublet, triplet, and so on.

ICHARG and MULT are used directly for RHF, UHF, ROHF. For GVB, these are implicit in the $SCF input, while for MCSCF or CI, these are implicit in $DRT/$CIDRT or $DET/$CIDET input. You must still give them correctly. * * * the next three control molecular geometry * * * COORD = choice for molecular geometry in $DATA. = UNIQUE only the symmetry unique atoms will be given, in Cartesian coords (default). = HINT only the symmetry unique atoms will be given, in Hilderbrandt style internals. = PRINAXIS Cartesian coordinates will be input, and transformed to principal axes. Please read the warning just below!!! = ZMT GAUSSIAN style internals will be input. = ZMTMPC MOPAC style internals will be input. = FRAGONLY means no part of the system is treated by ab initio means, hence $DATA is not given. The system is defined by $EFRAG.

Note: the choices PRINAXIS, ZMT, ZMTMPC require input of all atoms in the molecule. They also orient the molecule, and then determine which atoms are unique. The reorientation is likely to change the order of the atoms from what you input. When the point group contains a 3fold or higher rotation axis, the degenerate moments of inertia often cause problems choosing correct symmetry unique axes, in which case you must use COORD=UNIQUE rather than Z-matrices. Warning: The reorientation into principal axes is done only for atomic coordinates, and is not applied to the axis dependent data in the following groups: $VEC, $HESS, $GRAD,

Input Description

$CONTRL

2-14

$DIPDR, $VIB, nor Cartesian coords of effective fragments in $EFRAG. COORD=UNIQUE avoids reorientation, and thus is the safest way to read these. Note: the choices PRINAXIS, ZMT, ZMTMPC require the use of a group named $BASIS to define the basis set. The first two choices might or might not use $BASIS, as you wish. UNITS = distance units, any angles must be in degrees. = ANGS Angstroms (default) = BOHR Bohr atomic units = 0 = M Use Cartesian coordinates (default). If COORD=ZMT or ZMTMPC, and $ZMAT is not given: the internal coordinates will be those defining the molecule in $DATA. In this case, $DATA may not contain any dummy atoms. M is usually 3N-6, or 3N-5 for linear. For other COORD choices, or if $ZMAT is given: the internal coordinates will be those defined in $ZMAT. This allows more sophisticated internal coordinate choices. M is ordinarily 3N-6 (3N-5), unless $ZMAT has linear bends.

NZVAR

= M

NZVAR refers mainly to the coordinates used by OPTIMIZE or SADPOINT runs, but may also print the internal's values for other run types. You can use internals to define the molecule, but Cartesians during optimizations! * * * * * * * Pseudopotentials may be of two types: ECP (effective core potentials) which generate nodeless valence orbitals, and MCP (model core potentials) producing valence orbitals with the correct radial nodal structure. At present, ECPs have analytic nuclear gradients and Hessians, while MCPs have analytic nuclear gradients. PP = = NONE = READ = SBKJC = HW pseudopotential selection. all electron calculation (default). read ECP potentials in the $ECP group. use Stevens, Basch, Krauss, Jasien, Cundari ECP potentials for all heavy atoms (Li-Rn are available). use Hay, Wadt ECP potentials for heavy

Input Description

$CONTRL

2-15

= MCP

atoms (Na-Xe are available). use Huzinaga's Model Core Potentials. The correct MCP potential will be chosen to match the requested MCP valence basis set (see $BASIS). * * * * * * *

LOCAL

= = = = =

NONE BOYS RUEDNBRG POP

controls orbital localization. Skip localization (default). Do Foster-Boys localization. Do Edmiston-Ruedenberg localization. Do Pipek-Mezey population localization. See the $LOCAL group. Localization does not work for SCFTYP=GVB or CITYP. * * * * * * *

ISPHER = = -1

= 0

= +1

Spherical Harmonics option Use Cartesian basis functions to construct symmetry-adapted linear combination (SALC) of basis functions. The SALC space is the linear variation space used. (default) Use spherical harmonic functions to create SALC functions, which are then expressed in terms of Cartesian functions. The contaminants are not dropped, hence this option has EXACTLY the same variational space as ISPHER=-1. The only benefit to obtain from this is a population analysis in terms of pure s,p,d,f,g functions. Same as ISPHER=0, but the function space is truncated to eliminate all contaminant Cartesian functions [3S(D), 3P(F), 4S(G), and 3D(G)] before constructing the SALC functions. The computation corresponds to the use of a spherical harmonic basis.

QMTTOL = linear dependence threshhold Any functions in the SALC variational space whose eigenvalue of the overlap matrix is below this tolerence is considered to be linearly dependent. Such functions are dropped from the variational space. What is dropped is not individual basis functions, but rather some linear combination(s)

Input Description

$CONTRL

2-16

of the entire basis set that represent the linear dependent part of the function space. The default is a reasonable value for most purposes, 1.0E-6. When many diffuse functions are used, it is common to see the program drop some combinations. On occasion, in multi-ring molecules, we have raised QMTTOL to 3.0E-6 to obtain SCF convergence, at the cost of some energy. MAXIT = Maximum number of SCF iteration cycles. This pertains only to RHF, UHF, ROHF, or GVB runs. See also MAXIT in $MCSCF. (default = 30) * * * interfaces to other programs * * * MOLPLT = flag that produces an input deck for a molecule drawing program distributed with GAMESS. (default is .FALSE.) PLTORB = flag that produces an input deck for an orbital plotting program distributed with GAMESS. (default is .FALSE.) AIMPAC = flag to create an input deck for Bader's Atoms In Molecules properties code. (default=.FALSE.) For information about this program, see the URL http://www.chemistry.mcmaster.ca/aimpac FRIEND = string to prepare input to other quantum programs, choose from = HONDO for HONDO 8.2 = MELDF for MELDF = GAMESSUK for GAMESS (UK Daresbury version) = GAUSSIAN for Gaussian 9x = ALL for all of the above PLTORB, MOLPLT, and AIMPAC decks are written to file PUNCH at the end of the job. Thus all of these correspond to the final geometry encountered during jobs such as OPTIMIZE, SAPDOINT, IRC... In contrast, selecting FRIEND turns the job into a CHECK run only, no matter how you set EXETYP. Thus the geometry is that encountered in $DATA. The input is

Input Description

$CONTRL

2-17

added to the PUNCH file, and may require some (usually minimal) massaging. PLTORB and MOLPLT are written even for EXETYP=CHECK. AIMPAC requires at least RUNTYP=PROP. * * * NFFLVL used to determine energies and gradients away from equilibrium structures, at the coordinates given in $DATA. The method will use a Taylor expansion of the potential surface around the stationary point. See $EQGEOM, $HLOWT, $GLOWT. This may be used with RUNTYP=ENERGY or GRADIENT. = 2 uses only Hessian information, which gives a reasonable energy, but not such a good gradient. = 3 uses Hessian and 3rd nuclear derivatives in the Taylor expansion, producing more accurate values for the energy and for the gradient. * * * computation control switches * * * For the most part, the default is the only sensible value, and unless you are sure of what you are doing, these probably should not be touched. NPRINT = = = = = = = = = = = = = -7 -6 -5 -4 -3 -2 1 2 3 4 5 6 Print/punch control flag See also EXETYP for debug info. (options -7 to 5 are primarily debug) Extra printing from Boys localization. debug for geometry searches minimal output print 2e-contribution to gradient. print 1e-contribution to gradient. normal printing, no punch file extra printing for basis,symmetry,ZMAT extra printing for MO guess routines print out property and 1e- integrals print out 2e- integrals print out SCF data for each cycle. (Fock and density matrices, current MOs same as 7, but wider 132 columns output. This option isn't perfect.

Input Description = = = NOSYM = 0 = 1 7 8 9

$CONTRL

2-18

normal printing and punching (default) more printout than 7. The extra output is (AO) Mulliken and overlap population analysis, eigenvalues, Lagrangians, ... everything in 8 plus Lowdin population analysis, final density matrix. the symmetry specified in $DATA is used as much as possible in integrals, SCF, gradients, etc. (this is the default) the symmetry specified in the $DATA group is used to build the molecule, then symmetry is not used again. Some GVB or MCSCF runs (those without a totally symmetric charge density) require you request no symmetry.

ETOLLZ

= threshold to label molecular orbitals by Lz values. Small matrices of the Lz operator are diagonalized for the sets of MOs whose orbital energies are degenerate to within ETOLLZ. This option may be used in molecules with distorted linear symmetry for approximate labelling. Default: 1.0d-6 for linear, 0 (disable) if not.

INTTYP selects the integral package(s) used, all of which produce equally accurate results. This is therefore used only for debugging purposes. = BEST use the fastest integral code available for any particular shell quartet (default): s,p,L or s,p,d,L rotated axis code first. ERIC s,p,d,f,g precursor transfer equation code second, up to 5 units total ang. mom. Rys quadrature for general s,p,d,f,g,L, or for uncontracted quartets. = ROTAXIS means don't use ERIC at all, e.g. rotated axis codes, or else Rys quadrature. = ERIC means don't use rotated axis codes, e.g. ERIC code, or else Rys quadrature. = RYSQUAD means use Rys quadrature for everything. GRDTYP = BEST use Schlegel routines for spL gradient blocks, and Rys quadrature for all other gradient integrals. (default) = RYSQUAD use Rys quadrature for all gradient

Input Description

$CONTRL

2-19

integrals. This option is only slightly more accurate, but is rather slower. NORMF NORMP = 0 = 1 = 0 = 1 ITOL = = n = n normalize the basis functions (default) no normalization input contraction coefficients refer to normalized Gaussian primitives. (default) the opposite. primitive cutoff factor (default=20) products of primitives whose exponential factor is less than 10**(-n) are skipped. integrals less than 10.0**(-n) are not saved on disk. (default = 9). Direct SCF will calculate to a cutoff 1.0d-10 or 5.0d-11 depending on FDIFF=.F. or .T. proceed as usual skip computation of some properties which are not well parallelised. This includes bond orders and virial theorem, and can help parallel scalability if many CPUs are used. Note that NPRINT=-5 disables most property computations as well, so ISKPRP=1 has no effect in that case. (default: 0) * * * restart options * * * IREST = = -1 = = = = = GEOM 0 1 2 3 4 restart control options (for OPTIMIZE run restarts, see $STATPT) Note that this option is unreliable! reuse dictionary file from previous run, useful with GEOM=DAF and/or GUESS=MOSAVED. Otherwise, this option is the same as 0. normal run (default) 2e restart (1-e integrals and MOs saved) SCF restart (1-,2-e integrls and MOs saved) 1e gradient restart 2e gradient restart

ICUT

ISKPRP = 0 1

= select where to obtain molecular geometry = INPUT from $DATA input (default for IREST=0)

Input Description = DAF

$CONTRL

2-20

read from DICTNRY file (default otherwise)

As noted in the first chapter, binary file restart is not a well tested option! ==========================================================

Input Description

$SYSTEM

2-21

==========================================================

$SYSTEM

group

(optional)

This group provides global control information for your computer's operation. This is system related input, and will not seem particularly chemical to you! MWORDS = the maximum replicated memory which your job can use, on every node. This is given in units of 1,000,000 words (as opposed to 1024*1024 words), where a word is defined as 64 bits. (default=1) (In case finer control over the memory is needed, this value can be given in units of words with the old keyword MEMORY instead of MWORDS.) the grand total memory needed for the distributed data interface (DDI) storage, given in units of 1,000,000 words. See Chapter 5 of this manual for an extended explanation of running with MEMDDI.

MEMDDI =

note: the memory required on each processor for a run using p processors is therefore MEMDDI/p + MWORDS. The parallel runs that currently require MEMDDI are: SCFTYP=RHF MPLEVL=2 energy or gradient SCFTYP=UHF MPLEVL=2 energy or gradient SCFTYP=ROHF MPLEVL=2 OSPT=ZAPT energy or gradient SCFTYP=MCSCF MPLEVL=2 energy SCFTYP=MCSCF using the FULLNR or JACOBI convergers SCFTYP=MCSCF analytic hessian SCFTYP=any CITYP=ALDET, ORMAS, GUGA SCFTYP=any energy localization SCFTYP=RHF CCTYP=CCSD or CCSD(T) All other parallel runs should enter MEMDDI=0, for they use only replicated memory. Some serial runs execute the parallel code (on just 1 CPU), for there is only a parallel code. These serial runs must give MEMDDI as a result: SCFTYP=ROHF MPLEVL=2 OSPT=ZAPT gradient/property run SCFTYP=MCSCF analytic hessian TIMLIM = time limit, in minutes. Set to about 95 percent of the time limit given to the batch job (if you use a queueing system) so that GAMESS can stop

Input Description itself gently. PARALL =

$SYSTEM (default=525600.0 minutes)

2-22

a flag to cause the distributed data parallel MP2 program to execute the parallel algorithm, even if you are running on only one node. The main purpose of this is to allow you to do EXETYP=CHECK runs to learn what the correct value of MEMDDI needs to be. diagonalization control switch use a vectorized diagonalization routine if one is available on your machine, else use EVVRSP. (default) use EVVRSP diagonalization. This may be more accurate than KDIAG=0. use GIVEIS diagonalization (not as fast or reliable as EVVRSP) use JACOBI diagonalization (this is the slowest method) a flag to indicate whether or not GAMESS should produce a "core" file for debugging when subroutine ABRT is called to kill a job. This variable pertains only to UNIX operating systems. (default=.FALSE.)

KDIAG

= = 0 = 1 = 2 = 3

COREFL =

BALTYP = Parallel load balance scheme: = SLB uses static load balancing. = DLB uses dynamic load balancing (default). Dynamic load balancing attempts to spread out possibly unequal work assignments based on the rate at which different nodes complete tasks. For historical reasons, it is permissible to spell SLB as LOOP, and DLB as NXTVAL. MXSEQ2 = 300 (default) MXSEQ3 = 150 (default) Matrix/vector problem size in loops requiring either O(N**2) or O(N**3) work, respectively. Problems below these sizes are run purely serial, to avoid poor communication/computation ratios. NODEXT = array specifying node extentions in GDDI for each file. Non-zero values force no extension. E.g., NODEXT(40)=1 forces file 40 (file numbers

Input Description

$SYSTEM

2-23

are unit numbers used in GAMESS, see "rungms" or PROG.DOC) to have the name of $JOB.F40 on all nodes, rather than $JOB.F40, $JOB.F40.001, $JOB.F40.002 etc. This is convenient for FMO restart jobs, so that the file name need not be changed for each node, when copying the restart file. Note that on machines when several CPUs use the same directory (e.g., SMP) NODEXT should be zero. (default: all zeros) IOSMP = Parallelise I/O on SMP machines with multiple hard disks. Two parameters are specified, whose meaning should be clear from the example. iosmp(1)=2,6 2 refers to the number of HDDs per SMP box. 6 is the location of the character in the file names that switches HDDs, i.e. if HDDs are mounted as /work1 and /work2, then 6 refers to the position of the number 1 in /work1. The file system should permit disks attached with directory names differing by one symbol. (default: 0,0, disable the feature)

==========================================================

Input Description

$BASIS

2-24

==========================================================

$BASIS

group

(optional)

This group allows certain standard basis sets to be easily requested. There are three strategies here: GBASIS plus optional supplementations such as NDFUNC, EXTFIL to read basis sets from an external file that you provide, or BASNAM to develop customized basis sets in your input file. If this group is omitted, a fourth strategy is to give the basis set in the $DATA input, which is completely general. GBASIS requests various Gaussian basis sets. * * * segemented contractions * * * GBASIS = MINI - Huzinaga's 3 gaussian minimal basis set. Available H-Rn. = MIDI - Huzinaga's 21 split valence basis set. Available H-Rn. = STO - Pople's STO-NG minimal basis set. Available H-Xe, for NGAUSS=2,3,4,5,6. = N21 - Pople's N-21G split valence basis set. Available H-Xe, for NGAUSS=3. Available H-Ar, for NGAUSS=6. = N31 - Pople's N-31G split valence basis set. Available H-Ne,P-Cl for NGAUSS=4. Available H-He,C-F for NGAUSS=5. Available H-Kr, for NGAUSS=6, note that the bases for K,Ca,Ga-Kr were changed 9/2006. = N311 - Pople's "triple split" N-311G basis set. Available H-Ne, for NGAUSS=6. Selecting N311 implies MC for Na-Ar. = DZV - "double zeta valence" basis set. a synonym for DH for H,Li,Be-Ne,Al-Cl. (14s,9p,3d)/[5s,3p,1d] for K-Ca. (14s,11p,5d/[6s,4p,1d] for Ga-Kr. = DH - Dunning/Hay "double zeta" basis set. (3s)/[2s] for H. (9s,4p)/[3s,2p] for Li. (9s,5p)/[3s,2p] for Be-Ne. (11s,7p)/[6s,4p] for Al-Cl. = TZV - "triple zeta valence" basis set. (5s)/[3s] for H.

Input Description

$BASIS (10s,3p)/[4s,3p] for Li. (10s,6p)/[5s,3p] for Be-Ne. a synonym for MC for Na-Ar. (14s,9p)/[8s,4p] for K-Ca. (14s,11p,6d)/[10s,8p,3d] for Sc-Zn. - McLean/Chandler "triple split" basis. (12s,9p)/[6s,5p] for Na-Ar. Selecting MC implies 6-311G for H-Ne.

2-25

= MC

NGAUSS = the number of Gaussians (N). This parameter pertains only to GBASIS=STO, N21, N31, or N311. Note: Polarization functions and/or diffuse functions are to be added separately to these GBASIS values, which define only the atom's occupied orbitals, with keywords such as NDFUNC and DIFFSP. Pople GBASIS keywords require NGAUSS. * * * systematic basis set families * * * GBASIS = CCn - Dunning-type Correlation Consistent basis sets, officially called cc-pVnZ. Use n = D,T,Q,5,6 to indicate the level of polarization. These provide a hierachy of basis sets suitable for recovering the correlation energy. Available for H-He, Li-Ne, Na-Ar, Ca, Ga-Kr and for Sc-Zn for n=T,Q. ACCn - As CCn, but augmented with a set of diffuse functions, e.g. aug-cc-pVnZ. CCnC - As CCn, but augmented with tight functions for recovering core and core-valence correlation, e.g. cc-pCVnZ. ACCnC- As CCn, but augmented with both tight and diffuse functions, e.g. aug-cc-pCVnZ. PCn - Jensen Polarization Consistent basis sets. n = 0,1,2,3,4 indicates the level of polarization. (n=0 is unpolarized, n=1 is DZP, n=2 is TZ2P, etc.). These provide a hierachy of basis sets suitable for DFT and HF calculations. Available H-Ar. APCn - As PCn, but augmented with a set of diffuse functions. SPK-nZP - Sapporo family of non-relativistic bases, n=D,T,Q, available H-Xe SPK-AnZP - diffuse augmentation of the above.

= = = =

= = =

Input Description = SPKrnZP

$BASIS

2-26

= = = =

- Sapporo family of relativistic bases n=D,T,Q, available H-Xe. These should be used only with a relativistic transformation of the integrals, such as RELWFN=IOTC or RELWFN=DK. These sets are identical to SPK-nZP up to Ar. SPKrAnZP - diffuse augmentation of the above. KTZV - Karlsruhe valence triple zeta basis, as developed by Prof.Ahlrichs, see REFS.DOC. KTZVP- Karlsruhe valence triple zeta basis with a set of single polarization (P). KTZVPP-Karlsruhe valence triple zeta basis with a set of double polarization (PP).

Important notes about CC and PC basis sets: 1. Normally these basis sets are used only as spherical harmonics, see ISPHER=1 in $CONTRL. Failure to set ISPHER=1 will result in a) discrepancies in energy results for this basis set, compared to the literature or other programs. b) probable difficulties in convergence of SCF/DFT or CCSD amplitude equations, due to linear dependency. c) longer run times in correlated methods due to the retention of unimportant MOs. 2. The CC5, CC6, and PC4 basis sets (and corresponding augmented versions) contain h-functions, and CC6 contains i-functions. As GAMESS' integral codes are currently restricted to g-functions, these basis sets presently omit these functions, and therefore are not the standard sets. 3. The implementation of the cc-pVnZ basis sets for Al-Ar include one additional tight d-function, producing the socalled cc-pV(n+d)Z sets, which is found (J.Chem.Phys. 114, 9244(2001)) to improve the results. The same is true of the "aug-" counterpart. Note that the "core" versions of these elements (Al-Ar) don't have the extra d and should be regarded as inaccurate. 4. Note that both the CC and PC basis sets are generally contracted, which GAMESS can only handle by replicating the primitive basis functions, leading to a less than optimum performance in AO integral evaluation. 5. In case you are interested in scalar relativistic effects, the CCT-DK and CCQ-DK sets optimized for use with Douglas/Kroll are available for Sc-Kr. These will be used if you type GBASIS=CCT or CCQ along with RELWFN=DK, using

Input Description

$BASIS

2-27

NR sets for elements lighter than Sc. DK versions of ACCD or ACCT are available for Sc-Zn (but not Ga-Kr). Notes about the Sapporo family: 1. SPK is the international airport city code for Sapporo. 2. These should be used only in spherical harmonic form. 3. The relativistic bases were optimized at the 3rd order of the Douglas-Kroll transformation, with a Gaussian nuclei model, but can also be used with the infinite order twocomponent scheme IOTC (see RELWFN in $CONTRL). It would be very illogical to use these all-electron relativistic bases without turning on scalar relativity! 4. The basis sets were extracted from the data base of Segmented Gaussian Basis Sets, maintained by Takeshi Noro, Quantum Chemistry Group, Sapporo, Japan: http://setani.sci.hokudai.ac.jp/sapporo/Welcome.do The mapping between the data base names and the keywords used in GAMESS is (for n=D,T,Q): data base name keyword Sapporo-nZP SPK-nZP Sapporo-nZP+diffuse SPK-AnZP Sapporo-DK-nZP SPKrnZP Sapporo-DK-nZP+diffuse SPKrAnZP * * * Effective Core Potential (ECP) bases * * * GBASIS = SBKJC- Stevens/Basch/Krauss/Jasien/Cundari valence basis set, for Li-Rn. This choice implies an unscaled -31G basis for H-He. = HW - Hay/Wadt valence basis. This is a -21 split, available Na-Xe, except for the transition metals. This implies a 3-21G basis for H-Ne. * * * Model Core Potential (MCP) bases * * * Notes: Select PP=MCP in $CONTRL to automatically use the model core potential matching your basis choice below. References for these bases, and other information about MCPs can be found in the REFS.DOC chapter. Another family covering almost all elements is available in $DATA only. GBASIS = MCP-DZP, MCP-TZP, MCP-QZP a family of double, triple, and quadruple zeta

Input Description

$BASIS

2-28

quality valence basis sets, which are akin to the correlation consistent sets, in that these include increasing levels of polarization (and so do not require "supplements" like NDFUNC or DIFFSP) and must be used as spherical harmonics (see ISPHER). Availability: MCP-DZP: 56 elements Z=3-88, except V-Zn, Y-Cd, La, Hf-Hg MCP-TZP, MCP-QZP: 85 elements Z=3-88, except La The basis sets for hydrogen atoms will be the corresponding Dunning's cc-pVNZ (N=D,T,Q). = MCP-ATZP, MCP-AQZP MCP-TZP and MCP-QZP core potentials whose basis sets were augmented with diffuse functions Availability: same as for MCP-TZP, MCP-QZP = MCPCDZP, MCPCTZP, MCPCQZP based on MCP-DZP, MCP-TZP, MCP-QZP, with core-valence functions provided for the alkali and alkaline earth atoms Na through Ra. = MCPACDZP, MCPACTZP, MCPACQZP based on MCPCDZP, MCPCTZP, MCPCQZP, with core-valence functions provided for the alkali and alkaline earth atoms Na through Ra, and augmented with diffuse functions. The basis sets were extracted from the data base Segmented Gaussian Basis Sets, maintained by Takeshi Noro, Quantum Chemistry Group, Sapporo, Japan: http://setani.sci.hokudai.ac.jp/sapporo/Welcome.do The mapping between the data base names and the names used in GAMESS is data base name GAMESS keyword MCP/NOSeC-V-DZP MCP/NOSeC-V-TZP MCP/NOSeC-V-QZP MCP/NOSeC-V-TZP+diffuse MCP/NOSeC-V-QZP+diffuse MCP/NOSeC-CV-DZP MCP/NOSeC-CV-TZP MCP-DZP MCP-TZP MCP-QZP MCP-ATZP MCP-AQZP MCPCDZP MCPCTZP

Input Description MCP/NOSeC-CV-QZP

$BASIS MCPCQZP MCPACDZP MCPACTZP MCPACQZP

2-29

MCP/NOSeC-CV-DZP+diffuse MCP/NOSeC-CV-TZP+diffuse MCP/NOSeC-CV-QZP+diffuse

GBASIS = IMCP-SR1 and IMCP-SR2 valence basis sets to be used with the improved MCPs with scalar relativistic effects. These are available for transition metals except La, and the main group elements B-Ne, P-Ar, Ge, Kr, Sb, Xe, Rn. The 1 and 2 refer to addition of first and second polarization shells, so again don't use any of the "supplements" and do use spherical harmonics. = IMCP-NR1 and IMCP-NR2 closely related valence basis sets, but with nonrelativistic model core potentials. GBASIS = ZFK3-DK3, ZFK4-DK3, ZFK5-DK3, or ZFK3LDK3, ZFK4LDK3, ZFK5LDK3 These are a family of model core potential basis sets developed by Zeng/Fedorov/Klobukowski, for the p-block elements from 2p to 6p. The potentials were paramaterized taking into account both DK3 scalar relativistic and DK-SOC effects. The fundamental basis functions are from the Well-Tempered Basis Sets. The number after ZFK indicates the augmentation levels, e.g. ZFK3 means the diffuse functions from aug-cc-pVTZ are added, ZFK4 means from augcc-pVQZ, etc. The difference between ZFKn-DK3 and ZFKnLDK3 is that the common s and p exponents have been contracted as a single L-shell for the outermost s and p valence shells to save time in the "L" case. The s-block elements from 1s to 4s have also been put in the library. For H/He, all-electron aug-cc-pVnZ basis sets are used. For Li/Be, the relativistically contracted atomic natural orbital allelectron basis sets (ANO-RCC) are used. For Na/Mg, and K/Ca, unpublished MCP and basis sets based on ANO-RCC are available, although the potentials have not been extensively tested yet. No d-block elements can be used. * * * semiempirical basis sets * * * GBASIS = MNDO - selects MNDO model hamiltonian

Input Description = AM1 = PM3 = RM1

$BASIS - selects AM1 model hamiltonian - selects PM3 model Hamiltonian - selects RM1 model hamiltonian

2-30

Note: The elements for which these exist can be found in the 'further information' section of this manual. If you pick one of these, all other data in this group is ignored. Semi-empirical runs actually use valence-only Slater type orbitals (STOs), not Gaussian GTOs, but the keyword remains GBASIS. Except for NGAUSS, all other keywords such as NDFUNC, etc. will be ignored for these. If you add NGAUSS, STO-NG expansions of the valence STO functions in terms of Gaussians will be added to the log file. Plotting programs such as MacMolPlt can pick up this approximation to the STOs used up from the ouput, in order to draw the orbitals. The default NGAUSS=0 suppresses this output, but values up to 6 may be given to control the accuracy of the STO-NG printing. --- supplementary functions --NDFUNC = number of heavy atom polarization functions to be used. These are usually d functions, except for MINI/MIDI. The term "heavy" means Na on up when GBASIS=STO, HW, or N21, and from Li on up otherwise. The value may not exceed 3. The variable POLAR selects the actual exponents to be used, see also SPLIT2 and SPLIT3. (default=0) NFFUNC = number of heavy atom f type polarization functions to be used on Li-Cl. This may only be input as 0 or 1. (default=0) NPFUNC = number of light atom, p type polarization functions to be used on H-He. This may not exceed 3, see also POLAR. (default=0) DIFFSP = flag to add diffuse sp (L) shell to heavy atoms. Heavy means Li-F, Na-Cl, Ga-Br, In-I, Tl-At. The default is .FALSE. DIFFS = flag to add diffuse s shell to hydrogens. The default is .FALSE.

Input Description

$BASIS

2-31

Warning: if you use diffuse functions, please read QMTTOL in the $CONTRL group for numerical concerns. POLAR = = = = = = = exponent of polarization functions COMMON (default for GBASIS=STO,N21,HW,SBKJC) POPN31 (default for GBASIS=N31) POPN311 (default for GBASIS=N311, MC) DUNNING (default for GBASIS=DH, DZV) HUZINAGA (default for GBASIS=MINI, MIDI) HONDO7 (default for GBASIS=TZV)

SPLIT2 = an array of splitting factors used when NDFUNC or NPFUNC is 2. Default=2.0,0.5 SPLIT3 = an array of splitting factors used when NDFUNC or NPFUNC is 3. Default=4.00,1.00,0.25 The splitting factors are from the Pople school, and are probably too far apart. See for example the Binning and Curtiss paper. For example, the SPLIT2 value will usually cause an INCREASE over the 1d energy at the HF level for hydrocarbons. The actual exponents used for polarization functions, as well as for diffuse sp or s shells, are described in the 'Further References' section of this manual. This section also describes the sp part of the basis set chosen by GBASIS fully, with all references cited. Note that GAMESS always punches a full $DATA group. Thus, if $BASIS does not quite cover the basis you want, you can obtain this full $DATA group from EXETYP=CHECK, and then change polarization exponents, add Rydbergs, etc. * * * EXTFIL = a flag to read basis sets from an external file, defined by EXTBAS, rather than from a $DATA group. (default=.false.) Except for MCP basis sets, no external file is provided with GAMESS, thus you must create your own. The GBASIS keyword must give an 8 or less character string, obviously

Input Description

$BASIS

2-32

not using any internally stored names. Every atom must be defined in the external file by a line giving the chemical symbol, and this chosen string. Following this header line, give the basis in free format $DATA style, containing only S, P, D, F, G, and L shells, and terminating each atom by the usual blank line. The external file may have several families of bases in the same file, identified by different GBASIS strings. * * * This may only be used with COORD=UNIQUE or HINT! BASNAM = an array of names of customized basis set input groups. Built in basis sets can be used as parts of the basis sets. Obey the rule of no more than six characters starting with letters in the names, and avoid using any standard group names. This is best explained by an example where a core potential is used only on a transition metal, not the ligands: $contrl scftyp=rohf icharg=+3 mult=4 runtyp=gradient pp=read ispher=1 $end $system mwords=1 $end $guess guess=huckel $end $basis basnam(1)=metal, ligO,ligO,ligO,ligO,ligO,ligO, ligH,ligH,ligH,ligH,ligH,ligH, ligH,ligH,ligH,ligH,ligH,ligH $end $data Cr+3(H2O)6 complex...SBKJC & 6-31G(d) geometry Th CHROMIUM 24.0 .0000000000 .0 .0000000000 OXYGEN 8.0 .0000000000 .0 2.0398916104 HYDROGEN 1.0 .7757887450 .0 2.6122732372 $end ! core potential basis for Chromium $metal sbkjc $end ! $ligO normal 6-31G(d) for oxygen ligands

Input Description n31 6 d 1 ; 1 0.8 1.0 $end ! $ligH n31 6 $end $ecp Cr-ecp SBKJC O-ecp none O-ecp none O-ecp none O-ecp none O-ecp none O-ecp none H-ecp none ...snipped... H-ecp none $end

$BASIS

2-33

unpolarized basis for hydrogens

there must be 12 H's given here

=========================================================

Input Description

$DATA

2-34

==========================================================

$DATA group $DATAS group $DATAL group

(required) (if NESC chosen, for small component basis) (if NESC chosen, for large component basis)

This group describes the global molecular data such as point group symmetry, nuclear coordinates, and possibly the basis set. It consists of a series of free format card images. See $RELWFN for more information on large and small component basis sets. The input structure of $DATAS and $DATAL is identical to the COORD=UNIQUE $DATA input. ----------------------------------------------------------1TITLE a single descriptive title card.

----------------------------------------------------------2GROUP, NAXIS

GROUP is the Schoenflies symbol of the symmetry group, you may choose from C1, Cs, Ci, Cn, S2n, Cnh, Cnv, Dn, Dnh, Dnd, T, Th, Td, O, Oh. NAXIS is the order of the highest rotation axis, and must be given when the name of the group contains an N. For example, "Cnv 2" is C2v. "S2n 3" means S6. Use of NAXIS up to 8 is supported in each axial groups. For linear molecules, choose either Cnv or Dnh, and enter NAXIS as 4. Enter atoms as Dnh with NAXIS=2. If the electronic state of either is degenerate, check the note about the effect of symmetry in the electronic state in the SCF section of REFS.DOC. ---------------------------------------------------------In order to use GAMESS effectively, you must be able to recognize the point group name for your molecule. This presupposes a knowledge of group theory at about the level of Cotton's "Group Theory", Chapter 3.

Input Description

$DATA

2-35

Armed with only the name of the group, GAMESS is able to exploit the molecular symmetry throughout almost all of the program, and thus save a great deal of computer time. GAMESS does not require that you know very much else about group theory, although a deeper knowledge (character tables, irreducible representations, term symbols, and so on) is useful when dealing with the more sophisticated wavefunctions. Cards -3- and -4- are quite complicated, and are rarely given. A *SINGLE* blank card may replace both cards -3and -4-, to select the 'master frame', which is defined on the next page. If you choose to enter a blank line, skip to one of the -5- input sequences. Note! If the point group is C1 (no symmetry), skip over cards -3- and -4- (which means no blank card). ----------------------------------------------------------3For For For For For For X1, Y1, Z1, X2, Y2, Z2 C1 group, there is no card -3- or -4-. CI group, give one point, the center of inversion. CS group, any two points in the symmetry plane. axial groups, any two points on the principal axis. tetrahedral groups, any two points on a two-fold axis. octahedral groups, any two points on a four-fold axis.

----------------------------------------------------------4X3, Y3, Z3, DIRECT

third point, and a directional parameter. For CS group, one point of the symmetry plane, noncollinear with points 1 and 2. For CI group, there is no card -4-. For other groups, a generator sigma-v plane (if any) is the (x,z) plane of the local frame (CNV point groups). A generator sigma-h plane (if any) is the (x,y) plane of the local frame (CNH and dihedral groups).

Input Description

$DATA

2-36

A generator C2 axis (if any) is the x-axis of the local frame (dihedral groups). The perpendicular to the principal axis passing through the third point defines a direction called D1. If DIRECT='PARALLEL', the x-axis of the local frame coincides with the direction D1. If DIRECT='NORMAL', the x-axis of the local frame is the common perpendicular to D1 and the principal axis, passing through the intersection point of these two lines. Thus D1 coincides in this case with the negative y axis. ---------------------------------------------------------The 'master frame' is just a standard orientation for the molecule. By default, the 'master frame' assumes that 1. z is the principal rotation axis (if any), 2. x is a perpendicular two-fold axis (if any), 3. xz is the sigma-v plane (if any), and 4. xy is the sigma-h plane (if any). Use the lowest number rule that applies to your molecule. Some examples of these rules: Ammonia (C3v): the unique H lies in the XZ plane (R1,R3). Ethane (D3d): the unique H lies in the YZ plane (R1,R2). Methane (Td): the H lies in the XYZ direction (R2). Since there is more than one 3-fold, R1 does not apply. HP=O (Cs): the mirror plane is the XY plane (R4). In general, it is a poor idea to try to reorient the molecule. Certain sections of the program, such as the orbital symmetry assignment, do not know how to deal with cases where the 'master frame' has been changed. Linear molecules (C4v or D4h) must lie along the z axis, so do not try to reorient linear molecules. You can use EXETYP=CHECK to quickly find what atoms are generated, and in what order. This is typically necessary in order to use the general $ZMAT coordinates. * * * * Depending on your choice for COORD in $CONTROL,

Input Description if if if if if COORD=UNIQUE, COORD=HINT, COORD=CART, COORD=ZMT, COORD=ZMTMPC, follow follow follow follow follow

$DATA card card card card card sequence sequence sequence sequence sequence U U C G M

2-37

Card sequence U is the only one which allows you to define a completely general basis here in $DATA. Recall that UNIT in $CONTRL determines the distance units. ----------------------------------------------------------5UAtom input. Only the symmetry unique atoms are input, GAMESS will generate the symmetry equivalent atoms according to the point group selected above. if COORD=UNIQUE *************** NAME NAME, ZNUC, X, Y, Z

= 10 character atomic name, used only for printout. Thus you can enter H or Hydrogen, or whatever. ZNUC = nuclear charge. It is the nuclear charge which actually defines the atom's identity. X,Y,Z = Cartesian coordinates. if COORD=HINT ************* NAME,ZNUC,CONX,R,ALPHA,BETA,SIGN,POINT1,POINT2,POINT3 NAME = 10 character atomic name (used only for print out). ZNUC = nuclear charge. CONX = connection type, choose from 'LC' linear conn. 'CCPA' central conn. 'PCC' planar central conn. with polar atom 'NPCC' non-planar central conn. 'TCT' terminal conn. 'PTC' planar terminal conn. with torsion R = connection distance. ALPHA= first connection angle BETA = second connection angle SIGN = connection sign, '+' or '-' POINT1, POINT2, POINT3 = connection points, a serial number of a previously input atom, or one of 4 standard points: O,I,J,K

Input Description

$DATA

2-38

(origin and unit points on axes of master frame). defaults: POINT1='O', POINT2='I', POINT3='J' ref- R.L. Hilderbrandt, J.Chem.Phys. 51, 1654 (1969). You cannot understand HINT input without reading this. Note that if ZNUC is negative, the internally stored basis for ABS(ZNUC) is placed on this center, but the calculation uses ZNUC=0 after this. This is useful for basis set superposition error (BSSE) calculations. ---------------------------------------------------------* * * If you gave $BASIS, continue entering cards -5Uuntil all the unique atoms have been specified. When you are done, enter a " $END " card. * * * If you did not, enter cards -6U-, -7U-, -8U-. ----------------------------------------------------------6U- GBASIS, NGAUSS, (SCALF(i),i=1,4) GBASIS has exactly the same meaning as in $BASIS. You may choose from MINI, MIDI, STO, N21, N31, N311, DZV, DH, BC, TZV, MC, SBKJC, or HW. In addition, you may choose S, P, D, F, G, or L to enter an explicit basis set. Here, L means both an s and p shell with a shared exponent. In addition, GBASIS may be defined as MCP, to indicate that the current atom is represented by a model core potential, and valence basis set. An internally stored basis and potential will be applied (see REFS.DOC for the details). The MCP basis supplies only the occupied atomic orbitals, e.g. sp for a main group element, so please supplement with any desired polarization. In case the keyword MCP is followed by the keyword READ, everything will be taken from the input file, namely the basis functions are read using the sequence -6U-, -7U-, and -8U-, from lines following the "MCP READ" line. In addition, "MCP READ" implies that the parameters of the model core potentials, together with core basis functions are in the input stream, in a $MCP group. Other MCP bases are available in the $BASIS group, but note that to locate the MCP, the atom name must be a chemical symbol, that is "P" instead of "Phosphorus".

Input Description

$DATA

2-39

NGAUSS is the number of Gaussians (N) in the Pople style basis, or user input general basis. It has meaning only for GBASIS=STO, N21, N31, or N311, and S,P,D,F,G, or L. Up to 4 scale factors may be entered. If omitted, standard values are used. They are not documented as every GBASIS treats these differently. Read the source code if you need to know more. They are seldom given. ---------------------------------------------------------* * * If GBASIS is not S,P,D,F,G, or L, either add more shells by repeating card -6U-, or go on to -8U-. * * * If GBASIS=S,P,D,F,G, or L, enter NGAUSS cards -7U-. ----------------------------------------------------------7U- IG, ZETA, C1, C2 IG = a counter, IG takes values 1, 2, ..., NGAUSS. ZETA = Gaussian exponent of the IG'th primitive. C1 = Contraction coefficient for S,P,D,F,G shells, and for the s function of L shells. C2 = Contraction coefficient for the p in L shells. ---------------------------------------------------------* * * For more shells on this atom, go back to card -6U-. * * * If there are no more shells, go on to card -8U-. ----------------------------------------------------------8UA blank card ends the basis set for this atom. ---------------------------------------------------------Continue entering atoms with -5U- through -8U- until all are given, then terminate the group with a " $END " card. --- this is the end of card sequence U --COORD=CART input: ----------------------------------------------------------5C- Atom input. Cartesian coordinates for all atoms must be entered. They may be arbitrarily rotated or translated, but must possess the actual point group symmetry. GAMESS will reorient the

Input Description

$DATA

2-40

molecule into the 'master frame', and determine which atoms are the unique ones. Thus, the final order of the atoms may be different from what you enter here. NAME, ZNUC, X, Y, Z NAME = 10 character atomic name, used only for printout. Thus you can enter H or Hydrogen, or whatever. ZNUC = nuclear charge. It is the nuclear charge which actually defines the atom's identity. X,Y,Z = Cartesian coordinates. ---------------------------------------------------------Continue entering atoms with card -5C- until all are given, and then terminate the group with a " $END " card. --- this is the end of card sequence C --COORD=ZMT input: (GAUSSIAN style internals)

----------------------------------------------------------5GATOM

Only the name of the first atom is required. See -8G- for a description of this information. ----------------------------------------------------------6GATOM i1 BLENGTH

Only a name and a bond distance is required for atom 2. See -8G- for a description of this information. ----------------------------------------------------------7GATOM i1 BLENGTH i2 ALPHA

Only a name, distance, and angle are required for atom 3. See -8G- for a description of this information. ----------------------------------------------------------8GATOM ATOM i1 BLENGTH i2 ALPHA i3 BETA i4

is the chemical symbol of this atom. It can be followed by numbers, if desired, for example Si3.

Input Description

$DATA

2-41

The chemical symbol implies the nuclear charge. i1 defines the connectivity of the following bond. BLENGTH is the bond length "this atom-atom i1". i2 defines the connectivity of the following angle. ALPHA is the angle "this atom-atom i1-atom i2". i3 defines the connectivity of the following angle. BETA is either the dihedral angle "this atom-atom i1atom i2-atom i3", or perhaps a second bond angle "this atom-atom i1-atom i3". i4 defines the nature of BETA, If BETA is a dihedral angle, i4=0 (default). If BETA is a second bond angle, i4=+/-1. (sign specifies one of two possible directions). ---------------------------------------------------------o o o Repeat -8G- for atoms 4, 5, ... The use of ghost atoms is possible, by using X or BQ for the chemical symbol. Ghost atoms preclude the option of an automatic generation of $ZMAT. The connectivity i1, i2, i3 may be given as integers, 1, 2, 3, 4, 5,... or as strings which match one of the ATOMs. In this case, numbers must be added to the ATOM strings to ensure uniqueness! In -6G- to -8G-, symbolic strings may be given in place of numeric values for BLENGTH, ALPHA, and BETA. The same string may be repeated, which is handy in enforcing symmetry. If the string is preceeded by a minus sign, the numeric value which will be used is the opposite, of course. Any mixture of numeric data and symbols may be given. If any strings were given in -6G- to -8G-, you must provide cards -9G- and -10G-, otherwise you may terminate the group now with a " $END " card.

----------------------------------------------------------9GA blank line terminates the Z-matrix section.

----------------------------------------------------------10GSTRING VALUE

STRING is a symbolic string used in the Z-matrix. VALUE is the numeric value to substitute for that string.

Input Description

$DATA

2-42

---------------------------------------------------------Continue entering -10G- until all STRINGs are defined. Note that any blank card encountered while reading -10Gwill be ignored. GAMESS regards all STRINGs as variables (constraints are sometimes applied in $STATPT). It is not necessary to place constraints to preserve point group symmetry, as GAMESS will never lower the symmetry from that given at -2-. When you have given all STRINGs a VALUE, terminate the group with a " $END " card. --- this is the end of card sequence G --* * * * The documentation for sequence G above and sequence M below presumes you are reasonably familiar with the input to GAUSSIAN or MOPAC. It is probably too terse to be understood very well if you are unfamiliar with these. A good tutorial on both styles of Z-matrix input can be found in Tim Clark's book "A Handbook of Computational Chemistry", published by John Wiley & Sons, 1985. Both Z-matrix input styles must generate a molecule which possesses the symmetry you requested at -2-. If not, your job will be terminated automatically. COORD=ZMTMPC input: (MOPAC style internals)

----------------------------------------------------------5MATOM

Only the name of the first atom is required. See -8M- for a description of this information. ----------------------------------------------------------6MATOM BLENGTH

Only a name and a bond distance is required for atom 2. See -8M- for a description of this information. ----------------------------------------------------------7MATOM BLENGTH j1 ALPHA j2

Input Description

$DATA

2-43

Only a bond distance from atom 2, and an angle with repect to atom 1 is required for atom 3. If you prefer to hook atom 3 to atom 1, you must give connectivity as in -8M-. See -8M- for a description of this information. ----------------------------------------------------------8MATOM BLENGTH j1 ALPHA j2 BETA j3 i1 i2 i3

ATOM, BLENGTH, ALPHA, BETA, i1, i2 and i3 are as described at -8G-. However, BLENGTH, ALPHA, and BETA must be given as numerical values only. In addition, BETA is always a dihedral angle. i1, i2, i3 must be integers only. The j1, j2 and j3 integers, used in MOPAC to signal optimization of parameters, must be supplied but are ignored here. You may give them as 0, for example. ---------------------------------------------------------Continue entering atoms 3, 4, 5, ... with -8M- cards until all are given, and then terminate the group by giving a " $END " card. --- this is the end of card sequence M --========================================================== This is the end of $DATA! If you have any doubt about what molecule and basis set you are defining, or what order the atoms will be generated in, simply execute an EXETYP=CHECK job to find out!

Input Description

$ZMAT

2-44

==========================================================

$ZMAT

group

(required if NZVAR is nonzero in $CONTRL)

This group lets you define the internal coordinates in which the gradient geometry search is carried out. These need not be the same as the internal coordinates used in $DATA. The coordinates may be simple Z-matrix types, delocalized coordinates, or natural internal coordinates. You must input a total of M=3N-6 internal coordinates (M=3N-5 for linear molecules). NZVAR in $CONTRL can be less than M IF AND ONLY IF you are using linear bends. It is also possible to input more than M coordinates if they are used to form exactly M linear combinations for new internals. These may be symmetry coordinates or natural internal coordinates. If NZVAR > M, you must input IJS and SIJ below to form M new coordinates. See DECOMP in $FORCE for the only circumstance in which you may enter a larger NZVAR without giving SIJ and IJS. **** IZMAT defines simple internal coordinates **** IZMAT is an array of integers defining each coordinate. The general form for each internal coordinate is code number,I,J,K,L,M,N IZMAT =1 followed by two atom numbers. (I-J bond length) =2 followed by three numbers. (I-J-K bond angle) =3 followed by four numbers. (dihedral angle) Torsion angle between planes I-J-K and J-K-L. =4 followed by four atom numbers. (atom-plane) Out-of-plane angle from bond I-J to plane J-K-L. =5 followed by three numbers. (I-J-K linear bend) Counts as 2 coordinates for the degenerate bend, normally J is the center atom. See $LIBE. =6 followed by five atom numbers. (dihedral angle) Dihedral angle between planes I-J-K and K-L-M. =7 followed by six atom numbers. (ghost torsion) Let A be the midpoint between atoms I and J, and B be the midpoint between atoms M and N. This coordinate is the dihedral angle A-K-L-B. The atoms I,J and/or M,N may be the same atom number. (If I=J AND M=N, this is a conventional torsion). Examples: N2H4, or, with one common pair, H2POH.

Input Description

$ZMAT

2-45

Example - a nonlinear triatomic, atom 2 in the middle: $ZMAT IZMAT(1)=1,1,2, 2,1,2,3, 1,2,3 $END This sets up two bonds and the angle between them. The blanks between each coordinate definition are not necessary, but improve readability mightily. **** the next define delocalized coordinates **** DLC AUTO is a flag to request delocalized coordinates. (default is .FALSE.) is a flag to generate all redundant coordinates, automatically. The DLC space will consist of all non-redundant combinations of these which can be found. The list of redundant coordinates will consist of bonds, angles, and torsions only. (default is .FALSE.)

NONVDW is an array of atom pairs which are to be joined by a bond, but might be skipped by the routine that automatically includes all distances shorter than the sum of van der Waals radii. Any angles and torsions associated with the new bond(s) are also automatically included. The format for IXZMAT, IRZMAT, IFZMAT is that of IZMAT: IXZMAT is an extra array of simple internal coordinates which you want to have added to the list generated by AUTO. Unlike NONVDW, IXZMAT will add only the coordinate(s) you specify. IRZMAT is an array of simple internal coordinates which you would like to remove from the AUTO list of redundant coordinates. It is sometimes necessary to remove a torsion if other torsions around a bond are being frozen, to obtain a nonsingular G matrix. IFZMAT is an array of simple internal coordinates which you would like to freeze. See also FVALUE below, which is required input when IFZMAT is given. IFZMAT/FVALUE work with ordinary coordinate input using IZMAT, as well as with DLC, but in the former

Input Description

$ZMAT

2-46

case be careful that IFZMAT specifies coordinates that were already given in IZMAT. In addition, IFZMAT works only for IZMAT=1,2,3 type coordinates. See IFREEZ in $STATPT you wish to freeze regular or natural internal coordinates. FVALUE is an array of values to which the internal coordinates should be constrained. It is not necessary to input $DATA such that the initial values match these desired final values, but it is helpful if the initial values are not too far away. **** SIJ,IJS define natural internal coordinates **** SIJ is a transformation matrix of dimension NZVAR x M, used to transform the NZVAR internal coordinates in IZMAT into M new internal coordinates. SIJ is a sparse matrix, so only the non-zero elements are given, by using the IJS array described below. The columns of SIJ will be normalized by GAMESS. (Default: SIJ = I, unit matrix) IJS is an array of pairs of indices, giving the row and column index of the entries in SIJ. example - if the above triatomic is water, using IJS(1) = 1,1, 3,1, 1,2, 3,2, 2,3 SIJ(1) = 1.0, 1.0, 1.0,-1.0, 1.0 gives the matrix S= 1.0 0.0 1.0 1.0 0.0 -1.0 0.0 1.0 0.0

which defines the symmetric stretch, asymmetric stretch, and bend of water. references for natural internal coordinates: P.Pulay, G.Fogarasi, F.Pang, J.E.Boggs J.Am.Chem.Soc. 101, 2550-2560(1979) G.Fogarasi, X.Zhou, P.W.Taylor, P.Pulay J.Am.Chem.Soc. 114, 8191-8201(1992) reference for delocalized coordinates: J.Baker, A. Kessi, B.Delley J.Chem.Phys. 105, 192-212(1996)

Input Description

$ZMAT

2-47

==========================================================

Input Description

$LIBE

2-48

==========================================================

$LIBE

group

(required if linear bends are used in $ZMAT)

A degenerate linear bend occurs in two orthogonal planes, which are specified with the help of a point A. The first bend occurs in a plane containing the atoms I,J,K and the user input point A. The second bend is in the plane perpendicular to this, and containing I,J,K. One such point must be given for each pair of bends used. APTS(1)= x1,y1,z1,x2,y2,z2,... for linear bends 1,2,...

Note that each linear bend serves as two coordinates, so that if you enter 2 linear bends (HCCH, for example), the correct value of NZVAR is M-2, where M=3N-6 or 3N-5, as appropriate. ==========================================================

Input Description

$SCF

2-49

==========================================================

$SCF

group

relevant if SCFTYP = RHF, UHF, or ROHF, required if SCFTYP = GVB)

This group of parameters provides additional control over the RHF, UHF, ROHF, or GVB SCF steps. It must be given to define GVB open shell or perfect pairing wavefunctions. See $MCSCF for multireference inputs. DIRSCF = a flag to activate a direct SCF calculation, which is implemented for all the Hartree-Fock type wavefunctions: RHF, ROHF, UHF, and GVB. This keyword also selects direct MP2 computation. The default of .FALSE. stores integrals on disk storage for a conventional SCF calculation. FDIFF = a flag to compute only the change in the Fock matrices since the previous iteration, rather than recomputing all two electron contributions. This saves much CPU time in the later iterations. This pertains only to direct SCF, and has a default of .TRUE. This option is implemented only for the RHF, ROHF, UHF cases. Cases with many diffuse functions in the basis set, or large molecules, may sometimes be "mushy" at the end, rather than converging. Increasing ICUT in $CONTRL by one may help this, or consider turning this parameter off. ---- The next flags affect convergence rates. NOCONV = .TRUE. means neither SOSCF nor DIIS will be used. The default is .FALSE., making the choice of the primary converger as follows: for RHF, GVB, UHF, or ROHF (if Abelian): SOSCF for any DFT, or for non-Abelian groups: DIIS. DIIS = selects Pulay's DIIS interpolation. SOSCF = selects second order SCF orbital optimization. Once either DIIS or SOSCF are initiated, the following less important accelerators are placed in abeyance: EXTRAP = selects Pople extrapolation of the Fock matrix.

Input Description DAMP SHIFT RSTRCT DEM = = = =

$SCF

2-50

selects Davidson damping of the Fock matrix. selects level shifting of the Fock matrix. selects restriction of orbital interchanges. selects direct energy minimization, which is implemented only for RHF. (default=.FALSE.) EXTRAP T T DAMP F F SHIFT RSTRCT F F F F DIIS F/T F SOSCF T/F F

defaults for ab initio: semiempirical:

The above parameters are implemented for all SCF wavefunction types, except that DIIS will work for GVB only for those cases with NPAIR=0 or NPAIR=1. ---- These parameters fine tune the various convergers. CONV = SCF density convergence criteria. Convergence is reached when the density change between two consecutive SCF cycles is less than this in absolute value. One more cycle will be executed after reaching convergence. Less accuracy in CONV gives questionable gradients. The default is 1.0d-05, except runs involving CI, MP2, CC, or TDDFT use 1.0d-06 to obtain more crisply converged virtual orbitals.

SOGTOL = second order gradient tolerance. SOSCF will be initiated when the orbital gradient falls below this threshold. (default=0.25 au) ETHRSH = energy error threshold for initiating DIIS. The DIIS error is the largest element of e=FDS-SDF. Increasing ETHRSH forces DIIS on sooner. (default = 0.5 Hartree) MAXDII = Maximum size of the DIIS linear equations, so that at most MAXDII-1 Fock matrices are used in the interpolation. (default=10) SWDIIS = density matrix convergence at which to switch from DIIS to SOSCF. A value of zero means to keep using DIIS at all geometries, which is the default. However, it may be useful to have DIIS work only at the first geometry, in the

Input Description

$SCF

2-51

initial iterations, for example transition metal ECP runs which has a less good Huckel guess, and then use SOSCF for the final SCF iterations at the first geometry, and ever afterwards. A suggested usage might be DIIS=.TRUE. ETHRSH=2.0 SWDIIS=0.005. This option is not programmed for GVB. DEMCUT = Direct energy minimization will not be done once the density matrix change falls below this threshold. (Default=0.5) DMPCUT = Damping factor lower bound cutoff. The damping damping factor will not be allowed to drop below this value. (default=0.0) note: The damping factor need not be zero to achieve valid convergence (see Hsu, Davidson, and Pitzer, J.Chem.Phys., 65, 609 (1976), see the section on convergence control), but it should not be astronomical either. * * For see * * * * * * * * * * * * * * * * * * * * * more info on the convergence methods, the 'Further Information' section. * * * * * * * * * * * * * * * * * * *

---- orbital modification options ---The four options UHFNOS, VVOS, MVOQ, and ACAVO are mutually exclusive. The latter 3 require RUNTYP=ENERGY, and should not be used with any correlation treatment. UHFNOS = flag controlling generation of the natural orbitals of a UHF function. (default=.FALSE.) VVOS = flag controlling generation of Valence Virtual Orbitals. See J.Chem.Phys. 120, 2629-2637(2004). VVOs are a quantitative realization of the concept of "lowest unoccupied orbital" and are also useful for MCSCF starting orbitals. The implementation at present allows only RHF functions, elements up to Xe (excluding transition metals), and core potentials may not be used. The default is .FALSE. VVOS should be better MCSCF starting orbitals than either MVOQ or ACAVO type virtuals. MVOQ = 0 Skip MVO generation (default)

Input Description = n

$SCF

2-52

Form modified virtual orbitals, using a cation with n electrons removed. Implemented for RHF, ROHF, and GVB. If necessary to reach a closed shell cation, the program might remove n+1 electrons. Typically, n will be about 6. = -1 The cation used will have each valence orbital half filled, to produce MVOs with valence-like character in all regions of the molecule. Implemented for RHF and ROHF only. ACAVO = Flag to request Approximate Correlation-Adapted Virtual Orbitals. Implemented for RHF, ROHF, and GVB (w/o direct SCF). Default is .FALSE.

PACAVO =

Parameters used to define the ACAVO generating operator, which is defined as a*T + b*Vne + c*Jcore + d*Jval + e*Kcore + f*Kval The default, PACAVO(1)=0,0,0,0,0,-1, maximizes the exchange interaction with valence MOs (see for example J.L.Whitten, J.Chem.Phys. 56, 5458-5466(1972). The K-orbitals of D.Feller, E.R.Davidson J.Chem.Phys. 74, 3977-3979 are PACAVO(1)= 0.06,0.06,0.12,0.12,-0.06,-1.06, which is 0.06*F-K(valence). Of course, canonical virtuals are PACAVO(1)=1,1,2,2,-1,-1. ----- GVB wavefunction input ----The next parameters define the GVB wavefunction. See also MULT in the $CONTRL group. The GVB wavefunction assumes orbitals are in the order core, open, pairs. NCO = The number of closed shell orbitals. The default almost certainly should be changed! (default=0). The number of sets of open shells in the function. Maximum of 10. (default=0) An array giving the degeneracy of each open shell set. Give NSETO values. (default=0,0,0,...). The number of geminal pairs in the -GVBfunction. Maximum of 12. The default corresponds to open shell SCF (default=0).

NSETO NO

= =

NPAIR

Input Description

$SCF

2-53

CICOEF =

An array of ordered pairs of CI coefficients for the -GVB- pairs. (default = 0.90,-0.20,0.90,-0.20,...) For example, a two pair case for water, say, might be CICOEF(1)=0.95,-0.05,0.95,-0.05. If not normalized, as in the default, CICOEF will be. This parameter is useful in restarting a GVB run, with the current CI coefficients. COUPLE = A switch controlling the input of F, ALPHA, and BETA. (Default=.FALSE.) Input for F, ALPHA, BETA will be ignored unless you select this variable as .TRUE. F ALPHA BETA = = = An vector of fractional shell occupations. An array of A coupling coefficients, given in lower triangular order. An array of B coupling coefficients, given in lower triangular order.

Note: The default for F, ALPHA, and BETA depends on the state chosen. Defaults for the most commonly occuring cases are internally stored. See "Further Information" for other cases, including degenerate open shells. Note: ALPHA and BETA can be given for -ROHF- orbital canonicalization control, see "Further Information". ----- miscellaneous options ----NPUNCH = = = = NPREO 0 1 2 option for output to the PUNCH file do not punch out the final orbitals punch out the occupied orbitals punch out occupied and virtual orbitals The default is NPUNCH = 2.

= energy and orbital printing options, applying after other output options, for example NPRINT=-5 for no orbital output overrules this keyword. Orbitals from NPREO(1) to NPREO(2) and orbital energies from NPREO(3) to NPREO(4) are printed. Positive values indicate plain ordinal numbers. Non-positive values are relative to HOMO. For NPREO(1) and (3), 0 is HOMO, -1 is HOMO+1 etc.

Input Description

$SCF

2-54

For NPREO(2) and (4), 0 is HOMO, -1 is HOMO+1 etc. Numbers exceeding the total orbital count are automatically adjusted to the maximum value. Orbitals printed by NPREO(1) and NPREO(2) will always have the orbital energy labels attached, NPREO(3) to NPREO(4) define separate print-out of the orbital energies. HOMO here means the highest occupied orbital, assuming a singlet RHF orbital occupation, that is to say NE/2, no matter what SCFTYP is. To print only the HOMO and LUMO LCAO coefficients. and all orbital energies, enter: NPREO(1)=0,-1,1,9999 Default: 1,9999,2,1 (meaning print all orbitals, but no separate list of orbital energies). ----- options for virial scaling ----VTSCAL = A flag to request that the virial theorem be satisfied. An analysis of the total energy as an exact sum of orbital kinetic energies is printed. The default is .FALSE. This option is implemented for RHF, UHF, and ROHF, for RUNTYP=ENERGY, OPTIMIZE, or SADPOINT. Related input is: SCALF = initial exponent scale factor when VTSCAL is in use, useful when restarting. The default is 1.0. maximum number of iterations (at a single geometry) to satisfy the energy virial theorem. The default is 20. convergence criterion for the VT, which is satisfied when 2<T> + <V> + R x dE/dR is less than VTCONV. The default is 1.0D-6 Hartree.

MAXVT

VTCONV =

For more information on this option, which is most useful during a geometry search, see M.Lehd and F.Jensen, J.Comput.Chem. 12, 1089-1096(1991). * * * * * * * * * * * * * * * * * * * For more discussion of GVB/ROHF input see the 'further information' section

Input Description

$SCF * * * * * * * * * * * * * * * * * * *

2-55

==========================================================

Input Description

$SCFMI

2-56

==========================================================

$SCFMI

group

(optional, relevant if SCFTYP=RHF)

The Self Consistent Field for Molecular Interactions (SCF-MI) method is a modification of the usual Roothaan equations that avoids basis set superposition error (BSSE) in intermolecular interaction calculations, by expanding each monomer's orbitals using only its own basis set. Thus, the resulting orbitals are not orthogonal. The presence of a $SCFMI group in the input triggers the use of this option. The implementation is limited to ten monomers, treated at the RHF level. The energy, gradient, and therefore semi-numerical hessian are available. The SCF step may be run in direct SCF mode, and parallel calculation is also enabled. The calculation must use Cartesian Gaussian AOs only, not spherical harmonics. The SCF-MI driver differs from normal RHF calculations, so not all converger methods are available. Finally, this option is not compatible with electron correlation treatments (DFT, MP2, CI, or CC). The first 3 parameters must be given. All atoms of a fragment must appear consecutively in $DATA. NFRAGS = number of distinct fragments present. Both the supermolecule and its constituent monomers must be well described as closed shells by RHF wavefunctions. = an array containing the number of doubly MOs for each fragment. = an array containing the number of atomic basis functions located on each fragment. = maximum number of SCF-MI cycles, overriding the usual MAXIT value. (default is 50). = SCF-MI density convergence criteria. (default is 1.0d-10)

NF occupied MF ITER DTOL

Input Description ALPHA DIISON MXDIIS and

$SCFMI

2-57

= possible level shift parameter. (default is 0.0, meaning shifting is not used) = a flag to active the DIIS convergence. (default is .TRUE.) = the maximum number of previous effective Fock overlap matrices to be used in DIIS

(default=10) DIISTL = the density change value at which DIIS starts. (default=0.01)

A Huckel guess is localized by the Boys procedure onto each fragment to provide starting orbitals for each: ITLOC CNVLOC IOPT = maximum number of iteration in the localization step (Default is 50) = convergence parameter for the localization. (default is .01). = prints additional debug information. = 0 standard outout (default) = 1 print for each SCF-MI cycle MOs, overlap between the MOs, CPU times. = 2 print some extra informations in secular systems solution.

========================================================== "Modification of Roothan Equations to exclude BSSE from Molecular Interaction calculations" E. Gianinetti, M. Raimondi, E. Tornaghi Int. J. Quantum Chem. 60, 157-166 (1996) "Implementation of Gradient optimization algorithms and Force Constant computations in BSSE-free direct and conventional SCF approaches" A. Famulari, E. Gianinetti, M. Raimondi, M. Sironi Int. J. Quantum Chem. 69, 151-158 (1997)

Input Description

$DFT

2-58

==========================================================

$DFT

group

(relevant if DFTTYP is chosen) (relevant if SCFTYP=RHF,UHF,ROHF)

Note that if DFTTYP=NONE, an ab initio calculation will be performed, rather than density functional theory. This group permits the use of various one electron (usually empirical) operators instead of the true many electron Hamiltonian. Two programs are provided, METHOD= GRID or GRIDFREE. The programs have different functionals available, and so the keyword DFTTYP (which is entered in $CONTRL) and other associated inputs are documented separately below. Every functional that has the same name in both lists is an identical functional, but each METHOD has a few functionals that are missing in the other. The grid free implementation is based on the use of the resolution of the identity to simplify integrals so that they may be analytically evaluated, without using grid quadratures. The grid free DFT computations in their present form have various numerical errors, primarily in the gradient vectors. Please do not use the grid-free DFT program without reading the discussion in the 'Further References' section regarding the gradient accuracy. The grid based DFT uses a typical grid quadrature to compute integrals over the rather complicated functionals, using two possible angular grid types. Achieving a self-consistent field with DFT is rather more difficult than for normal HF, so DIIS is the default converger. Both DFT programs will run in parallel. See the two lists below for possible functionals in the two programs. See also the $TDDFT input group for excited states. METHOD = selects grid based DFT or grid free DFT. = GRID Grid based DFT (default) = GRIDFREE Grid free DFT

Input Description

$DFT

2-59

DFTTYP is given in $CONTRL, not here in $DFT! Possible values for the grid-based program are listed first, ----- options for METHOD=GRID ----DFTTYP = NONE means ab initio computation (default)

Many choices are given below, perhaps the most sensible are local DFT: SVWN pure DFT GGA: BLYP, PW91, B97-D, PBE/PBEsol hybrid DFT GGA: B3LYP, X3LYP, PBE0 pure DFT meta-GGA: revTPSS hybrid DFT meta-GGA: TPSSh, M06 but of course, everyone has their own favorite! pure exchange functionals: = SLATER Slater exchange = BECKE Becke 1988 exchange = GILL Gill 1996 exchange = OPTX Handy-Cohen exchange = PW91X Perdew-Wang 1991 exchange = PBEX Perdew-Burke-Ernzerhof exchange These will be used with no correlation functional at all. pure correlation functionals: = VWN Vosko-Wilk-Nusair correlation, using their electron gas formula 5 (VWN5) = VWN1 Vosko-Wilke-Nusair correlation, using their e- gas formula 1, with RPA params. = PZ81 Perdew-Zener 1981 correlation = P86 Perdew 1986 correlation = LYP Lee-Yang-Parr correlation = PW91C Perdew-Wang 1991 correlation = PBEC Perdew-Burke-Ernzerhof correlation = OP One-parameter Progressive correlation These will be used with 100% HF exchange, if chosen. combinations (partial list): SLATER exchange + VWN5 correlation Called LDA/LSDA in physics for RHF/UHF. = BLYP BECKE exchange + LYP correlation = SVWN

Input Description = = = = = = = = =

$DFT

2-60

BOP BECKE exchange + OP correlation BP86 BECKE exchange + P86 correlation GVWN GILL exchange + VWN5 correlation GPW91 GILL exchange + PW91 correlation PBEVWN PBE exchange + VWN5 correlation PBEOP PBE exchange + OP correlation OLYP OPTX exchange + LYP correlation PW91 means PW91 exchange + PW91 correlation PBE means PBE exchange + PBE correlation There's a nearly infinite set of pairings (well, 6*8), so we show only enough to give you the idea. In other words, pairs are formed by abbreviating the exchange functionals SLATER=S, BECKE=B, GILL=G, OPTX=O, PW91X=PW91, PBEX=PBE and matching them with any correlation functional, of which only two are abbreviated when used in combinations, PW91C=PW91, PBEC=PBE The pairings shown above only scratch the surface, but clearly, many possibilities, such as PW91PBE, are nonsense! pure DFT GGA functionals: empirical density functional #1, which is a modified BLYP from Adamson/Gill/Pople. PW91 Perdew/Wang 1991 PBE Perdew/Burke/Ernzerhof 1996 revPBE PBE as revised by Zhang/Yang RPBE PBE as revised by Hammer/Hansen/Norskov PBEsol PBE as revised by Perdew et al for solids HCTH93 Hamprecht/Cohen/Tozer/Handy's 1998 mod to B97, omitting HF exchange, fitting to 93 atoms and molecules HCTH120 later fit to 120 systems HCTH147 later fit to 147 systems HCTH407 later fit to 407 systems (best) SOGGA PBE revised by Zhang/Truhlar for solids MOHLYP metal optimized OPTX, half LYP B97-D Grimme's modified B97, with dispersion correction (this forces DC=.TRUE.)

= EDF1 = = = = = = = = = = = =

hybrid GGA functionals: = BHHLYP HF and BECKE exchange + LYP correlation = B3PW91 Becke's 3 parameter exchange hybrid, with PW91 correlation functional = B3LYP this is a hybrid method combining five

Input Description

$DFT

2-61

functionals, namely Becke + Slater + HF exchange, and LYP + VWN5 correlation. = B3LYP1 use VWN1 in place of VWN5, matching the e- gas formula chosen by some programs. = B97 Becke's 1997 hybrid functional = B97-1 Hamprecht/Cohen/Tozer/Handy's 1998 reparameterization of B97 = B97-2 Wilson/Bradley/Tozer's 2001 mod to B97 = B97-3 Keal/Tozer's 2005 mod to B97 = B97-K Boese/Martin's 2004 mod for kinetics = B98 Schmider/Becke's 1998 mode to B97, using their best "2c" parameters. = PBE0 a hybrid made from PBE = X3LYP HF+Slater+Becke88+PW91 exchange, and LYP+VWN1 correlation. Each includes some Hartree-Fock exchange, and also may use a linear combination of many DFT parts. range separated functionals: These are also known as "long-range corrected functionals". LC-BOP, LC-BLYP, or LC-BVWN are available by selecting BOP, BLYP, BVWN as well as setting the flag LC=.TRUE. (see LC below). Others are selected by a specific name: = CAMB3LYP coulomb attenuated B3LYP = wB97 omega separated form of B97 = wB97X wB97 with short-range HF exchange = wB97X-D dispersion corrected wB97X "double hybrid" GGA: = B2PLYP mixes BLYP, HF exchange, and MP2! It lacks analytic nuclear derivatives. See related inputs CHF and CMP2 below. "double hybrid" and "range separated": = wB97X-2 intended for use with GBASIS=CCT,CCQ,CC5 = wB97X-2L intended for use with GBASIS=N311 NGAUSS=6 NDFUNC=3 NFFUNC=1 NPFUNC=3 DIFFSP=.T. DIFFS=.T. Note: the B2PLYP family uses the conventional MP2 energy and may be used for closed shell or spin-unrestricted open shell cases. The wB97X-2 family uses the SCS-MP2 energy, and thus is limited to closed shell cases at present.

Input Description

$DFT

2-62

meta-GGA functionals: These are not hybridized with HF exchange, unless that is explicitly stated below. = VS98 Voorhis/Scuseria, 1998 = PKZB Perdew/Kurth/Zupan/Blaha, 1999 = tHCTH Boese/Handy's 2002 metaGGA akin to HCTH = tHCTHhyb tHCTH's hybrid with 15% HF exchange = BMK Boese/Martin's 2004 parameterization of tHCTHhyb for kinetics = TPSS Tao/Perdew/Staroverov/Scuseria, 2003 = TPSSh TPSS hybrid with 10% HF exchange = TPSSm TPSS with modified parameter, 2007 = revTPSS revised TPSS, 2009 = M05 Minnesota exchange-correlation, 2005 a hybrid with 28% HF exchange. = M05-2X M05, with doubled HF exchange, to 56% = M06 Minnesota exchange-correlation, 2006 a hybrid with 27% HF exchange. = M06-L M06, with 0% HF exchange (L=local) = M06-2X M06, with doubled HF exchange, to 54% = M06-HF M06 correlation, using 100% HF exchange = M08-HX M08 with 'high HF exchange' = M08-SO M08 of similar form, different params When the M06 family was created, Truhlar recommended M06 for the general situation, but see his "concluding remarks" in the M06 reference about which functional is best for what kind of test data set. An extensive bibliography for these functionals can be found in the 'Further References' section of this manual. Note that only a subset of these functionals can be used for TD-DFT energy or gradients. These subsets are listed in the $TDDFT input group. * * dispersion corrections * * *

DFT is notorious for failures to compute intra- and intermolecular dispersion interactions accurately. Two possible correction schemes are provided below. The first uses empirically chosen C6 and C8 coefficients, while the latter obtains these from the molecular DFT densities. At most, only one of the LRDFLG or DC options below may be chosen.

Input Description DC

$DFT

2-63

= a flag to turn on Grimme's empirical dispersion correction, involving scaled R**(-6) terms. N.B. This empiricism may also be added to plain Hartree-Fock, by choosing DFTTYP=NONE with DC=.T. Three different versions exist, see IDCVER. (default=.FALSE., except if DFTTYP=B97-D, wB97X-D)

IDCVER = 1 means 1st 2004 implementation. = 2 means 2nd 2006 implementation DFT-D2, default for B97-D, wB97X-D. = 3 means 3rd 2010 implementation DFT-D3, default for all others. Setting IDCVER will force DC=.TRUE. DCCHG = a flag to use Chai-Head-Gordon damping function instead of Grimme's 2006 function. Pertinent only for the DFT-D2 method. Forces DC=.TRUE. (default=.FALSE. except for wB97X-D) = a flag to turn on the computation of the E(3) nonadditive energy term. Pertinent only for DFT-D3, it forces DC=.TRUE. (default=.FALSE.)

DCABC

The following parameters govern Grimme's semiempirical dispersion term. They are basis set and functional dependent, so they exist for only a few DFTTYP. Default values are automatically selected and printed out in the output file for many common density functionals. The following keywords are for entering non-standard values. For DFT-D2 values, see also: R.Peverati and K.K.Baldridge J.Chem.Theory Comput. 4, 2030-2048 (2008). For DFT-D3 values, and a detailed explanation of each parameter, see: S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J.Chem.Phys. 132, 154104/1-19(2010) DCALP = alpha parameter in the DFT-D damping function (same as alpha6 in Grimme's DFT-D3 notation). Note also that alpha8 and alpha10 in DFT-D3 have constrained values of: alpha8 = alpha6 + 2, alpha10 = alpha8 + 2. Default=14.0 for DFT-D3 =20.0 for DFT-D2 =23.0 for DFT-D1

Input Description

$DFT =6.00 for DCCHG=.TRUE.

2-64

DCSR

= sR exponential parameter to scale the van der Waals radii (same as sR,6 in Grimme's DFT-D3 notation). Note also that sR,8 in DFT-D3 have a fixed value of 1.0. Optimized values are automatically selected for some of the more common functionals, otherwise, the default is 1.00 for DFT-D3, 1.10 for DFT-D2, and 1.22 for DFT-D1. = s6 linear parameter for scaling the C6 term. Optimized values are automatically selected for some of the more common functionals, otherwise, the default is 1.00. = s8 linear parameter for scaling the C8 term of DFT-D3. Pertinent only for DFT-D3. Optimized values are automatically selected for some of the more common functionals, otherwise, the default is 1.00.

DCS6

DCS8

The old keywords DCPAR and DCEXP were replaced by DCS6 and DCSR in 2010. Similarly, DCOLD has morphed into IDCVER. - - The Local Response Dispersion (LRD) correction includes atomic pair-wise -C6/R**6, -C8/R**8, and -C10/R**10 terms, whose coefficients are computed from the molecular system's electron density and its nuclear gradient. The nuclear gradient assumes the dispersion coefficients do not vary with geometry, which causes only a very small error in the gradient. Optionally, 3 and 4 center terms may be added, at the 1/R**6 level; in this case, nuclear gradients may not be computed at all. Since the three numerical parameters are presently known only for the long-range exchange corrected BOP functional, calculations may specify simply DFTTYP=LCBOPLRD. The "LCBOPLRD" functional will automatically select the following: DFTTYP=BOP LC=.TRUE. MU=0.47 LRDFLG=.TRUE. LAMBDA=0.232 KAPPA=0.600 RZERO=3.22 leaving only the choice for MLTINT up to you.

Input Description

$DFT

2-65

References for LRD are T.Sato, H.Nakai J.Chem.Phys. 131, 224104/1-12(2009) T.Sato, H.Nakai J.Chem.Phys. 133, 194101/1-9(2010) LRDFLG = flag choosing the Local Response Dispersion (LRD) C6, C8, and C10 corrections. Default=.FALSE. MLTINT = flag to add the 3 and 4 center 6th order terms, the default=.FALSE. Note that nuclear gradients are not available if these multi-center terms are requested. Three numerical parameters may be input. The defaults shown are optimized for the BOP functional with the LC correction for long-range exchange. LAMBDA = parameter adjusting the density gradient correction for the atomic and atomic pair polarizabilities. (default=0.232) KAPPA = parameter in the damping function (default=0.600) RZERO = parameter in the damping function (default=3.22) It may be interesting to see a breakdown of the total dispersion correction, using these keywords: PRPOL = print out atomic effective polarizabilities (default=.FALSE.) PRCOEF = N (default N=0) print out dispersion coefficient to N-th order. PRPAIR = print out atomic pair dispersion energies (default=.FALSE.) * * * range separation * * * LC = flag to turn on the long range correction (LC), which smoothly replaces the DFT exchange by the HF exchange at long inter-electron distances. (default=.FALSE.) This option can only be used with the Becke exchange functional (Becke) and a few correlation functionals, namely BLYP, BOP, and BVWN, only. For example, B3LYP has a fixed admixture of HF exchange, so it cannot work with the LC option.

Input Description

$DFT

2-66

See H.Iikura, T.Tsuneda, T.Yanai, and K.Hirao, J.Chem.Phys. 115, 3540 (2001). MU = A parameter for the long range correction scheme. (default=0.33)

Other range-separated options exist, invoked by naming the functional, such as DFTTYP=CAMB3LYP (see the DFTTYP keyword for a full list). * * * B2x-PLYP double hybrid functionals * * * B2xPLYP Double Hybrid functionals have the general formula: Exc = (1-cHF) * ExGGA + cHF * ExHF + (1-cMP2) * EcGGA + cMP2 * E(2) The next keywords allow the choice of cHF and cMP2. Both values must be between 0 and 1 (0-100%). CHF CMP2 = amount of HF exchange. (default=0.53) = amount of MP2. (default=0.27)

Some other common double hybrid functionals are available simply by chosing DFTTYP=B2PLYP, and changing the CHF and CMP2 parameters. Popular parametrizations are: CHF CMP2 -----------------------------------------B2-PLYP (default) | 0.53 | 0.27 | -----------------------------------------B2K-PLYP | 0.72 | 0.42 | -----------------------------------------B2T-PLYP | 0.60 | 0.31 | -----------------------------------------B2GP-PLYP | 0.65 | 0.36 | -----------------------------------------* * * Grid Input * * * Only one of the three grid types may be chosen for the run. The default (if no selection is made) is the Lebedev grid. In order to duplicate results obtained prior to April 2008, select the polar coordinate grid NRAD=96 NTHE=12 NPHI=24.

Input Description

$DFT

2-67

Energies can be compared if and only if the identical grid type and density is used, analogous to needing to compare with the identical basis set expansions. See REFS.DOC for more information on grids. See similar inputs in $TDDFT. Lebedev grid: NRAD NLEB = number of radial points in the Euler-MacLaurin quadrature. (default=96) = number of angular points in the Lebedev grids. (default=302). Possible values are 86, 110, 146, 170, 194, 302, 350, 434, 590, 770, 974, 1202, 1454, 1730, 2030...

The default for NLEB means that nuclear gradients will be accurate to about the default OPTTOL=0.00010 (see $STATPT), 590 approaches OPTTOL=0.00001, and 1202 is "army grade". The next two specify radial/angular in a single keyword: SG1 = a flag to select the "standard grid 1", which has 24 radial points, and various pruned Lebedev grids, from 194 down to 6. (default=.FALSE. This grid is very fast, but produces gradients whose accuracy reaches only OPTTOL=0.00050. This grid should be VERY USEFUL for the early steps of a geometry optimization. = two unpublished grids due to Curtis Janssen, implemented here differently than in MPQC: = 1 uses 95 radial points for all atoms, and prunes from a Lebedev grid whose largest size is 434, thus using about 15,000 grid points/atom. = 2 uses 155 radial points for all atoms, and prunes from a Lebedev grid whose largest size is 974, thus using about 71,000 grid points/atom. This is a very accurate grid, e.g. "army grade".

JANS

polar coordinate grid: NRAD NTHE = number of radial points in the Euler-MacLaurin quadrature. (96 is reasonable) = number of angle theta grids in Gauss-Legendre

Input Description

$DFT

2-68

quadrature (polar coordinates). (12 is reasonable) NPHI = number of angle phi grids in Gauss-Legendre quadrature. NPHI should be double NTHE so points are spherically distributed. (24 is reasonable)

The number of angular points will be NTHE*NPHI. The values shown give a gradient accuracy near the default OPTTOL of 0.00010, while NTHE=24 NPHI=48 approaches OPTTOL=0.00001, and "army grade" is NTHE=36 NPHI=72. * * * Grid Switching * * * At the first geometry of the run, pure HF iterations will be performed, since convergence of DFT is greatly improved by starting with the HF density matrix. After DFT engages, most runs (at all geometries, except for PCM or numerical Hessians) will use a coarser grid during the early DFT iterations, before reaching some initial convergence. After that, the full grid will be used. Together, these switchings can save considerable CPU time. SWOFF = turn off DFT, to perform pure SCF iterations, until the density matrix convergence falls below this threshold. This option is independent of SWITCH and can be used with or without it. It is reasonable to pick SWOFF > SWITCH > CONV in $SCF. SWOFF pertains only to the first geometry that the run computes, and is automatically disabled if you choose GUESS=MOREAD to provide initial orbitals. The default is 5.0E-3.

SWITCH = when the change in the density matrix between iterations falls below this threshhold, switch to the desired full grid (default=3.0E-4) This keyword is ignored if the SG1 grid is used. NRAD0 NLEB0 NTHE0 = same as NRAD, but defines initial coarse grid. default = smaller of 24 and NRAD/4 = same as NLEB, but defines initial coarse grid. default = 110 = same as NTHE, but defines initial coarse grid.

Input Description

$DFT

2-69

default = smaller of 8, NTHE/3 NPHI0 = same as NPHI, but defines initial coarse grid. default = smaller of 16, NPHI/3

technical parameters: THRESH = threshold for ignoring small contributions to the Fock matrix. The default is designed to produce no significant energy loss, even when the grid is as good as "army grade". If for some reason you want to turn all threshhold tests off, of course requiring more CPU, enter 1.0e-15. default: 1.0e-4/Natoms/NRAD/NTHE/NPHI GTHRE = threshold applied to gradients, similar to THRESH. < 1 assign this value to all thresholds = 1 use the default thresholds (default). > 1 divide default thresholds by this value. If you wish to increase accuracy, set GTHRE=10. The default introduces an error of roughly 1e-7 (a.u./bohr) in the gradient.

Input Description

$DFT

2-70

The keyword $DFTTYP is given in $CONTRL, and may have these values if the grid-free program is chosen: ----- options for METHOD=GRIDFREE ----DFTTYP = NONE means ab initio computation (default) exchange functionals: = XALPHA X-Alpha exchange (alpha=0.7) = SLATER Slater exchange (alpha=2/3) = BECKE Becke's 1988 exchange = DEPRISTO Depristo/Kress exchange = CAMA Handy et al's mods to Becke exchange = HALF 50-50 mix of Becke and HF exchange correlation functionals: = VWN Vosko/Wilke/Nusair correlation, formula 5 = PWLOC Perdew/Wang local correlation = LYP Lee/Yang/Parr correlation exchange/correlation functionals: = BVWN Becke exchange + VWN5 correlation = BLYP Becke exchange + LYP correlation = BPWLOC Becke exchange + Perdew/Wang correlation = B3LYP hybrid HF/Becke/LYP using VWN formula 5 = CAMB CAMA exchange + Cambridge correlation = XVWN Xalpha exchange + VWN5 correlation = XPWLOC Xalpha exchange + Perdew/Wang correlation = SVWN Slater exchange + VWN5 correlation = SPWLOC Slater exchange + PWLOC correlation = WIGNER Wigner exchange + correlation = WS Wigner scaled exchange + correlation = WIGEXP Wigner exponential exchange + correlation uses no auxiliary basis set for resolution of the identity, limiting accuracy. uses the 3rd generation of RI basis sets, These are available for the elements H to Ar, but have been carefully considered for H-Ne only. (DEFAULT)

AUXFUN = AUX0 = AUX3

THREE

= a flag to use a resolution of the identity to turn four center overlap integrals into three center integrals. This can be used only if no auxiliary basis is employed. (default=.FALSE.) ==========================================================

Input Description

$TDDFT

2-71

==========================================================

$TDDFT

group (relevant if TDDFT chosen in $CONTRL)

This group generates molecular excitation energies by time-dependent density functional theory computations (or time-dependent Hartree-Fock, also known as the Random Phase Approximation). The functional used for the excited states is necessarily the same one that is used for the reference state, specified by DFTTYP in $CONTRL. For conventional TD-DFT (TDDFT=EXCITE in $CONTRL), the orbitals are optimized for RHF or UHF type reference states. Analytic nuclear gradients are available for singlet excited states, while the energy of excited states of other multiplicities can be computed. For spin-flip TD-DFT (TDDFT=SPNFLP in $CONTRL), the calculation obtains orbitals for a reference state of either UHF or ROHF type, with MULT in $CONTRL determining the Ms quantum number of the reference. The reference state's Ms is set equal to the S value implied by $CONTRL's MULT=2S+1. The SF-TD-DFT then uses only determinants with Ms=S-1, due to the flip of one alpha spin into a beta spin. This means that target states (which are spin contaminated) will have multiplicities around the range S-1 to S, only. It is quite possible for some of the target states to have a lower energy than the reference!!! Nuclear gradients and properties are available. See just below for "limitations" below regarding the two different TD-DFT types. TDDFT is a single excitation theory. All of the caveats listed in the $CIS input group about states with double excitation character, need for Rydberg basis sets, greatly different topology of excited state surfaces, and so on apply here as well. Please read the introduction to the $CIS input group! If you use very large or very small Gaussian exponents, you may need to increase the number of radial grid points (the program prints advice in such cases). TDHF, TDDFT, and CIS are related in the following way:

Input Description

$TDDFT

2-72

DFT

-- Tamm/Dancoff approximation --> | TDHF CIS | V TDDFT TDDFT/TDA

Here TDHF means absorption of photons, to produce excited states (TDHF is called RPA in the physics community). This meaning of TDHF should not be confused with the photon scattering processes computed by RUNTYP=TDHF or TDHFX, which generate polarizabilities. Note, in particular, that CITYP=CIS is equivalent to using TDDFT=EXCITE DFTTYP=NONE TAMMD=.TRUE., provided the former is run with no frozen cores. Solvent effects for CIS calculations are therefore available via the TDDFT codes. Excited state properties are calculated using the TDDFT excited state electronic density only during gradient runs, or by setting TDPRP below. The TD-DFT codes excite all electrons, that is, there is no frozen core concept. Please see the 4th chapter of this manual for more information on both types of TD-DFT. "limitations" for TDDFT=EXCITE: Permissible values for DFTTYP are shown below. These include "NONE" which uses TDHF (i.e. the Random Phase Approximation), noting that extra states may need to be solved for in order to be sure of getting the first few states correctly. If nuclear gradients are needed, you may choose any of the following functionals: NONE SVWN, SOP, SLYP, OLYP, BVWN, BOP, BLYP (and their LC=.TRUE. versions) B3LYP, CAMB3LYP, B3LYP1, PBE, PBE0 For evaluation of just the excitation energies, you may use many more functionals, notably including the metaGGAs in the last three lines: NONE SVWN, SVWN1, SPZ81, SP86, SOP, SLYP, BVWN, BVWN1, BPZ81, BP86, BOP, BLYP, OLYP, B3LYP, CAMB3LYP, B3LYP1, B3PW91, X3LYP, PW91, PBE, PBE0 VS98, PKZB, M05, M05-2X, M06, M06-HF, M06-L, M06-2X, M08-HX, M08-SO TPSS, TPSSm, TPSSh, and revTPSS

Input Description

$TDDFT

2-73

The LC flag in $DFT automatically carries over to TDDFT runs. The LC option may be used with the "B" functionals, and (like the similar range-separated CAMB3LYP) is useful in obtaining better descriptions for charge-transfer excitations or Rydberg excitation energies than are the conventional exchange correlation functionals (whether pure or hybrid). The LC flag is also available for excited state gradient computation. Limits specific to the references for TDDFT=EXCITE are: For SCFTYP=RHF, excitation energies can be found for singlet or triplet coupled excited states. For singlet excited states only, analytic gradients and properties can be found, for either full TD-DFT or in the Tamm/Dancoff approximation. For RHF references, solvent effects can be included by EFP1 or PCM (or both together), for both TD-DFT excitation energies and their nuclear gradients. For SCFTYP=UHF, excited states with the same spin projection as the ground state are found. MULT in $CONTRL governs the number of alpha and beta electrons, hence Ms=(MULT-1)/2 is the only good quantum number for either the ground or excited states. Since U-TDDFT is a single excitation theory, excited states with <S> values near Ms and near Ms+1 will appear in the calculation. There are no properties other than the excitation energy, nor gradients, nor solvent effects, at present. "limitations" for TDDFT=SPNFLP: Permissible values for DFTTYP are fewer than the list shown above for conventional TD-DFT. In particular, no hybrid functional may be used (collinear approximation). The LC option for range-separation hybrids cannot be used, which also removes CAMB3LYP. Finally, no meta-GGA may be used. Note that spin-flip TD-DFT in the Tamm/Dancoff approximation using DFTTYP=NONE is equivalent to spin-flip CIS. MULT below is ignored, as the Ms of target states is fixed solely by MULT in $CONTRL. The spin-flip code operates only in the Tamm/Dancoff approximation, so TAMMD below is automatically .TRUE. Nuclear gradients and/or

Input Description

$TDDFT

2-74

excited state properties are available only in the gas phase. Solvation effects are available only for energy calculations, and only for EFP1 and C-PCM. --------NSTATE = Number of states to be found (excluding the reference state). The default is 1 more state. IROOT = State used for geometry optimization and property evaluation. (default=1) TDDFT=EXCITE counts the reference as 0, and this should be the lowest state. Hence IROOT=1 means the 1st excited state, just as you might guess. TDDFT=SPNFLP labels the reference state as 0, but this might not be the lowest state overall. The meaning of IROOT=1 is the lowest state, omitting the reference state from consideration. Hence IROOT=1 might specify the ground state! = Multiplicity (1 or 3) of the singly excited states. This keyword applies only when the reference is a closed shell. (default is 1) This parameter is ignored when TDDFT=SPNFLP. = a flag to request property computation for the state IROOT. Properties can only be obtained when the nuclear gradient is computable, see gradient restrictions noted in the introduction to this group. Properties require significant extra computer time, compared to the excitation energy alone, so the default is .FALSE. Properties are always evaluated during nuclear gradient runs, when they are a free by-product. is a flag selecting the Tamm/Dancoff approximation be used. This may be used with closed shell excitation energies or gradients, or open shell excitation energies. Default = .FALSE. This parameter is ignored by TDDFT=SPNFLP, which is only coded in the Tamm/Dancoff approximation.

MULT

TDPRP

TAMMD

Input Description NONEQ

$TDDFT

2-75

is a flag controlling PCM's solvent behavior: .TRUE. splits the dielectric constant into a bulk value (EPS in $PCM) and a fast component (EPSINF), see Cossi and Barone, 2001. The idea is that NONEQ=.t. is appropriate for vertical excitations, and .f. for adiabatic. (the default is .TRUE.) This keyword is ignored by TDDFT=SPNFLP. * * * Grid Selection * * *

The grid type and point density used in $TDDFT may be chosen independently of the values in $DFT. Excitation energies accurate to 0.01 eV may be obtained with grids that are much sparser than those needed for the ground state, and this is reflected in the defaults. Prior to April 2008, the default grid was NRAD=24 NTHE=8 NPHI=16. NRAD = number of radial grid points in Euler-Maclaurin quadrature, used in calculations of the second or third derivatives of density functionals. (default=48) = number of angular points in the Lebedev grid. (default=110) = number of theta grid points if a polar coordinate grid is used. = number of phi grid points if a polar coordinate grid is used. NPHI should be twice NTHE. = flag selecting "standard grid one". (default=.FALSE.)

NLEB NTHE NPHI SG1

See both $DFT and REFS.DOC for more information on grids. The "army grade" standard for $TDDFT is NRAD=96 combined with either NLEB=302 or NTHE=12/NPHI=24. the remaining parameters are technical in nature: CNVTOL = convergence tolerance in the iterative TD-DFT step. (default=1.0E-7)

Input Description

$TDDFT

2-76

MAXVEC = the maximum number of expansion vectors used by the solver's iterations, per state (default=50). The total size of the expansion space will be NSTATE*MAXVEC. NTRIAL = the number of initial expansion vectors used. (default is the larger of 5 and NSTATE). ==========================================================

Input Description

$CIS

2-77

==========================================================

$CIS

group

required when CITYP=CIS required when CITYP=SFCIS

The CIS method (singly excited CI) is the simplest way to treat excited states. By Brillouin's Theorem, a single determinant reference such as RHF will have zero matrix elements with singly substituted determinants. The ground state reference therefore has no mixing with the excited states treated with singles only. Reading the references given in Section 4 of this manual will show the CIS method can be thought of as a non-correlated method, rigorously so for the ground state, and effectively so for the various excited states. Some issues making CIS rather less than a black box method are: a) any states characterized by important doubles are simply missing from the calculation. b) excited states commonly possess Rydberg (diffuse) character, so the AO basis used must allow this. c) excited states often have different point group symmetry than the ground state, so the starting geometries for these states must reflect their actual symmetry. d) excited state surfaces frequently cross, and thus root flipping may very well occur. The normal CIS implementation allows the use of only RHF references, but can pick up both singlet and triplet excited states. Nuclear gradients are available, as are properties. The CIS run automatically includes computation of the dipole moments of all states, and all pairwise transition dipoles and oscillator strengths. The spin-flip type of CIS is very similar to spin-flip TDDFT (the $TDDFT group contains more information about how spin-flip runs select the target state's Ms by $CONTRL's MULT value). The reference state must be UHF or ROHF, with MULT in $CONTRL at least 3. The target states of the CIS have one lower Ms, after one alpha spin in the reference is flipped to beta. Nuclear gradients are possible. Solvent effects are not available for either CIS or SFCIS. It is worthwhile to look at the $TDDFT group, which is a very similar calculation. The TD-DFT program offers the

Input Description

$CIS

2-78

possibility of recovering some of the correlation energy, permits some solvent models, and can be used for MEX/CONICL surface intersection searches. The first six keywords are chemically important, while the remainder are mostly technical. NACORE = n Omits the first n occupied orbitals from the calculation (frozen core approximation). For CITYP=CIS, the default for n is the number of chemical core orbitals. For CITYP=SFCIS, the default, which is also the only possibility, is 0. NSTATE = IROOT = Number of states to be found (excluding the reference state). No default is provided. State for which properties and/or gradient will be calculated. Only one state can be chosen. The reference state is referred to as 0, and in the case of CITYP=SFCIS, might have a higher energy than some of the NSTATE target states. Flag to request the determination of CIS level properties, using the relaxed density. Relevant to RUNTYP=ENERGY jobs, although the default is .FALSE. because additional CPHF calculation will be required. Properties are an automatic byproduct of runs involving the CIS or SFCIS nuclear gradient. Type of CI Hamiltonian to use, if CITYP=CIS. SAPS spin-adapted antisymmetrized product of the desired MULT will be used (default) DETS determinant based, so both singlets and triplets will be obtained. Multiplicity (1 or 3) of the singly excited SAPS (the reference can only be singlet RHF). Only relevant for SAPS-based CITYP=CIS run, as SFCIS controls the Ms for target states by the value of MULT in $CONTRL. - - - - - - - - - - - -

CISPRP =

HAMTYP = = = MULT =

Input Description DIAGZN = = =

$CIS

2-79

Hamiltonian diagonalization method. DAVID use Davidson diagonalization. (default) FULL construct the full matrix in memory and diagonalize, thus determining all states (not recommended except for small cases). Flag to control whether approximate diagonal elements of the CIS Hamiltonian (based only on the orbital energies) are used in the Davidson algorithm. Note, this only affects the rate of convergence, not the resulting final energies. If set .FALSE., the exact diagonal elements are determined and used. Default=.TRUE. Dimension of the Hamiltonian submatrix that is diagonalized to form the initial CI vectors. The default is the greater of NSTATE*2 and 10. Maximum number of expansion basis vectors in the iterative subspace during Davidson iterations, before the expansion basis is truncated. The default is the larger of 8*NSTATE and NGSVEC. Maximum number of Davidson iterations. Default=50. Convergence criterion for Davidson eigenvectors. Eigenvector accuracy is proportional to DAVCVG, while the energy accuracy is proportional to its square. The default is 1.0E-05. Chooses type of CPHF solver to use. CONJG selects an ordinary preconditioned conjugate gradient solver. (default) DIIS selects a diis-like iterative solver. Flag to read CIS vectors from a $CISVEC group in the input file. Default is .FALSE. Flag to force the use of the minimal amount of memory in construction of the CIS Hamiltonian diagonal elements. This is only relevant when DGAPRX=.FALSE., and is meant for debug purposes. The default is .FALSE.

DGAPRX =

NGSVEC =

MXVEC

NDAVIT = DAVCVG =

CHFSLV = = = RDCISV = MNMEDG =

Input Description MNMEOP =

$CIS

2-80

Flag to force the use of the minimal amount of memory during the Davidson iterations. This is for debug purposes. The default is .FALSE.

==========================================================

$CISVEC

group

required if RDCISV in $CIS is chosen

This is formatted data generated by a previous CIS run, to be read back in as starting vectors. Sometimes molecular orbital phase changes make these CI vectors problematic. ==========================================================

Input Description

$MP2

2-81

==========================================================

$MP2

group

(relevant to SCFTYP=RHF,UHF,ROHF if MPLEVL=2)

Controls 2nd order Moller-Plesset perturbation runs, if requested by MPLEVL in $CONTRL. MP2 is implemented for RHF, high spin ROHF, or UHF wavefunctions, but see also $MRMP for MCSCF. Analytic gradients and the first order correction to the wavefunction (i.e. properties) are available for RHF, ROHF (if OSPT=ZAPT), and UHF. The $MP2 group is not usually given. See also the DIRSCF keyword in $SCF to select direct MP2. The spin-component-scaled MP2 (SCS-MP2) energy of Grimme is printed for SCFTYP=RHF references during energy runs. See also the keyword SCSPT below. Only the CODE=IMS program is able to do analytic gradients for SCS-MP2. Special serial codes exist for RHF or UHF MP2 energy or gradient, or the ROHF MP2 energy. Parallel codes using distributed memory are available for RHF, ROHF, or UHF MP2 gradients. In fact, the only way that ROHF MP2 gradients can be computed on one node is with the parallel code, using MEMDDI! MP2 energy values using solution models are computed by using the solvated SCF orbitals in the perturbation step. All of the MP2 nuclear gradient programs contain additional terms required for EFP, PCM, EFP plus PCM, or COSMO solvation models. NACORE = n Omits the first n occupied orbitals from the calculation. The default for n is the number of chemical core orbitals. NBCORE = MP2PRP= Same as NACORE, for the beta orbitals of UHF. It is almost always the same value as NACORE. a flag to turn on property computation for jobs jobs with RUNTYP=ENERGY. This is appreciably more expensive than just evaluating the second order energy correction alone, so the default is to skip properties. Properties are always computed during gradient runs, when they are an almost free byproduct. (default=.FALSE.)

Input Description

$MP2

2-82

OSPT=

selects open shell spin-restricted perturbation. This parameter applies only when SCFTYP=ROHF. Please see the 'further information' section for more information about this choice. = ZAPT picks Z-averaged perturbation theory. (default) = RMP picks RMP (aka ROHF-MBPT) perturbation theory. = the program implementation to use, choose from SERIAL, DDI, or IMS according to the following chart, depending on SCFTYP and whether the run involves gradients, UHF UHF ROHF ROHF ROHF energy gradient energy gradient energy OSPT=ZAPT ZAPT RMP SERIAL SERIAL SERIAL SERIAL DDI DDI DDI DDI RIMP2 -

CODE

RHF RHF energy gradient SERIAL DDI IMS RIMP2 SERIAL DDI IMS -

The default for serial runs (p=1) is CODE=IMS for RHF, and CODE=SERIAL for UHF or ROHF (provided PARALL is .FALSE. in $SYSTEM). When p>1 (or PARALL=.TRUE.), the default becomes CODE=DDI. However, if FMO is in use, the default for closed shell parallel runs is CODE=IMS. The "SERIAL" code for OSPT=RMP will run with modest scalability when p>1. The many different MP2 programs are written for different hardware situations. Here N is the number of atomic basis functions, and O is the number of correlated orbitals in the run: The original SERIAL programs use N**3 memory, and have larger disk files and generally takes longer than CODE=IMS. The IMS program uses N*O**2 memory, and places most of its data on local disks (so you must have good disk access), and will run in parallel...ideal for small clusters. Using this program on a node where the disks are of poor quality (SATA-type) and with many cores accessing that single disk may be very I/O bound. Adding more memory can make this program run more efficiently. Network traffic is modest when running in parallel.

Input Description

$MP2

2-83

The DDI program uses N**4 memory, but this is distributed across all nodes, and there is essentially no I/O...ideal for large parallel machines where the manufacturer has forgotten to include disk drives. MEMDDI must be given in $SYSTEM for these codes, so large problems may require many nodes to aggregate enough MEMDDI. The network traffic is high, so an Infiniband quality network or better preferred. Scalability is very good, for example, this program has been used up to 4,000 cores on Altix/ICE equipment. All of the programs just mentioned should generate the same numerical results, so select which one best matches your hardware. The RIMP2 program is an approximation to the true MP2 energy, using the "resolution of the identity" to reduce the amount of data stored (in memory and/or on disk), and also the total amount of computation. See the paper on this program for its reduced CPU and memory requirements. Network traffic is modest. The code has options within the $RIMP2 input to govern the use of replicated memory versus shared memory, as well as the use of disk storage versus distributed memory, so you can tune this to your hardware. References for the various programs are given in REFS.DOC. NOSYM = disables the orbital symmetry test completely. This is not recommended, as loss of orbital symmetry is likely to mean a bad calculation. It has the same meaning as the keyword in $CONTRL, but just for the MP2 step. (Default=0) transformed integral retention threshold, the default is 1.0d-9 (1.0d-12 in FMO runs).

CUTOFF =

The following keyword applies only to RHF references: SCSPT = spin component scaled MP2 energy selection. = NONE - the energy will be the normal MP2 value. This is the default. = SCS - the energy used for the potential surface will be the SCS energy value. Use of SCSPT=SCS causes gradients to be those for the SCSMP2 potential surface. For CODE=IMS, the nuclear gradient can be evaluated analytically. See NUMGRD in $CONTRL if

Input Description

$MP2

2-84

for some reason you wish to use the other two closed shell codes for SCS-MP2 gradients. The following keywords apply to any CODE=SERIAL MP2 run, or to parallel ROHF+MP2 runs using OSPT=RMP: LMOMP2= a flag to analyze the closed shell MP2 energy in terms of localized orbitals. Any type of localized orbital may be used. This option is implemented only for RHF, and its selection forces use of the METHOD=3 transformation, in serial runs only. The default is .FALSE. BASISMO solves the response equations during gradient computations in the MO basis. This is programmed only for RHF references without frozen core orbitals, when it is the default. BASISAO solves the response equations using AO integrals, for frozen core MP2 with a RHF reference, or for ROHF or UHF based MP2. controls memory usage. The default uses all available memory. Applies to CODE=SERIAL. (default=0) selects transformation method, 2 being the segmented transformation, and 3 being a more conventional two phase bin sort implementation. 3 requires more disk, but less memory. The default is to attempt method 2 first, and method 3 second. Applies only to CODE=SERIAL.

CPHFBS =

NWORD =

METHOD= n

AOINTS=

defines AO integral storage during conventional integral transformations, during parallel runs. DUP stores duplicated AO lists on each node, and is the default for parallel computers with slow interprocessor communication, e.g. ethernet. DIST distributes the AO integral file across all nodes, and is the default for parallel computers with high speed communications. Applies only to parallel OSPT=RMP runs.

==========================================================

Input Description

$RIMP2

2-85

===========================================================

$RIMP2

group

(optional, relevant if CODE=RIMP2 in $MP2)

This group controls the resolution of the identity MP2 program, which approximately evaluates the MP2 energy. The RI approximation greatly reduces the computer resources required, while suffering only a small error in the energies. Thus, very large atomic basis sets may be used. The input below controls both utilization of the computer resources, and the accuracy of the calculation. See also $AUXBAS, regarding the auxiliary basis set, whose choice also affects the accuracy of the calculation. The program is enabled for parallel calculation, and is tuned to today's SMP nodes. It is limited to energy calculations only, without any solvent effects, for RHF or UHF references. IAUXBF = 0 uses Cartesian Gaussians = 1 uses spherical harmonics for the auxiliary basis set used to expand the MP2 energy expression into products of 3-index matrices. The default is inherited from ISPHER. The next two control computer resources, trading memory for disk storage. GOSMP = flag requesting shared memory use. The default is .TRUE. in multi-core nodes, but .FALSE. in a uniprocessor. This option means only one copy of certain large matrices is stored per node. = a flag to store two and three center repulsion integrals in distributed memory (.TRUE.), or in disk files (.FALSE., which is the default). Selection of this flag requires MEMDDI in $SYSTEM. The default is .TRUE.

USEDM

The RI approximation reduces CPU time, memory requirements, and total disk storage requirements compared to exact calculation. Experimentation with these two keywords will let you tune the program to your hardware situation. For example, choosing GOSMP=.TRUE. and USEDM=.TRUE. will run without any extra disk files, while setting GOSMP=.TRUE.

Input Description

$RIMP2

2-86

and USEDM .FALSE. will minimize memory usage (and network usage) at the expense of doing disk I/O. Total memory usage per node can be obtained by running EXETYP=CHECK. Note the largest replicated memory printed during the RIMP2's output, dividing by 1000000 to get the correct input for MWORDS (round up a bit). Note the largest shared memory requirement printed, also dividing by 100000, and rounding up a bit. Note the distributed memory requirement, which is already in megawords, and is the correct input for MEMDDI. Then, assuming you use p total compute process on multiple n-way nodes, the memory per node is GBytes/node= 8(n*MWORDS + shared + n*MEMDDI/p)/1024 Turning off GOSMP reduces the shared memory to 0 but increases MWORDS, which is multiplied by the number of cores per node! Turning off USEDM leads to MEMDDI=0 by using disk storage instead. If additional memory is available, increasing MWORDS can lead to a reduction in the level of the occupied orbital batch, or "LV". Larger MWORDS permits a smaller LV, which will in turn reduce the required computational time, and the required network traffic or disk I/O. The value of LV used is the last line appearing after "CHECKING SIZE OF OCCUPIED ORBITAL BATCH". The next four control numerical accuracy, but see $AUXBAS which is even more influential in regards the accuracy! OTHAUX = flag to orthogonalize the RI basis set by diagonalization of the overlap matrix. If there is reason to suspect linear dependence may exist in the RI basis, select this option to have a more numerically stable result. Larger RI basis sets such as CCT and ACCT, in particular, may benefit from selecting this. (default=.FALSE.) STOL = threshold at which to remove small overlap matrix eigenvectors, ignored if OTHAUX=.FALSE. This keyword is analogous to QMTTOL in $CONTRL for the true AO basis. (default= 1.0d-6) = selects the procedure for removing redundancies when inverting the two-center, two-e- matrix.

IVMTD

Input Description

$RIMP2

2-87

= 0 use Cholesky decomposition (default) = 2 use diagonalization VTOL = threshold at which to remove redundancies. This is ignored unless IVMTD=2 (default= 1.0d-6)

Don't forget to see also the $AUXBAS input group! An example of this program follows. The molecule is taxol, with 1032 AOs and MOs in the 6-31G(d) basis, correlating 164 valence orbitals. The RI basis set used is SVP, which matches the true basis set in quality. There are 4175 AOs in the RI basis. The job was run on a single 8-way node (n=8, p=1,2,4,8), using MWORDS=50 (leading to LV=6), MEMDDI=580, and the largest shared memory needed is 95 million words. The total node memory is thus (8 bytes/word)*(8*50 + 95 + 8*580/ 8)/1024 = 8.4 GBytes easily fitting into a modern 16 GByte node. It reduces to (8 bytes/word)*(8*50 + 95 + 8*580/16)/1024 = 6.1 GB/node if two 8-way nodes are used. Scaling is p SCF RI-MP2 job total 1 7391 7919 15366 2 3718 4131 7860 4 1857 2290 4174 8 952 1488 2479 16 486 758 1276 using two 8-way nodes. numerical results are E(RI-MP2)= -2920.607512 versus the exact E(MP2)= -2920.606231 The 0.0013 error should be measured against the total 2nd order correlation energy, which is -8.7855, while noting the time for the 2nd order E is similar to the SCF time. ===========================================================

Input Description

$AUXBAS

2-88

===========================================================

$AUXBAS

group

(required if CODE=RIMP2 in $MP2)

This group specifies the auxiliary basis set used to define the resolution of the identity in the RI-MP2 method. The RI methods are formally exact if the RI basis set is complete, so selecting larger bases improves the results. However, this also increases the computational cost of the run! It is reasonable to use smaller RI basis sets when the AO basis is modest, and increase the RI basis when you use very large AO bases. CABNAM specifies built-in basis sets for the RI: = SVP Ahlrich's SVP basis, available H-Kr = TZVP Ahlrich's TZVP basis, available H-Ar = TZVPP Ahlrich's TZVPP basis, available H-Ar = CCD cc-pVDZ basis, available H-Ar = ACCD aug-cc-pVDZ basis, available H-Ar = CCT cc-pVTZ basis, available H-Ar = ACCT aug-cc-pVTZ basis, available H-Ar = XXXXX externally defined: see EXTCAB. CABNAM has no default, this is a required input! Note IAUXBF in $RIMP2 for selecting spherical harmonics versus Cartesian Gaussians. EXTCAB = flag to read the basis from an external file. (default is .FALSE.) This is analogous to EXTBAS in $BASIS: no external files are provided with GAMESS. The value for XXXX must be 8 or fewer letters, obviously avoiding the use of any built in auxiliary basis. Every atom present in your molecule must be defined in the external file by a line giving its chemical symbol, and this chosen string. Following this header line, give the basis in free format $DATA style, containing only S, P, D, F, and G shells, and terminating each atom by the usual blank line. The external file may have several families of bases in the same file, identified by different CABNAM strings. ===========================================================

Input Description

$CCINP

2-89

==========================================================

$CCINP

group

(optional, relevant for any CCTYP)

This group controls a coupled-cluster calculation of any type specified by CCTYP in $CONTRL. The reference orbitals may be RHF or high spin ROHF. If this input group is not given, as is usually the case, all valence electrons will be correlated. Excited state runs CCTYP=EOM-CCSD or CR-EOM also read this group to define the orbitals and to control the ground state CCSD step that preceeds computation of excitations. Excitation energies are possible only for a RHF reference. Parallel computation is possible for RHF references only, and only for CCTYP=CCSD or CCSD(T). Memory use in parallel runs is exotic, be certain to use EXETYP=CHECK (on one processor, with PARALL in $SYSTEM set) before running. See the "Further Information" section of this manual for more details. The first four inputs pertain to both RHF and ROHF cases: NCORE = gives the number of frozen core orbitals to be omitted from the CC calculation. The default is the number of chemical core orbitals. = the number of frozen virtual orbitals to be omitted from the calculation. (default is 0) = defines the maximum number of CCSD (or LCCD, CCD) iterations. This parameter also applies to ROHF's left CC vector solver, but not RHF's left vector. See MAXCCL for RHF. (default=30) = defines the convergence criterion for the cluster amplitudes, as 10**(-ICONV). The ROHF reference also uses this for its left eigenstate solver, but see CVGEOM in $EOMINP for RHF references. (default is 7, but it tightens to 8 for FMO-CC.)

NFZV MAXCC

ICONV

Input Description

$CCINP

2-90

**** the next group pertains to RHF reference only **** CCPRP = a flag to select computation of the CCSD level ground state density matrix (see also CCPRPE in $EOMINP for EOM-CCSD level excited states). The computation takes significant extra time, to obtain left eigenstates, so the default is .FALSE. except for CCTYP=CR-CCL or CR-EOML, where the work required for properties must be done anyway. This keyword is only available in serial runs.

Notes: CCSD is the only level at which properties can be obtained. Therefore this option can only be chosen for CCTYP=CCSD, CR-CCL, EOM-CCSD, or CR-EOM. The run will change CCTYP to EOM-CCSD if you choose CCSD, and will therefore read $EOMINP. However, if you don't select NSTATE in $EOMINP, your original CCTYP=CCSD will not include anything except the ground state in the EOM-CCSD. Note that the convergence criterion for left eigenstates will be CVGEOM in $EOMINP, which is set to obtain excitation energies, and may need tightening. Use of CCTYP=CR-EOM will do triples corrections, after doing the SD level properties. There is little reason to select any of these: MAXCCL = iteration limit on the left eigenstate needed by CCSD properties, or CR-CCL energies. This is just a synonym for MAXEOM in $EOMINP. If you want to alter the left state's convergence tolerance, use CVGEOM in $EOMINP. The right state convergence is set by MAXCC and ICONV above. NWORD = a limit on memory to be used in the CC steps. The default is 0, meaning all memory available will be used. = defines the restart option. If the value of IREST is greater or equal 3, program will restart from the earlier CC run. This requires saving the disk file CCREST from the previous CC run. Values of IREST between 0 and 3 should not be used. In general, the value of IREST is used by the program

IREST

Input Description

$CCINP

2-91

to set the iteration counter in the restarted run. The default is 0, meaning no restart is attempted. MXDIIS = defines the number of cluster amplitude vectors from previous iterations to be included in the DIIS extrapolation during the CCSD (or LCCD, CCD) iterative process. The default value of MXDIIS is 5 for all but small problems. The DIIS solver can be disengaged by entering MXDIIS = 0. It is not necessary to change the default value of MXDIIS, unless the CC equations do not converge in spite of increasing the value of MAXCC. AMPTSH = defines a threshold for eliminating small cluster amplitudes from the CC calculations. Amplitudes with absolute values smaller than AMPTSH are set to zero. The default is to retain all small amplitudes, meaning fully accurate CC iterations. Default = 0.0. **** the next group pertains to ROHF reference only **** There is little reason to select any of these. MULT = spin multiplicity to use in the CC computation. The value of MULT given in the $CONTRL group determines the spin state for the ROHF reference orbitals, and is the default for the CC step.

IOPMET = method for the CR-CC(2,3) triples correction. = 0 means try 1 and then try 2 (default) = 1, the high memory option This option uses the most memory, but the least disk storage and the least CPU time. = 2, the high disk option This option uses least memory, by storing a large disk file. Time is slightly more than IOPMET=1, but the disk file is (NO**3 * NU**3)/6 words, where NO = correlated orbitals, and NU= virtuals. = 3, the high I/O option This option requires slightly more memory than 2, and slightly more disk than 1, but does much I/O. It is also the slowest of the three choices. Check runs will print memory needed by all three options.

Input Description

$CCINP

2-92

KREST

= 0 fresh start of the CCSD equations (default) = 1 restart from AMPROCC file of a previous run

KMICRO = n performs DIIS extrapolation of the open shell CCSD, every n iterations (default is 6) Enter 0 to avoid using the DIIS converger. LREST = 0 fresh start of the left CCSD equations (default) = 1 restart from AMPROCC file of a previous run

LMICRO = n performs DIIS extrapolation of the open shell left equations, every n iterations (default is 5) Enter 0 to avoid using the DIIS converger. KMICRO and LMICRO are ignored for trivial problem sizes. ==========================================================

Input Description

$EOMINP

2-93

==========================================================

$EOMINP

group (optional, for CCTYP=EOM-CCSD, CR-EOM, or CR-EOML) (optional, for CCTYP=EA-EOM2 or IP-EOM2) (optional for CCSD properties, or CCTYP=CR-CCL)

This group controls the calculation of excited states by the equation of motion coupled cluster with single and double excitations, with optional triples corrections. It also pertains to electron attachment and detachment processes, which may result in the system being left in an excited state. The input group permits selection of how many states are computed (machine time is linear in the number of states). Since the default is only one excited state in the totally symmetric representation, it is usually necessary to give this group. The input also allows selection of various computational procedures. An excited state coupled cluster run consists of an RHF calculation, followed by a ground state CCSD (see the $CCINP group to control the ground state calculation, and the orbital range correlated), followed by an EOM-CCSD calculation. If CCTYP=CR-EOM, triples corrections based on the method of moments approach may follow these steps. The various types of triples corrections mentioned below, and other information, can be found in the "Further Information" section of this manual. --- state symmetry and state selection: GROUP the name of the Abelian group to be used, which may be only one of the groups shown in the table below. The default is taken from $DATA, and is reset to C1 if the group is non-Abelian. The purpose is to let the Abelian symmetry be turned off by setting GROUP=C1, if desired. Symmetry is used to help with the initial excited state selection, for controlling the EOMCC calculations, and for labeling the calculated states in the output (not to speed

Input Description

$EOMINP

2-94

up the calculations). NSTATE an array of up to 8 integers telling how many singlet excited states of each symmetry type should be computed. The default is NSTATE(1)=1,0,0,0,0,0,0,0 which means 1 excited totally symmetric singlet state is to be found. The ground state, which must lie in the totally symmetric irrep due to use of an RHF reference is always computed, and therefore should NOT be included in the number of totally symmetric excited states requested. There is no particular reason to think the first excited state will be totally symmetric, so most runs should give NSTATE input. Up to 10 states can be found in any irrep. Machine time is linear in the number of states to be found, so be realistic about how many states you solve for (particularly, with multi-root solvers). The choice of NSTATE(1)=0,0,0,0,0,0,0,0 means calculating the ground state only, yielding the new types of ground-state CR-CCSD(T) corrections labeled as types I, II, and III (see MTRIP). irreducible representation symmetry table: irrep 1 2 3 4 5 6 7 8 C1 A C2 A B Cs A' A'' Ci Ag Au C2v A1 A2 B1 B2 C2h Ag Au Bg Bu D2 A B1 B2 B3 D2h Ag Au B1g B1u B2g B2u B3g B3u Note that this differs from $DET, $MCQDPT, etc! IROOT selects the state whose energy is to be saved for further calculations (default IROOT(1)=1,0). The first integer lists the irrep number, from the same table as NSTATE. The second lists the number of the excited state. The default corresponds to the ground state (labeled as state 0), as this state must lie in the totally symmetric representation. IROOT(1)=3,2 means the second excited state of symmetry B1, if the

Input Description

$EOMINP

2-95

if the point group is C2v. The energy of the state selected is stored as the energy used for numerical derivative calculation, TRUDGE, etc. The energy saved will be the EOMCCSD value unless the triples correction are obtained, in which case the type III energy will be saved (if available) or else the type ID energy. If degenerate states are present, triples are evaluated for only one such state, namely the one with lower irrep number. The EOM-CCSD energies will be used to map an IROOT for a higher irrep number to this, but if the triples corrections alter the order of the states, the new IROOT may not pick up the state you are interested in. Fixes: pick the lower irrep number, or request states only in one symmetry type. IP-EOM and EA-EOM runs use the next three: MULT = target spin multiplicities of the states. = -1 means target both doublet and quartet states = 2 means consider only doublet states = 4 means consider only quartet states, which can be produced at the EOM-CCSD level by a double that unpairs two electrons, and attaches (or detaches) a third electron. The default for RHF is MULT=-1. If quartets are sought, be sure to use the guess procedure MINIT=1 so suitable starting guesses include these. This parameter is ignored if SCFTYP=ROHF, where the equations are not spin-adapted. Note that IP-EOM and EA-EOM always run through the ROHF codes, even if the reference is closed shell, but in the latter case the run is fully spin-adapted. = 0 this is not a restart = 1 restart data is read from AMPROCC file One use for this is to request additional states, with the restart taking any converged roots from disk, and doing an initial guess for additional states. You must not change MULT when restarting. = the number of unoccupied MOs in the active space for the EA-EOMCCSDt or IP-EOMCCSDt methods. For CCTYP=EA-EOM3A or IP-EOM3A based on a closed-shell reference, the active space consists of the NACT lowest unoccupied MOs of the RHF reference. In general, for

JREST

NACT

Input Description

$EOMINP

2-96

both SCFTYP=RHF and ROHF, NACT is the number of lowest unoccupied beta spin-orbitals to be included in the active space. This keyword ignored for other EOM runs. IP-EOM or EA-EOM runs will also require inputs for NSTATE, MINIT, NOACT and NUACT (or MOACT), and perhaps CVGEOM, MAXEOM, or other keywords in this group. * * * * * CCPRPE = a flag to select computation of the EOM-CCSD level excited state density matrices (see also CCPRP in $CCINP for ground states). The computation takes extra time, to obtain left eigenstates, so the default is .FALSE. Note: CCPRPE will evaluate excited states' dipole moments, and the transition moments and oscillator strengths between all states. This option can be chosen for CCTYP=EOMCCSD or CR-EOM, with the latter doing triples corrections after the SD level properties are obtained. Selecting this option, or CCPRP in $CCINP, requires extra time due to solving for the left eigenvectors (from the so-called "lambda" equation). CVGEOM will affect the accuracy of the computed properties. The resulting density matrices are square, not symmetric, and at present cannot be used for any property other than the dipole quantities. As a temporary expedient, they are output in the PUNCH file for possible use elsewhere. --- methods of converging the EOMCCSD equations and selecting triples corrections to EOMCCSD energies: MEOM selects the solver for the EOMCCSD calculations: 0 = one EOMCCSD root at a time, united iterative space for all calculated roots (default) 1 = one root at a time, separate iterative space for each calculated root 2 = the Hirao-Nakatsuji multi-root solver 3 = one root at a time, separate iterative space for all computed right/left roots. (compare to 1) 4 = one root at a time, united iterative spaces for each right/left root (compare to 0).

Input Description

$EOMINP

2-97

MEOM=0,1,2 obtain all the right eigenvectors first, and then if properties are being computed, proceed to compute the left eigenvectors. MEOM=3,4 obtain right and left eigenvectors simultaneously, and therefore should only be chosen if you are computing properties (see CCPRP/CCPRPE). the next two apply only to CCTYP=CR-EOM: MTRIP 1 = selects the type of noniterative triples corrections to EOMCCSD energies: compute the CR-EOMCCSD(T) triples corrections termed type I and II in the output. This is the default, which skips the iterative CISD calculations needed to construct the CR-EOMCCSD(T) triples corrections of type III. after performing an additional CISD calculation, evaluate all types of the CR-EOMCCSD(T) triples corrections, including types I, II, and III. This choice of MTRIP uses approximately 50 % more memory, but less CPU time than MTRIP=4. evaluate the CR-EOMCCSD(T) corrections of type III only. As with MTRIP=2, this calculation includes the iterative CISD calculation, which is needed to construct the type III triples corrections, in addition to the EOMCCSD and CR-EOMCCSD(T) calculations. carry out MTRIP=1 calculations, followed by MTRIP=3 calculations, thus evaluating all types of the CR-EOMCCSD(T) corrections (types I, II, and III in the output). As with MTRIP=2, this calculation includes the CISD iterations, which are needed to construct the type III triples corrections, in addition to the EOMCCSD and CR-EOMCCSD(T) calculations. Compared to MTRIP=2, this choice of MTRIP uses less memory, but more CPU time.

2 =

3 =

4 =

MCI

selects the solver for the CISD step, which is irrelevant unless MTRIP is bigger than 1. 1 = one root at a time, separate iterative space for each calculated root (default) 2 = the Hirao-Nakatsuji multi-root solver (slower)

Input Description

$EOMINP

2-98

--- initial guess for the EOMCCSD and possible CISD steps: MINIT selects the initial guess procedure for both the EOMCCSD and CISD iterations (when MTRIP>1). 1 = (not a default, but HIGHLY RECOMMENDED). Use EOMCCSd to start the EOMCCSD iterations and use CISd to start the CISD iterations during the CR-EOMCCSD(T), type III, calculations. This means that the initial guesses for the calculated states are defined using all single excitations (letter S in EOMCCSd and CISd) and a small subset of double excitations (the little d in EOMCCSd and CISd) defined by active orbitals or orbital range specified by the user. The inclusion of a small set of active doubles in addition to all singles in the initial guess facilitates finding excited states characterized by relatively large doubly excited amplitudes. This choice of MINIT is strongly recommended. (see NOACT, NUACT, and MOACT). 2 = Use CIS wave functions as initial guesses for the EOMCCSD and possible CISD calculations. This is the default, but may cause severe convergence difficulties or even miss some states entirely if the calculated states have significant doubly excited character. MINIT=1 is much better in these situations and strongly recommended, particularly when there is a chance of having low-lying states with nonnegligible bi-excited or multi-configurational character. the next three apply only to MINIT=1: NOACT NUACT the number of occupied MOs in the active space for the EOMCCSd and CISd initial guesses. the number of unoccupied MOs in the active space for the EOMCCSd and CISd initial guesses. The NOACT and NUACT variables are used only by MINIT=1, and are reset to 0 if MINIT=2. There are no default values of NOACT and NUACT and the user MUST provide NOACT and NUACT values when MINIT=1. The values of NOACT and NUACT should be small (5 or so), since they only describe the numbers of highest-energy occupied and lowest-energy unoccupied MOs that should

Input Description

$EOMINP

2-99

MOACT

help to capture the leading orbital excitations defining the excited states of interest (see an example below). The user should make sure that the active orbital range defined by NOACT and NUACT does not fall across degenerate orbitals (e.g., if NUACT is chosen such that only one of the two degenerate pi orbitals is included in the active orbital range for the EOMCCSd and CISd initial guesses, the user should increase NUACT at least by 1 to make sure that both pi orbitals are included in the active orbital set). See also the MOACT input for fine tuning. array allowing explicit selection of the active orbitals used to define the EOMCCSd and CISd initial guesses. If not provided, the MOACT array is filled such that the NOACT highest occupied and NUACT lowest unoccupied orbitals are selected. If MOACT array is given, the number of values in it must equal NOACT+NUACT. Sometimes, instead of defining larger NUACT values that increase memory requirements for the EOMCCSd and CISd initial guesses, it may be helpful to specify the unoccupied orbitals, since the lowest virtual orbitals of RHF, whenever there are diffuse functions in the basis set, may not be good at representing valence excited states. Here is an example in which the user is more selective about picking active unoccupied orbitals for the EOMCCSd and CISd initial guesses. In this example, the user picks the highest 3 occupied and selected 5 unoccupied orbitals of RHF as active for a 30-electron system (15 occupied orbitals total) and at least 30 orbitals total: MINIT=1 NOACT=3 NUACT=5 MOACT(1)=13,14,15, 19,20,24,25,30

--- iteration control: CVGEOM MAXEOM convergence criterion on the EOMCCSD excitation amplitudes R1 and R2 (default=1.0d-4). maximum number of iterations in the EOMCCSD calculations (default=50). For MEOM=0 or 1, this is the maximum number of iterations per

Input Description

$EOMINP

2-100

MICEOM

each calculated state. For MEOM=2, this is the maximum number of iterations for all states of the EOMCCSD multi-root procedure. maximum number of microiterations in the EOMCCSD calculations (default=80). Rarely used. For MEOM=1 (separate iterative space for each root), this is the maximum number of microiterations for each calculated state. For MEOM=0 or 2 (united iterative space for all calculated roots), this is the maximum number of microiterations for all calculated states. It is much better to perform calculations with MICEOM > MAXEOM (i.e., in a single iteration cycle). If for some reason the EOMCCSD convergence is very slow and the iterative space becomes very large, it may be worth changing the default MICEOM value to MICEOM < MAXEOM to reduce the disk usage. This is not going to happen too often and normally there is no need to change the default MICEOM value.

the next three apply only to CCTYP=CR-EOM, and only if the triples method MTRIP is greater than 1: CVGCI MAXCI convergence criterion for the CISD expansion coefficients (default=1.0d-4). maximum number of iterations in the CISD calculation (default=50). For MCI=1, this is the maximum number of iterations per each calculated CISD state. For MCI=2, this is the maximum number of iterations for all states of the CISD multi-root procedure. maximum number of microiterations in the CISD calculation (default=80). Rarely used. For MCI=1 (separate iterative space for each root), this is the maximum number of microiterations for each calculated state. For MCI=2 (united iterative space for all calculated roots), this is the maximum number of microiterations for all calculated states. In analogy to MICEOM, it is much better to perform the CISD calculations with MICCI > MAXCI (i.e., in a single iteration cycle).

MICCI

Input Description

$EOMINP

2-101

==========================================================

Input Description

$MOPAC

2-102

==========================================================

$MOPAC

group

(relevant if GBASIS=PM3, AM1, or MNDO)

This group affects only semi-empirical jobs, which are selected in $BASIS by keyword GBASIS. PEPTID = flag for peptide bond correction. By default a molecular mechanics-style torsion potential term is added for every peptide bond linkage found. The intent is to correct these torsions to be closer to planar than they would otherwise be in the semi-empirical model. Here, the peptide bond means any O H \\ / C----N / \ X One such torsion is added for O-C-N-H and one for O-C-N-X. This term is parameterized as in MOPAC6. Default=.TRUE. ==========================================================

Input Description

$GUESS

2-103

==========================================================

$GUESS

group

(optional, relevant for all SCFTYP's)

This group controls the selection of initial molecular orbitals. GUESS = Selects type of initial orbital guess. = HUCKEL Carry out an extended Huckel calculation using a Huzinaga MINI basis set, and project this onto the current basis. This is implemented for atoms up to Rn, and will work for any all electron or ECP basis set. (default for most runs) = HCORE Diagonalize the one electron Hamiltonian to obtain the initial guess orbitals. This method is applicable to any basis set, but does not work as well as the HUCKEL guess. = MOREAD Read in formatted vectors punched by an earlier run. This requires a $VEC deck, and you MUST pay attention to NORB below. = RDMINI Read in a $VEC deck from a converged calculation that used GBASIS=MINI and no polarization functions, and project these orbitals onto the current basis. Do not use this option if the current basis involve ECP basis sets. = MOSAVED (default for restarts) The initial orbitals are read from the DICTNRY file of the earlier run. = SKIP Bypass initial orbital selection. The initial orbitals and density matrix are assumed to be in the DICTNRY file. Mostly used for RUNTYP=HESSIAN when the hessian is being read in from the input. The next options are less general, being for Fragment Molecular Orbital runs, or Divide and Conquer runs: = FMO Read orbitals from the DICTNRY file, from previous FMO run with MODPRP=1. = HUCSUB Perform a Huckel guess in each subsystem of a Divide and Conquer run = DMREAD Read a density matrix from a formatted $DM

Input Description

$GUESS

2-104

group, produced by a previous Divide and Conquer run, see NDCPRT in $DANDC. All GUESS types except 'SKIP' permit reordering of the orbitals, carry out an orthonormalization of the orbitals, and generate the correct initial density matrix, for RHF, UHF, ROHF, and GVB, but note that correct computation of the GVB density requires also CICOEF in $SCF. The density matrix cannot be generated from the orbitals alone for MP2, CI, or MCSCF, so property evaluation for these should be RUNTYP=ENERGY rather than RUNTYP=PROP using GUESS=MOREAD. PRTMO = a flag to control printing of the initial guess. (default=.FALSE.) PUNMO = a flag to control punching of the initial guess. (default=.FALSE.) MIX = rotate the alpha and beta HOMO and LUMO orbitals so as to generate inequivalent alpha and beta orbital spaces. This pertains to UHF singlets only. This may require use of NOSYM=1 in $CONTRL depending on your situation. (default=.FALSE.) = The number of orbitals to be read in the $VEC group. This applies only to GUESS=MOREAD.

NORB

For -RHF-, -UHF-, -ROHF-, and -GVB-, NORB defaults to the number of occupied orbitals. NORB must be given for -CIand -MCSCF-. For -UHF-, if NORB is not given, only the occupied alpha and beta orbitals should be given, back to back. Otherwise, both alpha and beta orbitals must consist of NORB vectors. NORB may be larger than the number of occupied MOs, if you wish to read in the virtual orbitals. If NORB is less than the number of atomic orbitals, the remaining orbitals are generated as the orthogonal complement to those read. NORDER = Orbital reordering switch. = 0 No reordering (default) = 1 Reorder according to IORDER and JORDER. IORDER = Reordering instructions, giving the new molecular orbital order. This parameter applies to the common orbitals (both alpha and beta) except for UHF, where IORDER only affects the alpha MOs.

Input Description

$GUESS

2-105

Examples (let there be 10 occupied orbitals): transposition of HOMO and LUMO: IORDER(10)=11,10 a different transposition: IORDER(10)=15 IORDER(15)=10 a more general permutation: IORDER(8)=11,8,9,10 so the new orbital 10 is the original 9th. The default is IORDER(i)=i. JORDER = Reordering instructions. Same as IORDER, but for the beta MOs of UHF. INSORB = the first INSORB orbitals specified in the $VEC group will be inserted into the Huckel guess, making the guess a hybrid of HUCKEL/MOREAD. This keyword is meaningful only when GUESS=HUCKEL, and it is useful mainly for QM/MM runs where some orbitals (buffer) are frozen and need to be transferred to the initial guess vector set, see $MOFRZ. (default=0) * * * the next are 3 ways to clean up orbitals * * * PURIFY = flag to symmetrize starting orbitals. This is the most soundly based of the possible procedures. However it may fail in complicated groups when the orbitals are very unsymmetric. (default=.FALSE.) TOLZ TOLE = level below which MO coefficients will be set to zero. (default=1.0E-7) = level at which MO coefficients will be equated. This is a relative level, coefficients are set equal if one agrees in magnitude to TOLE times the other. (default=5.0E-5)

SYMDEN = project the initial density in order to generate symmetric orbitals. This may be useful if the HUCKEL or HCORE guess types give orbitals of impure symmetry (?'s present). The procedure will generate a fairly high starting energy, and thus its use may not be a good idea for orbitals of the quality of MOREAD. (default=.FALSE.)

Input Description

$GUESS

2-106

==========================================================

Input Description

$VEC $DM $MOFRZ

2-107

==========================================================

$VEC

group

(optional, relevant for all SCFTYP's) (required if GUESS=MOREAD)

This group consists of formatted vectors, as written onto file PUNCH in a previous run. It is considered good form to retain the titling comment cards punched before the $VEC card, as a reminder to yourself of the origin of the orbitals. For Morokuma decompositions, the names of this group are $VEC1, $VEC2, ... for each monomer, computed in the identical orientation as the supermolecule. For transition moment or spin-orbit coupling runs, orbitals for states one and possibly two are $VEC1 and $VEC2. ==========================================================

$DM

group

(relevant in Divide and Conquer runs)

This group consists of a formatted density matrix, read in exactly the format it was written. See GUESS=DM, and NDCPR in $DANDC. ==========================================================

$MOFRZ

group

(optional, relevant for RHF, ROHF, GVB)

This group controls freezing the molecular orbitals of your choice during the SCF procedure. If you choose this option, select DIIS in $SCF since SOSCF will not converge as well. GUESS=MOREAD is required in $GUESS. FRZ IFRZ = flag which triggers MO freezing. (default=.FALSE.) = an array of MOs in the input $VEC set which are to be frozen. There is no default for this.

==========================================================

Input Description

$STATPT

2-108

==========================================================

$STATPT

group

(for RUNTYP=OPTIMIZE or SADPOINT)

This group controls the search for stationary points. Note that NZVAR in $CONTRL determines if the geometry search is conducted in Cartesian or internal coordinates. METHOD = optimization algorithm selection. NR Pick from

Straight Newton-Raphson iterate. This will attempt to locate the nearest stationary point, which may be of any order. There is no steplength control. RUNTYP can be either OPTIMIZE or SADPOINT Rational Function Optimization. This is one of the augmented Hessian techniques where the shift parameter(s) is(are) chosen by a rational function approximation to the PES. For SADPOINT searches it involves two shift parameters. If the calculated stepsize is larger than DXMAX the step is simply scaled down to size. Quadratic Approximation. This is another version of an augmented Hessian technique where the shift parameter is chosen such that the steplength is equal to DXMAX. It is completely equivalent to the TRIM method. (default)

RFO

QA

SCHLEGEL The quasi-NR optimizer by Schlegel. CONOPT, CONstrained OPTimization. An algorithm which can be used for locating TSs. The starting geometry MUST be a minimum! The algorithm tries to push the geometry uphill along a chosen Hessian mode (IFOLOW) by a series of optimizations on hyperspheres of increasingly larger radii. Note that there currently are no restart capabilitites for this method, not even manually.

Input Description

$STATPT

2-109

OPTTOL = gradient convergence tolerance, in Hartree/Bohr. Convergence of a geometry search requires the largest component of the gradient to be less than OPTTOL, and the root mean square gradient less than 1/3 of OPTTOL. (default=0.0001) NSTEP = maximum number of steps to take. Restart data is punched if NSTEP is exceeded. The default is 50 steps for a minimum search, but only 20 for a transition state search, which benefit from relatively frequent Hessian re-evaluations. --- the next four control the step size --DXMAX = initial trust radius of the step, in Bohr. For METHOD=RFO, QA, or SCHLEGEL, steps will be scaled down to this value, if necessary. (default=0.3 for OPTIMIZE and 0.2 for SADPOINT) For METHOD=NR, DXMAX is inoperative. For METHOD=CONOPT, DXMAX is the step along the previous two points to increment the hypersphere radius between constrained optimizations. (default=0.1)

the next three apply only to METHOD=RFO or QA: TRUPD TRMAX TRMIN = a flag to allow the trust radius to change as the geometry search proceeds. (default=.TRUE.) = maximum permissible value of the trust radius. (default=0.5 for OPTIMIZE and 0.3 for SADPOINT) = minimum permissible value of the trust radius. (default=0.05)

--- the next three control mode following --IFOLOW = Mode selection switch, for RUNTYP=SADPOINT. For METHOD=RFO or QA, the mode along which the energy is maximized, other modes are minimized. Usually refered to as "eigenvector following". For METHOD=SCHLEGEL, the mode whose eigenvalue is (or will be made) negative. All other curvatures will be made positive.

Input Description

$STATPT

2-110

For METHOD=CONOPT, the mode along which the geometry is initially perturbed from the minima. (default is 1) In Cartesian coordinates, this variable doesn't count the six translation and rotation degrees. Note that the "modes" aren't from mass-weighting. STPT = flag to indicate whether the initial geometry is considered a stationary point. If .true. the initial geometry will be perturbed by a step along the IFOLOW normal mode with stepsize STSTEP. (default=.false.) The positive direction is taken as the one where the largest component of the Hessian mode is positive. If there are more than one largest component (symmetry), the first is taken as positive. Note that STPT=.TRUE. has little meaning with HESS=GUESS as there will be many degenerate eigenvalues.

STSTEP = Stepsize for jumping off a stationary point. Using values of 0.05 or more may work better. (default=0.01) IFREEZ = array of coordinates to freeze. These may be internal or Cartesian coordinates. For example, IFREEZ(1)=1,3 freezes the two bond lengths in the $ZMAT example, which was for a triatomic $CONTRL NZVAR=3 $END $ZMAT IZMAT(1)=1,1,2, 2,1,2,3, 1,2,3 $END while optimizing the angle. If NZVAR=0, so that this value applies to the Cartesian coordinates instead, the input of IFREEZ(1)=4,8 means to freeze the x coordinate of the 2nd and y coordinate of the 3rd atom. See also IFZMAT and FVALUE in $ZMAT, and IFCART below, as IFREEZ does not apply to DLC internals. In a numerical Hessian run, IFREEZ specifies Cartesian displacements to be skipped for a Partial Hessian Analysis. For more information: J.D.Head, Int.J.Quantum Chem. 65, 827, 1997

Input Description

$STATPT

2-111

H.Li, J.H.Jensen Theoret. Chem. Acc. 107, 211-219(2002) IFCART = array of Cartesian coordinates to freeze during a geometry optimization using delocalized internal coordinates. This probably works less well than IFREEZ when it freezes Cartesians. Only one of IFREEZ or IFCART may be chosen in a single run. IACTAT = array of "active atoms", which is a complimentary input to IFREEZ. Any atom *not* included in the list has its Cartesian coordinates frozen. Thus IACTAT(1)=3,-5,107,144,202,-211 allows 15 atoms, namely 3-5, 107, 144, and 202-211 to be optimized, while all other atoms are frozen. NZVAR in $CONTRL must be 0 when this option is chosen. IFREEZ and IACTAT are mutually exclusive. The latter acts by generating a IFREEZ for all atom coordinates not defined as "active", so users can input whichever list is shorter. --- The next two control the hessian matrix quality --HESS = selects the initial hessian matrix. = GUESS chooses an initial guess for the hessian. (default for RUNTYP=OPTIMIZE) = READ causes the hessian to be read from a $HESS group. (default for RUNTYP=SADPOINT) = RDAB reads only the ab initio part of the hessian, and approximates the effective fragment blocks. = RDALL reads the full hessian, then converts any fragment blocks to 6x6 T+R shape. (this option is seldom used). = CALC causes the hessian to be computed, see the $FORCE group. = the number of steps before the hessian is recomputed. If given as 0, the hessian will be computed only at the initial geometry if you choose HESS=CALC, and never again. If nonzero, the hessian is recalculated every IHREP steps, with the update formula used on other steps. (default=0)

IHREP

Input Description

$STATPT

2-112

HSSEND = a flag to control automatic hessian evaluation at the end of a successful geometry search. (default=.FALSE.) --- the next two control the amount of output --Let 0 mean the initial geometry, L mean the last geometry, and all mean every geometry. Let INTR mean the internuclear distance matrix. Let HESS mean the approximation to the hessian. Note that a directly calculated hessian matrix will always be punched, NPUN refers only to the updated hessians used by the quasi-Newton step. NPRT = 1 0 -1 -2 3 2 1 0 -1 -2 Print Print Print Print INTR INTR INTR INTR at at at at all, all, all, 0+L, orbitals orbitals orbitals orbitals at all at 0+L (default) never never

NPUN

Punch all orbitals and HESS at all Punch all orbitals at all same as 0, plus punch HESS at all Punch all orbitals at 0+L, otherwise only occupied orbitals (default) Punch occ orbitals at 0+L only Never punch orbitals

---- the following parameters are quite specialized ---PURIFY = a flag to help eliminate the rotational and translational degrees of freedom from the initial hessian (and possibly initial gradient). This is much like the variable of the same name in $FORCE, and will be relevant only if internal coordinates are in use. (default=.FALSE.) PROJCT = a flag to eliminate translation and rotational degrees of freedom from Cartesian optimizations. The default is .TRUE. since this normally will reduce the number of steps, except that this variable is set false when POSITION=FIXED is used during EFP runs. ITBMAT = number of micro-iterations used to compute the step in Cartesians which corresponds to the

Input Description

$STATPT The default is 5.

2-113

desired step in internals. UPHESS = SKIP BFGS POWELL POWELL MSP SCHLEGEL

do not update Hessian (not recommended) default for OPTIMIZE using RFO or QA default for OPTIMIZE using NR or CONOPT default for SADPOINT mixed Murtagh-Sargent/Powell update only choice for METHOD=SCHLEGEL

---- NNEG, RMIN, RMAX, RLIM apply only to SCHLEGEL ---NNEG = The number of negative eigenvalues the force constant matrix should have. If necessary the smallest eigenvalues will be reversed. The default is 0 for RUNTYP=OPTIMIZE, and 1 for RUNTYP=SADPOINT. = Minimum distance threshold. Points whose root mean square distance from the current point is less than RMIN are discarded. (default=0.0015) = Maximum distance threshold. Points whose root mean square distance from the current point is greater than RMAX are discarded. (default=0.1)

RMIN

RMAX

RLIM

= Linear dependence threshold. Vectors from the current point to the previous points must not be colinear. (default=0.07) ========================================================== * * * * * * * * * * * * * * * * * * * * * See the 'further information' section for some help with OPTIMIZE and SADPOINT runs * * * * * * * * * * * * * * * * * * * * *

Input Description

$TRUDGE

2-114

==========================================================

$TRUDGE

group

(required for RUNTYP=TRUDGE)

This group defines the parameters for a non-gradient optimization of exponents or the geometry. The TRUDGE package is a modified version of the same code from Michel Dupuis' HONDO 7.0 system, origially written by H.F.King. Presently the program allows for the optimization of 10 parameters. Exponent optimization works only for uncontracted primitives, without enforcing any constraints. Two non-symmetry equivalent H atoms would have their p function exponents optimized separately, and so would two symmetry equivalent atoms! A clear case of GIGO. Geometry optimization works only in HINT internal coordinates (see $CONTRL and $DATA groups). The total energy of all types of SCF wavefunctions can be optimized, although this would be extremely stupid as gradient methods are far more efficient. The main utility is for open shell MP2 or CI geometry optimizations, which may not be done in any other way with GAMESS. If your run requires NOSYM=1 in $CONTRL, you must be sure to use only C1 symmetry in the $DATA group. OPTMIZ = a flag to select optimization of either geometry or exponents of primitive gaussian functions. = BASIS for basis set optimization. = GEOMETRY for geometry optimization (default). This means minima search only, there is no saddle point capability. NPAR IEX = number of parameters to be optimized. = defines the parameters to be optimized. If OPTMIZ=BASIS, IEX declares the serial number of the Gaussian primitives for which the exponents will be optimized. If OPTMIZ=GEOMETRY, IEX define the pointers to the HINT internal coordinates which will be optimized.

Input Description

$TRUDGE

2-115

(Note that not all internal coordinates have to be optimized.) The pointers to the internal coordinates are defined as: (the number of atom on the input list)*10 + (the number of internal coordinate for that atom). For each atom, the HINT internal coordinates are numbered as 1, 2, and 3 for BOND, ALPHA, and BETA, respectively. P = Defines the initial values of the parameters to be optimized. You can use this to reset values given in $DATA. If omitted, the $DATA values are used. If given here, geometric data must be in Angstroms and degrees.

A complete example is a TCSCF multireference 6-31G geometry optimization for methylene, $CONTRL SCFTYP=GVB CITYP=GUGA RUNTYP=TRUDGE COORD=HINT $END $BASIS GBASIS=N31 NGAUSS=6 $END $DATA Methylene TCSCF+CISD geometry optimization Cnv 2 C H 6. LC 0.00 0.0 0.00 - O K 1. PCC 1.00 53. 0.00 + O K I $END $SCF NCO=3 NPAIR=1 $END $TRUDGE OPTMIZ=GEOMETRY NPAR=2 IEX(1)=21,22 P(1)=1.08 $END $CIDRT GROUP=C2V SOCI=.TRUE. NFZC=1 NDOC=3 NVAL=1 NEXT=-1 $END using GVB-PP(1), or TCSCF orbitals in the CI. The starting bond length is reset to 1.09, while the initial angle will be 106 (twice 53). Result after 17 steps is R=1.1283056, half-angle=51.83377, with a CI energy of -38.9407538472 Note that you may optimize the geometry for an excited CI state, just specify $GUGDIA NSTATE=5 $END $GUGDM IROOT=3 $END to find the equilibrium geometry of the third state (of five total states) of the symmetry implied by your $CIDRT. ==========================================================

Input Description

$TRURST

2-116

==========================================================

$TRURST

group RUNTYP=TRUDGE)

(optional, relevant for

This group specifies restart parameters for TRUDGE runs and accuracy thresholds. KSTART indicates the conjugate gradient direction in which the optimization will proceed. ( default = -1 ) -1 .... indicates that this is a non-restart run. 0 .... corresponds to a restart run. FNOISE accuracy of function values. Variation smaller than FNOISE are not considered to be significant (Def. 0.0005) TOLF accuracy required of the function (Def. 0.001) TOLR accuracy required of conjugate directions (Def. 0.05) For geometry optimization, the values which give better results (closer to the ones obtained with gradient methods) are: TOLF=0.0001, TOLR=0.001, FNOISE=0.00001 ==========================================================

Input Description

$FORCE

2-117

==========================================================

$FORCE

group

(optional, relevant for RUNTYP=HESSIAN,OPTIMIZE,SADPOINT) This group controls the computation of the hessian matrix (the energy second derivative tensor, also known as the force constant matrix), and an optional harmonic vibrational analysis. This can be a very time consuming calculation. However, given the force constant matrix, the vibrational analysis for an isotopically substituted molecule is very cheap. Related input is HESS= in $STATPT, and the $MASS, $HESS, $GRAD, $DIPDR, $VIB groups. Calculation of the hessian automatically yields the dipole derivative tensor, giving IR frequencies. Raman intensities are obtained by following with RUNTYP=RAMAN. METHOD = chooses the computational method: = ANALYTIC is a fully analytic calculation. This is implemented for SCFTYP=RHF, ROHF, GVB (for NPAIR=0 or 1, only), and MCSCF (for CISTEP=ALDET or ORMAS, only). This is the default for these cases. = SEMINUM does numerical differentiation of analytically computed first derivatives. This is the default for UHF, MCSCF using other CISTEPs, DFT, all solvent, models, relativistic corrections, and most MP2 or CI runs. = FULLNUM numerically twice differentiates the energy, which can be used by all other cases. It requires many energies (a check run will tell how many) and so it is mainly useful for systems with only very few symmetry unique atoms. The default for METHOD is to pick ANALYTIC over SEMINUM if that is programmed, and SEMINUM otherwise. FULLNUM will never be chosen unless you specifically request it. RDHESS = a flag to read the hessian from a $HESS group, rather than computing it. This variable pertains only to RUNTYP=HESSIAN. See also HESS= in the $STATPT group. (default is .FALSE.)

Input Description

$FORCE

2-118

PURIFY = controls cleanup Given a $ZMAT, the hessian and dipole derivative tensor can be "purified" by transforming from Cartesians to internals and back to Cartesians. This effectively zeros the frequencies of the translation and rotation "modes", along with their IR intensities. The purified quantities are punched out. Purification does change the Hessian slightly, frequencies at a stationary point can change by a wave number or so. The change is bigger at non-stationary points. (default=.FALSE. if $ZMAT is given) PRTIFC = prints the internal coordinate force constants. You MUST have defined a $ZMAT group to use this. (Default=.FALSE.) --- the next four apply to numeric differentiation ---NVIB = The number of displacements in each Cartesian direction for force field computation. This pertains only to METHOD=SEMINUM, as FULLNUM always uses double difference formulae. Move one VIBSIZ unit in each positive Cartesian direction. This requires 3N+1 evaluations of the wavefunction, energy, and gradient, where N is the number of SYMMETRY UNIQUE atoms given in $DATA. Move one VIBSIZ unit in the positive direction and one VIBSIZ unit in the negative direction. This requires 6N+1 evaluations of the wavefunction and gradient, and gives a small improvement in accuracy. In particular, the frequencies will change from NVIB=1 results by no more than 10-100 wavenumbers, and usually much less. However, the normal modes will be more nearly symmetry adapted, and the residual rotational and translational "frequencies" will be much closer to zero. (default) Displacement size (in Bohrs). This pertains to Both SEMINUM and FULLNUM. Default=0.01

= 1

= 2

VIBSIZ =

Input Description

$FORCE

2-119

Let 0 mean the Vib0 geometry, and D mean all the displaced geometries NPRT NPUN = 1 = 0 = 2 = 1 = 0 Print orbitals at 0 and D Print orbitals at 0 only (default) Punch all orbitals at 0 and D Punch all orbitals at 0 and occupied orbs at D Punch all orbitals at 0 only (default)

----- the rest control normal coordinate analysis ---VIBANL = flag to activate vibrational analysis. (the default is .TRUE. for RUNTYP=HESSIAN, and otherwise is .FALSE.) SCLFAC = scale factor for vibrational frequencies, used in calculating the zero point vibrational energy. Some workers correct for the usual overestimate in SCF frequencies by a factor 0.89. ZPE or other methods might employ other factors, see J.P.Merrick, D.Moran, L.Radom J.Phys.Chem.A 111, 11683-11700 (2007). The output always prints unscaled frequencies, so this value is used only during the thermochemical analysis. (Default is 1.0) TEMP = an array of up to ten temperatures at which the thermochemistry should be printed out. The default is a single temperature, 298.15 K. To use absolute zero, input 0.001 degrees. = an array of vibrational frequencies. If the frequencies are given here, the hessian matrix is not computed or read. You enter any imaginary frequencies as negative numbers, omit the zero frequencies corresponding to translation and rotation, and enter all true vibrational frequencies. Thermodynamic properties will be printed, nothing else is done by the run.

FREQ

PRTSCN = flag to print contribution of each vibrational mode to the entropy. (Default is .FALSE.)

Input Description

$FORCE

2-120

DECOMP = activates internal coordinate analysis. Vibrational frequencies will be decomposed into "intrinsic frequencies", by the method of J.A.Boatz and M.S.Gordon, J.Phys.Chem., 93, 1819-1826(1989). If set .TRUE., the $ZMAT group may define more than 3N-6 (3N-5) coordinates. (default=.FALSE.) PROJCT = controls the projection of the hessian matrix. The projection technique is described by W.H.Miller, N.C.Handy, J.E.Adams in J. Chem. Phys. 1980, 72, 99-112. At stationary points, the projection simply eliminates rotational and translational contaminants. At points with non-zero gradients, the projection also ensures that one of the vibrational modes will point along the gradient, so that there are a total of 7 zero frequencies. The other 3N-7 modes are constrained to be orthogonal to the gradient. Because the projection has such a large effect on the hessian, the hessian is punched both before and after projection. For the same reason, the default is .FALSE. to skip the projection, which is mainly of interest in dynamical calculations. ========================================================== There is a program ISOEFF for the calculation of kinetic and equilibrium isotope effects from the group of Piotr Paneth at the Technical University of Lodz. This program will accepts data computed by GAMESS (and other programs), and can be requested from paneth@p.lodz.pl

Input Description

$CPHF $MASS

2-121

==========================================================

$CPHF

group

(relevant for analytic RUNTYP=HESSIAN)

This group controls the solution of the response equations, also known as coupled Hartree-Fock. POLAR = a flag to request computation of the static polarizability, alpha. Because this property needs 3 additional response vectors, beyond those needed for the hessian, the default is to skip the property. (default = .FALSE.) CPHF = MO forms response equations from transformed MO integrals. (default for ROHF/GVB/MCSCF) = AO forms response equations from AO integrals, which takes less memory, and is programmed only for RHF wavefunctions. (default if RHF) = AODDI forms response equations from AO integrals, using distributed memory (see MEMDDI). This does AO integrals about 2x more than AO, but spreads the CPHF memory requirement out across multiple nodes. Coded only for RHF.

SOLVER = linear equation solver choice. This is primarily a debugging option. For RHF analytic Hessians, choose from CONJG (default), DIIS, ONDISK, not all of which will work for all CPHF= choices. For imaginary frequency dependent polarizability responses (MAKEFP jobs), choose GMRES (default), biconjugate gradient stabilized BCGST, DODIIS, or an explicit solver GAUSS. Most response equations have only one solver programmed, and thus ignore this keyword. NWORD = controls memory usage for this step. The default uses all available memory. (default=0)

==========================================================

$MASS

group (relevant for RUNTYP=HESSIAN, IRC, or DRC)

This group permits isotopic substitution during the computation of mass weighted Cartesian coordinates. Of course, the masses affect the frequencies and normal modes

Input Description of vibration.

$CPHF $MASS

2-122

AMASS = An array giving the atomic masses, in amu. The default is to use the mass of the most abundant isotope. Masses through element 104 are stored. example - $MASS AMASS(3)=2.0140 $END will make the third atom in the molecule a deuterium. ==========================================================

Input Description

$HESS $GRAD

2-123

==========================================================

$HESS

group (relevant for RUNTYP=HESSIAN if RDHESS=.TRUE.) (relevant for RUNTYP=IRC if FREQ,CMODE not given) (relevant for RUNTYP=OPTIMIZE,SADPOINT if HESS=READ)

Formatted force constant matrix (FCM), i.e. hessian matrix. This data is punched out by a RUNTYP=HESSIAN job, in the correct format for subsequent runs. The first card in the group must be a title card. A $HESS group is always punched in Cartesians. It will be transformed into internal coordinate space if a geometry search uses internals. It will be mass weighted (according to $MASS) for IRC and frequency runs. The initial FCM is updated during the course of a geometry optimization or saddle point search, and will be punched if a run exhausts its time limit. This allows restarts where the job leaves off. You may want to read this FCM back into the program for your restart, or you may prefer to regenerate a new initial hessian. In any case, this updated hessian is absolutely not suitable for frequency prediction! ==========================================================

$GRAD

group (relevant for RUNTYP=OPTIMIZE or SADPOINT) (relevant for RUNTYP=HESSIAN when RDHESS=.TRUE.) This

Formatted gradient vector at the $DATA geometry. data is read in the same format it was punched out.

For RUNTYP=HESSIAN, this information is used to determine if you are at a stationary point, and possibly for projection. If omitted, the program pretends the gradient is zero, and otherwise proceeds normally. For geometry searches, this information (if known) can be read into the program so that the first step can be taken instantly. ==========================================================

Input Description

$DIPDR $VIB $VIB2

2-124

==========================================================

$DIPDR

group

(relevant for RUNTYP=HESSIAN if RDHESS=.T.)

Formatted dipole derivative tensor, punched in a previous RUNTYP=HESSIAN job. If this group is omitted, then a vibrational analysis will be unable to predict the IR intensities, but the run can otherwise proceed. ==========================================================

$VIB

group

(relevant for RUNTYP=HESSIAN, METHOD=SEMINUM)

Formatted restart data, consisting of energies, gradients, and dipole moments. This data is read in the same format by which is was written to the RESTART file. Just add a " $END" card, and place this group into the input file to effect a restart. If the final gradient was written as zero, delete the entire last data set (energy, gradient, and dipole). This group can also be used to turn a less accurate single differencing run into a more accurate double differencing run (NVIB in $HESS). The mere presence of this group triggers the restart. ==========================================================

$VIB2

group

(relevant for hessians, METHOD=FULLNUM) (relevant for gradients, with NUMGRD=.TRUE.)

Formatted restart information, consisting of energy values, as written to the RESTART file. Just add a " $END" line at the bottom, and place this group into the input file to effect a restart. This group has the same name ($VIB2), but different contents, depending on whether you are restarting a numerical gradient or a fully numerical hessian job. The mere presence of this group triggers the restart. ===========================================================

Input Description

$VSCF

2-125

==========================================================

$VSCF

group

(optional, relevant to RUNTYP=VSCF)

This group governs the computation of vibrational frequencies including anharmonic effects. Besides the keywords shown below, the input file must contain a $HESS group (and perhaps a $DIPDR group), to start with previously obtained harmonic vibrational information. The VSCF method requires only energies, so any energy type in GAMESS may be used, perhaps with fully numerical harmonic vibrational information. Energies are sampled along the directions of the harmonic normal modes, and usually along pairs of harmonic normal modes, after which the nuclear vibrational wavefunctions are obtained. The dipole on the grid points may be used to give improved IR intensities. The most accurate calculation computes the potential surface directly, on all grid points, but this involves many energy evaluations. An attractive alternative is the Quartic Force Field approximation of Yagi et al., which computes a fit to the derivatives up to fourth order by computing a specialized set of points, after which this fit is used to generate the full grid of points for the solver. Since there are a great many independent energy evaluations, no matter which type of surface is computed, the VSCF method allows for computations in subgroups (much like the FMO method). Thus the $GDDI group will be read and acted upon, if found. Vibrational wavefunctions are obtained at an SCF-like level, termed VSCF, using product nuclear wavefunctions, along with an MP2-like correction to the vibrational energy, which is termed correlation corrected (cc-VSCF). In addition, vibrational energy levels based on second order degenerate pertubation theory (see VDPT) or a CI analog (see VCI) may be obtained. Most VSCF applications have been carried out with an electronic structure level of MP2 with triple zeta basis sets. This is thought to give accuracy to 50 wavenumbers for the larger fundamentals. Use of internal coordinates is known to give improved accuracy for lower frequencies, particularly in weakly bound clusters.

Input Description

$VSCF

2-126

Restarts involve the $VIBSCF group (which has different formats for each PETYP), and the READV keyword. Restarts are safest on the same machine, where normal mode phases are reproducible. References for the VSCF method, the QFF approximation, and the solvers are given in Chapter 4 of this manual, along with a number of sample applications. * * * * * The first input variables control the generation of the potential surface on which the nuclear vibrations occur: PETYP = DIRECT computes the full potential energy surface, according to NCOUP/NGRID. The total number of energy/dipole calculations for NCOUP=2 will be M*NGRID + (M*(M-1)/2)*NGRID*NGRID, where M is the number of normal modes. This is the default. = QFF the Quartic Force Field approximation to the potential surface is obtained. This is usually only slightly less accurate, but has a greatly reduced computational burden, namely 6*M + 12*M*(M-1)/2 energy/dipoles.

INTCRD = flag setting the coordinate system used for the grids. Any internal coordinates to be used must be defined in $ZMAT, using only 3N-6 simple coordinates (no DLC or natural internals), and of course you must give NZVAR in $CONTRL as well. The default is to use Cartesians (default .FALSE.) INTTYP = 0 default if INTCRD=.FALSE. (ignore this keyword) = 1 implies that the $ZMAT contains only stretches, bends, and torsions. It also selects an approximate transformation between Cartesian and internal coords. = 2 the other $ZMAT coordinates may be used, and the coordinate transformation will be iterated to convergence. (default if INTCRD=.TRUE.) NCOUP = the order of mode couplings included.

Input Description

$VSCF

2-127

= 1 computes 1-D grids along each harmonic mode = 2 adds additionally, 2-D grids along each pair of normal modes. (default=2) = 3 adds additionally, 3-D grids for mode triples, for PETYP=DIRECT only. NGRID = number of grid points to be used in solving for the anharmonic vibrational levels. In the case of PETYP=DIRECT, each of these grid points must be explicitly computed. For PETYP=QFF these grid points are obtained from a fitted quartic force field. Reasonable values are 8 or 16 for DIRECT, with 16 considered significantly more accurate. For PETYP=QFF, the generation of the solver grid is very fast, so use 16 always. (default=16) = step size for PETYP=DIRECT displacements. The maximum distance along each mode is a function of its frequency, amplitude(i)=sqrt(2*(AMP+1/2)/freq(i)) so that AMP resembles a vibrational quantum number. The default goes far enough past the classical turning points of the fundamentals to capture the relevant part of the surface. (default = 7.0) = step size for PETYP=QFF displacements. The step along each mode depends on the harmonic frequency, as well as this parameter, whose default is usually satisfactory (default=0.5)

AMP

STPSZ

In case the user wants to control each normal mode with a separate parameter, arrays of values may be given, using the keywords AMPX(1)=xx,yy,... or STPSZX(1)=xx,yy,zz... IMODE = array of modes for which anharmonic effects will be computed. IMODE(1)=10,19 computes anharmonic energies and wavefunctions for modes 10 and 19, only. In the current implementation, pairs of modes cannot be coupled, so NCOUP is forced to 1 if this option is specified. This approximation is intended for larger molecules, where the whole VSCF calculation is prohibitive. * * * * *

Input Description

$VSCF

2-128

The next set of keywords relates to the solver step which finds the vibrational states. The results always include VSCF and cc-VSCF (SCF and non-degenerate MP2-like solutions). Use of the restart option makes comparing the solvers very fast, compared to the time to generate the electronic potential energy surface's points. VDPT = option to use 2nd order degenerate perturbation theory, based on the ground and singly excited vibrational levels. Results for virtual CI within the same singly excited space will also be given. (default=.TRUE.) = option to use the virtual CI solver within a space of the ground and both singly and doubly excited vibrational levels. Selection of VCI turns VDPT off. (default=.FALSE.)

VCI

The solver always finds the ground vibrational state (v=0) by default, and defaults to finding the fundamentals (v=1 in every mode). It can rapidly find excited levels (such as all v=2) if restarted (see READV) from $VIBSCF, using the following to control the excitation levels: IEXC = 1 obtain fundamental frequencies (default) = 2 instead, obtain first overtones = 3 instead, obtain second overtones = 0 skip combination bands (default) = 1 add one additional quanta in other modes = 2 add two other quanta in one mode at a time. IEXC2 0 0 0 0 1 2 1 for H2O, which has only three modes: only 000 ground state, no transitions 000, and 100, 010, 001 (fundamentals) 000, and 200, 020, 002 (1st overtones) 000, and 300, 030, 003 (2nd overtones) 000, and 100, 010, 001, 110, 101, 110 (1st overtones and combinations) 000, and 100, 010, 001, 210, 201, 021 000, and 200, 020, 002, 120, 102, 012 between them, 1st and 2nd overtones, and all 2-1-0 combinations.

IEXC2

IEXC 0 1 2 3 1 1 2

Input Description

$VSCF

2-129

ICAS1, ICAS2 = starting and ending vibrations whose quanta are included. The default is all modes, ICAS1=1 and ICAS2=3N-6 (or 3N-5). SFACT = a numerical cutoff for small contributions in the solver. The default is 1d-4: 5d-3 or 1d-3 may affect accuracy of results, 1d-4 is safer, and 1d-5 might not converge. = scaling factor for pair-coupling potential. Sometimes when pair-coupling potential values are larger than the corresponding single mode values, they must be scaled down. It is seldom necessary to select a scaling other than unity. (Default=1.0) * * * * * The next two relate to simplified intensity computation. These simplifications are aimed at speeding up MP2 runs, if one does not care so much about intensities, and would like to eliminate the considerable extra time to compute MP2level dipoles. DMDR must not be used if overtones are being computed. DMDR = if true, indicates that the harmonic dipole derivative tensor $DIPDR will be read and used, rather than computing dipoles. (default=.FALSE.) = for MP2 electronic structure, a value of .FALSE. uses SCF level dipoles in order to save the time needed to obtain the MP2 density at every grid point. It is more accurate to use the DMDR flag instead of this option, if an MP2 level $DIPDR is available. (default=.TRUE.) * * * * These relate to the initial harmonic mode generation. Normally, a $HESS is provided, from which harmonic modes are obtained. It is possible to give the harmonic data explictly with the first two: RDFRQ = array of harmonic frequencies, starting from the smallest.

VCFCT

MPDIP

Input Description

$VSCF

2-130

CMODE

= array of normal mode displacements given in the same order as the frequencies read in RDFRQ. The data should be the x,y,z displacement of the first atom of the first mode, then x,y,z for the second atom, then going on to give each additional mode.

PROJCT = controls the projection of the hessian matrix (same meaning as in $FORCE). Default is .TRUE. which removes small mixings between rotations or translations and the harmonic modes. * * * * READV = flag to indicate restart data $VIBSCF should be read in to resume an interrupted calculation, or to obtain overtones in follow-on runs. (default is .FALSE.)

GEONLY = option to generate all points on the potential energy surface needed by the VSCF routine, without energy evaluations. The purpose of this is to prepare a set of geometries at which the energy is needed. A possible use for this is to obtain energies from a different program package, which might have an energy unavailable in GAMESS, but which lacks its own VSCF program. (default=.false.) ==========================================================

$VIBSCF

group

(optional, relevant to RUNTYP=VSCF)

This is restart data, as written to the disk file RESTART in a complete or partially completed previous run. Append a " $END", and also select READV=.TRUE. to read the data. $VIBSCF's contents are different for PETYP=DIRECT or QFF. The format of this group changed in December 2006, so that old groups can no longer be used. ==========================================================

Input Description

$GAMMA $EQGEOM $HLOWT $GLOWT

2-131

==========================================================

$GAMMA

group

required if RUNTYP=GAMMA

This group governs evaluation of the 3rd derivative of the energy with respect to nuclear coordinates, by finite differentiation of Hessians (see $FORCE options). NFCM = n describes the amount of restart data provided. The default is n=-1, to evaluate everything. A value of n means that n+1 $FCM groups are to be read from the file (hessian #0 means the equilibrium geometry). Restart data is read from a .gamma file, created by an earlier run.

DELTA = step size, default=0.01 Bohr PRTALL = flag to print full Hessian and Gamma matrix, the default is .FALSE. PRTSYM = flag to print unsymmetrical Gamma elements, the default is .FALSE. PRTBIG = flag to print large Gamma elements, default = .F. ==========================================================

$EQGEOM

group

required if NFFLVL=2 or 3 in $CONTRL

The coordinates of the stationary point, where the hessian and possibly 3rd derivative information was evaluated, in exactly the format it was printed by RUNTYP=GAMMA. ==========================================================

$HLOWT $GLOWT

group group

required if NFFLVL=2 or 3 in $CONTRL required if NFFLVL=3 in $CONTRL

These are the lower triangular parts of the hessian and 3rd derivative matrices, read in the same format as printed by an earlier RUNTYP=GAMMA. ==========================================================

Input Description

$IRC

2-132

==========================================================

$IRC

group

(relevant for RUNTYP=IRC)

This group governs the location of the intrinsic reaction coordinate (also called the minimum energy path, MEP), a steepest descent path in mass weighted coordinates, that connects the saddle point to reactants and products. The IRC serves a proof of the mechanism for a reaction, and is a starting point for reaction path dynamics. The IRC may be found for systems with QM atoms, EFP particles, or the combinations of QM and EFP particles, or QM plus the optional SIMOMM plug-in MM atoms. Restart data for RUNTYP=IRC is written into the PUNCH file. Information summarizing the reaction path is written to the TRAJECT file, which should be saved, appending these as various restarts are done. The graphics program MacMolPlt can display a movie of the entire mechanism, if you join the entire forward and entire backwards trajectory files, while changing the path distance parameter in the reverse part to a negative value. ----- there are five integration methods chosen by PACE. PACE = GS2 selects the Gonzalez-Schlegel second order method. This is the default method. Related input is:

GCUT

RCUT ACUT MXOPT IHUPD

cutoff for the norm of the mass-weighted gradient tangent (the default is chosen in the range from 0.00005 to 0.00020, depending on the value for STRIDE chosen below. cutoff for Cartesian RMS displacement vector. (the default is chosen in the range 0.0005 to 0.0020 Bohr, depending on the value for STRIDE) maximum angle from end points for linear interpolation (default=5 degrees) maximum number of contrained optimization steps for each IRC point (default=20) is the hessian update formula. 1 means Powell, 2 means BFGS (default=2)

Input Description GA

$IRC

2-133

is a gradient from the previous IRC point, and is used when restarting. OPTTOL is a gradient cutoff used to determine if the IRC is approaching a minimum. It has the same meaning as the variable in $STATPT. (default=0.0001) PACE = LINEAR selects linear gradient following (Euler's method). Related input is: STABLZ switches on Ishida/Morokuma/Komornicki reaction path stabilization. The default is .TRUE. DELTA initial step size along the unit bisector, if STABLZ is on. Default=0.025 Bohr. ELBOW is the collinearity threshold above which the stabilization is skipped. If the mass weighted gradients at QB and QC are almost collinear, the reaction path is deemed to be curving very little, and stabilization isn't needed. The default is 175.0 degrees. To always perform stabilization, input 180.0. READQB,EB,GBNORM,GB are energy and gradient data already known at the current IRC point. If it happens that a run with STABLZ on decides to skip stabilization because of ELBOW, this data will be punched to speed the restart. PACE = QUAD SAB GA selects quadratic gradient following. Related input is:

distance to previous point on the IRC. gradient vector at that historical point. selects the fourth order Adams-Moulton variable step predictor-corrector. Related input is:

PACE = AMPC4

GA0,GA1,GA2 which are gradients at previous points. PACE = RK4 selects the 4th order Runge-Kutta variable step method. There is no related input.

Input Description

$IRC

2-134

----- The next two are used by all PACE choices ----STRIDE = Determines how far apart points on the reaction path will be. STRIDE is used to calculate the step taken, according to the PACE you choose. The default is good for the GS2 method, which is very robust. Other methods should request much smaller step sizes, such as 0.10 or even 0.05. (default = 0.30 sqrt(amu)-Bohr) NPOINT = The number of IRC points to be located in this run. The default is to find only the next point. (default = 1)

----- The next two let you choose your output volume ----Let F mean the first IRC point found in this run, and L mean the final IRC point of this run. Let INTR mean the internuclear distance matrix. NPRT = 1 0 -1 -2 1 0 -1 -2 Print Print Print Print INTR INTR INTR INTR at at at at all, all, all, F+L, orbitals orbitals orbitals orbitals at all IRC points at F+L (default) never never

NPUN

Punch all orbitals at all IRC points Punch all orbitals at F+L, only occupied orbitals at IRC points between (default) Punch all orbitals at F+L only Never punch orbitals

----- The next two tally the reaction path results. The defaults are appropriate for starting from a saddle point, restart values are automatically punched out. NEXTPT = The number of the next point to be computed. STOTAL = Total distance along the reaction path to next IRC point, in mass weighted Cartesian space.

----- The following controls jumping off the saddle point.

Input Description

$IRC

2-135

If you give a $HESS group, FREQ and CMODE will be generated automatically. SADDLE = A logical variable telling if the coordinates given in the $DATA deck are at a saddle point (.TRUE.) or some other point lying on the IRC (.FALSE.). If SADDLE is true, either a $HESS group or else FREQ and CMODE must be given. (default = .FALSE.) Related input is: TSENGY = A logical variable controlling whether the energy and wavefunction are evaluated at the transition state coordinates given in $DATA. Since you already know the energy from the transition state search and force field runs, the default is .F. FORWRD = A logical variable controlling the direction to proceed away from a saddle point. The forward direction is defined as the direction in which the largest magnitude component of the imaginary normal mode is positive. (default =.TRUE.) EVIB = Desired decrease in energy when following the imaginary normal mode away from a saddle point. (default=0.0005 Hartree) FREQ = The magnitude of the imaginary frequency, given in cm**-1. CMODE = An array of the components of the normal mode whose frequency is imaginary, in Cartesian coordinates. Be careful with the signs! You must give FREQ and CMODE if you don't give a $HESS group, when SADDLE=.TRUE. The option of giving these two variables instead of a $HESS does not apply to the GS2 method, which must have a hessian input, even for restarts. Note also that EVIB is ignored by GS2 runs. * * For the * * * * * * * * * * * * * * * * * * hints about IRC tracking, see 'further information' section. * * * * * * * * * * * * * * * *

==========================================================

Input Description

$DRC

2-136

==========================================================

$DRC

group

(relevant for RUNTYP=DRC)

This group governs "direct dynamics", following the dynamical reaction coordinate, which is a classical trajectory based on quantum chemistry potential energy surfaces. These may be either ab initio or semi-empirical, and are computed "on the fly" as the trajectory proceeds. Because the vibrational period of a normal mode with frequency 500 wavenumbers is 67 fs, a DRC needs to run for many steps in order to sample a representative portion of phase space. Restart data can be found in the job's OUTPUT file, with important results summarized to the TRAJECT file. Almost all DRCs break molecular symmetry, so build your molecule with C1 symmetry in $DATA, or specify NOSYM=1 in $CONTRL. RUNTYP=DRC may not be used with EFP particles. NSTEP = The number of DRC points to be calculated, not including the initial point. (default = 1000) (default = 0.1 fs)

DELTAT = is the time step.

TOTIME = total duration of the DRC computed in a previous job, in fs. The default is the correct value when initiating a DRC. (default=0.0 fs) * * * In general, a DRC can be initiated anywhere, so $DATA might contain coordinates of the equilibrium geometry, or a nearby transition state, or something else. You must also supply an initial kinetic energy, and the direction of the initial velocity, for which there are a number of options: EKIN = The initial kinetic energy (default = 0.0 kcal/mol) See also ENM, NVEL, and VIBLVL regarding alternate ways to specify the initial value. VEL = an array of velocity components, in Bohr/fs. When NVEL is false, this is simply the direction

Input Description

$DRC

2-137

initial

of the velocity vector. Its magnitude will be automatically adjusted to match the desired kinetic energy, and it will be projected so that the translation of the center of mass is removed. Give in the order vx1, vy1, vz1, vx2, vy2, ...

NVEL

= a flag to compute the initial kinetic energy from the input VEL using the sum of mass*VEL*VEL/2. This flag is usually selected only for restarts. (default=.FALSE.) The next three allow the kinetic energy to be partitioned over all normal modes. The coordinates in $DATA are likely to be from a stationary point! You must also supply a $HESS group, which is the nuclear force constant matrix at the starting geometry.

VIBLVL = a flag to turn this option on (default=.FALSE.) VIBENG = an array of energies (in units of multiples of the hv of each mode) to be imparted along each normal mode. The default is to assign the zero point energy only, VIBENG(1)=0.5, 0.5, ..., 0.5 when HESS=MIN, and 0.0, 0.5, ..., 0.5 if HESS=TS. If given as a negative number, the initial direction of the velocity vector is along the reverse direction of the mode. "Reverse" means the phase of the normal mode is chosen such that the largest magnitude component is a negative value. An example might be VIBENG(4)=2.5 to add two quanta to mode 4, along with zero point energy in all modes. RCENG = reaction coordinate energy, in kcal/mol. This is the initial kinetic energy given to the imaginary frequency normal mode when HESS=TS. If this is given as a negative value, the direction of the velocity vector will be the "reverse direction", meaning the phase of the normal mode will be chosen so its largest component is negative. * * *

Input Description

$DRC

2-138

The next two pertain to initiating the DRC along a single normal mode of vibration. No kinetic energy is assigned to the other modes. You must also supply a $HESS group at the initial geometry. NNM = The number of the normal mode to which the initial kinetic energy is given. The absolute value of NNM must be in the range 1, 2, ..., 3N-6. If NNM is a positive/negative value, the initial velocity will lie in the forward/reverse direction of the mode. "Forward" means the largest normal mode component is a positive value. (default=0) = the initial kinetic energy given to mode NNM, in units of vibrational quanta hv, so the amount depends on mode NNM's vibrational frequency, v. If you prefer to impart an arbitrary initial kinetic energy to mode NNM, specify EKIN instead. (default = 0.0 quanta)

ENM

To summarize, there are 5 ways to initiate a trajectory: 1. VEL vector with NVEL=.TRUE. This is difficult to specify at your initial point, and so this option is mainly used when restarting your trajectory. The restart information is always in this format. 2. VEL vector and EKIN with NVEL=.FALSE. This will give a desired amount of kinetic energy in the direction of the velocity vector. 3. VIBLVL and VIBENG and possibly RCENG, to give some initial kinetic energy to all normal modes. 4. NNM and ENM to give quanta to a single normal mode. 5. NNM and EKIN to give arbitrary kinetic energy to a single normal mode. * * * The most common use of the next two is to analyze a trajectory with respect to the normal modes of a minimum energy geometry it travels around. NMANAL = a flag to select mapping of the mass-weighted Cartesian DRC coordinates and velocity (conjugate momentum) in terms of normal modes at a nearby

Input Description

$DRC

2-139

reference stationary point (which can be either a minimum or transition state). This reference geometry could in fact be the same as the initial point of the DRC, but does not need to be. If you choose this option, you must supply C0, HESS2, and a $HESS2 group corresponding to the reference stationary point. (default=.FALSE.) C0 = an array of the coordinates of the stationary reference point (the coordinates in $DATA might well be some other coordinates). Give in the order x1,y1,z1,x2,y2,... in Angstroms. * * * The next options apply to input choices which may read a $HESS at the initial DRC point, namely NNM or VIBLVL, or to those that read a $HESS2 at some reference geometry (NMANAL). HESS HESS2 = MIN indicates the hessian supplied for the initial geometry corresponds to a minimum (default). = TS indicates the hessian is for a saddle point. = MIN (default) or TS, the same meaning, for the reference geometry. These are used to decide if modes 1-6 (minimum) or modes 2-7 (TS) are to be excluded from the hessian as the translational and rotational contaminants. If the initial and reference geometries are the same, these two hessians will be duplicates of each other. The next variables can cause termination of a run, if molecular fragments get too far apart or close together. NFRGPR = Number of atom pairs whose distance will be checked. (default is 0) IFRGPR = Array of the atom pairs. 2 times NFRGPR values.

FRGCUT = Array for a boundary distance (in Bohr) for atom pairs to end DRC calculations. The run will stop if any distance exceeds the tolerance, or if a value is given as a negative number, if the

Input Description

$DRC

2-140

distance becomes shorter than the absolute value. In case the trajectory starts outside the bounds specified, they do not apply until after the trajectory reaches a point where the criteria are satisfied, and then goes outside again. Give NFRGPR values. * * * The final variables control the volume of output. Let F mean the first DRC point found in this run, and L mean the last DRC point of this run. NPRTSM = summarize the DRC results every NPRTSM steps, to the TRAJECT file. (default = 1) NPRT = 1 0 -1 2 1 0 -1 Print orbitals at all DRC points Print orbitals at F+L (default) Never print orbitals Punch all orbitals at all DRC points Punch all orbitals at F+L, and occupied orbitals at DRC points between Punch all orbitals at F+L only (default) Never punch orbitals

NPUN

==========================================================

Input Description

$MEX

2-141

===========================================================

$MEX

group

(relevant if RUNTYP=MEX)

This group governs a search for the lowest energy on the 3N-7 dimensional "seam" of intersection of two different electronic potential energy surfaces. Such Minimum Energy Crossing Points are important for processes such as spinorbit coupling that involve transfer from one surface to another, and thus are analogous to transition states on a single surface. The present program requires that the two surfaces differ in spin quantum number, or space symmetry, or both. Analytic gradients are used in the search. In case the two potential surfaces have identical spin and space symmetry, this kind of intersection point is referred to as a Conical Intersection. See $CONICL using RUNTYP=CONICAL instead. SCF1, SCF2 = define the molecular wavefunction types, possibly in conjunction with the usual MPLEVL and DFTTYP keywords.

MULT1, MULT2 = give the spin multiplicity of the states. Permissible combinations of wavefunctions are RHF with ROHF/UHF ROHF with ROHF UHF with UHF as well as their MP2 and DFT counterparts, and GVB with ROHF/UHF MCSCF with MCSCF (CISTEP=ALDET or GUGA only) NSTEP STPSZ = maximum number of search steps (default=50) = Step size during the search (default = 0.1D+00)

NRDMOS = = = = =

Initial orbitals can be read in 0 No initial orbitals (default) 1 Read in orbitals for first state (in $VEC1) 2 Read in orbitals for second state (in $VEC2) 3 Read in orbitals for both ($VEC1 and $VEC2)

Input Description NMOS1 NMOS2 NPRT

$MEX

2-142

= Number of orbitals for first state's $VEC1. = Number of orbitals for second state's $VEC2. = Printing orbitals = 0 No orbital printed out except at the first geometry (default) = 1 Orbitals are printed each geometry. If MCSCF is used, CI expansions are also printed.

Finer control of the convergence criterion: TDE = energy difference between two states (default = 1.0D-05)

TDXMAX = maximum displacement of coordinates (default = 2.0D-03) TDXRMS = root mean square displacement (default = 1.5D-03) TGMAX TGRMS = maximum of effective gradient between the two states (default = 5.0D-04) = root mean square effective gradient tolerance (default = 3.0D-04)

=========================================================== Usage notes: 1. Normally $CONTRL will not give SCFTYP or MULT keywords. SCF1 and SCF2 can be given in any order. The combinations permitted ensure roughly equal sophistication in the treatment of electron correlation. 2. After reading $MEX, SCFTYP and MULT will be set to the more complex of the two choices, which is considered to be RHF < ROHF < UHF < GVB < MCSCF. This permits the $SCF input defining a GVB wavefunction to be read and tested for correctness, in a GVB+ROHF run. Since only one SCFTYP is stored while reading the input, you might need to provide some keywords that are normally set by default for the other (such as ensuring DIIS is selected in $SCF if either of the states is UHF).

Input Description

$MEX

2-143

3. It is safest by far to prepare and read $VEC1 and $VEC2 groups so that you know what electronic states you start with. It is a good idea to regenerate both states at the end of the MEX search, to be sure that they remain as you began. 4. It is your responsibility to make sure that the states have a different space symmetry, or a different spin symmetry (or both). That is why note 3 is so important. 5. $GRAD1 and/or $GRAD2 groups containing gradients may be given to speed up the first geometry of the MEX search. 6. The search is even trickier than a saddle point search, for it involves the peaks and valleys of BOTH surfaces being generated. Starting geometries may be guessed as lying between the minima of the two surfaces, but the lowest energy on the crossing seam may turn out to be somewhere else. Be prepared to restart! 7. The procedure is a Newton-Raphson search, conducted in Cartesian coordinates, with a Lagrange multiplier imposing the constraint of equal energy upon the two states. The hessian matrices in the search are guessed at, and subjected to BFGS updates. Internal coordinates will be printed (for monitoring purposes) if you define $ZMAT, but the stepper operates in Cartesian coordinates only. No geometry constraints can be applied, apart from the point group in $DATA. A good paper to read about this kind of search is A.Farazdel, M.Dupuis J.Comput.Chem. 12, 276-282(1991)

Input Description

$CONICL

2-144

===========================================================

$CONICL

group

(relevant if RUNTYP=CONICAL)

This group governs a search for the lowest energy on the 3N-7 dimensional "seam" of intersection of two electronic potential energy surfaces of the same spin and space symmetry. Such Conical Intersections (CI) are important in photochemistry, where they serve as "funnels" for the transfer from an excited state to a lower state. See RUNTYP=MEX and the $MEX input for the simpler case where the two surfaces differ by either space or spin symmetry. Three search procedures are given, one of which requires the non-adiabatic coupling matrix element (NACME), and two others which do not require NACME information. The conical intersection search is available only for MCSCF (for which NACME are available) or for TD-DFT potential surfaces (where NACME are not available). The TD-DFT must be used in the Tamm/Dancoff approximation (see TAMMD in $TDDFT), but can be either conventional or spin-flip. The search utilizes some of the options of $STATPT, but note that the Schlegel stepper and HESS=CALC are not permitted. It may be reasonable to try the RFO stepper sometimes. The search can only be run in Cartesian coordinates. Restarts are possible only by updating the coordinates in $DATA. At present, the only solvation model that is supported is conventional TD-DFT with EFP1. OPTTYP = search procedure choice, see references below! = GPWNAC Gradient Projection with NACME, so this is only available for MCSCF. = BPUPD branching plane updating method (default) = PENALTY penalty-constrained optimization method Note that for MCSCF surfaces, if state-averaging is used, the program executes the code needed to produce NACME vectors, to producing the state-averaged gradients. There is essentially no extra time required to produce also the NACME, hence the GPWNAC stepper might as well be used.

Input Description

$CONICL

2-145

IXROOT = array of two states whose CI point is sought. For example, this might be IXROOT(1)=2,3 The roots are counted exactly the same as IROOT in the $DET or $TDDFT input groups. For the latter case, set IXROOT to 0 if you want the ground state to be one of the two surfaces searched on. There is no default for IXROOT! SYMOFF = flag to switch off point group symmetry, the default is .TRUE. DEBUG = flag to print debugging info, default is .FALSE.

The following are meaningful only for OPTTYP=PENALTY: TOLSTP = energy difference tolerance default=1d-6 Hartree TOLGRD = gradient convergence tolerance default=5d-3 Hartree/Bohr ALPHA SIGMA = parameter ensuring a singularity free penalty, default=0.02 Hartree = Lagrange multiplier for the penalty term. In case the energy gap between the states is not acceptable at the CI point, increase the value. default = 3.5 (unitless)

An understanding of the search procedures can be gained by reading the following papers: Gradient Projection with NACME: M.J.Bearpark, M.A.Robb, H.B.Schlegel Chem.Phys.Lett. 223, 269(1994) Branching Plane Updating method: S.Maeda, K.Ohno, K.Morokuma J.Chem.Theor Comput. 6, 1538(2010) Penalty constrained update method: B.G.Levine, C.Ko, J.Quenneville, T.J.Martinez Mol.Phys. 104, 1039(2006) B.G.Levine, J.D.Coe, T.J.Martinez J.Phys.Chem.B 112, 405(2008) A comparative study of the first two procedures is

Input Description

$CONICL

2-146

T.W.Keal, A.Koslowski, W.Thiel Theoret.Chem.Acc. 118, 837(2007) ===========================================================

Input Description

$MD

2-147

===========================================================

$MD

group

(relevant if RUNTYP=MD)

This group controls the molecular dynamics trajectory for a collection of quantum mechanical atoms and/or Effective Fragment Potential particles. A typical MD simulation starts with an equilibration phase, running long enough to produce a randomized structure and velocity distribution. Typically equilibration is done with an NVT ensemble, allowing the system to equilibrate to a desired temperature. A production run restarts with the positions and the velocity and quaternion data from the equilibration run, might use either a NVE or NVT ensemble, and collects radial distribution functions and other properties. Only a few properties are computed from the MD trajectory, apart from correct radial distribution functions. In particular, the pressures, diffusion constants, and heats of vaporization that appear on the printout (presently only for pure EFP runs) are from a preliminary code, which has not yet been verified. If the system contains only EFP particles, it may be placed in a periodic box, according to the minimum image convention. The optional periodic boundary conditions, along with cut-offs, are given in the $EFRAG input. See also the $EWALD input group for long-range electrostatic treatment if PBC is used. The first keywords relate to the steps: MDINT = MD integrator selection. = FROG (leapfrog). This is less accurate, and lacks the special ensemble stepper option NVTNH. = VVERLET (velocity Verlet) - default. = MD time step size, in seconds, default=1.0d-15, which is a femtosecond. selects a integrator step appropriate to the desired ensemble. This is only implemented for

DT NVTNH

Input Description

$MD

2-148

velocity Verlet. = 0 means use NVE Verlet stepping = 1 means use NVT Verlet stepping = 2 means use Nose/Hoover chain NVT Verlet stepping The default is 2 if either NVT option RSTEMP or RSRAND is chosen, but is 0 otherwise. NSTEPS = number of MD time steps to be found in this run, default=10000. TTOTAL = total time elapsed in the previous part of a MD trajectory which is being restarted (READ=.TRUE.). The default means this trajectory is a new one, or perhaps the start of a production phase of the MD. (default=0.0 seconds) * * * BATHT = bath temperature, in Kelvin (default=300.0) This value is used during NVT runs, or if the MD is initialized to a Maxwell-Boltzmann velocity distribution. * * * Two options exist to create NVT runs, to bring the system to a desired bath temperature. If neither is chosen, the ensemble is NVE: RSTEMP = flag to rescale the temperature. DTEMP default=.FALSE.

= temperature range for the RSTEMP option. The velocities are rescaled to the bath temperature if T < (BATHT-DTEMP) or T > (BATHT+DTEMP). The default is DTEMP=100.0 degrees.

RSRAND = flag to reset to Maxwell-Boltzmann distribution, using random numbers (same algorithm as MBT and MBR) to choose individual velocity magnitudes and directions. default=.FALSE. NRAND = number of steps for the RSRAND option. Reassign velocities (translational and rotational) every NRAND time steps. Default=1000.

Input Description

$MD

2-149

NVTOFF = step number at which to turn off either NVT thermostat, and switch to NVE. At this point, the NVTNH parameter will be reset to 0, and the PROD flag will be turned on, so that the production run will start (gathering and printing the RDF information to .log file). This keyword is also useful in NVE runs to postpone the accumulation of production information. The default means no switch to NVE (default=0). JEVERY = report simulation quantities (write info such as energies, temps, etc. to .log file) and collect RDF info each JEVERY time step. Default=10 KEVERY = write coordinates (to log and TRAJECT files), velocity/quaternion restart info (to the TRAJECT file and RDFs (to log file) at each KEVERY step. default=100 PROD = production run, at present this means only that information for radial distribution functions is collected, and printed. default=.FALSE. = spacing for radial bins in RDF calculations, default=0.02 Angstroms. = step number at which to begin collecting data for the other properties, such as pressure and diffusion constants. This should be a value between 1 and NSTEPS, as it counts off the current run's steps. Default=0.

DELR NPROP

PBCOUT = print PBC coordinates in the end of simulation (i.e. all molecules will be contained in one box) Default=.FALSE. * * * The following keywords control starting MD conditions. Normally an MD trajectory is initiated with both MBT and MBR chosen, while restarts would select only READ. The restart data is written to the TRAJECT file. To restart requires merging particle coordinates into $DATA and/or $EFRAG, and placing the $MD group below your existing $MD

Input Description

$MD

2-150

group, thus keeping your choices for the variables above (both $MD groups will be read). MBT MBR QRAND = get translational velocities from a random Maxwell-Boltzmann ensemble. Default=.FALSE. = get rotational velocities from a random MaxwellBoltzmann ensemble. Default=.FALSE. = if .TRUE., generate random quaternions, an option that is not normally chosen. if .FALSE., use EFP particle coordinates and the initial MBT/MBR assigned velocities to set correct quaternion data (default is .FALSE.) = read velocities (translational and rotational) and quaternions and their first and second derivatives from input file. Default is .FALSE. Set the other three values MBT/MBR/QRAND off if you choose restarting with READ.

READ

For READ=.TRUE., the following restart data is required. This data may be copied from the TRAJECT file, in exactly the format it was written out. The required data depends on your choice for the integrator, see MDINT above. In addition, you will need to update the particle coordinates in $DATA and/or $EFRAG, using data from the TRAJECT file. TVELQM(1)= quantum atom's translational velocities (both). TVEL(1)= array of EFP translational velocities (both). RVEL(1)= array of EFP rotational velocities (VVERLET). RMOM(1)= array of EFP rotational momenta (FROG). QUAT(1)= array of EFP quaternions (both). QUAT1D(1)= EFP quaternion first derivatives (VVERLET). QUAT2D(1)= EFP quaternion second derivatives (VVERLET). extra reading: "Computer Simulation of Liquids" M.P.Allen, D.J.Tildesley Oxford Science, 1987 "Understanding Molecular Simulation" D.Frenkel, B.Smit Academic Press, 2002 ===========================================================

Input Description

$RDF

2-151

==========================================================

$RDF

group

(relevant for RUNTYP=MD)

This group defines the pairs of atoms for which the radial distribution functions are to be computed, at the end of a molecular dynamics trajectory. The input is similar in style to $EFRAG, consisting of separate lines, with the word STOP ending each particular pair. Line 1. NRDF=<no.RDFs> gives the number of RDFs which should be computed. Line 2. <pair title> <FRAG1> <FRAG2> <no.pairs> gives a string for the printout (a good choice involves both atoms, such as ClCl), the name of the $FRAGNAME containing the first atom of the pair, the name of the $FRAGNAME group with the second atom of the pair, and how many such pairs exist. Line 3. <label> <num.atom1> <num.atom2> gives a label (arbitrary), the position of the atom within the $FRAG1 group, and the 2nd atom's within the $FRAG2. This line must be repeated <no.pairs> times. Line 4. STOP the word STOP ends this RDF's pair input. Lines 2-4 must then be repeated a total of <no.RDFs> times. An example will make this all clear. If there is only one type of fragment used, such as water (so $EFRAG contains only FRAGNAME=WATER), and assuming that this $WATER group defining the water EFP has atoms in the order O,H,H: $RDF nrdf=3 OO dum STOP OH dum dum dum dum

1 1 1 2 3

water 1 water 2 3 1 1

water water

1 4

Input Description STOP HH dum dum dum dum STOP $end

$RDF

2-152

2 2 3 3

water 2 3 2 3

water

==========================================================

Input Description

$GLOBOP

2-153

==========================================================

$GLOBOP

group

(relevant to RUNTYP=GLOBOP)

This controls a search for the global minimum energy. It is primarily intended for locating the best position for effective fragment "solvent" molecules, perhaps with an ab initio "solute" present. There are options for a single temperature Monte Carlo search, or a multiple temperature simulated annealing. Local minimization of some or all of the structures selected by the Monte Carlo is optional. See REFS.DOC for an overview of this RUNTYP. The coordinates of accepted structures are written to the file TRAJECT. A perl script named "globop_extract" is provided in the standard GAMESS distribution, which can extract the lowest energies (and matching coordinates) from the TRAJECT data set. RNDINI = flag to randomize the particles given in $EFRAG, usually choosing the particle at random, placing it near the center of the coordinate origin but in such a way that it does not collide with any particles placed earlier. The default is to use coordinates as given in $EFRAG (default .FALSE.) relevant only if RNDINI is .TRUE. RAND selects EFP particles in random order, as well as randomizing their coordinates. (default) STANDARD chooses the particles in the same order that they were given in $EFRAG, so only their positions are randomized.

RIORD

= = =

See REFS.DOC for some ideas on how to build clusters with these two inputs. TEMPI TEMPF = = initial temperature used in the simulation. (default = 20000 K) final temperature. If TEMPF is not given and NTEMPS is greater than 1, TEMPF will be calculated based on a cooling factor of 0.95. number of temperatures used in the simulation.

NTEMPS =

Input Description

$GLOBOP

2-154

If NTEMPS is not given but TEMPF is given, NTEMP will be calculated based on a cooling factor of 0.95. If neither NTEMP nor TEMPF is given, the job defaults to a single temperature Monte Carlo calculation. NFRMOV = NGEOPT = NTRAN NROT = = number of fragments to move on each step. (default=1) number of geometries to be evaluated at each temperature. (default = 100) number of translational steps in each block. (default=5) number of rotational steps in each block. (default=5) the number of blocks of steps can be set directly with this variable, instead of being calculated from NGEOPT, NTRAN, and NROT, according to NBLOCK=NGEOPT/(NTRAN+NROT) If NBLOCK is input, the number of geometries at each temperature will be taken as NGEOPT=NBLOCK*(NTRAN+NROT) Each block has NTRAN translational steps followed by NROT rotational steps. flag to enable geometry optimization to minimize the energy is carried out every NSTMIN steps. (default=.true.) After this number of geometry steps are taken, a local (Newton-Raphson) optimization will be carried out. If this variable is set to 1, a local minimization is carried out on every step, reducing the MC space to the set of local minima. Irrelevant if MCMIN is false. (default=10) if set to .TRUE., at the end of the run local minimizations are carried out on the final geometry and on the minimum-energy geometry. (default=.FALSE.) an array of length two. The first element is the

NBLOCK =

MCMIN

NSTMIN =

OPTN

SCALE

Input Description

$GLOBOP

2-155

initial maximum step size for the translational coordinates (Angstroms). The second element is the initial maximum stepsize for the rotational coordinates (pi-radians). (defaults = 1,1) AIMOVE = step range for moving ab initio atoms in the MC simulation. If set to zero, the ab initio atoms do not move in MC. The motion of ab initio atoms is unsophisticated, as the move consists only of shifting each Cartesian coordinate in the range of plus AIMOVE to minus AIMOVE atomic units. Ab initio atoms are allowed to relax during possible geometry optimizations implied by MCMIN/NSTMIN. (default=0.0) controls the rate at which information from successful steps is folded into the maximum step sizes for each of the 6*(number of fragments) coordinates. ALPHA varies between 0 and 1. ALPHA=0 means do not change the maximum step sizes, and ALPHA=1 throws out the old step sizes whenever there is a successful step and uses the successful step sizes as the new maxima. This update scheme was used with the Parks method where all fragments are moved on every step. It is normally not used with the Metropolis method. (default = 0) the desired acceptance ratio, the program tries to achieve this by adjusting the maximum step size. (default = 0.5) the factor used to update the maximum step size in the attempt to achive the desired acceptance ratio (DACRAT). If the acceptance ratio at the previous temperature was below DACRAT, the step size is decreased by multiplying it by UPDFAC. If the acceptance ratio was above DACRAT, the step size is increased by dividing it by DACRAT It should be between 0 and 1. (default = 0.95) the separation tolerence between atoms in the ab initio piece and atoms in the fragments, as well as between atoms in different fragments. If a step moves atoms closer than this tolerence, the

ALPHA

DACRAT =

UPDFAC =

SEPTOL =

Input Description

$GLOBOP

2-156

step is rejected. (default = 1.5 Angstroms) XMIN, XMAX, YMIN, YMAX, ZMIN, ZMAX = mimimum and maximum values for the Cartesian coordinates of the fragment. If the first point in a fragment steps outside these boundaries, periodic boundary conditions are used and the fragment re-enters on the opposite side of the box. The defaults of -10 for minima and +10 for maxima should usually be changed. BOLTWT = = = method for calculating the Boltzmann factor, which is used as the probability of accepting a step that increases the energy. STANDARD = use the standard Boltzmann factor, exp(-delta(E)/kT) (default) AVESTEP = scale the temperature by the average step size, as recommended in the Parks reference when using values of ALPHA greater than 0.

NPRT

= controls the amount of output, with = -2 reduces output below that of -1 = -1 reduces output further, needed for MCMIN=.true. = 0 gives minimal output (default) = 1 gives the normal GAMESS amount of output = 2 gives maximum output For large simulations, even IOUT=0 may produce a log file too large to work with easily. If geometry optimization is being done at each Monte Carlo generated structure, you can use the NPRT in $STATPT to further suppress output. controls the choice of random number generator. DEBUG uses a simple random number generator with a constant seed. Since the same sequence of random numbers is generated during each job, it is useful for debugging. RAND1 uses the simple random number generator used in DEBUG, but with a variable seed. RAND3 uses a more sophisticated random number generator described in Numerical Recipes, with a variable seed (default). array whose length is the number of fragments. It allows one or more fragments to be fixed

RANDOM = =

= =

IFXFRG =

Input Description

$GLOBOP

2-157

during the simulation. =0 allows the fragment to move during the run =1 fixes the fragment For example, IFXFRG(3)=1 would fix the third fragment, the default is IFXFRG(1)=0,0,0,...,0 ==========================================================

Input Description

$GRADEX

2-158

==========================================================

$GRADEX

group

(optional, for RUNTYP=GRADEXTR)

This group controls the gradient extremal following algorithm. The GEs leave stationary points parallel to each of the normal modes of the hessian. Sometimes a GE leaving a minimum will find a transition state, and thus provides us with a way of finding that saddle point. GEs have many unusual mathematical properties, and you should be aware that they normally differ a great deal from IRCs. The search will always be performed in cartesian coordinates, but internal coordinates along the way may be printed by the usual specification of NZVAR and $ZMAT. METHOD = algorithm selection. SR A predictor-corrector method due to Sun and Ruedenberg (default). JJH A method due to Jorgensen, Jensen and Helgaker. NSTEP DPRED STPT = maximum number of predictor steps to take. (default=50) = the stepsize for the predictor step. (default = 0.10) = a flag to indicate whether the initial geometry is considered a stationary point. If .TRUE., the geometry will be perturbed by STSTEP along the IFOLOW normal mode. (default = .TRUE.)

STSTEP = the stepsize for jumping away from a stationary point. (default = 0.01) IFOLOW = Mode selection option. (default is 1) If STPT=.TRUE., the intial geometry will be perturbed by STSTEP along the IFOLOW normal mode. Note that IFOLOW can be positive or negative, depending on the direction the normal mode should be followed in. The positive direction is defined as the one where the largest component of the Hessian eigenvector is positive.

Input Description

$GRADEX

2-159

If STPT=.FALSE. the sign of IFOLOW determines which direction the GE is followed in. A positive value will follow the GE in the uphill direction. The value of IFOLOW should be set to the Hessian mode which is parallel to the gradient to avoid miscellaneous warning messages. GOFRST = a flag to indicate whether the algorithm should attempt to locate a stationary point. If .TRUE., a straight NR search is performed once the NR step length drops below SNRMAX. 10 NR step are othen allowed, a value which cannot be changed. (default = .TRUE.) SNRMAX = upper limit for switching to straight NR search for stationary point location. (default = 0.10 or DPRED, whichever is smallest) OPTTOL = gradient convergence tolerance, in Hartree/Bohr. Used for optimizing to a stationary point. Convergence of a geometry search requires the rms gradient to be less than OPTTOL. (default=0.0001) HESS = selection of the initial hessian matrix, if STPT=.TRUE. = READ causes the hessian to be read from a $HESS group. = CALC causes the hessian to be computed. (default)

---- the next parameters apply only to METHOD=SR ---DELCOR = the corrector step should be smaller than this value before the next predictor step is taken. (default = 0.001) MYSTEP = maximum number of micro iteration allowed to bring the corrector step length below DELCOR. (default=20) SNUMH = stepsize used in the numerical differentiation of the Hessian to produce third derivatives. (default = 0.0001)

Input Description

$GRADEX

2-160

HSDFDB = flag to select determination of third derivatives. At the current geometry we need the gradient, the Hessian, and the partial third derivative matrix in the gradient direction. If .TRUE., the gradient is calculated at the current geometry, and two Hessians are calculated at SNUMH distance to each side in the gradient direction. The Hessian at the geometry is formed as the average of the two displaced Hessians. If .FALSE., both the gradient and Hessian are calculated at the current geometry, and one additional Hessian is calculated at SNUMH in the gradient direction. The default double-sided differentiation produces a more accurate third derivative matrix, at the cost of an additional wave function and gradient. (default = .TRUE.) ========================================================== * * See for * * * * * * * * * * * * * * * * * * * the 'further information' section some help with GRADEXTR runs. * * * * * * * * * * * * * * * * *

Input Description

$SURF

2-161

==========================================================

$SURF

group

(relevant for RUNTYP=SURFACE)

This group allows you to probe a potential energy surface along a small grid of points. Note that there is no option to vary angles, only distances. The scan can be made for any SCFTYP, or for the MP2 or CI surface. You may specify two rather different calculations to be done at each point on the grid, through the RUNTYPn, SCFTYPn, and electron correlation keywords. * * * below, 1 and 2 refer to different calculations * * * RUNTP1,RUNTYP2 = some RUNTYP supported in $CONTRL First RUNTYP=RUNTP1 and then RUNTYP=RUNTP2 will be performed, for each point on the grid. The second run is omitted if RUNTP2 is set to NONE. default: RUNTP1=ENERGY RUNTP2=NONE SCFTP1,SCFTP2 = some SCFTYP supported in $CONTRL default: SCFTYP in $CONTRL CITYP1,CITYP2 = some CITYP supported in $CONTRL default: CITYP in $CONTRL MPLEV1,MPLEV2 = some MPLEVL supported in $CONTRL default: MPLEVL in $CONTRL CCTYP1,CCTYP2 = some CCTYP supported in $CONTRL default: CCTYP in $CONTRL DFTYP1,DFTYP2 = some DFTTYP supported in $DFT default: DFTTYP in $DFT You may need to help by giving values in $CONTRL that will permit the program to estimate what is coming in the values here. For example, if you want to request hessians here, it may be good to give RUNTYP=HESSIAN in $CONTRL so that in its earliest stages of a job, the program can initialize for 2nd derivatives. There is less checking here than on $CONTRL input, so don't request something impossible such as two correlaton methods simultaneously, or analytic hessians for MP2, or other things that are impossible.

Input Description

$SURF

2-162

* * * below, 1 and 2 refer to different coordinates * * * IVEC1 IGRP1 = an array of two atoms, defining a coordinate from the first atom given, to the second. = an array specifying a group of atoms, which must include the second atom given in IVEC1. The entire group will be translated (rigidly) along the vector IVEC1, relative to the first atom given in IVEC1. = starting value of the coordinate, which may be positive or negative. Zero corresponds to the distance given in $DATA. = step size for the coordinate. If DISP1 is set to zero, then the keyword GRID1 is read.

ORIG1

DISP1

NDISP1 = number of steps to take for this coordinate. GRID1 = an array of grid points at which to compute the energy. This option is an alternative to the ORIG1, DISP1 input which produces an equidistant grid. To use GRID1, one has to set DISP1=0.0. The number of grid points is given in NDISP1, and is limite to at most 100 grid points. The input of GRID1(1)=ORIG1,ORIG1+DISP1,ORIG1+DISP1*2,... would reproduce an equidistant grid given by ORIG1 and DISP1.

ORIG1, DISP1, and GRID1 should be given in Angstrom. There are no reasonable defaults for these keywords. IVEC2, IGRP2, ORIG2, DISP2, NDISP2, GRID2 have the same meaning as their "1" counterparts, and permit you to make a two dimensional map along two displacement coordinates. If the "2" data are not input, the surface map proceeds in only one dimension. ==========================================================

Input Description

$LOCAL

2-163

==========================================================

$LOCAL

group (relevant if LOCAL=RUEDNBRG, BOYS, or POP)

This group allows input of additional data to control the localization methods. If no input is provided, the valence orbitals will be localized as much as possible, while still leaving the wavefunction invariant. There are many specialized options for Localized Charge Distribution analysis, and for EFP generation. N.B. Since Boys localization needs the dipole integrals, do not turn off dipole moment calculation in $ELMOM.

MAXLOC = maximum number of localization cycles. This applies to BOYS or POP methods only. If the localization fails to converge, a different order of 2x2 pairwise rotations will be tried. (default=250) CVGLOC = convergence criterion. The default provides LMO coefficients accurate to 6 figures. (default=1.0E-6) SYMLOC = a flag to restrict localization so that orbitals of different symmetry types are not mixed. This option is not supported in all possible point groups. The purpose of this option is to give a better choice for the starting orbitals for GVB-PP or MCSCF runs, without destroying the orbital's symmetry. This option is compatible with each of the 3 methods of selecting the orbitals to be included. If chosen in a run requesting VVOS (see $SCF), occupied and virtual orbitals will also not be permitted to mix in a localization of these two separate orbital spaces. (default=.FALSE.) ORIENT = a flag to request orientation of the localized orbitals for bond-order analysis. After the localization, the orbitals on each atom are rotated only among themselves, in order to direct the orbitals towards neighboring atom's orbitals, to which they are bonded. The density matrix, or bond-order matrix, of these Oriented LMOs is readily interpreted as atomic populations and

Input Description

$LOCAL

2-164

bond orders. This option can be used only for SCFTYP=MCSCF and LOCAL=RUEDNBRG. (default=.FALSE.) PRTLOC = a flag to control supplemental printout. The extra output is the rotation matrix to the localized orbitals, and, for the Boys method, the orbital centroids, for the Ruedenberg method, the coulomb and exchange matrices, for the population method, atomic populations. (default=.FALSE.) ----- The following keywords select the orbitals which are to be included in the localization. You may select from FCORE, NOUTA/NOUTB, or NINA/NINB, but may choose only one of these three groups. FCORE = flag to freeze all the chemical core orbitals present. All the valence orbitals will be localized. You must explicitly turn this option off to choose one of the other two orbital selection options. (default=.TRUE.) * * * NOUTA = number of alpha orbitals to hold fixed in the localization. (default=0)

MOOUTA = an array of NOUTA elements giving the numbers of the orbitals to hold fixed. For example, the input NOUTA=2 MOOUTA(1)=8,13 will freeze only orbitals 8 and 13. You must enter all the orbitals you want to freeze, including any cores. This variable has nothing to do with cows. NOUTB = number of beta orbitals to hold fixed in -UHFlocalizations. (default=0)

MOOUTB = same as MOOUTA, except that it applies to the beta orbitals, in -UHF- wavefunctions only. * * * NINA = number of alpha orbitals which are to be

Input Description

$LOCAL (default=0)

2-165

included in the localization. MOINA

= an array of NINA elements giving the numbers of the orbitals to be included in the localization. Any orbitals not mentioned will be frozen. = number of -UHF- beta MOs in the localization. (default=0) = same as MOINA, except that it applies to the beta orbitals, in -UHF- wavefunctions only.

NINB MOINB

ORMFUL = this flag is relevant only to CISTEP=ORMAS MCSCF localizations. By default, the localization is restricted such that the multiple active spaces are not mixed, leaving the total wavefunction invariant. It may be used to localize within the full range of active MOs. (Default is .FALSE.) ----- The following keywords are used for the localized charge distribution (LCD), a decomposition scheme for the energy, or multipole moments, or the first polarizability. See also LOCHYP in $FFCALC for the decomposition of hyperpolarizabilities. EDCOMP = flag to turn on LCD energy decomposition. Note that this method is currently implemented for SCFTYP=RHF and ROHF and LOCAL=RUEDNBRG only. The SCF LCD forces all orbitals to be localized, overriding input on the previous page. See also LMOMP2 in the $MP2 group. (default = .FALSE.) $LOCAL MOIDON = flag to turn on LMO identification and subsequent LMO reordering, and assign nuclear LCD automatically. (default = .FALSE.) DIPDCM = flag for LCD molecular dipole decomposition. (default = .FALSE.) QADDCM = flag for LCD molecular quadrupole decomposition. (default = .FALSE.)

Input Description

$LOCAL

2-166

POLDCM = flag to compute the static alpha polarizability, and its decomposition in terms of LCDs. The computation is done analytically, unless either of POLNUM or POLAPP is chosen. This method is implemented for SCFTYP=RHF or ROHF and LOCAL=BOYS or RUEDNBRG. (default=.FALSE., except that RUNTYP=MAKEFP turns this computation on, automatically. LMO dipole polarizabilities are the polarizability term in the EFP model) See also POLDYN in this group. POLNUM = flag to forces numerical rather than analytical calculation of the polarizabilities. This may be useful in larger molecules. The numerical polarizabilities of bonds in or around aromatic rings sometimes are unphysical. (default=.FALSE.) See D.R.Garmer, W.J.Stevens J.Phys.Chem. 93, 8263-8270(1989). POLDYN may not be used with this keyword. POLAPP = flag to force calculation of the polarizabilities using a perturbation theory expression. This may be useful in larger molecules. (default=.FALSE.) See R.M. Minikis, V. Kairys, J.H. Jensen J.Phys.Chem.A 105, 3829-3837(2001) POLDYN may not be used with this keyword. POLANG = flag to choose units of localized polarizability output. The default is Angstroms**3, while false will give Bohr**3. (default=.TRUE.) ZDO = flag for LCD analysis of a composite wavefunction, given in a $VEC group of a van der Waals complex, using the zero differential overlap approximation. The MOs are not orthonormalized and the intermolecular electron exchange energy is neglected. Also, the molecular overlap matrix is printed out. This is a very specialized option. (default = .FALSE.)

----- The following keywords can be used to define the nuclear part of an LCD. They are usually used to rectify mistakes in the automatic definition made when MOIDON=.TRUE. The index defining the

Input Description

$LOCAL

2-167

LMO number then refers to the reordered list of LMOs. NMOIJ IJMO = array giving the number of nuclei assigned to a particular LMO. = is an array of pairs of indices (I,J), giving the row (nucleus I) and column (orbital J) index of the entries in ZIJ and MOIJ. = arrays of integers K, assigning nucleus K as the site of the Ith charge of LCD J. = array of floating point numbers assigning a charge to the Ith charge of LCD J. = array of integers K, defining nucleus K as a proton.

MOIJ ZIJ IPROT

DEPRNT = a flag for additional decomposition printing, such as pair contributions to various energy terms, and centroids of the Ruedenberg orbitals. (default = .FALSE.) ----- The following keywords are used to build large EFPs from several RUNTYP=MAKEFP runs on smaller molecular fragments, by excluding common regions of overlap. For example, an EFP for n-octanol can be build from two MAKEFP runs, on n-pentane and n-pentanol, CH3CH2CH2CH2-CH2CH2CH2CH2OH CH3CH2CH2CH2[-CH3] [CH3]-CH2CH2CH2CH2OH by excluding operlapping regions shown in brackets from the two EFPs. See J.Phys.Chem.A 105, 3829-3837, (2001) for more information. NOPATM = array of atoms that define an area to be excluded from a DMA ($STONE) during a RUNTYP=MAKEFP run. All atomic centers specified, and the midpoints of any bonds to them, are excluded as expansion points. The density due to all LMOs primarily centered on these atoms are excluded from the DMA (see also KMIDPT). Furthermore, polarizability tensors for these LMOs are excluded.

Input Description

$LOCAL

2-168

KPOINT = array of "boundary atoms", those atoms that are covalently bonded to the atoms given in NOATM. KMIDPT = flag to indicate whether the density due to bond LMOs (and associated expansion points) between the NOPATM atoms and the KPOINT atoms are to be included in the DMA. (default = .TRUE.) NODENS = an array that specifies the atoms for which the associated electronic density will be removed before the multipole expansion. This provides an EFP with net integer charge. (P.A.Molina, H.Li, J.H.Jensen J.Comput.Chem. 24, 1972-1979(2003). The following keywords relate to the computation of imaginary frequency dynamic polarizabilities. This is useful in the development of the dispersion energy formula in the EFP2 model, but may also be computed separately, if wished. POLDYN = a flag to compute imaginary frequency dependent dynamic polarizabilities (alpha), by analytic means. (default=.FALSE., but .TRUE. if RUNTYP=MAKEFP) NDPFRQ = number of imaginary frequencies to compute. Default=1 for most runs, but=12 if RUNTYP=MAKEFP. DPFREQ = an array of imaginary frequencies to be used, entered as real numbers (absolute values). The default=0.0 for most runs, which is silly, because this just computes the normal static dipole polarizability! For RUNTYP=MAKEFP, the program uses 12 internally stored values, which serve as the roots for a Gauss-Legendre quadrature to extract the C6 dispersion coefficients. Given in atomic units. For more information, see I.Adamovic, M.S.Gordon Mol.Phys. 103, 379-387(2005).

========================================================== * * * * * * * * * * * * * * * * * *

Input Description For the the * *

$LOCAL hints about localizations, and LCD energy decomposition, see 'further information' section. * * * * * * * * * * * * * * * *

2-169

==========================================================

Input Description

$TRUNCN

2-170

==========================================================

$TRUNCN

group

(optional, relevant for RHF)

This group controls the truncation of some of the localized orbitals to just the AOs on a subset of the atoms. This option is particularly useful to generate localized orbitals to be frozen when the effective fragment potential is used to partition a system across a chemical bond. In other words, this group prepares the frozen buffer zone orbitals. This group should be used in conjunction with RUNTYP=ENERGY (or PROP if the orbitals are available) and either LOCAL=RUEDNBRG or BOYS, with MOIDON set in $LOCAL. DOPROJ = flag to activate MO projection/truncation, the default is to skip this (default=.FALSE.) AUTOID = forces identification of MOs (analogous to MOIDON in $LOCAL). This keyword is provided in case the localized orbitals are already present in $VEC, in which case this is a faster RUNTYP=PROP with LOCAL=NONE job. Obviously, GUESS=MOREAD. (default=.FALSE.) PLAIN = flag to control the MO tail truncation. A value of .FALSE. uses corresponding orbital projections, H.F.King, R.E.Stanton, H.Kim, R.E.Wyatt, R.G.Parr J. Chem. Phys. 47, 1936-1941(1967) and generates orthogonal orbitals. A value of .TRUE. just sets the unwanted AOs to zero, so the resulting MOs need to go through the automatic orthogonalization step when MOREAD in the next job. (default=.FALSE.) = an array specifying which MOs to be truncated. In most cases involving normal bonding, the options MOIDON or AUTOID will correctly identify all localized MOs belonging to the atoms in the zone being truncated. However, you can inspect the output, and give a list of all MOs which you want to be truncated in this array, in case you feel the automatic assignment is incorrect. Any orbital not in the truncation set, whether this is chosen automatically or by IMOPR, is left

IMOPR

Input Description

$TRUNCN

2-171

completely unaltered. - - There are now two ways to specify what orbitals are to be truncated. The most common usage is for preparation of a buffer zone for QM/MM computations, with an Effective Fragment Potential representing the non-quantum part of the system. This input is NATAB, NATBF, ICAPFR, ICAPBF, in which case the $DATA input must be sorted into three zones. The first group of atoms are meant to be treated in later runs by full quantum mechanics, the second group by frozen localized orbitals as a 'buffer', and the third group is to be substituted later by an effective fragment potential (multipoles, polarizabilities, ...). Note that in the DOPROJ=.TRUE. run, all atoms are still quantum atoms. NATAB NATBF = number of atoms to be in the 'ab initio' zone. = number of atoms to be in the 'buffer' zone. The program can obtain the number of atoms in the remaining zone by subtraction, so it need not be input.

In case the MOIDON or AUTOID options lead to confused assignments (unlikely in ordinary bonding situations around the buffer zone), there are two fine tuning values. ICAPFR = array indicating the identity of "capping atoms" which are on the border between the ab initio and buffer zones (in the ab initio zone). ICAPBK = array indicating the identity of "capping atoms" which are on the border between the buffer and EFP zones (in the effective fragment zone). See also IXCORL and IXLONE below. - - In case truncation seems useful for some other purpose, you can specify the atoms in any order within the $DATA group, by the IZAT/ILAT approach. You are supposed to give only one of these two lists, probably whichever is

Input Description shorter: IZAT ILAT

$TRUNCN

2-172

= an array containing the atoms which are NOT in the buffer zone. = an array containing the atoms which are in the buffer zone.

The AO coefficients of the localized orbitals present in the buffer zone which lie on atoms outside the buffer will be truncated. See also IXCORL and IXLONE below. - - The next two values let you remove additional orbitals within the buffer zone from the truncation process, if that is desirable. These arrays can only include atoms that are already in the buffer zone, whether this was defined by NATBF, or IZAT/ILAT. The default is to include all core and lone pair orbitals, not just bonding orbitals, as the buffer zone orbitals. IXCORL = an array of atoms whose core and lone pair orbitals are to be considered as not belonging to the buffer zone orbitals. IXLONE = an array of atoms for which only the lone pair orbitals are to be considered as not belonging to the buffer zone orbitals. The final option controls output of the truncated orbitals to file PUNCH for use in later runs: NPUNOP = = 1 = 2 punch out option for the truncated orbitals the MOs are not reordered. punch the truncated MOs as the first vectors in the $VEC MO set, with untransformed vectors following immediately after. (default)

==========================================================

Input Description

$ELMOM

2-173

==========================================================

$ELMOM

group

(not required)

This group controls electrostatic moments calculation. The symmetry properties of multipoles are discussed in A.Gelessus, W.Thiel, W.Weber J.Chem.Ed. 72, 505-508(1995) The quadrupole and octopole tensors on the printout are formed according to the definition of Buckingham. Caution: only the first nonvanishing term in the multipole charge expansion is independent of the coordinate origin chosen, which is normally the center of mass. IEMOM = 0 1 2 3 skip this property calculate monopole and dipole (default) also calculate quadrupole moments also calculate octopole moments - center of mass (default) - at each nucleus - at points given in $POINTS.

WHERE

= COMASS NUCLEI POINTS

OUTPUT = PUNCH, PAPER, or BOTH (default) * * the following are for atomic multipole moments * * The Cartesian atomic multipole moments printed are a generalization of Mulliken charges, generated by distributing density factors according to the atomic orbitals used. Only the first point is used as an expansion center, so generally only WHERE=COMASS or providing a single point make sense. For details refer to W.A.Sokalski, R.A.Poirier Chem.Phys.Lett. 98, 86-92(1983) K.M.Langner, P.Kedzierski, W.A.Sokalski, J.Leszczynski J.Phys.Chem.B 110, 9720-9727(2006) IAMM = 0 - skip generation of Atomic Multipole Moments n - generate atomic moments up to rank n The default is n=0, note that n may not exceed 12. = Flag to accumulate the atomic moments to their

CUM

Input Description

$ELMOM

2-174

local atom coordinates, if IAMM was selected. When .FALSE., the resulting moments are additive and sum up to corresponding molecular moments, printed by selecting IEMOM. Setting this flag to .TRUE. recombines the atomic moments to their local coordinates system, making them invariant of the reference frame. Default=.FALSE. IEMINT = 0 1 2 3 -2 -3 skip printing of integrals (default) print dipole integrals also print quadrupole integrals also print octopole integrals print quadrupole integrals only print octopole integrals only

==========================================================

Input Description

$ELPOT

2-175

==========================================================

$ELPOT

group

(not required)

This group controls electrostatic potential calculation. IEPOT = 0 skip this property (default) 1 calculate electric potential WHERE = COMASS NUCLEI POINTS GRID PDC center of mass at each nucleus (default) at points given in $POINTS at grid given in $GRID at points controlled by $PDC.

OUTPUT = PUNCH, PAPER, BOTH (default), or NONE This property is the electrostatic potential V(a) felt by a test positive charge, due to the molecular charge density, of both nuclei and electrons. If there is a nucleus at the evaluation point, that nucleus is ignored, avoiding a singularity. If this property is evaluated at the nuclei, it obeys the equation sum on nuclei(a) Z(a)*V(a) = 2*V(nn) + V(ne). The electronic portion of this property is called the diamagnetic shielding. ==========================================================

Input Description

$ELDENS

2-176

==========================================================

$ELDENS

group

(not required)

This group controls electron density calculation. IEDEN MORB = 0 skip this property (default) = 1 compute the electron density. = The molecular orbital whose electron density is to be computed. If zero, the total density is computed. (default=0) = COMASS NUCLEI POINTS GRID center of mass at each nucleus (default) at points given in $POINTS at grid given in $GRID

WHERE

OUTPUT = PUNCH, PAPER, or BOTH (default) IEDINT = 0 - skip printing of integrals (default) 1 - print the electron density integrals ==========================================================

Input Description

$ELFLDG

2-177

==========================================================

$ELFLDG

group

(not required)

This group controls electrostatic field and electric field gradient calculation. IEFLD = 0 - skip this property (default) 1 - calculate field 2 - calculate field and gradient = COMASS NUCLEI POINTS - center of mass - at each nucleus (default) - at points given in $POINTS

WHERE

OUTPUT = PUNCH, PAPER, or BOTH (default) IEFINT = 0 1 2 -2 skip printing these integrals (default) print electric field integrals also print field gradient integrals print field gradient integrals only

The Hellman-Feynman force on a nucleus is the nuclear charge multiplied by the electric field at that nucleus. The electric field is the gradient of the electric potential, and the field gradient is the hessian of the electric potential. The components of the electric field gradient tensor are formed in the conventional way, i.e. see D.Neumann and J.W.Moskowitz. ==========================================================

Input Description

$POINTS $GRID

2-178

==========================================================

$POINTS

group

(not required) which properties group must by an integer The next NPOINT the X, Y, and Z

This group is used to input points at will be computed. This first card in the contain the string ANGS or BOHR, followed NPOINT, the number of points to be used. cards are read in free format, containing coordinates of each desired point.

==========================================================

$GRID

group

(not required)

This group is used to input a grid (plane or cube) on which properties will be calculated. This group should be given if WHERE=GRID in $ELPOT or $ELDENS. This output will be in the PUNCH file whenever OUTPUT=PUNCH or BOTH. MODGRD = 0 generates 2-D grid (default) = 1 generates 3-D grid, also called "cube file", which can be visualized by several programs. ORIGIN(i) = coords of the lower left corner of the plot XVEC(i) = coords of the lower right corner of the plot YVEC(i) = coords of the upper left corner of the plot ZVEC(i) = coordinates of the diagonal corner of the 3-D grid, given if and only if MODGRD=1. SIZE = grid increment, default is 0.25. UNITS = units of the above four values, it can be either ANGS (the default) or BOHR. Note that XVEC and YVEC are not necessarily parallel to the X and Y axes, rather they are the axes which you desire to see plotted by the MEPMAP contouring program. ========================================================== * * For see * * * * * * * * * * * * * * * * * * * * conversion factors, and references the 'further information' section. * * * * * * * * * * * * * * * * * *

Input Description

$PDC

2-179

==========================================================

$PDC

group

(relevant if WHERE=PDC in $ELPOT)

This group determines the points at which to compute the electrostatic potential, for the purpose of fitting atomic charges to this potential. Constraints on the fit which determines these "potential determined charges" can include the conservation of charge, the dipole, and the quadrupole. PTSEL = determines the points to be used, choose GEODESIC to use a set of points on several fused sphere van der Waals surfaces, with points selected using an algorithm due to Mark Spackman. The results are similar to those from the Kollman/Singh method, but are less rotation dependent. (default) CONNOLLY to use a set of points on several fused sphere van der Waals surfaces, with points selected using an algorithm due to Michael Connolly. This is identical to the method used by Kollman & Singh (see below) CHELPG to use a modified version of the CHELPG algorithm, which produces a symmetric grid of points for a symmetric molecule. - no fit is performed. The potential at the points is instead output according to OUTPUT in $ELPOT. CHARGE - the sum of fitted atomic charges is constrained to reproduce the total molecular charge. (default) DIPOLE - fitted charges are constrained to exactly reproduce the total charge and dipole. QUPOLE - fitted charges are constrained to exactly reproduce the charge, dipole, and quadrupole.

CONSTR = NONE

Note: the number of constraints cannot exceed the number of parameters, which is the number of nuclei. Planar molecules afford fewer constraint equations, namedly two dipole constraints and three quadrupole constraints,

Input Description

$PDC

2-180

instead of three and five, repectively. * * the next 5 pertain to PTSEL=GEODESIC or CONNOLLY * * VDWSCL = scale factor for the first shell of VDW spheres. The default of 1.4 seems to be an empirical best value. Values for VDW radii for most elements up to Z=36 are internally stored. VDWINC = increment for successive shells (default = 0.2). The defaults for VDWSCL and VDWINC will result in points chosen on layers at 1.4, 1.6, 1.8 etc times the VDW radii of the atoms. LAYER = number of layers of points chosen on successive fused sphere VDW surfaces (default = 4)

Note: RUNTYP=MAKEFP's screening calculation changes the defaults to VDWSCL=0.5 or 0.8 depending on the type of Stone analysis, VDWINC=0.1, LAYER=25, and MAXPDC=100,000. NFREQ = flag for particular geodesic tesselation of points. Only relevant if PTSEL=GEODESIC. Options are: (10*h + k) for {3,5+}h,k tesselations -(10*h + k) for {5+,3}h,k tesselations Of course both nh and nk must be less than 10, so NFREQ must lie within the range -99 to 99. The default value is NFREQ=30 (=03)

PTDENS = density of points on the surface of each scaled VDW sphere (in points per square au). Relevant if PTSEL=CONNOLLY. Default=0.28 per au squared, which corresponds to 1.0 per square Angstrom, the default recommended by Kollman & Singh. * * * the next two pertain to PTSEL=CHELPG * * * RMAX DELR = maximum distance from any point to the closest atom. (default=3.0 Angstroms) = distance between points on the grid. (default=0.8 Angstroms)

Input Description

$PDC

2-181

MAXPDC = an estimate of the total number of points whose electrostatic potential will be included in the fit. (default=10000) CENTER = an array of coordinates at which the moments were computed. DPOLE QPOLE = the molecular dipole. = the molecular quadrupole.

PDUNIT = units for the above values. ANGS (default) will mean that the coordinates are in Angstroms, the dipole in Debye, and quadrupole in Buckinghams. BOHR implies atomic units for all 3. Note: it is easier to compute the moments in the current run, by setting IEMOM to at least 2 in $ELMOM. However, you could fit experimental data, for example, by reading it in here. ========================================================== There is no unique way to define fitted atomic charges. Smaller numbers of points at which the electrostatic potential is fit, changes in VDW radii, asymmetric point location, etc. all affect the results. A useful bibliography is U.C.Singh, P.A.Kollman, J.Comput.Chem. 5, 129-145(1984) L.E.Chirlain, M.M.Francl, J.Comput.Chem. 8, 894-905(1987) R.J.Woods, M.Khalil, W.Pell, S.H.Moffatt, V.H.Smith, J.Comput.Chem. 11, 297-310(1990) C.M.Breneman, K.B.Wiberg, J.Comput.Chem. 11, 361-373(1990) K.M.Merz, J.Comput.Chem. 13, 749(1992) M.A.Spackman, J.Comput.Chem. 17, 1-18(1996) Start your reading with the last paper shown.

Input Description

$RADIAL

2-182

==========================================================

$RADIAL

group

(relevant only to atoms)

This input data governs the computation of radial expectation values <r> and <r**2> for atomic orbitals. The atomic wavefunctions can be any SCFTYP except UHF. The atomic calculation should preserve radial degeneracy in p, d, or f shells, so UHF is not allowed, and furthermore, many atoms will require GVB or MCSCF inputs (see the 'Further References' section about doing atomic SCF). It is OK to use core potentials (MCP or ECP) or to apply scalar relativistic effects, so long as the calculation preserves degeneracy 2l+1 in every occupied shell. One should keep in mind that there is some arbitrariness in how different SCFTYPs canonicalize orbitals, so that individual orbitals may vary, for exactly the same total wavefunction. For example, ROHF orbitals within the doubly occupied set of orbitals change as a function of the A and B canonicalization inputs (see 'Further References'). Similar comments apply to orbitals from GVB or MCSCF. It is recommended that you do two runs, first to check if radial degeneracy is maintained (equal eigenvalues for all three p, or all five d orbitals). This preliminary run will help count which orbitals lie in degenerate shells, for MEMSH below. The quality of the numerical radial integration can be assessed from its closeness to 1.0. Radial wavefunctions can be printed, as an option. There are no defaults provided for the first three keywords, which are required inputs, if this group is given. NSHELL - number of atomic shells to be computed IDEGSH - an array of NSHELL values, giving the degeneracy of each shell (1, 3, 5, or 7) MEMSH RMAX - an array containing the sum of all IDEGSH values, listing the members of each shell. - maximum radius to be considered, in Bohr. The default is most appropriate for valence orbitals, which for bottom row elements may extend to five Angstrons (default=10.0). Inner shell orbitals

Input Description

$RADIAL

2-183

may require input of a smaller RMAX, to move some of the tick marks closer to the nucleus. NTICKS - radial increment is RMAX/NTICKS, so the default step size is 0.01 Bohr (default NTICKS=1001) PRTRAD - flag to print each shell's radial wavefunction at every radial tick mark (default is .FALSE.) The following example uses a basis that is too small to be converged, printing radial expectation values for manganese as 1s=0.0615, 3p=0.9156, 4s=3.4027, and 3d=1.1095: $contrl scftyp=rohf mult=6 ispher=1 $end $guess guess=huckel norder=1 iorder(10)=15,10,11,12,13,14 $end $basis gbasis=n31 ngauss=6 $end $scf rstrct=.true. $end $radial nshell=4 idegsh(1)=1,3,1,5 memsh(1)=1, 7,8,9, 10, 11,12,13,14,15 $end $data Mn atom...(4s)2(3d)5...6-S...spherical harmonics Dnh 2 Mn 25.0 $end ==========================================================

Input Description

$MOLGRF

2-184

==========================================================

$MOLGRF

group

(relevant only if you have MOLGRAPH)

This option provides an interface for viewing orbitals through a commercial package named MOLGRAPH, from Daikin Industries. Note that this option uses three disk files which are not defined in the GAMESS execution scripts we provide, since we don't use MOLGRAPH ourselves. You will need to define files 28, 29, 30, as generic names PRGRID, COGRID, MOGRID, of which the latter is passed to MOLGRAPH. GRID3D = a flag to generate 3D grid data. (default is .false.). TOTAL = a flag to generate a total density grid data. "Total" means the sum of the orbital densities given by NPLT array. (default is .false.). = numbers of grids. You can use different numbers for three axes. (default is MESH(1)=21,21,21). = boundary coordinates of a 3D graphical cell. The default is that the cell is larger than the molecular skeleton by 3 bohr in all directions. E.g., BOUND(1)=xmin,xmax,ymin,ymax,zmin,zmax

MESH BOUND

NPLOTS = number of orbitals to be used to generate 3D grid data. (default is NPLOTS=1). NPLT = orbital IDs. The default is 1 orbital only, the HOMO or SOMO. If the LOCAL option is given in $CONTRL, localized orbital IDs should be given. For example, NPLT(1)=n1,n2,n3,... = debug option, printing some of the grid data.

CHECK

If you are interested in graphics, look at the GAMESS web page for information about other graphics packages with GAMESS, particularly MacMolPlt and Avogadro, both are available for all common desktop operating systems. ==========================================================

Input Description

$STONE

2-185

==========================================================

$STONE

group

(optional)

This group defines the expansion points for Stone's distributed multipole analysis (DMA) of the electrostatic potential. The DMA takes the multipolar expansion of each overlap charge density defined by two Gaussian primitives, and translates it from the center of charge of the overlap density to the nearest expansion point. Some references for the method are A.J.Stone Chem.Phys.Lett. 83, 233-239 (1981) A.J.Stone, M.Alderton Mol.Phys. 56, 1047-1064(1985) A.J.Stone J.Chem.Theory and Comput. 1, 1128-1132(2005) The existence of a $STONE group in the input is what triggers the analysis. The first set of lines must appear as the first line after $STONE (enter a blank line if you make no choice), then enter as many choices as you wish, in any order, from the other sets. ---------------------------------------------------------BIGEXP <value> exponents larger than this are treated by the original Stone expansion, and those smaller by a numerical integration. The default is 0.0, meaning no numerical grid. The other parameters are meaningless if BIGEXP remains zero. number of radial grid points (default 100) number of angular grid points, choose one of the Lebedev grid values (default 590) degree of Becke smoothing (default=2) Radii choice, 0=constant, 1=Bragg-Slater, which is the default.

NRAD <nrad> NANG <nang> SMOOTH <nbecke> SMRAD <nbckrd>

---------------------------------------------------------ATOM i name, where ATOM is a keyword indicating that a particular

Input Description

$STONE atom is selected as an expansion center. is the number of the atom is an optional name for the atom. If not entered the name will be set to the name used in the $DATA input.

2-186

i name

---------------------------------------------------------ATOMS is a keyword selecting all nuclei in the molecule as expansion points. No other input on the line is necessary.

---------------------------------------------------------BONDS is a keyword selecting all bond midpoints in the molecule as expansion points. No other input on the line is necessary.

---------------------------------------------------------BOND i j name, where BOND i,j name is a keyword indicating that a bond midpoint is selected as an expansion center. are the indices of the atoms defining the bond, corresponding to two atoms in $DATA. an optional name for the bond midpoint. If omitted, it is set to 'BOND'.

---------------------------------------------------------CMASS is a keyword selecting the center of mass as an expansion point. No other input on the line is necessary.

---------------------------------------------------------POINT x y z name, where POINT x,y,z name is a keyword indicating that an arbitrary point is selected as an expansion point. are the coordinates of the point, in Bohr. is an optional name for the expansion point. If omitted, it is set to 'POINT'.

Input Description

$STONE

2-187

---------------------------------------------------------While making the EFPs for QM/MM run, a single keyword QMMMBUF is necessary. Adding additional keywords may lead to meaningless results. The program will automatically select atoms and bond midpoints which are outside the buffer zone as the multipole expansion points. QMMMBUF nmo, where is a keyword specifying the number of QM/MM buffer molecular orbitals, which must be the first NMO orbitals in the MO set. These orbitals must be frozen in the buffer zone, so this is useful only if $MOFRZ is given. is the number of buffer MO-s (if NMO is omitted, it will be set to the number of frozen MOs in $MOFRZ)

QMMMBUF

NMO

========================================================== The second and third moments on the printout can be converted to Buckingham's tensors by formula 9 of A.D.Buckingham, Quart.Rev. 13, 183-214 (1959) These can in turn be converted to spherical tensors by the formulae in the appendix of S.L.Price, et al. Mol.Phys. 52, 987-1001 (1984)

Input Description

$RAMAN

2-188

==========================================================

$RAMAN

group

(relevant for all SCFTYPs)

This input controls the computation of Raman intensity by the numerical differentiation produre of Komornicki and others. It is applicable to any wavefunction for which the analytic gradient is available, including some MP2 and CI cases. The calculation involves the computation of 19 nuclear gradients, one without applied electric fields, plus 18 no symmetry runs with electric fields applied in various directions. The numerical second differencing produces intensity values with 2-3 digits of accuracy. This run must follow an earlier RUNTYP=HESSIAN job, and the $GRAD and $HESS groups from that first job must be given as input. If the $DIPDR is computed analytically by this Hessian job, it too may be read in, if not, the numerical Raman job will evaluate $DIPDR. Once the data from the 19 applied fields is available, the $ALPDR tensor is evaluated. Then the nuclear derivatives of the dipole moment and alpha polarizability will be combined with the normal coordinate information to produce the IR and Raman intensity of each mode. To study isotopic substitution speedily, input the $GRAD, $HESS, $DIPDR, and $ALPDR groups along with the desired atomic masses in $MASS. The code does not permit semi-empirical or solvation models to be used. EFIELD = applied electric field strenth. The literature suggests values in the range 0.001 to 0.005. (default = 0.002 a.u.) ==========================================================

Input Description

$ALPDR

2-189

==========================================================

$ALPDR

group

(relevant for RUNTYP=RAMAN or HESSIAN)

Formatted alpha derivative tensor, punched by a previous RUNTYP=RAMAN job. If both $DIPDR and this group are found in the input file, the applied field computation will be skipped, to immediately evaluate IR and Raman intensities. If this group is found during RUNTYP=HESSIAN, the Raman intensities will be added to the output. You might want to run as RUNTYP=HESSIAN instead of RUNTYP=RAMAN in order to have access to PROJCT or the other options available in the $FORCE group. ==========================================================

Input Description

$NMR

2-190

==========================================================

$NMR

group

(optional, relevant if RUNTYP=NMR)

This group governs the analytic computation of the NMR shielding tensor for each nucleus, using the Gauge Invariant Atomic Orbital (GIAO) method, also known as London orbitals. The most useful input values are the first three printing options. The wavefunction must be RHF, the atomic basis set may be spdfg, the EFP model may be used to include solvent effects, and the McMurchieDavidson integrals used are not fast. ANGINT = a flag to control the evaluation of the perturbed two-electron integrals by increasing the angular momentum on the unperturbed 2e- integrals. With this selected, only two passes through the 2eNMR integral code are needed. Otherwise, six slow passes are needed, and option meant only for debugging purposes. (default=.TRUE.) INMEM A flag to carry all integrals in memory. If selected, the calculation will require several multiples of NAO**4. By default, the calculation will require space on the order of NATOMS*NAO**2, where NAO is the basis set dimension. This is useful for debugging. (default=.FALSE.)

The rest are print flags, in increasing order of the amount of output created, as well as decreasing order of interest. The default for all of these options is .FALSE. PDIA PPARA PEVEC PITER PRMAT Print diamagnetic term of the shielding tensor. Print paramagnetic term of the shielding tensor. Print eigenvectors of asymmetric shielding tensor. Print iteration data for the formation of the three first-order density matrices. Print the three first-order perturbed density matrices, the three first-order H matrices for

Input Description

$NMR

2-191

each nucleus, the unperturbed density matrix, and the nine second-order H matrices for each nucleus. POEINT PTEINT TEDBG Print all one-electron integrals. Print the perturbed two-electron integrals. Print VAST amounts of debugging information for the McMurchie-Davidson two-electron intgrals. Should only be used for the smallest test jobs.

==========================================================

Input Description

$MOROKM

2-192

==========================================================

$MOROKM group

(relevant if RUNTYP=EDA)

This performs an analysis of the energy contributions to dimerization (or formation of larger clusters of up to ten monomers), according to the Morokuma-Kitaura and/or Reduced Variational Space schemes. The analysis is limited to closed shell RHF monomers. In other words, the monomers should be distinct molecular species: avoid breaking chemical bonds! For more general energy decompositions, see the $LMOEDA input group. See also PIEDA in the FMO codes. Solvation models are not supported. MOROKM = a flag to request Morokuma-Kitaura decomposition. (default is .TRUE.) RVS = a flag to request "reduced variation space" decomposition. This differs from the Morokuma analysis. One or the other or both may be requested in the same run. (default is .FALSE.)

Generally speaking, RVS handles non-orthogonality of monomers better. When diffuse functions are used, the MOROKM analysis sometimes fails, but RVS will work. BSSE = a flag to request basis set superposition error be computed. You must ensure that CTPSPL is selected. This option applies only to MOROKM decompositions, as a basis superposition error is automatically generated by the RVS scheme. This is not the full Boys counterpoise correction, as explained in the reference. (default is .FALSE.) * * * The inputs here control how the RHF supermolecule, whose coordinates are given in the $DATA group, is divided into two or more monomers. IATM = An array giving the number of atoms in each of the monomer. Up to ten monomers may be defined. Your input in $DATA must have all the atoms in

Input Description

$MOROKM

2-193

the first monomer defined before the atoms in the second monomer, before the third monomer... The number of atoms belonging to the final monomer can be omitted. There is no sensible default for IATM, so don't omit it from your input. ICHM = An array giving the charges of the each monomer. The charge of the final monomer may be omitted, as it is fixed by ICH in $CONTRL, which is the total charge of the supermolecule. The default is neutral monomers, ICHM(1)=0,0,0,... = a flag to indicate all monomers are equivalent by symmetry (in addition to containing identical atoms). If so, which is not often true, then only the unique computations will be done. (default is .FALSE.) * * * CTPSPL = a flag to decompose the interaction energy into charge transfer plus polarization terms. This is most appropriate for weakly interacting monomers. (default is .TRUE.) CTPLX = a flag to combine the CT and POL terms into a single term. If you select this, you might want to turn CTPSPL off to avoid the extra work that that decomposition entails, or you can analyze both ways in the same run. (default is .FALSE.) = a flag to enable restarting, by reading the lines containing "FINAL ENERGY" from a previous run. The $EMORO group is single lines read under format A16,F20.10 containing the energies, and a card $END to complete. The 16 chars = anything. (default is .FALSE.)

EQUM

RDENG

========================================================== The present implementation has some quirks: 1. The initial guess of the monomer orbitals is not controlled by $GUESS. The program first looks for a $VEC1, $VEC2, ... group for each monomer. The orbitals must be

Input Description

$MOROKM

2-194

obtained for the identical coordinates which that monomer has within the supermolecule. If any $VECn groups are found, they will be MOREAD. If any are missing, the guess for that monomer will be constructed by HCORE. Check your monomer energies carefully! The initial guess orbitals for the supermolecule are formed from a block diagonal matrix containing the monomer orbitals. 2. The use of symmetry is turned off internally. 3. Spherical harmonics (ISPHER=1) may not be used. 4. There is no direct SCF option. File ORDINT will be a full C1 list of integrals. File AOINTS will contain whatever subset of these is needed for each particular decomposition step. So extra disk space is needed compared to RUNTYP=ENERGY. 5. This run type applies only to ab initio RHF treatment of the monomers. To be quite specific: this means that DFT (which involves a grid, not just integrals) will not work, nor will MOPAC's approximated 2e- integrals 6. This kind of calculation will run in parallel. Quirks 1, 3 and 4 can be eliminated by using PIEDA if only two monomers are present. For more monomers PIEDA results will slightly differ. PIEDA is a special case of FMO, q.v. References: C.Coulson in "Hydrogen Bonding", D.Hadzi, H.W.Thompson, Eds., Pergamon Press, NY, 1957, pp 339-360. C.Coulson Research, 10, 149-159 (1957). K.Morokuma J.Chem.Phys. 55, 1236-44 (1971). K.Kitaura, K.Morokuma Int.J.Quantum Chem. 10, 325 (1976). K.Morokuma, K.Kitaura in "Chemical Applications of Electrostatic Potentials", P.Politzer,D.G.Truhlar, Eds. Plenum Press, NY, 1981, pp 215-242. The method coded is the newer version described in the 1976 and 1981 papers. In particular, note that the CT term is computed separately for each monomer, as described in the words below eqn. 16 of the 1981 paper, not simultaneously. Reduced Variational Space: W.J.Stevens, W.H.Fink, Chem.Phys.Lett. 139, 15-22(1987). A comparison of the RVS and Morokuma decompositions can be found in the review article: "Wavefunctions and Chemical Bonding" M.S.Gordon, J.H.Jensen in "Encyclopedia of

Input Description

$MOROKM

2-195

Computational Chemistry", volume 5, P.V.R.Schleyer, editor, John Wiley and Sons, Chichester, 1998. BSSE during Morokuma decomposition: R.Cammi, R.Bonaccorsi, J.Tomasi Theoret.Chim.Acta 68, 271-283(1985). The present implementation: "Energy decomposition analysis for many-body interactions, and application to water complexes" W.Chen, M.S.Gordon J.Phys.Chem. 100, 14316-14328(1996)

Input Description

$LMOEDA

2-196

==========================================================

$LMOEDA

group

(relevant if RUNTYP=EDA)

This group governs the Localized Molecular Orbital Energy Decomposition Analysis, which is capable of more sophisticated treatment of "monomers" than the Morokuma or RVS schemes (see $MOROKM). For example, the wavefunctions of the monomers may be RHF, ROHF, or UHF, the DFT counterparts of each of these, the MP2 counterparts of each of these, or CCSD and CCSD(T) for RHF and ROHF references. Furthermore, division of the system into "monomers" can involve splitting chemical bond pairs, as the MMULT example below shows. If one or more monomers are open shell, to be treated by ROHF, use SCFTYP=ROHF in $CONTRL. Whenever a monomer has an even number of electrons, so that its MMULT=1 below, SCFTYP=ROHF (or UHF) automatically reduces to RHF on that monomer. Note that open shell monomers sometimes have more than one possible electron occupancy (for example, oxygen atom can fill 3 p orbitals by 4 electrons in various ways), in which case the energy decomposition isn't unique. MATOM = an array giving the number of atoms in each monomer. Up to ten monomers may be defined. Your input in $DATA must have all the atoms in the first monomer defined before the atoms in the second monomer, before the third monomer etc. The sum of the MATOM array must be equal to the total number in the supermolecule.

MCHARG = an array giving the charge of each monomer. Up to ten monomers may be defined. The sum of the charges in the monomers must be equal to the total charge of the supermolecule. MMULT = an array giving the multiplicity of each monomer. Up to ten monomers may be defined. A positive integer means alpha spin, a negative integer means beta spin. For example, if an ethane molecule is separated into two neutral CH3 groups, MMULT(1)=2,-2 or MMULT(1)=-2,2.

Input Description

$LMOEDA

2-197

SUPBAS = a flag to request Boys and Bernardi style counterpoise method for correcting basis set superposition errors. (default is .TRUE.). Usually it works well with Hartree-Fock and MP2 and coupled cluster methods, but less well with DFT methods due to SCF divergent problems. The paper describing this method is P.Su, H.Li J.Chem.Phys. 131, 014102/1-15(2009) Notes: 1. scalar relativistic effects can be handled by ECP or MCP, but at present, all electron treatment by RELWFN=IOTC or DK is not enabled. 2. the initial guess should be HCORE, as there is no option at present to read monomer orbitals. ==========================================================

Input Description

$QMEFP

2-198

===========================================================

$QMEFP

group

(relevant for RUNTYP=QMEFPEA)

This run type prints a detailed breakdown of QM/EFP1 and EFP1/EFP1 interaction energies, for combined quantum mechanics/effective fragment potential (QM/EFP) systems. The run first performs a gas phase QM calculation, and then includes the explicit EFP1 solvent molecules. Any QM calculation that supports EFP runs and also generates the QM density matrix may be used. Certain non-variational runs must therefore select as .TRUE. the approriate QM density matrix evaluation: see MPPRP in $MP2, TDPRP in $TDDFT, CCPRP in $CCINP, or CCPRPE in $EOM. Note that calculations for which the QM density is not available may not be performed, such as multi-reference MP2 or triples corrected CC methods. Very often, this entire input group is omitted, as the inputs are related to restarts. One very good reason for doing two steps is in case the EFP solvation changes the order of the excited states, so that two different IROOT values must be given to specify the target state. STEP1 is a flag requesting the gas phase step be run, but note that the EFP particles must be present in the input file's $EFRAG. is a flag requesting the QM+EFP step be run. the default for both is .TRUE. so that the full results are obtained in a single run.

STEP2

In case STEP1 is .FALSE., three restart data (which may be found in the PUNCH output file) must be given for the second step: STOTAL EMULT EREM total QM energy, without EFP molecules expectation value of the QM/EFP electrostatics for the isolated solute. expectation value of the QM/EFP remainder term, which is largely exchange repulsion, for the

Input Description isolated solute.

$QMEFP

2-199

Those QM methods which are not based on fully selfconsistent solutions of the QM/EFP interaction Hamiltonian (namely TDDFT, CIS, MP2, CCSD, EOM-CCSD) provide results which include the EFP's perturbation by the correlated density, and/or a particular excited state's density. This approach is termed "Method 2" in the following references: 1. P.Arora, L.V.Slipchenko, S.P.Webb, A.DeFusco, M.S.Gordon J.Phys.Chem.A 114, 6742-6750(2010) 2. A.DeFusco, J.Ivanic, M.W.Schmidt, M.S.Gordon J.Phys.Chem.A 115, 4574-4582(2011) ===========================================================

Input Description

$FFCALC

2-200

==========================================================

$FFCALC

group

(relevant for RUNTYP=FFIELD)

This group permits the study of the influence of an applied electric field on the wavefunction. The most common finite field calculation applies a sequence of fields to extract the linear polarizability and the first and second order hyperpolarizabilities (static alpha, beta, and gamma tensors). The method is general, because it relies on finite differencing of the energy values, and so works for all ab initio wavefunctions. If the dipole moments are available (true for SCF or CI functions, and see MPPROP in $MP2), the same tensors are formed by differencing the dipoles, which is more accurate. Some idea of the error in the numerical differentiations can be gleaned by comparing energy based and dipole based quantities. For analytic computation of static polarizabilities alpha, beta, and gamma (as well as frequency dependent NLO properties), for closed shell cases, see $TDHF and $TDHFX. For analytic computation of the static polarizability alpha, see POLAR in $CPHF. The standard computation obtains the polarizabilities, by double numerical differentiation. See ONEFLD to apply a single electric field, but for a more general approach to applied static fields, see $EFIELD. OFFDIA = .TRUE. computes the entire polarizability tensors, which requires a total of 49 wavefunction evaluations (some of gamma is not formed). = .FALSE. forms only diagonal components of the polarizabilities, using 19 wavefunctions. The default is .TRUE. ESTEP = step size for the applied electric field strength, 0.01 to 0.001 is reasonable. (default=0.001 a.u.)

The next parameters pertain to applying a field in only one direction:

Input Description

$FFCALC

2-201

ONEFLD = flag to apply one field (default=.FALSE.) SYM = a flag to specify when the field to be applied does not break the molecular symmetry. Since most fields do break the nuclear point group symmetry, the default is .FALSE.

EFIELD = an array of the three x,y,z components of the single applied field. LOCHYP = a flag to perform a localized orbital analysis of the alpha, beta, and gamma polarizabilities. See $LOCAL for similar analyses of the energy, multipole moments, or alpha tensor. References for this keyword are given below. Finite field calculations require large basis sets, and extraordinary accuracy in the wavefunction. To converge the SCF to many digits is sometimes problematic, but we suggest you use the input to increase integral accuracy and wavefunction convergence, for example $CONTRL ICUT=20 ITOL=30 $END $SCF CONV=1d-7 FDIFF=.FALSE. $END Examples of fields that do not break symmetry are a Zaxis field for an axial point group which is not centrosymmetric (i.e. C2v). However, a field in the X or Y direction does break the C2v symmetry. Application of a Zaxis field for benzene breaks D6h symmetry. However, you could enter the group as C6v in $DATA while using D6h coordinates, and regain the prospect of using SYM=.TRUE. If you wanted to go on to apply a second field for benzene in the X direction, you might want to enter Cs in $DATA, which will necessitate the input of two more carbon and hydrogen atom, but recovers use of SYM=.TRUE. References: J.E.Gready, G.B.Bacskay, N.S.Hush Chem.Phys. 22, 141-150(1977) H.A.Kurtz, J.J.P.Stewart, K.M.Dieter J.Comput.Chem. 11, 82-87(1990).

Input Description

$FFCALC

2-202

polarizability analysis: S.Suehara, P.Thomas, A.P.Mirgorodsky, T.Merle-Mejean, J.C.Champarnaud-Mesjard, T.Aizawa, S.Hishita, S.Todoroki, T.Konishi, S.Inoue Phys.Rev.B 70, 205121/1-7(2004) S.Suehara, T.Konishi, S.Inoue Phys.Rev.B 73, 092203/1-4(2006) ==========================================================

Input Description

$TDHF

2-203

==========================================================

$TDHF

group

(relevant for SCFTYP=RHF if RUNTYP=TDHF)

This group permits the analytic calculation of various static and/or frequency dependent polarizabilities, with an emphasis on important NLO properties such as second and third harmonic generation. The method is programmed only for closed shell wavefunctions, at the semi-empirical or ab initio level. Ab initio calculations may be direct SCF, or parallel, if desired, except INIG=2. Because the Fock matrices computed during the timedependent Hartree-Fock CPHF are not symmetric, you may not use symmetry. You must enter NOSYM=1 in $CONTRL! For a more general numerical approach to the static properties, see $FFCALC. For additional closed shell dynamic polarizabilities and spectra, see $TDHFX. NFREQ FREQ = Number of frequencies to be used. (default=1) = An array of energy values in atomic units. For example: if NFREQ=3 then FREQ(1)=0.0,0.1,0.25. By default, only the static polarizabilities are computed. (default is freq(1)=0.0) The conversion factor from wavenumbers to Hartree is to divide by 219,474.6. To convert a wavelength to Hartree, compute FREQ=45.56/lamda, lambda in nm. MAXITA = Maximum number of iterations for an alpha computation. (default=100) MAXITU = Maximum number of iterations in the second order correction calculation. This applies to iterative beta values and all gammas. (default=100) DIIS = use the DIIS extrapolation using residual induced Fock matrix (default=.TRUE.).

MAXDII = the maximum number of Fock matrices to be used in DIIS extrapolation (default=50).

Input Description ATOL BTOL

$TDHF

2-204

= Tolerance for convergence of first-order results. (default=1.0d-05) = Tolerance for convergence of second-order results. (default=1.0d-05)

RETDHF = a flag to choose starting points for iterative calculations from best previous results. (default=.true.) * * * the following NLO properties are available alpha polarizabilities are always calculated. INIB = 0 turns off all beta computation (default) = 1 calculates only noniterative beta = 2 calculate iterative and noniterative beta The next flags allow further BETA tuning = Calculate beta for second harmonic generation. = Calculate beta for electrooptic Pockels effect. = Calculate beta for optical rectification. = 0 turns off all gamma computation (default) = 1 calculates only noniterative gamma = 2 calculate iterative and noniterative gamma The next flags allow further GAMMA tuning = Calculate gamma for third harmonic generation. * * *

BSHG BEOPE BOR INIG

GTHG

GEFISH = Calculate gamma for electric-field induced second harmonic generation. GIDRI GOKE = Calculate gamma for intensity dependent refractive index. = Calculate gamma for optical Kerr effect.

These will be computed only if a nonzero energy (FREQ) is requested. The default for each flag is .TRUE., and they may be turned off individually by setting some .FALSE. Note however that the program determines the best way to

Input Description

$TDHF

2-205

calculate them. For example, if you wish to have the SHG results but no gamma results are needed, the SHG beta will be computed in a non-iterative way from alpha(w) and alpha(2w). However if you request the computation of the THG gamma, the second order U(w,w) results are needed and an iterative SHG calculation will be performed whether you request it or not, as it is a required intermediate. Only the following combinations make sense: INIB INIG giving FREQ(1)=0.0,0.1 e.g. w=0.1 0 0 static alpha, a(w) 1 0 static alpha,beta a(w),a(2w) noniterative b(OR), b(EOPE), b(SHG) 2 0 static alpha,beta a(w),a(2w) noniterative b(OR), b(EOPE), b(SHG) iterative b(OR), b(EOPE), b(SHG) 2 1 static alpha,beta,gamma a(w),a(2w) iterative b(OR), b(EOPE), b(SHG) noniterative g(THG), g(EFISH), g(IDRI), g(OKE) 2 2 static alpha,beta,gamma a(w),a(2w) iterative b(OR), b(EOPE), b(SHG) noniterative g(THG), g(EFISH), g(IDRI), g(OKE) iterative static gamma, g(OKE), g(THG), g(EFISH), g(IDRI), g(DC-OR) This is a quirky program: 1. INIG=2 only runs in serial, and only runs with AO integrals on disk. 2. ISPHER=1 may not be chosen. 3. INIB=1 and INIB=2 print the same components for OR, OPE, SHG, but different totals from the whole tensor. It is not clear which is correct. 4. units are not well specified on the output! References: for static polarizabilities, G.J.B.Hurst, M.Dupuis, E.Clementi J.Chem.Phys. 89, 385-395(1988) for dynamic polarizabilities, S.P.Karna, M.Dupuis J.Comput.Chem. 12, 487-504 (1991). P.Korambath, H.A.Kurtz, in "Nonlinear Optical Materials",

Input Description

$TDHF

2-206

ACS Symposium Series 628, S.P.Karna and A.T.Yeates, Eds. pp 133-144, Washington DC, 1996. Review: D.P.Shelton, J.E.Rice, Chem.Rev. 94, 3-29(1994). ==========================================================

Input Description

$TDHFX

2-207

==========================================================

$TDHFX

group

(relevent for SCF=RHF if RUNTYP=TDHFX)

This group permits the analytical determination of static and/or frequency dependent polarizabilities and hyperpolarizabilities (alpha, beta, and gamma), as well as their first- and second-order geometrical derivatives (of alpha and beta). This permits the prediction of dynamic (nonresonant) Raman and hyper-Raman spectra, yielding both intensities and depolarizations. The method is only available for closed shell systems (RHF). For other polarizability options, see $FFCALC and $TDHF. For ordinary Raman spectra, see $RAMAN. You must not use point group symmetry in this kind of calculation (except to enter the molecule's structure), so provide NOSYM=1. Since the derivative level is quite high, it is a good idea to converge the SCF problem crisply, CONV=1.0D-6. These options are not forced by the RUNTYP, so please use explicit input. The $TDHFX group acts as a script. Each keyword must be on a separate line, terminated by a $END. The available keywords are gathered into 3 sets. Those belonging to the first set must appear before the second set, which must appear before the third set. Set 1: Here is a list of keywords that specifies the number of parameters (electric fields and geometrical distortions) that will be taken into account in the computations. ALLDIRS = compute the responses for all the electric field directions (x,y,z). DIR idir = compute the responses for one electric field specific direction: x(idir=1), y(idir=2) and z(idir=3). USE_C USE_Q = do the computation in Cartesian coordinates. = do the computation in normal coordinates.

Input Description

$TDHFX

2-208

The default is ALLDIRS and USE_C. Set 2: The following two keywords must be specified before any computation that requires vibrational frequencies or normal modes of vibration: FREQ = compute the normal modes and the harmonic vibrational frequencies. Do a HESSIAN job.

FREQ2 = same as FREQ but store the second derivative of the monoelectronic Hamiltonian. Required if you want to determine geometrical second-order derivatives of properties. Set 3: The following keywords are related to the generalized iterative method to solve TDHF mixed derivative equations. They can be inserted anywhere in the $TDHFX group and change the behavior of the generalized iterative method for any of the following tasks that might be requested. DIIS = Use the DIIS method. This is the default method. NOACCEL = Do not use any accelerating method. ITERMAX imax = Specify the maximum number of iterations to obtain the converged solution. Default=100. CONV threshold = the threshold convergence criterion for the U response matrices. Default=1E-5. Below are the keywords to select a particular computation. The xx_NI version will call a non-iterative procedure. The laser energy (w) must be given in Hartree. Divide by 219,474.6 to convert a frequency in wavenumbers (cm-1) to a photon energy in Hartree. Wavelength (in nm) is 45.56/w, when w is in Hartree. Static polarizabilities may be obtained from w=0.0. MU = compute the dipole moment.

Input Description

$TDHFX

2-209

ALPHA w = compute the dynamic polarizability: alpha(-w;w). BETA w1 w2 / BETA_NI w1 w2 = compute the dynamic first hyperpolarizability: beta(-w1-w2;w1,w2). GAMMA w1 w2 w3 / GAMMA_NI w1 w2 w3 = compute the dynamic second hyperpolarizability: gamma(-w1-w2-w3;w1,w2,w3). POCKELS w / POCKELS_NI w = compute electro-optic Pockels effect: beta(-w;w,0). OR w / OR_NI w = optical rectification: beta(0;w,-w). SHG w / SHG_NI w = second harmonic generation: beta(-2w;w,w). KERR w / KERR_NI w = DC Kerr effect: gamma(-w;w,0,0). ESHG w / ESHG_NI w = electric field induced 2nd harm gen: gamma(-2w;w,w,0). THG w / THG_NI w = third harmonic generation: gamma(-3w;w,w,w). DFWM w / DFWM_NI w = degenerate four wave mixing gamma(-w;w,-w,w). See the review D.P.Shelton, J.E.Rice Chem.Rev. 94, 3-29(1994) for more information on the quantities just above. The next options are nuclear derivatives of some of the above. DMDX_NI = compute the dipole derivative matrix, the geometrical first derivative of MU. DADX w / DADX_NI w = compute the polarizability derivative matrix, the

Input Description

$TDHFX

2-210

geometrical first-order derivative of alpha(-w;w). DBDX w1 w2 / DBDX_NI w1 w2 = compute the geometrical first-order derivative of beta(-w1-w2;w1,w2). D2MDX2_NI = compute geometrical second derivatives of MU D2ADX2_NI w = compute geometrical second derivatives of alpha(-w;w). D2BDX2_NI w1 w2 = geometrical second derivatives of beta(-w1-w2;w1,w2). The next two keywords automatically select paths through the package generating the required intermediates (both polarizabilities and their nuclear derivatives) to form spectra. The most efficient path through the program will be selected automatically. RAMAN w = Summarize the Raman responses in a table, and if necessary, compute the geometrical first-order derivatives of alpha(-w;w). HRAMAN w = Summarize the hyper-Raman responses in a table, and if necessary, compute the geometrical firstorder derivatives of beta(-2w;w,w). The following keywords permit the deletion of disk files associated with the set of frequencies w1,w2,... FREE w1 FREE w1 w2 FREE w1 w2 w3 Below is an example of a TDHFX group: $TDHFX ALLDIRS USE_Q FREQ DIIS ITERMAX 100 CONV 0.1E-7

Input Description HRAMAN 0.02 FREE 0.02 FREE 0.02 0.02 HRAMAN 0.03 $END

$TDHFX

2-211

References: "Time Dependent Hartree-Fock schemes for analytic evaluation of the Raman intensities" O.Quinet, B.Champagne J.Chem.Phys. 115, 6293-6299(2001). "Analytical TDHF second derivatives of dynamic electronic polarizability with respect to nuclear coordinates. Application to the dynamic ZPVA correction." O.Quinet, B.Champagne, B.Kirtman J.Comput.Chem. 22, 1920-1932(2001). "Analytical time-dependent Hartree-Fock schemes for the evaluation of the hyper-Raman intensities" O.Quinet, B.Champagne J.Chem.Phys. 117, 2481-2488(2002). errata: JCP 118, 5692(2003) "Analytical time-dependent Hartree-Fock evaluation of the dynamically zero-point averaged (ZPVA) first hyperpolarizability" O.Quinet, B.Kirtman, B.Champagne J.Chem.Phys. 118, 505-513(2003). Computer quirks: 1. This package uses file numbers 201, 202, ... but some compilers (chiefly g77) may not support unit numbers above 99. The remedy is to use a different computer or compiler. 2. If you experience trouble running this package under AIX, degrade the optimization of subroutine JDDFCK in hss2b.src, by placing this line @PROCESS OPT(2) immediately before JDDFCK, recompile hss2b, and relink. ==========================================================

Input Description

$EFRAG

2-212

==========================================================

$EFRAG

group

(optional)

The Effective Fragment Potential (EFP) is a potential extracted from rigorous quantum mechanics, permitting the treatment of solvent molecules (or other types of subsystems) with a potential. There are two models, EFP1 and EFP2, with more accurate physics in the latter. For more information, see chapter 4 of this manual. EFP1 calculations are typically limited to a QM system with water molecules, the latter modeled by RHF-based or DFT-based potentials which are built into the program. If a QM system is present, the calculations (energy and analytic gradient) can treat it by RHF, UHF, ROHF, GVB, or MCSCF wavefunctions, with both DFT or MP2 correlation energy corrections to RHF, UHF, and ROHF. Closed shell TDDFT excited states can also use EFP1. The entire QM/EFP1 system can be embedded in a PCM continuum (see $PCM), except when the QM system is treated by MP2 or TD-DFT. EFP2 calculations should use COORD=FRAGONLY at the present time, as the QM/EFP2 interaction terms are under active development. The programming for EFP2/EFP2 interactions is completed. See RUNTYP=MAKEFP to create EFP2 potentials. This group gives the name and position of one or more effective fragment potentials. It consists of a series of free format card images, which may not be combined onto a single line! The position of a fragment is defined by giving any three points within the fragment, relative to the ab initio system defined in $DATA, since the effective fragments have a frozen internal geometry. All other atoms within the fragment are defined by information in the $FRAGNAME group. ----------------------------------------------------------1a line containing one or more of these options:

If you choose more options than are able to be fit on a single 80 character line, type an > character to continue onto the next line.

Input Description

$EFRAG

2-213

If you do not choose any of these options, input a blank line to accept defaults. COORD =CART =INT POLMETHD=SCF selects use of Cartesians coords to define the fragment position at line -3-. (default) selects use of Z-matrix internal coordinates at line -3-. indicates the induced dipole for each fragment due to the ab initio electric field and other fragment fields is updated only once during each SCF iteration. requests microiterations during each SCF iteration to make induced dipoles due to ab initio and other fragment fields self consistent amoung the fragments. (default) Both methods converge to the same dipolar interaction.

=FRGSCF

POSITION=OPTIMIZE Allows full optimization within the ab initio part, and optimization of the rotational and translational motions of each fragment. (default) =FIXED Allows full optimization of the ab initio system, but freezes the position of the fragments. This makes sense only with two or more fragments, as what is frozen is the fragments' relative orientation. =EFOPT the same as OPTIMIZE, but if the fragment gradient is large, up to 5 geometry steps in which only the fragments move may occur, before the geometry of the ab initio piece is relaxed. This may save time by reusing the two electron integrals for the ab initio system. NBUFFMO = n First n orbitals in the MO matrix are deemed to belong to the QM/MM buffer and will be excluded from

Input Description

$EFRAG

2-214

the interaction with the EFP region. This makes sense only if these first MOs are frozen via the $MOFRZ group. The next few inputs apply periodic boundary conditions, which is only possible if the system contains only EFP particles, with no ab initio atoms. The default is to use the minimum image convention, for all terms in the potentials, but see also the $EWALD input group in order to perform the long range electrostatic interactions in a more accurate manner. You may choose no more than one of the possible sets of cutoffs, with the switching function SWR1/SWR2 being the most physically reasonable. XBOX, YBOX, ZBOX = dimensions of the periodic box, which must be given in Angstroms. If these sizes are omitted, the simulation is an isolated cluster. = distance cutoffs for the switching function that gradually drops the interactions from full strength at SWR1 to zero at SWR2. Choose SWR2 <= min(XBOX/2,YBOX/2,ZBOX/2) and SWR1 <= SWR2 (typically 80%), to cut off interactions within a single box. In Angstrom a radial cutoff, implemented as a step function, which should be chosen like SWR2. In Angstrom = cutoffs (as step functions) beyond which effective fragment potential interactions are not computed, XCUT <= XBOX/2, etc. Angstroms

SWR1, SWR2

RCUT

XCUT, YCUT, ZCUT

For a simulation of 64 CCl4 molecules, PBC input might be xbox=21.77 ybox=21.77 zbox=21.77 swr1=8.0 swr2=10.0 Box sizes are typically chosen to give a correct value for the density of the system. The following turn off selected terms in the potentials, even if data for the term is found in the various $FRAGNAME input groups. These keywords are standalone strings,

Input Description

$EFRAG

2-215

without a value assigned to them. They allow data from potentials generated by MAKEFP runs to be kept in the $FRAGNAME, for possible future use. The first two are of interest in production runs, while the others are primarily meant for debugging purposes, as the latter terms are normally quite large. NOCHTR NODISP NOEXREP NOPOL NOPSCR = = = = = switch switch switch switch switch off off off off off charge transfer in EFP2 dispersion in EFP2 exchange repulsion (EFP1/EFP2) polarization (implies NOPSCR) polarization screening, only

The following parameters are related to screening of some terms in the potentials, when fragments are at close distances. Note that they are relevant only to EFP2 runs. Prior to May 2009, the defaults were ISCRELEC=0 ISCRPOL=0 ISCRDISP=0 at which time the defaults were changed to ISCRELEC=0 ISCRPOL=1 ISCRDISP=1 If you need to reproduce results or continue an ongoing set of computations, simply input the old defaults. ISCRELEC = fragment-fragment electrostatic screening, a correction for "charge penetration": E(elec) = E(multipoles) + E(chg.pen.) = 0 damping by various formulae is controlled by SCREEN1, SCREEN2, or SCREEN3 input sections in the $FRAGNAME group(s). If none are found, there will be no charge penetration screening of electrostatics. (default) = 1 use an overlap based damping correction E(chg.pen.)= -2(S**2/R)/sqrt(-2ln|S|) to the classical multipole energy. Since the overlap integrals used here, as well as in ISCRDISP must be evaluated as part of the exchange repulsion energy, there is essentially no overhead for selecting this. = fragment-fragment polarization screening. = 0 damping is controlled by POLSCR sections in the $FRAGNAME groups. If not found, there will be no screening. If POLSCR is found,

ISCRPOL

Input Description

$EFRAG

2-216

you must also use ISCRELEC=0 and SCREEN3. = 1 damping will use a Tang-Toennis style Gaussian formula, (1-exp(aR**2)(1+aR**2) where the default value of a=0.6. In order to change the 'a' parameter, give POLAB <a's value> STOP in the $FRAGNAME group. A smaller value may be useful for ionic EFPs. (default) ISCRDISP = fragment-fragment dispersion screening = 0 Use Tang-Toennies damping, with a fixed parameter a=1.5. = 1 use an overlap based damping factor, 1-S**2(1-2ln|S|+2ln**2|S|) instead. There is no parameterization, so there's no other input. (default) It is possible to choose ISCRELEC, ISCRPOL, and ISCRDISP independently, as they apply to distinct parts of the fragment-fragment effective potential, and apart from POLSCR/SCREEN3, are independently implemented. FRCPNT this keyword activates decomposing and printing the forces at the desired points in the EFP fragments, in additional to the traditional summing of the forces at the fragments' center-of-masses. This is useful for coarse graining the EFP data. If this option is selected, FORCE POINT section(s) must be given in the $FRAGNAME group(s).

----------------------------------------------------------2FRAGNAME=XXX

XXX is the name of the fragment whose coordinates are to be given next. XXX may not exceed 6 characters. Examples might be C6H6, BENZEN, DMSO, ... All information defining the EFP2-type fragment potential is given in a supplemental $XXX group, which is referred to below as a $FRAGNAME group.

Input Description

$EFRAG

2-217

Two different EFP1-type water potentials are internally stored. FRAGNAME=H2ORHF will select a water potential developed at the RHF/DZP level, while FRAGNAME=H2ODFT will select a potential corresponding to B3LYP/DZP (see $BASIS for the precise meaning of DZP). If you choose one of these internally stored potentials, you do not need to input either a $FRAGNAME or $FRGRPL groups. Since the EFP model consists of distributed multipoles and distributed polarizabilities, it is trivial to map some of the literature's simplified water potentials onto the EFP1 programming. For example, the octupole expansions used in EFP can be truncated to point charges (monopole term). So, FRAGNAME may also be any of the following water models: SPC, SPCE, TIP5P, TIP5PE, or POL5P Their EFP/EFP repulsion term is a typical 6-12 LennardJones form. Repulsion between the QM and EFP particles follows the EFP1 style, when used with a QM system. ----------------------------------------------------------3NAME NAME, X, Y, Z NAME, I, DISTANCE, J, BEND, K, TORSION (COORD=CART) (COORD=INT)

= the name of a fragment point. The name used here must match one of the points in $FRAGNAME. For the internally stored H2ORHF and H2ODFT potential, the atom names are O1, H2, and H3. = Cartesian coordinates defining the position of this fragment point RELATIVE TO THE COORDINATE ORIGIN used in $DATA. The choice of units is controlled by UNITS in $CONTRL.

X, Y, Z

I, DISTANCE, J, BEND, K, TORSION = the usual Z-matrix connectivity internal coordinate definition. The atoms I, J, K must be atoms in the ab initio system from in $DATA, or fragment points already defined in the current fragment or previously defined fragments. If COORD=INT, line -3- must be given a total of three times to define this fragment's position. If COORD=CART, line -3- must be given three times, which is sufficient to orient the rigid EFP particle. However, it

Input Description

$EFRAG

2-218

is good form to read in any remaining nuclei in the EFP, for example all 12 atoms in a benzene EFP, although only the first three lines determine the entire EFP's position, whenever you have the data for the extra nuclei. ---------------------------------------------------------Repeat lines -2- and -3- to enter as many fragments as you desire, and then end the group with a $END line. Note that it is quite typical to repeat the same fragment name at line -2-, to use the same type of fragment system at many different positions. ========================================================== * * * * * * * * * * * * * * * * * * * * * For tips on effective fragment potentials see the 'further information' section * * * * * * * * * * * * * * * * * * * * *

Input Description

$FRAGNAME

2-219

==========================================================

$FRAGNAME

group (required for each FRAGNAME given in $EFRAG)

This group gives all pertinent information for a given Effective Fragment Potential (EFP). This information falls into three categories, with the first two shared by the EFP1 and EFP2 models: electrostatics (distributed multipoles, screening) polarizability (distributed dipole polarizabilities) The EFP1 model contains one final term, fitted exchange repulsion whereas the EFP2 model contains a collection of terms, exchange repulsion, dispersion, charge transfer... An Effective Fragment Potential is input using several different subgroups. Each subgroup is specified by a particular name, and is terminated by the word STOP. You may omit any of the subgroups to omit that term from the EFP. All values are given in atomic units. To To To To To To To To To To To input input input input input input input input input input input monopoles, follow input sequence dipoles, follow input sequence quadrupoles, follow input sequence octopoles, follow input sequence electrostatic screening, follow input seq. polarizable points, follow input sequence polarizability screening, follow input seq. fitted "repulsion", follow input sequence Pauli exchange, follow input sequence dispersion, follow input sequence charge transfer, follow input sequence -EM-ED-EQ-EO-ES-P-PS-R-PE-D-CT-

The data contained in a $FRAGNAME is normally generated by performing a RUNTYP=MAKEFP using a standard $DATA group ab initio computation on the desired solvent molecule. A MAKEFP run will generate all terms for an EFP2 potential, including multipole screening parameters. The screening option is controlled by $DAMP and $DAMPGS input, and by you checking the final fitting parameters for reasonableness. Note that the ability to fit the "repulsion" term in an EFP1 potential is not included in GAMESS, meaning that EFP1 computations normally use built-in EFP1 water potentials.

Input Description

$FRAGNAME

2-220

----------------------------------------------------------1a single descriptive title card ----------------------------------------------------------2COORDINATES

COORDINATES signals the start of the subgroup containing the multipolar expansion terms (charges, dipoles, ...). Optionally, one can also give the coordinates of the polarizable points, or centers of exchange repulsion. -3NAME, X, Y, Z, WEIGHT, ZNUC

NAME is a unique string identifying the point. X, Y, Z are the Cartesian coordinates of the point, and must be in Bohr units. WEIGHT, ZNUC are the atomic mass and nuclear charge, and should be given as zero only for points which are not nuclei. In EFP1 potentials, the true nuclei will appear twice, once for defining the positive nuclear charge and its screening, and a second time for defining the electronic distributed multipoles. Repeat line -3- for each expansion point, and terminate the list with a "STOP". ---------------------------------------------------------Note: the multipole expansion produced by RUNTYP=MAKEFP comes from Stone's distributed multipole analysis (DMA). An alternative expansion, from a density based multipole expansion (DBME) performed on an adaptive grid is placed in the job's PUNCH file. This alternative multipole expansion may be preferable if large basis sets are in use (the DMA expansion is basis set sensitive). The DBME values can be inserted in place of the DMA values, for -EM-, -ED, -EQ-, and -EO- sections, if you wish. Experience suggests that DBME multipoles are about as accurate as those obtained using DMA. -EM1MONOPOLES

MONOPOLES signals the start of the subgroup containing

Input Description

$FRAGNAME

2-221

the electronic and nuclear monopoles. -EM2NAME, CHARGE1, CHARGE2

NAME must match one given in the COORDINATES subgroup. CHARGE1 = electronic monopole at this point. CHARGE2 = nuclear monopole at this point. Omit or enter zero if this is a bond midpoint or some other expansion point that is not a nucleus. Repeat -EM2- to define all desired charges. Terminate this subgroup with a "STOP". ----------------------------------------------------------ED1- DIPOLES DIPOLES signals the start of the subgroup containing the dipolar part of the multipolar expansion. -ED2NAME, MUX, MUY, MUZ

NAME must match one given in the COORDINATES subgroup. MUX, MUY, MUZ are the components of the electronic dipole. Repeat -ED2- to define all desired dipoles. Terminate this subgroup with a "STOP". ----------------------------------------------------------EQ1- QUADRUPOLES QUADRUPOLES signals the start of the subgroup containing the quadrupolar part of the multipolar expansion. -EQ2NAME, XX, YY, ZZ, XY, XZ, YZ

NAME must match one given in the COORDINATES subgroup. XX, YY, ZZ, XY, XZ, and YZ are the components of the electronic quadrupole moment. Repeat -EQ2- to define all desired quadrupoles. Terminate this subgroup with a "STOP". ----------------------------------------------------------EO1- OCTUPOLES (note: OCTOPOLES is misspelled) OCTUPOLES signals the start of the subgroup containing the octupolar part of the multipolar expansion.

Input Description -EO2-

$FRAGNAME

2-222

NAME, XXX, YYY, ZZZ, XXY, XXZ, XYY, YYZ, XZZ, YZZ, XYZ

NAME must match one given in the COORDINATES subgroup. XXX, ... are the components of the electronic octopole. Repeat -EO2- to define all desired octopoles. Terminate this subgroup with a "STOP". ----------------------------------------------------------ES1aSCREEN

SCREEN signals the start of the subgroup containing Gaussian screening (A*exp[-B*r**2]) for the distributed multipoles, which account for charge penetration effects. SCREEN pertains to ab initio-EFP multipole interactions, in contrast to the SCREENx groups defined just below for EFPEFP interactions. -ES1bNAME, A, B

NAME must match one given in the COORDINATES subgroup. A, B are the parameters of the Gaussian screening term. Repeat -ES1b- to define all desired screening points. Terminate this subgroup with a "STOP". ---------------------------------------------------------note: SCREENx input (any x) is only obeyed if ISCRELEC=0. SCREENx input will be ignored if ISCRELEC=1. One (and only one) of the following groups should appear to define the EFP-EFP multipole screening: -ES2aSCREEN1 or SCREEN2 or SCREEN3

SCREEN1 signals the start of the subgroup containing Gaussian screening (A*exp[-B*r**2]) for the distributed multipoles, which account for charge-charge penetration effects. SCREEN2 signals the start of the subgroup containing exponential screening (A*exp[-B*r]) for the distributed

Input Description

$FRAGNAME

2-223

multipoles, which account for charge-charge penetration effects. This is often the EFP-EFP screening of choice. SCREEN3 signals the start of the subgroup containing the screening terms (A*exp[-B*r]) for the distributed multipoles, which account for high-order penetration effects (higher terms means charge-charge, as for SCREEN1 or SCREEN2, but also charge-dipole, charge-quadrupole, and dipole-dipole and dipole-quadrupole terms). -ES2bNAME, A, B

NAME must match one given in the COORDINATES subgroup. A, B are the parameters of the exponential screening term. Repeat -ES2b- to define all desired screening points. Terminate this subgroup with a "STOP". ----------------------------------------------------------P1POLARIZABLE POINTS

POLARIZABLE POINTS signals the start of the subgroup containing the distributed dipole polarizability tensors, and their coordinates. This subgroup allows the computation of the polarization energy. -P2NAME, X, Y, Z

NAME gives a unique identifier to the location of this polarizability tensor. It might match one of the points already defined in the COORDINATES subgroup, but often does not. Typically the distributed polarizability tensors are located at the centroids of localized MOs. X, Y, Z are the coordinates of the polarizability point. They should be omitted if NAME did appear in COORDINATES. The units are controlled by UNITS= in $CONTRL. -P3XX, YY, ZZ, XY, XZ, YZ, YX, ZX, ZY

XX, ... are components of the distributed polarizability, which is not a symmetric tensor. XY means dMUx/dFy, where MUx is a dipole component, and Fy is a component of an applied field.

Input Description

$FRAGNAME

2-224

Repeat -P2- and -P3- to define all desired polarizability tensors, and terminate this subgroup with a "STOP". ----------------------------------------------------------PS1POLSCR

This section must not be given if ISCRPOL=1. If not given, when ISCRPOL=0, no polarization screening is performed. POLSCR signals the start of the subgroup containing the screening (by exp[-B*r]) for the induced dipoles. It pertains only to EFP-EFP interactions. It requires that you be using SCREEN3 damping of the multipole-multipole interactions! It applies to charge/induced dipole, dipole/induced dipole, quadrupole/induced dipole, and induced dipole/induced dipole terms. -PS2NAME, B

NAME must match one of the distributed dipole points given in the POLARIZABLE subgroup. B is the exponent of the exponential screening term, and a typical value is about 1.5. Repeat -PS2- to define all desired screening points. Terminate this subgroup with a "STOP". ---------------------------------------------------------FORCE POINT This section controls coarse graining of the gradient, if FRCPNT is selected in $EFRAG. The input consists of the coordinates of the desired points: COM x y z FP1 x y z FP2 x y x ... STOP where x,y,z are the coordinates of center of mass (COM) and also any desired "force points" FP1, FP2, ... Terminate this subgroup with a "STOP". ----------------------------------------------------------

Input Description

$FRAGNAME

2-225

EFP1 versus EFP2 The EFP1 model consists of a fitted potential, which is a remainder term, after taking care of electrostatics and polarization with the input described above. The fitted term is called a "repulsive potential" because its largest contribution stems from Pauli exchange repulsion. The fit actually contains several other interactions, since it is just a fit to the total interaction potential's remainder after subtracting the elecrostatic and polarization interactions. The EFP2 model uses analytic representations for exchange repulsion and other terms, and these are documented after the EFP1's "repulsive potential". ----------------------------------------------------------R1REPULSIVE POTENTIAL

See also the $FRGRPL input group, which defines the fit for the EFP1-EFP1 repulsion term. REPULSIVE POTENTIAL signals the start of the subgroup containing the fitted exchange repulsion potential, for the interaction between the fragment and the ab initio part of the system. This term also accounts, in part, for other effects, since it is a fit to a remainder. The fitted potential has the form N sum i -R2C * exp[-D * r**2] i i

NAME, X, Y, Z, N

NAME may match one given in the COORDINATES subgroup, but need not. If NAME does not match one of the known points, you must give its coordinates X, Y, and Z, otherwise omit these three values. N is the total number of terms in the fitted repulsive potential.

Input Description -R3C, D

$FRAGNAME

2-226

These two values define the i-th term in the repulsive potential. Repeat line -R3- for all N terms. Repeat -R2- and -R3- to define all desired repulsive potentials, and terminate this subgroup with a "STOP". ---------------------------------------------------------The following terms are part of the developing EFP2 model. This model replaces the "kitchen sink" fitted repulsion in the EFP1 model by analytic formulae. These formulae are to be specific for each kind of physical interaction, and to pertain to any solvent, not just water. The terms which are programmed so far are given below. ----------------------------------------------------------PE1-PE2-PE3-PE4PROJECTION BASIS SET PROJECTION WAVEFUNCTION n m FOCK MATRIX ELEMENTS LMO CENTROIDS

These four sections contain the data needed to compute the Pauli exchange repulsion, namely 1. the original basis set used to extract the potential. 2. the localized orbitals, expanded in that basis. 3. the Fock matrix, in the localized orbital basis. 4. the coordinates of the center of each localized orb. The information generated by a MAKEFP that follows these four strings is largely self explanatory. Note, however, that the orbitals (PE2) must have two integers giving the number of occupied orbitals -n- and the size of the basis set -m-. The PE2 and PE3 subsections do not contain STOP lines. ----------------------------------------------------------D1DYNAMIC POLARIZABLE POINTS

DYNAMIC POLARIZABLE POINTS signals the start of the subgroup containing the distributed imaginary frequency dipole polarizability tensors, and their coordinates. This information permits the computation of dispersion energies.

Input Description -D2NAME, X, Y, Z

$FRAGNAME

2-227

NAME gives a unique identifier to the location of this polarizability tensor. It might match one of the points already defined in the COORDINATES subgroup, but often does not. Typically the distributed polarizability tensors are located at the centroids of localized MOs. X, Y, Z are the coordinates of the polarizability point. They should be omitted if NAME did appear in COORDINATES. The units are controlled by UNITS= in $CONTRL. -D3XX, YY, ZZ, XY, XZ, YZ, YX, ZX, ZY

XX, ... are components of the distributed polarizability, which is not a symmetric tensor. XY means dMUx/dFy, where MUx is a dipole component, and Fy is a component of an applied field. Repeat -D2- and -D3- to define all desired polarizability tensors, and then repeat for all desired imaginary frequencies. MAKEFP jobs use 12 imaginary frequencies at certain internally stored values, to enable quadrature of these tensors, to form the C6 dispersion coefficient. Thus D2 and D3 input is repeated 12 times. Terminate this subgroup with a "STOP". ----------------------------------------------------------CT1- CANONVEC n m -CT2- CANONFOK These two sections contain the data needed to compute the charge transfer energy, namely 1. the canonical orbitals, expanded in the -PE1- basis. 2. the Fock matrix, in the canonical orbital basis. The information generated by a MAKEFP that follows these two strings is largely self explanatory. The MO and AO sizes given by -n- and -m- have the same meaning as for the -PE2- group. The CT1 group does not have a STOP line. ---------------------------------------------------------The EFP2 model presently can generate the energy for a system with an ab initio molecule and EFP2 solvents, if only Pauli exchange repulsion is used. The AI-EFP gradient

Input Description

$FRAGNAME

2-228

for this term is not yet programmed, nor are there AI-EFP codes for dispersion or charge transfer. Thus use of the EFP2 model, for all practical purposes, is limited to EFPEFP interactions only, via COORD=FRAGONLY. ========================================================== The entire $FRAGNAME group is terminated by a " $END".

Input Description

$FRGRPL

2-229

==========================================================

$FRGRPL

group

This group defines the inter-fragment repulsive potential for EFP1 potentials. It accounts primarily for exchange repulsions, but also includes charge transfer. Note that the functional form used for the fragment-fragment repulsion differs from that used for the ab initio-fragment repulsion, which is defined in the $FRAGNAME group. The form of the potential is N sum A * exp[-B * r] i i i ----------------------------------------------------------1PAIR=FRAG1 FRAG2

specifies which two fragment repulsions are being defined. $FRAGNAME input for the two names FRAG1 and FRAG2 must have been given. ----------------------------------------------------------2NAME1 NAME2 A B *or* NAME1 NAME2 'EQ' NAME3 NAME4

NAME1 must be one of the "NAME" points defined in the $FRAG1 group's REPULSION POTENTIAL section. Similarly NAME2 must be a point from the $FRAG2 group. In addition, NAME1 or NAME2 could be the keyword CENTER, indicating the center of mass of the fragment. A and B are the parameters of the fitted repulsive potential. The second form of the input allows equal potential fits to be used. The syntax implies that the potential between the points NAME1 and NAME2 should be taken the same as the potential previously given in this group for the pair of points NAME3 and NAME4. If there are NPT1 points in FRAG1, and NPT2 points in FRAG2, input line -2- should be repeated NPT1*NPT2 times.

Input Description

$FRGRPL

2-230

Terminate the pairs of potentials with a "STOP" card. Any pairs which you omit will be set to zero interaction. Typically the number of points on which fitted potentials might be taken to be all the nuclei in a fragment, plus the center of mass. ---------------------------------------------------------Repeat lines -1- and -2- for all pairs of fragments, then terminate the group with a $END line. ==========================================================

Input Description

$EWALD

2-231

==========================================================

$EWALD

group

(relevant for all-EFP runs with PBC)

This group controls evaluation of the electrostatic energy of EFP calculations by means of the Ewald sum formulae. This gives a more accurate evaluation of these long range interactions than the minimum image convention, which sums only up to a distance of one box, centered on each particle. Ewald sum formulae are not used for the other, shorter range interactions in the EFP model, such as exchange repulsion and polarization, which are always evaluated by the minimum image convention. This group is relevant if and only if a periodic box is defined in the $EFRAG input group. IFEWLD = a flag to activate Ewald sums for electrostatics The default is .FALSE. LEVEL = 1 means Ewald sum charge-charge interactions only, which is the default if IFEWLD is turned on. = 2 charge-charge, charge-dipole, dipole-dipole = 3 charge-charge, charge-dipole, dipole-dipole, and charge-quadrupole terms should be Ewald summed.

TNFOIL = a flag to select tin foil boundary conditions, which uses a metallic continuum past the cutoffs, instead of a vacuum. The default is .TRUE. BETA = parameter for the direct summation, in 1/Bohr. It should be 1.7/cutoff. Cutoffs are specified in $EFRAG, with the periodic box sizes, use a cutoff in units Angstrom in this formula, as the value 1.7 includes the conversion factor. The default=0.2 = number of reciprocal vectors in each direction. This should be kmax >= 3.2L/cutoff, where the radial cutoff, and box side L are both given in your $EFRAG. The default=10

KMAX

==========================================================

Input Description

$MAKEFP

2-232

==========================================================

$MAKEFP

group

(relevant if RUNTYP=MAKEFP)

This group controls generation of the effective fragment potential (EFP2 style) from the wavefunction of a single monomer. EFP generation is allowed for SCFTYP=RHF and ROHF. Multipole moments for electrostatics are always generated, and the default for the keywords below is to generate all additional terms.

FRAG

= a string of up to 8 letters to identify this EFP. For example, WATER or BENZENE or CH3OH or ... (default=FRAGNAME, which you can hand edit later)

SCREEN = a flag to generate screening information for the multipole electrostatics, and maybe polarizability screening. See $DAMP and $DAMPGS. (default=.TRUE. for RHF, so far ROHF is not coded) POL = a flag to generate dipole polarizabilities. (default=.TRUE.) See POLNUM in $LOCAL for an alternative way to generate the polarizabilities, which may be faster for large molecules. EXREP CHTR DISP = a flag to generate exchange repulsion parameters. (default=.TRUE.) = a flag to generate charge transfer parameters. (default=.TRUE. for RHF, so far ROHF is not coded) = a flag to generate information for dispersion. (default=.TRUE. for RHF, so far ROHF is not coded)

See also similar inputs NOPOL, NOEXREP, NOCHTR, NODISP in the $EFRAG input group, to ignore these terms if they are generated. ==========================================================

Input Description

$PRTEFP

2-233

==========================================================

$PRTEFP

group

(optional)

This group provides control for generating integer charge EFP fragments for constructing large EFPs. See P.A.Molina, H.Li, J.H.Jensen J.Comput.Chem. 24, 1971-1979 (2003) This group is mainly used in RUNTYP=MAKEFP runs. However, in MOPAC RUNTYP=ENERGY runs, the presence of a $PRTEFP group causes AM1 or PM3 charges to be printed and punched out in a suitable format for EFP calculations. NOPRT = an array specifying the atoms for which EFP multipole and polarizability points will not be printed/punched out. Example: For a molecule with the connectivity A1-A2-A3-A4-A5, NOPRT(1)=4,5 means that multipoles centered on atoms 4 and 5, and bond midpoints BO34 and BO45 are not part of the EFP.

MIDPRT = an array specifying atoms whose bond midpoints neglected by using NOPRT should be printed out. Example: MIDPRT(1)=3 forces the printout of bond midpoint BO34. The neglect of monopoles leads to EFPs with overall non-integer charge. The next keyword defines "collection points" to which the removed monopoles are added. Thus, the net charge of the EFP=ICHARG. The presence of this "fictitious" charge is compensated for by adding an opposing dipole to the collection point. NUMFFD = an array that defines (1) a collection point, (2) the number of atoms contributing to monopoles to this point, and (3) the numbers of the atoms. More than one collection point can be defined. An opposing dipole is calculated as -0.5Q*r (Q = sum of neglected monopoles, r = distance between collection point and nearest neglected monopole) and placed at the collection point. Example: NUMFFD(1)=3,2,4,5. The sum of monopoles

Input Description

$PRTEFP

2-234

at A4, A5, BO34 and BO45 (Q) is added to the A3 monopole. A dipole, -0.5Q*r, is placed on A3, where r is the distance between A3 and BO34. If MIDPRT(1)=3, Q does not include the BO34 monopole, r is the distance between BO34 and A4, and the resulting dipole is centered on BO34. ==========================================================

Input Description

$DAMP

2-235

==========================================================

$DAMP

group

(optional, relevant if RUNTYP=MAKEFP)

This group provides control over the screening of the charge term in the distributed multipole expansion used by the EFP model for electrostatic interactions, to account for charge penetration. See M.A.Freitag, M.S.Gordon, J.H.Jensen, W.A.Stevens J.Chem.Phys. 112, 7300-7306(2000) L.V.Slipchenko, M.S.Gordon J.Comput.Chem. 28, 276-291(2007) The screening exponents are optimized by fitting a damped multipolar electrostatic potential to the actual quantum mechanical potential of the wavefunction, computed on concentric layers of united spheres (namely, "GEODESIC" layers for WHERE=PDC in $ELPOT). See $STONE's generation of the unscreened classical multipoles, $PDC's generation of the true quantum potentia, and $DAMPGS. Different multipole damping functions can be generated. The first contains a single exponential form, (1 - beta*exp(-alpha*r)) and the second function is a single Gaussian form, (1 - beta*exp(-alpha*r**2)) The exponent 'alpha' values are optimized (normally with beta=one), with starting values defined in $DAMPGS. The exponential fit is used for fragment-fragment charge penetration screening, while the Gaussian fit is used in ab initio-fragment screening. See equations 28 and 4 in the reference. These two screen only the charge-charge interactions. It is also possible to generate a "higher order exponential" screening term, meaning that in addition to the charge-charge energy, also affects charge-dipole, charge-quadrupole, and dipole-dipole energy terms. Words of advice: 1. Higher order screening is usually similar in accuracy to just charge-charge screening, except in molecules without dipole moment, such as ethylene or benzene.

Input Description

$DAMP

2-236

2. If the bond midpoints have smaller charges, it may be more physically reasonable to screen only the atomic monopoles, see ISCCHG. 3. Use of the numerical Stone distributed multipole analysis may not be fully converged with respect to the level of highest used multipole moment (octapole) and corresponding energy terms (quadrupole-quadrupole), which makes screening much more problematic. 4. Accuracy of screening with the damping function of a single exponential form depends on a region of fitting the quantum mechanical electrostatic potential, i.e., a radius of first sphere with grid points (parameter VDWSCL in $PDC). A general trend is that for molecules with stronger electrostatic interaction, and, consequently, shorter intermolecular separations, e.g., methanol and water, smaller values of VDWSCL are preferable, whereas for weaker interacting molecules, e.g., dichloromethane and acetone, bigger VDWSCL values are more acceptable. Our recommended VDWSCL values are 0.4-0.5 for methanol, 0.5-0.8 for water, and 0.7-0.9 for weaker bonded molecules. Note that VDWSCL values of 1.0 and higher often result in not converged or badly converged damping parameters, and are not recommended. The default VDWSCL value is 0.7. 5. If the non-linear parameters alpha increase to 10, that term is effectively removed from the screening. This happens sometimes with buried atoms, and fairly often with bond mid-points. 6. Double check the numerical results carefully. ISCCHG = 0 use both atoms and bond midpoints as screening centers (the default) 1 use only atoms as screening centers IFTTYP = selects the type of multipole screening fit: 0 means generate a Gaussian fit, for use as SCREEN input in $FRAGNAME. 2 means generate an exponential charge-charge fit, for use as SCREEN2 input in $FRAGNAME. 3 means generate an exponential higher order fit, for use as SCREEN3 input in $FRAGNAME. If you wish to use Gaussian screening for EFP-EFP, simply copy the SCREEN output into a SCREEN1 section.

Input Description

$DAMP

2-237

IFTFIX = 0 means the coefficients in the fit (beta) are free parameters 1 means the coefficients are held to unity. In case the linear coefficients become large, and particularly if they are negative, a fit with unit coefficients is more reasonable. The default is to do both fits in one run, IFTTYP(1)=2,0, using unit coefficients, IFTFIX(1)=1,1. The remaining parameters are seldom given: NMAIN = the number of centers to receive a smaller alpha initial value, 2.0, which defaults to the number of atoms. The remaining centers, usually the bond midpoints, receive a larger starting value, 4.0. $DAMPGS gives more control of the values. = maximum iterations in the fit, default=30. = printing threshold for large deviations. The default is 100.0 kcal/mol.

MAXIT THRSH

==========================================================

Input Description

$DAMPGS

2-238

==========================================================

$DAMPGS group

(relevant if $DAMP was given)

This is a free-format, line by line input group that sets the initial values damping functions used to screen the multipole expansion. A check run may be helpful in listing the names of the expansion points that are chosen by MAKEFP jobs. Very often the input group contains only type -1- lines, and only in its second form. ----------------------------------------------------------1<exp.pt.> <nterms> or <exp.pt.>=<prev.exp.pt.> This line gives the name of the expansion point, and how many terms are in the damping function (always 1 at present). The second form of this line lets you equate the current point to some previous point's values in $DAMPGS, skipping line -2-. ----------------------------------------------------------2<coef> <exponent> The linear coefficient (usually 1.0) and exponent of this term in the damping function. Repeat -2- <nterms> times. If not given, the starting exponent for atoms is 2.0, and for bond midpoints, 4.0. ---------------------------------------------------------An example, for water, enforcing equivalent points, is: $dampgs or much more simply, O1 1 since the left is default exponents, 1.0 2.0 $dampgs H2 1 H3=H2 1.0 2.0 BO31=BO21 H3=H2 $end BO21 1 1.0 4.0 BO31=BO21 The "BO" is short for bond midpoint. $end ==========================================================

Input Description

$PCM

2-239

==========================================================

$PCM

group

(optional)

This group controls solvent effect computations using the Polarizable Continuum Model. If this group is found in the input file, a PCM computation is performed. The default calculation, chosen by selecting only the SOLVNT keyword, is to compute the electrostatic free energy. Appropriate numerical constants are provided for a wide range of solvents. Typical input might be as simple as $PCM SOLVNT=H2O $END There is in fact little need to give other PCM input data, except perhaps atomic radii in $PCMCAV if your molecule contains an unusual atom. Additional keywords (ICOMP, ICAV, IDISP, or IREP/IDP) allow for more sophisticated computations, namely cavitation, repulsion, and dispersion free energies. The methodology for these is general, but numerical constants are provided only for water. Alternatively, the PCM codes for electrostatics can be combined with U. Minnesota codes to implement the SMD solvation model. SMD combines the electrostatics with an alternative cavitation, dispersion, and solute structure reorganization (CDS) correction. Since SMD also changes the atomic radii, the electrostatics interaction is changed. See keyword SMD below (and the 4th chapter of this manual). Calculations are possible on either a solute embedded in a PCM continuum, or a system combining a solute & EFP explicit solvent molecules, embedded in a PCM continuum. The energy and/or nuclear gradients are programmed for RHF, ROHF, UHF, GVB, and MCSCF wavefunctions, and for DFT or MP2 level calculations using RHF, ROHF, and UHF. Closed shell TD-DFT excited states have analytic gradients, as well. Polarizabilities in solution may be found by RUNTYP=TDHF. Parallel computation is enabled, with scaling similar to the scaling of the corresponding gas phase calculation. PCM is not programmed for CI, Coupled Cluster, or semiempirical MOPAC runs.

Input Description

$PCM

2-240

See the Fragment Molecular Orbital section of the References chapter for information on using PCM within the FMO model. There is additional information on PCM in the References chapter of this manual. This includes information on which keyword combinations were default values in the past. IEF switch to choose the type of PCM model used. The default is -10, iterative C-PCM. = 0 isotropic dielectrics using the original formulation of PCM for dielectrics (D-PCM) = 1 anisotropic dielectric using the Integral Equation Formalism (IEF) of PCM, see $IEFPCM = 2 ionic solutions using IEF-PCM, see $IEFPCM = 3 isotropic dielectrics using IEF-PCM with matrix inversion solver, see $IEFPCM = -3 isotropic dielectric IEF-PCM with iterative solver, see $PCMITR. = 10 conductor-like PCM (C-PCM) with matrix inversion. Charge scaling is(Eps-1.0)/Eps =-10 C-PCM, with iterative solver. See $PCMITR.

C-PCM is normally a better choice than IEF-PCM. The iterative solvers chosen by IEF=-3 or -10 usually reproduce the energy of the explicit solvers IEF=3 or 10 to within 1.0d-8 Hartrees, and will be much faster and use less memory for large molecules. D-PCM should be considered obsolete, and choices 1 and 2 are seldom made. * * * SOLVNT = keyword naming the solvent, whose choices depend on use of non-SMD or SMD models. For the former, the eight numerical constants defining the solvent are internally stored for: WATER (or H2O) CH3OH C2H5OH CLFORM (or CHCl3) CTCL (or CCl4) METHYCL (or CH2Cl2) 12DCLET (or C2H4Cl2) BENZENE (or C6H6) TOLUENE (or C6H5CH3) CLBENZ (or C6H5Cl) NITMET (or CH3NO2) NEPTANE (or C7H16) CYCHEX (or C6H12) ANILINE (or C6H5NH2) ACETONE (or CH3COCH3)

Input Description

$PCM

2-241

THF DMSO (or DMETSOX) SMD has many additional solvents, see below. The default solvent name is "INPUT" which means you must give the numerical values defining some other solvent, as described below. * * * non-SMD calculations * * * The next set of parameters controls the computation: parameterization of the solvents, ICOMP which has an impact on the PCM electrostatics, and other keywords related to cavitation, dispersion, and repulsion corrections: ICAV, IDISP, IREP/IDP. ------ICOMP = Compensation procedure for induced charges. Gradient runs require ICOMP be 0 or 2 only. = 0 None. (default) = 1 Yes, each charge is corrected in proportion to the area of the tessera to which it belongs. = 2 Yes, using the same factor for all tesserae. = 3 Yes, with explicit consideration of the portion of solute electronic charge outside the cavity, by the method of Mennucci and Tomasi. See the $NEWCAV group.

Technical issues are: IEF=0 should normally choose ICOMP=2. Options IEF=1 or 2 are incompatible with gradients and must choose ICOMP=0, and presently contain bugs (do not choose these!). IEF=3 may not choose ICOMP=3, but if diffuse basis functions are in use, it may benefit from ICOMP=2. -----ICAV = calculate the cavitation energy, by the method of Pierotti and Claverie. The cavitation energy is computed at the end of the run (e.g. at the final geometry) as an additive constant to the energy. = 0 skip the computation (default) = 1 perform the computation.

If ICAV=1, the following parameter is relevant: TABS = the temperature, in Kelvin. (default=298.0)

Input Description

$PCM

2-242

------There are two procedures for the calculation of the repulsion and dispersion contributions to the free energy. Parameterizations were obtained for RHF cases, so the implementation permits their use only for RHF. IDISP is older, and is incompatible with IREP and/or IDP. Nuclear gradients are available for IDISP (select either ICLAV or ILJ in $DISREP). The older GEPOL-GB tessellation does some gradient terms numerically, which results in a less accurate gradient. IDISP = Calculation of both dispersion and repulsion free energy through the empirical method of Floris and Tomasi. = 0 skip the computation (default) = 1 perform the computation. See $DISREP group.

The next two options add repulsive and dispersive terms to the solute hamiltonian, in a more ab initio manner, by the method of Amovilli and Mennucci. These may be used only in single point energy calculations (see IDISP if you wish to use gradients). IREP = Calculation of repulsion free energy = 0 skip the computation (default) = 1 perform the computation. See $NEWCAV group. = Calculation of dispersion free energy = 0 skip the computation (default) = 1 perform the computation. See $DISBS group.

IDP

If IDP=1, then three additional parameters must be defined. The two solvent values correspond to water, and therefore these must be input for other solvents. WA = solute average transition energy. This is computed from the orbital energies for RHF, but must be input for MCSCF runs. (default=1.10) = ionization potential of solvent, in Hartrees. (default=0.451) = square of the zero frequency refractive index

WB ETA2

Input Description of the solvent.

$PCM (default=1.75)

2-243

--- the next 8 values define the solvent, if SOLVNT=INPUT: RSOLV = the solvent radius, in units Angstrom EPS = the dielectric constant EPSINF = the dielectric constant at infinite frequency. This value must be given only for RUNTYP=TDHF, if the external field frequency is in the optical range and the solvent is polar; in this case the solvent response is described by the electronic part of its polarization. Hence the value of the dielectric constant to be used is that evaluated at infinite frequency, not the static one (EPS). This value also must be given for TD-DFT/PCM, when NONEQ is selected in $TDDFT. For nonpolar solvents, the difference between the two is almost negligible. TCE = the thermal expansion coefficient, in units 1/K VMOL = the molar volume, in units ml/mol STEN = the surface tension, in units dyne/cm DSTEN = the thermal coefficient of log(STEN) CMF = the cavity microscopic coefficient Values for TCE, VMOL, STEN, DSTEN, CMF need to be given only for the case ICAV=1. Input of any or all of these values will override an internally stored value, if you have chosen a solvent by its name. * * * SMD calculations * * * The Solvation Model Density (SMD) uses the solute's quantum mechanical density (the D in the model's name) for IEF-PCM or C-PCM's electrostatics. It adds "CDS" corrections for cavitation, dispersion, and solvent structure, all of which have nuclear gradient contributions coded. The SMD model's parameters were developed using IEF-PCM and GEPOL cavity construction, but SMD may also be used with the more robust C-PCM model and FIXPVA cavity tessellation. SMD = a flag to select "Solvation Model Density". default=.FALSE. If chosen, naming the solvent by SOLVNT=xxx picks numerical values for the six SOLX keywords just below, which may then be omitted. The SMD model knows 178 solvents, see

Input Description

$PCM

2-244

chapter 4 of this manual for a listing. SOLA SOLB SOLC SOLG SOLH SOLN = Abraham's hydrogen bond acidity = Abraham's hydrogen bond basicity = aromaticity: fraction of non-H solvent atoms which are aromatic Carbon atoms = macroscopic surface tension at the air/solvent interface, in units of cal/mole/angstrom**2 = halogenicity: fraction of non-H solvent atoms which are F, Cl, or Br = index of refraction at optical frequencies at 298K, n-sub-20-super-D.

In addition to the parameters just above, SMD provides its own set of radii for each atom's sphere, so $PCMCAV input must not be given. Of course, if you choose SMD=.TRUE., with its built in CDS correction, you must select ICOMP=ICAV=IDISP=IREP=IDP=0! See also SMVLE in $SVP. * * * --- interface to Fragment Molecular Orbital method: IFMO specifies "n" for the n-body FMO expansion of the total electron density to be used in PCM. Nonzero IFMO can be used only within the regular FMO framework (q.v. for further FMO limitations). IFMO should be less or equal than NBODY in $FMO, Not all PCM options can be used with FMO! The following are explicitly permitted: IEF=-3,-10; ICOMP=0,1,2; MTHALL=2,4; IDISP=0,1; IDP=0; IREP=0,1. Gradient runs require ICOMP=0. IFMO may take the values of 0,1,2,3. (default=0)

--- the next set of keywords defines the molecular cavity, used for electrostatic (surface charge) calculations. See also $PCMCAV, $TESCAV, and $NEWCAV for other cavities. NESFP = option for spheres forming the cavity: = 0 centers spheres on each nucleus in the quantum solute, and every atom in EFP. (default) = N use N initial sphere, whose centers XE, YE, ZE and radii RIN must be specified in $PCMCAV.

Input Description

$PCM

2-245

The cavity generation algorithm may use additional spheres to smooth out sharp grooves, etc. If you are interested in smoother cavities, see the SVPE and SS(V)PE methods, which use a cavity based on isodensity surfaces. The following parameters control how many extra spheres are generated: OMEGA and FRO = GEPOL parameters for the creation of the 'added spheres' defining the solvent accessible surface. When an excessive number of spheres is created, which may cause problems of convergence, the value of OMEGA and/or FRO must be increased. For example, OMEGA from 40 to 50 ... up to 90, FRO from 0.2 ... up to 0.7. (defaults are OMEGA=40.0, FRO=0.7) RET = minimum radius (in A) of the added spheres. Increasing RET decreases the number of added spheres. A value of 100.0 (default) inhibits the addition of any spheres, while 0.2 fills in many. The use of added spheres is strongly discouraged.

MODPAR = cavity generation's parallelization option: 0 parallelize tessellation, 1= do not parallelize. The present parallel code is inefficient, so MODPAR=0 is recommended. (default=0) Don't confuse this with running PCM in parallel! MXSP MXTS = the maximum number of spheres. Default: MXATM parameter in GAMESS. = the maximum number of tesserae. Default: Nsph*NTSALL*2/3, where Nsph is the number of spheres (usually equal to the number of atoms). If less than 20 spheres are present, default is Nsph*NTSALL. For GEPOL-RT, NTSALL=960 is used in setting the default value. Note on MXSP and MXTS: PCM usually constructs more than one cavity (for example, a different one for the cavitation energy). MXSP and MXTS must be large enough to handle every possible cavity. --- arcane parameters:

Input Description

$PCM

2-246

IPRINT = 0 normal printing (default) = 1 turns on debugging printout IFIELD = At the end of a run, calculate the electric potential and electric field generated by the apparent surface charges. = 0 skip the computation (default) = 1 on nuclei = 2 on a planar grid If IFIELD=2, the following data must be input: AXYZ,BXYZ,CXYZ = each defines three components of the vertices of the plane where the reaction field is to be computed (in Angstroms) A ===> higher left corner of the grid B ===> lower left corner of the grid C ===> higher right corner of the grid NAB = vertical subdivision (A--B edge) of the grid NAC = horizontal subdivision (A--C edge) of the grid. ==========================================================

Input Description

$PCMCAV

2-247

==========================================================

$PCMCAV

group

(optional)

This group controls generation of the cavity holding the solute during Polarizable Continuum Model runs. The cavity is a union of spheres, according to NESFP given in $PCM. The data in this group supplements cavity data given in $PCM. It is unlikely that users will input anything here, except perhaps a few RIN values. The data given here must be in Angstrom units. XE,YE,ZE = arrays giving the coordinates of the spheres. if NESFP=0, the atomic positions will be used. if NESFP>0, you must supply NESFP values here. RADII = three tables of values (Angstroms!) are available: VANDW selects van der Waals radii (default) This table has radii for atoms H,He, B,C,N,O,F,Ne, Na,Al,Si,P,S,Cl,Ar, K,As,Se,Br,Kr, Rb,Sb,Te,I, Cs,Bi internally tabulated, otherwise give RIN. = VDWEFP, similar to VANDW, except that radii not tabulated by VANDW are assigned as 1.60A. This option is most useful for protein-EFP calculations. = SUAHF, the simplified united atomic radii will be be used for the array RIN, namely H:0.01 C:1.77 N:1.68 O:1.59 P:2.10 S:2.10 For the other elements with Z<16, 1.50 is used. For the elements with Z>16, 2.30 will be applied. RIN = an array giving the sphere radii. Radii given here will overwrite the values selected by RADII's tables. RIN values are multiplied by ALPHA, see just below. if NESFP=0, the program will look up the internally data according to the RADII keyword. if NESFP>0, give NESFP values. Example: Suppose the 4th atom in your molecule is Fe, but all other atoms have van der Waals radii. You decide a good guess for Fe is twice the covalent radius: $PCMCAV RIN(4)=2.33 $END. Due to ALPHA, traditionally 1.2, the Fe radius will be 2.796.

Input Description

$PCMCAV

2-248

The source for the van der Waals radii is "The Elements", 2nd Ed., John Emsley, Clarendon Press, Oxford, 1991, except for C,N,O where the Pisa group's experience with the best radii for PCM treatment of singly bonded C,N,O atoms is taken. The radii for a few transition metals are given by A.Bondi, J.Phys.Chem. 68, 441-451(1964). ALPHA = an array of scaling factors, for the definition of the solvent accessible surface. If only the first value is given, all radii are scaled by the same factor. (default is ALPHA(1)=1.2)

EPSHET = an array of dielectric constants, for each atom in the heterogeneous CPCM. The default is to use the same dielectric for every atom, namely the value of EPS in $PCM. (only if IEF=10 or -10). The default EPSHET(1)=X,X,X,X where EPS=X means homogeneous CPCM. ==========================================================

Input Description

$TESCAV

2-249

==========================================================

$TESCAV

group

(optional)

This group controls the tessellation procedure for the cavity surfaces in PCM computations. The default values for this group will normally be satisfactory. Use of the FIXPVA mechanism for dividing the surface of the atomic spheres into tesserae should allow for convergent PCM geometry optimizations. To converge to small OPTTOL values may require the use of internal coordinates, since the tessellation amounts to a finite grid (so the PCM energy is not strictly rotationally invariant). Cartesian geometry optimizations may require a high density of tesserae on the cavity surface: NTSALL=240 (or 960) This may require raising the maximum number of tesserae, see MXTS in $PCM. It is reasonable to just try internal coordinates first, as this should be sufficient w/o increasing the tesserae density. See also IFAST=1 in $PCMGRD. --- The first two arrays control the density of tesserae and the method to generate the tesserae. INITS = array defines the initial number of tesserae for each sphere. Only 60, 240 and 960 are allowed, but the value can be different for each sphere. (Default is INITS(1)=60,60,60,...) See NTSALL.

METHOD =

array defining the tessellation method for each sphere. The value can be different for each sphere. The default is 4 for all spheres, e.g. METHOD(1)=4,4,4,... See also MTHALL. = 1 GEPOL-GB, "Gauss-Bonet" tessellation. = 2 GEPOL-AS, "area scaling" tessellation. = 3 GEPOL-RT, "regular tessellation". = 4 FIXPVA, "Fixed points with variable area". FIXPVA gives smooth potential surfaces during geometry optimizations, works with the $PCM options ICAV, IDISP, IDP, and IRP, and is the preferred tessellation method. --- The next three parameters are presets for filling the arrays INITS and METHOD with identical values.

Input Description

$TESCAV

2-250

NTSALL = MTHALL = MTHAUT =

60, 240 or 960 (default = 60) All values in the array INITS are set to NTSALL 1, 2, 3, or 4 (default = 4) All values in the array METHOD are set to MTHALL 0 or 1 (default = 0) If RUNTYP=OPTIMIZE and frozen atoms are defined by IFCART, MTHAUT=1 will select METHOD=1 for frozen atoms. See also AUTFRE and NTSFRZ.

note: Explicitly defining INITS and METHOD from the input deck will overrule the presets from NTSALL, MTHALL and/or MTHAUT. --- The following two parameters control GEPOL-RT AREATL = The area criterion (A*A) for GEPOL-RT. Tesserae with areas < AREATL at the boundary of intersecting spheres will be neglected. Default=0.010 A*A. Smaller AREATL cause larger number of tesserae. AREATL < 0.00010 is not recommended. Controls (by scaling) the distance within which tesserae are considered "close" to the boundary. Such tesserae will be recursively divided into smaller ones until their areas are < AREATL. The default (= 1.0) means the distance is the square root of the tessera area. A large BONDRY value like 1000.0 will lead to fine tessellation for the entire surface with all tessera areas < AREATL.

BONDRY =

--- The next two parameters are only relevant if MTHAUT=1 AUTFRE = NTSFRZ = Distance (A) for frozen atoms to be treated as moving atoms when MTHAUT=1. Default=2.0 A. 60, 240 OR 960, initial tessera number for frozen atoms. Default=60

==========================================================

Input Description

$NEWCAV

2-251

==========================================================

$NEWCAV

group

(optional)

This group controls generation of the "escaped charge" cavity, used when ICOMP=3 or IREP=1 in $PCM. This cavity is used only to calculate the fraction of the solute electronic charge escapes from the original cavity. IPTYPE = choice for tessalation of the cavity's spheres. = 1 uses a tetrahedron = 2 uses a pentakisdodecahedron (default) ITSNUM = m, the number of tessera to use on each sphere. if IPTYPE=1, input m=30*(n**2), with n=1,2,3 or 4 if IPTYPE=2, input m=60*(n**2), with n=1,2,3 or 4 (default is 60) *** the next three parameters pertain to IREP=1 *** RHOW PM NEVAL = density, relative to liquid water (default = 1.0) = molecular weight (default = 18.0) = number of valence electrons on solute (default=8)

The defaults for RHOW, PM, and NEVAL correspond to water, and therefore must be correctly input for other solvents. ==========================================================

Input Description

$PCMGRD

2-252

==========================================================

$PCMGRD

group

(optional) It

This group controls the PCM gradient computations. is of a technical nature, and is seldom given. IPCDER = selects different methods for PCM gradients 1 use Ux(q) approximation (C-PCM and IEF-PCM), or use charge-derivative method (D-PCM). This is the default for D-PCM. 2 Variable-Tessera-Number Approximation. Implemented only for C-PCM and IEF-PCM, and the default for GEPOL-AS tesselation. 3 The same as 2, but for FIXPVE tessellation. The program will pick the correct default for IPCDER! note: If ICAV = 1 or IDISP = 1 in $PCM, the derivatives of the cavitation energy or dispersion-repulsion, respectively, will automatically be calculated. You must be using the following input: $PCM ICAV=1 IDISP=1 $END $DISREP ICLAV=1 $END IFAST

= Controls the PCM calculations for RUNTYP=OPTIMIZE. 0 update PCM charges at each SCF cycle at every geometry (default) 1 update PCM charges at each SCF cycle for the initial geometry. For the subsequent geometries, calculate PCM charges at the first SCF cycle and use the PCM charges for the following SCF cycles; after the density change falls below DENTOL, update the PCM charges one time (to save CPU time).

==========================================================

Input Description

$IECPCM

2-253

==========================================================

$IEFPCM

group

(optional)

This group defines data for the integral equation formalism version of PCM solvation. It includes special options for ionic or anisotropic solutions. The next two sets are relevant only for anisotropic solvents, namely IEF=1: EPS1, EPS2, EPS3 = diagonal values of the dielectric permittivity tensor with respect to the laboratory frame. The default is EPS in $PCM EUPHI, EUTHE, EUPSI = Eulerian angles which give the rotation of the solvent orientation with respect to the lab frame. The term lab frame means $DATA orientation. The default for each is zero degrees. The next two are relevant to ionic solvents, namely IEF=2: EPSI = the ionic solutions's dielectric, the default is EPS from $PCM. DISM = the ionic strength, in Molar units (mol/dm**3) The default is 0.0 ==========================================================

Input Description

$PCMITR

2-254

==========================================================

$PCMITR

group

(optional, for IEF=-3 or -10 in $PCM)

This group provides control over the iterative isotropic IEF-PCM calculation. See C.S.Pomelli, J.Tomasi, V.Barone Theoret.Chem.Acc. 105, 446-451(2001) H.Li, C.S.Pomelli, J.H.Jensen Theoret.Chem.Acc. 109, 71-84(2003) MXDIIS = Maximum size of the DIIS linear equations, the value impacts the amount of memory used by PCM. Memory=2*MXDIIS*NTS, where NTS is the number of tesserae. MXDIIS=0 means no DIIS, instead the point Jacobi iterative method will be used. (Default=50) Maximum number of iters in phase 1. (Default=50) Maximum number of iters in phase 2. (Default=50)

MXITR1 = MXITR2 =

note: if MXDIIS is larger than both MXITR1 and MXITR2 MXDIIS will be reset to be the larger of these two. THRES = Convergence threshold for the PCM Apparent Surface Charges (ASC). (Default=1.0D-08) Loose threshold used in the early SCF cycles when the density change is above DENSLS. If THRSLS < THRESH, this option is turned off. Default is 5.0D-04. If the density change is above DENSLS the loose threshold THRSLS applies. (Default = 0.01 au) 1, Directly compute the electronic potential at each tessera and the ASC potential at the electronic coordinates, with no disk storage. (Default) 0, Compute and save above data to hard disk.

THRSLS =

DENSLS = IDIRCT =

Keywords for region wise multipole expansion of ASCs in approximating interaction among tesserae:

Input Description

$PCMITR

2-255

(C.S.Pomelli, J.Tomasi THEOCHEM 537, 97-105(2001)) IMUL = = = = = RCUT1 = Region wise multipole expansion order in the approximate interaction among tesserae. 0, Neglected (Only for test purposes) 1, Monopole 2, Monopole+Dipole 3, Monopole+Dipole+Quadrupole (Default) Cutoff radius (Angstrom) for interactions among tesserae. If RCUT1 is larger than your option is effectively turned mid-range Default=15.0 A molecule, the off.

RCUT2

Cutoff radius (Angstrom) for long range interactions among tesserae. Default=30.0 A

The remaining keywords apply only to PCM calculations with a QM/EFP solute (see Li et al.) Keywords for region wise multipole expansion of ASCs in approximating interaction between ASCs and QM region: IMGASC = 1, Use region wise multipole expansion of ASCs to compute the ASC potential at QM region. 0, no use of the multipole expansion method. (default) Cutoff radius (Angstrom) for used of the IMGASC multipole expansion (Default=20.0 A)

RASC

Keywords for multipole expansion of the QM region in approximating the QM region potential: IMGABI = 0, multipole expansion of the QM region is turned off (default). 1, turn multipole expansion of the QM region on. Cutoff radius (Angstrom) for used of the IMGABI multipole expansion (Default=4.0 A)

RABI

Keywords for the coupling of PCM and EFP polarizability tensors: IEFPOL = 1, PCM ASCs induce EFP dipoles.(default)

Input Description

$PCMITR

2-256

0, PCM ASCs do not induce EFP dipoles. REFPOL = When IEFPOL=1, if the distance (Angstrom) between a polarizability point and a tessera is less than REFPOL, they are considered too close and the field from the tessera will not induce dipole for the polarizability point. Default=0.0 A means always induce the dipole.

==========================================================

Input Description

$DISBS

2-257

==========================================================

$DISBS

group

(optional)

This group defines auxiliary basis functions used to evaluate the dispersion free energy by the method of Amovilli and Mennucci. These functions are used only for the dispersion calculation, and thus have nothing to do with the normal basis given in $BASIS or $DATA. If the input group is omitted, only the normal basis is used for the IDP=1 dispersion energy. NADD XYZE = the number of added shells = an array giving the x,y,z coordinates (in bohr) of the center, and exponent of the added shell, for each of the NADD shells.

NKTYPE = an array giving the angular momenta of the shells An example placing 2s,2p,2d,1f on one particular atom, $DISBS NADD=7 NKTYP(1)= 0 0 1 1 XYZE(1)=2.9281086 0.0 2.9281086 0.0 2.9281086 0.0 2.9281086 0.0 2.9281086 0.0 2.9281086 0.0 2.9281086 0.0 2 2 3 .0001726 .0001726 .0001726 .0001726 .0001726 .0001726 .0001726 0.2 0.05 0.2 0.05 0.75 0.2 0.2 $END

==========================================================

Input Description

$DISREP

2-258

==========================================================

$DISREP

group

(optional)

This group controls evaluation of the dispersion and repulsion energies by the empirical method of Floris and Tomasi. The group must be given when IDISP=1 in $PCM, whenever the solvent is not water. Only one of the two options ICLAV or ILJ should be selected. Due to its lack of parameters, almost no one chooses ILJ. ICLAV = selects Claverie's disp-rep formalism. = 0 skip computation. = 1 Compute the solute-solvent disp-rep interaction as a sum over atom-atom interactions through a Buckingham-type formula (R^-6 for dispersion, exp for repulsion). (default) Ref: Pertsin-Kitaigorodsky "The atom-atom potential method", page 146. ILJ = selects a Lennard-Jones formalism. = 0 skip computation. (default) = 1 solute atom's-solvent molecule interaction is modeled by Lennard-Jones type potentials, R^-6 for dispersion, R^-12 for repulsion).

---- the following data must given for ICLAV=1: RHO N NT = solvent numeral density = number of atom types in the solvent molecule = an array of the number of atoms of each type in a solvent molecule RDIFF = distances between the first atoms of each type and the cavity DKT = array of parameters of the dis-rep potential for the solvent RWT = array of atomic radii for the solvent The defaults are appropriate for water, RHO=3.348D-02 N=2 NT(1)=2,1 RDIFF(1)=1.20,1.50 DKT(1)=1.0,1.36 RWT(1)=1.2,1.5

Input Description DKA

$DISREP

2-259

= array of parameters of the dis-rep potential for the solute. Defaults are provided for some common elements: H: 1.00 Be: 1.00 B: 1.00 C: 1.00 N: 1.10 O: 1.36 P: 2.10 S: 1.40 = array of atomic radii for the solute to compute dis-rep. Defaults are provided for some common elements: H: 1.20 Be: 1.72 B: 1.72 C: 1.72 N: 1.60 O: 1.50 P: 1.85 S: 1.80

RWA

Other elements have DKA and RWA values of 0.0 and so must be given in the input deck, or the dispersion/repulsion energy will be 0. For EFP/PCM calculations, only QM atoms need DKA and RWA values to calculate the DIS-REP energy. ---- the following data must given for ILJ=1: RHO EPSI = solvent numeral density = an array of energy constants referred to each atom of the solute molecule. SIGMA = an array of typical distances, relative to each solute atom ==========================================================

Input Description

$SVP

2-260

==========================================================

$SVP

group

(optional)

The presence of this group in the input turns on use of the Surface and Simulation of Volume Polarization for Electrostatics (SS(V)PE) solvation model, or the more exact Surface and Volume Polarization for electrostatics (SVPE) model. These model the solvent as a dielectric continuum, and are available with either an isodensity or spherical cavity, around the solute. A semi-empirical correction for short-range electrostatics may be chosen. The solute may be described only by RHF, UHF, ROHF, GVB, or MCSCF wavefunctions. The energy is reported as a free energy, which includes the factor of 1/2 that accounts for the work of solvent polarization assuming linear response. Gradients are not yet available. Typical use of either the SS(V)PE or the SVPE method will involve a prior step to do an equivalent calculation on the given solute in the gas phase. This provides a set of orbitals that can be used as a good initial guess for the subsequent run including solvent. It also provides the gas phase energy that can be subtracted from the energy in solvent to obtain the electrostatic contribution to the free energy of solvation. The solvation free energy is the difference in the "FINAL" energy found in the gas phase and solvated runs (not to be confused with the "reaction field energy" found on the solvated output). Many runs will be fine with all parameters set at their default values. The most important parameters a user may want to consider changing are: NVLPL = treatment of volume polarization 0 - SS(V)PE method, which simulates volume polarization by effectively folding in an additional surface polarization (default) N - SVPE method, which explicitly treats volume polarization with N extra layers

DIELST = static dielectric constant of solvent (default = 78.39, appropriate for water) IVERT = 0 do an equilibrium calculation (default)

Input Description

$SVP

2-261

1 do a nonequilibrium calculation to get the final state of a vertical excitation - this requires that IRDRF=1 to read the $SVPIRF input group that was punched with IPNRF=1 in a run on the initial state - note that a meaningful result is obtained only if the initial and final states both come from the same wavefunction/basis set/ geometry/solvation model. DIELOP = optical dielectric constant of solvent this only relevant if IVERT=1 (default 1.776, appropriate for water) EGAS = gas phase energy (optional): if given, the program will output the free energy of solvation and the change in solute internal energy due to solvation. note that a meaningful result is obtained only if EGAS comes from the same wavefunction/basis set/ geometry as is used in the solvation calculation = flag to turn on a semi-empirical correction for local electrostatic effects based on the electric field's normals to the surface cavity. This also adds cavitation/dispersion/solvent structure (CDS) effects drawn from the SMD model, see SMD in $PCM. (Default=.FALSE.)

SMVLE

ISHAPE = sets the shape of the cavity surface 0 - electronic isodensity surface (default) 1 - spherical surface RHOISO = value of the electronic isodensity contour used to specify the cavity surface, in electrons/bohr**3 (relevant if ISHAPE=0; default=0.001) RADSPH = sphere radius used to specify the cavity surface. A positive value means it is given in Bohr, negative means Angstroms. (relevant if ISHAPE=1; default is half the distance between the outermost atoms plus 1.4 Angstroms) INTCAV = selects the surface integration method 0 - single center Lebedev integration (default) 1 - single center spherical polar integration, not recommended; Lebedev is far more efficient

Input Description

$SVP

2-262

NPTLEB = number of Lebedev-type points used for single center surface integration. The default value has been found adequate to obtain the energy to within 0.1 kcal/mol for solutes the size of monosubstituted benzenes. (relevant if INTCAV=0) Valid choices are 6, 14, 26, 38, 50, 86, 110, 146, 170, 194, 302, 350, 434, 590, 770, 974, 1202, 1454, 1730, 2030, 2354, 2702, 3074, 3470, 3890, 4334, 4802, 5294, or 5810. (default=1202) NPTTHE, NPTPHI = number of (theta,phi) points used for single center surface integration. These should be multiples of 2 and 4, respectively, to provide symmetry sufficient for all Abelian point groups. (relevant if INTCAV=1; defaults = 8,16; these defaults are probably too small for all but the tiniest and simplest of solutes.) TOLCHG = a convergence criterion on the program variable named CHGDIF, which is the maximum change in any surface charge from its value in the previous iteration (default=1.0D-7). This is checked in each SCF iteration, although the actual value is not printed until final convergence is reached. The single-center surface integration approach may fail for certain highly nonspherical molecular surfaces. The program will automatically check for this and bomb out with a warning message if need be. The single-center approach succeeds only for what is called a star surface, meaning that an observer sitting at the center has an unobstructed view of the entire surface. Said another way, for a star surface any ray emanating out from the center will pass through the surface only once. Some cases of failure may be fixed by simply moving to a new center with the ITRNGR parameter described below. But some surfaces are inherently nonstar surfaces and cannot be treated with this program until more sophisticated surface integration approaches are implemented. ITRNGR = translation of cavity surface integration grid 0 - no translation (i.e., center the grid at the origin of the atomic coordinates) 1 - translate to center of nuclear mass

Input Description 2 - translate to 3 - translate to 4 - translate to non-Hydrogen 5 - translate to in Bohr 6 - translate to in Angstroms

$SVP

2-263

center of nucl. charge (default) midpoint of outermost atoms midpoint of outermost atoms user-specified coordinates, user-specified coordinates,

TRANX, TRANY, TRANZ = x,y,z coordinates of translated cavity center, relevant if ITRNGR=5 or 6. (default = 0,0,0) IROTGR = rotation of cavity surface integration grid 0 - no rotation 1 - rotate initial xyz axes of integration grid to coincide with principal moments of nuclear inertia (relevant if ITRNGR=1) 2 - rotate initial xyz axes of integration grid to coincide with principal moments of nuclear charge (relevant if ITRNGR=2; default) 3 - rotate initial xyz axes of integration grid through user-specified Euler angles as defined by Wilson, Decius, Cross ROTTHE, ROTPHI, ROTCHI = Euler angles (theta, phi, chi) in degrees for rotation of the cavity surface integration grid, relevant if IROTGR=3. (default=0,0,0) IOPPRD = choice of the system operator form. The default symmetric form is usually the most efficient, but when the number of surface points N is big it can require very large memory (to hold two N by N matrices). The nonsymmetric form requires solution of two consecutive system equations, and so is usually slower, but as trade-off requires less memory (to hold just one N by N matrix). The two forms will lead to slightly different numerical results, although tests documented in the third reference given in Further Information show that the differences are generally less than the inherent discretization error itself and so are not meaningful. 0 - symmetric form (default)

Input Description

$SVP

2-264

1 - nonsymmetric form The remaining parameters below are rather specialized and rarely of concern. They should be changed from their default values only for good reason by a knowledgeable user. TOLCAV = convergence criterion on maximum deviation of calculated vs. requested RHOISO (relevant if ISHAPE=0; default=1.0D-10) ITRCAV = maximum number of iterations to allow before giving up in search for isodensity surface. (relevant if ISHAPE=0; default=99) NDRCAV = highest analytic density derivative to use in the search for isodensity surface. 0 - none, use finite differences (default) 1 - use analytic first derivatives LINEQ = selects the solvers of linear equatio solver equations that determine the effective point charges on the cavity surface. 0 - use LU decomposition in memory if space permits, else switch to LINEQ=2 1 - use conjugate gradient iterations in memory if space permits, else use LINEQ=2 (default) 2 - use conjugate gradient iterations with the system matrix stored externally on disk.

CVGLIN = convergence criterion for solving linear equations by the conjugate gradient iterative method (relevant if LINEQ=1 or 2; default = 1.0D-7) CSDIAG = a factor to multiply diagonal elements to improve the surface potential matrix, S. (default = 1.104, optimal for Lebedev integration) IRDRF = a flag to read in a set of point charges as an initial guess to the reaction field. 0 - no initial guess reaction field (default) 1 - read point charges from $SVPIRF input group. It is up to the user to be sure that the number of charges read is appropriate.

Input Description

$SVP

2-265

IPNRF

= a flag to punch the final reaction field. 0 - no punch (default) 1 - punch in format of $SVPIRF input group

==========================================================

Input Description

$SVPIRF

2-266

==========================================================

$SVPIRF

group

(optional; relevant for SVP runs)

Formatted card images of reaction field point charges, as punched by setting IPNRF=1 in a previous SVP run. These can be used by setting IRDRF=1 in a subsequent SVP run to provide an initial guess to the reaction field. These charges from the initial state are required if IVERT=1 in $SVP to do a vertical excitation calculation on the final state. ==========================================================

Input Description

$COSGMS

2-267

==========================================================

$COSGMS

group

(optional)

The presence of this group in the input turns on the use of the conductor-like screening model (COSMO) with molecular shaped cavity for closed and open shell HF, DFT, and MP2. Open shells may be high spin-restricted or any sort of spin-unrestricted case. The energy and/or the gradient can be computed for each of these. The implementation of the COSMO cavity has a limit of about 150-200 atoms. Like other limits in GAMESS, this can be raised according to directions in the Programmer's Reference. EPSI = the dielectric constant, 80 is often used for H2O This parameter must be given, except for the perfect conductor approximation (see PRFCND).

PRFCND = perfect conductor approximation, sets EPSI equal to infinity. Relevant only if EPSI is not given. (default=.FALSE.) COSRAD = the multiplicative factor for the van der Waals radii used for cavity construction. (default=1.2) NSPA DISEX OUTCHG = the number of surface points on each atomic sphere that form the cavity. (default=92) = parameter for the refinement of crevices (default=10.0D+00) select the method for the correction of the outlying charge error (OCE). = DMULTI sets the multipole expansion method. = DBLCAV sets the double cavity method (default).

COSWRT = flag to generate the .cosmo output file, used as input to the COSMO-RS program, from the company COSMOlogic. A replacement output source file is needed (full version of cosprt.src). Users need to sign a special license agreement to enable this option, see http://ocikbws.uzh.ch/gamess COSWRT forces PRFCND=.T. and requires GBASIS=KTZVP

Input Description

$COSGMS

2-268

and DFTTYP=BP86, because COSMO-RS is parametrized for use only with this specific setup. (default=.FALSE.) DCOSMO = flag to use the DCOSMO-RS method. This requires reading in a supplementary .pot file, obtained by processing COSWRT's .cosmo output with the COSMO-RS software. (default is .FALSE.) COSBUG = flag to turn on debugging printout. Additional information on the COSMO model can be found in the References chapter of this manual. ==========================================================

Input Description

$SCRF

2-269

==========================================================

$SCRF

group

(optional)

The presence of this group in the input turns on the use of the Kirkwood-Onsager spherical cavity model for the study of solvent effects. The method is implemented for RHF, UHF, ROHF, GVB and MCSCF wavefunctions and gradients, and so can be used with any RUNTYP involving the gradient. The method is not implemented for MP2, CI, any of the semiempirical models, or for analytic hessians. DIELEC = the dielectric constant, 80 is often used for H2O RADIUS = the spherical cavity radius, in Angstroms G = the proportionality constant relating the solute molecule's dipole to the strength of the reaction field. Since G can be calculated from DIELEC and RADIUS, do not give G if they were given.

========================================================== Additional information on the SCRF model can be found in the Further Information chapter.

Input Description

$ECP

2-270

==========================================================

$ECP

group

(required if PP=READ in $CONTRL)

This group lets you read in effective core potentials, for some or all of the atoms in the molecule. You can use built in potentials for some of the atoms if you like. This is a free format (positional) input group. Since the input is a little tricky, it is good to look at the two examples at the end of this group. *** Give a card set -1-, -2-, and -3- for each atom *** -card 1PNAME, PTYPE, IZCORE, LMAX+1

PNAME is a 8 character descriptive tag for this potential. If PNAME is repeated later, for the same type of element, the previously defined potential is copied to this atom. No other information should be given on this card, and cards -2- and -3- must be skipped. Do not use this "copy" option when there is no core potential, instead type "NONE" over and over again. PTYPE = GEN = SBKJC a general potential should be read. look up the Stevens/Basch/Krauss/Jasien/ Cundari potential for this type of atom. = HW look up the Hay/Wadt built in potential for this type of atom. = NONE treat all electrons on this atom. IZCORE is the number of core electrons to be removed. Obviously IZCORE must be an even number, or in other words, all core orbitals being removed must be completely occupied. LMAX is the maximum angular momentum occupied in the core orbitals being removed (usually). Give IZCORE and LMAX only if PTYPE is GEN. *** For the first occurence of PNAME, if PTYPE is GEN, *** *** then give cards -2- and -3-. Otherwise go to -1-. *** *** Card sets -2- and -3- are repeated LMAX+1 times The potential U(LMAX+1) is given first, followed by U(L)-U(LMAX+1), for L=1,LMAX. ***

Input Description

$ECP

2-271

-card 2-

NGPOT

NGPOT is the number of Gaussians in this part of the local effective potential. -card 3CLP,NLP,ZLP (repeat this card NGPOT times)

CLP is the coefficient of this Gaussian in the potential. NLP is the power of r for this Gaussian, 0 <= NLP <= 2. ZLP is the exponent of this Gaussian. Note that PTYPE lets you to type in one or more atoms explicitly, while using built in data for other atoms. By far the easiest way to use the SBKJC potential for all atoms in the formic acid molecule is to request PP=SBKJC in $CONTRL. But here we show two alternatives. Note that both examples copy one oxygen potential to the other, and both explicitly declare there is no potential on every hydrogen. Assume that the atoms in $DATA are generated in the order C, H, O, O, H. The first way is to look up the program's internally stored SBKJC potentials one atom at a time: $ECP C-ECP H-ECP O-ECP O-ECP H-ECP $END SBKJC NONE SBKJC NONE core electrons atoms must must be given atoms.

The second oxygen duplicates the first, no are removed on hydrogen. The order of the follow that generated by $DATA. All atoms here in $ECP, not just the symmetry unique

The second example reads all SBKJC potentials explicitly: $ECP C-ECP GEN 2 1

Input Description 1

$ECP

2-272

----- CARBON U(P) -----0.89371 1 8.56468 2 ----- CARBON U(S)-U(P) ----1.92926 0 2.81497 14.88199 2 8.11296 H-ECP NONE O-ECP GEN 2 1 1 ----- OXYGEN U(P) -----0.92550 1 16.11718 2 ----- OXYGEN U(S)-U(P) ----1.96069 0 5.05348 29.13442 2 15.95333 O-ECP H-ECP NONE $END Again, the 2nd oxygen copies from the first. It is handy to use the rest of card -2- as a descriptive comment. As a final example, for antimony we have LMAX+1=3 (there are core d's). One must first enter U(f), followed by U(s)-U(f), U(p)-U(f), U(d)-U(f). ==========================================================

Input Description

$MCP

2-273

==========================================================

$MCP

group (required if MCP READ was given on card -6U-)

This group lets you read in model core potentials, for some or all of the atoms in the molecule. This is a fixed format input group. For the review of the MCP method, see M.Klobukowski, S.Huzinaga, and Y.Sakai, pp. 49-74 in J. Leszczynski, "Computational Chemistry", vol. 3 (1999) . *** Give input -1-, -2-, ..., -9- for each MCP atom *** -card 1ANAT ANAT is a 8 character name for the MCP atom. It must match the name given for that atom in the $DATA group.

-card 2- NOAN, (NO(IS),NG(IS), IS=1,4) FORMAT(9I3) IS = 1, 2, 3, 4 for s, p, d, and f symmetry, resp. NOAN is the number of terms in the MCP NO(IS) is the number of core orbitals in symmetry IS NG(IS) is the number of basis functions used to expand the core orbitals in symmetry IS -card 3ZEFF ZEFF, MCPFMT FORMAT(F10.2, A8)

is the number of valence electrons, e.g. 7.0 for Fluorine MCPFMT is the format for reading floating-point numbers in the MCP data -card 4(ACOEF(L), L=1,NOAN) FORMAT(MCPFMT)

ACOEF(L) is the L-th coefficient in the expansion of the model core potential; more than one line may be provided ACOEF(L) is the defined as A(l) in Eq. (38) of the MCP review paper. -card 5(AEXPN(L), L=1,NOAN) FORMAT(MCPFMT)

AEXPN(L) is the L-th exponent in the expansion of the model core potential; more than one line may be provided

Input Description

$MCP

2-274

AEXPN(L) is the defined as alpha(l) in Eq. (38) of the MCP review paper. -card 6(NINT(L), L=1,NOAN) FORMAT(10I3)

NINT(L)

is the power of R in the expansion of the model core potential; NINT(L) is defined as n(l) in Eq. (38) of the MCP review paper.

*** For each symmetry IS present in the core orbitals *** *** read the card set -7-, -8-, and -9*** -card 7(BPAR(K), K=1,NO(IS)) FORMAT(MCPFMT) BPAR(K) is the constant in the core projector operator, B(k) in Eq. (41) of the review. -card 8(EX(I), I=1,NG(IS)) FORMAT(MCPFMT) EX(I) is the exponent of the I-th Gaussian function used to expand the core orbitals *** Repeat -9- for each core orbital in symmetry IS *** -card 9C(I) (C(I), I=1,NG(IS)) FORMAT(MCPFMT) expansion coefficients of the core orbital

The following example input file is for H2CO, and by the way, provides another example of COORD=HINT. ! $CONTRL RUNTYP=ENERGY $DATA Formaldehyde H2CO CNV 2 C 6.0 LC 0.00 MCP READ L 3 1 18.517235 2 2.5787547 3 0.58994362 L 1 1 0.17330638 L 1 1 0.60957120E-01 D 1; 1 0.600 1.0 COORD=HINT PP=MCP $END

0.0 0.0 - O K <<<< this is an MCP atom <<<< (311/311/1) basis -0.16370140 0.22673090E-01 -0.26304451 0.19109693 0.58040872 0.50918856 1.0000000 1.0000000 1.0000000 1.0000000

Input Description

$MCP

2-275

8.0 LC 1.2031 MCP READ L 3 1 44.242510 2 6.2272700 3 1.4361751 L 1 1 0.40211473 L 1 1 0.12688798 D 1; 1 1.154 1.0 H 1.0 TZV P 1; 1 $END PCC 1.100 1.1012 1.0

0.0 0.0 - O K <<<< this is an MCP atom <<<< (311/311/1) basis -0.13535836 0.17372951E-01 -0.30476423 0.16466813 0.43955753 0.46721611 1.0000000 1.0000000 1.0000000 1.0000000

121.875 0.0 + O K I <<<< not an MCP atom, TZV+pol basis

<<<< start of the MCP data <<<< empty lines allowed MCP for C NR (2S/2P) S(2)P(2) <<<< comment <<<< empty lines allowed C <<<< MCP for the atom C 2 1 14 <<<< NOAN, NO(1), NG(1) 4.00(4D15.8) <<<< ZEFF, MCPFMT .41856306 .99599513E-01 <<<< ACOEF 16.910482 7.4125554 <<<< AEXPN 0 0 <<<< NINT 22.676882 <<<< B(1s) 26848.283 8199.1206 2798.3668 1048.2982 423.36984 181.26843 81.068295 37.403931 17.629539 8.4254263 4.0611964 1.9672294 .95541420 .46459041 .10743274D-03 .21285491D-03 .99343100D-03 .28327774D-02 .83154481D-02 .21694082D-01 .52916004D-01 .11618593D+00 .21812785D+00 .32180986D+00 .29375407D+00 .10974353D+00 .70844050D-02 .17825971D-02 MCP for O 2 O NR (2S/2P) S(2)P(4) <<<< MCP for the atom O

$MCP

1 16 6.00(4D15.8) .31002267 .27178756E-01

Input Description 25.973731 0 0 41.361784 57480.749 829.06758 31.542773 1.6077662 .85822477D-04 .76877460D-02 .22782741D+00 .55937988D-02 $END 13.843290

$MCP

2-276

17270.167 346.04791 14.815300 .77153240 .18173691D-03 .20823429D-01 .33492260D+00 .16121923D-02

5766.9282 151.12147 7.0298236 .37052330 .84803428D-03 .52424753D-01 .28833079D+00 .10915544D-04

2107.0076 68.233250 3.3561489 .17799002 .25439914D-02 .11864010D+00 .93046197D-01 .21431633D-03

==========================================================

Input Description

$RELWFN

2-277

==========================================================

$RELWFN

group

(optional)

This group is relevant if RELWFN in $CONTRL chose one of the relativistic transformations (DK, RESC, or NESC) for elimination of the small components of relativistic wavefunctions, to produce a corrected single component wavefunction. For DK or RESC, only one electron integral corrections are added, whereas for NESC, corrections to two electron integrals are accounted for by means of a relativistically averaged basis set. All relativistic methods in GAMESS neglect two-electron corrections coming from pVp integrals. The 3rd order DK transformation will normally afford the most sound results, from a theoretical point of view. Analytic gradients are programmed for both RESC and NESC computations. For DK, all non-relativistic gradient terms are analytic, while the relativistic contributions are evaluated numerically by a double difference formula. During geometry optimizations, in rare cases, the number of nearly linearly independent functions in the Resolution of the Identity (RI) used to evaluate the most difficult integrals may change at some new geometry. If so, the job will quit with an error message, and the user must restart it again manually. For IOTC, DK, or RESC, ordinary basis sets are used. This however is a misleading statement, for while any basis set will run, accurate answers may be hard to obtain without the use of basis sets constructed using the relativistic approximations. Certainly at least the contraction coefficients must be modified to account for effects such as the s orbital size contraction under relativity, but the reoptimization of exponents may also be important. Experience suggests that large uncontracted basis sets using non-relativistic exponents are probably OK, but standard contractions from NR atomic calculations can lead to spurious results. As a rule of thumb, elements H-Xe might perhaps be OK, but for heavier elements, use relativistically derived basis sets.

Input Description

$RELWFN

2-278

There are two possible basis set choices for IOTC, DK, or RESC calculations. The Sapporo relativistic segmented contractions are available for elements down to Xenon (see GBASIS=SPKrnZP or SPKrAnZP). DK3 basis sets for H-Lr obtained at U. of Tokyo exist in the form of general contractions, http://www.riken.jp/qcl/ publications/dk3bs/periodic_table.html which gives the EPAPS data published by T.Tsuchiya, M.Abe, T.Nakajima, K.Hirao J.Chem.Phys. 115,4463-4472(2001) A program to extract this web page into GAMESS's format is provided with GAMESS, see file ~/gamess/tools/dk3.f. Light to medium atom main group (H-Kr) DK2 bases exist, look for the names cc-pVnZ_DK on http://www.emsl.pnl.gov:2080/forms/basisform.html For NESC, you must provide three basis sets, for the large and small components and an averaged one, which are given in $DATAL, $DATAS, $DATA, respectively. The only possible choice for these basis sets is due to Dyall, and these are available from http://www.emsl.pnl.gov:2080/forms/basisform.html Their names are similar to cc-pVnZ(pt/sf/lc), pt=point or fi=finite nucleus, sf for spin-free and the final field is lc=large component ($DATAL), sc=small component ($DATAS), and wf is a typo for Foldy-Wouthuysen 2e- basis ($DATA). In GAMESS you can only use point nucleus approximation. The need to input three basis sets means that you cannot use a $BASIS group, and you must use COORD=UNIQUE style input in the various $DATA's. The three $DATA groups must contain identical information except for the primitive expansion coefficients, as the three basis sets must have the same exponents. In case the option to treat only some atoms relativistically is chosen, all non-relativistic atoms must have identical basis input in all three groups. The finite size of nuclei is not taken into account, so do not use any basis set obtained including this effect. For NESC, the one electron part of the spin-orbit operator can be corrected, while for RESC, one can compute spin-orbit coupling with relativistic corrections to both one and two electron SOC integrals, unless internal uncontraction is requested (in this case only 1 electron

Input Description

$RELWFN

2-279

SOC integrals are modified). It should be noted that internally uncontracted basis sets containing very large exponents have large SOC integrals, thus the average asymmetry due to RESC appears larger (before contraction). For any order DK, the 1e- SOC integrals are corrected only to first order (DK1). It has been observed by many people that even the first order correction is small, and thus it should be sufficient. The IOTC treatment of scalar relativity has not yet been adapted to perform DK1 spinorbit corrections. Please use 3rd order DK if you use NESOC=1. * * * the next parameter applies only to RELWFN=DK: NORDER gives the order of the DK transformation to be applied to the one-electron potential: 1 corresponds to the free particle 2 is the most commonly implemented DK method. It has all relativistic corrections to second order. (default) 3 represents 3rd order DK transformation. It does not include all 3rd order relativity corrections, in the sense of collecting all terms in the same order of c (speed of light), due to using only a 2nd order form of the Coulomb potential (1/rij). However, DK3 gives the closest approximation to the Dirac-Coulomb equation of all methods here. MODEQR is the mode of quasi-relativistic calculation. These options pertain to the DK or RESC methods. The default is 1 (or 3 if ISPHER=1 in $CONTRL). These are additive (bitwise) options, meaning you must enter 5 to request options 1+4: = 0 use the input contracted atomic basis set for the Resolution of the Identity (RI) used to simplify the pVp relativistic integrals in order to evaluate them in closed form. Use of this option will reproduce RESC results prior to June 2001. As the accuracy of the RI is compromised, this option is not recommended. = 1 use the Gaussian primitives constituting the input contracted atomic basis set to define the

Input Description

$RELWFN

2-280

RI. This produces a considerable increase in accuracy of the integrals. = 2 HONDO's implementation of the RI for RESC is mimicked, namely for ISPHER=+1, the space used for the RI will have no spherical contaminants, similar to the MO space. This option is not available for RESC gradients. = 4 avoid redundant exponents when splitting L shells into s and p, when generating the internally uncontracted basis set. This is necessary if you are using s or p primitives with the same exponents as in some L shell. This is unlikely to occur, but if so, the L shell must be entered before the s or p. Option 4 requires 1. = 8 use 128 bit precision in the RIs. Select this option if your exponent range is larger than 64 bits can handle (for example, if your basis set's s primitive's exponents run from 1e+14 to 1e-2, 16 orders, exhausting the 14-16 decimal places that 64 bits supports on most machines). Note that setting this option also reduces numerical noise in the gradient. This option can be used with or without the internal uncontraction. 1. 128 bit math can be very slow, depending on your CPU and/or compiler's support for it. Only relativistic 1e- integrals use 128 bits. 2. If your FORTRAN library does not support the REAL*16 data type (128 bits), the code compiles itself in 64 bit mode, and will halt if you ask for 128 bits. NESOC = Douglas-Kroll style 1st order relativistic corrections for SOC integrals. Relevant only if OPERAT=HSO1, HSO2P, or HSO2, for RUNTYP=TRANSITN. = 0 no corrections (default for no relativity) = 1 apply correction to one-electron spin-orbit integrals (default if RESC, NESC, or DK scalar relativity options are chosen). This is not yet implemented for RELWFN=IOTC.

NRATOM the number of different elements to be treated nonrelativistically. For example, in Pb3O4, to

Input Description

$RELWFN

2-281

treat only lead relativistically, enter NRATOM=1. The elements to be treated nonrelativistically are defined by CHARGE. (default=0) For NESC, this parameter affects the choice of the basis sets, you should use identical large, small, and averaged basis set for such atoms. For DK or RESC, MODEQR=1 won't uncontract to the primitives of such atoms. CHARGE is an array containing nuclear charges of the atoms to be treated nonrelativistically. (e.g. CHARGE(1)=8.0, to drop all oxygen atoms) CLIGHT gives the speed of light (atomic units), introduced as a parameter in order to reproduce exactly results published with a slightly different choice. Default: 137.0359895 * * * the next parameters are used only with DK or RESC: QMTTOL same as in $CONTRL, but used for the preparation of the RI space. It is sensible to use a value smaller than $CONTRL, if desired. (default: from $CONTRL). QRTOL parameter for relativistic gradients. RESC: tolerance for equating nearly degenerate eigenvalues of the kinetic energy and overlaps, when evaluating the gradient. Values that are too large (>1e-6) can cause numerical errors in the gradient, approximately on the same order as QRTOL. Too small values can add very large values to the gradient due to division by numbers that are zero within machine precision that are not avoided with this tolerance filter. The recommended values for MODEQR=1 are 1e-6 for gold to 1e-7 for silver. For MODEQR=0, 1d-8 or smaller can be used. (default = smaller of 1d-8 or QMTTOL). DK: Coordinate offset in bohr for the numerical differentiation of the relativistic contributions to the gradient (analagous to VIBSIZ in $HESS, but applied to gradients). Note that the offset is applied to linear combinations of Cartesian

Input Description

$RELWFN

2-282

coordinates that conserve symmetry, and have the translations and rotations projected out; the change in Cartesian coordinates is equal to the offset times the expansion coefficient. Default: 1e-2. NVIB The number of offsets per coordinate (similar to NVIB in $FORCE). NVIB can be 1 or 2 (or -1 or -2). This parameter applies only to DK gradients. Positive values correspond to the projected mode, in which translations, rotations, and any modes which are not totally symmetric are projected out. Negative values correspond to using Cartesian coordinates. In most cases projected modes are superior; however they can cause slight distortions away from the true symmetry -IF- you specify lower symmetry than the molecule actually possesses. (default=2)

==========================================================

Input Description

$EFIELD

2-283

==========================================================

$EFIELD
This external general, energies EVEC

group

(not required)

group permits the study of the influence of an electric field on the molecule. The method is and so works for all wavefunctions, and for both and nuclear gradients. = an array of the three x,y,z components of the applied electric field, in a.u., where 1 Hartree/e*bohr = 5.1422082(15)D+11 V/m A typical size for the EVEC components is therefore about 0.001 a.u. = a flag to specify when the field breaks the the molecular symmetry. Since most fields break symmetry, the default is .FALSE.

SYM

========================================================== Restrictions: analytic hessians are not available, but numerical hessians are. Because an external field causes a molecule with a dipole to experience a torque, geometry optimizations must be done in Cartesian coordinates only. Internal coordinates eliminate the rotational degrees of freedom, which are no longer free. A nuclear hessian calculation will have two rotational modes with non-zero "frequency", caused by the torque. A gas phase molecule will rotate so that the dipole moment is anti-parallel to the applied field. To carry out this rotation during geometry optimization will take many steps, and you can help save much time by inputting a field opposite the molecular dipole. There is also a stationary point at higher energy with the dipole parallel to the field, which will have two imaginary frequencies in the hessian. These will appear as the first two modes in a hessian run, but will not have the i for imaginary included on the printout since they are rotational modes. sign conventions: Dipole vectors are considered to point from the negative end of the molecule to the positive end. Thus HCl at the MP2/aug-cc-pVDZ level's geometry of R=1.2831714 has a positive dipole, if we place Cl at the origin and H along

Input Description

$EFIELD

2-284

the positive z-axis. The sign convention on applied fields is such that a +1 charge particle feels a force in the positive direction under a positive field, namely, as if there was a negative plate at large +Z and a positive plate at large -Z. Hence positive fields enhance HCl's dipole: EVEC(z) E(MP2) mu(MP2) -0.001 -460.2567905970 1.112875 -0.0001 -460.2571917846 1.153172 0.0 -460.2572372416 1.157646 +0.0001 -460.2572828745 1.162119 +0.001 -460.2577014871 1.202350 and the higher energy for each negative EVEC means HCl would prefer to turn around in the field. Thus, one use for this group is calculation of the electric dipole by finite differencomg, for wavefunctions that cannot yield molecular properties due to not having a relaxed density matrix. Perform two RUNTYP=ENERGY jobs per component, with fields 0.001 and -0.001 a.u. The central difference formula for each component of the dipole is mu = 2.541766*(E(+0.001)-E(-0.001)/0.002, in Debye. The differentiation using data from HCl gives 1.157635. For an application to molecular ionization in intense fields generated by lasers, see H.Kono, S.Koseki, M.Shiota, Y.Fujimura J.Phys.Chem.A 105, 5627-5636(2001) ==========================================================

Input Description

$INTGRL

2-285

==========================================================

$INTGRL

group

(optional)

This group controls AO integral formats. Probably the only values that should ever be selected are QFMM or NINTIC, as the program picks sensible values otherwise. QFMM = a flag to use the quantum fast multipole method for linear scaling Fock matrix builds. This is available for RHF, UHF, and ROHF wavefunctions, and for DFT, but not with any other correlation treatment. You must select DIRSCF=.TRUE. in $SCF if you use this option. The RHF and closed shell DFT gradients also uses QFMM techniques. The Optimal Parameter FMM code will run at a comparable speed to a ordinary run doing all integrals for molecules about 15 Angstroms in size, and should run faster for 20 Angstroms or more. See also the $FMM group. (default=.FALSE.)

SCHWRZ = a flag to activate use of the Schwarz inequality to predetermine small integrals. There is no loss of accuracy when choosing this option, and there are appreciable time savings for bigger molecules. Default=.TRUE. for over 5 atoms, or for direct SCF, and is .FALSE. otherwise. NINTMX = Maximum no. of integrals in a record block. (default=15000 for J or P file, =10000 for PK) NINTIC = Controls storage of integrals in memory, with any remaining integrals will be stored on disk. Caution: memory set aside for this parameter is unavailable to the quantum chemistry methods. Positive NINTIC indicate the number of integrals, negative the amount of memory used for integrals and labels (in words). At present NINTIC works robustly for RHF, ROHF, or UHF, is thought to work for GVB or MCSCF and mostly works for sequential MP2 as well. Direct SCF does not use this option! (default=0).

Input Description

$INTGRL

2-286

Various antiquated or antediluvian parameters follow: NOPK = 0 PK integral option on, which is permissible for RHF, UHF, ROHF, GVB energy/gradient runs. = 1 PK option off (default for all jobs). Must be off for anything with a transformation.

NORDER = 0 (default) = 1 Sort integrals into canonical order. There is little point in selecting this option, as no part of GAMESS requires ordered integrals. See also NSQUAR through NOMEM. NSQUAR = 0 Sorted integrals will be in triangular canonical order (default) = 1 instead sort to square canonical order. NDAR = Number of direct access logical records to be used for the integral sort (default=2000) LDAR = Length of direct access records (site dependent) NBOXMX = 200 Maximum number of bins. NWORD = 0 Memory to be used (default=all of it). NOMEM = 0 If non-zero, force external sort. The following parameters control integral restarts. IST=JST=KST=LST=1 NREC=1 INTLOC=1 Values shown are defaults, and mean not restarting. ==========================================================

Input Description

$FMM

2-287

==========================================================

$FMM

group

(relevant if QFMM selected in $INTGRL)

This group controls the quantum fast multipole method evaluation of Fock matrices. The defaults are reasonable, so there is little need to give this input. ITGERR = Target error in final energy, to 10**-(ITGERR) Hartree. The accuracy is usually better than the setting of ITGERR, in fact QFMM runs should suffer no loss of accuracy or be more accurate than a conventional integral run (default=7). QOPS = a flag to use the Quantum Optimum Parameter Searching technique, which finds an optimum FMM parameter set. (Default=.TRUE.)

If QOPS=.FALSE., the ITGERR value is not used. In this case the user should specify the following parameters: NP NS IWS IDPGD IEPS = the highest multipole order for FMM (Default=15). = the highest subdivision level (Default=2). = the minimum well-separateness (Default=2). = point charge approximation error (10**(-IDPGD)) of the Gaussian products (Default=9). = very fast multipole method (vFMM) error, (10**(-IEPS)) (Default=9)

==========================================================

Input Description

$TRANS

2-288

==========================================================

$TRANS

group

(optional for -CI- or -MCSCF-) (relevant to analytic hessians) (relevant to energy localization)

This group controls the integral tranformation. MP2 integral transformations are controlled instead by the $MP2 input group. There is little reason to give any but the first variable. DIRTRF = a flag to recompute AO integrals rather than storing them on disk. The default is .FALSE. for MCSCF and CI runs. If your job reads $SCF, and you select DIRSCF=.TRUE. in that group, a direct transformation will be done, no matter how DIRTRF is set. Note that the transformation may do many passes over the AO integrals for large basis sets, and thus the direct recomputation of AO integrals can be very time consuming. CUTTRF = Threshold for keeping transformed two electron integrals. (default= 1.0d-9, except FMO=1.0d-12) IPURFY = orbital purification, like PURIFY in $GUESS. = 0 skip orbital purification before transform. = 1 perform purification once per geometry, for example, in the first iteration of MCSCF only. = 2 purify during every MCSCF iteration. The default is 0. Use of 2 causes example 9 to take one more iteration to converge, due to the small upsetting of the orbitals between each iteration by this purification. This option is useful if PURIFY in $GUESS at the initial geometry is insufficient purification. NOSYM = disables the orbital symmetry test completely. This is not recommended, as loss of orbital symmetry is likely to mean a calculation is turning into garbage. It has the same meaning as the keyword in $CONTRL, but pertains to just the integral transform. (Default is 0)

Input Description

$TRANS

2-289

The remaining keywords refer almost entirely to the serial integral transformation codes, not the distributed memory routines: MPTRAN = method to use for the integral transformation. the default is try 0, then 1, then 2. 0 means use the incore method 1 means use the segmented method. 2 means use the alternate method, which uses less memory than 2, but much more disk. NWORD = Number of words of fast memory to allow. uses all available memory. (default=0) Zero

AOINTS = AO integral storage during parallel runs. It pertains only to CPHF=MO analytic Hessians. DUP stores duplicated AO lists on each node. DIST distributes the AO integral file across all nodes. =========================================================

Input Description

$FMO

2-290

==========================================================

$FMO

group

(optional, activates FMO option)

The presence of this group activates the Fragment Molecular Orbital option, which divides large molecules (think proteins or clusters) into smaller regions for faster computation. The small pieces are termed 'monomers' no matter how many atoms they contain. Calculations within monomers, then 'dimer' pairs, and optionally 'trimer' sets act so as to approximate the wavefunction of the full system. The quantum model may be SCF, DFT, MP2, CC, MCSCF, TDDFT, or CI. Sample inputs, and auxiliary programs, and other information may be found in the GAMESS source distribution in the directory ~/gamess/tools/fmo. NBODY = n-body FMO expansion: 0 only run initial monomer guess (maybe remotely useful to create the restart file, or as an alternative to EXETYP=CHECK). 1 run up to monomer SCF 2 run up to dimers (FMO2, the default) 3 run up to trimers (FMO3) = switch to turn on EFMO 0 = use FMO 1 = use EFMO = switch to freeze the electronic state of some fragments. FMO/FD and FMO/FDD require RUNTYP=OPTIMIZE and two layers in FMO. 0 = regular FMO 1 = FMO/FD (frozen domain) 3 = FMO/FDD (frozen domain and dimers) I. The following parameters define layers. NLAYER = the number of layers (default: 1) MPLEVL = an array specifying n in MPn PT for each layer, n=0 or 2. (default: all 0s).

IEFMO

MODFD

Input Description

$FMO

2-291

Note that MCQDPT is not available and therefore one may not choose this for MCSCF. DFTTYP = an array specifying the DFT functional type for each layer. (default: DFTTYP in $DFT). See $DFT for possible functionals. Only gridbased DFT is supported (all functionals). SCFTYP = an array specifying SCF type for each layer. At present the only valid choices are RHF, ROHF, and MCSCF (default: SCFTYP in $CONTRL for all). CCTYP = an array specifying CC type for each layer, which may be only the following choices from $CONTRL: LCCD, CCD, CCSD, CCSD(T), CCSD(T), CCSD(TQ), CR-CCL, or non-size extensive R-CC or CR-CC. Since FMO's CC methods involve adding corrections from pairs of monomers together, it is better to choose a size extensive method. = an array specifying TDDFT type for each layer, of the same kind as TDDFT in $CONTRL. Default: TDDFT in $CONTRL for all layers. = an array specifying CI type for each layer, see CITYP in $CONTRL. At present, only CIS may be used (FMO1-CIS energy only, i.e., nbody=1). Default: CITYP from $CONTRL, for all layers. II. Parameters defining FMO fragments: NFRAG LAYER = the number of FMO fragments (default: 1) = an array defining the layer for each fragment. Default: all fragments in layer 1, i.e., LAYER(1)=1,1,1,...,1

TDTYP

CITYP

FRGNAM = an array of names for each fragment (each 1-8 character long) (default: FRG00001,FRG00002...). INDAT = an array assigning are supported (the INDAT(1): if it is otherwise INDAT(1) atoms to fragments. Two styles choice is made based on nonzero, choice (a) is taken, is ignored and choice (b) is

Input Description

$FMO

2-292

taken): a) INDAT(i)=m assigns atom i is to fragment m. INDAT(i) must be given for each atom. b) the style is a1 a2 ... ak 0 b1 b2 ... bm 0 ... Elements a1...ak are assigned to fragment 1, then b1...bm are assigned to fragment 2,etc. An element is one of the following: I or I -J where I means atom I, and a pair I,-J means the range of atoms I-J. There must be no space after the "-"! Example: indat(1)=1,1,1,2,2,1 is equivalent to indat(1)=0, 1,-3,6,0, 4,5,0 Both assign atoms 1,2,3 and 6 to fragment 1, and 4,5 to fragment 2. ICHARG = an array of charges on the fragments (default: all 0 charges) MULT = an array of multiplicities for each fragment. At most one fragment is allowed to differ from a singlet, and then only for the ROHF or MCSCF fragment. (default: all 1's)

SCFFRG = an array giving the SCF type for each fragment. At present, the only choice is one ROHF or one MCSCF fragment: all the rest must be RHF. The values in SCFTYP overwrite SCFFRG, that is, if you want to do a 2-layer calculation, the first layer being RHF and the other MCSCF, then you would use SCFTYP(1)=RHF,MCSCF and SCFFRG(N)=MCSCF, where you should replace N by your MCSCF fragment number. Then the first layer will be all RHF and the other will have one MCSCF fragment. In special cases, some SCFFRG values may be set to NONE, in which case SCF is not performed. This is useful in conjunction with ATCHRG. (default: SCFTYP in $CONTRL). MOLFRG = an array listing fragments for selective FMO, where not all dimers (and/or trimers) are

Input Description

$FMO

2-293

computed. Setting MOLFRG imposes various restrictions, such as RUNTYP=ENERGY only. See MODMOL. Default: all 0. IACTFG = array specifying fragments in the active domain in FMO/FD(D). Ranges can be specified as in INDAT, so INDAT(1)=1,2,-5,8 means fragments 1,2,3,4,5,8. All IACTFG fragments should be in the 2nd layer, and the interfragment distance between fragments in IACTFG and the 1st layer's fragments should not be zero (i.e., no detached bonds between them). Default: all zeroes. NOPFRG = printing and other additive options, specified for each fragment, 1 set the equivalent of $CONTRL NPRINT=7 (printing option). Useful if you want to print orbitals only for a few selected monomers. 2 set MVOQ to +6 to obtain better virtual orbitals (ENERGY runs only, useful mostly to prepare good initial orbitals for MCSCF). 4 generate cube file for the specified fragment, the grid being chosen automatically. (default: all 0s) 64 use frozen atomic charges (defined in ATCHRG) instead of the variational ones to compute converged fragment densities, to describe the electrostastic field from a fragment acting upon other fragments. 128 apply options 1 and 4 above only at the final SCF iteration (correlation or GRADIENT only). NACUT = automatically divides a molecule into fragments by assigning NACUT atoms to each fragment (useful for something like water clusters). This sets FRGNAM and INDAT, so they need not be given. If 0, the automatic option is disabled. (default: 0)

IEXCIT = options for FMO based TDHF, TDDFT, or CI calculations: IEXCIT(1): ordinal number for the excited state fragment. There is no default for IEXCIT(1), you should always set it. IEXCIT(2): chooses the many-body level excitation n, e.g.

Input Description

$FMO

2-294

for FMOn-TDDFT. n=1 means only the fragment given in IEXCIT(1) will be excited. n=2 adds dimer corrections (from fragment pairs involving IEXCIT(1)). IEXCIT(2) must not exceed NBODY. Default: 1. IEXCIT(3): (relevant for FMO2-TDDFT only) = 0 economic mode: only TDDFT dimer calculations are performed (skipping all other dimers). = 1 all dimer calculations are performed to obtain not just the excitation but also the total excited state energy. Default: 0. IEXCIT(4): excited state matching method in FMO2-TDDFT used to determine which excitations in dimers correspond to those in the TDDFT fragment given in IEXCIT(1). Default=2. = 0 trivial or identity matching (assume the same order of the excited states in monomers and dimers. = 1 match the dominant orbital pair (aka DRF) coefficient. = 2 match the whole excitation vector. Methods 1 and 2 try to match monomer dimer orbitals first, and then use DRF coefficients. In difficult cases (i.e., if the orbitals in a dimer are very delocalised), methods 1 and 2 may not be able to find the right transition, so some visual checking is recommended. ATCHRG = array of atomic charges, to be used with NOPFRG, set for some fragments to 64 (i.e., to freeze some of fragment electrostatic potentials during SCC). Nota bene: the order of atoms in ATCHRG is not the same as in FMOXYZ. In ATCHRG, you should specify atomic charges for all atoms in fragment 1, then for fragment 2 etc, as a single array. For covalently connected fragments there are formally divided atoms (some redundant), and ATCHRG should then list charges for them as well, all in the exact order of atoms in which fragments are defined in FMO. The number of entries in ATCHRG is NATFMO+NBDFG, where NATFMO is the number of atoms in $FMOXYZ and NBDFG is the number of bonds defined in FMOBND. NATCHA = option applicable to molecular clusters made

Input Description

$FMO

2-295

exclusively of the same molecules. Only NATCHA atoms are then specified in ATCHRG, and the rest are copied from the first set. RAFO = array of three thresholds defining model systems in FMO/AFO. All of them are multiplicative factors applied to distances. Two atoms are considered covalently bonded if they are separated by the predefined distance determined by their van der Waals radii. Larger RAFO values make further separated atoms to be considered as bonded.

All atoms within RAFO(1) distance from BDA or BAA are included into the model system in AFO ($FMOBND lists BDAs and BAAs in this order as BDA BAA). Atoms within RAFO(2) from the set defined by RAFO(1) are replaced by hydrogens. AO coefficients expanding localized orbitals to be frozen are saved for use in FMO for atoms within RAFO(3) from BDA or BAA. A nonzero RAFO(1) turns on FMO/AFO, else FMO/HOP is used. Default: 0,0,0. MODMOL = additive options for dimers and trimers in the selective FMO based on MOLFRG. 1 only do selected correlated calculations, 0 do selected correlated and all SCF dimers/trimers. This is the default. 2 modifies the choice of dimers/trimers to those within MOLFRG; else (0) to those involving exactly one fragment from MOLFRG. 4 do not store NFRAG**3 arrays in FMO3, to be used with MODMOL=2, to reduce memory in special cases. No property summary will be provided, just whatever is printed in SCF for each trimer. III. Parameters defining FMO approximations MODESP = options for ESP calculations. 0 the original distance definition (uniform), 1 an improved distance definition (many-body consistent, applied to unconnected n-mers), 2 an improved distance definition (many-body consistent, applied to all n-mers). (default: 0 (FMO2) or 1 (FMO3)) MODGRD = 0 subtract the external potential from the

Input Description

$FMO

2-296

Lagrangian (default). 1 do not do that. 2 add ESP derivatives(MODESP should be 0) 8 add Mulliken charge derivatives to MODGRD=2 16 do not add HOP derivatives 32 add CPHF-related terms needed for the fully analytic gradient, which are implemented only for FMO2-RHF, with no EFP or PCM. This option also requires entering RESPPC=0. Note that other terms should be added, too, so MODGRD=42 (=2+8+32) gives a fully analytic gradient. Default: 10 (=2+8, for FMO2) or 0 (for FMO3). RESPAP = cutoff for Mulliken atomic population approx, namely, usage of only diagonal terms in ESPs. It is applied if the distance between two monomers is less than RESPAP, the distance is relative to van der Waals radii; e.g. two atoms A and B separated by R are defined to have the distance equal to R/(RA+RB), where RA and RB are van der Waals radii of A and B). RESPAP has no units, as may be deduced from the formula. RESPAP=0.0 disables this approximation. (default: 0.0) RESPPC = cutoff for Mulliken atomic point charge approximation, namely replacing 2e integral contributions in ESPs by effective 1e terms). See RESPAP. (default: 2.0 (FMO2) or 2.5 (FMO3)) RESDIM = cutoff for approximating the SCF energy by electrostatic interaction (1e terms), see RESPAP. This parameter must be nonzero for ab initio electron correlation methods. RESDIM=0 disables this approximation. (default: 2.0 (FMO2) or RITRIM(1)+RITRIM(3) for FMO3 energy, 0 for FMO3 gradient) RCORSD = cutoff that is compared to the distance between two monomers and all dynamic electron correlation during the dimer run is turned off if the distance is larger than this cutoff. RCORSD must be less than or equal to RESDIM and it affects only MP2, CC, CI, and TDDFT.

Input Description

$FMO

2-297

(default: 2.0 (FMO2), RITRIM(1)+RITRIM(4) for FMO3 energy, 0 for FMO3 gradient) RITRIM = an array of 4 thresholds determining neglect of 3-body terms (FMO3 only). The first three are for uncorrelated trimers and the exact definition can be found in the source code. The fourth one neglects correlated trimers with the separation larger than the threshold value. RITRIM(4) should not exceed RITRIM(3). (default: 1.25,-1.0,2.0,2.0, which corresponds to the medium accuracy with medium basis sets, see REFS.DOC). SCREEN = an array of two elements, alpha and beta, giving the exponent and the multiplicative factor defining the damping function 1-beta*exp(-alpha*R**2). This damping function is used to screen the potential due to point charges of bond detached atoms and it can only be applied for RESPPC=-1, i.e., when ESP is approximated by point charges. Default: 0,0 (no screening). Other sensible values are 1,1.

VDWRAD = array of van der Waals radii in Angstrom, one for each atom in the periodic table. Reasonable values are set only for a few light atoms and otherwise a value of 2.5 is used. VDWRAD values are used only to compute distance between fragments and thus somewhat affect all distance-based approximations. ORSHFT = orbital shift, the universal constant that multiplies all projection operators. The value of 1e+8 was sometimes erroneously quoted instead of the actual value of 1e+6 in some FMO publications. (default: 1e+6). MAXKND = the maximum number of hybrid orbital sets (one set is given for each basis set located at the atoms where bonds are detached). See also $FMOHYB. (default: 10) MAXCAO = the maximum number of hybrid orbitals in an LMO set. (default: 5)

Input Description

$FMO

2-298

MAXBND = the maximum number of detached bonds. (default: NFG*2+1) ==========================================================

Input Description

$FMOPRP

2-299

==========================================================

$FMOPRP

group

(optional for FMO runs)

Options setting up SCF convergers, parallelization and properties are given here. I. Parameters for SCF convergers and initial guess MAXIT CONV = the maximum number of monomer SCF iterations. (default 30) = monomer SCF energy convergence criterion. It is considered necessary to set CONV in $SCF to a value less or equal to the CONV in $FMO. Usually 1e-7 works well, but for poorly converging monomer SCF (frequently seen with DFT) one order, smaller value for CONV in $SCF is recommended, (1e-7 in $FMO and 1e-8 in $SCF) (default: 1e-7).

NGUESS = controls initial guess (cumulative options, add all options desired) (default=2): 1 run free monomer SCF 2 if set, dimer density/orbitals are constructed from the "sum" of monomer quantities, otherwise Huckel guess will be used. 4 insert HMO projection operator in Huckel guess 8 apply dimer HO projection to dimer initial guess 16 do RHF for each dimer and trimer, then run DFT. 128 do not use orbitals from the previous geometry during geometry optimization. This is mostly useful for multilayer optimizations, when this choice must always be set if basis sets differ . 512 reorder initial orbitals manually using $GUESS options (IORDER), applies to MCSCF layers only. IJVEC = Index array enabling reading $VEC groups defining initial orbitals for individual runs (monomers and dimers). This consists of pairs: ifg1,jfg1, ifg2,jfg2, ... The first pair indexes $VEC1 with ifg1,jfg1, the second pair handles $VEC2 etc. ifg,jfg defines a dimer if both are non-zero or a monomer if jfg is zero. The first 0,0 pair ends

Input Description

$FMOPRP

2-300

the list, which means if $VEC1, $VEC3, $VEC4 are given only $VEC1 will be used. (default: all 0s; at most 100 can be given) MODORB = controls whether orbitals and energies are exchanged between fragments (additive options). 1 exchange orbitals if set, otherwise densities 2 exchange energies DFT, ROHF, and MCSCF require MODORB=3, otherwise use MODORB=0 for efficiency. (Default: 0 for RHF, 3 for DFT/ROHF/MCSCF.) MCONV = an array specifying SCF convergers for each FMO step. Individually (MCONV(2) is for monomers, MCONV(4) for dimers, MCONV(9) for trimers). Each array element is set to A1+A2+A3, where A1 determines SCF and A2 MCSCF convergers, and A3 is the direct/conventional bit common for all SCF methods. MCONV is an additive option: A1(SCF): A2(MCSCF): A3(direct) 1 EXTRAP 1024 FOCAS 256 FDIFF 2 DAMPH 2048 SOSCF 512 DIRSCF 4 VSHIFT 4096 DROPC 8 RSTRCT 8192 CANONC 16 DIIS 16384 FCORE 32 DEM 32768 FORS 64 SOSCF 65536 NOCI 131072 EKT 262144 LINSER 524288 JACOBI 1048576 QUD There are some limitations on joint usage for each that can be understood from $SCF or $MCSCF. If set to -1, the defaults given in $SCF or $MCSCF are used. See MCONFG. (default: all -1's).

MCONFG = an array specifying SCF convergers for each fragment during the monomer SCF runs. The value -1 means use the default (defined by MCONV). The priority in which convergers are chosen is: MCONFG (highest), if not defined MCONV, if not defined, $SCF (lowest). This option is useful in case of poor convergence caused by charge fluctuations and SCF converger problems in particular, SOSCF instability for poor

Input Description initial guess.

$FMOPRP Default: all -1.

2-301

ESPSCA = scale factors for up to nine initial monomer SCF iterations. ESPs will be multiplied by these factors, to soften the effect of environment and help convergence. At most nine factors can be defined. (default: all 1.0's) CNVDMP = damping of SCF convergence, that is, loosen convergence during the initial monomer SCF iterations to gain speed. CONV in $SCF and ITOL and ICUT in $CONTRL are modified. CONV is set roughly to min(DE/CNVDMP,1e-4), where DE is the convergence in energy at the given monomer SCF iteration. It is guaranteed that CONV,ITOL and ICUT at the end will be set to the values given in $SCF. Damping is disabled if CNVDMP is 0. Reasonable values are 10-100. Care should be taken for restart jobs: since restart jobs do not know how well FMO converged, restart jobs start out at the same rough values as nonrestart jobs, if CNVDMP is used. Therefore for restart jobs either set CNVDMP appropriately for the restart (i.e., normally 10-100 times larger than for the original run) or turn this option off, otherwise regressive convergence can incur additional iterations (default: 0). COROFF = parameter turning off DFT in initial monomer SCF, similar to SWOFF. COROFF is used during monomer SCF, and it turns off DFT until monomer energies converge to this threshold. If COROFF is nonzero, SWOFF is ignored during monomer SCF, but is used for dimers and trimer iterations. Setting COROFF=1e-3 and SWOFF=0 usually produces good DFT convergence. COROFF may be thought as a macroanalogue of SWOFF. If monomer SCF converges poorly (>25 iterations), it is also recommended to raise CONV in $SCF to 1e-8 (if CONV in $FMO is 1e-7). Default:1.0E-3 (0.0 skips this option). NPCMIT = the maximum number of FMO/PCM[m] iterations, applicable to m>1 only (for m=1, $FMOPRP MAXIT is used). NPCMIT=2 can be thought as having special meaning: it is used to define FMO/PCM[l(m)] runs

Input Description

$FMOPRP

2-302

by forcing the FMO/PCM loop run only twice, which corresponds to determining PCM charges during the first iteration (and the m-body level) and then using them during the second iteration (l-body). For FMO/PCM[l(m)] only l=1 is implemented and "m" is given in $PCM IFMO. Default: 30. CNVPCM = convergence threshold for FMO/PCM[m] iterations, applicable to m>1 only (for m=1, $FMOPRP CONV is used). CNVPCM is applied to the total FMO energy Default: 1.0D-07 Hartree. PCMOFF = parameter turning PCM off in initial monomer SCF iterations, analogous to COROFF. PCM is turned off, until convergence reaches PCMOFF. PCMOFF=0 disables this feature. Default: 0.0 NCVSCF = an array of 2 elements to alter SCF convergers. After NCVSCF(1) monomer SCF iterations the SCF converger will switch between SOSCF <-> FULLNR. This option is useful in converging difficult cases in the following way: $SCF diis=.t. soscf=.f. $end $FMOPRP NCVSCF(1)=2 mconv(4)=65 $end This results in the initial 2 monomer SCF iterations being done with DIIS, then a switch to SOSCF occurs. mconv(4)=65 switches to SOSCF for dimers. Note that NCVSCF(1) will only overwrite MCONV, but not MCONFG. The SCF converger in MCONV(2) will be enforced after NCVSCF(2) monomer SCF iterations, overwriting MCONFG as well. This is useful for the most obnoxiously converging cases. See other FMO documentation. Default: 9999,9999 (which means do not use). NAODIR = a parameter to decide whether to enforce DIRSCF. Useful for incore integral runs in parallel. NAODIR is the number of AO orbitals that is expected to produce 100,000,000 non-zero integrals. Using this and assuming NAO**3.5 dependence, the program will then guess how many integrals will each n-mer have and whether they will fit into the available memory. If they are determined not to fit, DIRSCF will be set true.

Input Description

$FMOPRP

2-303

This option overwrites MCONV but not MCONFG. If set to 0, then the default in-core integral strategy is used. (default=0) II. Parameters defining parallel execution MODPAR = parallel options (additive options) 1 turns on/off heavy job first strategy (reduces waiting on remaining jobs at barrier points) (see also 8) 4 broadcast all fragments done by a group at once rather than fragment by fragment. 8 alters the behavior of fragment initialixation: if set, fragments are always done in the reverse order (nfg, nfg-1, ...1) because distance calculation costs decrease in the same order and they usually prevail over making Huckel orbitals or running free monomer SCF. Note that during SCC (monomer SCF) iterations the order in which monomers are done is determined by MODPAR=1. 16 if set, hybrid orbital projectors will not be parallelized (may be useful on slow networks) 32 reserved 64 Broadcast F40 for FMO restarts. F40 should only be precopied to the grand master scratch directory and it should NOT exist on all slaves. (default: 13, which is 1+4+8) 256 Replace I/O to fragment density file by parallel broadcasts from group masters NGRFMO = an array that sets the number of GDDI groups during various stages of the calculation. The first ten elements are used for layer 1, the next 10 for layer 2, etc. ngrfmo(1) monomer SCF ngrfmo(2) dimers ngrfmo(3) trimers ngrfmo(4) correlated monomers ngrfmo(5) separated dimers ngrfmo(6) SCF monomers in FMO-MCSCF (MCSCF monomer will be done with ngrfmo(1) groups) ngrfmo(7) SCF dimers in FMO-MCSCF (MCSCF dimer be done with ngrfmo(2) groups) ngrfmo(8-10) reserved If any of them is zero, the corresponding stage

Input Description runs with If NGRFMO NGROUP in (default:

$FMOPRP

2-304

the previously defined number of groups. option is used, it is recommended to set $GDDI to the total number of nodes. 0,0,0,0).

MANNOD = manually define node division into groups. Contrary to MANNOD in $GDDI and here it is defined for each FMO stage (see NGRFMO) in each layer. If MANNOD values are set at all, it is required that they be given corresponding to the first nonzero NGRFMO value. The MANNOD values should be given for each nonzero NGRFMO. E.g. ngrfmo(1)=6,3,0,0,0, 0,0,0,0,0, 4,3 mannod(1)=4,2,2,2,2,2, 5,5,4, 4,4,3,3, 6,6,2 where 6 groups are defined for monomers in layer 1, then 3 for dimers in layer 1, and 4 and 3 groups for monomers and dimers in layer 2. (default: all -1 which means do not use). III. Orbital conversion File F40 that contains orbital density can be manipulated in some way to change the information stored in it without running any FMO calculations. Such conversion requires irest=2 and the basis sets in the input should define the old (before conversion) format. The results will be stored in F30. You should then rename it to F40 and use in a consequent run (with irest>=2). Two basic conversion types are supported: A) changing RHF into MCSCF and B) changing basis sets for RHF. RHF and MCSCF use different stucture of the restart file (F40) and therefore conversion is necessary. For type A the following orbital reordering manipulation before storing the results can be done, for example $guess guess=modaf norder=1 iorder(28)=34,28 Type B is typically used for preparing good initial orbitals for hard to converge cases. E.g., you can use something like 6-21G to converge the orbitals and then convert F40 to be used with 6-311G*. At present there is a limitation that only density based (MODORB=0) files may be converged, i.e. you cannot do it for DFT and MCSCF.

Input Description

$FMOPRP

2-305

MAXAOC = The new (i.e., after conversion) maximum number of AOs per fragment. If you don't know what it should be you can run a CHECK job with the new basis set and find the number in "Max AOs per frg:". If this number is equal to the old value, then type A is chosen. IBFCON = the array giving pairs of the old and new numbers of AOs for each atom in $DATA (type B only). MAPCON = maps determining how to copy old orbitals into new (type B only). See the example. Example: $DATA contains only H and O (in this order), F40 was computed with 6-31G and you want to convert to 6-31G**. One water per fragment. MAXAOC=25 25=5*2+15=new basis size for 6-31G** IBFCON(1)=2,5, 9,15 2 and 5 for H (6-31 and 6-31G**), 9 and 15 for O MAPCON(1)=1,2,0,0,0, 1,2,3,4,5,6,7,8,9,0,0,0,0,0,0 Here we copy the two s functions of each H, and add p polarization p to each H (3 0's), and similarly we copy nine s,p functions for O, and add d polarization (6 0's) In order to construct MAPCON, you should know in what order Gaussian primitives are stored. The easiest way to learn this is to run a simple calculation and check the output (SHELL information). IV. Printing, properties, restart, and dimensions. NPRINT = controls print-out (bit additive) bits 1-2 0 normal output 1 reduced output (recommended for single points) 2 minimum output (recommended for optimizations) 4 print interfragment distances. Note: any of RESPAP, RESPPC, or RESDIM must be non-zero or otherwise nothing will be printed. If you only want the distances but no approximations, set the thresholds to huge values, e.g. resdim=1000. 8 print Mulliken charges Note: RESPPC must be set (non-zero), see above. 64 print atomic coordinates for each fragment

Input Description

$FMOPRP

2-306

PRTDST = array of three print-out thresholds: 1. print all pairs of fragments separated by less than PRTDST(1). 2. print a warning if two fragments are closer than PRTDST(2), intended mostly to monitor suspicious geometries during optimization. 3. print a warning if two fragments are closer than PRTDST(3) and have no detached bond between them, intended to check input. PRTDST(3) values should slightly exceed the longest detached bond in the system. Using zero for PRTDST(1) and PRTDST(2) turns them off. Similarly, use PRTDST(3)=-1 to turn it off. PRTDST has no units, as it applies to unitless FMO distances (e.g., 0.5 means half the sum of van der Waals radii for the closest pair of atoms). (default: 0.0,0.5,0.6) IREST = restart level (all non-zero values require file .F40 with restart data be precopied to each node). (unless MODPAR=64 is set) See CNVDMP 0 no restart 2 restart monomer SCF (SCC). 4 restart dimers. Requires monomer energies be given in $FMOENM. Some or no dimer energies may also be given in $FMOEND, in which case those dimers with energies will not be run. Usually the only property that can be obtained with IREST=4 is the energy. The only exception is: a) IREST=1024 was set when monomer SCF was run and b) the property restart files (*.F38*) from each node were saved and copied to the scratch directory for the IREST=1028 job. If these two conditions are met, gradient and ES moments can be restarted with IREST=1028. 1024 write property restart files during monomer SCF and/or use them to restart gradient and/or ES moments. No other property may be restarted. Default: 0.

MODPRP = some extra FMO properties (bit additive) 1 total electron density (AO-basis matrix, written to F10: useful to create initial orbitals for ab initio).

Input Description

$FMOPRP

2-307

2 reserved. 4 electron density on a grid, cube file. 8 electron density on a grid, file. 16 automatically generate grid Only one bit out of 4 and 8 Default: 0. NGRID

produces a Gaussian produces a sparse cube for modprp = 4 or 8. may be set.

= three integers, giving the number of 3D grid points for monomers with NOPFRG=4 in x,y and z directions (default 0,0,0).

GRDPAD = Grid padding. Contributions to density on grid will be restricted to the box surrounding an n-mer with each atom represented by a sphere of GRDPAD vdW radii. In general the finer effects one is interested in, the larger GRDPAD should be. For example, if one plots not density, but density differences and a very small cutoff is used, then a larger value of GRDPAD (2.5 or 3.0) may be preferred. Default: 2.0. IMECT = The partitioning method for the interfragment charge transfer (computed from Mulliken charges). IMECT pertains only to those dimers between which a bond is detached. IMECT=0,1,2,3,4 are supported (see source code). (default: 4) V. Interaction analysis (PIEDA) IPIEDA = 0 skip the analysis (default) 1 perform brief PL-state analysis (FMO pair interactions) 2 perform full PL-state analysis with the PL0state data. N0BDA = gives the number of detached bonds. This parameter should be set to a nonzero value only in runs that produce BDA pair energies. (default: 0) = array of the detached bond lengths, whose number is N0BDA. R0BDA must be given if E0BDA is used.

R0BDA

Input Description

$FMOPRP

2-308

E0BDA EFMO0

= the array of BDA pair energies, whose number is N0BDA*4. = the array of the free state fragment energies, first NFRAG correlated, then NFRAG uncorrelated values.

EPL0DS = monomer polarization energies, first NFRAG values of PL0d, then NFRAG values of PL0s, then NFRAG values of PL0DI. EINT0 = the total components for the PL0 state: ES0, EX0, CT+mix0, DI0.

None of the PIEDA input values (except IPIEDA) are to be manually prepared, all should come from the punch file of preceeding calculations. The brief order of IPIEDA=2 execution is: 1. run FMO0. 2. compute BDA energies (if detached bonds are present), using sample files in tools/fmo/pieda. To do this, one needs only R0BDA for a given system. R0BDA is punched by any FMO run at the very beginning, so NBODY=0 type of run might be used to generate it. 3. The results of (1) are EFMO0; the results of (2) are E0BDA; use them to run PL0, whose results will be EPL0DS and EINT0. 4. Run PL with the results of (1),(2) and (3). The alternative is to run IPIEDA=1, which requires none of the above data, but it will use E0BDA is available. ==========================================================

Input Description

$FMOXYZ

2-309

==========================================================

$FMOXYZ

group

(given for FMO runs)

This group provides an analog of $DATA for $FMO, except that no explicit basis set is given here. It contains any nonzero number of lines of the following type: A.N Q X Y Z A is the dummy name of an atom. N is an optional basis set number (if omitted, it will be set to 1). N is intended for mixed basis set runs, for example, if you want to put diffuse functions on carboxyl groups. Q is the atomic charge. Z is the integer atomic charge. X, Y and Z are Cartesian coordinates. These obey UNITS given in $CONTRL. There is no default, this group must always be given for FMO runs. Alternatively, you may use the chemical symbol instead of Q. Note that "A" is ignored in all cases, but must be given. Here is how $DATA is used in FMO: Each atom given in $DATA defines the basis set for that atom type, entirely omitting Cartesian coordinates (which are in $FMOXYZ). There are two ways to input basis sets in FMO. I. easy! This works only if you want to use the same built-in basis set for all atoms. It is possible to use EXTFIL as usual for externally defined basis sets. 1. Define $BASIS as usual 2. Put each atom type in $DATA, e.g. for (H2O)2, $DATA H2O C1 ! FMO does not support symmetry, so always use C1 H 1 O 8

Input Description $end II. advanced.

$FMOXYZ

2-310

This allows you to mix basis sets, have multiple layers or a non-standard without involving EXTFIL. 1. Do not define $BASIS. 2. Put each atom type in $DATA, followed by basis set, either explicit or built in. The names of atoms in $DATA have the following format, where brackets indicate optional parameters: S[.N][-L] N and L may be omitted (taking the default value of 1), S is the atom name (discarded upon reading), N is the basis set ordinal number, L is the layer. S[.N][-L] may not exceed 8 characters. Example: 2-layer water dimer. In the first layer, you want to use STO-3G for the first molecule and your own basis set for the second. In the second layer, you want to use 6-31G and 6-31G* for the first and second molecules, respectively. $DATA water dimer (H2O)2 C1 H-1 1 ! explanation: layer 1, basis 1 (STO-3G) for Hydr. sto 3 O-1 8 sto 3 ! explanation: layer 1, basis 1 (STO-3G) for Oxygen

H.2-1 1 ! layer 1, basis 2 (manual) for hydrogen s 1 ; 1 2.0 1 O.2-1 8 s 2 1 100.0 2 10.0 l 1 1 5.0 1 ! explanation: layer 1, basis 2 (manual) for Oxygen 0.8 0.6 1

Input Description H-2 1 n31 6 O-2 8 n31 6

$FMOXYZ

2-311

! explanation: layer 2, basis 1 (6-31G) for Hydr. ! explanation: layer 2, basis 1 (6-31G) for Oxygen

H.2-2 1 ! layer 2, basis 2 (6-31G* = 6-31G) for Hydrogen n31 6 O.2-2 8 ! explanation: layer 2, basis 2 (6-31G*) for Oxygen n31 6 d 1 ; 1 0.8 1 $end Your $FMOXYZ matching this $DATA will then look as follows: $FMOXYZ O 8 x y z H 1 x y z H 1 x y z O.2 8 x y z H.2 1 x y z H.2 1 x y z $END Note that if you define mixed basis sets for the atoms where bond detachment occurs (do not do this for basis sets with diffuse functions), then you should provide all required sets in $FMOHYB as well, and define $FMOBND properly. ==========================================================

Input Description

$OPTFMO

2-312

==========================================================

$OPTFMO

group

(relevant if RUNTYP=OPTFMO)

This group controls the search for stationary points using optimizers developed for the Fragment Molecular Orbital (FMO) method. There is no restriction on the number of atoms in the molecule, whereas optimising FMO with standard optimizers (RUNTYP=OPTIMIZE) has a restriction to 2000 atoms (unless you rebuild your GAMESS appropriately). OPTFMO runs may be restarted by providing the updated coordinates in $FMOXYZ and, optionally, optimization restart data (punched out for each step) in $OPTRST (the data differs for each method). METHOD = optimization method STEEP steepest descent CG conjugate gradient BFGSL approximate BFGS numeric updates of the inverse Hessian, that do not require explicitly storing that matrix. HSSUPD numeric updates of the inverse Hessian Default: HSSUPD. HESS = initial inverse Hessian for METHOD=HSSUPD GUESS diagonal guess of 3 READ read from F38 (advanced option) Default: GUESS.

UPDATE = inverse Hessian update scheme for METHOD=HSSUPD BFGS Broyden-Fletcher-Goldfarb-Shanno DFP Davidon-Fletcher-Powell Default: BFGS. OPTTOL = gradient convergence tolerance, in Hartree/Bohr. Convergence of a geometry search requires the largest component of the gradient to be less than OPTTOL, and the root mean square gradient less than 1/3 of OPTTOL. (default=0.0001) NSTEP = maximum number of steps to take. Restart data are punched at each step. (default=200)

IFREEZ = array of coords to freeze during optimization.

Input Description

$OPTFMO

2-313

The usage is the same as for the similar option in $STATPT. IACTAT = array of active (not frozen) atoms in geometry optimizations, see $STATPT for its description. STEP = initial step factor. This multiplies the gradient to prevent large steps. The values of 0.1-0.2 are considered useful in the vicinity of minimum, and 0.5-1.0 is probably OK at the start. (default: 1)

STPMIN = the minimum permitted value of dynamically chosen STEP size (see STPFAC). (default: 0) STPMAX = the maximum permitted value of dynamically chosen STEP size (see STPFAC). (default: 1) STPFAC = Dynamic adjustment of STEP. If the energy goes down considerably, the new STEP is set to the old STEP multiplied by 1/STPFAC, if the energy goes up significantly, STEP is set to STEP*STPFAC, both constrained by STPMIN and STPMAX. The default is 1, which means do not use dynamic adjustment. The value 0.9 may be useful if dynamically adjusted steps are desired. ==========================================================

Input Description

$FMOLMO

2-314

==========================================================

$FMOHYB

group (optional, for FMO runs) (this group was previously known as $FMOLMO)

Hybrid orbitals are used to describe bond detachment when dividing a molecule into fragments. These are the familiar sp3 orbitals for C, plus the 1s core orbital. One set is given for each basis set used. The number of basis functions L1 (see below) should match your basis set(s). This group is not required if no detached bonds are present, for example in water clusters, where the FMO boundaries do not detach bonds. FMO/AFO also does not use $FMOHYB and this group may be omitted. Format: NAM1 L1 M1 I1,1 J1,1 C1,1 C2,1 C3,1 ... CL1,1 ... I1,M1 J1,M1 C1,M1 C2,M1 C3,M1 ... CL1,M1 NAM2 L2 M2 I2,1 J2,1 C1,1 C2,1 C3,1 ... CL1,1 ... I2,M2 J2,M2 C1,M2 C2,M2 C3,M2 ... CL2,M2 where NAM are set names (up to 8 characters long), L1 is the basis set size, M1 is the number of hybrid orbitals in this set. Ci,j are LCAO coefficients (i is AO, j is MO) so it is the transposed matrix of what is usually considered. Ii,j and Ji,j are bond assignment numbers, defining to which side the corresponding projection operator is added. Usually one of each pair of I and J is 1, and the other 0. (default: nothing, that is, no detached bonds). Orbitals to be put into $FMOHYB are provided for many common basis sets (see gamess/tools/fmo/HMO). ==========================================================

Input Description

$FMOBND

2-315

==========================================================

$FMOBND
runs)

group

(optional, for FMO

The atom indices involved in the bond detachment are given, in pairs for each bond. Bonds are always detached between fragments, layers in multilayer FMO are defined fragmentwise, i.e., whole fragments are assigned to layers. -I1 J1 NAM1,1 NAM1,2 ... NAM1,n ICH1 IMUL1 -I2 J2 NAM2,1 NAM2,2 ... NAM2,n ICH2 IMUL2... I and J are positive integers giving absolute atom indices. NAMs are hybrid orbital set names, defined in $FMOHYB. Each line is allowed to have different set of NAMs, which can happen if different type of bonds are detached, for example, one line describing C-C bond and another C-N. Every bond given is detached in such a way that the I-atom will get nothing of it, effectively remove one electron (1/2 of a single covalent bond) from its fragment. The Jatom will get all of the bond and thus adds one electron to its fragment (e.g., formally heterolytic assignment, although in practice all electrons remain through the Coulomb field). The number 'n' above is the number of layers. ICH and IMUL are ignored in FMO/HOP. For FMO/AFO, they define the charge and multiplicity of the model system constructed for the given bond (both 0 by default). IMUL follows the same rules and in $CONTRL. In FMO/AFO any name should be used in place of NAM as NONE, if ICH or MUL should be specified, otherwise only -I and J may be given (i.e., omitting NAM, ICH and MUL). (default: nothing, that is, no detached bonds). Example, for a two-layer run with STO-3G and 6-31G* in the first and second layers, respectively. $FMOBND -10 15 STO-3G 6-31G* -20 27 STO-3G 6-31G* $END ==========================================================

Input Description

$FMOENM $FMOEND $OPTRST

2-316

==========================================================

$FMOENM

group

(optional, for FMO runs)

This group defines monomer energies for restart jobs. The group should be taken from a previous run. The format is IFG and ILAY, followed by 4 monomer energies, of which only the first two are used (noncorrelated and correlated). IFG is the fragment number and ILAY is the layer number. This group is required for FMO restarts IREST=4. ==========================================================

$FMOEND

group

(optional, for FMO runs)

Dimer energies for restart jobs. The group should be taken from a previous run. The format is IFG, JFG and ILAY, followed by 2 dimer energies, (E'IJ and Tr(deltaDIJ*VIJ)). IFG and JFG describe the dimer and ILAY is the layer number. This group is optional for FMO restarts IREST=4 and is otherwise ignored. Note that for parallel restarts, $FMOEND groups from all nodes should be collected and merged into one group. ==========================================================

$OPTRST

group

(optional, for RUNTYP=OPTFMO)

Restart data for FMO geometry optimizations. The data inside vary for each optimization method, and are supposed to be taken from a previous run (from the punch file). ==========================================================

Input Description

$GDDI

2-317

==========================================================

$GDDI

group

(parallel runs only)

This group controls the partitioning of a large set of processors into sub-groups of processors, each of which might compute separate quantum chemistry tasks. If there is more than one processor in a group, the task assigned to that group will run in parallel within that group. Note that the implementation of groups in DDI requires that the group boundaries be on SMP nodes, not individual processors. At present, only two procedures in GAMESS can utilize processor groups, namely the FMO method which breaks large calculations into many small ones, or VSCF, which has to evaluate the same energy at many geometries. For example, the FMO method can farm out different monomer or dimer computations to different processor subgroups. This is advantageous, as the monomers are fairly small, and therefore do not scale to very many processors, although the monomer, dimer, and maybe trimer calculations are numerous, and can be farmed out on a large parallel system. NGROUP = the number of groups in GDDI. Default is 0 which means standard DDI (all processes in one group). PAROUT = flag to create punch and log files for all nodes. It is recommended to set this flag to .TRUE. if you switch the number of groups on the fly (such as in FMO). BALTYP = load balancing at the group level, otherwise similar to the one in $SYSTEM. BALTYP in $SYSTEM is used for intragroup load balancing and the one in $GDDI for intergroup. It is very seldom when .FALSE. is useful (default: .FALSE.). MANNOD = manual node division into groups. Subgroups must split up on node boundaries (a node contains one or more cores). Provide an array of node counts, whose sum must equal the number of nodes fired up when GAMESS is launched. Note the distinction between nodes and cores, also

Input Description

$GDDI

2-318

called processers, If you are using six quad-core nodes, you might enter NGROUP=3 MANNOD(1)=2,2,2 so that eight CPUs go into each subgroup. If MANNOD is not given (the most common case), the NGROUP groups are chosen to have equal numbers of nodes in them. For example, a 8 node run that asks for NGROUP=3 will set up 3,3,2 nodes/group. Note on memory usage in GDDI: Distributed memory MEMDDI is allocated globally, MEMDDI/p words per computing process, where p is the total number of processors. This means an individual subgroup has access to MANNOD(i)*ncores*MEMDDI/p words of distributed memory. Thus, if you use groups of various sizes, each group will have different amounts of distributed memory (which can be desirable if you have fragments of various sizes in FMO). ===========================================================

Input Description

$ELG

2-319

===========================================================

$ELG

group

(polymer elongation calculation)

This group of parameters provides control of elongation calculations, which steadily increase the size of aperiodic polymers, by adding attacking monomers to the end of an existing chain. The existing chain consists of two parts: an A region, with a frozen electron density, farthest from the new monomer, and a B region at whose end the monomer attacks. The wavefunction of the B region and the new monomer are optimized quantum mechanically. Disk files containing integrals and/or wavefunction information must be saved from one elongation run to the next. A large number of examples are provided with the source code distribution, see ~/gamess/tools/elg for this, perhaps starting with the (gly)5, (gly)6, (gly)7 examples. See the literature cited below for more help. NELONG = a flag to activate an elongation calculation, 0 means normal GAMESS run (default) 1 same as 0 but without reorientation of geometry 2 means elongation starting cluster calculation, this initiates a chain's A and B regions. 3 implies the monomer elongation of the chain. NATM = NUMBER OF ATOMS IN A-REGION Coordinates of the A-region atoms must be listed at the beginning of the input geometry in $DATA

NASPIN = multiplicity of the A-region NTMLB NCT = NUMBER OF TERMINAL ATOMS IN B-REGION = CONTROLLER FOR AO-CUT 0 means no AO-cut 1 means AO-cut activated = PRINT LEVEL 0 minimum printing (default) 3 debugging printing = LOCAL DENSITY OF STATES CALCULATION

IPRI

LDOS

Input Description

$ELG

2-320

0 means no LDOS calculation 1 means LDOS calculation I2EA = READ-IN 2E-INTEGRALS FOR A-REGION 0 means A-region 2e-integrals are recalculated 1 means A-region 2e-integrals are read from a previous calculation = Flag to shift one unpaired electron to the A- or the B-region, for covalently bonded A and B. .TRUE. means shift one electron to B-region .FALSE. means shift one electron to A-region

ATOB

For more information on this method, see A.Imamura, Y.Aoki, K.Maekawa J.Chem.Phys. 95, 5419-5431(1991) Y.Aoki, A.Imamura J.Chem.Phys. 97, 8432-8440(1992) Y.Aoki, S.Suhai, A.Imamura Int.J.Quantum Chem. 52, 267-280(1994) Y.Aoki, S.Suhai, A.Imamura J.Chem.Phys. 101, 10808-10823(1994) and particularly the new implementation described in "Application of the elongation method to nonlinear optical properties: finite field approach for calculating static electric (hyper)polarizabilities" F.L.Gu, Y.Aoki, A.Imamura, D.M.Bishop, B.Kirtman Mol.Phys. 101, 1487-1494(2003) "A new localization scheme for the elongation method" F.L.Gu, Y.Aoiki, J.Korchowiec, A.Imamura, B.Kirtman J.Chem.Phys. 121, 10385-10391(2004) "Elongation method with cutoff technique for linear SCF scaling" J.Korchowiec, F.L.Gu, A.Imamura, B.Kirtman, Y.Aoki Int.J.Quantum Chem. 102, 785-794(2005) "Elongation method at Restricted Open-Shell Hartree-Fock level of theory" J.Korchowiec, F.L.Gu, Y.Aoki Int.J.Quantum Chem. 105, 875-882(2005) ==========================================================

Input Description

$DANDC

2-321

==========================================================

$DANDC

group

(optional, relevant if SCFTYP=RHF or UHF)

This group controls the divide-and-conquer (DC) SCF calculations, in which the total 1-electron density matrix is obtained as sum of subsystem density matrices. In this calculation, the total system is partitioned into several disjoint subsystems (central regions). A subsystem density matrix is expanded by bases in the central region and its neighboring enviromental region (buffer). The present implementation allows energy and analytic nuclear gradients, for HF, DFT, and semi-empirical runs, for SCFTYP=RHF or UHF only. The discrete EFP and various continuum solvation models are available. DC correlation energies are also available for either MP2 and CC, see $DCCORR, without nuclear gradients. Dynamic and static polarizabilities (but no hyperpolarizabilities) based on DC-HF are available by specifying RUNTYP=TDHF (not TDHFX). The initial guess is given by a density matrix, not orbitals. The only available options are GUESS=HUCKEL, HCORE, HUCSUB, DMREAD, and MOREAD (the latter means orbitals for the entire system). For a review paper on Divide-and-Conquer in GAMESS: M.Kobayashi, H.Nakai in Linear-Scaling Techniques in Computational Chemistry and Physics: Methods and Applications (Springer), Chap. 5 (2011) For more information on the DC-SCF method, see W.Yang, T.-S.Lee J.Chem.Phys. 103, 5674-5678(1995) T.Akama, M.Kobayashi, H.Nakai J.Comput.Chem. 28, 2003-2012(2007) T.Akama, A.Fujii, M.Kobayashi, H.Nakai Mol.Phys. 105, 2799-2804(2007) T.Akama, M.Kobayashi, H.Nakai Int.J.Quant.Chem. 109, 2706-2713(2009) M.Kobayashi, T.Yoshikawa, H.Nakai Chem.Phys.Lett. 500, 172-177(2010) [open-shell] M.Kobayashi, T.Kunisada, T.Akama, D.Sakura, H.Nakai J.Chem.Phys. 134, 034105/1-11(2011) [gradient]

Input Description

$DANDC

2-322

For more information on DC-MP2 and DC-CC, see M.Kobayashi, Y.Imamura, H.Nakai J.Chem.Phys. 127, 074103/1-7(2007) M.Kobayashi, H.Nakai J.Chem.Phys. 129, 044103/1-9(2008) M.Kobayashi, H.Nakai J.Chem.Phys. 131, 114108/1-9(2009) M.Kobayashi, H.Nakai Int.J.Quant.Chem. 109, 2227-2237(2009) For more information on DC-TDHF polarizability, see T.Touma, M.Kobayashi, H.Nakai Chem.Phys.Lett. 485, 247-252(2010) Of course, the trick to methods that divide up a large problem into small ones is to control the errors that result. A simple way to set up a DC-MP2 calculation is with atomic partitions: $contrl scftyp=rhf mplevl=2 runtyp=energy $end $system mwords=25 $end $scf dirscf=.true. $end $dandc dcflg=.true. subtyp=atom bufrad=8.0 $end $dccorr dodccr=.true. rbufcr=5.0 $end $guess guess=hucsub $end (if DC-SCF is used) This leads to as many subsystems as there are atoms, with the buffer region around the central atom being defined by a radius. This input recognizes that exchange effects in Hartree-Fock are longer range than correlation, and thus uses dual level radii. It may be reasonable to simply do a conventional and thus fully accurate SCF computation by DCFLG=.FALSE., obtaining only the MP2 correlation energy by the divide and conquer method. Faster run times may result from other partitionings, such as manually dividing a protein into subsystems containing a single amino acid. DCFLG = Note: flag to activate DC-SCF calculation. (default=.FALSE.) If you want to treat only the correlated MP2/CC procedure in the DC manner, after a standard HF calculation, this option may be set to .FALSE. chooses a method to construct disjoint subsystems (central region). individual atom is 1 subsystem.

SUBTYP = = ATOM

Input Description

$DANDC

2-323

(default if NSUBS=0 or not given) = MANUAL manually selects using NSUBS and LBSUBS keywords. (default if NSUBS>=1) = CARD reads from card. $SUBSCF is used for SCF and $SUBCOR for MP2/CC calculation. = AUTO constructs subsystems automatically by dividing total system by cubic grid. Grid size can be set by SUBLNG. = AUTBND considers bond strength after AUTO. NSUBS = number of subsystems when SUBTYP=MANUAL.

LBSUBS = an array assigning atoms to subsystems. The style is the same as INDAT keyword in $FMO. Two styles are supported (the choice is made based on LBSUBS(1): if it is nonzero, choice (a) is taken, otherwise LBSUBS(1) is ignored and choice (b) is taken): a) LBSUBS(i)=m assigns atom i is to subsystem m. LBSUBS(i) must be given for each atom. b) the style is a1 a2 ... ak 0 b1 b2 ... bm 0 ... Elements a1...ak are assigned to subsystem 1, then b1...bm are assigned to subsystem 2,etc. An element is one of the following: I or I -J where I means atom I, and a pair I,-J means the range of atoms I-J. There must be no space after the "-"! Example: LBSUBS(1)=1,1,1,2,2,1 is equivalent to LBSUBS(1)=0, 1,-3,6,0, 4,5,0 Both assign atoms 1,2,3 and 6 to subsystem 1, and 4,5 to subsystem 2. SUBLNG = grid length of cube used in SUBTYP=AUTO or AUTBND. This value should be in the unit given by UNITS keyword in $CONTRL. (default=2.0 Angstroms). BUFTYP = chooses a method to construct buffer region. = RADIUS selects atoms included in spheres centered at atoms in the central region (default). The radius is given by BUFRAD keyword for

Input Description

$DANDC

2-324

DC-SCF and by the RBUFCR keyword in $DCCORR for DC-MP2/CC. = RADSUB selects subsystems containing one or more atom(s) which is included in spheres centered at atoms in the central region. This selection can avoid cutting bonds within each subsystem. = CARD reads from $SUBSCF or $SUBCOR card. Only available when SUBTYP=CARD. BUFRAD = buffer radius in DC-SCF calculation. This value should be in the units given by UNITS keyword in $CONTRL (default=5.0 Angstroms). FRBETA = inverse temperature parameter of Fermi function used in DC-SCF procedure in a.u. (default=200.0) Reducing this value may improve SCF convergence but may obtain worse total energy. MXITDC = maximum number of iteration cycles for determining Fermi level (default=100). Usually, you need not care about this keyword. FTOL = Fermi function cutoff factor (default=15.0). = p The value of Fermi function less than 10**(-p) is considered as 0. The value greater than [1 - 10**(-p)] is considered as 1. DC print-out option which is the sum of followings (default=0). not used (reserved). prints density matrix ($DM section) on punch. prints energy corresponding to each subsystem. Gives correct energy only in HF calculation. prints orbitals in each subsystem.

NDCPRT = = +1 = +2 = +4 = +8 IORBD =

selects molecular orbital in total system whose electron density is to be computed. Print format is given in $ELDENS. = -1, -2, ... correspond to HOMO, HOMO-1, ... = 1, 2, ... correspond to LUMO, LUMO+1, ... = 0 no calculation (default).

In the DC-SCF procedure, the available SCF acceleration techniques are DIIS, DAMP, EXTRAP as well as DC-DIIS and

Input Description

$DANDC

2-325

VFON which are specific to the DC-SCF. In DC-SCF calculation, only DIIS is used by default. DC-DIIS (DIIDCF=.TRUE.) is not normally needed for convergence. The following keywords control (DC-)DIIS convergence: DIITYP = selects the error vector used in the standard DIIS extrapolation = FDS Pulay's modified DIIS (e=FDS-SDF). Although this type of error vector behaves well in standard SCF, it may not for DC-SCF. = DELTAF Pulay's original DIIS (e[i]=F[i]-F[i-1]), or so-called Anderson mixing (default). uses orthogonal basis (in entire system) for DIIS extrapolation. Normally, this does not make sense in DC-SCF run. .FALSE. uses atomic basis function for DIIS extrapolation (default).

DIIQTR = .TRUE.

EXTDII = energy error threshold in absolute value for exiting DIIS (default=0.0). PEXDII = percentage threshold of energy error change for exiting DIIS (default=1.0). PEXDII is preferential to EXTDII. DIIDCF = a flag to activate DC-DIIS interpolation (default=.FALSE.). ETHRDC = energy error threshold for initiating DC-DIIS. Increasing ETHRDC forces DC-DIIS on sooner (default = 1.D-4 if DIIDCF=.TRUE.). The following keywords control the convergence acceleration based on the varying fractional occupation number (VFON). The final electronic temperature is given by FRBETA. FONTYP = = DIIER = NONE selects the variation pattern of electronic temperature (beta) in SCF iteration logarithmic variation with respect to DIIS error. no variation (default).

Input Description

$DANDC

2-326

BETINI = initial beta value in a.u. (default = FRBETA/4 for FONTYP=DIIER). FONSTA = threshold to start variation of beta (default=1.0 for FONTYP=DIIER). FONEND = threshold to stop variation of beta (default=1.D-4 for FONTYP=DIIER). When FONTYP=DIIER, the beta value used in the iteration (of which the DIIS error is DIISer) is the following: beta = BETINI [for DIISER>FONSTA] = FRBETA [for DIISER<=FONEND] = FRBETA + C_FON * Log(DIISer/FONEND) [otherwise] where (C_FON = (BETINI-FRBETA) / Log(FONSTA/FONEND) Option for the type of nuclear gradient: NDCGRD = selects the DC-SCF gradient implementation = 0 use a formula proposed by Yang and Lee in 1995 = 1 use a formula proposed by Kobayashi et al. in 2011 (default)

Next are options for printing density of states (DOS). DOSITV = Interval between plot points in Hartree. The default is zero,meaning no DOS print-out. If you print out DOS, DOSITV=0.05 may be sufficient. DOSRGL = Left end of the plot range in Hartree. (default=-2.0) DOSRGR = Right end of the plot range in Hartree. (default=+2.0) BDOS = Inverse temperature parameter (beta) for distributing states. This value should not be given because it is set to be equivalent to FRBETA in $DANDC by default.

==========================================================

Input Description

$DCCORR

2-327

==========================================================

$DCCORR

group (optional) relevant for MPLEVL=2 relevant for CCTYP=LCCD, CCD, CCSD, CCSD(T), R-CC

This group controls the linear-scaling DC-based MP2 or CC calculations. In this method, subsystem correlation energy is evaluated in each subsystem by means of subsystem MOs. Total correlation energy is obtained by summing up subsystem contributions. The present implementation allows only RHF reference. DC-MP2 calculations can be run in parallel (using CODE=DDI, IMS, or SERIAL in $MP2), but DC-CC is limited to serial execution. DC-MP2 with CODE=IMS is only compatible with DIRSCF=.TRUE. Coupled cluster code is only available for CCTYP=LCCD, CCD, CCSD, CCSD(T), or R-CC. No solvation models are available. This group must be given if the "double-hybrid" DFT is used (e.g., DFTTYP=B2PLYP). Note: Although $DANDC input is usually used together to select subsystem and buffer information, DC-SCF calculation is not indispensable to perform DC correlation calculation. You can perform DC correlation calculation without DC-SCF by setting DCFLG=.FALSE. in $DANDC and DODCCR=.TRUE. For more information (and references), see $DANDC. DODCCR = a flag to activate DC-MP2/CC calculation. This is forced to be .TRUE. if DCFLG=.TRUE. in $DANDC. This keyword enables to perform DC-MP2/CC calculation after standard (non-DC) RHF. RBUFCR = buffer radius used in DC-MP2/CC calculation. This value should be in the unit given by UNITS option in $CONTRL. By default, RBUFCR is set to be equal to BUFRAD in $DANDC. This keyword is mainly used to perform so-called dual-buffer DC-MP2/CC calculations, see the paper on the DC-CC method for more details. RMKORB = a flag to remake orbitals in each subsystems. This

Input Description

$DCCORR

2-328

is forced to be .TRUE. if RBUFCR is different from BUFRAD in $DANDC or standard HF calculation was performed. Apart from these cases, RMKORB=.FALSE. by default. This keyword is meant for debug purposes. HFFRM = a flag to use the Fermi level determined in the preceding HF calculations even when RMKORB=.TRUE. (default=.FALSE.) The Fermi level is used to classify the subsystem orbitals into occupied and virtual ones. Usually, this option does not change the results except for the use of diffuse basis functions. = a parameter determining proportion of occupied contribution. This should be between 0 and 1. The proportion of virtual contribution becomes [1 - WOCC]. (default=1.0) This is forced to be 1.0 in DC-CC calculation, except when WOCC=0.0, which only calculates virtual contribution. We recommend 1.0 to obtain accurate results. a flag to disable MP2 calculation for virtual contributions. This is forced to be .FALSE. if WOCC is not 1.0, and to be .TRUE. in DC-CC calculation. = .TRUE. Performs DC-MP2 calculation only for occupied contributions. This option will accelerate the CPU time. (default) = .FALSE. Performs DC-MP2 calculation for occupied and virtual contributions. specifies the partitioning for (T) correction. This is only relevant to CCTYP=CCSD(T) or R-CC. = XY (two-digit integer) uses [X,Y] type partitioning defined in the following article: J.Chem.Phys.131,114108(2009) (default=00)

WOCC

ONLYOC =

ITPART =

ISTCOR = restart option for DC-MP2/CC. = 0 does DC-MP2/CC calculation from the beginning (default). = n reads subsystem correlation energies corresponding to subsystem 1-(n-1) from input

Input Description

$DCCORR

2-329

and perform DC-MP2/CC calculation from n-th subsystem. $MP2RES and $CCRES inputs are required for DC-MP2 and DC-CC calculations, respectively. FZCORE = a flag to freeze core electrons in DC-MP2 or DC-CC calculation. Other frozen orbital options options such as NACORE in $MP2 and NCORE in $CCINP do not pertain to DC-MP2/CC calculations. The default is .TRUE. to freeze cores.

==========================================================

Input Description

$SUBSCF $SUBCOR

2-330

==========================================================

$SUBSCF group $SUBCOR group

(relevant during Divide and Conquer)

These groups specify the central and buffer regions when SUBTYP=CARD or BUFTYP=CARD in $DANDC. $SUBSCF is used for DC SCF and $SUBCOR is for DC-MP2/CC. If BUFTYP is not CARD, only central region is specified by these groups. They consist of free format integer numbers of which the style is like this: $SUBSCF ! SUBSYSTEM 1 1 3 -5 0 2 6 -8 0 0 ! SUBSYSTEM 2 2 6 -9 11 0 1 3 4 10 12 -14 0 0 ! SUBSYSTEM 3 ... $END Lines starting with ! are comments neglected when reading. First, atoms in the central region of subsystem 1 is specified according to the (b) style of LBSUBS in $DANDC. A single 0 separates the central and buffer region of the same subsystem. Then, specify atoms in the buffer region of subsystem 1. A double 0 separates subsystems. These are iterated until all subsystems are specified. In the above case, the subsystems are the followings: Subsystem 1 central: buffer : Subsystem 2 central: buffer : 1,3,4,5 2,6,7,8 2,6,7,8,9,11 1,3,4,10,12,13,14

==========================================================

Input Description

$MP2RES $CCRES

2-331

==========================================================

$MP2RES group $CCRES group

(restart data for DC-MP2 runs) (restart data for DC-CC runs)

Restart data (consisting of subsystem correlation energies) for Divide and Conquer correlation calculations. The appropriately named input group is required if ISTCOR is selected in $DCCORR. The format of these two groups is slightly different for DC-MP2 or DC-CC, but the data should be given in exactly the same format that it was written to file RESTART, adding only a $END line. Examples: $MP2RES 1 -0.133110332082E+00 2 -0.130740147906E+00 3 -0.130483660838E+00 $END $CCRES 2 1 2 3 4 $END -0.135031928183E+00 -0.132589691149E+00 -0.132673391144E+00 -0.133163592168E+00 -0.132440119981E+00 -0.131009546477E+00 -0.130832334600E+00 -0.131377855474E+00 0.000E+00 0.000E+00 0.000E+00 -0.133110332082E+00 -0.130740147906E+00 -0.130483660838E+00

The integer in the first line indicates the CC method. ==========================================================

Input Description

$FFDATA $FFPDB

2-332

==========================================================

$FFDATA group $FFPDB group

(optional, relevant if QuanPol is used) (optional, relevant if QuanPol is used)

QuanPol (quantum chemistry polarizable force field program) can perform MM, QM/MM or QM/MM/Continuum solvent MD simulation or geometry optimization, using HF, DFT, GVB, MCSCF, MP2 or TDDFT wavefunctions. To use QuanPol, either $FFDATA or $FFPDB needs to be present, to define the MM atoms. Quantum atoms, if any, are given in $DATA as usual. After the initial input giving QuanPol's options, one gives either explicit coordinates (in which case this group must be named $FFDATA) or Protein Data Bank coordinates (in which case this is $FFPDB). Force field data sets are located by the environment variable QUANPOL. ----------------------------------------------------------1DT one or more lines, containing one or more options: = MD time step size. Default=1.0D-15 seconds.

NSTEPS = number of MD and OPTIMIZE steps. Default=1000. OPTTOL = geometry optimization gradient criterion. Default=1.0D-04 hartree/bohr NPROP JOUT = start to calculate properties after NPROP steps. Default=0 = report simulation information such as energies and temperature to log file every JOUT steps. Default=1. = write coordinates to the log file every KOUT steps. Default=100 = special action control = 314159 to create the $FFDATA group for a molecule using the information in LOUT314159.PAR file.

KOUT LOUT

Input Description

$FFDATA $FFPDB

2-333

ITSTAT = = = = =

flag to enable the thermostat (velocity scaling) 0 no thermostat (default) 1 velocity scaling 2 Berenedsen thermostat 3 Andersen thermostat

IPSTAT = flag to enable the barostat (volume scaling) = 0 no barostat (default) = 1 Berenedsen barostat after NPROP steps. A barostat is meaningful only for PBC system. For spherical systems with a soft-wall, volume and pressure are self-adjusted. TEMP0 PRES0 = bath temperature. Default=298.15 K. = bath pressure. Default=1.0 bar. A pre-equilibrium system may show huge positive or negative pressures like 100,000 bar. An equilibrium system may show pressures fluctuating by several hundreds bar.

INTALG = MD integrator algorithm. = 1 Beeman algorithm (default) = 2 velocity verlet algorithm NRANDOM= selects the seed for QuanPol's random number generator: = 0 use fixed seeds for reproducibility (default) = 1 use time/date to generate seeds QuanPol uses a 16-bit pseudo-random integer generator with a cycle length 6953607871644. See Wichmann & Hill, Appl.Statist. 31, 188-190 (1982) Fixed and time/date seeds should give the same randomness. Using fixed seeds, serial MD jobs are reproducible; parallel MD jobs are reproducible for ~500 steps. MXFFAT MXBOND MXANGL MXDIHR MXDIHB maximum number maximum number maximum number maximum number maximum number (i.e. improper MXWAGG = maximum number = = = = = of MM atoms. of bonds. of bond angles. of dihedral rotation angles. of dihedral bending angles. torsion in CHARMM). of wagging angles.

Input Description

$FFDATA $FFPDB

2-334

MXCMAP = maximum number of CHARMM correction map cases. All of these are for memory allocation purposes. Default varies from 10,000 to 100,000, depending on the number of processors. MXLIST = maximum number of non-bond MM atoms around a given MM atom. Default=1400 is good for SWR2=12. BUFLIST= The width of the buffer region for the non-bond list. Default = 2.0 angstrom. A new non-bond list will be generated if any atom moves more than half BUFLIST since the last updating of the non-bond list. IADDWAT= = = = ITYPWAT= = = = specifies how 0 No adding 1 Add water 2 Add water to add water molecules to the system water (default) in PBC master box in a sphere

selects the water model. (the default is 301) 301 Nonpolarizable flexible 3-point model 302 Polarizable flexible 3-point model 303 SPC/Fw model by Wu/Tepper/Voth, see J.Chem.Phys. 124, 024503(2006). = 304 flexible TIP3P as implemented in CHARMM22/27.

Water models 301 and 302 are optimized using SWR1=10, SWR2=12, SWMODE=3, 510 waters, PBC, at 298.15 K and 1 bar. Density, O-O rdf, self-diffusion coefficient are good and not size-sensitive. Dielectric constants are ~70 for 301, ~56 for 302 when 510 waters are used, and are ~110 for 301, ~96 for 302 when 2187 waters are used. JADDNA1= JADDK1 = = = IADDNA1= IADDK1 = IADDCA2= IADDMG2= IADDCL1= flag to add NA+ ions to DNA/RNA PO4- sites. flag to add K+ ions to DNA/RNA PO4- sites. 0 skip (default) 1 Add NA+/K+ ions to all possible PO4- sites number number number number number of of of of of Na+ K+ Ca2+ Mg2+ Clions ions ions ions ions randomly randomly randomly randomly randomly added. added. added. added. added. Default=0. Default=0. Default=0. Default=0. Default=0.

CENTER = X, Y, Z

Input Description

$FFDATA $FFPDB

2-335

define the center of the PBC master box or the sphere center. If not found, it will be automatically calculated. Use the same CENTER for restart jobs. XBOX,YBOX,ZBOX = size of the periodic box in Angstrom. Default 1.0D+30 means no PBC is imposed. RCUT RCUTQ = radial cutoff of MM-MM interactions in angstrom. = radial cutoff of QM-MM interactions in angstrom.

SWMODE = selects the switching function mode, default=3 Note that shifting functions operate on the range zero to SWR2, while switching functions work in the tail region, from SWR1 to SWR2. = 1 atom-atom switching function. Tests show that atom-atom SWF gives incorrect water structure and properties. = 2 group-group switching function. Terminal atoms (H, F, Cl,... and carbonyl O) will be grouped to their node atoms. Tests show that group-group SWF can give a correct water structure. = 3 the atom-atom shifting function S(r)=(1-r/SWR2)**2 is used for charge-charge interaction. The same shifting function is used by the ENCAD and ilMM codes. In addition, this option means that group-group switching function is used for both charge-charge and Lennard-Jones interactions in the range between SWR1 and SWR2. Set SWR1=SWR2 to turn off the switching, but keep the shifting. = 4 similar to SWMODE=3, but with the atom-atom shifting function S(r)=[1-(r/SWR2)**2]**2. which is one of the CHARMM shifting functions. Switching function is used as in option 3. = 5 similar to SWMODE=3, but the atom-atom shifting function is choosen to mimic a dielectric reaction field for charge-charge interaction. RXNEPS & SWR2 are required. The shifting function is Eq (5) in Rick, J.Chem.Phys. 120, 6085 (2004)

Input Description

$FFDATA $FFPDB Switching function is used as in option 3.

2-336

The switching function implemented in QuanPol is W(r) = 1 - 10*D**3 + 15*D**4 - 6*D**5 with D = (r**2 - SWR1**2)/(SWR2**2-SWR1**2) SWR1,SWR2 = distance cutoffs for the switching function that gradually drops the interactions from full strength at SWR1 to zero at SWR2. In angstrom. For MM atoms only. SWR1Q,SWR2Q = same as SWR1 and SWR2, but for QM-MM interactions. SPHRAD = radius of the sphere containing the QM/MM system. Default is a huge value, meaning no sphere. A Lennard-Jones type potential is applied to keep the heavy atoms in the sphere. For each such atom: V=4*SPHEPS*{[SPHSIG/(r-R)]**12 - [SPHSIG/(r-R)]**6} R = SPHRAD + [2**(1/6)-1]*SPHSIG V = -SPHEPS when r = SPHRAD - SPHSIG SPHEPS = Lennard-Jones epsilon parameter for SPHRAD. Default = 0.15 kcal/mol is good for water. Proper values should be determined empirically. SPHSIG = Lennard-Jones sigma parameter for SPHRAD. Default = 1.5 A is good for water. Proper values should be close to the radii of the solvent atoms, which are usually around 1.5. IRXNFLD= flag to enable spherical reaction field model = 0 no reaction field (default) = 1 image charge method, currently only for pure MM system = 60, 240, 960, 3840 to choose surface charge method and define the number of surface elements. Available for MM and QM/MM. RXNEPS = dielectric constant in RXNFLD (default = 1.0) RXNRAD = radius of sphere in angstrom (default = 1.0D+30). SPHRAD is required. For water solvent,

Input Description

$FFDATA $FFPDB

2-337

RXNRAD = SPHRAD + 0.60 A RXNEPS = 78.39 SPHEPS = 0.15 SPHSIG = 1.50 are strongly suggested. RDF = NRDF, NAME1, NAME2, ... = specifies the number of pairs for the radial distribution function calculation, and the names of the atoms. Must give NRDF pairs of names. Default for NDRF is 0. The RDF will be calculated every JOUT steps.

DELRDF = specifies the radial increment in the radial distribution function calculation. Default= 0.02 angstrom. DIFFUSE= NDFS, NAME1, NAME2, ... = specifies the number of atoms for diffusion coefficient calculation, and the names of the atoms. Must give NDFS names. Default is NDFS=0. TIMDFS = time interval for diffusion coefficient calculation. Default = 3.0D-12 seconds is good for water. Can be larger, but should not be smaller. There must be sufficient displacement in order to apply the statistical formula. NATPDB = number of atoms in the PDB file. If $FFPDB is used, NATPDB will be automatically determined. The main usage is for restart jobs in which only $FFDATA is provided. NFIXPDB= fix the coordinates of PDB atoms for the initial NFIXPDB steps of an MD or OPTIMIZE procedure. This is useful for initial solvent equilibration. Reasonable values are 1000-10000. Default = 0. NRIJ = NRIJ, I1, J1, I2, J2, ... = specifies up to 20 pairs of atoms to print out their distances at every JOUT steps. Useful when one wants to monitor H-bond distances. Default NRIJ = 0.

Input Description

$FFDATA $FFPDB

2-338

NRMSD

= flag root-mean-square-displacement calculation. = 0 skip = 1 calculate RMSD from the initial coordinates at every JOUT steps. = flag radius of gyration calculation (see TIMGYRA). = 0 skip = 1 calculate radius of gyration using formula: R=SQRT[sum(m*r*r)/sum(m)] r: distance from COM m: atom mass So R is mass-weighted RMS distance from COM.

NGYRA

TIMGYRA= time interval for radius of gyration calculation. Default=1.0D-12 seconds. Can be larger or smaller. NRALL = flag to activate internuclear distance calculation (see TIMRALL). = 0 skip = 1 calculate internuclear distances and compare to those in the initial structure. Unsigned and RMS displacements will be printed out.

TIMRALL= time interval for internuclear distance calculation. Default = 1.0D-12 seconds. Can be larger or smaller, but frequent calculation slows down the MD. NDIEL = flag MD simulation of dielectric constant. = 0 skip (default) = 1 calculate dielectric constant using formula: Eps = 1 + (<M**2> - <M>**2)/(3kT<V>) M = total dipole of the master box or sphere k = Boltzmann constant T = temperature V = volume When spherical systems are used, a sphere with radius = SPHRAD-SPHSIG is used to calculate M and V. Tests show this gives Eps very similar to those from PBC simulations. When induced point dipoles are used, each dipole is decomposed into two point charges at the opposite sites of the point dipole. These charges are considered for M calculation. One

Input Description

$FFDATA $FFPDB

2-339

of them may be relocated when PBC is imposed, or may be excluded if it is outside of the sphere. AANAM = a name for the LOUT=314159 purpose. This name should be in the LOUT314159.TOP file. Give any name, if no intention to use LOUT314159.TOP. = this is used only in $FFDATA to duplicate the input molecule in 3D space NFOLD times. Reasonable values are 0, 3, 6, 9, 12 and 15, which leads to 1, 8, 64, 512, 4096 and 32768 copies. 0-20 can be used. Default=0, no action. = specifies the spacing when NFOLD is active. The value should be calculated using density. Default= 0.0 angstrom. flag to include MM charges flag to include MM polarization flag to include MM Lennard-Jones flag to include CHARMM correction map for proteins For all of these, = 1 include (default) = 0 exclude

NFOLD

RFOLD

IDOCHG = IDOPOL = IDOLJ = IDOCMAP=

NFFTYP = select the force field type = 20022, which is CHARMM22/27 (default) WT14 = scaling factor for 1-4 LJ, charge-charge and polarization interactions. Default 1.00

RETAIN = retaining factor (0.0 - 1.0, default 0.5) for MM force field covalent terms that involve only QM atoms, one of which is a boundary atom with repulsion potentials in place of a frontier MM atom. Using 0.5 is reasonable for weakened boundary bonds. Use 0.0 if the boundary bonds are not weakened. The retaining factor for MM covalent terms involving only QM atoms (none of which is a boundary atom in place of a frontier MM atom) is always 0.0 and cannot be changed from the input deck. QMREP = NQMREP, IATOM1, NTERM1, C11, Z11, C12, Z12 ...,

Input Description

$FFDATA $FFPDB

2-340

IATOM2, NTERM2, C21, Z21, C22, Z22 ... = specify effective Gaussian repulsion potentials at boundary QM/MM atoms (typically H atoms in place of alpha carbons of a peptide) to produce the desired longer bond lengths. NQMREP = number of QM atoms with Gaussian potentials. Up to 200 atoms. IATOMn = QM atom sequential number in $DATA NTERMn = number of Gaussians at IATOMn. Up to 4 C11,.. = strength part of the Gaussian, e/bohr Z11,.. = radial part of the Gaussian, 1/bohr**2 Must enter NTERMn pairs of C and Z for atom IATOMn. For example, to define 1 Gaussian for QM atom 1 and 3 Gaussians for QM atom 7, give QMREP=2,1,1,3.0,3.0,7,3,8.0,6.0,3.0,3.0,0.3,1.0 For H atom forming C-H bond, a single Gaussian with C=3.0 Z=3.0 is a good option. The remainder of this group depends on whether it is a $FFDATA or a $FFPDB!

Input Description

$FFDATA $FFPDB

2-341

--------------------------------------------------------**** the following inputs pertain to $FFDATA **** -2the input is given in subsections with a keyword at the start of the subsection, and STOP at its end. Z = The name of the atom. = nuclear charge of the atom = Cartesian coordinates in angstrom

COORDINATES NAME, NUC, X, Y, NAME NUC X,Y,Z STOP

PARAMETERS NAME, MASS, Q, POL, SIGMA, EPSILON, SIGMA2, EPSILON2 NAME = The name of the atom. Q = Force field charge (e) on the atom. POL = Polarizability of the atom, in A**3 SIGMA = Lennard-Jones parameter in angstrom. CHARMM uses RMIN/2. QuanPol will automatically check whether it is SIGMA or RMIN/2. EPSILON = Lennard-Jones parameter in kcal/mol SIGMA2, EPSILON2 = the LJ parameters for select 1-4 cases in CHARMM. Give zeros if not these. Give the same number of lines as specified in the COORDINATES section STOP QMMMREP N, C1, Z1, C2, Z2, C3, Z3, C4, Z4 N = number of Gaussian type potentials. currently only 4 is allowed. C1 - C4 = strength factor of the potential Z1 - Z4 = radial factor of the potential give the same number of lines as specified in the COORDINATES section STOP BOND

Input Description

$FFDATA $FFPDB

2-342

SERIAL#, ATOM1, ATOM2, BFC, R0 SERIAL# = serial number of the bond. this is only for notation purpose. ATOM1 = serial number in COORDINATES section for the first atom in the bond. ATOM2 = same as ATOM1, but for the second atom. BFC = bond force constant in kcal/mol/A**2 R0 = equilibrium bond length in angstrom. STOP ANGLE SERIAL#, ATOM1, ATOM2, ATOM3, AFC, ANGLE0 SERIAL# = serial number of the angle. this is only for notation purpose. ATOM1 = serial number in COORDINATES section for the first atom in the angle. ATOM2 = same as ATOM1, but for the second atom. ATOM3 = same as ATOM1, but for the third atom. AFC = angle bending force constant in kcal/mol/rad**2 ANGLE0 = equilibrium angle in degree. STOP DIHROT SERIAL#, ATOM1, ATOM2, ATOM3, ATOM4, VROT, N, GAMMA SERIAL# = serial number of the dihedral rotation angle. This is only for notation purpose. ATOM1 = serial number in COORDINATES section for the first atom in the dihedral rotation angle. ATOM2 = same as ATOM1, but for the second atom. ATOM3 = same as ATOM1, but for the third atom. ATOM4 = same as ATOM1, but for the fourth atom. VROT = rotational barrier in kcal/mol N = multiplicity, an integer. GAMMA = the phase factor in degree. STOP DIHBND SERIAL#, ATOM1, ATOM2, ATOM3, ATOM4, DBFC, DIHB0 SERIAL# = serial number of the dihedral bending (improper torsion) angle. this is only for notation purpose. ATOM1 = serial number in COORDINATES section

Input Description

$FFDATA $FFPDB

2-343

ATOM2 ATOM3 ATOM4 DBFC DIHB0 STOP

= = = = =

for the first atom in the dihedral bending angle. same as ATOM1, but for the second atom. same as ATOM1, but for the third atom. same as ATOM1, but for the fourth atom. dihedral bending force constant in kcal/mol/rad**2 equilibrium dihedral bending angle in degree.

CMAP SERIAL#, ATOM1, ATOM2, ATOM3, ATOM4, ATOM5, ITYPE SERIAL# = serial number of the CHARMM correction map phi,psi couples. this is only for notation purpose. ATOM1 = serial number in COORDINATES section for the first atom in the phi angle (the carbonyl carbon of an amino acid residue) of the peptide backbone in a phi,psi couple. ATOM2 = serial number in COORDINATES section for the second atom in the phi angle (peptide N atom) of a phi,psi couple. this is the first atom of the psi angle. ATOM3 = serial number in COORDINATES section for the third atom in the phi angle (the alpha C atom) of a phi,psi couple. this is the 2nd atom of the psi angle. ATOM4 = serial number in COORDINATES section for the fourth atom in the phi angle (a carbonyl carbon) of a phi,psi couple. this is the third atom of the psi angle. ATOM5 = serial number in COORDINATES section for the fourth atom in the psi angle (the next peptide N atom). ITYPE = specifies the two amino acid residues a phi,psi couple belongs to. =1 alanine-alanine (most cases) =2 alanine-proline =3 glycine-glycine/glycine-proline =4 proline-alanine =5 proline-proline (here alanine stands for any amino acid residue other than glycine and proline)

Input Description STOP

$FFDATA $FFPDB

2-344

When $FFPDB is given, CMAP is automatically generated for restart jobs, via $FFDATA input. WAGGING SERIAL#, ATOM2, ATOM3, ATOM4, ATOM1, WFC SERIAL# = serial number of the wagging angle. this is only for notation purpose. ATOM2 = serial number in COORDINATES section for the second atom in the wagging angle. ATOM3 = same as ATOM2, but for the third atom. ATOM4 = same as ATOM2, but for the fourth atom. ATOM1 = same as ATOM2, but for the first atom. WFC = wagging force constant kcal/mol/rad**2 STOP Use a $END line to end $FFDATA. ---------------------------------------------------------**** the following inputs pertain to $FFPDB **** -2- Simply paste a PDB text file into $FFPDB will work. (1). H atoms must be added beforehand and appear at the correct places. Currently QuanPol cannot add H atoms or any other missing atoms. (2). PDB format is enforced. Sequential numbers are not used by QuanPol. Chemical symbols are used. (3). Rename the atom at the very end of each chain as 'OXT' or 'HXT', and delete the 'TER' lines. Multiple chains are allowed. (4). SSBOND lines are required to define S-S bonds. Use a $END line to end $FFPDB. ==========================================================

Input Description

$CIINP

2-345

The remaining groups apply only to MCSCF and CI runs. * * * * * * * * * * * * * * * For hints on how to do MCSCF see the 'further information' * * * * * * * * * * * * * * * * * * * and CI section * * * *

==========================================================

$CIINP

group

(optional, relevant for any CITYP)

This group is the control box for Graphical Unitary Group Approach (GUGA) CI calculations or determinant based CI. Each step which is executed potentially requires a further input group described later. NRNFG = An array of 10 switches controlling which steps of a CI computation are performed. 1 means execute the module, 0 means don't. NRNFG(1) = Generate the configurations. See either $CIDRT or $CIDET input. (default=1) NRNFG(2) = Transform the integrals. See $TRANS. (default=1) NRNFG(3) = determinants: skip the CI iterations. GUGA: Sort integrals and calculate the Hamiltonian matrix, see $CISORT and $GUGEM. (default=1) NRNFG(4) = determinants: meaningless GUGA: Diagonalize the Hamiltonian matrix, see $GUGDIA or $CIDET. (default=1) NRNFG(5) = Construct the one electron density matrix, and generate NO's. See $GUGDM or $CIDET. (default=1) NRNFG(6) = Construct the two electron density matrix. See $GUGDM2 or $CIDET. (default=0 normally, but 1 for CI gradients) NRNFG(7) = Construct the Lagrangian of the CI function. Requires DM2 matrix exists. See $LAGRAN. (default=0 normally, but 1 for CI gradients) This does not apply to determinants. NRNFG(8-10) are not used. Users are not encouraged to change these values, as the defaults are quite reasonable.

Input Description

$CIINP

2-346

NPFLG = An array of 10 switches to produce debug printout. There is a one to one correspondance to NRNFG, set to 1 for output. (default = 0,0,0,0,0,0,0,0,0,0) The most interesting is NPFLG(2)=1 to see the transformed 1e- integrals, NPFLG(2)=2 adds the very numerous transformed 2e- integrals to this. IREST = n Restart the -CI- at stage NRNFG(n). ==========================================================

Input Description

$DET $GEN $CIDET $CIGEN

2-347

==========================================================

$DET group (required by MCSCF if CISTEP=ALDET or ORMAS) $GEN group (required by MCSCF if CISTEP=GENCI) $CIDET group (required if CITYP=ALDET, ORMAS, or FSOCI) $CIGEN group (required if CITYP=GENCI)
This group describes the determinants to be used in a MCSCF or CI wavefunction: a) For full CI calculations (ALDET) the $DET/$CIDET will generate a full list of determinants. If the CI is part of an MCSCF, this means the MCSCF is of the FORS type (which is also known as CASSCF). b) For Occupation Restricted Multiple Active Space (ORMAS) CI, the input in $ORMAS will partition the active orbitals defined here into separate spaces, that is, provide both $DET/$CIDET and $ORMAS. c) For Full Second Order CI, provide $CIDET and $SODET inputs. d) For a general CI (meaning user specified space orbital products) provide $DET/$CIDET plus $GEN/$CIGEN and most likely $GCILST (according to the keyword GLIST). In the above, group names for MCSCF/CI jobs are separated by a slash. Determinants contain several spin states, in contrast to configuration state functions. The Sz quantum number of each determinant is the same, but the Hamiltonian eigenvectors will have various spins S=Sz, Sz+1, Sz+2, ... so NSTATE may need to account for states of higher spin symmetry. In Abelian groups, you can specify the exact spatial symmetry you desire. GLIST = general determinant list option The keyword GLIST must not be given in a $DET or $CIDET input group! These both generate full determinant lists, automatically. = INPUT means an input $GCILST group will be read. = EXTRNL means the list will be read from a disk file GCILIST generated in an earlier run. = SACAS requests generation of sevaral CAS spaces of different space symmetries, specified by

Input Description

$DET $GEN $CIDET $CIGEN

2-348

the input IRREPS. This option is intended for state averaged calculations for cases of high symmetry, where degenerate irreps of the true group may fall into different irreps of the Abelian subgroup used. * * * The next four define the orbital spaces * * * There is no default for NCORE, NACT, and NELS: NCORE NACT NELS SZ = total number of orbitals doubly occupied in all determinants. = total number of active orbitals. = total number of active electrons. = azimuthal spin quantum number for each of the determinants, two times SZ is therefore the number of excess alpha spins in each determinant. The default is SZ=S, extracted from the MULT=2S+1 given in $CONTRL.

* * * The following determine the state symmetry * * * GROUP = name of the point group. The default is to copy this from $DATA, if that group is Abelian (C1, Ci, Cs, C2, C2v, C2h, D2, or D2h). If not, the point group used will be C1 (no symmetry). specifies the spatial symmetry of the state. Of course these names are the standard group theory symbols for irreducible representations: C1 A Ci Ag Au Cs AP APP (P stands for prime, i.e. ') C2 A B C2v A1 A2 B1 B2 C2h Ag Bu Bg Au D2 A B1 B2 B3 D2h Ag B1g B2g B3g Au B1u B2u B3u Default is STSYM being the totally symmetric state, listed as the first column above. The free format scanner is not able to read quotes

STSYM =

Input Description

$DET $GEN $CIDET $CIGEN

2-349

so the letters "P" must be used in Cs. IRREPS = specifies the symmetries of the GLIST=SACAS space determinant list. This variable should always be an array, as a single symmetry is more quickly obtained by the regular full CI code. The values given are more primitive than STSYM, being the following integers, not strings: IRREPS= 1 2 3 4 5 6 7 8 meaning C1 A Ci Ag Au Cs A' A'' C2 A B C2v A1 A2 B1 B2 C2h Ag Bu Bg Au D2 A B1 B2 B3 D2h Ag B1g B2g B3g Au B1u B2u B3u * * * the following control the diagonalization * * * NSTATE = Number of CI states to be found, including the ground state. The default is 1, meaning ground state only. The maximum number of states is 100. See also IROOT below (two places). PRTTOL = Printout tolerance for CI coefficients, the default is to print any larger than 0.05. ANALYS = a flag to request analysis of the CI energy in terms of single and double excitation pair correlation energies. This is normally used in CI computations, rather than MCSCF, and when the wavefunction is dominated by a single reference, as the analysis is done in terms of excitations from the determinant with largest CI coefficient. The defalt is .FALSE. ITERMX = Maximum number of Davidson iterations per root. The default is 100. A CI calculation will fail if convergence is not obtained before reaching the limit. MCSCF computations will not bomb if the iteration limit is reached, instead the last CI vector is used to proceed into the next orbital update. In cases with very large active

Input Description

$DET $GEN $CIDET $CIGEN

2-350

spaces, it may be faster to input ITERMX=2 or 3 to allow the program to avoid fully converging the CI eigenvalue problem during the early MCSCF iterations. For small active spaces, it is best to allow the CI step to be fully converged on every iteration. CVGTOL = Convergence criterion for Davidson eigenvector routine. This value is proportional to the accuracy of the coeficients of the eigenvectors found. The energy accuracy is proportional to its square. The default is 1.0E-5, but 1E-6 if gradients, MPLEVL, CITYP, or FMO selected). NHGSS = dimension of the Hamiltonian submatrix which is diagonalized to obtain the initial guess eigenvectors. The determinants forming the submatrix are chosen on the basis of a low diagonal energy, or if needed to complete a spin eigenfunction. The default is 300.

NSTGSS = Number of eigenvectors from the initial guess Hamiltonian to be included in the Davidson's iterative scheme. It is seldom necessary to include extra states to obtain convergence to the desired states. The default equals NSTATE. MXXPAN = Maximum number of expansion basis vectors in the iterative subspace during the Davidson iterations before the expansion basis is truncated. The default is the larger of 10 or 2*NSTGSS. Larger values might help convergence, do not decrease this parameter below 2*NSTGSS. CLOBBR = a flag to erase the disk file containing CI vectors from the previous MCSCF iteration. The default is to use these as starting values for the current iteration's CI. If you experience loss of spin symmetry in the CI step, reverse the default, to always take the CI from the top. Default = .FALSE. * * * the following control the 1st order density * * *

Input Description

$DET $GEN $CIDET $CIGEN

2-351

The following pertain to CI calculations by CITYP=xxx (not the CI step within MCSCF jobs). Similar keywords apply to MCSCF runs, see just below. PURES = flag to say that IROOT and NGFLGDM just below should count only those states whose S value is a match to that implied by MULT in $CONTRL. Thus, PURES=.TRUE. (the default) allows selection of S1 as IROOT=2 (the second singlet), even if there is a T1 state (and maybe others!) between S0 and S1. Of course, NSTATE must be large enough to reach S1 (at least 3, if there is a T1 between S0 and S1). Setting PURES to .FALSE. ignores the spin of each state when using IROOT and NFLGDM. = the root whose density is saved on the disk file for subsequent property analysis. Only one root can be saved, and the default value of 1 means the ground state. Be sure to set NFLGDM to form the density of the state you are interested in! IROOT has a similar meaning for MCSCF, see below.

IROOT

NFLGDM = Array controlling each state's density formation. 0 -> do not form density for this state. 1 -> form density and natural orbitals for this state, print and punch occ.nums. and NOs. 2 -> same as 1, plus print density over MOs. 3 -> same as 2, plus print properties for this state (see $ELMOM, $ELPOT, et cetera). The default is NFLGDM(1)=1,0,0,...,0 meaning only ground state NOs are generated. * * * the following control the state averaged * * * * * * 1st and 2nd order density matrix computation * * * The following keywords apply to the CI step within the MCSCF iterations. See just above for similar inputs pertaining to CITYP=xxx calculations. PURES = a flag controlling the spin purity of the state avaraging. If true, the WSTATE array pertains to the lowest states of the same S value as is given by the MULT keyword in $CONTRL. In this

Input Description

$DET $GEN $CIDET $CIGEN

2-352

case the value of NSTATE will need to be bigger than the total number of weights given by WSTATE if there are other spin states present at low energies. If false, it is possible to state average over more than one S value, which might be of interest in spin-orbit coupling jobs. The default is .TRUE. WSTATE = An array of up to 100 weights to be given to the densities of each state in forming the average. The default is to optimize a pure ground state, WSTATE(1)=1.0,0.0,...,0.0 A small amount of the ground state can help the convergence of excited states greatly. Gradient runs are possible only with pure states. Be sure to set NSTATE above appropriately! IROOT = the MCSCF state whose energy will be used as the desired value. The default means to use the average (according to WSTATE) of all states as the FINAL energy, which of course is not a physically meaningful quantity. This is mostly useful for the numerical gradient of a specific state obtained with state averaged orbitals. (default=0). IROOT has a similar meaning for CI, see above.

==========================================================

Input Description

$ORMAS

2-353

==========================================================

$ORMAS

group

(required by MCSCF if CISTEP=ORMAS) (required for CITYP=ORMAS)

This group partitions an active space, defined in $DET or $CIDET, into Occupation Restricted Multiple Active Spaces (ORMAS). All possible determinants satisfying the occupation restrictions (and of course the space symmetry restriction given in $DET/$CIDET) will be generated. This group's usefulness lies in reducing the large number of determinants present in full CI calculations with large active spaces. There are no sensible defaults for these inputs, but if the group is entirely omitted, a full CI calculation will be performed. That is, the defaults are NSPACE=1, MSTART(1)=NCORE+1, MINE(1)=NELS, MAXE(1)=NELS meaning all active orbitals are in one partition. NSPACE MSTART = number of orbital groups you wish to partition the active space (NACT in $DET/$CIDET) into. = an array of NSPACE integers. These specify where each orbital group starts in the full list. You must not overlook the NCORE core orbitals in computing MSTART values. Space I runs from orbital MSTART(I) up to orbital MSTART(I+1)-1, or NACT+NCORE if I is the last space, I=NSPACE.

IMPORTANT !!!! Remember to make sure your orbitals have been reordered to suit MSTART, using NORDER in $GUESS. MINE = an array of NSPACE integers. These specify the minimum numbers of electrons that must always occupy the orbital groups. In other words, MINE(I) is the minimum number of electrons that can occupy space I in any of the determinants. = an array of NSPACE integers. These specify the maximum numbers of electrons that must always occupy the orbital groups. In other words, MAXE(I) is the maximum number of electrons that can occupy space I in any of the determinants.

MAXE

Input Description

$ORMAS

2-354

The number of active electrons is NELS in $DET or $CIDET, and the program will check that MINE/MAXE values are consistent with this total number. BLOCK = a flag to request that for CI calculations (but not CISTEP=ORMAS in MCSCF) that the generation of natural orbitals prevent any mixing between the NSPACE different orbital subspaces. This means that the NOs are not the true NOs, but they can be used in MOREAD to exactly reproduce the ORMAS CI energy, which is invariant to rotations within the orbital subspaces. (Default = .FALSE.) = a flag to request Davidson-style +Q corrections. If this is not sensible for your CI choice, the program will not print this correction, anyway. The default is .TRUE. = a flag to choose storage in memory of some intermediates. This is very large, and slower in the case of many occupied orbitals, but helpful with a smaller number of orbitals. Therefore the default for this is .TRUE. for MCSCF runs, but .FALSE. during CI computations.

QCORR

FDIRCT

*** See REFS.DOC for more information on using ORMAS *** ==========================================================

Input Description

$CEEIS

2-355

==========================================================

$CEEIS

group

(optional, for extrapolation to FCI limit)

The method termed Correlation Energy Extrapolation by Intrinsic Scaling (CEEIS) allows one to extrapolate sequences of CI energies, computed with the ORMAS program, to what is effectively the full CI limit for a given basis set. Typically, the energy for SD and SDT excitation levels using all orbitals (m=M, meaning occupied + all virtuals) is combined, using certain scaling relations, with explicit computations using m orbitals for quadruple, quintuple... excitations (x), using a smaller m for each higher excitation, to obtain the extrapolated FCI limit, within an estimated error bar. When this is done for several basis sets, it is possible to extrapolate the individual full CI energies to the limit of the complete basis set. A series of papers combines complete basis set CEEIS energies with scalar relativistic, spin-orbit, and long range electrostatic corrections to produce a very accurate rotational-vibrational spectrum of F2, see L.Bytautas, T.Nagata, M.S.Gordon, K.Ruedenberg J.Chem.Phys. 127, 164317/1-20 (2007) L.Bytautas, N.Matsunaga, T.Nagata, M.S.Gordon, K.Ruedenberg J.Chem.Phys. 127, 204301/1-12 (2007) L.Bytautas, N.Matsunaga, T.Nagata, M.S.Gordon, K.Ruedenberg J.Chem.Phys. 127, 204313/1-19 (2007) L.Bytautas, K.Ruedenberg J.Chem.Phys. 130, 204101/1-14 (2009) The input description below is quite terse. A full description of how to use CEEIS with ORMAS is provided in a separate file (a Word document) named ~/gamess/tools/ci-tools/ceeis/CEEIS.doc containing a much more detailed description of how to do this kind of calculation. This document explains how to use an Excel spreadsheet to allow visual checking of the energy data that are being extrapolated. Several input examples are given in the same directory. ENREF = reference energy, usually either a zero-excited ORMAS reference wavefunction, or some SCF level energy (if the reference is one determinant).

Input Description

$CEEIS

2-356

ISTPEX = highest excitation level considered by the CEEIS, the default is 8 (octuple excitations). M1M2EX = an array to specify the various ORMAS computations to be performed, at each excitation level x. 0's start the specification of m values for each level x=3,4,...ISTPEX. Some examples follow, M1M2EX(1)= 0,0,0, 0,7,10,-14,20 0,7,10,-14 ISTEPX=5 The final two zero's on the first (SDT) line mean do the SDT computations with the entire virtual space, and also for all m values used at the higher excitations. The SDTQ energies are found for m=7,10,11,12,13,14,20, that is, the minus sign implies all values in the range 10-14. The SDTQ5 computations do not include m=20. If there is not enough memory to do the entire SDT calculation, this can be extrapolated (losing accuracy in the entire CEEIS process), by input such as M1M2EX(1)= 0,7,10,-14,20,27, 0,7,10,-14,20 0,7,10,-14 ISTEPX=5 Changing the 0,0 part of the triples line to what is shown extrapolates from m=27. Note that it is an error not to include the same m values that higher excitations will use. There is no input for doubles, as in all cases the program will generate the SD energy for the entire virtual space, and additional SD energies for the m values chosen for use by the higher excitation levels. M1M2EX(1)= all 0's will carry out a fully automated CEEIS using MMIN to MMIN+4, testing convergence, possibly adding MMIN+5 to MMIN+9 and so forth. IDELTM = range increment for the m1,m2 ranges given as {m1,-m2} in M1M2EX. Default=1. ISCHME = extrapolation choice (the default is 1) for energy increments (DEMAT = differences of EMAT values): = 1 means extrapolate excitation level "x" by DEMAT(m,x) = a*DEMAT(m,x-2) + b = 2 means extrapolate quadruples as above, but x=5+6 or x=7+8,... are extrapolated together: DEMAT(m,x) = A*DEMAT(m,2) + B*DEMAT(m,3) + C In this case energies for odd excitation levels

Input Description

$CEEIS

2-357

are not needed, and their computation can be avoided by making the odd levels in M1M2EX be the same input for 5+6, 7+8, ... MMIN = "m" value of the lowest virtual orbital to be considered in the extrapolation. The default is NCORE + 1 + MAX(no. valence e-, no. valence orbs), which is in fact the lowest "m" that should ever be used.

XTRTOL = an array of thresholds for each extrapolated energy E(x), if the automated CEEIS is being used. default = 2D-4 Hartree for all levels x. NSEXT = an array containing NSPACE entries. Each entry corresponds to an ORMAS orbital group defined by MSTART in $ORMAS, and can be either 0 or 1. An entry of 1 means include excitations from this space during the CEEIS. 0 means do not include any such excitations, meaning electrons in this subspace are NOT being correlated, apart from the correlation built into the original ORMAS. The final entry in the list is the virtual space, and must be given as 1. The default is all 1's. that the CEEIS calculation is being which case energies provided in the are read, and only the missing be calculated. Default = .FALSE.

RESTRT = a flag to say restarted, in $CEDATA group energies will

IEXPND = expands the excitation level in restarts, e.g. if the previous data was computed for ISTPEX=6, and you now wish to use ISTPEX=8, enter IEXPND=2 to add two more columns to the matrix EMAT(m,x) being read in $CEDATA. ==========================================================

$CEDATA

group

(optional restart data for CEEIS runs)

This group contains previously computed ORMAS energies, forming the EMAT array, to be used to restart CEEIS runs. It is required if RESTRT in $CEEIS is true. ==========================================================

Input Description

$GCILST

2-358

==========================================================

$GCILST

group

(required by MCSCF if CISTEP=GENCI) (required if CITYP=GENCI)

This group defines space products to be used in the general CI calculation, or in a MCSCF wavefunction. The input is free format. Line 1: NSPACE ISYM The first line gives the total number of space products to be entered in the second lines. The option ISYM can be omitted, or given as 0, in which case the program will verify that all space products typed in the second lines indeed have the spatial symmetry defined by STSYM in the $GEN or $CIGEN input groups. If ISYM is 1, the user is indicating that more than one space symmetry is known to be in the list, that this is intentional, and the program should proceed with the calculation. This might be of use in state averaging two representations in a group that has more than two total representations, and therefore faster than turning symmetry off completely by GROUP=C1. ISYM=2 has the same meaning but turns on additional printing. Line 2 is repeated NSPACE times. Each line 2 contains NACT integers, which must be 0, 1, or 2, and therefore tells the occupation of each of the active orbitals in each space product. An example input is: $GEN GLIST=INPUT NELS=6 NACT=4 SZ=0.0 $END $GCILST 5 2 2 2 0 2 1 2 1 2 0 2 2 2 2 0 2 0 2 2 2 $END which generates 6 Ms=0 determinants, much less than the 16 determinants in a C1 symmetry full list for 6 e- in 4 MOs. The second space product above generates two determinants. All space products with singly occupied orbitals are used to form all possible determinants, to ensure that the final

Input Description

$GCILST

2-359

states are eigenfunctions of the S**2 operator (meaning they will be pure spin states). Note that there is no way at present to generate lists such as singles and doubles from a single reference. Convergence of MCSCF calculations with arbitrary lists of space products will depend on how well chosen your list is, and may very well require the use of FULLNR or JACOBI convergers. A utility program to pre-select the important part of CI expansions with high excitation levels, based on information from CI-SDT calculations, is distributed with the source code. See the file ~/gamess/tools/ci-tools/select/readme.1st for more information. ==========================================================

Input Description

$GMCPT

2-360

==========================================================

$GMCPT

group

(relevant if CISTEP=GMCCI in $MCSCF) (relevant if MRPT=GMCPT in $MRMP)

This group specifies the determinants to be used in a general MCSCF wavefunction. Additional inputs give the necessary information to compute a 2nd order perturbation energy correction to the MCSCF energy of such a MCSCF reference, by choosing MPLEVL=2 in $CONTRL and MRPT=GMCPT. The PT is of quasidegenerate type, in which several MCSCF states can be perturbed simultaneously. After 2nd order correction to both its diagonal and off-diagonal matrix elements, this model Hamiltonian is diagonalized to give the GMC-QDPT energies. The diagonalization also yields some information about the remixing of the reference states at 2nd order. Of course, the program can also be used to obtain the 2nd order correction to the energy of just one state. GMC-QDPT is therefore analogous to the two equivalent MCQDPT programs (MRPT=MCQDPT or DETMRPT) for CAS-type references, but allows more general types of MCSCF reference. Compared to those programs, there are also choices for the 0-th order states, for the orbital energies, and for the treatment of external excitations. The letters GMCPT should be understood as standing for GMC-QDPT, and have been shortened only because of the constraints on input group names to 6 or fewer letters. At the present time, this program does not support EXETYP=CHECK. It is enabled for parallel execution. 1. data to specify active space and electronic state: NMOFZC: number of frozen core orbitals, during the PT the shape of these orbitals will be optimized in the MCSCF stage, so they are "frozen" in the sense of not being correlated in the PT. The default is the number of chemical core orbitals. NMODOC: number of orbitals restricted to double occupancy

Input Description

$GMCPT

2-361

during MCSCF, but which are correlated in the PT calculation. In other words, the filled valence orbitals. (no default). (It is possible to enter a different keyword NMOCOR which is the total number of doubly occupied orbitals, and NMOFZC. In this case the program will obtain NMODOC by subtraction, namely NMODOC = NMOCOR - NMOFZC). NMOACT: number of active orbitals in the MCSCF (no default) NMOFZV: number of virtual orbitals to be omitted from the PT step. The default is 0, retaining all virtuals. NELACT: number of active electrons. Since the default is computed from the total number of electrons given in $DATA and $CONTRL's ICHARG, minus 2*NMOFZC minus 2*NMODOC, there is little reason to input this. MULT: SZ: STSYM: multiplicity of the state, with the default being taken from MULT in $CONTRL. spin projection quantum number for determinants, default is (MULT-1)/2 The symmetry of the electronic state. See $DET for possible values: use AP/APP in Cs, not primes. Default is the totally symmetric representation.

If you are treating a system with degenerate states in an appropriate Abelian subgroup of the true group, up to three STSYM values can be given, to specify all components of that originally degenerate state. For example, STSYM(1)=b1u,b2u,b3u generates all P states for an atom running in the Abelian subgroup D2h.

2. data to specify the MCSCF CI (and PT's reference CI): The type of general MCSCF reference is specified by REFTYP, which can be MRX, ORMAS, or RAS: REFTYP= MRX means multi-reference determinant list, plus excitations (default). The determinants will be

Input Description

$GMCPT

2-362

given in a $PDET group, and the keywords NPDET and NEXCIT defined below are required. REFTYP= RAS means the active space is divided into three subspaces, known as RAS1, RAS2, and RAS3. Keywords MSTART and NEXCIT defined below are required. For example, MSTART(1)=4,6,9 defines a RAS with three orbitals in the NMOFZC/NMODOC spaces, while the RAS1, RAS2, and RAS3 subspaces contain 2, 3, and NMOACT-5 orbitals. It remains only to specify the excitation level NEXCIT between these spaces. REFTYP= ORMAS defines even more general subspaces than RAS, and requires inputs NSPACE, MSTART, MINE, and MAXE. These have the same meaning as the $ORMAS keywords. NPDET is the number of parent determinants, to be given as NPDET lines in the $PDET group. A value is required for REFTYP=MRX. is an excitation level. A value is required for REFTYP=MRX or REFTYP=RAS. is the number of subspaces into which the active space is divided. Required for REFTYP=ORMAS. is an array telling the starting MO of each orbital space. It is required for REFTYP=RAS and ORMAS. is an array giving the minimum number of electrons occupying each subspace. Required for REFTYP=ORMAS. is an array giving the maximum number of electrons occupying each subspace. Required for REFTYP=ORMAS.

NEXCIT NSPACE MSTART MINE MAXE

NSPACE, MSTART, MINE, and MAXE have the same meaning as in the $ORMAS group. See $ORMAS, and also in the MCSCF/CI section of REFS.DOC, for help in understanding the power of the ORMAS type of reference determinant list. 3. data to define the reference CI states: KSTATE is an array of states to be used. As an example, KSTATE(1)=0,1,0,1 means use states 2 and 4. The

Input Description

$GMCPT

2-363

default is the ground state, KSTATE(1)=1,0,0... WSTATE is a set of weights for each state. The default is equal weight assigned to every state selected by KSTATE (WSTATE(1)=1.0, 1.0, 1.0, ...) specificies which state's energy should be saved for use in numerical gradient evaluation. IROOT counts only for those states included by KSTATE, so KSTATE(1)=0,1,0,1 and IROOT=2 refers to the second root computed (4th overall). Default: IROOT=1. spin adaptation (default=0) 0 means off, 1 means on (strictly), -1 means on (loosely). Proper spin states are picked up automatically so this input is usually skipped. See NSOLUT in this context. a flag to turn off space symmetry use, i.e. STSYM. .FALSE. will ignore symmetry (default=.TRUE.) a flag to ignore spin symmetry, i.e. MULT. Give as .FALSE. to ignore the spin (default=.TRUE.)

IROOT

ISPINA

KNOSYM KNOSPN

The next few influence the Davidson CI diagonalization, and are quite similar to $MCQDPT keywords, so the description here is terse. NSOLUT is the number of roots to be obtained. If there are not enough states of the correct spin found in the first NSOLUT states to satisfy KSTATE/WSTATE, increase this parameter to find enough. is the maximum number of Davidson iterations to find the states (default=200) is the convergence criterion on the CI coefficient convergence (default= 1.0d-6) is a convergence criterion on the total energy of the states. This is ignored if given as a negative number. (default = -1.0d-12 Hartree) maximum expansion space size in the Davidson diagonalization subspace (default=100)

MXITER THRCON THRENE

MAXBAS

Input Description

$GMCPT

2-364

MDI

dimension of the initial guess subspace used to initiate the Davidson iterative CI solver. See NHGSS in $DET for more information (default=300). 4. data to define perturbation theory computation:

KXGMC

a flag to choose the 0-th order Hamiltonian used, when more than one state is included by KSTATE and WSTATE. KXGMC has no impact on single state runs. .TRUE. selects Granovsky's XMCQDPT equations for the zero-th order Hamiltonian, see A.A.Granovsky, J.Chem.Phys. 134, 214113(2011). .FALSE. selects the original definition of the unperturbed Hamiltonian. The default is .TRUE. selects wavefunction analysis (default=1) 0 means off, 1 means on (external), -1 means on (internal orbitals). This will compute the approximate weight of the MCSCF reference CI in the first order wavefunction. It is therefore a very useful diagnostic for the quality of the calculation, as the MCSCF state should be a high percentage. The formula for the decomposition is changed from the original CAS-type MCQDPT (REFWGT in $MCQDPT), see Miyajima, Watanabe, and Nakano's reference cited below. Select IWGT=0 if the fastest speed is desired. flag to request canonicalization (default=.TRUE.) Canonicalization within the core, virtual, and any rotationally invariant active subspaces yields a well defined theoretical model. You would not normally turn this option off. flag for treating (ij)->(ab) exitations .TRUE. means treating this type of term by the traditional MCQDPT formulae .FALSE. uses a MP2-type formula when this type of term arises between two identical determinants, while using zero otherwise. This is thought to be better in terms of size-consistency. (default) KROT has an impact on run times and on the numerical result. See the paper cited below by

IWGT

KFORB

KROT

Input Description

$GMCPT

2-365

Ebisuzaki, Watanabe, and Nakano for details. THRWGT threshold weight on the square of CI coefficients, for determinant selection. Any determinants that are excluded from the reference list due to THRWGT are treated in the outer space of the perturbation. Give as a negative number to retain all of the determinants, even those of very little importance, in the reference of the perturbation treatment. The default is 1.0d-8.

KSZDOE

flag to use spin (Sz) dependent orbital energies. This variable is ignored for singlet state(s), or if SZ is chosen as 0. If .TRUE., alpha and beta orbital energies are not the same, Ealp(i) = h(i,i) + sum_kl { Dalp(k,l)[(ii|kl)-(il|ki)] +Dbet(k,l) (ii|kl)} Ebet(i) = h(i,i) + sum_kl { Dbet(k,l)[(ii|kl)-(il|ki)] +Dalp(k,l) (ii|kl)} If .FALSE. both sets use the energies E(i) = h(i,i) + sum_kl D(k,l)[(ii|kl)-1/2*(il|ki)] = [Ealp(i)+Ebet(i)]/2 from the total density D(k,l)=Dalp(k,l)+Dbet(k,l) Default=.TRUE. threshold on generator constants. Default=1.0d-9 Raising lowers accuracy but produces speedups. Lowering to 1.0d-12 should give full accuracy for benchmarking purposes. threshold to ignore |<I|V|nu>/dE|, which is not a very effective screening, and its use is thus not recommended. Default is 1.0 which should not screen anything. Possible values are 0.05-0.10, since many |<I|V|nu>/dE| are around 0.02-0.03.

THRGEN

THRHDE

The next two deal with the so-called "intruder state avoidance". There are theoretical difficulties with either one. THRDE just drops terms, so the potential surface may have small discontinuities. EDSHFT always shifts results a little bit, even if no small denominators (aka intruder states) are actually present. Clearly both are "band-

Input Description

$GMCPT

2-366

aids"! Note that the first ISA technique is turned on, by default. THRDE is a threshold to simply drop out any term whose energy denominator is too small. The default for this is 0.005 Hartree. Change to zero to turn this option off. is the same as the same keyword in $MCQDPT. The denominators D are changed to D + EDSHFT/D. Turn off THRDE if you select this option. A reasonable value to try is 0.02, the default is 0.0.

EDSHFT

5. miscellaneous data CEXCEN = string defining the units for the excitation energy. Choose from these 4 strings (any case): eV (default), cm-1, Kcal/mol, KJ/mol DDTFPT = a flag requesting the distributed data integral transformation be used, if the run is parallel. This option requires MEMDDI in $SYSTEM. If there is not enough memory to allow this, turn this option off to use an alternate parallel transformation (DEFAULT=.TRUE.). Note: There are additional technical parameters in the $GMCPT group, documented in the source code file gmcpt.src. ---In case it is desirable for the GMC-QDPT program to reproduce results obtained by the DETMRPT/MCQDPT programs: a) use a CAS-SCF reference in the MCSCF step b) select REFTYP=ORMAS here, and enter NSPACE=1, giving only one value for MSTART, MINE, MAXE c) retain the entire CAS reference in the internal determinant's perturbation space, THRWGT=-1.0 d) select the original external determinant space's perturbation treatment, KROT=.FALSE. e) use equal alpha/beta orbital energies, KSZDOE=.FALSE. f) in multi-state mode, select KXGMC off, to reproduce those program's 0-th order reference states g) ensure ISA is turned off, THRDE= -1.0

Input Description

$GMCPT

2-367

h) perhaps adjust numerical parameters to full accuracy, to increase the no. of decimals: THRGEN=1D-12, THRHDE=1D+10. References for GMC-QDPT: a) H.Nakano, R.Uchiyama, K.Hirao J.Comput.Chem. 23, 1166-1175(2002) b) M.Miyajima, Y.Watanabe, H.Nakano J.Chem.Phys. 124, 044101/1-9(2006) c) R.Ebisuzaki, Y.Watanabe, H.Nakano Chem.Phys.Lett. 442, 164-169(2007) The first paper introduced the theory, with further developments including reference state weights given in the second. The present computer code is based on the efficient formulation involving ionized intermediate determinants, as described in the third paper. ==========================================================

Input Description

$PDET/$ADDDET/$REMDET

2-368

==========================================================

$PDET

group

(required if NPDET>0 in $GMCPT)

This group defined the "parent" determinants, which will be excited to excitation level NEXCIT. There must be a total of NPDET determinants given in the group. Each determinant may have spaces at the front or rear, but not embedded within the string. An example, presuming NPDET=3, is $PDET 2200 2+-0 2-+0 $END ==========================================================

$ADDDET $REMDET

group group

(optional, if NPDET>0 in $GMCPT) (optional, if NPDET>0 in $GMCPT)

These two groups add (or remove) determinants from the reference list. The first line in the group tells how many determinants are contained in the group. $ADDDET/$REMDET 2 2002 +-02 $END These two determinants would be generated if the $PDET list was used with NEXCIT=2 (or higher), but this $REMDET would remove them from the generated total reference CI. ==========================================================

Input Description

$SODET

2-369

==========================================================

$SODET

group

(required if CITYP=FSOCI)

This group controls a full second order CI calculation using determinants (see also the keyword SOCI in $CIDRT). Most of the characteristics of the active space (such as NCORE, NACT, NELS) must be given in a $CIDET group, as a preliminary full CI according to $CIDET will be made. The FCI states will then used as the initial guess for the full second order CI. A few additional parameters may be given in this group, but many runs will not need to give any of these. NEXT NSOST = the number of external orbitals to be included. The default is the entire virtual MO space. = the number of states to be found in the SOCI. The default is copied from NSTATE in $CIDET.

MAXPSO = maximum expansion space size used in the SOCI. The default is copied from MXXPAN in $CIDET. ORBS = MOS means use the MCSCF orbitals, which should be allowed to undergo canonicalization (see the CANONC keyword in $MCSCF), or the input $VEC group in case SCFTYP=NONE. (default) NOS means to instead use the natural orbitals of the MCSCF.

==========================================================

Input Description

$DRT $CIDRT

2-370

==========================================================

$DRT group $CIDRT group

(required by MCSCF if CISTEP=GUGA) (required if CITYP=GUGA)

This group describes the Configuration State Functions (CSFs) used by the MCSCF or CI calculation. The Distinct Row Table (DRT) is the means by which the Graphical Unitary Group Approach (GUGA) specifies configurations. The group is spelled $DRT for MCSCF runs, and $CIDRT for CI runs. The main difference in these is NMCC versus NFZC. There is no default for GROUP, and you must choose one of FORS, FOCI, SOCI, or IEXCIT. GROUP = the name of the point group to be used. This is usually the same as that in $DATA, except for RUNTYP=HESSIAN, when it must be C1. Choose from the following: C1, C2, CI, CS, C2V, C2H, D2, D2H, C4V, D4, D4H. If your $DATA group is not listed, choose only C1 here. FORS = flag specifying the Full Optimized Reaction Space set of configuration should be generated. This is usually set true for MCSCF runs, but if it is not, see FORS in $MCSCF. (Default=.FALSE.) = flag specifying first order CI. In addition to the FORS configurations, all singly excited CSFs from the FORS reference are included. Default=.FALSE. = flag specifying second order CI. In addition to the FORS configurations, all singly and doubly excited configurations from the FORS reference are included. (Default=.FALSE.)

FOCI

SOCI

IEXCIT= electron excitation level, for example 2 will lead to a singles and doubles CI. This variable is computed by the program if FORS, FOCI, or SOCI is chosen, otherwise it must be entered. INTACT= flag to select the interacting space option. See C.F.Bender, H.F.Schaefer J.Chem.Phys. 55, 4798-4803(1971). The CI will include only those

Input Description

$DRT $CIDRT

2-371

CSFs which have non-vanishing spin couplings with the reference configuration. Note that when the Schaefer group uses this option for high spin ROHF references, they use Guest/Saunders orbital canonicalization. * * the next variables define the single reference * * The single configuration reference is defined by filling in the orbitals by each type, in the order shown. The default for each type is 0. Core orbitals, which are always doubly occupied: NMCC = number of MCSCF core MOs (in $DRT only). NFZC = number of CI frozen core MOs (in $CIDRT only). Internal orbitals, which are partially occupied: NDOC = number of doubly occupied MOs in the reference. NAOS = number of alpha occupied MOs in the reference, which are singlet coupled with a corresponding number of NBOS orbitals. NBOS = number of beta spin singly occupied MOs. NALP = number of alpha spin singly occupied MOs in the reference, which are coupled high spin. NVAL = number of empty MOs in the reference. External orbitals, occupied only in FOCI or SOCI: NEXT = number of external MOs. If given as -1, this will be set to all remaining orbitals (apart from any frozen virtual orbitals). NFZV = number of frozen virtual MOs, never occupied. * * the next two help with state symmetry * * STSYM= The symmetry of the electronic state. See $DET for possible values: use AP/APP in Cs, not primes. Default is the totally symmetric representation.

note: This option overwrites whatever symmetry is implied by NALP/NAOS/NBOS. It is easier to pick STSYM than to allow its inference from the singly occupied orbitals, which is a relic of ancient input files. NOIRR= controls labelling of the CI state symmetries. = 1 no labelling (default)

Input Description

$DRT $CIDRT

2-372

= 0 usual labelling. This can be very time consuming if the group is non-Abelian. =-1 fast labelling, in which all CSFs with small CI coefficients are ignored. This can produce weights quite different from one, due to ignoring small coefficients, but overall seems to work OK. Note that it is normal for the weights not to sum to 1 even for NOIRR=0 because for simplicity the weight determination is focused on the relative weights rather than absolute. However weight do not sum to one only for row-mixed MOs. = -2,-3... fast labelling and sets SYMTOL=10**NOIRR for runs other than TRANSITN. All irreps with weights greater than SYMTOL are considered. * * * the final choices are seldom used * * * MXNINT = Buffer size for sorted integrals. (default=20000) Adjust this upwards if the program tells you to, which may occur in cases with large numbers of external orbitals. MXNEME = Buffer size for energy matrix. NPRT (default=10000)

= Configuration printout control switch. This can consume a HUMUNGUS amount of paper! 0 = no print (default) 1 = print electron occupancies, one per line. 2 = print determinants in each CSF. 3 = print determinants in each CSF (for Ms=S-1).

==========================================================

Input Description

$MCSCF

2-373

==========================================================

$MCSCF

group

(for SCFTYP=MCSCF)

This group controls the MCSCF orbital optimization step. The difference between the five convergence methods is outlined in the Further Information chapter, which you should carefully study before trying MCSCF computations. --- the next chooses the configuration basis --CISTEP = ALDET chooses the Ames Lab. determinant full CI, and requires $DET input. (default) = ORMAS chooses an Occupation Restricted Multiple Active Space determinant CI, requiring both $DET and $ORMAS inputs. = GUGA chooses the graphical unitary group CSFs, and requires $DRT input. This is the only value usable with the QUAD converger. = GENCI chooses the Ames Laboratory general CI, and requires $GEN input. = GMCCI chooses the Kyushu University general CI, and requires $GMCPT input. --- the next five choose the orbital optimizer --FOCAS = a flag to select a method with a first order convergence rate. (default=.FALSE.) Parallel runs with FOCAS do not use MEMDDI. = a flag selecting an approximately second order convergence method, using an approximate orbital hessian. (default=.TRUE.) Parallel runs with SOSCF do not use MEMDDI.

SOSCF

FULLNR = a flag selecting a second order method, with an exact orbital hessian. (default=.FALSE.) Parallel runs with FULLNR require input of MEMDDI. QUAD = a flag to pick a fully quadratic (orbital and CI coefficient) optimization method, which is applicable to FORS or non-FORS wavefunctions. QUAD may not be used with state-averaging. (default = .FALSE.) This converger can be used only in serial runs.

Input Description

$MCSCF

2-374

JACOBI = a flag to pick a program that minimizes the MCSCF energy by a sequence of 2x2 Jacobi orbital rotations. This is very systematic in forcing convergence, although the number of iterations may be high and the time longer than the other procedures. This option does not compute the orbital Lagrangian, hence at present nuclear gradients may not be computed. (default = .FALSE.) This converger can be used only in serial runs. Note that FOCAS must be used only with FORS=.TRUE. in $DRT. The other convergers are usable for either FORS or non-FORS wavefunctions, although convergence is always harder in the latter case, when FORS below must be set .FALSE. --- the next apply to all convergence methods --ACURCY = the major convergence criterion, the maximum permissible asymmetry in the Lagrangian matrix. (default=1E-5, but 1E-6 if MPLEVL, CI, or FMO is selected.) ENGTOL = a secondary convergence criterion, the run is considered converged when the energy change is smaller than this value. (default=1.0E-10) MAXIT MICIT = Maximum number of iterations (default=100 for FOCAS, 60 for SOSCF, 30 for FULLNR or QUAD) = Maximum number of microiterations within a single MCSCF iteration. (default=5 for FOCAS or SOSCF, or 1 for FULLNR or QUAD) = The maximum memory to be used, the default is to use all available memory. (default=0)

NWORD

CANONC = a flag to cause formation of the closed shell Fock operator, and generation of canonical core orbitals. This will order the MCC core by their orbital energies. (default=.TRUE.) FORS = a flag to specify that the MCSCF function is of

Input Description

$MCSCF

2-375

the Full Optimized Reaction Space type, which is sometimes known as CAS-SCF. .TRUE. means omit active-active rotations from the optimization. Since convergence is usually better with these rotations included, the default is sensible: for FOCAS: .TRUE., for FULLNR or QUAD: .FALSE. for FULLNR or QUAD, and for SOSCF: .TRUE. for ALDET/GUGA but .FALSE. for ORMAS/GENCI) It is seldom a good idea to enter this keyword. EKT = a flag to cause generation of extended Koopmans' theorem orbitals and energies. (Default=.FALSE.) For this option, see R.C.Morrison and G.Liu, J.Comput.Chem., 13, 1004-1010 (1992). Note that the process generates non-orthogonal orbitals, as well as physically unrealistic energies for the weakly occupied MCSCF orbitals. The method is meant to produce a good value for the first I.P.

NPUNCH = MCSCF punch option (analogous to $SCF NPUNCH) 0 do not punch out the final orbitals 1 punch out the occupied orbitals 2 punch out occupied and virtual orbitals The default is NPUNCH = 2. NPFLG = an array of debug print control. This is analagous to the same variable in $CIINP. Elements 1,2,3,4,6,8 make sense, the latter controls debugging the orbital optimization.

--- the next refers to SOSCF optimizations --NOFO = number of FOCAS iterations before switching to the SOSCF converger. May be 0, 1, ... (default=1). One FOCAS iteration at the first geometry permits a canonicalization of the virtual space to occur, which is likely to be crucial for convergence. = set to 1 to remove redandant orbital Lagrangian elements in FMO-MCSCF. Note that corresponding orbital rotations will still be optimised but not considered when deciding whether a run converged. This option is only in effect if detached bonds

MCFMO

Input Description

$MCSCF

2-376

are present (for which redundant orbitals exist). Default: 1. (This variable is irrelevant except to FMO runs) --- the next three refer to FOCAS optimizations --CASDII = threshold to start DIIS (default=0.05) CASHFT = level shift value (default=1.0) NRMCAS = renormalization flag, 1 means do Fock matrix renormalization, 0 skips (default=1) --- the next applies to the QUAD method --(note that all FULLNR input is also relevant to QUAD) QUDTHR = threshold on the orbital rotation parameter, SQCDF, to switch from the initial FULLNR iterations to the fully quadratic method. (default = 0.05) --- The JACOBI converger accepts FULLNR options ----- NORB, NOROT, MOFRZ, and FCORE as input ----- all remaining input applies only to FULLNR --DAMP = damping factor, this is adjusted by the program as necessary. (default=0.0)

METHOD = DM2 selects a density driven construction of the Newton-Raphson matrices. (default). = TEI selects 2e- integral driven NR construction. See the 'further information' section for more details concerning these methods. TEI is slow! LINSER = a flag to activate a method similar to direct minimization of SCF. The method is used if the energy rises between iterations. It may in some circumstances increase the chance of converging excited states. (default=.FALSE.) FCORE = a flag to freeze optimization of the MCC core orbitals, which is useful in preparation for RUNTYP=TRANSITN jobs. Setting this flag will automatically force CANONC false. This option

Input Description

$MCSCF

2-377

is incompatible with gradients, so can only be used with RUNTYP=ENERGY. It is a good idea to decrease TOLZ and TOLE in $GUESS by two orders of magnitude to ensure the core orbitals are unchanged during input. (default=.FALSE.) --- the last four FULLNR options are seldom used --DROPC = a flag to include MCC core orbitals during the CI computation. The default is to drop them during the CI, instead forming Fock operators which are used to build the correct terms in the orbital hessian. (default = .TRUE.) = the number of orbitals to be included in the optimization, the default is to optimize with respect to the entire basis. This option is incompatible with gradients, so can only be used with RUNTYP=ENERGY. (default=number of AOs given in $DATA). = an array of orbitals to be frozen out of the orbital optimization step (default=none frozen). = an array of up to 250 pairs of orbital rotations to be omitted from the NR optimization process. The program automatically deletes all core-core rotations, all act-act rotations if FORS=.T., and all core-act and core-virt rotations if FCORE=.T. Additional rotations are input as I1,J1,I2,J2... to exclude rotations between orbital I running from 1 to NORB, and J running up to the smaller of I or NVAL in $TRANS.

NORB

MOFRZ NOROT

==========================================================

Input Description

$MRMP

2-378

==========================================================

$MRMP

group

(relevant if SCFTYP=MCSCF, MPLEVL=2)

This group allows you to specify which multi-reference perturbation program is executed. The results from these programs should never be called "CASPT2". That method is similar in spirit, but is a different set of equations, which are not numerically identical to those used below. The first two programs should be called MRMP when applied to a single state, and MCQDPT when applied to more than one state. See REFS.DOC for details about different multireference PTs. MRPT = DETMRPT requests a determinant program. The MCSCF computation must use CISTEP=ALDET, as this program inherits orbital spaces, and state selection options only from a $DET group. See $DETPT for related input. (default for most runs) = MCQDPT requests a CSF (GUGA based) program. Its advantages compared to DETMRPT are that it can do spin-orbit MRPT, apply energy denominator shifts in case of so-called "intruder states", or find the weight of the MCQDPT zeroth order state. CISTEP can be ALDET or GUGA, your choice. See $MCQDPT for related input. (default for RUNTYP=TRANSITN) = GMCPT requests a determinant based program that can use non-CAS type reference functions, including ORMAS or user defined lists. See $GMCPT for related input and more info.

Both the DETMRPT and MCQDPT programs produce numerically identical results, if you select a tight value of THRGEN=1D-12 for the latter program (in some cases you may also need to tighten their CI convergence criteria). Eight or more decimal place energy agreement between the two codes has been observed, when being careful about these cutoffs. This is true whether the codes are running in single state mode, which the literature calls MRMP, or in multi-state mode, which the literature calls MCQDPT.

Input Description

$MRMP

2-379

Generally speaking, the determinant code uses direct CI technology to avoid disk I/O, and is much faster when used with larger active spaces (particularly above 12 active orbitals). The determinant code uses essentially no disk space beyond that required by the MCSCF itself. The determinant code uses native integral transformation codes, including the distributed memory parallel transformation. However, the determinant code is perhaps a bit slower when there is a small active space and very many filled valence orbitals included in the PT. Both codes exploit distributed memory parallelization. The determinant program is relatively complete control of state weights and careful to read in only canonicalized virtual MOs if you pick RDVECS=.TRUE. new, and still lacks canonicalization. Be core, active, and with this program.

RDVECS = a flag controlling whether the orbitals should be MCSCF optimized in this run. A value of .TRUE. means that your converged MCSCF orbitals are being given in $VEC, and the program will branch to the perturbation treatement. (default=.FALSE.) notes: If you select RDVECS, and are not doing spin-orbit coupling with the CSF program, $GUESS method GUESS=MOREAD is used to process the orbitals. Its options such as NORB and PURIFY will apply to reading the $VEC group, and as always, MOREAD in $GUESS will orthogonalize. If you are the CSF program for spin-orbit coupling, $GUESS is ignored, and the $VEC or $VECn group must contain all virtuals. The orbitals will not be reorthogonalized unless you select the MODVEC option. In either case, if your orbitals are not orthogonal, you are better off repeating MCSCF with RDVECS=.FALSE.! MODVEC = 0 skip orthogonalization (default) = 1 do orthogonalization in the SO-MCQDPT program. ==========================================================

Input Description

$DETPT

2-380

==========================================================

$DETPT group

(relevant if SCFTYP=MCSCF and MPLEVL=2)

This input group applies to the determinant-based multi-reference perturbation theory program, if chosen by MRPT=DETMRPT in $MRMP group. When applied to only one state, the theory is known as multi-reference Moller-Plesset (MRMP), but the term MCQDPT is used when this theory is used in its multi-state form. Please note that this perturbation theory is not the same thing as the CASPT2 theory, and should -NEVER- be called that. A more complete discussion may be found in the 'Further Information' chapter. NVAL = number of filled valence orbitals in the MCSCF to be included in the dynamic correlation treatment. This is analogous to NMODOC in the $MCQDPT group. The number of frozen cores orbitals is found by subtracting NVAL from NCORE in $DET, so that you need not specify the chemical core's size. Also, there is no input for specifying the active space, which is inherited from $DET. The default for NVAL correlates valence orbitals, but freezes any chemical cores. = number of external orbitals to use. The default means to use all of them (default=-1). = a flag to use MCSCF natural orbitals rather than canonicalized orbitals as the basis of the PT. This changes the numerical results!!!

NEXT NOS

Omitting NPTST, IPTST, and WPTST is the simplest option, meaning that any state with a non-zero WSTATE in $DET is included in the pertubation. Canonicalization of the orbitals is normally done by the MCSCF program, see CANONC in $MCSCF. However, if not, or if the state weights are changed, the canonicalization is done in the perturbation code, according to CANON in this group. The default is the most computationally efficient. CANON = flag to request canonicalization. Default=.TRUE.

Input Description

$DETPT

2-381

Turning off canonicalization is for experimental purposes, so most runs should not avoid it. The canonicalization will be done in the perturbation code under three circumstances, RDVECS=.TRUE. was used, at the first geometry, the MCSCF step skipped canonicalization, or you enter NPTST/IPTST/SPTST information. Canonicalization uses the state averaged density matrix to build the "standard Fock operator", and involves diagonalizing its diagonal sub-blocks. NPTST = the number of states to include in generation of the unperturbed CAS states. If NPTST is chosen, spins of the states will be ignored, like using PURES=.F. in $DET, so you must be careful in your matching IPTST input. = an array of CAS-CI states to be included in the perturbation theory, give NPTST values. = an array of state weights. Like NPTST/IPTST, the default for WPTST is derived from WSTATE in $DET.

IPTST WPTST

example: NPTST=3 IPTST(1)=1,3,5 might be used to include three singlets, S0,S1,S2 in a MCQDPT-type treatment, but skip over T1 and T2. You will have done an earlier CI or MCSCF run, in order to know that you need NPTST five or higher to capture the lowest three singlets, and that these singlets appear where they do. NSTATE in $DET must be at least 5 in this example, to find enough roots. EDSHFT is the same as the same keyword in $MCQDPT. The denominators D are changed to D + EDSHFT/D. Reasonable values are 0.02 to 1D-4, if you need any shift at all. The default is 0.0.

==========================================================

Input Description

$MCQDPT

2-382

==========================================================

$MCQDPT

group

(relevant if SCFTYP=MCSCF and MPLEVL=2)

Controls 2nd order MCQDPT (multiconfiguration quasidegenerate perturbation theory) runs, if requested by MPLEVL=2 in $CONTRL. MCQDPT2 is implemented only for FORS (aka CASSCF) wavefunctions. The MCQDPT method is a multistate, as well as multireference perturbation theory. The implementation is a separate program, interfaced to GAMESS, with its own procedures for determination of the canonical MOs, CSF generation, integral transformation, CI in the reference CAS, etc. Therefore some of the input in this group repeats data given elsewhere, particularly for $DET/$DRT. Analytic gradients are not available. Spin-orbit coupling may be treated as a perturbation, included at the same time as the energy perturbation. If spin-orbit calculations are performed, the input groups for each multiplicity are named $MCQD1, $MCQD2, ... rather than $MCQDPT. Parallel calculation is enabled. When applied to only one state, the theory is known as multi-reference Moller-Plesset (MRMP), but the term MCQDPT is used when this theory is used in its multi-state form. Please note that this perturbation theory is not the same thing as the CASPT2 theory, and should -NEVER- be called that. A more complete discussion may be found in the 'Further Information' chapter. *** MCSCF reference wavefunction *** NEL MULT = = total number of electrons, including core. (default from $DATA and ICHARG in $CONTRL) spin multiplicity (default from $CONTRL) Number of orbitals in FORS active space (default is the active space in $DET or $DRT) number of frozen core orbitals, NOT correlated in the perturbation calculation. (default is number of chemical cores) number of orbitals which are doubly occupied in every MCSCF configuration, that is, not active

NMOACT = NMOFZC = NMODOC =

Input Description

$MCQDPT

2-383

NMOFZV =

orbitals, which are to be included in the perturbation calculation. (The default is all valence orbitals between the chemical core and the active space) number of frozen virtuals, NOT occupied during the perturbation calculation. The default is to use all virtuals in the MP2. (default=0)

If the input file does not provide a $DET or $DRT, the user must give NMOFZC, NMODOC, and NMOACT correctly here. STSYM = The symmetry of the target electronic state(s). See $DET for possible values: use AP/APP in Cs, not primes. This must be given, and need not match the state symmetry used in optimizing the orbitals by $DET or $DRT, although it often does. Default is the totally symmetric representation. NOSYM = 0 use CSF symmetry (see the STSYM keyword). off diagonal perturbations vanish if states are of different symmetry, so the most efficient computation is a separate run for every space symmetry. (default) 1 turn off CSF state symmetry so that all states are treated at once. STSYM is ignored. Presently this option does not seem to work!! -1 Symmetry purify the orbitals. Since $GUESS is not read by MCQDPT runs, this option can be used as a substitute for its PURIFY. After cleaning the orbitals, they are reorthogonalised within each irrep and within each group (core, double, active, virtual) separately. Since this occurs without MCSCF optimization if you have chosen to use RDVECS in $MRMP, it is *your* responsibility to ensure that any purification of the orbitals is small enough that the CAS energies for the original CASSCF and the CAS-CI performed during the MCQDPT are the same! *** perturbation specification *** KSTATE= state is used (1) or not (0) in the MCQDPT2. Maximum of 20 elements, including zeros. For example, if you want the perturbation correction to the second and the fourth roots,

Input Description

$MCQDPT

2-384

KSTATE(1)=0,1,0,1 See also WSTATE. (default=1,0,0,0,0,0,0,...) XZERO a flag to choose the 0-th order Hamiltonian used, when more than one state is included by KSTATE and WSTATE. XZERO has no impact on single state runs. .TRUE. selects Granovsky's XMCQDPT equations for the zero-th order Hamiltonian, see A.A.Granovsky, J.Chem.Phys. 134, 214113(2011). .FALSE. selects the original definition of the unperturbed Hamiltonian. The default is .FALSE. *** Intruder State Removal *** EDSHFT = energy denominator shifts. See also REFWGT. (default=0.0,0.0)

Intruder State Avoidance (ISA) calculations can be made by changing the energy denominators around poles (where the denominator is zero). Each denominator x is replaced by x + EDSHFT/x, so that far from the poles (when x is large) the effect of such change is small. EDSHFT is an array of two values, the first is used in spin-free MCQDPT, and the second is for spin-orbit MCQDPT. Both values are used if RUNTYP=TRNSTN, only the first is used otherwise. A suggested pair of values is 0.02,0.1, but experimentation with your system is recommended. Setting these values to zero is ordinary MCQDPT, whereas infinite collapses to the MCSCF reference. Note that the energy denominators (which are ket-dependent in MCQDPT) are changed in a different way for each ketvector, that is, for each row in MCQDPT Hamiltonian matrix. In other words, the zeroth order energies are not "universal", but state specific. This is strictly speaking an inconsistency in defining zeroth order energies that are usually chosen "universally". In order to maintain continuity when studying a PES, one usually uses the same EDSHFT values for all points on PES. In order to study the potential surface for any extended range of geometries, it is recommended to use ISA, as it is quite likely that one or more regions of the PES will be unphysical due to intruder states.

Input Description

$MCQDPT

2-385

For an example of how intruder states can appear at some points on the PES, see Figures 1,2,7 of K.R.Glaesemann, M.S.Gordon, H.Nakano Phys.Chem.Chem.Phys. 1, 967-975(1999) and also H.A.Witek, D.G.Fedorov, K.Hirao, A.Viel, P.-O.Widmark J.Chem.Phys. 116, 8396-406(2002) For a discussion of intruder state removal from MCQDPT, see H.A.Witek, Y.-K.Choe, J.P.Finley, K.Hirao J.Comput.Chem. 23, 957-965(2002) REFWGT = a flag to request decomposition of the second order energy into internal, semi-internal, and external contributions, and to obtain the weight of the MCSCF reference in the 1st order wave function. This option significantly increases the run time! When you run in parallel, only the transformation steps will speed up, as the PT part of the reference weight calculation has not been adapted for speedups (default=.FALSE.) The EDSHFT option does not apply if REFWGT is used. One purpose of using REFWGT is to try to understand the nature of the intruder states. *** Canonical Fock orbitals *** IFORB = 0 omit this step. = 1 determine the canonical Fock orbitals. (default) = 3 canonicalise the Fock orbitals averaged over all $MCQDx input groups.

This option pertains only to RUNTYP=TRANSITN. It is primarily meant to include spin-orbit coupling perturbation into the energy perturbation, but could also be used in conjunction with OPERAT=DM to calculate only the second order energy perturbation. IFORB=3 means that WSTATE is used as follows: In each $MCQDx group, the WSTATE weights are divided by the total number of states (sum(i) IROOTS(i)), so the sum over all WSTATE values in all $MCQDx groups is normalized to sum to 1. Thus there is no normalization to 1 within each $MCQDx group. This option might be used to speed up an atomic MCQDPT, e.g. if computing the 3-P ground state of carbon, one would want to average over all three spatial components of the P

Input Description

$MCQDPT

2-386

term, to be sure of spatial degeneracy, but then run the perturbation using symmetry, separately on the B1g+B2g+B3g subspecies (within D2h) of a P term. It is very important to give weights appropriate for the symmetry, the input requires care. WSTATE = weight of each CAS-CI state in computing the closed shell Fock matrix. You must enter 0.0 whenever the same element in KSTATE is 0. In most cases setting the WSTATEs for states to be included in the MCQDPT to equal weights is the best, and this is the default.

*** Miscellaneous options *** ISELCT is an option to select only the important CSFs for inclusion into the CAS-CI reference states. Set to 1 to select, or 0 to avoid selection of CSFs (default = 0) All CSFs in a preliminary complete active space CI whose CI coefficients exceed the square root of THRWGT are kept in a smaller CI to determine the zero-th order states. Note that the CSFs with smaller coefficients, while excluded from the reference states, are still used during the perturbation calculation, so most of their energy contribution is still retained. This can save appreciable computer time in cases with large active spaces. weight threshold for retaining CSFs in selected configuration runs. In quantum mechanics, the weight of a CSF is the square of its CI coefficient. (default=1d-6) threshold for one-, two-, and three-body density matrix elements in the perturbation calculation. The default gives about 5 decimal place accuracy in energies. Increase to 1.0D-12 if you wish to obtain higher accuracy, for example, in numerical gradients (default=1D-8). Tightening THRGRN and perhaps CI diagonalization should allow 7-8 decimal place agreement with the determinant code.

THRWGT =

THRGEN =

Input Description

$MCQDPT

2-387

THRENE = THRCON = MDI =

threshold for the energy convergence in the Davidson's method CAS-CI. (default=-1.0D+00) threshold for the vector convergence in the Davidson's method CAS-CI. (default=1.0D-06) dimension of small Hamiltonian diagonalized to prepare initial guess CI states. (default=50) maximum number of expansion vectors in the Davidson diagonalization subspace (e.g. MXXPAN). (default=50) number of states to be solved for in the Davidson's method, this might need to exceed the number of states in the perturbation treatment in order to "capture" the correct roots. maximum number of iterations to permit in the Davidson's diagonalization. print option, 0 gives normal printout, while <0 gives debug print (e.g. -1, -5, -10, -100) In particular, LPOUT=-1 gives more detailed timing information. (default=0)

MXBASE =

NSOLUT =

NSTOP LPOUT

= =

The next three parameters refer to parallel execution: DOORD0 = a flag to select reordering of AO integrals which speeds the integral transformations. This reduces disk writes, but increases disk reads, so you can try turning it off if your machine has slow writes. (default=.TRUE.) access 2e- integral file on every node, at the same time. This affects only runs with DOORD0 true, and it may be useful to turn this off in the case of SMP nodes sharing a common disk drive. (default=.TRUE.) a flag to delete file 56 containing halftransformed integrals after it has been used. This reduces total disk requirements

PARAIO =

DELSCR =

Input Description

$MCQDPT (default=.FALSE.)

2-388

if this file is big.

Note that parallel execution will be more effective if you use distributed memory, MEMDDI in $SYSTEM. Using AOINTS=DIST in $TRANS is likely to be helpful in situations with relatively poor I/O rates compared to communication, e.g. SMP enclosures forced to share a single scratch disk system. See PROG.DOC for more information on parallel execution. Finally, there are additional very specialized options, described in the source code routine MQREAD: IROT, LENGTH, MAXCSF, MAXERI, MAXROW, MXTRFR, THRERI, MAINCS, NSTATE ==========================================================

Input Description

$CASCI

2-389

==========================================================

$CASCI

group

(relevant to SCFTYP=RHF MPLEVL=2)

This group carries out the Improved Virtual Orbital Complete Active Space CI method of Freed, Chaudhuri, and co-workers. IVO-CASCI starts with a RHF reference, and then generates IVOs, which are used in a CI computation within an active space chosen by the user. The input consists of this group, the $MCQDPT group, and perhaps a $IVOORB group, along with SCFTYP=RHF and MPLEVL=2. MULT in $CONTRL applies to the SCF reference, while MULT in $MCQDPT selects the spin of the IVO-CASCI state(s). Doublets are treated by using a cation RHF reference. IVOCAS = a flag to turn on IVO-CASCI computation. This is usually the only input required (default=.FALSE.) MOLIST = a flag to request complete control over the active space specification. The default uses the parameters in $MCQDPT to select from the IVOs with the lowest energy. (default=.FALSE.) DEGENR = a flag to indicate the HOMO is degenerate. The program should set this for you. PRINT = a flag to print debugging info (default=.FALSE.)

The user should request IFORB=0 in $MCQDPT to suppress its generation of canonical orbitals, so that the IVOs are used. A Huckel guess is usually fine. The $MCQDPT should define the active orbitals taken from the IVO set by giving NMOFZC, NMODOC, and NMOACT, and the electronic state is specified by that group's MULT, NSTATE, and NSTSYM. References: D.M.Potts, C.M.Taylor, R.K.Chaudhuri, K.F.Freed J.Chem.Phys. 114, 2592-2600(2001) R.K.Chaudhuri, K.F.Freed, S.A.Abrash, D.M.Potts J.Mol.Spectrosc. 547, 83-96(2001) R.K.Chaudhuri, K.F.Freed J.Chem.Phys. 126, 114103/1-6(2007) A simple example follows,

Input Description

$CASCI

2-390

$contrl scftyp=rhf mplevl=2 runtyp=energy ispher=1 $end $casci IVOCAS=.true. $end $mcqdpt mult=3 stsym=b1 nstate=1 iforb=0 nel=8 nmofzc=1 nmodoc=2 nmoact=2 $end $basis gbasis=ccd $end $guess guess=huckel $end $data Methylene...3-B-1 state...RHF/cc-pVDZ Cnv 2 C H 6.0 1.0 $end 0.0 0.0 .0000000000 .9813851814 .0289123030 .4758735367

The result for the 1st order energy will be -38.9156231594, which is a full CI within a two orbital space, generated by the IVO process, rather than a more expensive MCSCF run. ==========================================================

$IVOORB
$CASCI)

group

(relevant if MOLIST=.T. in

In case the IVOs are not generated in the desired order, this group can fully specify the orbital counts in each irreducible representation. line 1: NIRREP - gives the total number of irreps line 2: NDIM, NCORE, NDOC, NUNOCC, NSING - for this irrep, gives its total dimension, the number of core MOs in the CASCI, and 3 parameters which define the active orbitals: filled, empty, and singly occupied (0,1 only) in the reference. Repeat NIRREP times. A 6 active e- example is $IVOORB 2 59 4 2 2 0 26 0 1 1 0 $END ==========================================================

Input Description

$CISORT $GUGEM

2-391

The input groups $CISORT, $GUGEM, $GUGDIA, $GUGDM, $GUGDM2, $LAGRAN, and $TRFDM2 pertain only to GUGA CI, chosen by either CITYP=GUGA or CISTEP=GUGA. The most important of these values may be given for determinant runs (using the same keyword spellings) in the $DET group. ==========================================================

$CISORT

group

(relevant for GUGA -CI- or -MCSCF-)

This group provides further control over the sorting of the transformed molecular integrals into the order the GUGA program requires. NDAR LDAR = Number of direct access records. (default = 2000) = Length of direct access record (site dependent)

NBOXMX = Maximum number of boxes in the sort. (default = 200) NWORD = Number of words of fast memory to use in this step. A value of 0 results in automatic use of all available memory. (default = 0) = 0 (set to one to force out of memory algorithm)

NOMEM

==========================================================

$GUGEM

group

(relevant for GUGA -CI- or -MCSCF-)

This group provides further control over the calculation of the energy (Hamiltonian) matrix. CUTOFF = Cutoff criterion for the energy matrix. (default=1.0E-8) NWORD = not used.

==========================================================

Input Description

$GUGDIA

2-392

==========================================================

$GUGDIA

group

(relevant for GUGA -CI- or -MCSCF-)

This group provides control over the Davidson method diagonalization step. NSTATE = Number of CI states to be found, including the ground state. (default=1, ground state only.) You can solve for any number of states, but only 100 can be saved for subsequent sections, such as state averaging. See IROOT in $GUGDM/$GUGDM2. PRTTOL = Printout tolerance for CI coefficients (default = 0.05) MXXPAN = Maximum no. of expansion basis vectors used before the expansion basis is truncated. (default=30) ITERMX = Maximum number of iterations (default=50) CVGTOL = Convergence criterion for Davidson eigenvector routine. This value is proportional to the accuracy of the coeficients of the eigenvector(s) found. The energy accuracy is proportional to its square. (default=1.0d-5, but 1E-6 if gradients, MPLEVL, CITYP, or FMO selected). NWORD = Number of words of fast memory to use in this step. A value of zero results in the use of all available memory. (default = 0)

MAXHAM = specifies dimension of Hamiltonian to try to store in memory. The default is to use all remaining memory to store this matrix in memory, if it fits, to reduce disk I/O to a minimum. MAXDIA = maximum dimension of Hamiltonian to send to an incore diagonalization. If the number of CSFs is bigger than MAXDIA, an iterative Davidson procedure is invoked. Default=100 NIMPRV = Maximum no. of eigenvectors to be improved every iteration. (default = nstate)

Input Description

$GUGDIA

2-393

NSELCT = Determines initial guess to eigenvectors. = 0 -> Unit vectors corresponding to the NSTATE lowest diagonal elements and any diagonal elements within SELTHR of them. (default) < 0 -> First abs(NSELCT) unit vectors. > 0 -> use NSELCT unit vectors corresponding to the NSELCT lowest diagonal elements. SELTHR = Guess selection threshold when NSELCT=0. (default=0.01) NEXTRA = Number of extra expansion basis vectors to be included on the first iteration. NEXTRA is decremented by one each iteration. This may be useful in "capturing" vectors for higher states. (default=5) On AXP processors, enter as 0 to avoid core dumps. KPRINT = Print flag bit vector used when NPFLG(4)=1 in the $CIINP group (default=8) value 1 bit 0 print final eigenvalues value 2 bit 1 print final tolerances value 4 bit 2 print eigenvalues and tolerances at each truncation value 8 bit 3 print eigenvalues every iteration value 16 bit 4 print tolerances every iteration Inputs for a multireference Davidson correction, in case the orbitals are from a MCSCF. NREF EREF = number of CSFs in the MCSCF (full CI) job. = the energy of the MCSCF reference.

==========================================================

Input Description

$GUGDM

2-394

==========================================================

$GUGDM

group

(relevant for GUGA -CI-)

This group provides further control over formation of the one electron density matrix. See NSTATE in $GUGDIA. NFLGDM = Array controlling each state's density formation. 0 -> do not form density for this state. 1 -> form density and natural orbitals for this state, print and punch occ.nums. and NOs. 2 -> same as 1, plus print density over MOs. The default is NFLGDM(1)=1,0,0,...,0 meaning only ground state NOs are generated. Note that forming the 1-particle density for a state is negligible compared to diagonalization time for that state. IROOT = The root whose density matrix is saved on desk for later computation of properties. You may save only one state's density per run. By default, this is the ground state (default=1).

WSTATE = An array of up to 100 weights to be given to the 1 body density of each state. The averaged density will be used for property computations, as well as "state averaged natural orbitals". The default is to use NFLGDM/IROOT, unless WSTATE is given, when NFLGDM/IROOT are ignored. It is not physically reasonable to average over any CI states that are not degenerate, but it may be useful to use WSTATE to produce a totally symmetric density when the states are degenerate. IBLOCK = Density blocking switch. If nonzero, the off diagonal block of the density above row IBLOCK will be set to zero before the (now approximate) natural orbitals are found. One use for this is to keep the internal and external orbitals in a FOCI or SOCI calculation from mixing, where IBLOCK is the highest internal orbital. (default=0) NWORD = Number of words of memory to use. all available memory (default=0). Zero means use

==========================================================

Input Description

$GUGDM2

2-395

==========================================================

$GUGDM2

group

(relevant for GUGA -CI- or -MCSCF-)

This group provides control over formation of the 2-particle density matrix. WSTATE = An array of up to 100 weights to be given to the 2 body density of each state in forming the DM2. The default is to optimize a pure ground state. (Default=1.0,99*0.0) A small amount of the ground state can help the convergence of excited states greatly. Gradient runs are possible only with pure states. IROOT = the MCSCF state whose energy will be used as the desired value. The default means to use the average (according to WSTATE) of all states as the FINAL energy, which of course is not a physically meaningful quantity. This is mostly useful for the numerical gradient of a specific state obtained with state averaged orbitals. (default=0). Be sure to set NSTATE in $GUGDIA appropriately! CUTOFF = Cutoff criterion for the 2nd-order density. (default = 1.0E-9) NWORD = Number of words of fast memory to use in sorting the DM2. The default uses all available memory. (default=0). = 0 uses in memory sort, if possible. = 1 forces out of memory sort. = Number of direct access records. (default=4000) = Length of direct access record (site dependent)

NOMEM NDAR LDAR

NBOXMX = Maximum no. of boxes in the sort. (default=200) ==========================================================

Input Description

$LAGRAN

2-396

==========================================================

$LAGRAN

group

(relevant for GUGA -CI- gradient)

This group provides further control over formation of the CI Lagrangian, a quantity which is necessary for the computation of CI gradients. NOMEM = = NWORD = NDAR LDAR 0 form in core, if possible 1 forces out of core formation 0 (0=use all available memory)

= 4000 = Length of each direct access record (default is NINTMX from $INTGRL)

==========================================================

Input Description

$TRFDM2

2-397

==========================================================

$TRFDM2

group

(relevant for GUGA -CI- gradient)

This group provides further control over the back transformation of the 2 body density to the AO basis. NOMEM = = = NWORD = 0 transform and sort in core, if possible 1 transform in core, sort out of core, if poss. 2 transform out of core, sort out of core 0 (0=use all available memory)

CUTOFF= 1.0D-9, threshold for saving DM2 values NDAR LDAR = 2000 = Length of each direct access record (default is system dependent)

NBOXMX= 200 ========================================================== Usually neither $LAGRAN or $TRFDM2 group are given. Since these groups are normally used only for CI gradient runs, we list here the restrictions on the GUGA CI gradients: a) SCFTYP=RHF, only b) no FZV orbitals in $CIDRT, all MOs must be used. c) the derivative integrals are computed in the 2nd derivative code, which is limited to spd basis sets. d) the code does not run in parallel. e) Use WSTATE in $GUGDM2 to specify the state whose gradient is to be found. Use IROOT in $GUGDM to specify the state whose other properties will be found. These must be the same state! f) excited states often have different symmetry than the ground state, so think about GROUP in $CIDRT. g) the gradient can probably be found for any CI for which you have sufficient disk to do the CI itself. Time is probably about 2/3 additional. See also $CISGRD for CI singles gradients. ===========================================================

Input Description

$TRANST

2-398

$TRANST

group

(relevant for RUNTYP=TRANSITN) (only for CITYP=GUGA or MPLEVL=2)

This group controls the evaluation of the radiative transition moment, or spin orbit coupling (SOC). An SOC calculation can be based on variational CI wavefunctions, using GUGA CSFs, or based on 2nd order perturbation theory using the MCQDPT multireference perturbation theory. These are termed SO-CI and SO-MCQDPT below. The orbitals are typically obtained by MCSCF computations, and since the CI or MCQDPT wavefunctions are based on those MCSCF states, the zero-th order states are referred to below as the CAS-CI states. SOC jobs prepare a model Hamiltonian in the CAS-CI basis, and diagonalize it to produce spinmixed states, which are linear combinations of the CAS-CI states. If scalar relativistic corrections were included in the underlying spin-free wavefunctions, it is possible either to include or to neglect similar corrections to the spin-orbit integrals, see keyword NESOC in $RELWFN. An input file to perform SO-CI will contain SCFTYP=NONE CITYP=GUGA MPLEVL=0 RUNTYP=TRANSITN while a SO-MCQDPT calculation will have SCFTYP=NONE CITYP=NONE MPLEVL=2 RUNTYP=TRANSITN The SOC job will compute a Hamiltonian matrix as the sum of spin-free terms and spin-orbit terms, H = H-sf + H-so. For SO-CI, the matrix H-sf is diagonal in the CAS-CI state basis, with the LS-coupled CAS-CI energies as the diagonal elements, and H-so contains only off-diagonal couplings between these LS states, H-sf = CAS-CI spin-free E H-so = CAS SOC Hamiltonian (e.g. HSO1, HSO2P, HSO2) For SO-MCQDPT, the additional input PARMP defines these matrices differently. For PARMP=0, the spin-free term has diagonal and off-diagonal MCQDPT perturbations: H-sf - CAS-CI spin-free E + 2nd order spin-free MCQDPT H-so - CAS SOC Hamiltonian For PARMP not equal to 0, the spin orbit operator is also included into the perturbing Hamiltonian of the MCQDPT: H-sf - CAS-CI spin-free E + 2nd order spin-free MCQDPT H-so - CAS SOC Hamiltonian + 2nd order SO-MCQDPT Pure transition moment calculations (OPERAT=DM) are presently limited to CI wavefunctions, so please use only

Input Description

$TRANST

2-399

CITYP=GUGA MPLEVL=0. The transition moments computed by SO-MCQDPT runs (see TMOMNT flag) will form the transition density for the CAS-CI zeroth order states rather than the 1st order perturbed wavefunctions. Please see REFS.DOC for additional information on what is actually a fairly complex input file to prepare. OPERAT selects the type of transition being computed. = DM calculates radiative transition moment between states of same spin, using the dipole moment operator. (default) = HSO1 one-electron Spin-Orbit Coupling (SOC) = HSO2P partial two electron and full 1e- SOC, namely core-active 2e- contributions are computed, but active-active 2e- terms are ignored. This generally captures >90% of the full HSO2 computation, but with spin-orbit matrix element time similar to the HSO1 calculation. = HSO2 one and two-electron SOC, this is the full Pauli-Breit operator. = HSO2FF one and two-electron SOC, the form factor method gives the same result as HSO2, but is more efficient in the case of small active spaces, small numbers of CAS-CI states, and large atomic basis sets. This final option applies only to SO-CI. PARMP = controls inclusion of the SOC terms in SO-MCQDPT, for OPERAT=HSO1 (default=1) or for HSO2P/HSO2 (default=3) only. 0 - no SOC terms should be included in the MCQDPT corrections at 2nd order, but they will be included in the CAS states on which the MCQDPT (i.e. up to 1st order) 1 - include the 1e- SOC perturbation in MCQDPT -1 - defined under "3", read on... 3 - full 1-electron and partial 2-electron in the form of the mean field perturbation (this is very similar to HSO2P, but in the MCQDPT2 perturbation). Only doubly occupied orbitals (NMODOC) are used for the core 2e terms. If the option is set to -1, then all core orbitals (NMOFZC+NMODOC) are used. Neither

Input Description

$TRANST

2-400

calculation includes extra diagrams including filled orbitals, so both are "partial". PARMP=3 (or -1) has almost no extra cost compared to PARMP=1, but can only be used with OPERAT=HSO2 or HSO2P. The options -1 and 3 are not rigorously justified, contrary to HOS2P for a SO-CI, as 2e integrals with 2 core indices appear in the second order in two ways. There is a meanfield addition to 1e integrals, which is included when you choose PARMP=3 or -1. But, there are separate terms from additional diagrams that are not implemented, so that there is some imbalance in including the partial 2e correction. Nevetheless, it may be better to include such "partial" partial 2e contributions than not to. Note that at first order in the energy (the CAS-CI states) the N-electron terms are treated exactly as specified by OPERAT. NFFBUF = sets buffer size for form factors in SO-MCQDPT. (applies only to OPERAT = HSO1, HSO2 or HSO2P). This is a very powerful option that speeds up SO-MCQDPT calculations by precomputing the total multiplicative factor in front of each diagram so that the latter is computed only once (this is in fact what happens in MCQDPT). It is not uncommon for this option to speed up calculations by a factor of 10. Since this option forces running the SO-CASCI part twice (due to the SO-MCQDPT Hamiltonian being non-Hermitian), it is possible that in rare cases NFFBUF=0 may perform similarly or better. The upper bound for NFFBUF is NACT**2, where NACT=NOCC-NFZC. Due to the sparseness of the coupling constants it is usually sufficient to set NFFBUF to 3*NACT. To use the older way of dynamically computing form factors and diagrams on the fly, set NFFBUF to 0. Default: 3*(NOCC-NFZC) It is advisable to tighten up the convergence criteria in the $MCQDx groups since SOC is a fairly small effect, and the spin-free energies should be accurately computed, for example THRCON=1e-8 THRGEN=1e-10. PARMP has a rather different meaning for OPERAT=HSO2FF: It refers to the difference between ket and bra's Ms, -1 do matrix elements for ms=-1 only 0 do matrix elements for ms=0 only 1 do matrix elements for ms=1 only

Input Description

$TRANST

2-401

-2 do matrix elements for all ms (0, 1, and -1), which is the default. -3 calculates form factors so they can be saved * * * next defines the orbitals and wavefunctions * * * NUMCI = For SO-CI, this parameter tells how many CI calculations to do, and therefore defines how many $DRTx groups will be read in. For SO-MCQDPT, this parameter tells how many MCQDPT calculations to do, and therefore defines how many $MCQDx groups will be read in. (default=1) IROOTS, IVEX, NSTATE, and ENGYST below will all have NUMCI values. NUMCI may not exceed 64. You may wish to define one $DRTx or $MCQDx group for each spatial symmetry representation occuring within each spin multiplicity, as the use of symmetry during these separate calculations may make the entire job run much faster. NUMVEC = the meaning is different depending on the run: a) spin-orbit CI (SO-CI), Gives the number of different MO sets. This can be either 1 or 2, but 2 can be chosen only for FORS/CASSCF or FCI wavefunctions. (default=1) If you set NUMVEC=2 and you use symmetry in any of the $DRTx groups, you may have to use STSYM in the $DRT groups since the order of orbitals from the corresponding orbital transformation is unpredictable. b) spin-orbit perturbation (SO-MCQDPT), The option to have different MOs for different states is not implemented, so your job will have only one $VEC1 group, and IVEX will not normally be input. The absolute value of NUMVEC should be be equal to the value of NUMCI above. If NUMVEC positive, the orbitals in the $VEC1 will be used exactly as given, whereas if NUMVEC is a negative number, the orbitals will be canonicalized according to IFORB in $MCQDx. Using NUMVEC=-NUMCI and IFORB=3 in all $MCQDx to canonicalize over all states is recommended. Note that $GUESS is not read by this RUNTYP! Orbitals must be in $VEC1 and possibly $VEC2 input groups.

Input Description

$TRANST

2-402

NFZC

= For SO-CI, this is equal to NFZC in each $DRTx group. When NUMVEC=2, this is also the number of identical core orbitals in the two vector sets. For SO-MCQDPT, this should be NMOFZC+NMODOC given in each of the $MCQDx groups. The default is the number of AOs given in $DATA, this is not very reasonable. = the number of occupied orbitals. For SO-CI this should be NFZC+NDOC+NALP+NAOS+NBOS+NVAL, but add the external orbitals if the CAS-CI states are CI-SD or FOCI or SOCI type instead of CAS. For SO-MCQDPT enter NUMFZC+NUMDOC+NUMACT. The default is the number of AOs given in $DATA, which is not usually correct.

NOCC

Note: IROOTS, NSTATE, ENGYST, IVEX contain NUMCI values. IROOTS = array containing the number of CAS-CI states to be used from each CI or MCQDPT calculation. The default is 1 for every calculation, which is probably not a correct choice for OPERAT=DM runs, but is quite reasonable for the HSO operators. The total number of states included in the SOC Hamiltonian is the summation of the NUMCI values of IROOTS times the multiplicity of each CI or MCQDPT. See also ETOL/UPPREN. NSTATE = array containing the number of CAS-CI states to be found by diagonalising the spin-free Hamiltonians. Of these, the first IROOTS(i) states will be used to find transition moments or SOC. Obviously, enter NSTATE(i) >= IROOTS(i). The default for NSTATE(i) is IROOTS(i), but might be bigger if you are curious about the additional energies, or to help the Davidson diagonalizer. NSTATE is ignored by SO-MCQDPT runs, and you must ensure that your IROOTS input corresponds to the KSTATE option in $MCQDx. ETOL = energy tolerance for CI state elimination. This applies only to SO-CI and OPERAT=HSO1,2,2P. After each CI finds NSTATE(i) CI roots for each $DRTx, the number of states kept in the run is

Input Description

$TRANST

2-403

normally IROOTS(i), but ETOL applies the further constraint that the states kept be within ETOL of the lowest energy found for any of the $DRTx. The default is 100.0 Hartree, so that IROOTS is the only limitation. UPPREN = similar to ETOL, except it is an absolute energy, instead of an energy difference. IVEX = Array of indices of $VECx groups to be used for each CI calculation. The default for NUMVEC=2 is IVEX(1)=1,2,1,1,1,1,1..., and of course for NUMVEC=1, it is IVEX(1)=1,1,1,1,1... This applies only to CITYP=GUGA jobs.

ENGYST = energy values to replace the spin-free energies. This parameter applies to SO-CI only. A possible use for this is to use first or second order CI energies (FOCI or SOCI in $DRT) on the diagonal of the Hamiltonian (obtained in some earlier runs) but to use only CAS wavefunctions to evaluate off diagonal HSO matrix elements. The CAS-CI is still conducted to get CI coefs, needed to evaluate the off diagonal elements. Enter MXRT*NUMCI values as a square array, by the usual FORTRAN convention (that is, MXRT roots of $DRT1, MXRT roots of $DRT2 etc), in hartrees, with zeros added to fill each column to MXRT values. MXRT is the maximum value in the IROOTS array. (the default is the computed CAS-CI energies) See B.Schimmelpfennig, L.Maron, U.Wahlgren, C.Teichteil, H.Fagerli, O.Gropen Chem.Phys.Lett. 286, 261-266(1998). * * * the next pertain only to spin-orbit runs * * * ISTNO if given as positive values: an array of one or two state indices which govern computation of the density matrix of one state, or the transition density of two states. if given as negative values: one state-averaged density with equal weights. ISTNO(1)=5 state-specific density of state 5 ISTNO(1)=1,2 transition density between 1 and 2

Input Description

$TRANST

2-404

ISTNO(1)=-1,-6 state-average all states 1 to 6 The default is ISTNO(1)=0,0 meaning no density. Computation of the density gives access to the full Gaussian property package, except Mulliken populations. At present, computation of the transition density does just that, without any oscillator strengths. If the computation is of SO-MCQDPT type, the density or transition density that is computed will be that for the unperturbed SO-CASCI states. DEGTOL = array of two tolerances to help define what states are considered degenerate. This is ignored except for linear molecules or atoms. The purpose is to decide what states are grouped together during the determination of simultaneous eigenstates of the spin-orbit Hamiltonian and Jz. DEGTOL(1) is in wavenumbers, and defines which spin-orbit states have the same energy. DEGTOL(2) is in units of electrons, and defines which natural orbitals are considered to be degenerate. If the Jz values in your run seem incorrect, tighten or relax the two degeneracy tolerances to get the correct groupings of the states. Default= 0.02,0.002 RSTATE = sets the zero energy level format: ndrt*1000+iroot for adiabatic state (root) 0000 sets zero energy to the lowest diabatic root default: 1001 (1st root in $DRT1 or $MCQD1) ZEFTYP specifies effective nuclear charges to use. = TRUE uses true nuclear charge of each atom, except protons are removed if an ECP basis is being used (default). = 3-21G selects values optimized for the 3-21G basis, but these are probably appropriate for any all electron basis set. Rare gases, transition metals, and Z>54 will use the true nuclear charges. = SBKJC selects a set obtained for the SBKJC ECP basis set, specifically. It may not be sensible to use these for other ECP sets. Rare gases, lanthanides, and Z>86 will use

Input Description

$TRANST the true nuclear charges.

2-405

ZEFF

= an array of effective nuclear charges, overriding the charges chosen in ZEFTYP. Note that effective nuclear charges can be used for any HSO type OPERAT, but traditionally these are used mainly for HSO1 as an empirical correction to the omission of the 2e- term, or to compensate for missing core orbitals in ECP runs.

ONECNT = uses a one-center approximation for SOC integrals: = 0 compute all SOC integrals without approximations = 1 compute only one-center 1e and 2e SOC integrals = 2 compute all 1e, but only one-center 2e integrals Numerical tests indicate the error of the one-center approximation (ONECNT=1) is usually on the order of a few wavenumbers for Li-Ne (a bit larger for F) and its errors appear to become negligible for anything heavier than Ne. ONECNT=1 appears to give a better balanced description than ONECNT=2. Very careful users can check how well the approximation works for their particular system by using ONECNT=0, then ONECNT=1, to compare the results. One important advantage of ONECNT=1/2 is that this removes the dependence of SOC 2e integrals upon the molecular geometry. This means the program needs to compute SOC 2e integrals only once for a given set of atoms and then they can be read by using SOC integral restart. RUNTYP=SURFACE automatically takes advantage of this fact. JZ controls the calculation of Jz eigenvalues = 0 do not perform the calculation = 1 do the calculation By default, Jz is set to 1 for molecules that are recognised as linear (this includes atoms!). Jz cannot be computed for nonlinear molecules. The matrix of Jz=Lz+Sz operator is constructed between spin-mixed states (eigenvalues of Hso). Setting Jz to 1 can enforce otherwise avoided (by symmetry) calculations of SOC matrix elements. JZ applies only to HSO1,2,2P.

TMOMNT = flag to control computation of the transition

Input Description

$TRANST

2-406

dipole moment between spin-mixed wavefunctions (that is, betweeen eigenvectors of the Pauli-Breit Hamiltonian). Applies only to HSO1,2,2P. (default is .FALSE.) SKIPDM = flag to omit(.TRUE.) or include(.FALSE.) dipole moment matrix elements during spin-orbit coupling. Usually it takes almost no addition effort to calculate <R> excluding some cases when the calculation of forbidden by symmetry spin-orbit coupling matrix elements <Hso> may have to be performed since <R> and <Hso> are computed simultaneously. Applies only to HSO1,2,2P. Since the lack of a MCQDPT density matrix means there are no MCQDPT dipole moments at present, SO-MCQDPT jobs will compute the dipole matrix elements for the CAS-CI states only. However, the dipole moments in the spin-mixed states will be computed with the MCQDPT mixing coefficients. (default is .TRUE.) IPRHSO = controls output style for matrix elements (HSO*) =-1 do not output individual matrix elements otherwise these are accumulative: = 0 term-symbol like kind of labelling: labels contain full symmetry info (default) = 1 all states are numbered consequently within each spin multiplicity (ye olde style) = 2 output only nonzero (>=1e-4) matrix elements PRTPRM = flag to provide detailed information about the composition of the spin-mixed states in terms of adiabatic states. This flag also provides similar information about Jz (if JZ set). (default is .FALSE.) LVAL = additional angular momentum symmetry values: For the case of running an atom: LVAL is an array of the L values (L**2 = L(L+1)) for each $MCQD/$DRT group (L=0 is S, 1 is P, etc.) For the case of running a linear molecule: LVAL is an array that gives the |Lz| values. Note that real-valued wavefunctions (e.g. Pi-x, Pi-y) have Lz and -Lz components mixed, so you should input |Lz| as 1 and 1 for both Pi-x and Pi-y.

Input Description

$TRANST

2-407

This parameter should not be given for a nonlinear polyatomic system. Default: all set to -1 (that is, do not use these additional symmetry labels. It is the user's responsibility to ensure the values' correctness. Note that for SO-MCQDPT useful options in $MCQDPT are NDIAOP and KSTATE. They enable efficient separation of atomic/linear symmetry irreps). It is acceptable to set only some values and leave others as -1, if only some groups have definite values. Note that normally Lz values are printed at the end of the log file, so its easy to double check the initial values for LVAL. For the case of atoms LVAL drastically reduces the CPU time, as it reduces a square matrix to tridiagonal form. For the case of linear molecules the savings at the spin-orbit level are somewhat less, but they are usually quite significant at the preceding spin-free MCQDPT step. MCP2E = Model Core Potential SOC 2e contributions. Note that MCP 1e contributions are handled as in case of all-electron runs because MCP orbitals contain all proper nodes). = 0 do not add the MCP 2e core-active contribution, but add any other 2e- terms asked for by OPERAT. = 1 add this contribution, but no other 2e SOC term. This is recommended, and the default. = 2 add this contribution and the 2e- contributions requested by OPERAT, for any e- which are being treated by quantum mechanics (not MCP cores). Note that for MCP2E=0 and 2, HSO2, HSO1, HSO2P values of OPERAT are supported for the explicit 2e- contributions. The recommended approach is to assume that MCP alone can capture all the 2e SOC, for this use MCP2E=1 OPERAT=HSO2P. The entire 2econtribution is achieved with MCP2E=2 OPERAT=HSO2. If your MCP leaves out many core electrons as particles, MCP2E=2 OPERAT=HSO2P can be tested to see if it adds a sizable amount to SOC, compared to MCP2E=1 OPERAT=HSO2P).

Input Description

$TRANST

2-408

MCP2E=2 OPERAT=HSO1 is an illegal combination. MCP2E=1 OPERAT=HSO1 is illogical since the MCP 2e integrals are computed but not used anywhere. The following table explains MCP2E and gives all useful combinations: MCP2E/OPERAT 2e SOC contributions SOC 2e ints 2 HSO2 MCPcore-CIact + CIcore-CIact MCP+basis + CIact-CIact 2 HSO2P MCPcore-CIact + CIcore-CIact MCP+basis 1 HSO2P MCPcore-CIact MCP using the following orbital space definitions: MCPcore orbitals whose e- are replaced by MCP CIcore always doubly occupied CIact MOs allowed to have variable occupation * * * expert mode HSO control options * * * MODPAR = parallel options, which are independent bit options, 0=off, 1=on. Bit 1 refers only to HSO2FF, bit 2 to HSO1,2,2P. Enter a decimal value 0, 1, 2, 3 meaning binary 00, 01, 10, 11. bit 1 = 0/1 (HSO2FF) uses static/dynamic load balancing in parallel if available, otherwise use static load balancing. Dynamic algorithm is usually faster but may utilize memory less efficiently, and I/O can slow it down. Also, dynamical algorithm forces SAVDSK=.F. since its unique distribution of FFs among nodes implies no savings from precalculating form factors. bit 2 = 0/1 (HSO1,2,2P) duplicate/distribute SOC integrals in parallel. If set, 2e AO integrals and the four-index transformation are divided over nodes (distributed), and SOC MO integrals are then summed over nodes. The default is 3, meaning both bits are set on (11)

PHYSRC = flag to force the size of the physical record to be equal to the size of the sorting buffers. This option can have a dramatic effect on the efficency. Usually, setting PHYSRC=.t. is helpful if the code complains that low memory enforces SLOWFF=.TRUE., or you set it yourself. For large active spaces and large memory (more precisely, if

Input Description

$TRANST

2-409

reclen is larger than the physical record size) PHYSRC=.TRUE. can slow the code down. Setting PHYSRC to .true. forces SLOWFF to be .false. See MODPAR. (default .FALSE.) (only with HSO2FF) RECLEN = specifies the size of the record on file 40, where form factors are stored. This parameter significantly affects performance. If not specified, RECLEN have to be guessed, and the guess will usually be either an overestimate or underestimate. If the former you waste disk space, if the latter the program aborts. Note that RECLEN will be different for each pair of multiplicities and you must specify the maximum for all pairs. The meaning of this number is how many non-zero form factors are present given four MO indices. You can decrease RECLEN if you are getting a message "predicted sorting buffer length is greater than needed..." Default depends on active space. (only HSO2FF) SAVDSK = flag to repeat the form factor calculation twice. This avoids wasting disk space as the actually required record size is found during the 1st run. (default=.FALSE.) (only with HSO2FF) SLOWFF = flag to choose a slower FF write-out method. By default .FALSE., but this is turned on if: 1) not enough memory for the fast way is available 2) the maximum usable memory is available, as when the buffer is as large as the maximum needed, then the "slow FF" algorythm is faster. Generally SLOWFF=.true. saves up to 50% or so of disk space. See PHYSRC. (only with HSO2FF) ACTION controls disk file DAFL30 reuse. = NORMAL calculate the form factors in this run. = SAVE calculate, and store the form factors on disk for future runs with the same active space characteristics. = READ read the form factors from disk from an earlier run which used SAVE. (default=NORMAL) (only with HSO2FF) Note that currently in order to use ACTION = SAVE or READ you should specify MS= -1, 0, or 1

Input Description

$TRANST

2-410

* * * some control tolerances * * * NOSYM= -1 forces use of symmetry-contaminated orbitals symmetry analysis, otherwise the same as NOSYM=0 = 0 fully use symmetry = 1 do not use point group symmetry, but still use other symmetries (Hermiticity, spin). = 2 use no symmetry. Also, include all CSFs for HSO1, 2, 2P. = 3 force the code to assume the symmetry specified in $DATA is the same as in all $DRT groups, but is otherwise identical to NOSYM=-1. This option saves CPU time and money(memory). Since the $DRT works by mapping non-Abelian groups into their highest Abelian subgroup, do not use NOSYM=3 for non-Abelian groups. SYMTOL = relative error for the matrix elements. This parameter has a great impact upon CPU time, and the default has been chosen to obtain nearly full accuracy while still getting good speedups. (default=1.0E-4) * * * the remaining parameters are not so important * * * PRTCMO = flag to control printout of the corresponding orbitals. (default is .FALSE.) HSOTOL = HSO matrix elements are considered zero if they are smaller than HSOTOL. This parameter is used only for print-out and statistics. (default=1.0E-1 cm-1) TOLZ TOLE = MO coefficient zero tolerance (as for $GUESS). (default=1.0E-8) = MO coefficient equating tolerance (as for $GUESS). (default=1.0E-5)

========================================================== * * * * * * * * * * * * * * * * * * * For information on RUNTYP=TRANSITN,

Input Description

$TRANST

2-411

see the 'further information' section * * * * * * * * * * * * * * * * * * *

Input Description

group name index

2-412

Here is an alphabetical listing of all input group names:

ADDDET, 368 ALPDR, 189 AUXBAS, 88 BASIS, 24 CASCI, 389 CCINP, 89 CCRES, 331 CEDATA, 357 CEEIS, 355 CIDET, 347 CIDRT, 370 CIGEN, 347 CIINP, 345 CIS, 77 CISORT, 391 CISVEC, 80 CONTRL, 6, 144 COSGMS, 267 CPHF, 121 DAMP, 235 DAMPGS, 238 DANDC, 321 DATA, 34 DATAL, 34 DATAS, 34 DCCORR, 327 DET, 347 DETPT, 380 DFT, 58 DIPDR, 124 DISBS, 257 DISREP, 258 DM, 107 DRC, 136 DRT, 370 ECP, 270 EFIELD, 283 EFRAG, 212 ELDENS, 176 ELFLDG, 177 ELG, 319 ELMOM, 173 ELPOT, 175 EOMINP, 93 EQGEOM, 131 EWALD, 231 FFCALC, 200 FFDATA, 332 FFPDB, 332 FMM, 287 FMO, 290 FMOEND, 316 FMOENM, 316 FMOHYB, 314 FMOPRP, 299 FMOXYZ, 309 FORCE, 117 FRAGNAME, 219 FRGRPL, 229 GAMMA, 131 GCILST, 358 GDDI, 317 GEN, 347 GLOBOP, 153 GLOWT, 131 GMCPT, 360 GRAD, 123 GRADEX, 158 GRID, 178 GUESS, 103 GUGDIA, 392 GUGDM, 394 GUGDM2, 395 GUGEM, 391 HESS, 123 HLOWT, 131 QMEFP, 198 IEFPCM, 253 INTGRL, 285 IRC, 132 IVOORB, 390 LAGRAN, 396 LIBE, 48 LMOEDA, 196 LOCAL, 163 MAKEFP, 232 MASS, 121 MCP, 273 MCQDPT, 382 MCSCF, 373 MD, 147 MEX, 141 MOFRZ, 107 MOLGRF, 184 MOPAC, 102 MOROKM, 192 MP2, 81 MP2RES, 331 MRMP, 378 NEWCAV, 251 NMR, 190 OPTFMO, 312 OPTRST, 316 ORMAS, 353 PCM, 239 PCMCAV, 247 PCMGRD, 252 PCMITR, 254 PDC, 179 PDET, 368 POINTS, 178 PRTEFP, 233 RADIAL, 182 RAMAN, 188 RDF, 151 RELWFN, 277 REMDET, 368 RIMP2, 85 SCF, 49 SCFMI, 56 SCRF, 269 SODET, 369 STATPT, 108 STONE, 185 SUBCOR, 330 SUBSCF, 330 SURF, 161 SVP, 260 SVPIRF, 266 SYSTEM, 21 TDDFT, 71 TDHF, 203 TDHFX, 207 TESCAV, 249 TRANS, 288 TRANST, 398 TRFDM2, 397 TRUDGE, 114 TRUNCN, 170 TRURST, 116 VEC, 107 VEC1, 107 VEC2, 107 VIB, 124 VIB2, 124 VIBSCF, 130 VSCF, 125 ZMAT, 44

Input Examples (24 March 2010) ****************************** * * * Section 3 - Input Examples * * * ******************************

3-1

The distribution of GAMESS contains a number of short examples, named EXAM*.INP. You should run all of these tests to be sure you have installed GAMESS correctly. The answers are shown in the comments preceeding each of the short input tests. The "correct" answers were obtained on a IBM computer using the xlf compiler, and other machines may differ in the last energy digit, or the last couple of gradient digits. Please note the existence of a script named ~/gamess/tools/checktst/checktst to assist in verifying the numerical results. The examples are listed in the rest of this section, and serve a secondary purpose as a useful tutorial about GAMESS input files. Example ------1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Description ----------RHF geometry optimization UHF + gradient ROHF + gradient GVB + gradient RHF + CI gradient MCSCF geometry optimization RHF + gradient RHF + MP2 gradient MCSCF + MCQDPT energy correction RHF + hessian RHF IRC closed shell DFT geometry opt. RHF properties CI transition moment GVB/ROHF on 2-pi-u state GVB/ROHF on 3-P state GVB/ROHF + hessian RHF + hessian, effective core pot. spin-orbit coupling exponent TRUDGE optimization OS-TCSCF hessian UHF + UMP2 gradient PM3 geometry optimization

CH2 CH2 CH2 CH2 CH2 CH2 HPO H2O H2O H2O HCN HCCH H2O H2O C2Si CH2 P2 NH ICH3 H3CN SiH3-

Input Examples

3-2

24 H2O SCRF test case 25 ? internal coordinate example 26 H3PO localized orbital test 27 NH3 DRC example 28 H2O-NH3 Morokuma decomposition 29 FNH2OH surface scan 30 HCONH2(H2O)3 effective fragment solvation 31 CH3OH PCM test case 32 HNO coupled cluster test 33 HCN ORMAS-MCSCF illustration 34 H2CO CIS optimization 35 As relativity via Douglas-Kroll 36 C2H4 MCSCF analytic hessian 37 (H2O)3 Fragment Molecular Orbital RHF 38 AsH3 model core potential optimization 39 CH4 Raman and hyper-Raman spectra 40 CH2 minimum energy crossing point search 41 CO excitation energy/gradient by TD-DFT 42 CN numerical gradient for open shell CC 43 CH4 heat of formation 44 (HF)6 divide-and-conquer MP2 energy The following will not run in parallel: 05 - CI gradient is not enabled for parallel execution 23,25,27 - MOPAC is not enabled for parallel execution 32,42 - only RHF-based CCSD and CCSD(T) runs in parallel 39 - RUNTYP=TDHFX is not enabled for parallel execution

Input Examples

3-3

! EXAM01. ! 1-A-1 CH2 RHF geometry optimization using GAMESS. ! ! Although internal coordinates are used (COORD=ZMAT), ! the optimization is done in Cartesian space (NZVAR=0). ! This run uses a criterion (OPTTOL) on the gradient ! which is tighter than is normally used. ! ! This job tests the sp integral module, the RHF module, ! and the geometry optimization module. ! ! Using the default search METHOD=STANDARD, ! FINAL E= -37.2322678015, 8 iters, RMS grad= .0264308 ! FINAL E= -37.2308175316, 7 iters, RMS grad= .0320881 ! FINAL E= -37.2375723414, 7 iters, RMS grad= .0056557 ! FINAL E= -37.2379944431, 6 iters, RMS grad= .0017901 ! FINAL E= -37.2380387832, 8 iters, RMS grad= .0003391 ! FINAL E= -37.2380397692, 6 iters, RMS grad= .0000030 ! $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END $SYSTEM TIMLIM=2 MEMORY=100000 $END $STATPT OPTTOL=1.0E-5 $END $BASIS GBASIS=STO NGAUSS=2 $END $GUESS GUESS=HUCKEL $END $DATA Methylene...1-A-1 state...RHF/STO-2G Cnv 2 C H H 1 rCH 1 rCH

2 aHCH

rCH=1.09 aHCH=110.0 $END

Input Examples

3-4

! EXAM02. ! 3-B-1 CH2 UHF calculation on methylene ground state. ! ! This test uses the default choice, COORD=UNIQUE, to ! enter the molecule. Only the symmetry unique atoms ! are given, and they must be given in the orientation ! which GAMESS expects. ! ! This job tests the UHF energy and the UHF gradient. ! In addition, the orbitals are localized. ! ! The initial energy is -37.228465066. ! The FINAL energy is -37.2810867258 after 11 iterations. ! The unrestricted wavefunction has <S**2> = 2.013. ! Mulliken, Lowdin charges on C are -0.020584, 0.018720. ! The spin density at Hydrogen is -0.0167104. ! The dipole moment is 0.016188. ! The RMS gradient is 0.027589766. ! FINAL localization sums are 30.57 and 25.14 Debye**2. ! $CONTRL SCFTYP=UHF MULT=3 RUNTYP=GRADIENT LOCAL=BOYS $END $SYSTEM TIMLIM=1 MEMORY=100000 $END $BASIS GBASIS=STO NGAUSS=2 $END $GUESS GUESS=HUCKEL $END $DATA Methylene...3-B-1 state...UHF/STO-2G Cnv 2 Carbon Hydrogen $END 6.0 1.0 0.0 0.82884 0.7079

Input Examples

3-5

! EXAM03. ! 3-B-1 CH2 ROHF calculation on methylene ground state. ! The wavefunction is a pure triplet state (<S**2> = 2), ! and so has a higher energy than the second example. ! ! For COORD=CART, all atoms must be given, and as in the ! present case, these may be in an unoriented geometry. ! GAMESS deduces which atoms are unique, and orients ! the molecule appropriately. The geometry here is thus ! identical to the second example. ! ! This job tests the ROHF wavefunction and gradient code. ! It also tests the direct SCF procedure. ! ! The initial energy is -37.228465066. ! The FINAL energy is -37.2778767089 after 7 iterations. ! Mulliken, Lowdin charges on C are -0.020346, 0.019470. ! The Hydrogen atom spin density is 0.0129735. ! The dipole moment is 0.025099 Debye. ! The RMS gradient is 0.027505548 ! $CONTRL SCFTYP=ROHF MULT=3 RUNTYP=GRADIENT COORD=CART $END $SYSTEM TIMLIM=1 MEMORY=100000 $END $SCF DIRSCF=.TRUE. $END $BASIS GBASIS=STO NGAUSS=2 $END $GUESS GUESS=HUCKEL $END $DATA Methylene...3-B-1 state...ROHF/STO-2G Cnv 2 Hydrogen Carbon Hydrogen $END 1.0 6.0 1.0 0.82884 -0.82884 0.7079 0.7079 0.0 0.0

Input Examples

3-6

! EXAM04. ! 1-A-1 CH2 TCSCF calculation on methylene. ! The wavefunction has two configurations, exciting ! the carbon sigma lone pair into the out of plane p. ! ! Note that the Z-matrix used to input the molecule ! can include identifying integers after the element ! symbol, and that the connectivity can then be given ! using these labels rather than integers. ! ! This job tests the GVB wavefunction and gradient. ! ! The initial GVB-PP(1) energy is -37.187342653. ! The FINAL energy is -37.2562020559 after 10 iters. ! The GVB CI coefs are 0.977505 and -0.210911, giving ! a pair overlap of 0.64506. ! Mulliken, Lowdin charges for C are 0.020810, 0.055203. ! The dipole moment is 1.249835. ! The RMS gradient = 0.019618475. ! $CONTRL SCFTYP=GVB RUNTYP=GRADIENT COORD=ZMT $END $SYSTEM TIMLIM=1 MEMORY=100000 $END $BASIS GBASIS=STO NGAUSS=2 $END $SCF NCO=3 NSETO=0 NPAIR=1 $END $DATA Methylene...1-A-1 state...GVB...one geminal pair...STO-2G Cnv 2 C1 H1 H2 C1 rCH C1 rCH

H1 aHCH

rCH=1.09 aHCH=99.0 $END ! normally a GVB-PP calculation will use GUESS=MOREAD $GUESS GUESS=HUCKEL $END

Input Examples

3-7

! EXAM05 ! CH2 CI calculation. ! The wavefunction is RHF + CI-SD, within the minimal ! basis, containing 55 configurations. Two CI roots ! are found, and the gradient of the higher state is ! then computed. ! ! Note that CI gradients have several restrictions, ! which are further described in the $LAGRAN group. ! ! FINAL energy of RHF = -38.3704885128 after 10 iters. ! State 1 EIGENvalue = -38.4270674136, c(1) = 0.970224 ! State 2 EIGENvalue = -38.3130036824, c(29) = 0.990865 ! The upper state dipole moment is 0.708275 Debye. ! The upper state has RMS gradient 0.032264079 ! $CONTRL SCFTYP=RHF CITYP=GUGA RUNTYP=GRADIENT $END $SYSTEM TIMLIM=3 MEMORY=300000 $END $BASIS GBASIS=STO NGAUSS=3 $END $GUESS GUESS=HUCKEL $END ! look at all state symmetries, by using C1 symmetry $CIDRT GROUP=C1 IEXCIT=2 NFZC=1 NDOC=3 NVAL=3 $END ! ground state is 1-A-1, 1st excited state is 1-B-1 $GUGDIA NSTATE=2 $END ! compute properties of the 1-B-1 state $GUGDM NFLGDM(1)=1,1 IROOT=2 $END ! compute gradient of the 1-B-1 state $GUGDM2 WSTATE(1)=0.0,1.0 $END $DATA Methylene...CI...STO-3G basis Cnv 2 Carbon Hydrogen $END 6.0 1.0 0.0 0.82884 0.7079

Input Examples

3-8

! EXAM06. ! 1-A-1 CH2 MCSCF methylene geometry optimization. ! The two configuration ansatz is the same as used in ! the fourth example. ! ! The optimization is done in internal coordinates, ! as NZVAR is non-zero. Since a explicit $ZMAT is ! given, these are used for the internal coordinates, ! rather than those used to enter the molecule in ! the $DATA. (Careful examination of this trivial ! triatomic's input shows that $ZMAT is equivalent ! to $DATA in this case. You would normally give ! $ZMAT only if it is somehow different.) ! This job tests the MCSCF wavefunction and gradient. ! At the initial geometry: ! The initial energy is -37.187342653, ! the FINAL E= -37.2562020559 after 14 iterations, ! the RMS gradient is 0.0256396. ! After 4 steps, ! FINAL E= -37.2581791686, RMS gradient=0.0000013, ! r(CH)=1.1243359, ang(HCH)=98.8171674 $CONTRL SCFTYP=MCSCF RUNTYP=OPTIMIZE NZVAR=3 COORD=ZMT $END $SYSTEM TIMLIM=5 MEMORY=300000 $END $BASIS GBASIS=STO NGAUSS=2 $END $DATA Methylene...1-A-1 state...MCSCF/STO-2G Cnv 2 C H 1 rCH H 1 rCH 2 aHOH rCH=1.09 aHOH=99.0 $END $ZMAT IZMAT(1)=1,1,2, 1,1,3, 2,2,1,3 $END ! Normally one starts a MCSCF run with converged SCF ! orbitals, as Huckel orbitals normally do not converge. ! Even if they do converge, the extra iterations are ! very expensive, so use MOREAD for your runs! ! $GUESS GUESS=HUCKEL $END ! ! two active electrons in two active orbitals ! The ground 3-B-1 state is of different symmetry so we ! need only solve for the lowest A-1 symmetry root. ! $DET STSYM=A1 NCORE=3 NACT=2 NELS=2 NSTATE=1 $END

Input Examples

3-9

Input Examples

3-10

! EXAM07. ! 1-A' HPO RHF calculation using GAMESS. ! This job tests the HONDO integral & gradient packages, ! due to the d function on phosphorus. The input also ! illustrates the use of a more flexible basis set than ! the methylene examples. ! Although HUCKEL would be better, HCORE is tested. ! ! The initial energy is -397.591192627, ! the FINAL E= -414.0945320854 after 18 iterations, ! The dipole moment is 2.535169. ! The RMS gradient is 0.023723942. ! $CONTRL SCFTYP=RHF RUNTYP=GRADIENT $END $SYSTEM TIMLIM=20 MEMORY=300000 $END $GUESS GUESS=HCORE $END $DATA HP=O ... 3-21G+* RHF calculation at STO-2G* geometry Cs Phosphorus 15.0 N21 3 L 1 1 0.039 D 1 1 0.55 Oxygen N21 8.0 3 -0.3527854 1.36412

1.0 1.0 1.439

1.0

Hydrogen 1.0 N21 3 $END

Input Examples

3-11

! EXAM08. ! 1-A-1 H2O RHF + MP2 gradient calculation. ! This job generates RHF orbitals which should be saved ! for use with EXAM9. This run, together with EXAM9, ! shows a much more typical MCSCF calculation, which ! should always be started with some sort of SCF MOs. ! This job also tests the 2nd order Moller-Plesset code. ! ! The FINAL E is -75.5854099058 after 10 iterations. ! E(MP2) is -75.7060361996, RMS grad=0.017449524 ! dipole moments are SCF=2.435689, MP2=2.329368 ! $CONTRL SCFTYP=RHF MPLEVL=2 RUNTYP=GRADIENT $END $SYSTEM TIMLIM=2 MEMORY=100000 memddi=1 parall=.true. $END $BASIS GBASIS=N21 NGAUSS=3 $END $GUESS GUESS=HUCKEL $END $DATA Water...RHF/321G...exp.geom...R(OH)=0.95781,A(HOH)=104.4776 Cnv 2 OXYGEN HYDROGEN $END 8.0 1.0 0.0 0.7572157 0.5865358

Input Examples

3-12

! EXAM09. ! 1-A-1 H2O 2nd order MC-QDPT calculation ! This job finds the Full Optimized Reaction Space ! MCSCF (or CAS-SCF) wavefunction for water. Its ! initial RHF orbitals are taken from EXAM08. ! The MCSCF wavefunction contains 65 determinants, ! not all of which are singlets, of course. ! The second order perturbation theory correction ! to the MCSCF energy is then obtained, using a ! determinant code as well. ! ! MCSCF: ! On the 1st iteration, the energy is -75.601726236. ! The FINAL MCSCF E= -75.6386218843 after 14 iters, ! with c(1) = 0.9884456 and dipole moment = 2.301620 ! MRMP (single state MCQDPT) E(MP2) = -75.7109705643 ! $CONTRL SCFTYP=MCSCF MPLEVL=2 $END $SYSTEM TIMLIM=1 $END $BASIS GBASIS=N21 NGAUSS=3 $END ---- EXPERIMENTAL GEOM, R(OH)=0.95781A, HOH=104.4776 DEG. $DATA WATER...3-21G BASIS...FORS-MCSCF...EXPERIMENTAL GEOMETRY Cnv 2 Oxygen 8.0 Hydrogen 1.0 0.0 0.7572157 0.5865358 $END $GUESS GUESS=MOREAD NORB=13 $END $DET NCORE=1 NACT=6 NELS=8 $END ---- CONVERGED 3-21G $VEC 1 1 0.98323195E+00 ... vectors deleted 13 3 0.35961579E+00 $END WATER VECTORS, E=-75.585409913 - - 0.95883436E-01 0.00000000E+00 ... to save paper ... 0.28728587E+00 0.35961579E+00

Input Examples

3-13

! EXAM 10. ! This run duplicates the first column of table 6 in ! Y.Yamaguchi, M.Frisch, J.Gaw, H.F.Schaefer, and ! J.S.Binkley J.Chem. Phys. 1986, 84, 2262-2278. ! ! FINAL energy at the VIB 0 geometry is -74.9659012159. ! ! If run with METHOD=ANALYTIC, ! the FREQuencies are 2170.05, 4140.00, and 4391.07 ! the INTENSities are 0.17129, 1.04807, and 0.70930 ! the mean POLARIZABILITY is 0.40079 ! ! If run with METHOD=NUMERIC, NVIB=2, ! the FREQuencies are 2170.14, 4140.18, and 4391.12 ! the INTENSities are 0.17169, 1.04703, and 0.70909 ! $CONTRL SCFTYP=RHF RUNTYP=HESSIAN UNITS=BOHR NZVAR=3 $END $SYSTEM TIMLIM=4 MEMORY=100000 $END $FORCE METHOD=ANALYTIC $END $CPHF POLAR=.TRUE. $END $BASIS GBASIS=STO NGAUSS=3 $END $DATA Water at the RHF/STO-3G equilibrium geometry CNV 2 OXYGEN 8. 0.0 0.0 0.0702816679 HYDROGEN 1. 0.0 1.4325665478 -1.1312080153 $END $ZMAT IZMAT(1)=1,1,2, 1,1,3, 2,2,1,3 $END $GUESS GUESS=HUCKEL $END

Input Examples

3-14

! EXAM 11. ! 1A' HCN RHF Intrinsic Reaction Coordinate ! This job tests the reaction path finder. The reaction ! is followed back to the HNC isomer. Four points on the ! IRC (counting the saddle point) are found, ! Pt. R(N-C) R(N-H) A(HNC) Energy distance ! T.S. 1.22136 1.43764 52.993 -91.5648510 0.0 ! 1 1.22533 1.33296 58.476 -91.5673097 0.29994 ! 2 1.22802 1.23827 64.747 -91.5735346 0.59986 ! 3 1.22974 1.16350 72.039 -91.5814775 0.89968 ! $CONTRL SCFTYP=RHF RUNTYP=IRC NZVAR=3 $END $SYSTEM TIMLIM=5 MEMORY=400000 $END $IRC PACE=GS2 SADDLE=.TRUE. TSENGY=.TRUE. FORWRD=.FALSE. NPOINT=3 $END $GUESS GUESS=HUCKEL $END $ZMAT IZMAT(1)=1,1,2 1,1,3 2,2,1,3 $END $BASIS GBASIS=STO NGAUSS=3 $END $DATA HYDROGEN CYANIDE...STO-3G...INTRINSIC REACTION COORDINATE CS NITROGEN 7.0 -.0004620071 .0002821165 .0000000000 CARBON 6.0 1.2208931990 -.0003427488 .0000000000 HYDROGEN 1.0 .8654562191 1.1478852258 .0000000000 $END $HESS ENERGY IS -91.5648510307 E(NUC) IS 23.4154954113 1 1 1.10665682E+00 1.58946320E-02 0.00000000E+00... ... 2nd derivatives deleted to save paper ... 9 2-8.04548379E-09 0.00000000E+00 0.00000000E+001.42096449E-08 $END

Input Examples

3-15

! EXAM 12. ! This job illustrates linear bends, for acetylene, and ! tests the closed shell LDA density functional program. ! ! At the input geometry, ! the FINAL E= -765352334525 after 12 iterations, ! and the RMS gradient is 0.0944557. ! ! At the final geometry, 5 steps later, ! the FINAL E= -76.5841347569, RMS gradient=0.0000007, ! R(CC)=1.21193 and R(CH)=1.07797. ! $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE NZVAR=5 $END $SYSTEM TIMLIM=2 $END $DFT DFTTYP=SVWN $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 $END $GUESS GUESS=HUCKEL $END ! Note, this OPTTOL is smaller than the accuracy of the ! integration grid actually supports (see REFS.DOC) $STATPT OPTTOL=0.00001 $END $DATA Acetylene geometry optimization in internal coordinates Dnh 4 CARBON 6.0 0.0 0.0 0.70 HYDROGEN 1.0 0.0 0.0 1.78 $END $ZMAT IZMAT(1)=1,1,2, 1,1,3, 1,2,4, 5,1,2,4, 5,2,1,3 $END ------- XZ is 1st plane for both bends ------$LIBE APTS(1)=1.0,0.0,0.0,1.0,0.0,0.0 $END

Input Examples

3-16

! EXAM 13. ! This run duplicates the POLYATOM calculation of ! D.Neumann + J.W.Moskowitz, J.Chem.Phys. 49,2056(1968) ! SCF convergence is a bit better today, so some of the ! results are not precisely the same. ! ! V(NE) = -199.1343264099 ! V(EE) = 37.8955167210 T = 75.9557584991 ! V(NN) = 9.2390200836 E(TOT)= -76.0440311061 ! Mulliken charge(O)=-0.647397 Bond Order=0.905 ! Density: O=286.491824 H=0.404989 ! Moments: DZ= 2.093290 ! QXX=-2.388658 QYY= 2.495388 QZZ=-0.106730 ! OXXZ=-0.890362 OYYZ= 2.186853 OZZZ=-1.296490 ! Electric field/gradient: H(YZ)=+/-0.365168 ! O(Z)=-0.060033 H(Y)=+/-0.006572 H(Z)=0.001233 ! O(XX)=1.904867 O(YY)=-1.735891 O(ZZ)=-0.168977 ! H(XX)=0.301208 H(YY)=-0.258153 H(ZZ)=-0.043055 ! Potential: V(O)=-22.330374 V(H)=-1.006648 ! $CONTRL SCFTYP=RHF RUNTYP=ENERGY UNITS=BOHR ISPHER=1 $END $SYSTEM TIMLIM=15 MEMORY=300000 $END $GUESS GUESS=HUCKEL $END $ELMOM IEMOM=3 $END $ELFLDG IEFLD=2 $END $ELPOT IEPOT=1 $END $ELDENS IEDEN=1 $END $DATA Water...properties test...(10,5,2/4,1)/[5,3,2/2,1] basis Cnv 2 Oxygen 8.0 S 2 1 31.3166 2 76.232 S 3 1 290.785 2 1424.0643 3 4643.4485 S 2 1 4.6037 2 12.8607 S 2 1 0.9311 2 9.7044 S 1 1 0.2825 P 3

0.243991 0.152763 0.904785 0.121603 0.029225 0.264438 0.458240 1.051534 -0.140314 1.0

Input Examples 1 2 3 P 1 P D 1 D 1 1 1 1 1 1.5 0.5 0.0 1.0 1.0 1.428036 0.817238 0.231208 0.032828 1.0 1.0 1.0957706 1 0.21373 0.71706 1.0 1.0 7.90403 35.1832 2.30512 0.124190 0.019580 0.394730

3-17

Hydrogen 1.0 S 3 1 0.65341 2 2.89915 3 19.2406 S 1 1 0.17758 P 1 1 1.0 $END

Input Examples

3-18

! EXAM 14. ! CI transition moments. Water, using RHF/STO-3G MOs. ! All orbitals are occupied, transition is 1-1A1 to 2-1A1. ! ! E(STATE 1)= -75.0101113548, E(STATE 2)= -74.3945819375 ! Dipole LENGTH is <Q>=0.392614 ! Dipole VELOCITY is <d/dQ>=0.368205 ! $CONTRL SCFTYP=NONE CITYP=GUGA RUNTYP=TRANSITN UNITS=BOHR $END $SYSTEM TIMLIM=1 MEMORY=100000 $END $BASIS GBASIS=STO NGAUSS=3 $END ! standard SD-CI calculation $DRT1 GROUP=C2V IEXCIT=2 NFZC=1 NDOC=4 NVAL=2 $END $TRANST NFZC=1 IROOTS(1)=2 $END $DATA WATER MOLECULE...STO-3G...TRANSITION MOMENT CNV 2 OXYGEN HYDROGEN $END 8.0 1.0 0.0 0.0 0.0 1.428 0.0 -1.096

--- RHF ORBITALS --- GENERATED AT 09:24:04 18-FEB-88 WATER MOLECULE...STO-3G...TRANSITION MOMENT E(RHF)= -74.9620539825, E(NUC)= 9.2384802989, 8 ITERS $VEC1 1 1 9.94117078E-01 2.66680164E-02 0.00000000E+00 ... ... vectors deleted to save paper ... 7 2-8.42653177E-01 8.42653177E-01 $END

Input Examples

3-19

! EXAM 15. ! C2- diatom, in the electronic state doublet-pi-u. ! This illustrates a open shell SCF calculation, using ! fed in coupling coefficients, and the GVB/ROHF code. ! ! The FINAL energy is -75.5579181071 after 8 iterations. ! $CONTRL SCFTYP=GVB MULT=2 ICHARG=-1 UNITS=BOHR $END $SYSTEM TIMLIM=15 MEMORY=300000 $END $BASIS GBASIS=DH NDFUNC=1 POLAR=DUNNING $END $DATA C2-...DOUBLET-PI-UNGERADE...OPEN SHELL SCF DNH 4 CARBON $END $GUESS $SCF 6.0 0.0 0.0 -1.233

GUESS=MOREAD NORB=30 NORDER=1 IORDER(5)=7,5,6 $END NCO=5 NSETO=1 NO=2 COUPLE=.TRUE. F(1)=1.0, 0.75 ALPHA(1)=2.0, 1.5, 1.00 BETA(1)=-1., -.75, -0.5 $END

--- RHF ORBITALS --- GENERATED AT 14:05:16THU MAR 24/88 CC R(C-C) = 2 * 1.233 BOHR BAS=831+1D E(RHF)= -75.3856001855, E(NUC)= 14.5985401460, 18 ITERS $VEC 1 1-7.06500288E-01-1.39103044E-03-3.57452331E-04 ... ... vectors deleted to save paper ... $END

Input Examples

3-20

! EXAM 16. ! ROHF/GVB on Si 3-P state, using Gordon's 6-31G basis. ! ! The purpose of this example is two-fold, namely to ! show off the open shell capabilities of the GVB code, ! and to emphasize that the 6-31G basis for Si in GAMESS ! is Mark Gordon's version. The basis stored in GAMESS is ! completely optimized, whereas Pople's uses the core from ! from a 6-21G set, reoptimizing only the -31G part. ! The energy from Pople's basis would be only -288.828405. ! ! Jacobi diagonalization is intrinsically slow, but ! results in pure subspecies in degenerate p irreps. ! In fact, these may be labeled in the highest Abelian ! subgroup of the atomic point group Kh. ! ! The FINAL energy is -288.8285729745 after 7 iterations. ! $CONTRL SCFTYP=GVB MULT=3 $END $SYSTEM TIMLIM=2 MEMORY=100000 KDIAG=3 $END $BASIS GBASIS=N31 NGAUSS=6 $END $DATA Si...3-P term...ROHF in full Kh symmetry Dnh 2 Silicon $END $GUESS $SCF 14. GUESS=HUCKEL $END NCO=6 NSETO=1 NO=3 COUPLE=.TRUE. F(1)=1.0, 0.333333333333333 ALPHA(1)=2.0, 0.66666666666667, 0.16666666666667 BETA(1)=-1.0, -0.33333333333333, -0.16666666666667

$END

Input Examples ! EXAM 17. ! Analytic hessian for an open shell SCF function. ! Methylene's 1-B-1 excited state. ! FINAL energy= -38.3334724780 after 8 iterations. ! The FREQuencies are 1224.19, 3563.44, 3896.23 ! The INTENSities are 0.13317, 0.21652, 0.14589 ! The mean POLARIZABILITY is 0.53018 ! $CONTRL SCFTYP=GVB MULT=1 RUNTYP=HESSIAN UNITS=BOHR $END $SYSTEM TIMLIM=4 MEMORY=100000 $END $CPHF POLAR=.TRUE. $END $BASIS GBASIS=STO NGAUSS=3 $END $SCF NCO=3 NSETO=2 NO(1)=1,1 NPAIR=0 $END $ZMAT IZMAT(1)=1,1,2, 1,1,3, 2,2,1,3 $END $GUESS GUESS=HUCKEL $END $DATA METHYLENE...1-B-1 STATE...ROHF...STO-3G BASIS CNV 2 CARBON HYDROGEN $END 6.0 1.0 0.0 0.0 0.0 1.8913952563 0.0041647278 0.7563907037

3-21

Input Examples

3-22

! EXAM 18. ! effective core potential...diatomic P2...RHF/CEP-31G* ! See Stevens,Basch,Krauss, J.Chem.Phys. 81,6026-33(1984). ! GAMESS FINAL E= -12.6956518702, FREQ=913.17 ! A separate run gives E(P)= -6.32635 so De=26.95 kcal/mol ! $CONTRL SCFTYP=RHF RUNTYP=HESSIAN ECP=SBKJC NZVAR=1 $END $SYSTEM TIMLIM=15 MEMORY=900000 $END $GUESS GUESS=HUCKEL $END $ZMAT IZMAT(1)=1,1,2 $END $DATA diatomic phosphorous Dnh 4 PHOSPHORUS 15.0 0.9393077548 SBKJC D 1 1 0.45 1.0 $END 0.0000000000 0.0000000000

Input Examples ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! EXAM 19. Spin-orbit coupling example. This run duplicates the results shown in Table 3 of T.R.Furlani, H.F.King, J.Chem.Phys. 82, 5577-83(1985), GAMESS 1e-= 114.3851, 2e-= -49.4168, lit=114.38,-49.42

3-23

Energies for the singlet CI are State= 1 Energy = -54.868531216 (1-delta) State= 2 Energy = -54.868531216 (1-delta) State= 3 Energy = -54.798836731 (1-sigma-plus) Energies for the triplet CI are State= 1 Energy = -54.938225701 (3-sigma-minus) Final energy of all 6 levels in the pi**2 configuration, after diagonalization of the spin-orbit Hamiltonian, are BREIT RELATIVE E= -15296.570, -15296.432, -15296.432, BREIT RELATIVE E= 0.0, 0.0, and +15296.570 wavenumbers. If run as OPERAT=HSO1, with ZEFF taken as true atomic Z, then inclusion of only the 1e- operator is 114.3851, and ZEFF RELATIVE E= -15296.859, -15296.432, -15296.432, ZEFF RELATIVE E= 0.0, 0.0, and +15296.859 wavenumbers. Why are there six levels? The singlet-delta is two roots, the singlet-sigma-plus is a third. During the CI, the spatial triplet-sigma-minus is one CSF, with alpha/alpha spin, hence IROOTS=3,1. The final spin-orbit Hamiltonian includes all three triplet spin states, namely adding the ab+ba and beta/beta triplets. So, 2+1+3=6 levels. You can work out for yourself these have the quantum number omega=0,0,1,2. Only the omega=0 states can interact, raising the triplet's degeneracy and slightly affecting the singlet-sigma-plus state's position. Note that the lower multiplicity DRT1 is done in C1 symmetry to generate both components of the delta state.

$CONTRL SCFTYP=NONE MULT=3 CITYP=GUGA RUNTYP=TRANSITN UNITS=BOHR $END $SYSTEM TIMLIM=2 MEMORY=900000 $END $BASIS GBASIS=N31 NGAUSS=6 $END $TRANST OPERAT=HSO2 NFZC=3 NOCC=5 NUMVEC=1 NUMCI=2 IROOTS(1)=3,1 $END $DRT1 GROUP=C1 IEXCIT=2 NFZC=3 NDOC=1 NVAL=1 $END $DRT2 GROUP=C4V IEXCIT=2 NFZC=3 NALP=2 $END $DATA Imidogen radical Cnv 4 Nitrogen 7.0

Input Examples

3-24

Hydrogen 1.0 0.0 0.0 1.9748 $END --- ROHF ORBITALS --- GENERATED AT 12:04:18 29 MAR 90 ( 88) IMIDOGEN RADICAL E(ROHF)= -54.9382257007, E(NUC)= 3.5446627507, 8 ITERS $VEC1 ...orbitals omitted to save space... $END

Input Examples

3-25

! EXAM 20. ! Optimize an orbital exponent. ! The SBKJC basis for I consists of 5 gaussians, in a -41 ! type split. The exponent of a diffuse L shell for ! iodide ion is optimized (6th exponent overall). The ! optimal exponent turns out to be 0.036713, with a ! corresponding FINAL energy of -11.3010023066 ! $CONTRL SCFTYP=RHF RUNTYP=TRUDGE ICHARG=-1 ECP=SBKJC $END $SYSTEM TIMLIM=30 MEMORY=300000 $END $TRUDGE OPTMIZ=BASIS NPAR=1 IEX(1)=6 $end $GUESS GUESS=HUCKEL $END $DATA I- ion Dnh 2 Iodine 53.0 SBKJC L 1 1 0.02 1.0 $END

Input Examples

3-26

! EXAM 21. ! Open shell two configuration SCF analytic hessian. ! M.Duran, Y.Yamaguchi, H.F.Schaefer III ! J.Phys.Chem. 1988, 92, 3070-3075. ! Least motion insertion of CH into H2, which leads to ! a 3rd order hypersaddle point on the 2-B-1 surface. ! ! Literature values are ! FINAL E=-39.25104, C1=0.801, C2=-0.598 ! FREQ= 4805i, 1793i, 1317i, 989, 2914, 3216 ! mean POLARIZABILITY=2.05 ! GAMESS obtains ! FINAL E=-39.2510351249, C1=0.801141, C2=-0.598476 ! FREQ= 4805.53i, 1793.00i, 1317.43i, ! FREQ= 988.81, 2913.52, 3216.42 ! INTENS= 4.54563, 0.09731, 0.00768 ! mean POLARIZABILITY=2.04655 ! $CONTRL SCFTYP=GVB MULT=2 RUNTYP=HESSIAN $END $SYSTEM TIMLIM=25 MEMORY=100000 $END $CPHF POLAR=.TRUE. $END $GUESS GUESS=MOREAD NORB=16 NORDER=1 IORDER(4)=6,4,5 $END $SCF NCO=3 NSETO=1 NO=1 NPAIR=1 CICOEF(1)=0.7,-0.7 $END $DATA Insertion of CH into H2...OS-TCSCF ansatz...DZ basis CNV 2 CARBON 6.0 0.0000000000 S 6 1 4232.61 0.002029 2 634.882 0.015535 3 146.097 0.075411 4 42.4974 0.257121 5 14.1892 0.596555 6 1.9666 0.242517 S 1 1 5.1477 1.0 S 1 1 0.4962 1.0 S 1 1 0.1533 1.0 P 4 1 18.1557 0.018534 2 3.9864 0.115442 3 1.1429 0.386206 4 0.3594 0.640089 P 1 1 0.1146 1.0 0.0000000000 -0.0001357549

Input Examples HYDROGEN 1.0 0.0000000000 DH 0 1.2 1.2 HYDROGEN 1.0 0.0000000000 DH 0 1.2 1.2 0.0000000000 0.4152229538

3-27 1.0922959062 -1.4824967459

$END --- these are 2-A1 ROHF vectors ----- ROHF ORBITALS --- GENERATED AT 08:23:42 27 JUN 90 (178) INSERTION OF CH INTO H2...OS-TCSCF ANSATZ...DZ BASIS E(ROHF)= -39.2316245004, E(NUC)= 8.0760320442, 12 ITERS $VEC 1 1 6.01223299E-01 4.37813104E-01 ... ... vectors deleted to save paper ... 16 4-2.12429766E-02 $END

Input Examples ! EXAM22. ! ! 3-A-2 H3CN UMP2/6-31G*//UHF/6-31G* ! ! The FINAL UHF energy= -94.0039683697 after 14 iters. ! E(MP2)= -94.2315757668, with RMS grad=0.003359454 ! Dipoles for HF and MP2 are 2.049391 and 2.098487 D. ! $CONTRL SCFTYP=UHF MULT=3 RUNTYP=GRADIENT MPLEVL=2 COORD=ZMT $END $SYSTEM TIMLIM=5 MWORDS=1 MEMDDI=1 PARALL=.TRUE. $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=0 $END $GUESS GUESS=HUCKEL $END $DATA Methylnitrene...UHF/6-31G* structure Cnv 3 N C H H H 1 2 2 2 rCN rCH rCH rCH

3-28

1 1 1

aHCN aHCN aHCN

3 120.0 3 -120.0

rCN=1.4329216 rCH=1.0876477 aHCN=110.21928 $END

Input Examples

3-29

! EXAM23. ! semiempirical calculation, using the MOPAC/GAMESS combo ! AM1 gets the geometry disasterously wrong! ! ! initial geometry, MNDO AM1 PM3 ! FINAL HEAT OF FORMATION 105.14088 93.45997 46.89387 ! RMS gradient 0.0818157 0.1008587 0.0366232 ! final geometry (# steps), 8 11 10 ! FINAL HEAT OF FORMATION 46.45649 -1.81716 -2.79647 ! RMS gradient 0.0000246 0.0000294 0.0000015 ! r(SiH) 1.42117 1.45813 1.52104 ! a(HSiH) 101.962 120.000 96.280 ! ! At the final PM3 geometry, the charge on Si is -.4681, ! and the dipole moment is 2.345322 Debye. ! $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT ICHARG=-1 $END $SYSTEM TIMLIM=5 MEMORY=200000 $END $BASIS GBASIS=PM3 $END $DATA Silyl anion...comparison of semiempirical models Cnv 3 Si H 1 H 1 H 1 rSiH rSiH rSiH

2 aHSiH 2 aHSiH

aHSiH

-1

rSiH=1.15 aHSiH=110.0 $END

Input Examples

3-30

! EXAM24. ! Self-consistent reaction field test, of water in water. ! Cavity radius is calculated from the 1.00 g/cm**3 density. ! FINAL energy is -74.9666740755 after 12 iterations ! Induced dipole= -0.03663, RMS gradient= 0.033467686 ! $contrl scftyp=rhf runtyp=gradient coord=zmt $end $system memory=300000 $end $basis gbasis=sto ngauss=3 $end $guess guess=huckel $end $scrf radius=1.93 dielec=80.0 $end $data water in water, arbitrary geometry Cnv 2 O H 1 rOH H 1 rOH 2 aHOH rOH = 0.95 aHOH = 104.5 $end

Input Examples

3-31

! EXAM25. ! Illustration of coordinate systems for geometry searches. ! Arbitrary molecule, chosen to illustrate ring, methyl on ! ring, methine H10, imino in ring, methylene in ring. ! ! H8 H9 ! \| ! H7-C6 O1---O5 H13 ! \ / \ / ! C2 C4 ! / \ / \ ! H10 N3 H12 ! | ! H11 ! ! The initial AM1 energy is -48.6594935 ! initial RMS final E final RMS #steps ! Cartesians 0.0200113 -48.7022520 0.0000304 50 ! dangling Z-mat 0.0600637 ... OO bond crashes on 1st step ! good Z-matrix 0.0232915 -48.7022510 0.0000285 21 ! deloc. coords. 0.0176452 -48.7022537 0.0000267 22 ! nat. internals 0.0209442 -48.7022570 0.0000183 15 ! $contrl scftyp=rhf runtyp=optimize coord=zmt $end $system memory=300000 $end $statpt hess=guess nstep=100 nprt=-1 npun=-2 $end $basis gbasis=am1 $end $guess guess=huckel $end $data Illustration of coordinate systems C1 O C 1 rCOa N 2 rCNa 1 aNCO C 3 rCNb 2 aCNC 1 wCNCO O 4 rCOb 3 aOCN 2 wOCNC C 2 rCC 1 aCCO 5 wCCOO H 6 rCH1 2 aHCC1 1 wHCCO1 H 6 rCH2 2 aHCC2 1 wHCCO2 H 6 rCH3 2 aHCC3 1 wHCCO3 H 2 rCHa 1 aHCOa 5 wHCOOa H 3 rNH 2 aHNC 1 wHNCO H 4 rCHb 5 aHCOb 1 wHCOOb H 4 rCHc 5 aHCOc 1 wHCOOc

Input Examples rCOa=1.43 rCNa=1.47 rCNb=1.47 rCOb=1.43 aNCO=106.0 aCNC=104.0 aOCN=106.0 wCNCO=30.0 wOCNC=-30.0 rCC=1.54 aCCO=110.0 wCCOO=-150.0 rCH1=1.09 rCH2=1.09 rCH3=1.09 aHCC1=109.0 aHCC2=109.0 aHCC3=109.0 wHCCO1=60.0 wHCCO2=-60.0 wHCCO3=180.0 rCHa=1.09 aHCOa=110.0 wHCOOa=100.0 rNH=1.01 aHNC=110.0 wHNCO=170.0 rCHb=1.09 rCHc=1.09 aHCOb=110.0 aHCOc=110.0 wHCOOb=150.0 wHCOOc=-100.0 $end To use Cartesian coordinates: --- $contrl nzvar=0 $end To use conventional Z-matrix, with a dangling O-O bond: --- $contrl nzvar=33 $end

3-32

To use well chosen internals, with all 5 ring bonds defined: --- $contrl nzvar=33 $end --- $zmat izmat(1)=1,1,2, 1,2,3, 1,3,4, 1,4,5, 1,5,1, 2,1,2,3, 2,5,4,3, 3,5,1,2,3, 3,1,5,4,3, 1,6,2, 2,6,2,1, 3,6,2,1,5, 1,6,7, 1,6,8, 1,6,9, 2,7,6,2, 2,8,6,2, 2,9,6,2,

Input Examples 3,7,6,2,1, 3,8,6,2,1, 3,9,6,2,1, 1,10,2, 2,10,2,1, 3,10,2,1,5, 1,11,3, 2,11,3,2, 3,11,3,2,1, 1,12,4, 2,12,4,5, 3,12,4,5,1, 1,13,4, 2,13,4,5, 3,13,4,5,1 $end To use delocalized coordinates: --- $contrl nzvar=33 $end --- $zmat dlc=.true. auto=.true. $end

3-33

To use natural internal coordinates: $contrl nzvar=44 $end $zmat izmat(1)=1,1,2, 1,2,3, 1,3,4, 1,4,5, 1,5,1, ! ring ! 2,5,1,2, 2,1,2,3, 2,2,3,4, 2,3,4,5, 2,4,5,1, 3,5,1,2,3, 3,1,2,3,4, 3,2,3,4,5, 3,3,4,5,1, 3,4,5,1,2, 1,2,6, 2,6,2,1, 2,6,2,3, 4,6,2,1,3, ! methyl C ! 1,6,7, 1,6,8, 1,6,9, ! methyl Hs ! 2,7,6,8, 2,8,6,9, 2,9,6,7, 2,9,6,2, 2,7,6,2, 2,8,6,2, 3,7,6,2,1, 1,10,2, 2,10,2,1, 2,10,2,3, 2,10,2,6, ! methine ! 1,11,3, 2,11,3,2, 2,11,3,4, 4,11,3,2,4, ! imino ! 1,12,4, 1,13,4, ! methylene ! 2,12,4,13, 2,12,4,3, 2,13,4,3, 2,12,4,5, 2,13,4,5 ijS(1)=1,1, 2,2, 3,3, 4,4, 6,6, 7,6, 8,6, 9,6,10,6, 7,7, 8,7, 9,7,10,7, 11,8,12,8,13,8,14,8,15,8, 11,9,12,9, 14,9,15,9, 16,10, 17,11,18,11, 20,13, ! 23,16, 24,16, 25,16, 26,16, 27,16, 28,16, 23,17, 24,17, 25,17, 24,18, 25,18, 26,19, 27,19, 28,19, 27,20, 28,20, 29,21, 30,22, 31,23,32,23,33,23, 32,24,33,24, methine ! 34,25, 35,26,36,26, 37,27, ! imino ! 38,28, 39,29, ! methylene ! 40,30, 41,30, 42,30, 43,30, 44,30, 41,31, 42,31, 43,31, 44,31, 41,32, 42,32, 43,32, 44,32, 21,14, 22,15, 5,5, ! ring !

19,12,

! methyl C ! methyl Hs

Input Examples 41,33, 42,33, 43,33, 44,33

3-34

Sij(1)=1.0, 1.0, 1.0, 1.0, 1.0, ! ring ! 1.0, -0.8090, 0.3090, 0.3090, -0.8090, -1.1180, 1.8090, -1.8090, 1.1180, 0.3090, -0.8090, 1.0, -0.8090, 0.3090, -1.8090, 1.1180, -1.1180, 1.8090, 1.0, 1.0,-1.0, 1.0, ! methyl C ! 1.0, 1.0, 1.0, ! methyl Hs ! 1.0, 1.0, 1.0,-1.0,-1.0,-1.0, 2.0,-1.0,-1.0, 1.0,-1.0, 2.0,-1.0,-1.0, 1.0,-1.0, 1.0, 1.0, 2.0,-1.0,-1.0, 1.0,-1.0, ! methine ! 1.0, 1.0,-1.0, 1.0, ! imino ! 1.0, 1.0, ! methylene ! 4.0, 1.0, 1.0, 1.0, 1.0, 1.0,-1.0, 1.0,-1.0, 1.0, 1.0,-1.0,-1.0, 1.0,-1.0,-1.0, 1.0 $end

Input Examples

3-35

! EXAM26 ! Localized orbital test...Phys.Chem. 1984, 88, 382-389 ! ! FINAL Energy= -415.2660357363 in 11 iters ! ! If you localize only the valence orbitals, by commenting ! out the $LOCAL group below, the ! Boys localization sum is 204.693589 ! Ruedenberg localization sum is 5.081667 ! population localization sum is 4.610528 ! ! The SCF localized charge decomposition forces all MOs ! to be localized, so the final diagonal sum is 28.389125. ! The nuclear charge assigned to oxygen "lone pairs" is ! redistributed so the total nuclear P and O charges are ! correct. The energies for the PO bond, PH bonds, ! and O lone pairs are -37.273022, -27.364212, -26.363865. ! The corresponding dipoles are 2.041, 3.484, and 3.465. ! ! To analyze MP2 valence contributions, choose MPLEVL=2, ! and turn EDCOMP and DIPDCM off. The results should be ! E(MP2)=-415.4952200908, and contributions of PO bond, ! PH bonds, and O lone pairs to the correlation energy are ! -0.0442096, -0.0237793, and -0.0378790, respectively. ! $contrl scftyp=rhf runtyp=energy local=ruednbrg mplevl=0 $end $system memory=750000 $end $mp2 lmomp2=.true. $end $local edcomp=.true. moidon=.true. dipdcm=.true. ijmo(1)= 1,11, 2,11, 1,12, 2,12, 1,13, 2,13 zij(1)=1.666666667,0.333333333,1.6666666667,0.333333333, 1.666666667,0.333333333 moij(1)= 2,1, 2,1, 2,1 nnucmo(11)=2,2,2 $end $basis gbasis=n21 ngauss=3 ndfunc=1 $end $data phosphine oxide...3-21G* basis...localized orbital test Cnv 3 P 15.0 O 8.0 H 1.0 $end 0.0000000000 1.2335928631 0.0 0.0 1.4701 -0.6421021244

Input Examples

3-36

! EXAM27. ! NH3 semi-empirical DRC calculation ! ! The dynamic reaction coordinate is initiated at the ! planar inversion transition state, with a velocity ! parallel to the mode with imaginary frequency. The ! reactive trajectory is given one kcal/mole energy in ! excess of the amount needed to traverse the barrier. ! The trajectory is analyzed in terms of the equilibrium ! geometry's coordinates and normal modes. Because ! this is a test run, the trajectory is stopped after ! a much too short time interval. ! ! The last point on the trajectory has ! T=0.00163, V=-9.12874, E=-9.12710, ! q(L6)=-0.153112, p(L6)=-0.014313, ! velocity(H,z)=0.028857623667 $CONTRL SCFTYP=RHF RUNTYP=DRC $END $SYSTEM MEMORY=300000 $END $BASIS GBASIS=AM1 $END $DATA ammonia...DRC starting from the planar transition state C1 NITROGEN 7.0 0.0000000000 0.0000000000 0.0000000000 HYDROGEN 1.0 -0.4882960784 0.8457536168 0.0000000000 HYDROGEN 1.0 -0.4882960784 -0.8457536168 0.0000000000 HYDROGEN 1.0 0.9765921567 0.0000000000 0.0000000000 $END $DRC NPRTSM=1 NSTEP=10 DELTAT=0.1 NMANAL=.TRUE. EKIN=1.0 VEL(1)=0.0 0.0 -0.1128, 0.0 0.0 0.5213, 0.0 0.0 0.5213, 0.0 0.0 0.5213 C0(1)=0.0000000000 0.0000000000 0.0291576578 -0.4692651161 0.8127910232 -0.3097192193 -0.4692651161 -0.8127910232 -0.3097192193 0.9385302321 0.0000000000 -0.3097192193 $END $HESS ENERGY IS -9.1354556210 E(NUC) IS 6.8369847904 1 1 6.16231432E-01 3.45452916E-11-1.03923982E-05 ... ... 2nd derivatives deleted to save paper ... 12 3 1.38181166E-10 5.72335505E-02 $END

Input Examples ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! EXAM28. Morokuma energy decomposition. This run duplicates a result from Table 16 of H.Umeyama, K.Morokuma, J.Am.Chem.Soc. 99,1316(1977) ES= EX= PL= CT= MIX= total GAMESS -14.02 8.98 -1.12 -2.37 -0.43 -8.96 literature -14.0 9.0 -1.1 -2.4 -0.4 -9.0

3-37

Enter $LMOEDA instead of $MOROKM for an alternative energy analysis, supporting many more calculations.

$contrl scftyp=rhf runtyp=eda coord=zmt $end $system timlim=1 $end $basis gbasis=n31 ngauss=4 $end $guess guess=huckel $end $morokm iatm(1)=3 $end $data water-ammonia dimer...4-31G basis set Cs H O H N H H H 1 2 2 4 4 4 rOH rOH R rNH rNH rNH

1 1 3 3 3

aHOH aHOH aHNaxis aHNaxis aHNaxis

3 0.0 1 180.0 5 +120.0 5 -120.0

rOH=0.956 aHOH=105.2 rNH=1.0124 aHNaxis=112.1451 R=2.93 $end

! makes HNH=106.67

Input Examples

3-38

! EXAM29. surface scan ! The scan is done over a 3x3 grid centered on the SCF ! transition state for the SN2 type reaction ! F- + NH2OH -> F-NH2-OH anion -> FNH2 + OH! ! Groups 1 and 2 are F and OH, and their distance from ! the N is varied antisymmetrically, which is more or ! less what the IRC should be like. The results seem to ! indicate that the MP2/3-21G saddle point would shift ! further into the product channel, since the higher ! MP2 energies occur at shorter r(NF) and longer r(NO): ! ! FINAL E= -229.0368324615, E(MP2)= -229.3873302375 ! FINAL E= -229.0356378402, E(MP2)= -229.3866642673 ! FINAL E= -229.0309266321, E(MP2)= -229.3822094777 ! FINAL E= -229.0372146702, E(MP2)= -229.3923234074 ! FINAL E= -229.0385440296, E(MP2)= -229.3936486644 ! FINAL E= -229.0367369562, E(MP2)= -229.3913683073 ! FINAL E= -229.0328601144, E(MP2)= -229.3918932009 ! FINAL E= -229.0364643934, E(MP2)= -229.3948325500 ! FINAL E= -229.0372478250, E(MP2)= -229.3943498144 ! ! A more conclusive way to tell this would be to compute ! single point MP2 energies along the SCF IRC, since the ! true reaction path always curves, and thus does not lie ! along rectangular grid points. ! $contrl scftyp=rhf runtyp=surface icharg=-1 coord=zmt mplevl=2 $end $system memory=500000 timlim=30 memddi=2 $end $surf ivec1(1)=2,1 igrp1=1 ivec2(1)=2,5 igrp2(1)=5,6 disp1= 0.10 ndisp1=3 orig1=-0.10 disp2=-0.10 ndisp2=3 orig2= 0.10 $end $basis gbasis=n21 ngauss=3 $end $guess guess=huckel $end $data F-NH2-OH exchange (inspired by J.Phys.Chem. 1994,98,7942-4) Cs F N H H O H 1 2 2 2 5 rNF rNH rNH rNO rOH

1 1 3 2

aFNH aFNH aONH aHON

3 aHNH +1 4 aONH -1 1 180.0

rNF=1.7125469

Input Examples rNH=0.9966981 rNO=1.9359887 rOH=0.9828978 aFNH=90.18493 aONH=79.34339 aHON=100.78851 aHNH=108.57000 $end

3-39

Input Examples ! ! ! ! ! ! ! ! ! ! EXAM30 Test of water EFP ... formamide/three water complex FINAL E= -169.0085352303 after 12 iterations RMS gradient=0.008099469 The geometry below combines a computed gas phase structure for formamide, with three waters located in a cylic fashion whose positions approximate the minimum structure of W.Chen and M.S.Gordon. This approximate structure lies about 11 mHartee above the actual minimum. $contrl scftyp=rhf runtyp=gradient coord=zmt $end $system memory=300000 $end $basis gbasis=dh npfunc=1 ndfunc=1 $end $data formamide with three effective fragment waters C1 C O 1 rCO N 1 rCN 2 aNCO H 3 rNHa 1 aCNHa 2 0.0 H 3 rNHb 1 aCNHb 2 180.0 H 1 rCH 2 aHCO 4 180.0 rCO=1.1962565 rCN=1.3534065 rNHa=0.9948420 rNHb=0.9921367 rCH=1.0918368 aNCO=124.93384 aCNHa=119.16000 aCNHb=121.22477 aHCO=122.30822 $end $efrag coord=int fragname=H2ORHF O1 4 1.926 3 175.0 H2 7 0.9438636 4 117.4 H3 7 0.9438636 8 106.70327 fragname=H2ORHF O1 8 1.901 7 175.0 H2 10 0.9438636 8 110.0 H3 10 0.9438636 11 106.70327 fragname=H2ORHF H2 2 1.951 1 150.0 O1 13 0.9438636 2 177.0 H3 14 0.9438636 13 106.70327 $end

3-40

1 180.0 3 -175.0 4 95.0 4 0.0 4 -5.0 8 -95.0 3 0.0 3 0.0 3 140.0

Input Examples

3-41

! EXAM31. ! methanol in PCM water...RHF geometry optimization ! FINAL E= -115.0425099569, 10 iters, RMS Grad= 0.0019075 ! FINAL E= -115.0425563041, 7 iters, RMS Grad= 0.0006106 ! FINAL E= -115.0425615962, 6 iters, RMS Grad= 0.0001950 ! FINAL E= -115.0425621855, 5 iters, RMS Grad= 0.0000403 ! FINAL E= -115.0425622093, 4 iters, RMS Grad= 0.0000309 ! FINAL E= -115.0425622106, 3 iters, RMS Grad= 0.0000033 ! ! ------RESULTS OF PCM CALCULATION ------! FREE ENERGY IN SOLVENT = -115.0425622106 A.U. ! INTERNAL ENERGY IN SOLVENT = -115.0346408480 A.U. ! DELTA INTERNAL ENERGY = .0000000000 A.U. ! ELECTROSTATIC INTERACTION = -.0079213626 A.U. ! PIEROTTI CAVITATION ENERGY = .0000000000 A.U. ! DISPERSION FREE ENERGY = .0000000000 A.U. ! REPULSION FREE ENERGY = .0000000000 A.U. ! TOTAL INTERACTION = -.0079213626 A.U. ! TOTAL FREE ENERGY IN SOLVENT = -115.0425622106 A.U. ! $contrl scftyp=rhf runtyp=optimize nzvar=12 $end $system mwords=2 $end $pcm solvnt=water $end $basis gbasis=n31 ngauss=6 ndfunc=1 $end $guess guess=huckel $end $zmat izmat(1)=1,1,2, 1,2,3, 1,3,4, 1,3,5, 1,3,6, 2,1,2,3, 2,2,3,4, 2,2,3,5, 2,2,3,6, 3,1,2,3,4, 3,1,2,3,5, 3,1,2,3,6 $end $statpt opttol=1d-5 $end $data Methanol in PCM water...starting at gas phase geom Cs H O C H H 1.0 8.0 6.0 1.0 1.0 $end -1.0616171503 -0.6870131482 0.7093551399 1.0836641283 1.0975386849 0.8036449245 -0.0653470836 0.0291827007 0.5408321444 -0.9797829903 0.0000000000 0.0000000000 0.0000000000 0.8835398105 0.0000000000

Input Examples

3-42

! EXAM32. ! Test of Coupled-Cluster energy for HNO ! The basis set used is 6-31G(d,p), with 35 AOs. ! An advanced non-iterative triples energy is ! computed, which should be better than CCSD(T). ! The two chemical core orbitals are not correlated. ! ! RHF FINAL E= -129.7891059395 after 13 iters ! Highest level result is E(CR-CC(2,3))= -130.1517479953 ! ! Other results are ! 19 CCSD iterations needed to converge T1 and T2. ! E(MBPT(2)) = -130.1278985212, aka MP2 energy ! E(CCSD) = -130.1398314377 ! The T1 diagnostic is 0.01448788, and the largest T2 ! amplitude is for the pi->pi* double, namely -0.146352. ! It takes 15 iterations to converge the left eigen! state (lambda equation). A number of other ! "completely renormalized" energies are computed, with ! CR-CCL aka CR-CC(2,3),D being considered the best. ! The CCSD level dipole is 1.658371 Debye ! ! The "standard" E(CCSD(T)) is not computed by this run, ! change to CCTYP=CCSD(T) to see that. ! $contrl scftyp=rhf cctyp=cr-ccl runtyp=energy nzvar=3 $end $system timlim=2 $end $guess guess=huckel $end $basis gbasis=n31 ngauss=6 ndfunc=1 npfunc=1 $end $zmat izmat(1)=1,1,2, 1,2,3, 2,1,2,3 $end $data HNO...CR-CC(2,3) computation in small DZP basis Cs H 1.0 N 7.0 O 8.0 $end -0.3153213523 0.0188021294 1.1940439356 0.9784305023 0.0012704060 0.0007180427 0.0 0.0 0.0

Input Examples

3-43

! EXAM 33. ! This job illustrates occupation restricted multiple ! active space MCSCF, for HCN. ! ! The multiple active spaces are sigma, pi-x, and pi-y. ! The excitation level between these three spaces can be ! limited to 0, 1, or 2. The number of determinants in ! each such ORMAS-MCSCF are ! excitation MINE MAXE # dets energy gradient ! 0 6,2,2 6,2,2 2,610 -93.014905 0.04394 ! 1 5,1,1 7,3,3 11,290 -93.014905 0.04394 ! 2 4,0,0 8,4,4 15,410 -93.022394 0.04510 ! full CI 2,0,0 10,4,4 15,876 -93.022407 0.04511 ! Full CI of 10 valence electrons in 9 valence orbitals ! is well within the capabilities of CISTEP=ALDET, but ! this example is meant to illustrate using occupational ! restrictions to limit the number of determinants. ! Note the singles between spaces don't contribute any ! energy because in this case the singles determinants ! all have the wrong total space symmetry. ! ! FINAL E= -93.0223942017, 11 iters, RMS grad=0.045100935 ! $contrl scftyp=mcscf runtyp=gradient nzvar=3 $end $system mwords=5 memddi=1 $end $basis gbasis=n31 ngauss=6 ndfunc=1 npfunc=1 $end $zmat izmat(1)=1,1,2, 1,2,3, 5,1,2,3 $end $libe apts(1)=1.0,0.0,0.0 $end ! reordering is sigma before pi-x before pi-y before empty $guess guess=moread norb=35 norder=1 iorder(3)=3,4,5,10,14, 6,9, 7,8, 11,12,13 $end $mcscf soscf=.true. cistep=ormas $end $det ncore=2 nact=9 nels=10 $end $ormas nspace=3 mstart(1)=3,8,10 mine(1)=4,0,0 maxe(1)=8,4,4 $end ! ! ! ! --------------uncomment the following lines to convert this run from a MCSCF nuclear gradient, into a 2nd order perturbation theory energy correction using GMCQDPT. E(MP2)= -93.1328290859, reference wt= 96.974% $contrl runtyp=energy mplevl=2 $end $system mwords=10 memddi=10 $end $mcscf soscf=.true. cistep=gmcci $end $gmcpt nmofzc=2 nmodoc=0 nmoact=9 reftyp=ormas nspace=3 mstart(1)=3,8,10 mine(1)=4,0,0 maxe(1)=8,4,4 $end $mrmp mrpt=gmcpt $end

Input Examples $data HCN...6-31G(d,p) MCSCF using ORMAS...RHF geometry Cnv 4 H C N 1.0 6.0 7.0 $end 0.0 0.0 -1.0589956 0.0 0.0 0.0 0.0 0.0 1.1327718

3-44

--- CLOSED SHELL MO's --- GENERATED Mon, Jan 13, 2003 E(RHF)= -92.8771381048, with MVOQ=4 used to make virtuals. $VEC ...orbitals deleted... $END

Input Examples

3-45

! EXAM34. ! CIS treatment of excited states of formaldehyde. ! ! EXCITED STATE 1's E=-113.7017742428, RMS=0.0290048 ! The S0->S1 transition dipole is (0,0,0.006029), ! and the S0 -> S1 transition energy is 4.56 eV. ! ! geometry optimization would lead in 18 steps to ! -113.7053624528, at r(CO)=1.2553, r(CH)=1.0854, ! a(HCO)= 117.74, with C's pyramidalization= 24.88. ! This reproduces the fourth line of Table III in ! Foresman et al. J.Phys.Chem. 96, 135-149(1992), ! using no frozen core orbitals in order to do so. ! Since it is well known that the geometry of this ! state lies within Cs symmetry, the initial guess ! geometry below is very slightly bent into Cs. ! $contrl scftyp=rhf cityp=cis runtyp=gradient nzvar=6 $end $system timlim=1 $end $basis gbasis=n31 ngauss=6 ndfunc=1 diffsp=.t. $end $guess guess=huckel $end $cis hamtyp=saps mult=1 nacore=0 nstate=1 istate=1 $end $zmat izmat(1)=1,1,2, 1,2,3, 1,2,4, 2,1,2,3, 2,1,2,4, 4,1,2,4,3 $end $data Formaldehyde CIS/6-31+G(d) 1(n->pi*) state optimization Cs O C H 8.0 6.0 1.0 $end .01 .0 -0.01 -.8669736159 .3455497481 .9295804473 .0 .0 .9376713430

Input Examples ! EXAM35. ! As atom...Test of relativistic energy correction, ! by the Douglas-Kroll transformation to 3rd order. ! ! the FINAL DK3 energy is -2259.0955118230 ! web page says -2259.095511826 ! ! convergence of the DK transformation is typical, ! 0th order -2234.2372862734 (non-relativistic) ! 1st order -2264.6131852344 ! 2nd order -2258.9450216276 ! 3rd order -2259.0955118230 ! in that 1st order way undershoots, 2nd order comes ! back close, and 3rd order is not insubstantial. ! Compare with -2259.456841 which is the point ! nucleus Dirac-Coulomb numerical Hartree-Fock from ! L.Visscher, K.G.Dyall ! At.Data Nucl.Data Tables 67, 207-224(1997) ! ! The uncontracted 20s15p9d basis set below is from ! T.Tsuchiya, M.Abe, T.Nakajima, K.Hirao ! J.Chem.Phys. 115, 4463-4472(2001) ! using exponents downloaded from the web page of ! this group at the University of Tokyo. A general ! contraction of this basis can easily be obtained, ! by manipulating the $VEC coefs produced by this run. ! The semicolon divides two lines of input that happen ! to be given on a single physical line of the file. ! $contrl scftyp=rohf mult=4 relwfn=dk ispher=1 $end $system mwords=2 $end $relwfn norder=3 $end $guess guess=huckel $end $data illustration of 3rd order Douglas-Kroll for As Dnh 2 Arsenic 33.0 S 1 ; 1 7.2421890D+07 S 1 ; 1 7.7040750D+06 S 1 ; 1 1.3365730D+06 S 1 ; 1 3.0394350D+05 S 1 ; 1 8.3289250D+04 S 1 ; 1 2.5994450D+04 S 1 ; 1 8.9795770D+03 S 1 ; 1 3.3667950D+03 S 1 ; 1 1.3464700D+03 S 1 ; 1 5.6774580D+02 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

3-46

Input Examples S S S S S S S S S S P P P P P P P P P P P P P P P D D D D D D D D D 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2.4923080D+02 1.1199520D+02 4.6328140D+01 2.2611220D+01 1.0910110D+01 4.5498340D+00 2.1494630D+00 1.0337510D+00 3.0892460D-01 1.1206710D-01 4.9515580D+04 8.4637830D+03 2.2908560D+03 7.7965970D+02 3.0545690D+02 1.3097990D+02 5.9698960D+01 2.8408790D+01 1.3883000D+01 6.6102210D+00 3.0821260D+00 1.3919830D+00 4.8254700D-01 1.9228260D-01 7.2849660D-02 7.1896480D+02 2.0798400D+02 7.9590850D+01 3.4514110D+01 1.5730540D+01 7.2805600D+00 3.3000700D+00 1.4173160D+00 5.4472730D-01 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0

3-47

$end

Input Examples

3-48

! EXAM36 ! analytic hessian for determinant MCSCF, at the ! transition state for C=C rotation in ethylene ! ! There are 38 AOs and 36 MOs using spherical harmonics. ! The 4e-, 4 orbital active space (CC sigma, pi, pi*, and ! sigma* orbitals) generates a total of 36 determinants. ! ! FINAL E= -77.9753563834 after 14 iterations ! imaginary FREQ= 1847.32i ! true FREQ= 319.87(2), 1005.72(2), 1082.80, 1578.13 ! true FREQ= 1605.72, 3311.13, 3315.17, 3405.91(2) ! the lowest true vibration is the most intense, 1.09748 ! $contrl scftyp=mcscf runtyp=hessian ispher=1 $end $system mwords=1 memddi=5 timlim=50 $end $basis gbasis=n31 ngauss=6 ndfunc=1 $end $guess guess=moread norb=36 norder=1 iorder(3)=4,5,6,7, 3,8,9,10 $end $det ncore=6 nact=4 nels=4 $end $data C2H4 at rotational saddle point...sigma,pi,pi*,sigma* active Dnd 2 C H $end How to prepare the starting orbitals, also take note of the orbital reordering to select the CC sigma: --- $contrl scftyp=rohf mult=3 runtyp=energy $end --- $scf mvoq=2 $end --- $guess guess=huckel norder=0 $end --- OPEN SHELL ORBITALS --- Tue Apr 6 10:00:30 2004 E(ROHF)= -77.9570103652 $VEC 1 1 7.04639833E-01... ... 36 8 3.55118554E-02-8.89989950E-03-3.55118554E-02 $END 6.0 1.0 0.0000000000 0.6500976762 0.0000000000 0.6500976762 0.7486926908 1.3062796706

Input Examples

3-49

! EXAM 37. ! water trimer...illustration of FMO method on clusters ! ! A total of 21 energies are computed in this run, ! of which the very first and last are -75.0201194583 ! and -149.9943977172, from various monomer and dimer ! calculations. Combined together, the results for ! 2-body FMO-RHF are: ! Euncorr(2)= -224.910612407, RMS GRADIENT = 0.0267805 ! ! Explicit RHF/STO-3G calculation on these coords has ! E= -224.9112662623, grad=0.0269349 ! ! See ../gamess/tools/fmo for larger examples based on ! published data and examples involving bond fractioning. ! $contrl scftyp=rhf runtyp=gradient $end $system timlim=2 $end $basis gbasis=sto ngauss=3 $end $fmo nfrag=3 icharg(1)=0,0,0 frgnam(1)=frag01,frag02,frag03 indat(1)=1,1,1, 2,2,2, 3,3,3 $end $fmoprp nprint=0 $end $fmoxyz O O .000000 .000000 .000000 H H .000000 .000000 .957200 H H .926627 .000000 -.239987 O O 2.542027 .893763 -1.001593 H H 1.991815 1.623962 -1.284979 H H 2.958433 .581215 -1.804806 O O .162059 2.462918 -1.477183 H H -.189749 1.755643 -.936605 H H -.375542 2.449889 -2.269046 $end $data Basis set input, with no atomic coordinates C1 h-1 1 c-1 6 n-1 7 o-1 8 $end

Input Examples ! EXAM 38. ! Analytic gradients for Model Core Potentials, ! with a DZP quality basis, for BiCl3. Model Core ! Potentials account for scalar relativity effects, ! and preserve all valence orbital radial nodes. ! ! The latter point stands in contrast to the ! Effective Core Potential (ECP) pseudopotentials. ! ! FINAL RHF E= -116.3966190322, RMS grad= 0.0053955 ! FINAL RHF E= -116.3972798590, RMS grad= 0.0036800 ! FINAL RHF E= -116.3976422769, RMS grad= 0.0014246 ! FINAL RHF E= -116.3976891713, RMS grad= 0.0001135 ! FINAL RHF E= -116.3976900830, RMS grad= 0.0000485 ! FINAL RHF E= -116.3976902416, RMS grad= 0.0000001 ! $contrl scftyp=rhf runtyp=optimize pp=mcp ispher=1 coord=zmt nzvar=6 $end $system timlim=5 mwords=4 $end $basis gbasis=mcp-dzp $end $statpt opttol=1.0d-5 $end $data BiCl3 Cnv 3 Bi Cl Cl Cl 1 rBiCl 1 rBiCl 1 rBiCl

3-50

2 aClBiCl 2 aClBiCl

3 aClBiCl +1

rBiCl=2.48 aClBiCl=99.0 $end

Input Examples ! ! ! ! ! ! ! EXAM 39. The non-resonant Raman and hyper-Raman spectra of CH4

3-51

Please see the actual file, supplied with GAMESS, for its very long preamble about the inadequacy of the basis set used below, and how to interpret the output.

$contrl scftyp=rhf runtyp=tdhfx nosym=1 ispher=0 $end $system mwords=1 $end $basis gbasis=n21 ngauss=3 $end $guess guess=huckel $end $scf dirscf=.true. conv=1d-6 $end $force method=analytic $end $cphf cphf=AO polar=.false. $end $tdhfx FREQ2 DADX 0.04 DADX_NI 0.04 DBDX 0.04 0.04 DBDX_NI 0.04 0.04 RAMAN 0.04 HRAMAN 0.04 D2ADX2_NI 0.04 D2BDX2_NI 0.04 0.04 $end $data methane RHF Td C H $END 6.0 1.0 0.0 0.6252197764 0.0 0.6252197764 0.0 0.6252197764

Input Examples ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! EXAM40. CH2 singlet/triplet...minimum energy crossing. Ansatz is full valence MCSCF in cc-pVDZ basis, 25 AOs and 24 MOs, using spherical harmonics. It is well known that the ground state of CH2 (A.Kalemos, T.H.Dunning, A.Mavridis, J.F.Harrison Can.J.Chem. 82, 684-693(2004)) is a triplet, but that the singlet state becomes the lowest surface at small angles. In this basis, the states have their minima at r(CH) a(HCH) Energy 3-B-1 1.10155 130.9955 -38.9605726 1-A-1 1.13868 99.9417 -38.9415486 and we know there is a crossing of these states somewhere. Starting between the minima, near R=1.11 and angle=115, where triplet E= -38.9565003, dE/dZ(C)=+.0259717 singlet E= -38.9359506, dE/dZ(C)=-.0411344, the seam minimization stops in 13 steps at C 0.0 .0000000000 .0977833873 H 0.0 -.8659658151 -.6448916937 H 0.0 .8659658151 -.6448916937 which is R=1.1408, angle=98.77, actually just inside the 1-A-1's bond angle. This MEX point is the "transition state" for spin-orbit-coupling induced inter-system-crossing (ISC) between these two surfaces, see N.Matsunaga, S.Koseki, M.S.Gordon J.Chem.Phys. 104, 7988-7996(1996). Note that the MEX's energy and structure are very similar to the singlet state's minimum: Energy of First State = -38.941516 Energy of Second State = -38.941513 Energy Difference = .000003 Max Effective Gradient = .000009 RMS Effective Gradient = .000005 Max Change of X = .000023 RMS change of X = .000011 PARALLEL GRADIENT (in seam) has RMS=.026456 $contrl $basis $guess $zmat $mex $det1 $det2 runtyp=mex ispher=1 nzvar=3 $end gbasis=ccd $end guess=moread norb=24 $end izmat(1)=1,1,2, 1,1,3, 2,2,1,3 $end scf1=mcscf mult1=3 nmos1=24 scf2=mcscf mult2=1 nmos2=24 nrdmos=3 $end stsym=B1 ncore=1 nact=6 nels=6 $end stsym=A1 ncore=1 nact=6 nels=6 $end

3-52

Input Examples $data methylene...cc-pVDZ basis set Cnv 2 Carbon Hydrogen $end 6.0 1.0 0.0 0.936 -0.596 -38.9565003122

3-53

3-B-1 state: E(MCSCF)= $VEC1 ...snipped... $END 1-A-1 state: E(MCSCF)= $VEC2 ...snipped... $END

-38.9359506088

Input Examples ! EXAM 41. ! This job illustrates TDDFT/BLYP/6-31+G(d) for ! the 3 lowest singlet excited states of CO. ! Note the use of diffuse functions in the basis ! set, since excited states often have Rydberg ! character. ! ! The geometry is optimized at the BLYP level, ! and is slightly longer than R0(exp)=1.128323. ! experimental Te is 8.06 to 1-pi, ! 8.17 to 1-sigma-minus ! Computational results on the log file show you ! that these two states arise from sigma->pi*, ! and pi->pi* excitations, respectively. ! ! ground state FINAL E= -113.3036657017, in 18 iters ! ! state excitation transition dipole oscillator ! ev x y z strength ! 0 sig+ .000 ! 1 pi 8.107 .6618 .1110 .0000 .089 ! 2 pi 8.107 .1110 -.6618 .0000 .089 ! 3 sig- 9.407 .0000 .0000 .0000 .000 ! ! RMS gradient of 1st excited state= 0.091670657 ! $contrl scftyp=rhf dfttyp=blyp tddft=excite runtyp=gradient $end $system timlim=10 mwords=7 $end $tddft nstate=3 mult=1 iroot=1 $end $guess guess=huckel $end $basis gbasis=N31 ngauss=6 diffsp=.T. ndfunc=1 $end $data CO...excitation to the three lowest singlet states Cnv 4 C O 6.0 8.0 $end 0.0 0.0 0.0 0.0 0.0 1.1497297

3-54

Input Examples EXAM 42. ! numerical gradient for PH3, using CCTYP=CR-CCL ! there are 40 AOs, 38 MOs, 5 frozen cores, so ! 4 valence orbitals correlated by 29 virtuals. ! ! This tests the numerical gradient driver, and also ! emphasizes that the Dunning correlation consistent ! basis sets should be used in spherical harmonic form. ! ! Since this molecule has two totally symmetric degrees ! of freedom, 1 numerical gradient requires 5 energies: ! at the input geometry, and at a pair of geometries ! displaced along each totally symmetric direction. ! ! See METHOD=FULLNUM in $FORCE for numerical hessians, ! and RUNTYP=FFIELD for numerical polarizabilities. ! ! E(RHF)= -342.4761838200, E(CCSD)= -342.6400065656, ! T1 diag=0.01066308, mu(CCSD)= 0.717048 Debye ! standard E(CCSD(T)) is not generated by this run. ! ! E(CR-CCL)= E(CR-CC(2,3)= -342.6433870011, ! RMS gradient= 0.004511564 ! $contrl scftyp=rhf cctyp=cr-ccl runtyp=gradient numgrd=.true. ispher=1 coord=zmt nzvar=6 $end $system timlim=5 mwords=2 $end $basis gbasis=ccd $end $data PH3...RHF/cc-pVDZ geometry Cnv 3 P H H H 1 rPH 1 rPH 1 rPH

3-55

2 aHPH 2 aHPH

3 aHPH +1

rPH=1.412958 aHPH=95.2045121 $end

Input Examples EXAM 42. ! numerical gradient for CN, using open shell CC(2,3). ! ! This tests the numerical gradient driver, and also ! emphasizes that the Dunning correlation consistent ! basis sets should be used in spherical harmonic form. ! ! A numerical gradient computation requires the energy ! at the molecule's actual geometry, plus energies at ! a pair of geometries displaced along each of its ! totally symmetric directions. ! A diatomic has 1 totally symmetric degree of freedom, ! so this run requires 3 energies for 1 gradient. ! ! See METHOD=FULLNUM in $FORCE for numerical hessians, ! and RUNTYP=FFIELD for numerical polarizabilities. ! ! There are 30 AOs, 28 MOs, 2 frozen cores, so 5 alpha ! and 4 beta valence electrons are correlated. ! ! E(ROHF)= -92.1960778308, E(CCSD)= -92.4767618032, ! the CR-CCL energy E(CC(2,3)) = -92.4930167395, ! and RMS gradient= 0.029652621 at the CC(2,3) level. ! (will optimize to -92.4941853332 at 1.1966876) ! $contrl scftyp=rohf cctyp=cr-ccl mult=2 nzvar=1 runtyp=gradient numgrd=.true. ispher=1 $end $system timlim=5 $end $basis gbasis=ccd $end $zmat izmat(1)=1,1,2 $end $ccinp maxcc=50 $end $data CN...experimental geometry...X-2-sigma-plus state Cnv 4 C N 6.0 7.0 $end 0.0 0.0 0.0 0.0 0.0 1.1718

3-56

Input Examples ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! !

3-57

EXAM 43. methane G3(MP2,CCSD(T)) heat of formation 6-31G(d) has 23 AOs and 23 MOs, G3Large has 79 AOs and 74 MOs. -------------------------------------------------------MP2/6-31G(D) = -40.332552 CCSD(T)/6-31G(D)= -40.355850 MP2/G3MP2LARGE = -40.404248 BASIS CONTRIBUT = -.071696 ZPE(HF/6-31G(D)= .042659 ZPE SCALE FACTOR= .892900 HLC = -.036680 FREE ENERGY = .030480 THERMAL ENERGY = .050629 THERMAL ENTHALPY= .051573 HEAT OF FORMATION (0K): -16.01 KCAL/MOL HEAT OF FORMATION (298K): -17.83 KCAL/MOL -------------------------------------------------------The literature, namely JCP 110,4705(1999), says the heat of formation by G3(MP2,QCISD(T)) = -17.8 @ 298 This run substitutes the standard CCSD(T) energy for QCI, as considered by L.A.Curtiss, K.Ragavachari, P.C.Redfern, A.G.Baboul, J.A.Pople Chem.Phys.Lett. 314, 101-107(1999) RUNTYP=G3MP2 performs a sequence of computations, First, using the 6-31G(d) Cartesian GTO basis set: HF geometry optimization (much like runtyp=optimize) HF frequencies and ZPE evaluation (runtyp=hessian) MP2 geometry, with no frozen cores (runtyp=optimize) CCSD(T) energy calculation (runtyp=energy) Then, using the G3Large basis, as spherical harmonics: MP2 energy calculation, with frozen cores All these intermediate energies are then gathered together by the G3 recipe to produce the results. Note that there is no particular input. The two basis sets that are used, and the switch from Cartesian to spherical harmonics is handled internally, so there is no $BASIS group. The necessary asis sets are available for H-Ca, Ga-Kr. Parallel computation is enabled. The reference state must be RHF at present. You can assist the run by giving a converged HF/6-31G(d) geometry in $DATA, although this is not necessary. $contrl scftyp=rhf runtyp=g3mp2 $end $system timlim=5 mwords=2 memddi=5 $end $scf dirscf=.true. $end $data Methane...G3(MP2,CCSD(T)) Td C H 6.0 1.0 $end 0.0000000 0.6375302 0.0000000 0.6375302 0.0000000 0.6375302

Input Examples

3-58

! EXAM 44. ! Hydrogen fluoride hexamer...(HF)6 ! using the divide-and-conquer (DC) method ! ! Divide-and-conquer HF and MP2 energies are: ! FINAL DC-RHF E= -599.9471636844, 14 iters ! E(MP2)= -600.7388336079 ! An explicit MP2/6-31G calculation yields: ! RHF E= -599.9475140963, 12 iters ! MP2 E= -600.7399209860 ! ! CCSD calculation requires changing one keyword in ! $CONTRL. The divide-and-conquer CCSD energy is ! E(CCSD)= -600.7487442686 ! compared to the explicit CCSD/6-31G calculation: ! CCSD ENERGY= -600.7485966549 ! $CONTRL SCFTYP=RHF RUNTYP=ENERGY MPLEVL=2 COORD=ZMT $END $SYSTEM MWORDS=1 $END $BASIS GBASIS=N31 NGAUSS=6 $END $GUESS GUESS=HUCSUB $END $DCCORR DODCCR=.TRUE. RBUFCR=3.0 $END $DANDC DCFLG=.TRUE. BUFRAD=5.0 BUFTYP=RADSUB NSUBS=6 LBSUBS(1)=1,2,3,4,5,6,1,2,3,4,5,6 $END $DATA zigzag hexamer (HF)6 C1 F F 1 rFF F 2 rFF 1 aHFH F 3 rFF 2 aHFH 1 180.0 F 4 rFF 3 aHFH 2 180.0 F 5 rFF 4 aHFH 3 180.0 H 1 rHFL 2 aHFH 3 180.0 H 2 rHF 3 aHFH 4 180.0 H 3 rHF 4 aHFH 5 180.0 H 4 rHF 5 aHFH 6 180.0 H 4 rFH 3 aHFH 2 180.0 H 5 rFH 4 aHFH 3 180.0 rFF=2.5 rHF=0.97 rFH=1.43 aHFH=116.0 rHFL=0.97 $END

Further Information (5 May 2011) *********************************** * * * Section 4 - Further Information * * * ***********************************

4-1

This section of the manual contains both references, and hints on how to do things. The following is a list of the topics covered: Computational References________________________________________________ 5 Basis Set References ___________________________________________________ 17 Spherical Harmonics ___________________________________________________ 29 How to do RHF, ROHF, UHF, and GVB calculations ________________________ 30
general considerations_______________________________________________________ 30 direct SCF ________________________________________________________________ 31 convergence accelerators ____________________________________________________ 34 high spin open shell SCF (ROHF) _____________________________________________ 37 other open shell SCF cases (GVB) _____________________________________________ 39 true GVB perfect pairing runs ________________________________________________ 43 the special case of TCSCF____________________________________________________ 45 a caution about symmetry____________________________________________________ 45

How to do MCSCF (and CI) calculations___________________________________ 47

MCSCF implementation _____________________________________________________ 48 orbital updates_____________________________________________________________ 49 CI coefficient optimization ___________________________________________________ 52 determinant CI ____________________________________________________________ 54 CSF CI ___________________________________________________________________ 58 starting orbitals ____________________________________________________________ 62 miscellaneous hints _________________________________________________________ 64 MCSCF references _________________________________________________________ 65

Second Order Perturbation Theory________________________________________ 69

RHF and UHF reference MP2 ________________________________________________ 69 high spin ROHF reference MP2_______________________________________________ 70 GVB based MP2 ___________________________________________________________ 72 MCSCF reference perturbation theory _________________________________________ 73

Coupled-Cluster Theory_________________________________________________ 77
available computations (ground states) _________________________________________ 80

Further Information

4-2

available computations (excited states) _________________________________________ 88 density matrices and properties _______________________________________________ 94 excited state example________________________________________________________ 98 resource requirements ______________________________________________________ 99 restarts in ground-state calculations __________________________________________ 104 initial guesses in excited-state calculations _____________________________________ 106 eigensolvers for excited-state calculations ______________________________________ 107 references and citations required in publications ________________________________ 109

Density Functional Theory _____________________________________________ 116

DFTTYP keywords ________________________________________________________ 116 grid-free DFT_____________________________________________________________ 117 DFT with grids ___________________________________________________________ 118 Time Dependent Density Functional Theory (TD-DFT) __________________________ 120 references for DFT ________________________________________________________ 122

Summary of excited state methods _______________________________________ 133 Geometry Searches and Internal Coordinates ______________________________ 135
quasi-Newton Searches _____________________________________________________ 135 the nuclear Hessian ________________________________________________________ 138 coordinate choices _________________________________________________________ 139 the role of symmetry _______________________________________________________ 144 practical matters __________________________________________________________ 145 saddle points _____________________________________________________________ 147 mode following____________________________________________________________ 149

Intrinisic Reaction Coordinate Methods___________________________________ 151 Gradient Extremals ___________________________________________________ 156 Continuum Solvation Methods __________________________________________ 162
Self Consistent Reaction Field (SCRF) ________________________________________ 162 Polarizable Continuum Model (PCM) _________________________________________ 163 SVPE and SS(V)PE. _______________________________________________________ 172 Conductor-like screening model (COSMO) ____________________________________ 176

The Effective Fragment Potential Method _________________________________ 178

terms in an EFP___________________________________________________________ 179 constructing an EFP1 ______________________________________________________ 180 constructing an EFP2 ______________________________________________________ 181 current limitations_________________________________________________________ 182 practical hints for using EFPs _______________________________________________ 183 global optimization ________________________________________________________ 185

Further Information

4-3

QM/MM across covalent bonds ______________________________________________ 187 Simpler potentials _________________________________________________________ 189 references ________________________________________________________________ 190

The Fragment Molecular Orbital method__________________________________ 196

Surfaces and solids ________________________________________________________ 198 FMO variants ____________________________________________________________ 199 Effective fragment molecular orbital method (EFMO) ___________________________ 200 Guidelines for approximations with FMO3_____________________________________ 200 How to perform FMO-MCSCF calculations ____________________________________ 201 How to perform multilayer runs _____________________________________________ 202 How to mix basis sets in FMO _______________________________________________ 202 How to perform FMO/PCM calculations ______________________________________ 203 How to perform FMO/EFP calculations _______________________________________ 204 Geometry optimizations for FMO ____________________________________________ 204 Pair interaction energy decomposition analysis (PIEDA) _________________________ 204 Excited states _____________________________________________________________ 206 Selective FMO ____________________________________________________________ 206

Frozen domains ______________________________________________________ 206

Analyzing and visualizing the results__________________________________________ 207 Parallelization of FMO runs with GDDI _______________________________________ 207 Limitations of the FMO method in GAMESS___________________________________ 207 Restarts with the FMO method ______________________________________________ 208 Note on accuracy __________________________________________________________ 209 FMO References __________________________________________________________ 209

MOPAC Calculations within GAMESS ___________________________________ 214 Molecular Properties and Conversion Factors______________________________ 217
Polarizabilities ____________________________________________________________ 218

Localized Molecular Orbitals ___________________________________________ 220 Transition Moments and Spin-Orbit Coupling______________________________ 226
states____________________________________________________________________ 227 orbitals __________________________________________________________________ 228 symmetry ________________________________________________________________ 229 spin orbit details __________________________________________________________ 230 input nitty-gritty __________________________________________________________ 232 references ________________________________________________________________ 233 examples_________________________________________________________________ 235

Further Information

4-4

For people who are newcomers to computational chemistry, it may be helpful to study an introductory book. First, some texts about quantum chemistry: "Ab Initio Molecular Orbital Theory" W.J.Hehre, L.Radom, J.A.Pople, P.v.R.Schleyer Wiley and Sons, New York, 1986 "Modern Quantum Chemistry" (now a Dover paperback) A.Szabo, N.S.Ostlund McGraw-Hill, 1989 "Quantum Chemistry, 6th Edition" I.N.Levine Prentice Hall, 2008 Then, a few books more focused on computation: "Introduction to Quantum Mechanics in Chemistry" M.A.Ratner, G.C.Schatz Prentice Hall, 2000 "Introduction to Computational Chemistry, 2nd Edition" Frank Jensen Wiley and Sons, Chichester, 2006 "Molecular Modeling Basics" Jan H. Jensen CRC Press, Boca Raton, 2010 Frank's book is an outstanding survey of methods, basis sets, properties, and other topics. Jan's book is a good complement to Frank's, staying at a simpler level, using GAMESS input examples. It has an accompanying online blog, http://molecularmodelingbasics.blogspot.com

Further Information

4-5

Computational References
GAMESS M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.J.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.Su, T.L.Windus, M.Dupuis, J.A.Montgomery J.Comput.Chem. 14, 1347-1363 (1993) M.S.Gordon, M.W.Schmidt pp 1167-1189 in "Theory and Applications of Computational Chemistry, the first forty years" C.E.Dykstra, G.Frenking, K.S.Kim, G.E.Scuseria (editors), Elsevier, Amsterdam, 2005. HONDO These papers describes many of the algorithms in detail, and much of these applies also to GAMESS: "The General Atomic and Molecular Electronic Structure System: HONDO 7.0" M.Dupuis, J.D.Watts, H.O.Villar, G.J.B.Hurst Comput.Phys.Comm. 52, 415-425(1989) "HONDO: A General Atomic and Molecular Electronic Structure System" M.Dupuis, P.Mougenot, J.D.Watts, G.J.B.Hurst, H.O.Villar in "MOTECC: Modern Techniques in Computational Chemistry" E.Clementi, Ed. ESCOM, Leiden, the Netherlands, 1989, pp 307-361. "HONDO: A General Atomic and Molecular Electronic Structure System" M.Dupuis, A.Farazdel, S.P.Karna, S.A.Maluendes in "MOTECC: Modern Techniques in Computational Chemistry" E.Clementi, Ed. ESCOM, Leiden, the Netherlands, 1990, pp 277-342. M.Dupuis, S.Chin, A.Marquez in "Relativistic and Electron Correlation Effects in Molecules", G.Malli, Ed. Plenum Press, NY 1994, pp 315-338. sp integrals and gradient integrals inner axis sp integration is done by McMurchie/Davidson J.A.Pople, W.J.Hehre J.Comput.Phys. 27, 161-168(1978) H.B.Schlegel, J.Chem.Phys. 77, 3676-3681(1982) spd integrals by rotated axis/McMurchie-Davidson K.Ishimura, S.Nagase Theoret.Chem.Acc. 120, 185-189(2008) McMurchie/Davidson integrals L.E.McMurchie, E.R.Davidson J.Comput.Phys. 26, 218-231(1978) spdfg integrals "Numerical Integration Using Rys Polynomials"

Further Information

4-6

H.F.King and M.Dupuis J.Comput.Phys. 21,144(1976) "Evaluation of Molecular Integrals over Gaussian Basis Functions" M.Dupuis,J.Rys,H.F.King J.Chem.Phys. 65,111-116(1976) "Molecular Symmetry and Closed Shell HF Calculations" M.Dupuis and H.F.King Int.J.Quantum Chem. 11,613(1977) "Computation of Electron Repulsion Integrals using the Rys Quadrature Method" J.Rys,M.Dupuis,H.F.King J.Comput.Chem. 4,154-157(1983) ERIC spdfg integrals "Recursion Formula for Electron Repulsion Integrals Over Hermite Polynomials" G.D.Fletcher Int.J.Quantum Chem. 106, 355-360(2006) spdfg gradient integrals "Molecular Symmetry. II. Gradient of Electronic Energy with respect to Nuclear Coordinates" M.Dupuis and H.F.King J.Chem.Phys. 68,3998(1978) although the implementation is much newer than this paper. spd hessian integrals "Molecular Symmetry. III. Second derivatives of Electronic Energy with respect to Nuclear Coordinates" T.Takada, M.Dupuis, H.F.King J.Chem.Phys. 75, 332-336 (1981) the Q matrix, and integral transformation symmetry E.Hollauer, M.Dupuis J.Chem.Phys. 96, 5220 (1992) spdfg effective core potential (ECP) integral/derivatives C.F.Melius, W.A.Goddard Phys.Rev.A 10,1528-1540(1974) L.R.Kahn, P.Baybutt, D.G.Truhlar J.Chem.Phys. 65, 3826-3853 (1976) M.Krauss, W.J.Stevens Ann.Rev.Phys.Chem. 35, 357-385(1985) J.Breidung, W.Thiel, A.Komornicki Chem.Phys.Lett. 153, 76-81(1988) B.M.Bode, M.S.Gordon J.Chem.Phys. 111, 8778-8784(1999) See also the papers listed for SBKJC and HW basis sets. model core potential (MCP) reviews S.Huzinaga Can.J.Chem. 73, 619-628(1995) M.Klobukowski, S.Huzinaga, Y.Sakai, in Computational Chemistry: Reviews of current trends, volume 3, pp 49-74, edited by J.Leszczynski, World Scientific, Singapore, 1999. Quantum fast multipole method (QFMM) E.O.Steinborn, K.Ruedenberg Adv.Quantum Chem. 7, 1-81(1973)

Further Information L.Greengard "The Rapid Evaluation of Potential Fields in Particle Systems" (MIT, Cambridge, 1987) C.H.Choi, J.Ivanic, M.S.Gordon, K.Ruedenberg J.Chem.Phys. 111, 8825-8831(1999) C.H.Choi, K.Ruedenberg, M.S.Gordon J.Comput.Chem. 22, 1484-1501(2001) C.H.Choi J.Chem.Phys. 120, 3535-3543(2004) RHF C.C.J.Roothaan Rev.Mod.Phys. 23, 69-89(1951)

4-7

UHF J.A.Pople, R.K.Nesbet

J.Chem.Phys 22, 571-572(1954)

high-spin coupled ROHF C.C.J.Roothaan Rev.Mod.Phys. 32, 179-185(1960) R.McWeeny, G.Diercksen J.Chem.Phys. 49,4852-4856(1968) M.F.Guest, V.R.Saunders Mol.Phys. 28, 819-828(1974) J.S.Binkley, J.A.Pople, P.A.Dobosh Mol.Phys. 28, 1423-1429(1974) E.R.Davidson Chem.Phys.Lett. 21,565-567(1973) K.Faegri, R.Manne Mol.Phys. 31,1037-1049(1976) H.Hsu, E.R.Davidson, and R.M.Pitzer J.Chem.Phys. 65,609-613(1976) B.N.Plakhutin, E.V.Gorelik, N.N.Breslavskaya J.Chem.Phys. 125, 204110/1-10(2006) B.N.Plakhutin, E.R.Davidson J.Phys.Chem.A 113, 12386-12395(2009) E.R.Davidson, B.N.Plakhutin J.Chem.Phys. 132, 184110/1-14(2010) K.R.Glaesemann, M.W.Schmidt J.Phys.Chem.A 114, 8772-8777(2010) GVB and low-spin coupled ROHF F.W.Bobrowicz and W.A.Goddard, in Modern Theoretical Chemistry, Vol 3, H.F.Schaefer III, Ed., Chapter 4. DFT and TD-DFT All appropriate references are included in the section on density functional theory included below. MCSCF - see reference list in the subsection below determinant CI full CI (ALDET) and general CI (GENCI), J.Ivanic, K.Ruedenberg Theoret.Chem.Acc. 106, 339-351(2001) occupation restricted multiple active space (ORMAS), J.Ivanic J.Chem.Phys. 119, 9364-9376, 9377-9385(2003)

Further Information configuration state function CI (GUGA) B.Brooks and H.F.Schaefer J.Chem. Phys. 70,5092(1979) B.Brooks, W.Laidig, P.Saxe, N.Handy, and H.F.Schaefer, Physica Scripta 21, 312(1980). CIS energy and gradient J.B.Foresman, M.Head-Gordon, J.A.Pople, M.J.Frisch J.Phys.Chem. 96, 135-149(1992) R.M.Shroll, W.D.Edwards Int.J.Quantum Chem. 63, 1037-1049(1997) the parallel CIS implementation in GAMESS is described in S.P.Webb Theoret.Chem.Acc. 116, 355-372(2006) which has a nice review of other excited state methods. spin-flip CIS: A.I.Krylov Chem.Phys.Lett. 338, 375(2001)

4-8

closed, unrestricted open shell 2nd order Moller-Plesset J.A.Pople, J.S.Binkley, R.Seeger Int. J. Quantum Chem. S10, 1-19(1976) M.J.Frisch, M.Head-Gordon, J.A.Pople, Chem.Phys.Lett. 166, 275-280(1990) C.M.Aikens, S.P.Webb, R.L.Bell, G.D.Fletcher, M.W.Schmidt, M.S.Gordon Theoret.Chem.Acc., 110, 233-253(2003) with the TCA "overview article" being a thorough review of the single determinant MP2 gradient equations. CODE=SERIAL is generally based on the CPL paper above, as described in the HONDO references given above. The next two document CODE=DDI for RHF and UHF, G.D.Fletcher, M.W.Schmidt, M.S.Gordon Adv.Chem.Phys. 110, 267-294(1999) C.M.Aikens, M.S.Gordon J.Phys.Chem.A, 108, 3103-3110(2004) The next two document CODE=IMS for RHF, K.Ishimura, P.Pulay, S.Nagase J.Comput.Chem. 27, 407-413(2006) K.Ishimura, P.Pulay, S.Nagase J.Comput.Chem. 28, 2034-2042(2007) The next documents code=RIMP2 for RHF and UHF, M.Katouda, S.Nagase Int.J.Quantum Chem. 109, 2121-2130(2009) Spin Component Scaled MP2 (SCS-MP2) S.Grimme

Further Information J.Chem.Phys. 118, 9095-9102(2003) spin restricted open shell MP2, ZAPT energy T.J.Lee, D.Jayatilaka Chem.Phys.Lett. 201, 1-10(1993) T.J.Lee, A.P.Rendell, K.G.Dyall, D.Jayatilaka J.Chem.Phys. 100, 7400-7409(1994) nuclear gradients for ZAPT The next two document the CODE=DDI program, G.D.Fletcher, M.S.Gordon, R.L.Bell Theoret.Chem.Acc. 107, 57-70(2002) C.M.Aikens, G.D.Fletcher, M.W.Schmidt, M.S.Gordon J.Chem.Phys. 124, 014107/1-14(2006) spin restricted open shell MP2, RMP method P.J.Knowles, J.S.Andrews, R.D.Amos, N.C.Handy, J.A.Pople Chem.Phys.Lett. 186, 130-136 (1991) W.J.Lauderdale,J.F.Stanton,J.Gauss,J.D.Watts,R.J.Bartlett Chem.Phys.Lett. 187, 21-28(1991)

4-9

multiconfigurational quasidegenerate perturbation theory H.Nakano J.Chem.Phys. 99, 7983-7992(1993) Coupled-Cluster Equation of Motion Coupled-Cluster (EOMCC) this is a subset of the relevant papers: P.Piecuch, S.A.Kucharski, K.Kowalski, M.Musial, Comput.Phys.Commun. 149, 71-96(2002) K.Kowalski, P.Piecuch, J.Chem.Phys. 120, 1715-1738 (2004) P.Piecuch, S.A.Kucharski, K.Kowalski, M.Musial Comput.Phys.Commun. 149, 71-96(2002). parallel CCSD(T) program J.L.Bentz, R.M.Olson, M.S.Gordon, M.W.Schmidt, R.A.Kendall Comput.Phys.Commun. 176, 589-600(2007) R.M.Olson, J.L.Bentz, R.A.Kendall, M.W.Schmidt, M.S.Gordon J.Comput.Theoret.Chem. 3, 1312-1328(2007) Any publication describing the results of ground-state and/or excited-state calculations using the equation of motion coupled-cluster and/or completely renormalized EOMCCSD(T) options (CCTYP=EOM-CCSD or CR-EOM) obtained with GAMESS should reference the specific papers appearing in the printout. For more references to the primary literature for both types of coupled-cluster methods, see the section "Coupled-Cluster theory" below.

Further Information

4-10

RHF/ROHF/TCSCF coupled perturbed Hartree Fock "Single Configuration SCF Second Derivatives on a Cray" H.F.King, A.Komornicki in "Geometrical Derivatives of Energy Surfaces and Molecular Properties" P.Jorgensen J.Simons, Ed. D.Reidel, Dordrecht, 1986, pp 207-214. "A parallel Distributed data CPHF algorithm for analytic Hessians" Y.Alexeev, M.W.Schmidt, T.L.Windus, M.S.Gordon J.Comput.Chem. 28, 1685-1694(2007). Y.Osamura, Y.Yamaguchi, D.J.Fox, M.A.Vincent, H.F.Schaefer J.Mol.Struct. 103, 183-186(1983) M.Duran, Y.Yamaguchi, H.F.Schaefer J.Phys.Chem. 92, 3070-3075(1988) "A New Dimension to Quantum Chemistry" Y.Yamaguchi, Y.Osamura, J.D.Goddard, H.F.Schaefer Oxford Press, NY 1994 MCSCF coupled perturbed Hartree-Fock M.R.Hoffman, D.J.Fox, J.F.Gaw, Y.Osamura, Y.Yamauchi, R.S.Grev, G.Fitzgerald, H.F.Schaefer, P.J.Knowles, N.C.Handy J.Chem.Phys. 80, 2660-2668(1984) the book by Osamura, Goddard, and Schaefer just mentioned. T.J.Dudley, R.M.Olson, M.W.Schmidt, M.S.Gordon J.Comput.Chem. 27, 353-362(2006) non-adiabatic coupling matrix element (NACME) J.C.Tully, chapter 5 (pp 217-267) in "Dynamics of Molecular Collisions - Part B", edited by W.H.Miller, Plenum Press, NY, 1976. B.H.Lengsfield, D.R.Yarkony, chapter 1 (pp. 1-71) in "State-selected and state-to-state in-molecule reaction dynamics- Part 2, theory", edited by M.Baer and C.-Y.Ng, John Wiley, NY, 1992. harmonic vibrational analysis in Cartesian coordinates W.D.Gwinn J.Chem.Phys. 55,477-481(1971) Normal coordinate decomposition analysis J.A.Boatz and M.S.Gordon, J.Phys.Chem. 93, 1819-1826(1989). Partial Hessian vibrational analysis H.Li, J.H.Jensen, Theoret.Chem.Acc. 107, 211-219(2002) anharmonic vibrational spectra (VSCF) a review of VSCF: R.B.Gerber, J.O.Jung in "Computational Molecular Spectroscopy" P.Jensen, P.R.Bunker, eds. Wiley and Sons, Chichester, 2000, pp 365-390.

Further Information the basic method for VSCF and cc-VSCF: G.M.Chaban, J.O.Jung, R.B.Gerber J.Chem.Phys. 111, 1823-1829(1999) the QFF approximation: K.Yagi, K.Hirao, T.Taketsugu, M.W.Schmidt, M.S.Gordon J.Chem.Phys. 121, 1383-1389(2004) the VDPT solver: N.Matsunaga, G.M.Chaban, R.B.Gerber J.Chem.Phys. 117, 3541-3547(2002) solver for larger systems: L.Pele, B.Brauer, R.B.Gerber Theoret.Chem.Acc. 117, 69-72(2007) use of internal coordinates, and thermochemistry B.Njegic, M.S.Gordon J.Chem.Phys. 125, 224102/1-12(2006) applications of RUNTYP=VSCF: G.M.Chaban, J.O.Jung, R.B.Gerber J.Phys.Chem.A 104, 2772-2779(2000) J.Lundell, G.M.Chaban, R.B.Gerber Chem.Phys.Lett. 331, 308-316(2000) K.Yagi, T.Taketsugu, K.Hirao, M.S.Gordon J.Chem.Phys. 113, 1005-1017(2000) G.M.Chaban, R.B.Gerber, K.C.Janda J.Phys.Chem.A 105, 8323-8332(2001) A.T.Kowal Spectrochimica Acta A 58, 1055-1067(2002) G.M.Chaban, S.S.Xantheas, R.B.Gerber J.Phys.Chem.A 107, 4952-4956(2003) G.M.Chaban J.Phys.Chem.A 108, 4551-4556(2004) Y.Miller, G.M.Chaban, R.B.Gerber J.Phys.Chem.A 109, 6565-6574(2005) Y.Miller, G.M.Chaban, R.B.Gerber Chem.Phys. 313, 213-224(2005) C.A.Brindle, G.M.Chaban, R.B.Gerber, K.C.Janda Phys.Chem.Chem.Phys. 7, 945-954(2005) G.M.Chaban, R.M.Gerber Theoret.Chem.Acc. 120, 273-279(2008)

4-11

Raman spectrum A.Komornicki, J.W.McIver J.Chem.Phys. 70, 2014-2016(1979) G.B.Bacskay, S.Saebo, P.R.Taylor Chem.Phys. 90, 215-224(1984) static polarizabilities: H.A.Kurtz, J.J.P.Stewart, K.M.Dieter J.Comput.Chem. 11, 82-87 (1990) dynamic polarizabilities: P.Korambath, H.A.Kurtz, in "Nonlinear Optical Materials",

Further Information ACS Symposium Series 628, S.P.Karna and A.T.Yeates, Eds. pp 133-144, Washington DC, 1996. nuclear derivatives of dynamic polarizabilities, and dynamic Raman and hyper-Raman: O.Quinet, B.Champagne J.Chem.Phys. 115, 6293-6299(2001) O.Quinet, B.Champagne B.Kirtman J.Comput.Chem. 22, 1920-1932(2001) O.Quinet, B.Champagne J.Chem.Phys. 117, 2481-2488(2002) O.Quinet, B.Kirtman, B.Champagne J.Chem.Phys. 118, 505-513(2003) Geometry optimization and saddle point location J.Baker J.Comput.Chem. 7, 385-395(1986). T.Helgaker Chem.Phys.Lett. 182, 503-510(1991). P.Culot, G.Dive, V.H.Nguyen, J.M.Ghuysen Theoret.Chim.Acta 82, 189-205(1992).

4-12

Dynamic Reaction Coordinate (DRC) J.J.P.Stewart, L.P.Davis, L.W.Burggraf, J.Comput.Chem. 8, 1117-1123 (1987) S.A.Maluendes, M.Dupuis, J.Chem.Phys. 93, 5902-5911(1990) T.Taketsugu, M.S.Gordon, J.Phys.Chem. 99, 8462-8471(1995) T.Taketsugu, M.S.Gordon, J.Phys.Chem. 99, 14597-604(1995) T.Taketsugu, M.S.Gordon, J.Chem.Phys. 103, 10042-9(1995) M.S.Gordon, G.Chaban, T.Taketsugu J.Phys.Chem. 100, 11512-11525(1996) T.Takata, T.Taketsugu, K.Hirao, M.S.Gordon J.Chem.Phys. 109, 4281-4289(1998) T.Taketsugu, T.Yanai, K.Hirao, M.S.Gordon THEOCHEM 451, 163-177(1998) Energy orbital localization C.Edmiston, K.Ruedenberg Rev.Mod.Phys. 35, 457-465(1963). R.C.Raffenetti, K.Ruedenberg, C.L.Janssen, H.F.Schaefer, Theoret.Chim.Acta 86, 149-165(1993) Boys orbital localization S.F.Boys, "Quantum Science of Atoms, Molecules, and Solids" P.O.Lowdin, Ed, Academic Press, NY, 1966, pp 253-262. See the first paper on oriented localized orbitals if you wish to know the true origin of "Boys localization" Population orbital localization J.Pipek, P.Z.Mezey J.Chem.Phys. 90, 4916(1989). Oriented localized orbitals J.Ivanic, G.M.Atchity, K.Ruedenberg Theoret.Chem.Acc. 120, 281-294(2008)

Further Information J.Ivanic, K.Ruedenberg Theoret.Chem.Acc. 120, 295-305(2008) Valence Virtual Orbitals (VVOS) W.C.Lu, C.Z.Wang, M.W.Schmidt, L.Bytautas, K.M.Ho, K.Ruedenberg J.Chem.Phys. 120, 2629-2637 and 2638-2651(2004) W.C.Lu, C.Z.Wang, T.L.Chan, K.Ruedenberg, K.M.Ho Phys.Rev.B 70, 041101-1/4(2004)

4-13

Mulliken Population Analysis R.S.Mulliken J.Chem.Phys. 23, 1833-1840, 1841-1846, 2338-2342, 2343-2346(1955) so called "Lowdin Population Analysis" This should be described as "a Mulliken population analysis (ref M1-M4 above) based on symmetrically orthogonalized orbitals (ref L)", where reference L is P.-O.Lowdin Adv.Chem.Phys. 5, 185-199(1970) Lowdin populations are not invariant to rotation if the basis set used is Cartesian d,f,...: I.Mayer, Chem.Phys.Lett. 393, 209-212(2004). Bond orders and valences M.Giambiagi, M.Giambiagi, D.R.Grempel, C.D.Heymann J.Chim.Phys. 72, 15-22(1975) I.Mayer, Chem.Phys.Lett. 97,270-274(1983), 117,396(1985). M.S.Giambiagi, M.Giambiagi, F.E.Jorge Z.Naturforsch. 39a, 1259-73(1984) I.Mayer, Theoret.Chim.Acta 67, 315-322(1985). I.Mayer, Int.J.Quantum Chem. 29, 73-84(1986). I.Mayer, Int.J.Quantum Chem. 29, 477-483(1986). The same formula (apart from a factor of two) may also be seen in equation 31 of the second of these papers (the bond order formula in the 1st of these is not the same formula): T.Okada, T.Fueno Bull.Chem.Soc.Japan 48, 2025-2032(1975) T.Okada, T.Fueno Bull.Chem.Soc.Japan 49, 1524-1530(1976) a review about bond orders: I. Mayer, J.Comput.Chem. 28, 204-221(2007). Direct SCF J.Almlof, K.Faegri, K.Korsell J.Comput.Chem. 3, 385-399 (1982) M.Haser, R.Ahlrichs J.Comput.Chem. 10, 104-111 (1989) DIIS (Direct Inversion in the Iterative Subspace) P.Pulay J.Comput.Chem. 3, 556-560(1982)

Further Information SOSCF G.Chaban, M.W.Schmidt, M.S.Gordon Theor.Chem.Acc. 97, 88-95(1997) T.H.Fischer, J.Almlof J.Phys.Chem. Modified Virtual Orbitals (MVOs) C.W.Bauschlicher, Jr. J.Chem.Phys.

4-14

96,9768-74(1992) 72,880-885(1980)

Thermochemistry (RUNTYP=G3MP2) G3(MP2,CCSD(T)) is defined in L.A.Curtiss, K.Ragavachari, P.C.Redfern, A.G.Baboul, J.A.Pople Chem.Phys.Lett. 314, 101-107(1999) based on various other G3 basis set/method papers: L.A.Curtiss, P.C.Redfern, K.Raghavachari, V.Rassolov, J.A.Pople J.Chem.Phys. 110, 4703-4709(1999) L.A.Curtiss, P.C.Redfern, K.Raghavachari, V.Rassolov, J.A.Pople J.Chem.Phys. 114, 9287-9295(2001) L.A.Curtiss, P.C.Redfern, K.Raghavachari, V.Rassolov, J.A.Pople J.Chem.Phys. 109,7764-7776(1998) L.A.Curtiss, K.Ragavachari Theoret.Chem.Acc. 108, 61-70(2002) EVVRSP, in memory diagonalization S.T.Elbert Theoret.Chim.Acta 71,169-186(1987) Davidson eigenvector method E.R.Davidson J.Comput.Phys. 17,87(1975) "Matrix Eigenvector Methods" p. 95-113 in "Methods in Computational Molecular Physics", edited by G.H.F.Diercksen and S.Wilson, D.Reidel Publishing, Dordrecht, 1983. M.L.Leininger, C.D.Sherrill, W.D.Allen, H.F.Schaefer, J.Comput.Chem. 22, 1574-1589(2001) DK (Douglas-Kroll relativistic transformation) M.Douglas, N.M.Kroll Ann.Phys. 82, 89-155(1974) B.A.Hess Phys.Rev. A33, 3742-3748(1986) G.Jansen, B.A.Hess Phys.Rev. A39, 6016-6017(1989) T.Nakajima, K.Hirao J.Chem.Phys. 113, 7786-7789(2000) T.Nakajima, K.Hirao Chem.Phys.Lett. 329, 511-516(2000) W.A.DeJong, R.J.Harrison, D.A.Dixon J.Chem.Phys. 114, 48-53(2001) A.Wolf, M.Reiher, B.A.Hess J.Chem.Phys. 117, 9215-26(2002) T.Nakajima, K.Hirao J.Chem.Phys. 119, 4105-4111(2003) (and see just below for DK1 during SOC) IOTC (Infinite-Order Two-Component) relativy correction M.Barysz, A.J.Sadlej J.Chem.Phys. 116, 2696-2704(2002) M.Barysz, Progress in Theoretical Chemistry and Physics, Kluwer Academic Publishers, 349-397(2002)

Further Information D.Kedziera, M.Barysz, A.J.Sadlej Struct.Chem. 15, 369-377(2004) D.Kedziera, M.Barysz, J.Chem.Phys. 121, 6719-6727(2004) M.Barysz, L.Mentel, J.Leszczynski J.Chem.Phys. 130, 164114/1-7(2009) RESC (Relativistic Elimination of Small Components) T.Nakajima, K.Hirao Chem.Phys.Lett. 302, 383-391(1999) T.Nakajima, T.Suzumura, K.Hirao Chem.Phys.Lett. 304, 271(1999) D.G.Fedorov, T.Nakajima, K.Hirao Chem.Phys.Lett. 335, 183-187(2001) NESC (Normalized Elimination of Small Components) K.G.Dyall J.Comput.Chem. 23, 786-793(2002)

4-15

Spin-orbit coupling and transition moments Many references can be found in the section on this topic below. For the 1st order Douglas-Kroll transformation of the 1e- part of the spin orbit operator, see T.Zeng, D.G.Fedorov, M. Klobukowski J.Chem.Phys. 131, 124109/1-17 (2009) T.Zeng, D.G.Fedorov, M.Klobukowski J.Chem.Phys. 132, 074102/1-15 (2010) GIAO NMR R.Ditchfield Mol.Phys. 27, 789-807(1974) M.A.Freitag, B.Hillman, A.Agrawal, M.S.Gordon J.Chem.Phys. 120, 1197-1202(2004) Solvation models: EFP, SCRF, PCM, or COSMO. All appropriate references are included in the sections on these topics included below. MOPAC 6 J.J.P.Stewart J.Computer-Aided Molecular Design 4, 1-105 (1990) References for parameters for individual atoms may be found on the printout from your runs. MacMolPlt B.M.Bode, M.S.Gordon J.Mol.Graphics Mod. 16, 133-138(1998)

quantum chemistry parallelization in GAMESS for SCF, see the main GAMESS paper quoted above. T.L.Windus, M.W.Schmidt, M.S.Gordon, Chem.Phys.Lett. 216, 375-379(1993) T.L.Windus, M.W.Schmidt, M.S.Gordon, Theoret.Chim.Acta 89, 77-88 (1994)

Further Information

4-16

T.L.Windus, M.W.Schmidt, M.S.Gordon, in "Parallel Computing in Computational Chemistry", ACS Symposium Series 592, Ed. by T.G.Mattson, ACS Washington, 1995, pp 16-28. K.K.Baldridge, M.S.Gordon, J.H.Jensen, N.Matsunaga, M.W.Schmidt, T.L.Windus, J.A.Boatz, T.R.Cundari ibid, pp 29-46. G.D.Fletcher, M.W.Schmidt, M.S.Gordon Adv.Chem.Phys. 110, 267-294 (1999) H.Umeda, S.Koseki, U.Nagashima, M.W.Schmidt J.Comput.Chem. 22, 1243-1251 (2001) C.H.Choi, K.Ruedenberg J.Comput.Chem. 22, 1484-1501(2001) D.G.Fedorov, M.S.Gordon ACS Symp.Series 828, 1-22(2002) H.Li, C.S.Pomelli, J.H.Jensen Theoret.Chem.Acc. 109, 71-84(2003) C.M.Aikens, M.S.Gordon J.Phys.Chem.A 108, 3103-3110(2004) H.M.Netzloff, M.S.Gordon J.Comput.Chem. 25, 1926-1936(2004) T.J.Dudley, R.M.Olson, M.W.Schmidt, M.S.Gordon J.Comput.Chem. 27, 353-362(2006) C.M.Aikens, G.D.Fletcher, M.W.Schmidt, M.S.Gordon J.Chem.Phys. 124, 014107/1-14(2006) Y.Alexeev, M.W.Schmidt, T.L.Windus, M.S.Gordon J.Comput.Chem. 28, 1685-1694(2007). R.M.Olson, J.L.Bentz, R.A.Kendall, M.W.Schmidt, M.S.Gordon J.Comput.Theoret.Chem. 3, 1312-1328(2007) J.L.Bentz, R.M.Olson, M.S.Gordon, M.W.Schmidt, R.A.Kendell Comput.Phys.Commun., 176, 589-600 (2007). G.D.Fletcher Mol.Phys. 105, 2971-2976(2007) The Distributed Data Interface (DDI), which is the computer science layer underneath the parallel quantum chemistry G.D.Fletcher, M.W.Schmidt, B.M.Bode, M.S.Gordon Comput.Phys.Commun. 128, 190-200 (2000) R.M.Olson, M.W.Schmidt, M.S.Gordon, A.P.Rendell Proc. of Supercomputing 2003, IEEE Computer Society. This does not exist on paper, but can be downloaded at http://www.sc-conference.org/sc2003/tech_papers.php D.G.Fedorov, R.M.Olson, K.Kitaura, M.S.Gordon, S.Koseki J.Comput.Chem. 25, 872-880(2004).

Further Information

4-17

Basis Set References

An excellent review of the relationship between the atomic basis used, and the accuracy with which various molecular properties will be computed is: E.R.Davidson, D.Feller Chem.Rev. 86, 681-696(1986). STO-NG H-Ne Na-Ar, K,Ca,Ga-Kr Rb,Sr,In-Xe Sc-Zn,Y-Cd Ref. Ref. Ref. Ref. Ref. 1 and 2 2 and 3 ** 4 5 6

1) W.J.Hehre, R.F.Stewart, J.A.Pople J.Chem.Phys. 51, 2657-2664(1969). 2) W.J.Hehre, R.Ditchfield, R.F.Stewart, J.A.Pople J.Chem.Phys. 52, 2769-2773(1970). 3) M.S.Gordon, M.D.Bjorke, F.J.Marsh, M.S.Korth J.Am.Chem.Soc. 100, 2670-2678(1978). ** the valence scale factors for Na-Cl are taken from this paper, rather than the "official" Pople values in Ref. 2. 4) W.J.Pietro, B.A.Levi, W.J.Hehre, R.F.Stewart, Inorg.Chem. 19, 2225-2229(1980). 5) W.J.Pietro, E.S.Blurock, R.F.Hout,Jr., W.J.Hehre, D.J. DeFrees, R.F.Stewart Inorg.Chem. 20, 3650-3654(1980). 6) W.J.Pietro, W.J.Hehre J.Comput.Chem. 4, 241-251(1983).

MINI/MIDI

H-Xe

Ref. 9

9) "Gaussian Basis Sets for Molecular Calculations" S.Huzinaga, J.Andzelm, M.Klobukowski, E.Radzio-Andzelm, Y.Sakai, H.Tatewaki Elsevier, Amsterdam, 1984. This book is referred to in certain circles as "the green book" based on the color of its cover. The MINI bases are three Gaussian expansions of each atomic orbital. The exponents and contraction coefficients are optimized for each element, and s and p exponents are not constrained to be equal. As a result these bases give much lower energies than does STO-3G. The valence MINI orbitals of main group elements are scaled by factors optimized by John Deisz at North Dakota State University. Transition metal MINI bases are not scaled. The MIDI bases are derived from the MINI sets by floating the outermost

Further Information

4-18

primitive in each valence orbitals, and renormalizing the remaining 2 gaussians. MIDI bases are not scaled by GAMESS. The transition metal bases are taken from the lowest SCF terms in the s**1,d**n configurations. 3-21G H-Ne Na-Ar K,Ca,Ga-Kr,Rb,Sr,In-Xe Sc-Zn Y-Cd Ref. Ref. Ref. Ref. Ref. 10 11 12 13 14 (also 6-21G) (also 6-21G)

10) J.S.Binkley, J.A.Pople, W.J.Hehre J.Am.Chem.Soc. 102, 939-947(1980). 11) M.S.Gordon, J.S.Binkley, J.A.Pople, W.J.Pietro, W.J.Hehre J.Am.Chem.Soc. 104, 2797-2803(1982). 12) K.D.Dobbs, W.J.Hehre J.Comput.Chem. 7,359-378(1986) 13) K.D.Dobbs, W.J.Hehre J.Comput.Chem. 8,861-879(1987) 14) K.D.Dobbs, W.J.Hehre J.Comput.Chem. 8,880-893(1987)

N-31G

references for H He Li Be B C-F Ne Na-Al Si P-Cl Ar K-Kr

4-31G 15 23 19,24 20,24 17 15 23 18

5-31G 15 23

16

6-31G 15 23 19 20 19 16 23 22 21 ** 22 22 26

15) R.Ditchfield, W.J.Hehre, J.A.Pople J.Chem.Phys. 54, 724-728(1971). 16) W.J.Hehre, R.Ditchfield, J.A.Pople J.Chem.Phys. 56, 2257-2261(1972). 17) W.J.Hehre, J.A.Pople J.Chem.Phys. 56, 4233-4234(1972). 18) W.J.Hehre, W.A.Lathan J.Chem.Phys. 56,5255-5257(1972). 19) J.D.Dill, J.A.Pople J.Chem.Phys. 62, 2921-2923(1975). 20) J.S.Binkley, J.A.Pople J.Chem.Phys. 66, 879-880(1977). 21) M.S.Gordon Chem.Phys.Lett. 76, 163-168(1980) ** - Note that the built in 6-31G basis for Si is not that given by Pople in reference 22. The Gordon basis gives a better wavefunction, for a ROHF calculation in full atomic (Kh)

Further Information

4-19

symmetry, 6-31G Energy virial Gordon -288.828573 1.999978 Pople -288.828405 2.000280 See the input examples for how to run in Kh. 22) M.M.Francl, W.J.Pietro, W.J.Hehre, J.S.Binkley, M.S.Gordon, D.J.DeFrees, J.A.Pople J.Chem.Phys. 77, 3654-3665(1982). 23) Unpublished, copied out of GAUSSIAN82. 24) For Li and Be, 4-31G is actually a 5-21G expansion. 25) V.A.Rassolov, J.A.Pople, M.A.Ratner, T.L.Windus J.Chem.Phys. 109, 1223-1229(1998) 26) A.V.Mitin, J.Baker, P.Pulay J.Chem.Phys. 118, 7775-7782(2003) - not in GAMESS. 27) V.A.Rassolov, M.A.Ratner, J.A.Pople, P.C.Redfern, L.A.Curtiss J.Comput.Chem. 22, 976-984(2001). Note that reference 27 renames basis sets published earlier as "6-31G*" in references 25 and 32. GAMESS was changed to use the 6-31G* basis sets from reference 27 for K, Ca, and Ga-Kr in September 2006. Sc-Zn remain those of ref. 25. Extended basis sets --> 6-311G 28) R.Krishnan, J.S.Binkley, R.Seeger, J.A.Pople J.Chem.Phys. 72, 650-654(1980). --> valence double zeta "DZV" sets: "DH" basis - DZV for H, Li-Ne, Al-Ar 30) T.H.Dunning, Jr., P.J.Hay Chapter 1 in "Methods of Electronic Structure Theory", H.F.Schaefer III, Ed. Plenum Press, N.Y. 1977, pp 1-27. Note that GAMESS uses inner/outer scale factors of 1.2 and 1.15 for DH's hydrogen (since at least 1983). To get Thom's usual basis, scaled 1.2 throughout: HYDROGEN 1.0 x, y, z DH 0 1.2 1.2 DZV for K,Ca 31) J.-P.Blaudeau, M.P.McGrath, L.A.Curtiss, L.Radom J.Chem.Phys. 107, 5016-5021(1997) "BC" basis - DZV for Ga-Kr 32) R.C.Binning, Jr., L.A.Curtiss J.Comput.Chem. 11, 1206-1216(1990) Note, this basis set is available only by GBASIS=DZV, since it is no longer considered to be the 6-31G substitute.

Further Information --> valence triple zeta "TZV" sets: TZV for H,Li-Ne 40) T.H. Dunning, J.Chem.Phys. 55 (1971) 716-723. TZV for Na-Ar - also known as the "MC" basis 41) A.D.McLean, G.S.Chandler J.Chem.Phys. 72,5639-5648(1980). TZV for K,Ca 42) A.J.H. Wachters, J.Chem.Phys. 52 (1970) 1033-1036. (see Table VI, Contraction 3). TZV for Sc-Zn (taken from HONDO 7) This is Wachters' (14s9p5d) basis (ref 42) contracted to (10s8p3d) with the following modifications 1. the most diffuse s removed; 2. additional s spanning 3s-4s region; 3. two additional p functions to describe the 4p; 4. (6d) contracted to (411) from ref 43, except for Zn where Wachter's (5d)/[41] and Hay's diffuse d are used. 43) A.K. Rappe, T.A. Smedley, and W.A. Goddard III, J.Phys.Chem. 85 (1981) 2607-2611 Valence only basis sets (ECPs and MCPs)

4-20

SBKJC ECP, these are -31G splits for main group, bigger for transition metals (available Li-Rn): 50) W.J.Stevens, H.Basch, M.Krauss J.Chem.Phys. 81, 6026-6033 (1984) 51) W.J.Stevens, M.Krauss, H.Basch, P.G.Jasien Can.J.Chem. 70, 612-630 (1992) 52) T.R.Cundari, W.J.Stevens J.Chem.Phys. 98, 5555-5565(1993) HW ECP, these are -21 splits (sp exponents not shared) transition metals (not built in at present, although they will work if you type them in): 53) P.J.Hay, W.R.Wadt J.Chem.Phys. 82, 270-283 (1985) main group (available Na-Xe) 54) W.R.Wadt, P.J.Hay J.Chem.Phys. 82, 284-298 (1985) see also 55) P.J.Hay, W.R.Wadt J.Chem.Phys. 82, 299-310 (1985) Model core potentials (MCP): To understand the model core potential formalism itself, see the review articles S.Huzinaga Can.J.Chem. 73, 619-628(1995)

Further Information

4-21

M.Klobukowski, S.Huzinaga, Y.Sakai, in Computational Chemistry: Reviews of current trends, volume 3, pp 49-74, edited by J.Leszczynski, World Scientific, Singapore, 1999. The MCP-xZP,MCP-AxZP,MCP-CxZP, MCP-ACxZP families: 60) Y.Sakai, E.Miyoshi, M.Klobukowski, S.Huzinaga, "Model potentials for main group elements", J. Chem. Phys. 106, 8084-8092 (1997). 61) E. Miyoshi, Y. Sakai, K. Tanaka, M. Masamura, "Relativistic dsp-model core potentials for main group elements in the fourth, fifth and sixth row and their applications", J. Mol. Struct. (THEOCHEM) 451, 73-79 (1998) 62) Y. Sakai, E. Miyoshi, H. Tatewaki, "Model core potentials for the lanthanides", J. Mol. Struct. (THEOCHEM) 451, 143-150 (1998) 63) E.Miyoshi, H.Mori, R.Hirayama, Y.Osanai, T.Noro, H.Honda, M.Klobukowski "Compact and efficient basis sets of s- and p-block elements for model core potential method" J.Chem.Phys. 122, 074104/1-8(2005) 64) M. Sekiya, T. Noro, Y. Osanai, E. Miyoshi, T. Koga, "Relativistic Correlating Basis Sets for Lanthanide Atoms from Ce to Lu", J. Comput. Chem. 27, 463 (2006) 65) H. Anjima, S. Tsukamoto, H. Mori, H. Mine, M. Klobukowski, E. Miyoshi, "Revised Model Core Potentials of s-Block Elements", J. Comput. Chem. 28, 2424-2430 (2007) 66) Y. Osanai, M. S. Mon, T. Noro, H. Mori, H. Nakashima, M. Klobukowski, E. Miyoshi, "Revised model core potentials for first-row transition-metal atoms from Sc to Zn", Chem. Phys. Lett. 452, 210-214 (2008) 67) Y. Osanai, E. Soejima, T. Noro, H. Mori, M. Ma San, M. Klobukowski, E. Miyoshi, "Revised model core potentials for second-row transition metal atoms from Y to Cd", Chem. Phys. Lett. 463, 230-234 (2008) 68) H. Mori, K. Ueno-Noto, Y. Osanai, T. Noro, T. Fujiwara, M. Klobukowski, E. Miyoshi, "Revised model core potentials for third-row transition-metal atoms from Lu to Hg", Chem. Phys. Lett. 476, 317-322 (2009) the iMCP (improved model core families) are: 71) C.C.Lovallo, M.Klobukowski J.Comput.Chem. 24, 1009-10015(2003) 72) C.C.Lovallo, M.Klobukowski

Further Information J.Comput.Chem. 25, 1206-1213(2004)

4-22

the ZFK (Zeng, Fedorov, Klobukowski) family for sp block: 72) T.Zeng, D.G.Fedorov, M. Klobukowski J.Chem.Phys. 133, 114107/1-11 (2010) For additional information, see also T.Zeng, D.G.Fedorov, M. Klobukowski J.Chem.Phys. 131, 124109/1-17 (2009) T.Zeng, D.G.Fedorov, M.Klobukowski J.Chem.Phys. 132, 074102/1-15 (2010) The MCP family, built into the $DATA group only: 75) Y.Sakai, E.Miyoshi, M.Klobukowski, S.Huzinaga, "Model potentials for molecular calculations. I. The sd-MP set for transition metal atoms Sc-Hg", J. Comput. Chem. 8 (1987) 226-255. 76) Y.Sakai, E.Miyoshi, M.Klobukowski, S.Huzinaga, "Model potentials for molecular calculations. II. The spd-MP set for transition metal atoms Sc-Hg", J. Comput. Chem. 8 (1987) 256-264. 77) Y.Sakai, E.Miyoshi, M.Klobukowski, S.Huzinaga, "Model potentials for main group elements", J. Chem. Phys. 106 (1997) 8084-8092. 78) E.Miyoshi, Y.Sakai, K.Tanaka, M.Masamura "Relativistic dsp-Model Core Potentials for Main Group Elements in the 4th, 5th, and 6th-Row and Applications" J. Mol. Struct. (Theochem), 451 (1998) 73-79. 79) Y.Sakai, E.Miyoshi, H.Tatewaki "Model Core Potentials for the Lanthanides" J. Mol. Struct. (Theochem), 451 (1998) 143-150. Systematic basis set families: Polarization Consistent basis sets (PC-n): 81) F.Jensen J.Chem.Phys. 115, 9113-9125(2001). erratum J.Chem.Phys. 116, 3502(2002). 82) F.Jensen J.Chem.Phys. 116, 7372-7379(2002). 83) F.Jensen J.Chem.Phys. 117, 9234-9240(2002). 84) F.Jensen J.Chem.Phys. 118, 2459-2463(2003). 85) F.Jensen, T.Helgaker J.Chem.Phys. 121, 3463-3470(2004). 86) F.Jensen, J.Phys.Chem.A in press (2007). Correlation Consistent bases (CCn, ACCn, CCnC, ACCnC): The official names for these "Dunning-style" basis sets are, respectively,

Further Information cc-pVnZ, aug-cc-pCVnZ, cc-CVnZ, and aug-cc-CVnZ. Please see the Pacific Northwest National Laboratory web page http://www.emsl.pnl.gov/forms/basisform.html for references to these basis sets. Kirk Peterson's very thorough bibliography can be found at http://tyr0.chem.wsu.edu/~kipeters/Pages/cc_append.html Sapporo (SPK) basis set family first, the non-relativistic sets, S1. H.Tatewaki, T.Koga J.Chem.Phys. 104, 8493(1996) S2. H.Tatewaki, T.Koga, H.Takashima Theoret.Chem.Acc. 96, 243(1997) S3. T.Koga, H.Tatewaki, Y.Satoh Theoret.Chem.Acc. 102, 105(1999) S4. T.Koga, S.Yamamoto, T.Shimazaki, H.Tatewaki, Theoret.Chem.Acc. 108, 41(2002) then, the relativistic sets, S6. T.Noro, M.Sekiya, T.Koga, S.L.Saito Chem.Phys.Lett. 481, 229-233(2009) Karlsruhe basis sets (group of Reinhart Ahlrichs) 91) A.Schaefer, H.Horn, R.Ahlrichs J.Chem. Phys. 97,2571 (1992). 92) A.Schaefer, C.Huber, R.Ahlrichs J.Chem. Phys. 100, 5829 (1994). Polarization exponents: STO-NG* 100) J.B.Collins, P. von R. Schleyer, J.S.Binkley, J.A.Pople J.Chem.Phys. 64, 5142-5151(1976).

4-23

3-21G*. See also reference 12. 101) W.J.Pietro, M.M.Francl, W.J.Hehre, D.J.DeFrees, J.A. Pople, J.S.Binkley J.Am.Chem.Soc. 104,5039-5048(1982) 6-31G* and 6-31G**. See also reference 22 above. 102) P.C.Hariharan, J.A.Pople Theoret.Chim.Acta 28, 213-222(1973) multiple polarization, and f functions 103) M.J.Frisch, J.A.Pople, J.S.Binkley J.Chem.Phys. 80, 3265-3269 (1984). Anion diffuse functions:

Further Information 3-21+G, 3-21++G, etc. 105) T.Clark, J.Chandrasekhar, G.W.Spitznagel, P. von R. Schleyer J.Comput.Chem. 4, 294-301(1983) 106) G.W.Spitznagel, Diplomarbeit, Erlangen, 1982. -----------STO-NG*

4-24

means d orbitals are used on third row atoms only. The original paper (ref 100) suggested z=0.09 for Na and Mg, and z=0.39 for Al-Cl. We prefer to use the same exponents as are used in 3-21G* and 6-31G*, so we know we're looking at changes in the sp basis, not the d exponent. means d orbitals on main group elements in the third and higher periods. Not defined for the transition metals, where there are p's already in the basis. Except for alkalis and alkali earths, the 4th and 5th row zetas are from Huzinaga, et al. (ref 9). The exponents are normally the same as for 6-31G*. means d orbitals on second and third row atoms. We use Mark Gordon's z=0.395 for Silicon, as well as his fully optimized sp basis (ref 21). This is often written 6-31G(d) today. For the first row transition metals, the * means an f function is added. The transition metal 3d 6-31G orbital is NOT of triple zeta quality, and thus is probably not very accurate. means the same as 6-31G*, except that p functions are added on hydrogens. This is often written 6-31G(d,p) today.

3-21G*

6-31G*

6-31G**

6-311G** means p orbitals on H, and d orbitals elsewhere. The exponents were derived from correlated atomic states, and so are considerably tighter than the polarizing functions used in 6-31G**, etc. This is often written 6-311G(d,p) today. The exponents for 6-31G* for C-F are disturbing, in that each atom has exactly the same value. Dunning and Hay (ref 30) have recommended a better set of exponents for second row atoms and a slightly different value for H. 2p, 3p, 2d, 3p polarization sets are usually thought of as arising from applying splitting factors to the 1p and 1d values. For example, SPLIT2=2.0, 0.5 means to double and

Further Information

4-25

halve the single value. The default values for SPLIT2 and SPLIT3 are taken from reference 103, and were derived with correlation in mind. The SPLIT2 values often produce a higher (!) HF energy than the singly polarized run, because the exponents are split too widely. SPLIT2=0.4,1.4 will always lower the SCF energy (the values are the unpublished personal preference of MWS), and for SPLIT3 we might suggest 3.0,1.0,1/3. With all this as background, we are ready to present the tables of polarization exponents that are built into GAMESS. Please note that the names associated with each column are only generally descriptive. The column marked "COMMON" is obtained from both Pople (mostly his 6-31G, but using Gordon's value for Silicon) and Huzinaga (from the "green book"). The exponents for K-Kr under "Dunning" are from Curtiss, et al., not Thom Dunning, and so on. The exponents are for d functions unless otherwise indicated.

Further Information Polarization exponents, chosen by POLAR= in $BASIS: COMMON -----1.1(p) 1.1(p) 0.2 0.4 0.6 0.8 0.8 0.8 0.8 0.8 0.175 0.175 0.325 0.395 0.55 0.65 0.75 0.85 0.2 0.2 N/A 0.207 0.246 0.293 0.338 0.389 0.443 0.11 0.11 0.04485 0.0502 0.8(f) 0.2289 0.2772 0.3277 0.3810 0.4366 0.4948 0.260 0.229 N/A 0.141 0.202 0.273 0.315 0.338 0.318 POPN31 -----POPN311 ------0.75(p) 0.75(p) 0.200 0.255 0.401 0.626 0.913 1.292 1.750 2.304 DUNNING ------1.0(p) 1.0(p) HUZINAGA -------1.0(p) 1.0(p) 0.076(p) 0.164(p) 0.388 0.600 0.864 1.154 1.496 1.888 0.061(p) 0.101(p) 0.198 0.262 0.340 0.421 0.514 0.617 0.039(p) 0.059(p) N/A

4-26

H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc-Zn Ga Ge As Se Br Kr Rb Sr

HONDO7 -----1.0(p) 1.0(p) 0.32 0.50 0.72 0.98 1.28 1.62 2.00 0.157 0.234 0.311 0.388 0.465 0.542 0.619 0.696

0.70 0.75 0.80 0.85 0.90 1.00

N/A

N/A

0.034(p) 0.048(p)

A blank means the value equals the "COMMON" column. Common d polarization for all sets ("green book"): In Sn Sb Te I Xe 0.160 0.183 0.211 0.237 0.266 0.297 Tl Pb Bi Po At Rn 0.146 0.164 0.185 0.204 0.225 0.247 see f exponents on next page...

Further Information f polarization functions, from reference 103: Li Be B C N O F Ne 0.15 0.26 0.50 0.80 1.00 1.40 1.85 2.50 Na Mg Al Si P S Cl Ar 0.15 0.20 0.25 0.32 0.45 0.55 0.70 --

4-27

Anions usually require diffuse basis functions to properly represent their spatial diffuseness. The use of diffuse sp shells on atoms in the second and third rows is denoted by a + sign, also adding diffuse s functions on hydrogen is symbolized by ++. These designations can be applied to any of the Pople bases, e.g. 3-21+G, 3-21+G*, 6-31++G**. The following exponents are for L shells, except for H. For H-F, they are taken from ref 105. For Na-Cl, they are taken directly from reference 106. These values may be found in footnote 13 of reference 103. For Ga-Br, In-I, and Tl-At these were optimized for the atomic ground state anion, using ROHF with a flexible ECP basis set, by Ted Packwood at NDSU. H 0.0360 Li 0.0074 Na 0.0076

Be 0.0207 Mg 0.0146

B 0.0315 Al 0.0318 Ga 0.0205 In 0.0223 Tl 0.0170

C 0.0438 Si 0.0331 Ge 0.0222 Sn 0.0231 Pb 0.0171

N 0.0639 P 0.0348 As 0.0287 Sb 0.0259 Bi 0.0215

O 0.0845 S 0.0405 Se 0.0318 Te 0.0306 Po 0.0230

F 0.1076 Cl 0.0483 Br 0.0376 I 0.0368 At 0.0294

Additional information about diffuse functions and also Rydberg type exponents can be found in reference 30.

Further Information

4-28

The following atomic energies are UHF (RHF on 1-S states), p orbitals are not symmetry equivalent, using the default scale factors. They may be useful in picking a basis of the desired accuracy. Atom state STO-2G H 2-S -.454397 He 1-S -2.702157 Li 2-S -7.070809 Be 1-S -13.890237 B 2-P -23.395284 C 3-P -36.060274 N 4-S -53.093007 O 3-P -71.572305 F 2-P -95.015084 Ne 1-S -122.360485 Na 2-S -155.170019 Mg 1-S -191.507082 Al 2-P -233.199965 Si 3-P -277.506857 P 4-S -327.564244 S 3-P -382.375012 Cl 2-P -442.206260 Ar 1-S -507.249273 Atom state DH H 2-S -.498189 He 1-S -Li 2-S -7.431736 Be 1-S -14.570907 B 2-P -24.526601 C 3-P -37.685571 N 4-S -54.397260 O 3-P -74.802707 F 2-P -99.395013 Ne 1-S -128.522354 Na 2-S -Mg 1-S -Al 2-P -241.855079 Si 3-P -288.829617 P 4-S -340.689043 S 3-P -397.468667 Cl 2-P -459.435938 Ar 1-S -STO-3G -.466582 -2.807784 -7.315526 -14.351880 -24.148989 -37.198393 -53.719010 -73.804150 -97.986505 -126.132546 -159.797148 -197.185978 -239.026471 -285.563052 -336.944863 -393.178951 -454.546015 -521.222881 6-311G -.499810 -2.859895 -7.432026 -14.571874 -24.527020 -37.686024 -54.397980 -74.802496 -99.394158 -128.522553 --------3-21G -.496199 -2.835680 -7.381513 -14.486820 -24.389762 -37.481070 -54.105390 -74.393657 -98.845009 -127.803825 -160.854065 -198.468103 -240.551046 -287.344431 -339.000079 -395.551336 -457.276552 -524.342962 MC -----------161.845587 -199.606558 -241.870014 -288.847782 -340.711346 -397.498023 -459.473412 -526.806626 6-31G -.498233 -2.855160 -7.431236 -14.566764 -24.519492 -37.677837 -54.385008 -74.780310 -99.360860 -128.473877 -161.841425 -199.595219 -241.854186 -288.828598 -340.689008 -397.471414 -459.442939 -526.772151 SCF limit* -0.5 -2.861680 -7.432727 -14.573023 -24.529061 -37.688619 -54.400935 -74.809400 -99.409353 -128.547104 -161.858917 -199.614636 -241.876699 -288.854380 -340.718798 -397.504910 -459.482088 -526.817528

* M.W.Schmidt and K.Ruedenberg, J.Chem.Phys. 71, 3951-3962(1979). These are ROHF energies in Kh symmetry. H-Xe can be found in Phys.Rev.A 46, 3691-3696(1992).

Further Information

4-29

Spherical Harmonics
The implementation of ISPHER in $CONTRL does not rely on using a spherical harmonic basis set, in fact the atomic basis remains the Cartesian Gaussians. Instead, certain MOs formed from particular combinations of the Cartesian Gaussians (for example, xx+yy+zz) are deleted from the MO space. Thus a run with ISPHER=1 will have fewer MOs than AOs. Since neither the occupied nor virtual MOs contain any admixture of xx+yy+zz, the resulting energy and wavefunction is exactly equivalent to the use of a spherical harmonic basis. The log file output will contain expansions of each MO in terms of 6 d's, 10 f's, and 15 g's, and the $VEC also contains the same expansion over Cartesian Gaussians. Both the matrix in your log file and in $VEC will contain fewer MOs than AOs, the exact number of MOs used is printed in the initial guess section of the log file. It should be possible to read such $VEC groups into runs with different settings of ISPHER, should you choose to do so. The advantage of this approach is that intelligence in the generation of symmetry orbitals combined with the capability to drop linearly dependent MO combinations means that the details of ISPHER are located only in the orbital optimization code, where the variational spaces are simply reduced in size to eliminate the undesired contaminant functions. This means that none of the integral routines need be modified, as the atomic basis remains the Cartesian Gaussians. The disadvantage is that AO integral files run over the Cartesian Gaussians, and thus are not reduced in size. Of course transformed MO integrals and various computations in correlated calculations are reduced in size, since the number of MOs may be greatly reduced. Computationally, the advantages of ISPHER=1 are not limited to the reduced CPU time associated with fewer total MOs. Questions about d orbital participation as measured by Mulliken populations are cleanly addressed when the d's usage in the MOs does not contain any contamination from the s shape xx+yy+zz. Less obviously, the use of spherical harmonics frequently greatly reduces problems with linear dependency, that exhibit as poor SCF convergence.

Further Information

4-30

How to do RHF, ROHF, UHF, and GVB calculations

general considerations
These four SCF wavefunctions are all based on Fock operator techniques, even though some GVB runs use more than one determinant. Thus all of these have an intrinsic N**4 time dependence, because they are all driven by integrals in the AO basis. This similarity makes it convenient to discuss them all together. In this section we will use the term HF to refer generically to any of these four wavefunctions, including the multi-determinate GVB-PP functions. $SCF is the main input group for all these HF wavefunctions. As will be discussed below, in GAMESS the term ROHF refers to high spin open shell SCF only, but other open shell coupling cases are possible using the GVB code. Analytic gradients are implemented for every possible HF type calculation possible in GAMESS, and therefore numerical hessians are available for each. Analytic hessian calculation is implemented for RHF, ROHF, and any GVB case with NPAIR=0 or NPAIR=1. Analytic hessians are more accurate, and much more quickly computed than numerical hessians, but require additional disk storage to perform an integral transformation, and also more physical memory. The second order Moller-Plesset energy correction (MP2) is implemented for RHF, UHF, ROHF, and MCSCF wavefunctions. Analytic gradients may be obtained for MP2 with RHF, UHF, or ROHF reference wavefunctions, and MP2 level properties are therefore available for these, see MP2PRP in $MP2. All other cases give properties for the SCF function. Direct SCF is implemented for every possible HF type calculation. The direct SCF method may not be used with DEM convergence. Direct SCF may be used during energy, gradient, numerical or analytic hessian, CI or MP2 energy correction, or localized orbital computations.

Further Information

4-31

direct SCF
Normally, HF calculations proceed by evaluating a large number of two electron repulsion integrals, and storing these on a disk. This integral file is read in once during each HF iteration to form the appropriate Fock operators. In a direct HF, the integrals are not stored on disk, but are instead reevaluated during each HF iteration. Since the direct approach *always* requires more CPU time, the default for DIRSCF in $SCF is .FALSE. Even though direct SCF is slower, there are at least two reasons why you may want to consider using it. The first is that it may not be possible to store all of the integrals on the disk drives attached to your computer. Second, what you are really interested in is reducing the wall clock time to obtain your answer, not the CPU time. Workstations, particularly nodes with multiple CPUs and only one disk subsystem, may have modest hardware I/O capabilities. Other environments such as a mainframe shared by many users may also have very poor CPU/wall clock performance for I/O bound jobs such as conventional HF. You can estimate the disk storage requirements for conventional HF using a P or PK file by the following formulae: nint = 1/sigma * 1/8 * N**4 Mbytes = nint * x / 1024**2 Here N is the total number of basis functions in your run, which you can learn from an EXETYP=CHECK run. The 1/8 accounts for permutational symmetry within the integrals. Sigma accounts for the point group symmetry, and is difficult to estimate accurately. Sigma cannot be smaller than 1, in no symmetry (C1) calculations. For benzene, sigma would be almost six, since you generate 6 C's and 6 H's by entering only 1 of each in $DATA. For water sigma is not much larger than one, since most of the basis set is on the unique oxygen, and the C2v symmetry applies only to the H atoms. The factor x is 12 bytes per integral for basis sets smaller than 255, and 16 otherwise. Finally, since integrals that are very close to zero need not be stored on disk, the actual power dependence is not as bad as N**4, and in fact in the limit of very large molecules can be as low as N**2. Thus plugging in sigma=1 should give you an upper bound to the actual disk space needed. If the estimate exceeds your available disk storage, your only recourse is direct HF.

Further Information

4-32

What are the economics of direct HF? Naively, if we assume the run takes 10 iterations to converge, we must spend 10 times more CPU time computing the integrals on each iteration. However, we do not have to waste any CPU time reading blocks of integrals from disk, or in unpacking their indices. We also do not have to waste any wall clock time waiting for a relatively slow mechanical device such as a disk to give us our data. There are some less obvious savings too, as first noted by Almlof. First, since the density matrix is known while we are computing integrals, we can use the Schwarz inequality to avoid doing some of the integrals. In a conventional SCF this inequality is used to avoid doing small integrals. In a direct SCF it can be used to avoid doing integrals whose contribution to the Fock matrix is small (density times integral=small). Secondly, we can form the Fock matrix by calculating only its change since the previous iteration. The contributions to the change in the Fock matrix are equal to the change in the density times the integrals. Since the change in the density goes to zero as the run converges, we can use the Schwarz screening to avoid more and more integrals as the calculation progresses. The input option FDIFF in $SCF selects formation of the Fock operator by computing only its change from iteration to iteration. The FDIFF option is not implemented for GVB since there are too many density matrices from the previous iteration to store, but is the default for direct RHF, ROHF, and UHF. So, in our hypothetical 10 iteration case, we do not spend as much as 10 times more time in integral evaluation. Additionally, the run as a whole will not slow down by whatever factor the integral time is increased. A direct run spends no additional time summing integrals into the Fock operators, and no additional time in the Fock diagonalizations. So, generally speaking, a RHF run with 10-15 iterations will slow down by a factor of 2-4 times when run in direct mode. The energy gradient time is unchanged by direct HF, and this is a large time compared to HF energy, so geometry optimizations will be slowed down even less. This is really the converse of Amdahl's law: if you slow down only one portion of a program by a large amount, the entire program slows down by a much smaller factor. To make this concrete, here are some times for GAMESS for a job which is a RHF energy for a SbC4O2NH4. These

Further Information

4-33

timings were obtained an extremely long time ago, on a DECstation 3100 under Ultrix 3.1, which was running only these tests, so that the wall clock times are meaningful. This system is typical of Unix workstations in that it uses SCSI disks, and the operating system is not terribly good at disk I/O. By default GAMESS stores the integrals on disk in the form of a P supermatrix, because this will save time later in the SCF cycles. By choosing NOPK=1 in $INTGRL, an ordinary integral file can be used, which typically contains many fewer integrals, but takes more CPU time in the SCF. Because the DECstation is not terribly good at I/O, the wall clock time for the ordinary integral file is actually less than when the supermatrix is used, even though the CPU time is longer. The run takes 13 iterations to converge, the times are in seconds. # nonzero integrals # blocks skipped CPU time (ints) CPU time (SCF) CPU time (job total) wall time (job total) P supermatrix 8,244,129 55,841 709 1289 2123 3468 ordinary file 6,125,653 55,841 636 1472 2233 3200

When the same calculation is run in direct mode (integrals are processed like an ordinary integral disk file when running direct), iteration 1: # nonzero integrals # blocks skipped iteration 13: # nonzero integrals # blocks skipped CPU time (job total) wall time (job total) FDIFF=.TRUE. 6,117,416 60,208 3,709,733 105,278 6719 6764 FDIFF=.FALSE. 6,117,416 60,208 6,122,912 59,415 7851 7886

Note that elimination of the disk I/O dramatically increases the CPU/wall efficiency. Here's the bottom line on direct HF: best direct CPU / best disk CPU = 6719/2123 = 3.2 best direct wall/ best disk wall= 6764/3200 = 2.1 Direct SCF is slower than conventional disk SCF, but not outrageously so! From the data in the tables, we can see that the best direct method spends about 6719-1472 = 5247 seconds doing integrals. This is an increase of about 5247/636 = 8.2 in the time spent doing integrals, in a run

Further Information

4-34

that does 13 iterations (13 times evaluating integrals). 8.2 is less than 13 because the run avoids all CPU charges related to I/O, and makes efficient use of the Schwarz inequality to avoid doing many of the integrals in its final iterations.

convergence accelerators
Generally speaking, the simpler the HF function, the better its convergence. In our experience, the majority of RHF and ROHF runs converge readily from GUESS=HUCKEL. UHF often takes considerably more iterations than either of these, due to the extremely common occurrence of heavy spin contamination. GVB runs typically require GUESS=MOREAD, although the Huckel guess usually works for NPAIR=0. GVB cases with NPAIR greater than one are particularly difficult. Unfortunately, not all HF runs converge readily. The best way to improve your convergence is to provide better starting orbitals! In many cases, this means to MOREAD orbitals from some simpler HF case. For example, if you want to do a doublet ROHF, and the HUCKEL guess does not seem to converge, do this: Do an RHF on the +1 cation. RHF is typically more stable than ROHF, UHF, or GVB, and cations are usually readily convergent. Then MOREAD the cation's orbitals into the neutral calculation which you wanted to do at first. GUESS=HUCKEL does not always start with the correct electronic configuration. It may be useful to use PRTMO in $GUESS during a CHECK run to examine the starting orbitals, and then reorder them with NORDER if that seems appropriate. Of course, by default GAMESS uses the convergence procedures which are usually most effective. Still, there are cases which are difficult, so the $SCF group permits you to select several alternative methods for improving convergence. Briefly, these are EXTRAP. This extrapolates the three previous Fock matrices, in an attempt to jump ahead a bit faster. This is the most powerful of the old-fashioned accelerators, and normally should be used at the beginning of any SCF run. When an extrapolation occurs, the counter at the left of the SCF printout is set to zero.

Further Information

4-35

DAMP. This damps the oscillations between several successive Fock matrices. It may help when the energy is seen to oscillate wildly. Thinking about which orbitals should be occupied initially may be an even better way to avoid oscillatory behaviour. SHIFT. Level shifting moves the diagonal elements of the virtual part of the Fock matrix up, in an attempt to uncouple the unoccupied orbitals from the occupied ones. At convergence, this has no effect on the orbitals, just their orbital energies, but will produce different (and hopefully better) orbitals during the iterations. RSTRCT. This limits mixing of the occupied orbitals with the empty ones, especially the flipping of the HOMO and LUMO to produce undesired electronic configurations or states. This should be used with caution, as it makes it very easy to converge on incorrectly occupied electronic configurations, especially if DIIS is also used. If you use this, be sure to check your final orbital energies to see if they are sensible. A lower energy for an unoccupied orbital than for one of the occupied ones is a sure sign of problems. DIIS. Direct Inversion in the Iterative Subspace is a modern method, due to Pulay, using stored error and Fock matrices from a large number of previous iterations to interpolate an improved Fock matrix. This method was developed to improve the convergence at the final stages of the SCF process, but turns out to be quite powerful at forcing convergence in the initial stages of SCF as well. By giving ETHRSH as 10.0 in $SCF, you can practically guarantee that DIIS will be in effect from the first iteration. The default is set up to do a few iterations with conventional methods (extrapolation) before engaging DIIS. This is because DIIS can sometimes converge to solutions of the SCF equations that do not have the lowest possible energy. For example, the 3-A-2 small angle state of SiLi2 (see M.S.Gordon and M.W.Schmidt, Chem.Phys.Lett., 132, 294-8(1986)) will readily converge with DIIS to a solution with a reasonable S**2, and an energy about 25 milliHartree above the correct answer. A SURE SIGN OF TROUBLE WITH DIIS IS WHEN THE ENERGY RISES TO ITS FINAL VALUE. However, if you obtain orbitals at one point on a PES without DIIS, the subsequent use of DIIS with MOREAD will probably not introduce any problems. Because DIIS is quite powerful, EXTRAP, DAMP, and SHIFT are all turned off once DIIS begins to work. DEM and RSTRCT will still be in use, however.

Further Information

4-36

SOSCF. Approximate second-order (quasi-Newton) SCF orbital optimization. SOSCF will converge about as well as DIIS at the initial geometry, and slightly better at subsequent geometries. There's a bit less work solving the SCF equations, too. The method kicks in after the orbital gradient falls below SOGTOL. Some systems, particularly transition metals with ECP basis sets, may have Huckel orbitals for which the gradient is much larger than SOGTOL. In this case it is probably better to use DIIS instead, with a large ETHRSH, rather than increasing SOGTOL, since you may well be outside the quadratic convergence region. SOSCF does not exhibit true second order convergence since it uses an approximation to the inverse hessian. SOSCF will work for MOPAC runs, but is slower in this case. SOSCF will work for UHF, but its convergence may be better than DIIS. SOSCF will work for non-Abelian cases, but may encounter problems if the open shell is degenerate. It should be clear that SOSCF and DIIS are the two work-horse convergers, with DAMP (and possibly SHIFT) useful in cases where the initial guess is such that these two are not engaged immediately. If you compute many different types of molecules, you will find cases where SOSCF works but DIIS does not, but also cases where DIIS works but SOSCF does not (although often both will work). If you do not obtain convergence with one of these, try the other one! If you still have problems, attempt to get better starting orbitals. DEM. Direct energy minimization should be your last recourse. It explores the "line" between the current orbitals and those generated by a conventional change in the orbitals, looking for the minimum energy on that line. DEM should always lower the energy on every iteration, but is very time consuming, since each of the points considered on the line search requires evaluation of a Fock operator. DEM will be skipped once the density change falls below DEMCUT, as the other methods should then be able to affect final convergence. While DEM is working, RSTRCT is held to be true, regardless of the input choice for RSTRCT. Because of this, it behooves you to be sure that the initial guess is occupying the desired orbitals. DEM is available only for RHF. The implementation in GAMESS resembles that of R.Seeger and J.A.Pople, J.Chem.Phys. 65, 265-271(1976). Simultaneous use of DEM and DIIS resembles the ADEM-DIOS method of H.Sellers, Chem.Phys.Lett. 180, 461-465(1991). DEM does not work with direct SCF.

Further Information

4-37

high spin open shell SCF (ROHF)

Open shell SCF calculations are performed in GAMESS by both the ROHF code and the GVB code. Note that when the GVB code is executed with no pairs, the run is NOT a true GVB run, and should be referred to in publications and discussion as a ROHF calculation. Low spin couplings are possible with the GVB program. The ROHF module in GAMESS can handle any number of open shell electrons, provided these have a high spin coupling. For example: one open shell, doublet: $CONTRL SCFTYP=ROHF MULT=2 $END two open shells, triplet: $CONTRL SCFTYP=ROHF MULT=3 $END m open shells, high spin: $CONTRL SCFTYP=ROHF MULT=m+1 $END John Montgomery (who was then at United Technologies) is responsible for the ROHF implementation in GAMESS. The following discussion is due to him, dating from 1988 when his method of forming a combined Fock operator was included in GAMESS. Other choices (Euler and two "canonical" sets) were added to the table in 2009/2010. The Fock matrix in the MO basis has the form closed open virtual closed F2 | Fb | (Fa+Fb)/2 ----------------------------------open Fb | F1 | Fa ----------------------------------virtual (Fa+Fb)/2 | Fa | F0 where Fa and Fb are the usual alpha and beta Fock matrices any UHF program produces. All ROHF methods agree on these, as they are the variational conditions that separate the doubly occupied, alpha occupied, and empty orbital spaces. The diagonal blocks can be written F2 = Acc*Fa + Bcc*Fb F1 = Aoo*Fa + Boo*Fb F0 = Avv*Fa + Bvv*Fb Some choices for the canonicalization coefficients to define the diagonal blocks are Acc Bcc Aoo Boo Avv Bvv Guest and Saunders 1/2 1/2 1/2 1/2 1/2 1/2 Roothaan single matrix -1/2 3/2 1/2 1/2 3/2 -1/2 Davidson/1988 1/2 1/2 1 0 1 0 Binkley, Pople, Dobosh 1/2 1/2 1 0 0 1 McWeeny and Diercksen 1/3 2/3 1/3 1/3 2/3 1/3 Faegri and Manne 1/2 1/2 1 0 1/2 1/2

Further Information

4-38

GVB program/Euler 1/2 1/2 1/2 0 1/2 1/2 "canonical 1" 0 1 1 0 1 0 "canonical 2" (2S+1)/2S -1/2S 0 1 -1/2S (2S+1)/2S See below for how these last two rows connect to ionization events. The 1988 GAMESS ROHF program using a now deleted Davidson-type ROHF produced final orbitals matching the line above. This differs from the choices made in Davidson's own MELD program. The MELD program itself has always done a "cleanup" of the virtual space, after convergence, using Avv=Bvv=1/2, producing orbitals which are the same as Faegri/Manne. If MELD's MP2 option is chosen, the occupied space is also altered after convergence, using Aoo=Boo=1/2, which is the Guest/Saunders line above. Thus the term "Davidson orbitals" is used here to refer to the behavior of the now-deleted 1988 ROHF code in GAMESS, which didn't have either type of final orbital cleanup. The choice of the diagonal blocks is arbitrary, as ROHF is converged when the off diagonal blocks go to zero. The exact choice for these blocks can however have an effect on the convergence rate. This choice also affects the MO coefficients, and orbital energies, as the different choices produce different canonical orbitals within the three subspaces. All methods, however, will give identical total wavefunctions, and hence identical properties such as gradients and hessians. Some of the perturbation theories for open shell cases are defined in terms of a particular canonicalization, if so, GAMESS automatically canonicalizes after convergence so the desired orbitals and energies are given to the perturbation theory codes. The default coupling case in GAMESS is the Roothaan single matrix set. Note that pre-1988 versions of GAMESS produced "Davidson" orbitals. If you would like to fool around with any of these other canonicalizations, the Acc, Aoo, Avv and Bcc, Boo, Bvv parameters can be input as the first three elements of ALPHA and BETA in $SCF. For example, the McWeeny/Diercksen canonicalization, in double precision, is obtained by $scf couple=.true. alpha(1)=0.333333333333333333, 0.333333333333333333, 0.666666666666666667 beta(1)=0.666666666666666667, 0.333333333333333333, 0.333333333333333333 $end

Further Information

4-39

Here is some idea of the range of eigenvalues that result from using the various canonicalization schemes in the table above. The system is 6-31G nitrogen atom, all runs give E= -54.3820511123 (matching all 10 decimals): 1s 2s 2p "3p" "3s" Roothaan -15.5514 -0.5306 -0.1774 +0.7666 +0.8704 McWeeny,Diercksen -15.6214 -0.8745 -0.1183 +0.8984 +0.9684 Davidson -15.6355 -0.9432 -0.5657 +0.8457 +0.9292 Guest,Saunders -15.6355 -0.9432 -0.1774 +0.9248 +0.9880 Binkley,Pople,Dob. -15.6355 -0.9432 -0.5657 +1.0039 +1.0469 Faegri,Manne -15.6355 -0.9432 -0.5657 +0.9248 +0.9880 GVB (aka Euler) -15.6355 -0.9432 -0.2828 +0.9248 +0.9880 "canonical 1" -15.5933 -0.7370 -0.5657 +0.8457 +0.9292 "canonical 2" -15.7065 -1.2863 +0.2109 +1.0567 +1.0861 Since the ionization potential (IP) for a 2p electron in Nitrogen is 0.53 Hartree, it is clear that most of the orbital energies above do not approximately predict this IP. Recent work by Boris Plakhutin and co-workers (see the 3 papers in the ROHF references above) leads to two sets of orbitals and eigenvalues, for the prediction of both IP and electron affinities (EA), for various ionization events, starting from a high spin ROHF state: canonical 1 (to produce high spin final states) A1 = remove beta e- from filled space, B1 = remove alpha e- from open shell, C1 = attach alpha e- to virtual space. canonical 2 (to produce low spin final states) A2 = remove alpha e- from filled space, B2 = attach beta e- to filled space, C2 = attach beta e- to virtual space. Correct handling of spin requires the value of the spin S of the initial state in the 2nd canonicalization set. Two different ROHF runs are necessary to get all six EA and IP processes. Additional discussion about ROHF orbital energies may be found in K.R.Glaesemann, M.W.Schmidt J.Phys.Chem.A 114, 8772-8777(2010) [available on-line] along with a demonstration of the non-uniqueness of ROHFbased perturbation theories.

other open shell SCF cases (GVB)

Genuine GVB-PP runs will be discussed later in this section. First, we will consider how to do open shell SCF with the GVB part of the program.

Further Information It is possible to do other open shell cases with the GVB code, which can handle the following cases: one open shell, doublet: $CONTRL SCFTYP=GVB MULT=2 $END $SCF NCO=xx NSETO=1 NO(1)=1 $END two open shells, triplet: $CONTRL SCFTYP=GVB MULT=3 $END $SCF NCO=xx NSETO=2 NO(1)=1,1 $END two open shells, singlet: $CONTRL SCFTYP=GVB MULT=1 $END $SCF NCO=xx NSETO=2 NO(1)=1,1 $END

4-40

Note that the first two cases duplicate runs which the ROHF module can do better. Note that all of these cases are really ROHF, since the default for NPAIR in $SCF is 0. Many open shell states with degenerate open shells (for example, in diatomic molecules) can be treated as well. There is a sample of this in the 'Input Examples' section of this manual. If you would like to do any cases other than those shown above, you must derive the coupling coefficients ALPHA and BETA, and input them with the occupancies F in the $SCF group. Mariusz Klobukowski of the University of Alberta has shown how to obtain coupling coefficients for the GVB open shell program for many such open shell states. These can be obtained from Appendix A of the book "A General SCF Theory" by Ramon Carbo and Josep M. Riera, Springer-Verlag (1978). The basic rule is (1) (2) (3) F(i) = 1/2 * omega(i) ALPHA(i) = alpha(i) BETA(i) = - beta(i),

where omega, alpha, beta are symbols used in these Tables. Values for the excited terms in the p**N configurations were extracted from C.F.Jackels and E.R.Davidson Int. J. Quantum Chem. 8, 707-714(1974), which also explains the idea of averaging over equivalent determinants to enforce a symmetric density matrix, and thus preserve radial symmetry in the atomic orbitals. The variable NSETO should give the number of open shells, and NO should give the degeneracy of each open

Further Information shell. Thus the 5-S state of carbon would have NSETO=2, and NO(1)=1,3.

4-41

Some specific examples for all terms in each of the atomic p**N configurations follow. Be sure to give all the digits, as these values are part of a double precision energy formula! ! p**1 2-P state $CONTRL SCFTYP=GVB MULT=2 $END $SCF NCO=xx NSETO=1 NO=3 COUPLE=.TRUE. F(1)= 1.0 0.16666666666667 ALPHA(1)= 2.0 0.33333333333333 0.00000000000000 BETA(1)= -1.0 -0.16666666666667 -0.00000000000000 p**2 3-P state $CONTRL SCFTYP=GVB MULT=3 $END $SCF NCO=xx NSETO=1 NO=3 COUPLE=.TRUE. F(1)= 1.0 0.33333333333333 ALPHA(1)= 2.0 0.66666666666667 0.16666666666667 BETA(1)= -1.0 -0.33333333333333 -0.16666666666667

$END

$END

For the 1-D excited to ALPHA(3)=0.1 and For the 1-S excited to ALPHA(3)=0.0 and !

state, change the open-shell parameters BETA(3)= +0.03333333333333 state, change the open-shell parameters BETA(3)= +0.33333333333333

p**3 4-S state $CONTRL SCFTYP=ROHF MULT=4 $END which is equivalent to $CONTRL SCFTYP=GVB MULT=4 $END $SCF NCO=xx NSETO=1 NO=3 COUPLE=.TRUE. F(1)= 1.0 0.50000000000000 ALPHA(1)= 2.0 1.00000000000000 0.50000000000000 BETA(1)= -1.0 -0.50000000000000 -0.50000000000000

$END

For 2-D, use ALPHA(3)= 0.4 and BETA(3)= -0.2 for 2-P, use ALPHA(3)= 0.33333333333333 and BETA(3)= 0.0 ! p**4 3-P state $CONTRL SCFTYP=GVB MULT=3 $END $SCF NCO=xx NSETO=1 NO=3 COUPLE=.TRUE. F(1)= 1.0 0.66666666666667 ALPHA(1)= 2.0 1.33333333333333 0.83333333333333 BETA(1)= -1.0 -0.66666666666667 -0.50000000000000

$END

For 1-D, use ALPHA(3)= 0.76666666666667 and BETA(3)= -0.3 for 1-S, use ALPHA(3)= 0.66666666666667 and BETA(3)= 0.0

Further Information ! p**5 2-P state $CONTRL SCFTYP=GVB MULT=2 $END $SCF NCO=xx NSETO=1 NO=3 COUPLE=.TRUE. F(1)= 1.0 0.83333333333333 ALPHA(1)= 2.0 1.66666666666667 1.33333333333333 BETA(1)= -1.0 -0.83333333333333 -0.66666666666667

4-42

$END

Coupling constants for the highest spin states in the d**N configurations are from the book "Handbook of Gaussian Basis Sets", R.Poirier, R.Kari, I.G.Csizmadia, Elsevier, Amsterdam, 1985. ! d**1 2-D state $CONTRL SCFTYP=GVB MULT=2 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE. ALPHA(1)= 2.0, 0.20, 0.00 BETA(1)=-1.0,-0.10, 0.00 $END d**2 average of 3-F and 3-P states $CONTRL SCFTYP=GVB MULT=3 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE. ALPHA(1)= 2.0, 0.40, 0.05 BETA(1)=-1.0,-0.20,-0.05 $END d**3 average of 4-F and 4-P states $CONTRL SCFTYP=GVB MULT=4 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE. ALPHA(1)= 2.0, 0.60, 0.15 BETA(1)=-1.0,-0.30,-0.15 $END d**4 5-D state $CONTRL SCFTYP=GVB MULT=5 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE. ALPHA(1)= 2.0, 0.80, 0.30 BETA(1)=-1.0,-0.40,-0.30 $END d**5 6-S state $CONTRL SCFTYP=ROHF MULT=6 $END d**6 5-D state $CONTRL SCFTYP=GVB MULT=5 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE. ALPHA(1)= 2.0, 1.20, 0.70 BETA(1)=-1.0,-0.60,-0.50 $END d**7 average of 4-F and 4-P states $CONTRL SCFTYP=GVB MULT=4 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE.

F(1)=1.0,0.1

F(1)=1.0,0.2

F(1)=1.0,0.3

F(1)=1.0,0.4

! !

F(1)=1.0,0.6

F(1)=1.0,0.7

Further Information ALPHA(1)= 2.0, 1.40, 0.95 BETA(1)=-1.0,-0.70,-0.55 ! $END

4-43

d**8 average of 3-F and 3-P states $CONTRL SCFTYP=GVB MULT=3 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE. ALPHA(1)= 2.0, 1.60, 1.25 beta(1)=-1.0,-0.80,-0.65 $end d**9 2-D state $CONTRL SCFTYP=GVB MULT=2 $END $SCF NCO=xx NSETO=1 NO=5 COUPLE=.TRUE. ALPHA(1)= 2.0, 1.80, 1.60 BETA(1)=-1.0,-0.90,-0.80 $END

F(1)=1.0,0.8

F(1)=1.0,0.9

Note that GAMESS can do a proper calculation on the ground terms for the d**2, d**3, d**7, and d**8 configurations only by means of state averaged MCSCF. For d**8, use $contrl scftyp=mcscf mult=3 $end $det group=c1 ncore=xx nact=5 nels=8 nstate=10 wstate(1)=1,1,1,1,1,1,1,0,0,0 $end to correctly average the 7 lowest roots (3-F) with no weight given to the highest three roots (3-P). Although this is done with the SCFTYP=MCSCF program, this is a SCF type calculation since only the orbitals, and not any CI coefficients, are optimized in this run. Open shell cases such as s**1,d**n are probably most easily tackled with the state-averaged MCSCF program. The ORMAS CI code may be convenient in fixing the number of electrons found in each open shell.

true GVB perfect pairing runs

True GVB runs are obtained by choosing NPAIR nonzero. If you wish to have some open shell electrons in addition to the geminal pairs, you may add the pairs to the end of any of the GVB coupling cases shown above. The GVB module assumes that you have reordered your MOs into the order: NCO double occupied orbitals, NSETO sets of open shell orbitals, and NPAIR sets of geminals (with NORDER=1 in the $GUESS group). Each geminal consists of two orbitals and contains two singlet coupled electrons (perfect pairing). The first MO of a geminal is probably heavily occupied (such as a

Further Information

4-44

bonding MO u), and the second is probably weakly occupied (such as an antibonding, correlating orbital v). If you have more than one pair, you must be careful that the initial MOs are ordered u1, v1, u2, v2..., which is -NOTthe same order that RHF starting orbitals will be found in. Use NORDER=1 to get the correct order. These pair wavefunctions are actually a limited form of MCSCF. GVB runs are much faster than MCSCF runs, because the natural orbital u,v form of the wavefunction permits a Fock operator based optimization. However, convergence of the GVB run is by no means assured. The same care in selecting the correlating orbitals that you would apply to an MCSCF run must also be used for GVB runs. In particular, look at the orbital expansions when choosing the starting orbitals, and check them again after the run converges. GVB runs will be carried out entirely in orthonormal natural u,v form, with strong orthogonality enforced on the geminals. Orthogonal orbitals will pervade your thinking in both initial orbital selection, and the entire orbital optimization phase (the CICOEF values give the weights of the u,v orbitals in each geminal). However, once the calculation is converged, the program will generate and print the nonorthogonal, generalized valence bond orbitals. These GVB orbitals are an entirely equivalent way of presenting the wavefunction, but are generated only after the fact. Convergence of true GVB runs is by no means as certain as convergence of RHF, UHF, ROHF, or GVB with NPAIR=0. You can assist convergence by doing a preliminary RHF or ROHF calculation, and use these orbitals for GUESS=MOREAD. Few, if any, GVB runs with NPAIR non-zero will converge without using GUESS=MOREAD. Generation of MVOs during the preliminary SCF can also be advantageous. In fact, all the advice outlined for MCSCF computations below is germane, for GVB-PP is a type of MCSCF computation. The total number of electrons in the GVB wavefunction is given by the following formula: NE = 2*NCO + sum 2*F(i)*NO(i) + 2*NPAIR i The charge is obtained by subtracting the total number of protons given in $DATA. The multiplicity is implicit in the choice of alpha and beta constants. Note that ICHARG

Further Information

4-45

and MULT must be given correctly in $CONTRL anyway, as the number of electrons from this formula is double checked against the ICHARG value.

the special case of TCSCF

The wavefunction with NSETO=0 and NPAIR=1 is called GVB-PP(1) by Goddard, two configuration SCF (TCSCF) by Schaefer or Davidson, and CAS-SCF with two electrons in two orbitals by others. Note that this is just semantics, as these are identical. This is a very important type of wavefunction, as TCSCF is the minimum acceptable treatment for singlet biradicals. The TCSCF wavefunction can be obtained with SCFTYP=MCSCF, but it is usually much faster to use the Fock based SCFTYP=GVB. Because of its importance, the TCSCF function (together with open shells, if desired) permits analytic hessian computation.

a caution about symmetry

Caution! Some exotic calculations with the GVB program do not permit the use of symmetry. The symmetry algorithm in GAMESS was "derived assuming that the electronic charge density transforms according to the completely symmetric representation of the point group", Dupuis/King, JCP, 68, 3998(1978). This may not be true for certain open shell cases, and in fact during GVB runs, it may not be true for closed shell singlet cases! First, consider the following correct input for the singlet-delta state of NH: $CONTRL SCFTYP=GVB NOSYM=1 $END $SCF NCO=3 NSETO=2 NO(1)=1,1 $END for the x**1y**1 state, or for the x**2-y**2 state, $CONTRL SCFTYP=GVB NOSYM=1 $END $SCF NCO=3 NPAIR=1 CICOEF(1)=0.707,-0.707 $END Neither gives correct results, unless you enter NOSYM=1. The electronic term symbol is degenerate, a good tip off that symmetry cannot be used. However, some degenerate states can still use symmetry, because they use coupling constants averaged over all degenerate states within a single term, as is done in EXAM15 and EXAM16. Here the "state averaged SCF" leads to a charge density which is symmetric, and these runs can exploit symmetry. Secondly, since GVB runs exploit symmetry for each of the "shells", or type of orbitals, some calculations on

Further Information

4-46

totally symmetric states may not be able to use symmetry. An example is CO or N2, using a three pair GVB to treat the sigma and pi bonds. Individual configurations such as (sigma)**2,(pi-x)**2,(pi-y*)**2 do not have symmetric charge densities since neither the pi nor pi* level is completely filled. Correct answers for the sigma-plus ground states result only if you input NOSYM=1. Problems of the type mentioned should not arise if the point group is Abelian, but will be fairly common in linear molecules. Since GAMESS cannot detect that the GVB electronic state is not totally symmetric (or averaged to at least have a totally symmetric density), it is left up to you to decide when to input NOSYM=1. If you have any question about the use of symmetry, try it both ways. If you get the same energy, both ways, it remains valid to use symmetry to speed up your run. And beware! Brain dead computations, such as RHF on singlet O2, which actually is a half filled degenerate shell, violate the symmetry assumptions, and also violate nature. Use of partially filled degenerate shells always leads to very wild oscillations in the RHF energy, which is how the program tries to tell you to think first, and compute second. Configurations such as pi**2, e**1, or f2u**4 can be treated, but require GVB wavefunctions and F, ALPHA, BETA values from the sources mentioned.

Further Information

4-47

How to do MCSCF (and CI) calculations

Multi-configuration self consistent field (MCSCF) wavefunctions are the most general SCF possible. MCSCF allows for a natural description of chemical processes involving the separation of electrons (bond breaking, electronic excitation, etc), which are often not well represented using the single configuration SCF methods. MCSCF wavefunctions, as the name implies, contain more than one configuration, each of which is multiplied by a configuration interaction (CI) coefficient, optimized to determine its weight. In addition, the shapes of the orbitals used to form each of the configurations are optimized, just as in a simpler SCF, to self consistency. Typically every different chemical problem requires that an MCSCF wavefunction be designed to treat it, on a case by case basis, by choosing an "active space". For example, one may be interested in describing the reactivity of a particular functional group, instead of elsewhere in the molecule. So, the active electrons and active orbitals will be those that are "active" on that functional group. Orbitals elsewhere in the molecule just remain doubly occupied, as for RHF. This means some attention must be paid to orbitals in order to obtain the desired results. Procedures for the selection of configurations (which amounts to choosing the number of active electrons and active orbitals), for the two mathematical optimizations just mentioned, ways to interpret the resulting MCSCF wavefunction, and treatments for dynamical electron correlation of MCSCF wavefunctions are the focus of a review article: "The Construction and Interpretation of MCSCF wavefunctions" M.W.Schmidt and M.S.Gordon, Annu.Rev.Phys.Chem. 49,233-266(1998) One section of this article is devoted to the problem of designing the correct active space to treat your problem. Additional reading is listed at the end of this section. These pages describe a powerful and mature MCSCF program, allowing computation of the MCSCF energy, nuclear gradient, and nuclear hessian for pure states. Stateaveraged energies can be obtained. Efficient perturbative treatments of the dynamical correlation energy for all

Further Information

4-48

electrons, whether in active and filled orbitals, are provided. Effective procedures for generating starting orbitals are available. Localized orbital analysis of the final active orbitals is provided. If desired, spin-orbit couplings or transition moments can be found (see elsewhere in this chapter). Of course, parallel computation has been enabled. The most efficient technique implemented in GAMESS for finding the dynamic correlation energy of MCSCF is second order perturbation theory, in the variant known as MCQDPT (known as MRMP for one state). MCQDPT is discussed in a different section of this chapter. The use of CI, probably in the form of second order CI, will be described below, en passant, during discussion of the input defining the configurations for MCSCF. Selection of a CI following any type of SCF (except UHF) is made with CITYP in the $CONTRL group, and masterminded by $CIINP.

MCSCF implementation
With the exception of the QUAD converger, the MCSCF program is of the type termed "unfolded two-step" by Roos. This means the orbital and CI coefficient optimizations are separated. The latter are obtained in a conventional CI diagonalization, while the former are optimized by a separate orbital improvement step. Each MCSCF iteration (except for the JACOBI and QUAD convergers) consists of the following steps: 1) transformation of AO integrals to the current MO basis, 2) generation of the Hamiltonian matrix and optimization of the CI coefficients by a Davidson diagonalization, 3) generation of the first and second order density matrix, 4) improvement of the molecular orbitals. During the first iteration at the first geometry, you will receive verbose output from each of these steps, but each subsequent iteration produce only a single summary line. The CI problem in steps two and three has four options for the many electron basis, namely ALDET, ORMAS, or GENCI using determinants, or GUGA using CSFs. This choice is made with the keyword CISTEP in $MCSCF. Much more will be said below about the differences between determinants and CSFs. The word "configuration" will be used throughout this section to refer to either determinants or CSFs, when a generic term is needed for the many-electron functions.

Further Information

4-49

Most people use CSF and configuration interchangeably, so please note the distinction made here. The orbital update in step four has five options, namely FOCAS, SOSCF, FULLNR, JACOBI, and QUAD, listed here in roughly the order of their increasing mathematical sophistication, convergence characteristics, and of course, their computer resource requirements. Again, these are chosen by keywords in the $MCSCF group. More will be said just below about the relative merits of these. Depending on the converger chosen, the program will select the appropriate kind of integral transformation at step one. There's seldom need to try to fine tune this, but note that the $TRANS group allows you to choose an AO integral direct transformation, with the DIRTRF flag. The type of CI and the type of orbital converger are to some extent "mix and match". This is particularly true for the two full CI programs, GUGA or ALDET, where either produces exactly the same CI density matrices. Here is a chart of the ways to combine CI and orbital optimizers: parallel run's orbital transformation CI computation via CISTEP= converger memory GUGA ALDET GENCI ORMAS --------- --------------------- ----- ----FOCAS replicated ok ok silly silly SOSCF replicated ok ok ok ok FULLNR distributed ok ok ok ok QUAD serial ok xx xx xx JACOBI serial ok ok ok ok "xx" means QUAD converger is coded only for CISTEP=GUGA. "silly" means that this converger ignores active-active rotations, so these runs are likely to be divergent, or perhaps converge to a false solution. "serial" means this can only run sequentially at present. The next two sections provide more information on the two mathematical optimizations, first how the orbital shape is refined, and then the determinantion of CI coefficients.

orbital updates
There are presently five orbital improvement options, namely FOCAS, SOSCF, FULLNR, JACOBI, and QUAD. All but the JACOBI update run in parallel. Each converger is discussed briefly below, in order of increasing robustness. The most commonly used convergers are SOSCF and FULLNR.

Further Information

4-50

The input to control the orbital update step is the $MCSCF group, where you can pick the convergence procedure. Most of the input in this group is rather specialized, but note in particular MAXIT and ACURCY, which control the convergence behavior. FOCAS is a first order, complete active space MCSCF optimization procedure. It is based on a novel approach due to Meier and Staemmler, using very fast but numerous microiterations to improve the convergence of what is intrinsically a first order method. Since FOCAS requires only one virtual orbital in the integral transformation to compute the Lagrangian (whose asymmetry is the orbital gradient, and must fall below ACURCY at convergence), the total MCSCF job may take less time than a second order method, even though it may require many more iterations to converge. The use of microiterations is crucial to FOCAS' ability to converge. It is important to take a great deal of care choosing the starting orbitals. SOSCF is a method built upon the FOCAS code, which seeks to combine the speed of FOCAS with approximate second order convergence properties. Thus SOSCF is an approximate Newton-Raphson, based on a diagonal guess at the orbital hessian, and in fact has much in common with the SOSCF option in $SCF. Its time requirements per iteration are like FOCAS, with a convergence rate better than FOCAS but not as good as true second order. Storage of only the diagonal of the orbital hessian allows the SOSCF method to be used with much larger basis sets than exact second order methods. Because SOSCF usually requires the least CPU time, disk space, and memory needs, it is the default. Good convergence by the SOSCF method requires that you prepare starting orbitals carefully, and read in all MOs in $VEC, as providing canonicalized virtual orbitals increases the diagonal dominance of the orbital hessian. Parallel computations are possible with SOSCF, but only to a modest number of nodes. FULLNR means a full Newton-Raphson orbital improvement step is taken, using the exact orbital hessian. FULLNR is a robust convergence method, and normally takes the fewest iterations to converge. Computing the exact orbital hessian requires two virtual orbital indices be included in the integral transformation, making this step quite time consuming, and of course memory for storage of the orbital hessian must be available. Because both the transformation and orbital improvement steps of FULLNR are time consuming,

Further Information

4-51

FULLNR is not the default. You may want to try FULLNR when convergence is difficult, assuming you have already tried preparing good starting orbitals by the hints below. The serial FULLNR code uses the augmented hessian matrix approach to solve the Newton-Raphson equations. There are two suboptions for computation of the orbital hessian: DM2 is faster, but takes more memory than TEI. The parallel implementation of FULLNR avoids explicit storage of the orbital hessian, by recomputing the product of the hessian times orbital rotation vector during the subiterations solving the Newton-Raphson problem. The partial integral transformation used to set up the FULLNR converger has been changed to use distributed memory, and will scale like the MP2 energy/gradient programs, to many nodes. Parallel FULLNR requires large MEMORY only for the CI step (if the active space is big), but always requires a large MEMDDI. The parallel FULLNR program is essentially diskless, apart from storage of converged CI vectors. The JACOBI method uses a series of 2 by 2 orbital rotations by an angle predicted to lower the energy. This should essentially ensure convergence after sweeping through all possible orbital pairs enough times. The procedure was created to converge selected (general) determinant MCSCF functions, but of course it can be used will full lists as well in difficult cases. The JACOBI calculation will consist of a full four index transformation over all MOs before the iterations begin. Each iteration consists of 1. a small 4 index transformation over active orbitals 2. optimization of the CI vector 3. generation of the 1e- and 2e- density matrices 4. sweeps over Jacobi rotations, using MO integrals in memory to generate each rotation, with a subsequent update after each pair is rotated. 5. when sufficient energy lowering has been achieved, begin a new iteration. This procedure never generates the orbital Lagrangian! Unfortunately this means that at present it is not possible to compute nuclear gradients. Due to lack of a Lagrangian, ACURCY is of course irrelevant, so the convergence test is on ENGTOL. QUAD uses a fully quadratic, or second order approach and is thus the most powerful MCSCF converger. The QUAD code is programmed only for CISTEP=GUGA. QUAD runs begin with normal unfolded FULLNR iterations, until the orbitals approach convergence sufficiently. QUAD then begins the

Further Information

4-52

simultaneous optimization of CI coefficients and orbitals, and convergence should be obtained in 3-4 additional MCSCF iterations. The QUAD method requires building the full electronic hessian, including orbital/orbital, orbital/CI, and CI/CI blocks, which is a rather big matrix. In principle, this is the most robust method available, but it is limited to perhaps 50-100 CSFs only, because it is a memory hog. QUAD may be helpful in converging excited electronic states, but note that you may not use state averaging with QUAD. In practice, QUAD has not received very much use compared to the unfolded convergers.

CI coefficient optimization
Determinants or configuration state functions (CSFs) may be used to form the many electron basis set. It is necessary to explain these in a bit of detail so that you can understand the advantages of each. A determinant is a simple object: a product of spin orbitals with a given Sz quantum number, that is, the number of alpha spins and number of beta spins are a constant. Matrix elements involving determinants are correspondingly simple, but unfortunately determinants are not necessarily eigenfunctions of the S**2 operator. To expand on this point, consider the four familiar 2efunctions which satisfy the Pauli principle. Here u, v are space orbitals, and a, b are the alpha and beta spin functions. As you know, the singlet and triplets are: S1 = (uv + vu)/sqrt(2) * (ab - ba)/sqrt(2) T1 = (uv - vu)/sqrt(2) * aa T2 = (uv - vu)/sqrt(2) * (ab + ba)/sqrt(2) T3 = (uv - vu)/sqrt(2) * bb It is a simple matter to multiply out S1 and T2, and to expand the two determinants which have Sz=0, D1 = |ua vb| D2 = |va ub| This reveals that S1 = (D1+D2)/sqrt(2) or D1 = (S1 + T2)/sqrt(2) T2 = (D1-D2)/sqrt(2) D2 = (S1 - T2)/sqrt(2) Thus, one must take a linear combination of determinants in order to have a wavefunction with the desired total spin. There are two important points to note: a) A two by two Hamiltonian matrix over D1 and D2 has eigenfunctions with -different- spins, S=0 and S=1. b) use of all determinants with Sz=0 does allow for the construction of spin adapted states. D1+D2, or D1-D2, are -not- spin contaminated.

Further Information

4-53

By itself, a determinant such as D1 is said to be "spin contaminated", being a fifty-fifty admixture of singlet and triplet. (It is curious that calculations with just one such determinant are often called "singlet UHF", when this is half triplet!). Of course, some determinants are spin adapted all by themselves, for example the spin adapted functions T1 and T3 above are single determinants, as are the closed shells S2 = (uu) * (ab - ba)/sqrt(2). S3 = (vv) * (ab - ba)/sqrt(2). It is possible to perform a triplet calculation, with no singlet states present, by choosing determinants with Sz=1 such as T1, since then no state with Sz=0 exists in the determinant basis set (as is required when S=0). To summarize, the eigenfunctions of a Hamiltonian formed by determinants with any particular Sz will be spin states with S=Sz, S=Sz+1, S=Sz+2, ... but will not contain any S values smaller than Sz. CSFs are an antisymmetrized combination of a space orbital product, and a spin adapted linear combination of simple alpha-beta products. Namely, the following CSF C1 = A (uv) * (ab-ba)/sqrt(2) which has a singlet spin function is identical to S1 above if you write out what the antisymmetrizer A does, and the CSFs C2 = A (uv) * aa C3 = A (uv - vu)/sqrt(2) * (ab + ba)/sqrt(2) C4 = A (uv) * bb equal T1-T3. Since the three triplet CSFs have the same energy, GAMESS works with the simpler form C2. Singlet and triplet computations using CSFs are done in separate runs, because when spin-orbit coupling is not considered, the Hamiltonian is block diagonal in a CSF basis. Technical information about the CSFs is that they use YamanouchiKotani spin couplings, and matrix elements are obtained using a GUGA, or graphical unitary group approach. Determinant and CSF are both primarily used for MCSCF wavefunctions, but can be used in CI (see CITYP in $CONTRL). Other comparisons between the determinant and CSF implementations, as they exist in GAMESS today, are determinants CSFs parallel execution yes yes direct CI yes no use Abelian group symmetry yes yes state average mixed spins yes no first order density yes yes state averaged densities yes yes

Further Information

4-54

analytic nuclear hessian yes no can form CI Lagrangian no yes In nearly every circumstance the determinant CI will run faster than GUGA, so it is the default. Here are timings for N electrons in N orbitals, no symmetry used: N in N ALDET GENCI --- GUGA --8 1 1 1 0 10 8 38 19 33 12 228 3122 534 2209 14 7985 -15377 130855 The reason there are two numbers under GUGA is that the first is for writing the loops (Hamiltonian data) to disk, and the second is for the actual diagonalization. Note that the GUGA Hamiltonian time alone is greater than the entire ALDET computation! The ALDET program does not store anything on disk, and so runs at CPU/wall ratios of 1. The quality of the initial guess of the CI eigenvector in the various determinant codes is much better than in the GUGA CSF code, so the chances of converging to an incorrect excited state root is much less. Finally, determinant input is generally easier. No wonder determinants are now the default configurations! Two of the determinant CI programs, namely ALDET or ORMAS (but not GENCI) have been changed to use replicated memory parallelism, with modest scaling. The GUGA program is parallel in its solving, but not its Hamiltonian generation, and as already noted, its H formation takes more time than the entire determinant CI (translation: use CISTEP=ALDET, not CISTEP=GUGA). The GENCI program will run as a serial bottleneck (no speedup) in parallel runs. The next two sections describe in detail the input for specification of the configurations, either determinants or CSFs.

determinant CI
Three determinant CI codes are provided for MCSCF, one for full CI spaces (ALDET), another named the Occupation Restricted Multiple Active Spaces (ORMAS), and finally there is a program for arbitrary (selected) determinant lists (GENCI). For straight CI, but not MCSCF, there is a fourth program, the full second order CI (CITYP=FSOCI), whose purpose is MR-CISD. ALDET is a full CI within the chosen active space. It is possible to go up to 16 electrons in 16 orbitals, if

Further Information

4-55

your computer has a lot of memory. ALDET is the only CISTEP for which analytic nuclear hessian is possible, and it is also the most scalable CI code (using replicated memory to store CI vectors). A sample input for ALDET is $DET STSYM=B1 NSTATE=3 NCORE=xx NELS=8 NACT=6 $END Keywords in this group actually relate to all determinant programs, and are described below. The $DET input group is basic to all determinant CI codes. Keywords GROUP and STSYM specify the desired spatial symmetry of the determinants. Most runs need give only the orbital and electron counts: NCORE, NACT, and NELS. The number of electrons is 2*NCORE+NELS, and will be checked against the charge implied by ICHARG. The MULT given in $CONTRL is used to determine the desired Sz value, by extracting S from MULT=2S+1, then by default Sz=S. If you wish to include lower spin multiplicities, which will increase the CPU time of the run, but will let you know what the energies of such states are, just input a smaller value for SZ. The states whose orbitals will be MCSCF optimized will be those having the requested MULT value, unless you choose otherwise with the PURES flag. The remaining parameters in the $DET group give extra control over the diagonalization process. Most are not given in normal circumstances, except NSTATE, which you may need to adjust to produce enough roots of the desired MULT value. The only important keyword which has not been discussed is the WSTATE array, giving the weights for each state in forming the first and second order density matrix elements, which drive the orbital update methods. Note that analytic gradients are available only when the WSTATE array is a unit vector, corresponding to a pure state, such as WSTATE(1)=0,1,0 which permits gradients of the first excited state to be computed. When used for state averaged MCSCF, WSTATE is normalized to a unit sum, thus input of WSTATE(1)=1,1,1 really means a weight of 0.33333... for the each of the states being averaged. ORMAS (Occupation Restricted Multiple Active Space) is a program designed to limit the size of the full CI problem, and may be useful when the number of active orbitals is 10 or higher. By dividing your total active space into multiple subspaces, and specifying a range of electrons to occupy each subspace, most of the full CI's effect can be included. ORMAS generates a full CI within each orbital subspace, taking the product of each small full CI to generate the determinant list.

Further Information Here are some ideas on how to use ORMAS, which is a very flexible CI program:

4-56

a) single reference, arbitrary excition level CI-X, from a closed shell reference: $det ncore=y nact=z nels=10 (y+z=entire basis) $ormas nspace=2 mstart(1)=y+1,y+6 mine(1)=10-x,0 maxe(1)=10,x This excites the 5 doubly occupied orbitals, to the desired excitation level of X. An open shell example of CI-SD from ...22111 might be $contrl mult=4 $det ncore=y nact=z nels=7 (y+z=entire basis) $ormas nspace=3 mstart(1)=y+1,y+3,y+6 mine(1)=2,1,0 maxe(1)=4,5,2 No more than 2e- are allowed to be promoted from the doubly occupied or singly occupied spaces, and no more than 2 are allowed to enter the singly occupied or empty spaces. b) simple product of active spaces For example, consider furan, with two active subspaces. Keeping the 5 true core and the 4 CH bonds in the core space, the sigma subspace might contains 5 ring sigma, one oxygen lone pair, and 5 ring sigma antibonds, with a total of 12 e-. The pi active space contains 5 pi orbitals and 6 e-: $det ncore=9 nact=16 nels=18 $ormas nspace=2 mstart(1)=10,21 mine(1)=12,6 maxe(1)=12,6 Having the minimum and maximum electron counts the same is what makes this the simple product of two separate active spaces. In other words, this is similar to the QCAS procedure of Nakano and Hirao, but ORMAS limits only the total electron counts, not separately the numbers of alpha and beta e-, in other words all spin couplings are used. c) flexible occupancy between active subspaces Imagine that you are interested in excited states of formaldehyde, some of which will have Rydberg character, dominated by single excitations into diffuse orbitals. H2CO's valence states arise from 3 orbitals, the CO pi and pi* and one oxygen lone pair. Placing the O sp lone pair and three sigma bonds into the filled space, and centering diffuse s,p,d shells on the carbon:

Further Information $det $ormas

4-57

ncore=6 nact=12 nels=4 nspace=2 mstart(1)=7,10 mine(1)=3,0 maxe(1)=4,1 This is a 4e-, 3 orbital n,pi,pi* space to describe valence states, and excites one electron into the 9 diffuse orbitals to describe Rydberg states. It is many fewer determinants than a 4e- in 12 orbital FCI. d) RAS-like CI The previous example is reminiscent of Roos' RAS-SCF. In fact ORMAS can do RAS-SCF, which is three spaces: the lowest space is allowed to excite only a few electrons, a middle space that is the rest, and a top space into which only a few electrons can be excited. Suppose there are 10 e-, 10 orbitals, that the bottom and top spaces involve 3 orbitals, and that a "few" means specifically 2 e-: $det ncore=20 nact=10 nels=10 $end $ormas nspace=3 mstart(1)=21,24,28 mine(1)=4,2,0 maxe(1)=6,6,2 However, ORMAS can use more than 3 orbital subspaces. e) first or second order CI. Consider C2H4, with a 4 orbital active space of CC sigma, pi, pi*, and sigma*. In order to correlate the four valence CH orbitals by double excitations, an MCSCF based on $DET, followed by SOCI based on $CIDET and $ORMAS, is: $contrl scftyp=mcscf cityp=ormas $mcscf cistep=aldet $det ncore=6 nact=4 nels=4 $cidet ncore=2 nact=y nels=12 (y=rest of basis) $ormas nspace=3 mstart(1)=3,7,11 mine(1)=6,2,0 maxe(1)=8,6,2 which permits singles and doubles out of the CH and CC spaces, into the CC and external spaces. ORMAS is a full CI (or several full CI's) within each orbital subspace. However, ORMAS does not generate all excitation levels between spaces (just those implied by the minimum and maximum electron counts you give). This means ORMAS MCSCF runs must optimize active-active rotations between the subspaces, and therefore you should expect better convergence from FULLNR than SOSCF. ORMAS is sure to require orbital reordering. For the furan example just mentioned, there is no reason to expect that the RHF occupied orbitals will not have the filled sigma and pi orbitals intermingled. You must use the

Further Information

4-58

NORDER and IORDER keywords in $GUESS to carefully partition starting orbitals into sigma and pi subspaces. The selected (general) determinant list is used if CISTEP=GENCI, and the list is controlled by two input groups. The first is $GEN, which is identical to $DET except for inclusion of an additional keyword GLIST=INPUT. This reads the determinants (as space products) from an additional input group $GCILST. Completely arbitrary choices for the space products may be made, but peculiar lists may lead to poor MCSCF convergence. The FOCAS converger should not be used, as it assumes full CI spaces. If you are doing straight CI calculations, the required input for each determinant CITYP is: ALDET needs $CIDET ORMAS needs $CIDET and $ORMAS GENCI needs $CIDET and $CIGEN and probably $GCILST FSOCI needs $CIDET and $SODET In other words, $CIDET replaces $DET, and $CIGEN replaces $GEN, but the keywords in the groups mean the same thing. The reason for different names is to allow CI calculations to follow MCSCF in the same run, without clashing input group names.

CSF CI
The GUGA-based CSF package was originally a set of different programs, so its input is spread over several input groups. The CSFs are specified by a $CIDRT group in the case of CITYP=GUGA, and by a $DRT group for MCSCF wavefunctions. Thus it is possible to perform an MCSCF defined by a $DRT input (or perhaps using $DET during the MCSCF), and follow this with a second order CI defined by a $CIDRT group, in the same run. The remaining input groups used by the GUGA CSFs are $CISORT, $GUGEM, $GUGDIA, and $GUGDM2 for MCSCF runs, with the latter two being the most important, and in the case of CI computations, $GUGDM and possibly $LAGRAN groups are relevant. Perhaps the most interesting variables outside the $DRT/$CIDRT group are NSTATE in $GUGDIA to include excited states in the CI computation, IROOT in $GUGDM to select the CI state for properties, and WSTATE in $GUGDM2 to control which state's orbitals are optimized, and possible state-averaging.

Further Information

4-59

The $DRT and $CIDRT groups are almost the same, with the only difference being orbitals restricted to double occupancy are called MCC in $DRT, and FZC in $CIDET. Therefore the rest of this section refers only to "$DRT". The CSFs are specified by giving a reference CSF, together with a maximum degree of electron excitation from that single CSF. The MOs in the reference CSF are filled in the order MCC or FZC first, followed by DOC, AOS, BOS, ALP, VAL, and EXT (the Aufbau principle). AOS, BOS, and ALP are singly occupied MOs. ALP means a high spin alpha coupling, while AOS/BOS are an alpha/beta coupling to an open shell singlet. This requires the value NAOS=NBOS, and their MOs alternate. An example is NFZC=1 NDOC=2 NAOS=2 NBOS=2 NALP=1 NVAL=3 which gives the reference CSF FZC,DOC,DOC,AOS,BOS,AOS,BOS,ALP,VAL,VAL,VAL This is a doublet state with five unpaired electrons. VAL orbitals are unoccupied only in the reference CSF, they will become occupied as the other CSFs are generated. This is done by giving an excitation level, either explicitly by the IEXCIT variable, or implicitly by the FORS, FOCI, or SOCI flags. One of these four keywords must be chosen, and during MCSCF runs, this is usually FORS. Consider another simpler example, for an MCSCF run, NMCC=3 NDOC=3 NVAL=2 which gives the reference CSF MCC,MCC,MCC,DOC,DOC,DOC,VAL,VAL having six electrons in five active orbitals. MCSCF calculations are usually of the Full Optimized Reaction Space (FORS) type. Some workers refer to FORS as CASSCF, complete active space SCF. These are the same, but the keyword is spelled FORS in GAMESS. In the present instance, choosing FORS=.TRUE. gives an excitation level of 4, as the 6 valence electrons have only 4 holes available for excitation. MCSCF runs typically have only a small number of VAL orbitals. It is common to summarize this example as "six electrons in five orbitals". The next example is a first or second order multireference CI wavefunction, where NFZC=3 NDOC=3 NVAL=2 NEXT=-1 leads to the reference CSF FZC,FZC,FZC,DOC,DOC,DOC,VAL,VAL,EXT,EXT,... FOCI or SOCI is chosen by selecting the appropriate flag, the correct excitation level is automatically generated. Note that the -1 for NEXT causes all remaining MOs to be included in the external orbital space. One way of viewing

Further Information

4-60

FOCI and SOCI wavefunctions is as all singles, or all singles and doubles, from the entire MCSCF wavefunction as a reference. An equivalent way of saying this is that all CSFs with N electrons (in this case N=6) distributed in the valence orbitals in all ways (that is the FORS MCSCF wavefunction) make up the reference wavefunction. To this, FOCI adds all CSFs with N-1 electrons in active and 1 electron in external orbitals. SOCI adds all CSFs with N-2 electrons in active orbitals and 2 in external orbitals. SOCI is often prohibitively large, but is also a very accurate wavefunction. SOCI can also be performed with determinants, as CITYP=FSOCI, or CITYP=ORMAS. The latter may be the most efficient way to generate SOCI energies. For larger molecules, where SOCI is impractical, the most effective way to recover dynamic correlation energy is the multireference perturbation method. Sometimes people use the CI package for ordinary single reference CI calculations, such as NFZC=3 NDOC=5 NVAL=34 which means the reference RHF wavefunction is FZC FZC FZC DOC DOC DOC VAL VAL ... VAL and in this case NVAL is a large number conveying the total number of -virtual- orbitals into which electrons are excited. The excitation level would be given as IEXCIT=2, perhaps, to perform a SD-CI. All excitations smaller than the value of IEXCIT are automatically included in the CI. Note that NVAL's spelling was chosen to make the most sense for MCSCF calculations, and so it is a bit of a misnomer here. Before going on, there is a quirk related to single reference CI that should be mentioned. Whenever the single reference contains unpaired electrons, such as NFZC=3 NDOC=4 NALP=2 NVAL=33 some "extra" CSFs will be generated. The reference here can be abbreviated 2222 11 000 000 000 000 000 000 000 000 000 000 000 Supposing IEXCIT=2, the following CSF 2200 22 000 011 000 000 000 000 000 000 000 000 000 will be generated and used in the CI. Most people would prefer to think of this as a quadruple excitation from the reference, but acting solely on the reasoning that no more than two electrons went into previously vacant NVAL orbitals, the GUGA CSF package decides it is a double. So, an open shell SD-CI calculation with GAMESS will not give the same result as other programs, although the result for any such calculation with these "extras" is correctly computed. Note that if you also select the INTACT option,

Further Information the the are not

4-61

extra space products are eliminated, but that some of spin couplings for the truly IEXCIT'd space products also eliminated. Note that this kind of problem does arise if you use ORMAS!

As was discussed above, the CSFs are automatically spin-symmetry adapted, with S implicit in the reference CSF. The spin quantum number you appear to be requesting in $DRT (basically, S = NALP/2) will be checked against the value of MULT in $CONTRL. The total number of electrons, 2*NMCC(or NFZC) + 2*NDOC + NAOS + NBOS + NALP will be checked against the input given for ICHARG. The CSF package is also able to exploit spatial symmetry, which like the spin and charge, is implicitly determined by the choice of the reference CSF. The keyword GROUP in $DRT governs the use of spatial symmetry. The CSF program works with Abelian point groups, which are D2h and any of its subgroups. However, $DRT allows the input of some (but not all) higher point groups. For nonAbelian groups, the program automatically assigns the orbitals to an irrep in the highest possible Abelian subgroup. For the other non-Abelian groups, you must at present select GROUP=C1. Note that when you are computing a Hessian matrix, many of the displaced geometries are asymmetric, hence you must choose C1 in $DRT (however, be sure to use the highest symmetry possible in $DATA!). The symmetry of the reference CSF given in your $DRT is one way to determine the symmetry of the CSFs which are generated. As an example, consider a molecule with Cs symmetry, and these two reference CSFs ...MCC...DOC DOC VAL VAL ...MCC...DOC AOS BOS VAL Suppose that the 2nd and 3rd active MOs have symmetries a' and a". Both of these generate singlet wavefunctions, with 4 electrons in 4 active orbitals, but the former constructs 1-A' CSFs, while the latter generates 1-A" CSFs. However, if the 2nd and 3rd orbitals have the same symmetry type, an identical list of CSFs is generated. The alternative is to enter the spatial symmetry with the STSYM keyword. In cases with high point group symmetry, it may be possible to generate correct state degeneracies only by using no symmetry (GROUP=C1) when generating CSFs. As an example, consider the 2-pi ground state of NO. If you use GROUP=C4V, which will be mapped into its highest Abelian subgroup C2v, the two components of the pi state will be

Further Information

4-62

seen as belonging to different irreps, B1 and B2. The only way to ensure that both sets of CSFs are generated is to enforce no symmetry at all, so that CSFs for both components of the pi level are generated. This permits state averaging (WSTATE(1)=0.5,0.5) to preserve cylindrical symmetry. It is however perfectly feasible to use C4v or D4h symmetry in $DRT when treating sigma states. The use of spatial symmetry decreases the number of CSFs, and thus the size of the Hamiltonian that must be computed. In molecules with high symmetry, this may lead to faster run times with the GUGA CSF code, compared to the determinant code.

starting orbitals
The first step is to partition the orbital space into core, active, and external sets, in a manner which is sensible for your chemical problem. This is a bit of an art, and the user is referred to the references quoted at the end of this section. Having decided what MCSCF to perform, you now must consider the more pedantic problem of what orbitals to begin the MCSCF calculation with. You should always start an MCSCF run with orbitals from some other run, by means of GUESS=MOREAD. Do not expect to be able to use HUCKEL! At the start of a MCSCF problem, use orbitals from some appropriate converged SCF run. A realistic example of an MCSCF calculation is examples 8 and 9. Once you get an MCSCF to converge, you can and should use these MCSCF MOs at other nearby geometries (MOREAD will apply an appropriate Schmidt orthogonalization). Starting from SCF orbitals can take a little bit of care. Most of the time (but not always) the orbitals you want to correlate will be the highest occupied orbitals in the SCF. Fairly often, however, the correlating orbitals you wish to use will not be the lowest unoccupied virtuals of the SCF. You will soon become familiar with NORDER=1 in $GUESS, as reordering is needed in 50% or more cases. The occupied and especially the virtual canonical SCF MOs are often spread out over regions of the molecule other than "where the action is". Orbitals which remedy this can generated by two additional options at almost no CPU cost. One way to improve upon the SCF orbitals as starting MOs is to generate valence virtual orbitals (VVOs). These

Further Information

4-63

are constructed by projection of internally stored atomic core and valence orbitals onto the SCF orbitals, so by construction, the resulting virtual orbitals are valence in character. See VVOS in $SCF. An alternative choice, not usually as good, are the modified virtual orbitals. MVOs are obtained by diagonalizing the Fock operator of a very positive ion, within the virtual orbital space only. As implemented in GAMESS, MVOs can be obtained at the end of any RHF, ROHF, or GVB run by setting MVOQ in $SCF nonzero, at the cost of a single SCF cycle. Typically, we use MVOQ=+6. Generating MVOs does not change any of the occupied SCF orbitals of the original neutral, but gives more valence-like LUMOs. Another way to improve SCF starting orbitals is by a partial localization of the occupied orbitals. Typically MCSCF active orbitals are concentrated in the part of the molecule where bonds are breaking, etc. Canonical SCF MOs are normally more spread out. By choosing LOCAL=BOYS along with SYMLOC=.TRUE. in $LOCAL, you can get orbitals which are localized, but still retain orbital symmetry to help speed the MCSCF along. In groups with an inversion center, a SYMLOC Boys localization does not change the orbitals, but you can instead use LOCAL=POP. Localization tends to order the orbitals fairly randomly, so be prepared to reorder them appropriately. Pasting the virtuals from a MVOQ run onto the occupied orbitals of a SYMLOC run (both can be done in the same SCF computation) gives the best possible set of starting orbitals. If you also take the time to design your active space carefully, select the appropriate starting orbitals from this combined $VEC, and inspect your converged results, you will be able to carry out MCSCF computations correctly. Convergence of MCSCF is by no means guaranteed. Poor convergence can invariably be traced back to either a poor initial selection of orbitals, or poor design of the active space. The best advice is, before you even start: "Look at the orbitals." "Then, look at the orbitals again". Later, if you have any trouble: "Look at the orbitals some more". Few people are able to see the orbital shapes in the LCAO matrix in a log file, and so need a visualization program. In particular, you should download a copy of MacMolPlt from http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html

Further Information

4-64

This runs on all popular desktop operating systems, MAC OS X, Linux, and Windows, making it easy to see your orbital shapes. Even if you don't have any trouble, look at the orbitals to see if they converged to what you expected, and have reasonable occupation numbers. It is particularly useful to check the oriented localized MCSCF orbitals (see the discussion of this in the section on localized orbitals in this section for more information). MCSCF is by no means the sort of "black box" that RHF is these days, so please look very carefully at your final results.

miscellaneous hints
It is very helpful to execute a EXETYP=CHECK run before doing any MCSCF or CI run. The CHECK run will tell you the total number of configurations and check the charge and multiplicity and electronic state symmetry, based on your input. The CHECK run also lets the program feel out the memory that will be required to actually do the run. Thus the CHECK run can potentially prevent costly mistakes, or tell you when a calculation is prohibitively large. A very common MCSCF wavefunction has 2 electrons in 2 active MOs. This is the simplest possible wavefunction describing a singlet diradical. While this function can be obtained in an MCSCF run (using NACT=2 NELS=2 or NDOC=1 NVAL=1), it can be obtained much faster by use of the GVB code, with one GVB pair. This GVB-PP(1) wavefunction is also known in the literature as two configuration SCF, or TCSCF. The two configurations of this GVB are equivalent to the three configurations used in this MCSCF, as orbital optimization in natural form (configurations 20 and 02) causes the coefficient of the 11 configuration to vanish. If you are using a large active space (say, 12 or more orbitals), the main bottleneck in the MCSCF calculation is the formation and diagonalization of the Hamiltonian, not the integral transformation and orbital updates. Of course, since determinants are much faster than CSFs, and do not use large disk files, you should use determinants for large active spaces. In this case, you would be wise to switch to FULLNR, which will minimize the total number of iterations, and thus the number of CI calculations. Note that by selecting ITERMX=5 in $DET or $GEN, you can avoid fully converging the CI during each MCSCF iteration, saving a bit of time. Since each iteration's CI

Further Information

4-65

calculation starts with the previous iteration's result, the CI vectors will become fully converged during the MCSCF cycles. The total run time may decrease, although a few additional MCSCF iterations may be required. For small active spaces, where the CI step takes trivial time, you should use a bigger ITERMX to ensure fully converged CI states are generated every iteration. If you choose to use ORMAS, a general determinant CI, or if you select an CSF excitation level IEXCIT smaller than that needed to generate the FORS space, you must use the SOSCF, JACOBI, or FULLNR method as these can optimize active-active rotations. Be sure to set FORS=.FALSE. in $MCSCF when for non-full CI cases, or else very poor convergence will result. Actually, the convergence for incomplete active spaces is likely to be poorer than for full active spaces, anyway. A good way to check the active space is to localize the orbitals, to see if they resemble the atomic orbitals which you imagined formed the bonds, antibonds, and lone pairs in the active space. The ORIENT keyword in $LOCAL will print a density matrix analysis, showing active electron bonding and antibonding patterns (see reference 18/19 below). - - - - The MCSCF technology in GAMESS is the result of some considerable programming effort: The FOCAS, serial FULLNR, and QUAD convergers were adapted from Michel Dupuis' HONDO program. The SOSCF converger was written by Galina Chaban, the parallel FULLNR converger is due to Graham Fletcher, and the JACOBI converger is due to Joe Ivanic. The GUGA CI programs were written by Bernie Brooks and others, while all determinant CI codes (ALDET, GENCI, ORMAS, and FSOCI) stem from Joe Ivanic. Analytic nuclear Hessians were programmed by Tim Dudley. The CSF-based multireference pertubation program was written by Haruyuki Nakano, with a determinant implementation provided by Joe Ivanic. Shiro Koseki and Dmitri Fedorov are responsible for the spinorbit coupling and transition moment codes. The expertise of Klaus Ruedenberg in MCSCF wavefunctions has been the inspiration for many of these developments!

MCSCF references
There are several review articles about MCSCF listed below. Of these, the first two are a nice overview of the subject, the final 3 are more technical.

Further Information 1.

4-66

2a.

2b.

3. 4. 5.

"The Construction and Interpretation of MCSCF wavefunctions" M.W.Schmidt and M.S.Gordon, Ann.Rev.Phys.Chem. 49,233-266(1998) "The Multiconfiguration SCF Method" B.O.Roos, in "Methods in Computational Molecular Physics", edited by G.H.F.Diercksen and S.Wilson D.Reidel Publishing, Dordrecht, Netherlands, 1983, pp 161-187. "The Multiconfiguration SCF Method" B.O.Roos, in "Lecture Notes in Quantum Chemistry", edited by B.O.Roos, Lecture Notes in Chemistry v58, Springer-Verlag, Berlin, 1994, pp 177-254. "Optimization and Characterization of a MCSCF State" J.Olsen, D.L.Yeager, P.Jorgensen Adv.Chem.Phys. 54, 1-176(1983). "Matrix Formulated Direct MCSCF and Multiconfiguration Reference CI Methods" H.-J.Werner, Adv.Chem.Phys. 69, 1-62(1987). "The MCSCF Method" R.Shepard, Adv.Chem.Phys. 69, 63-200(1987).

There is an entire section on the choice of active spaces in Reference 1. As this is a matter of great importance, here are two alternate presentations of the design of active spaces: 6. "The CASSCF Method and its Application in Electronic Structure Calculations" B.O.Roos, in "Advances in Chemical Physics", vol.69, edited by K.P.Lawley, Wiley Interscience, New York, 1987, pp 339-445. 7. "Are Atoms Intrinsic to Molecular Electronic Wavefunctions?" K.Ruedenberg, M.W.Schmidt, M.M.Gilbert, S.T.Elbert Chem.Phys. 71, 41-49, 51-64, 65-78 (1982). Two papers germane to the FOCAS implementation are 8. "An Efficient first-order CASSCF method based on the renormalized Fock-operator technique." U.Meier, V.Staemmler Theor.Chim.Acta 76, 95-111(1989) 9. "Modern tools for including electron correlation in electronic structure studies" M.Dupuis, S.Chen, A.Marquez, in "Relativistic and Electron Correlation Effects in Molecules and Solids", edited by G.L.Malli, Plenum, NY 1994

Further Information The paper germane to the the SOSCF converger is 10. "Approximate second order method for orbital optimization of SCF and MCSCF wavefunctions" G.Chaban, M.W.Schmidt, M.S.Gordon Theor.Chem.Acc. 97: 88-95(1997) Two papers germane to the FULLNR converger, and two discussing implementation details are

4-67

11. "General second order MCSCF theory: A Density Matrix Directed Algorithm" B.H.Lengsfield, III, J.Chem.Phys. 73,382-390(1980). 12. "The use of the Augmented Matrix in MCSCF Theory" D.R.Yarkony, Chem.Phys.Lett. 77,634-635(1981). 13. M.Dupuis, P.Mougenot, J.D.Watts, in "Modern Techniques in Theoretical Chemistry", E.Clementi, editor, ESCOM, Leiden, 1989, chapter 7. 14. "A parallel multi-configuration self-consistent field algorithm" G.D.Fletcher, Mol.Phys. 105, 2971-2976(2007) The paper describing the JACOBI converger is 15. "A MCSCF method for ground and excited states based on full optimizatons of successive Jacobi rotations" J.Ivanic, K.Ruedenberg J.Comput.Chem. 24, 1250-1262(2003) For determinant CI codes, see 16. "Identification of deadwood in configuration spaces through general direct configuration interaction" J.Ivanic, K.Ruedenberg Theoret.Chem.Acc. 106, 339-351(2001) 17. "Direct configuration interaction and multiconfigurational self-consistent-field method for multiple active spaces with variable occupancies. Part I.Method Part II.Applications" J.Ivanic J.Chem.Phys. 119, 9364-9376 and 9377-9385(2003) For CSFs, see 18. "GUGA approach to the electron correlation problem" B.R.Brooks, H.F.Schaefer J.Chem.Phys. 70, 5092-5106(1979)

Further Information Orientation of localized MCSCF active orbitals for bonding analysis: 19. J.Ivanic, G.M.Atchity, K.Ruedenberg Theoret.Chem.Acc. 120, 281-294(2008) 20. J.Ivanic, K.Ruedenberg Theoret.Chem.Acc. 120, 295-305(2008)

4-68

Further Information

4-69

Second Order Perturbation Theory

The perturbation theory techniques available in GAMESS expand to the second order energy correction only, but permit use of nearly any zeroth order SCF wavefunction. Since MP2 theory for systems well described by the chosen zeroth order reference recovers about 80-85% of the dynamical correlation energy (assuming the use of large basis sets), MP2 is often a computationally effective theory. For higher accuracy, you can instead choose the more time consuming coupled cluster theory. When using MPLEVL=2, it is important to ensure that your system is well described at zeroth order by your choice of SCFTYP. The input for second order pertubation calculations based on SCFTYP=RHF, UHF, or ROHF is found in $MP2, while for SCFTYP=MCSCF, see $MRMP. By default, frozen core MP2 calculations are performed.

RHF and UHF reference MP2

These methods are well defined, due to the uniqueness of the Fock matrix definitions. These methods are also well understood, so there is little need to say more, except to point out an overview article on RHF or UHF MP2 gradients: C.M.Aikens, S.P.Webb, R.L.Bell, G.D.Fletcher, M.W.Schmidt, M.S.Gordon Theoret.Chem.Acc. 110, 233-253(2003) The distributed memory parallel MP2 gradient program is described in G.D.Fletcher, M.W.Schmidt, M.S.Gordon Adv.Chem.Phys. 110, 267-294(1999) and that for UMP2 in C.M.Aikens, M.S.Gordon J.Phys.Chem.A 108, 3103-3110(2004) One point which may not be commonly appreciated is that the density matrix for the first order wavefunction for the RHF and UHF case, which is generated during gradient runs or if properties are requested in the $MP2 group, is of the type known as "response density", which differs from the more usual "expectation value density". The eigenvalues of the response density matrix (which are the occupation numbers of the MP2 natural orbitals) can therefore be greater than 2 for frozen core orbitals, or even negative

Further Information

4-70

values for the highest 'virtual' orbitals. The sum is of course exactly the total number of electrons. We have seen values outside the range 0-2 in several cases when the single configuration HF wavefunction is not an appropriate description of the system, and thus these occupancies may serve as a guide to the wisdom of using a HF reference: M.S.Gordon, M.W.Schmidt, G.M.Chaban, K.R.Glaesemann, W.J.Stevens, C.Gonzalez J.Chem.Phys. 110,4199-4207(1999)

high spin ROHF reference MP2

There are a number of open shell perturbation theories described in the literature. It is important to note that these methods give different results for the second order energy correction, reflecting ambiguities in the selection of the zeroth order Hamiltonian and in defining the ROHF Fock matrices. See K.R.Glaesemann, M.W.Schmidt J.Phys.Chem.A 114, 8772-8777(2010) for a figure showing 4 different ROHF-based perturbation theory potentials, which are highly parallel, but have different total energy values. Two of the perturbation theories mentioned below, RMP and ZAPT, are available in GAMESS using SCFTYP=ROHF (see OSPT in $MP2). Nuclear gradients can be obtained for ZAPT. The OPT1 results can be generated using MPLEVL=2 with SCFTYP=MCSCF, using an active space where every orbital is singly occupied with the highest MULT possible (which is single-determinant). One theory is known as RMP, which it should be pointed out, is entirely equivalent to the ROHF-MBPT2 method. The theory is as UHF-like as possible, and can be chosen in GAMESS by selection of OSPT=RMP. The second order energy is defined by 1. P.J.Knowles, J.S.Andrews, R.D.Amos, N.C.Handy, J.A.Pople Chem.Phys.Lett. 186, 130-136(1991) 2. W.J.Lauderdale, J.F.Stanton, J.Gauss, J.D.Watts, R.J.Bartlett Chem.Phys.Lett. 187, 21-28(1991). The submission dates are in inverse order of publication dates, and -both- papers should be cited when using this method. Here we will refer to the method as RMP in keeping with much of the literature. The RMP method diagonalizes the alpha and beta Fock matrices separately, so their occupied-occupied and virtual-virtual blocks are canonicalized. This generates two distinct orbital sets, whose double excitation contributions are processed by the

Further Information

4-71

usual UHF MP2 program, but an additional energy term from single excitations is required. RMP's use of different orbitals for different spins adds to the CPU time required for integral transformations, of course. just like UMP2. RMP is invariant under all of the orbital transformations for which the ROHF itself is invariant. Unlike UMP2, the second order RMP energy does not suffer from spin contamination, since the reference ROHF wave-function has no spin contamination. The RMP wavefunction, however, is spin contaminated at 1st and higher order, and therefore the 3rd and higher order RMP energies are spin contaminated. Other workers have extended the RMP theory to gradients and hessians at second order, and to fourth order in the energy, 3. W.J.Lauderdale, J.F.Stanton, J.Gauss, J.D.Watts, R.J.Bartlett J.Chem.Phys. 97, 6606-6620(1992) 4. J.Gauss, J.F.Stanton, R.J.Bartlett J.Chem.Phys. 97, 7825-7828(1992) 5. D.J.Tozer, J.S.Andrews, R.D.Amos, N.C.Handy Chem.Phys.Lett. 199, 229-236(1992) 6. D.J.Tozer, N.C.Handy, R.D.Amos, J.A.Pople, R.H.Nobes, Y.Xie, H.F.Schaefer Mol.Phys. 79, 777-793(1993) We deliberately omit references to the ROMP precursor of the RMP formalism. RMP gradients are not available. The Z-averaged perturbation theory (ZAPT) formalism for ROHF perturbation theory is the preferred implementation of open shell spin-restricted perturbation theory (OSPT=ZAPT in $MP2). The ZAPT theory has only a single set of orbitals in the MO transformation, and therefore runs in a time similar to the RHF perturbation code. The second order energy is free of spin-contamination, but some spincontamination enters into the first order wavefunction (and hence properties). This should be much less contamination than for OSPT=RMP. For these reasons, OSPT=ZAPT is the default open shell method. References for ZAPT are 7. T.J.Lee, D.Jayatilaka Chem.Phys.Lett. 201, 1-10(1993) 8. T.J.Lee, A.P.Rendell, K.G.Dyall, D.Jayatilaka J.Chem.Phys. 100, 7400-7409(1994) The formulae for the seven terms in the ZAPT energy are clearly summarized in the paper 9. I.M.B.Nielsen, E.T.Seidl J.Comput.Chem. 16, 1301-1313(1995) The ZAPT gradient equations are found in 10. G.D.Fletcher, M.S.Gordon, R.L.Bell Theoret.Chem.Acc. 107, 57-70(2002)

Further Information

4-72

11. C.M.Aikens, G.D.Fletcher, M.W.Schmidt, M.S.Gordon J.Chem.Phys. 124, 014107/1-14(2006) We would like to thank Tim Lee for his gracious assistance in the implementation of the ZAPT energy. There are a number of other open shell theories, with names such as HC, OPT1, OPT2, and IOPT. The literature for these is 12. I.Hubac, P.Carsky Phys.Rev.A 22, 2392-2399(1980) 13. C.Murray, E.R.Davidson Chem.Phys.Lett. 187,451-454(1991) 14. C.Murray, E.R.Davidson Int.J.Quantum Chem. 43, 755-768(1992) 15. P.M.Kozlowski, E.R.Davidson Chem.Phys.Lett. 226, 440-446(1994) 16. C.W.Murray, N.C.Handy J.Chem.Phys. 97, 6509-6516(1992) 17. T.D.Crawford, H.F.Schaefer, T.J.Lee J.Chem.Phys. 105, 1060-1069(1996) The latter two of these give comparisons of the various high spin methods, and the numerical results in ref. 17 are the basis for the conventional wisdom that restricted open shell theory is better convergent with order of the perturbation level than unrestricted theory. Paper 8 has some numerical comparisons of spin-restricted theories as well. We are aware of one paper on low-spin coupled open shell SCF perturbation theory 18. J.S.Andrews, C.W.Murray, N.C.Handy Chem.Phys.Lett. 201, 458-464(1993) but this is not implemented in GAMESS. See the MCSCF reference perturbation code for this case.

GVB based MP2

This is not implemented in GAMESS. Note that the MCSCF perturbation program discussed below should be able to develop the perturbation corrections to open shell singlets, by using a $DRT input such as NMCC=N/2-1 NDOC=0 NAOS=1 NBOS=1 NVAL=0 which generates a single CSF if the two open shells have different symmetry, or for a one pair GVB function NMCC=N/2-1 NDOC=1 NVAL=1 which generates a 3 CSF function entirely equivalent to the two configuration TCSCF, a.k.a GVB-PP(1). For the record, note that if we attempt a triplet state with the MCSCF program, NMCC=N/2-1 NDOC=0 NALP=2 NVAL=0

Further Information

4-73

we get a result equivalent to the OPT1 open shell method described above, not the RMP or ZAPT result. It is possible to generate the orbitals with a simpler SCF computation than the MCSCF $DRT examples just given, and read them into the MCSCF based MP2 program described below, by RDVECS=.TRUE..

MCSCF reference perturbation theory

Just as for the open shell case, there are several ways to define a multireference perturbation theory. The most noteworthy are the CASPT2 method of Roos' group, the MRMP2 method of Hirao, the closely related MCQDPT2 method of Nakano, and the MROPTn methods of Davidson. Although the total energies of each method are different, energy differences should be rather similar. In particular, the MRMP/MCQDPT method implemented in GAMESS gives results for the singlet-triplet splitting of methylene in close agreement to CASPT2, MRMP2(Fav), and MROPT1, and differs by 2 Kcal/mole from MRMP2(Fhs), and the MROPT2 to MROPT4 methods. The MCQDPT method implemented in GAMESS is a multistate perturbation theory due to Nakano. If applied to 1 state, it is the same as the MRMP model of Hirao. When applied to more than one state, it is of the philosophy "perturb first, diagonalize second". This means that perturbations are made to both the diagonal and off-diagonal elements to give an effective Hamiltonian, whose dimension equals the number of states being treated. The effective Hamiltonian is diagonalized to give the second order state energies. Diagonalization after inclusion of the off-diagonal perturbation ensures that avoided crossings of states of the same symmetry are treated correctly. Such an avoided crossing is found in the LiF molecule, as shown in the first of the two papers on the MCQDPT method: H.Nakano, J.Chem.Phys. 99, 7983-7992(1993) H.Nakano, Chem.Phys.Lett. 207, 372-378(1993) The closely related single state "diagonalize, then perturb" MRMP model is discussed by K.Hirao, Chem.Phys.Lett. 190, 374-380(1992) K.Hirao, Chem.Phys.Lett. 196, 397-403(1992) K.Hirao, Int.J.Quant.Chem. S26, 517-526(1992) K.Hirao, Chem.Phys.Lett. 201, 59-66(1993) Computation of reference weights and energy contributions is illustrated by H.Nakano, K.Nakayama, K.Hirao, M.Dupuis J.Chem.Phys. 106, 4912-4917(1997)

Further Information

4-74

T.Hashimoto, H.Nakano, K.Hirao J.Mol.Struct.(THEOCHEM) 451, 25-33(1998) Single state MCQDPT computations are very similar to MRMP computations. A beginning set of references to the other multireference methods used includes: P.M.Kozlowski, E.R.Davidson J.Chem.Phys. 100, 3672-3682(1994) K.G.Dyall J.Chem.Phys. 102, 4909-4918(1995) B.O.Roos, K.Andersson, M.K.Fulscher, P.-A.Malmqvist, L.Serrano-Andres, K.Pierloot, M.Merchan Adv.Chem.Phys. 93, 219-331(1996). and a review article is available comparing these methods, E.R.Davidson, A.A.Jarzecki in "Recent Advances in Multireference Methods" K.Hirao, Ed. World Scientific, 1999, pp 31-63. The CSF (GUGA-based) MRMP/MCQDPT code was written by Haruyuki Nakano, and was interfaced to GAMESS by him in the summer of 1996. This program makes extensive use of disk files during its specialized transformations and the perturbation steps. Its efficiency is improved if you can add extra physical memory to reduce the number of file reads. In practice we have used this program up to about 12 active orbitals, and with very large disks, to about 500 AOs. In 2005, Joe Ivanic programmed a determinant based MRMP/MCQDPT program. This uses the normal integral transformation routines already present in GAMESS, and direct CI technology to avoid disk I/O. The determinant program is able to handle larger active spaces than the CSF program, and has already been used for cases with 16 electrons in 16 orbitals, and basis sets up to 500 AOs. When proper care is taken with numerical cutoffs, such as CI vector convergence and the generator cutoff in the CSF code, both programs produce identical results. Both are enabled for parallel execution. The more mature CSF program has several interesting options not found in the determinant program: perturbative treatment of spin-orbit coupling, energy denominators which are a band-aid for the horribly named "intruder states", and the ability to find the weight of the MCSCF reference in the 1st order wavefunction. Neither program produces a density matrix for property evaluation, nor are analytic gradients programmed. We end with an input example to illustrate open shell and multireference pertubation computations on the ground state of NH2 radical:

Further Information ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! 2nd order perturbation test on NH2, following T.J.Lee, A.P.Rendell, K.G.Dyall, D.Jayatilaka J.Chem.Phys. 100, 7400-7409(1994), Table III. State is 2-B-1, 69 AOs, either 1 or 49 CSFs. For 1 CSF E(ROHF) E(ZAPT) [E(ZAPT) E(RMP) E(OPT1) [E(OPT1) reference, = -55.5836109825 = -55.7763947115 = -55.7763947289 at lit's ZAPT geom] = -55.7772299958 = -55.7830422945 = -55.7830437413 at lit's OPT1 geom]

4-75

For 49 CSF full valence MCSCF reference, CSFs: E(MRMP2) = -55.7857440268 dets: E(MRMP2) = -55.7857440267 $contrl $system $guess $mcscf scftyp=mcscf mplevl=2 runtyp=energy mult=2 $end mwords=1 memddi=1 $end guess=moread norb=69 $end fullnr=.true. $end

! ! ! ! !

Next set of lines carry out a MRMP computation, after a preliminary MCSCF orbital optimization. $det using determinants stsym=B1 ncore=1 nact=6 nels=7 $end

! -----------

using CSFs, for the very same calculation. $mcscf cistep=guga $end $drt group=c2v stsym=B1 fors=.t. nmcc=1 ndoc=3 nalp=1 nval=2 $end $mrmp mrpt=mcqdpt $end $mcqdpt stsym=B1 nmofzc=1 nmodoc=0 nmoact=6 $end lines carry out a single reference OPT1. stsym=B1 ncore=4 nact=1 nels=1 $end mrpt=mcqdpt rdvecs=.true. $end nmofzc=1 nmodoc=3 nmoact=1 stsym=B1 $end

! Next --- $det --- $mrmp --- $mcqdpt

! Next lines are single reference RMP and/or ZAPT --- $contrl scftyp=rohf $end --- $mp2 ospt=rmp $end $data 2-B-1 state...TZ2Pf basis, RMP geom. of Lee, et al. Cnv 2 Nitrogen 7.0

Further Information S 6 1 13520.0 0.000760 2 1999.0 0.006076 3 440.0 0.032847 4 120.9 0.132396 5 38.47 0.393261 6 13.46 0.546339 S 2 1 13.46 0.252036 2 4.993 0.779385 S 1 ; 1 1.569 1.0 S 1 ; 1 0.5800 1.0 S 1 ; 1 0.1923 1.0 P 3 1 35.91 0.040319 2 8.480 0.243602 3 2.706 0.805968 P 1 ; 1 0.9921 1.0 P 1 ; 1 0.3727 1.0 P 1 ; 1 0.1346 1.0 D 1 ; 1 1.654 1.0 D 1 ; 1 0.469 1.0 F 1 ; 1 1.093 1.0 Hydrogen 1.0 0.0 0.7993787 0.6359684 S 3 ! note that this is unscaled 1 33.64 0.025374 2 5.058 0.189684 3 1.147 0.852933 S 1 ; 1 0.3211 1.0 S 1 ; 1 0.1013 1.0 P 1 ; 1 1.407 1.0 P 1 ; 1 0.388 1.0 D 1 ; 1 1.057 1.0 $end OPT1 geom: H 1.0 RMP geom: H 1.0 ZAPT geom: H 1.0 0.0 0.7998834 0.6369401 0.0 0.7993787 0.6359684 0.0 0.7994114 0.6357666

4-76

E(ROHF)= -55.5836109825, E(NUC)= 7.5835449477, 9 ITERS $VEC ...omitted... $END

Further Information

4-77

Coupled-Cluster Theory
The single-reference coupled-cluster (CC) theory, employing the exponential wave function ansatz |Psi0> = exp(T) |Phi> = exp(T1+T2+...) |Phi>, where T1, T2, etc. are the singly excited (1-particle-1hole), doubly excited (2-particle-2-hole), etc. components of the cluster operator T and |Phi> is the singledeterminantal reference state (e.g., the Hartree-Fock determinant), is widely recognized as one of the most accurate methods for describing ground electronic states of atoms and molecules. CC approaches provide the best compromise between relatively low computer costs and high accuracy. They are particularly effective in accounting for the dynamical correlation effects. For example, the CCSD(T) approach, which is a No**2 * Nu**4 (or N**6) procedure in the iterative CCSD steps and a No**3 * Nu**4 (or N**7) procedure in the non-iterative steps related to the calculation of triples (T3) energy corrections, is capable of providing results of the CISDTQ or better quality (CISDTQ is an iterative No**4 * Nu**6 or N**10 procedure) when closed-shell molecules are examined. Here and elsewhere in this section, No and Nu are the numbers of correlated occupied and unoccupied orbitals. Symbol N designates a measure of the system size in the following sense: N=2 means a simultaneous increase of the number of correlated electrons and basis functions by a factor of two. Unlike single- and multi-reference CI methods and some variants of multi-reference perturbation theory, all standard CC methods, such as CCSD or CCSD(T), provide a size extensive description of molecular systems, i.e. no loss of accuracy occurs due to the mere increase of the system size when CC calculations are performed. Thanks to numerous advances in both the formal aspects of CC theory and the development of efficient computer codes, the single-reference CC approaches, such as CCSD and CCSD(T), are nowadays routinely used in calculations for non-degenerate closed- and open-shell electronic ground states of atomic and molecular systems with up to 50 or so correlated electrons and up to 200-300 or so basis functions. The application of the local correlation formalism within the context of CC theory enables one to extend the applicability of the CCSD(T) and similar CC approaches to systems with approximately 100 light atoms

Further Information

4-78

(hundreds of correlated electrons and > 1000 basis functions). Generalizations of CC theory to open-shell, quasi-degenerate, and excited states are possible, via the multi-reference, renormalized, extended, equation-ofmotion, and response CC formalisms, and some of these extensions (for example, the equation-of-motion CC methods for excited states) have become as popular as the multireference CI, multi-reference perturbation theory, or CASSCF methods. We should also add that CC theory is a fundamental many-body formalism, whose applicability ranges from electronic structure of atoms and molecules and nuclear physics to extended systems, phase transitions, condensed matter theory, theories of homogeneous electron gas, and relativistic quantum field theory, to mention a few examples. Examples of applications of quantum chemical CC methods in ab initio calculations for atomic nuclei using modern nucleon-nucleon interactions by Piecuch and co-workers are listed in the reference section below. A number of review articles have been written over the years and it is difficult to cite all of them here. We recommend that users of GAMESS planning to use CC/EOMCC methods read one or more reviews listed below: "Coupled-cluster theory" J. Paldus, in S. Wilson and G.H.F. Diercksen (Eds.), Methods in Computational Molecular Physics, NATO Advanced Study Institute, Series B: Physics, Vol. 293, Plenum, New York, 1992, pp. 99-194. "Applications of post-Hartree-Fock methods: a tutorial." R.J. Bartlett and J.F. Stanton, in K.B. Lipkowitz and D.B.Boyd (Eds.), Reviews in Computational Chemistry, Vol. 5, VCH Publishers, New York, 1994, pp. 65-169. "Coupled-Cluster Theory: Overview of Recent Developments" R.J. Bartlett, in D.R. Yarkony (Ed.), Modern Electronic Structure Theory, Part I, World Scientific, Singapore, 1995, pp. 1047-1131. "Achieving chemical accuracy with coupled-cluster theory" T.J. Lee and G.E. Scuseria, in S.R. Langhoff (Ed.), Quantum Mechanical Electronic Structure Calculations with Chemical Accuracy, Kluwer, Dordrecht, The Netherlands, 1995, pp. 47-108. "Coupled-cluster Theory" J. Gauss, in Encyclopedia of Computational Chemistry, P.v.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H.F. Schaefer III, P.R. Schreiner (Eds.) Wiley, Chichester, U.K., 1998, Vol. 1, pp. 615-636. "A Critical Assessment of Coupled Cluster Method in Quantum Chemistry"

Further Information

4-79

J. Paldus and X. Li, Adv. Chem. Phys. 110, 1-175 (1999), "EOMXCC: A New Coupled-Cluster Method for Electronically Excited States" P. Piecuch and R.J. Bartlett, Adv. Quantum Chem. 34, 295-380 (1999). "An Introduction to Coupled Cluster Theory for Computational Chemists" T.D.Crawford, H.F.Schaefer in K.B. Lipkowitz and D.B.Boyd (Eds.), Reviews in Computational Chemistry, Vol. 14, VCH Publishers, New York, 2000, pp. 33-136. "In Search of the Relationship between Multiple Solutions Characterizing Coupled-Cluster Theories" P. Piecuch and K. Kowalski, in J. Leszczynski (Ed.), Computational Chemistry: Reviews of Current Trends, Vol. 5, World Scientific, Singapore, 2000), pp. 1-104. "Recent Advances in Electronic Structure Theory: Method of Moments of Coupled-Cluster Equations and Renormalized Coupled-Cluster Approaches" P. Piecuch, K. Kowalski, I.S.O. Pimienta, M.J. McGuire, Int. Rev. Phys. Chem. 21, 527-655 (2002). "New Alternatives for Electronic Structure Calculations: Renormalized, Extended, and Generalized Coupled-Cluster Theories" P. Piecuch, I.S.O. Pimienta, P.-F. Fan, and K. Kowalski, in J. Maruani, R. Lefebvre, and E. Brandas (Eds.), Progress in Theoretical Chemistry and Physics, Vol. 12, Advanced Topics in Theoretical Chemical Physics, Kluwer, Dordrecht, 2003, pp. 119-206. "Coupled Cluster Methods" J. Paldus, in Handbook of Molecular Physics and Quantum Chemistry, edited by S. Wilson (Wiley, Chichester, 2003), Vol. 2, pp. 272-313. "Method of Moments of Coupled-Cluster Equations: A New Formalism for Designing Accurate Electronic Structure Methods for Ground and Excited States" P. Piecuch, K. Kowalski, I.S.O. Pimienta, P.-D. Fan, M. Lodriguito, M.J. McGuire, S.A. Kucharski, T. Kus, and M. Musial, Theor. Chem. Acc. 112, 349-393 (2004). "Noniterative Coupled-Cluster Methods for Excited Electronic States" P. Piecuch, M. Wloch, M. Lodriguito, and J.R. Gour, in Progress in Theoretical Chemistry and Physics, Vol. 15, Recent Advances in the Theory of Chemical and Physical Systems," edited by S. Wilson, J.-P. Julien, J. Maruani, E. Brandas, and G. Delgado-Barrio (Springer, Berlin, 2006), pp. XXX-XXXX, in press. "Bridging Quantum Chemistry and Nuclear Structure Theory:

Further Information

4-80

Coupled-Cluster Calculations for Closed- and Open-Shell Nuclei" P. Piecuch, M. Wloch, J.R. Gour, D.J. Dean, M. HjorthJensen, and T. Papenbrock, in V. Zelevinsky (Ed.), Nuclei and Mesoscopic Physics: Workshop on Nuclei and Mesoscopic Physics WNMP 2004, AIP Conference Proceedings, Vol. 777, AIP Press, 2005, pp. 28-45. These reviews point to the other review articles and many original papers. The list of original papers relevant to CC/EOMCC methods implemented in GAMESS is provided below.

available computations (ground states)

The CC programs incorporated in GAMESS enable user to perform conventional LCCD, CCD, CCSD, CCSD[T] (also known as CCSD+T(CCSD)), CCSD(T), and CCSD(TQ) calculations, renormalized (R) and completely renormalized (CR) CCSD[T], CCSD(T), and CCSD(TQ) calculations, and calculations using the rigorously size extensive completely renormalized CRCC(2,3) (or CR-CCSD(T)L) approach for closed-shell RHF references. Performance of the ground-state CC methods has been discussed in a number of places (cf. the review articles mentioned above and references listed at the end of the "Coupled-Cluster Theory" section). Methods such as, for example, CCSD(T), CR-CC(2,3), and CCSD(TQ) provide excellent results for molecules in or near the equilibrium geometries. Almost all CC methods are excellent in describing dynamical correlation, while being relatively inexpensive and easy to use. One must remember, however, that the conventional single-reference CC methods, such as CCSD(T), should not be applied to bond breaking, diradicals, and other quasi-degenerate states, particularly (but not only) when the RHF determinant is used as a reference. In some of the most frequent cases of electronic quasi-degeneracies, including single-bond breaking and diradicals, the CR-CCSD(T), CR-CCSD(TQ), and CR-CC(2,3)= CR-CCSD(T)L methods can be used instead. The recently proposed CR-CC(2,3) approach seems particularly promising in this regard, although the CR-CCSD(T) and CR-CCSD(TQ) approaches are very useful as well. The CR-CC(2,3) method has costs similar to those characterizing the CCSD(T) approach, while providing the results of the very high, full CCSDT, quality for diradicals and single-bond breaking where CCSD(T) fails. At the same time, the accuracy of CRCC(2,3) calculations is comparable to or, sometimes, even better than that obtained with the conventional CCSD(T) approach for closed-shell molecules near the equilibrium

Further Information

4-81

geometries. Just like CCSD(T), the CR-CC(2,3) approximation is rigorously size extensive, while working much better than CCSD(T) when non-dynamical correlation effects become large. CR-CC(2,3) (CCTYP=CR-CCL) is among the most attractive ground-state CC options in GAMESS, providing GAMESS users with the highly accurate energies in the closed-shell, single-bond breaking, and diradical regions of molecular potential energy surfaces, and a number of one-electron properties calculated at the CCSD level at a price of single, relatively inexpensive calculation of the CCSD(T) type. One of the interesting features of GAMESS that can be particularly useful in high accuracy calculations for closed-shell systems is the presence of the (TQ) corrections to CCSD energies among various ground-state CC options. This includes the factorized CCSD(TQ),b method suggested by Kowalski and Piecuch, which describes triples effects at the CCSD(T) level, using noniterative steps that scale as N**7 with the system size, while providing information about the dominant effects due to quadruply excited clusters. The CCSD(TQ),b method is closely related to its CCSD(TQf) predecessor proposed by Kucharski and Bartlett. In fact, if desired, one can extract the CCSD(TQf) energy from the information printed in the GAMESS output when CCTYP=CCSD(TQ) or CR-CC(Q) as follows: CCSD + [R1-CCSD(TQ),A CCSD] * [CCSD(TQ),A DENOMINATOR] (the R1-CCSD(TQ),A method in the GAMESS output represents one of the renormalized CCSD(TQ) approaches, termed RCCSD(TQ)-1,a, which are discussed below). The differences between the CCSD(TQ),b and CCSD(TQf) methods are minimal and the accuracies and costs of both approaches are virtually identical. In particular, both methods use relatively inexpensive noniterative steps that scale as N**6 or N**7 with the system size to determine the quadruples corrections. The unique features of the ground-state CC code in GAMESS are the renormalized (R) and completely renormalized (CR) CCSD[T], CCSD(T), and CCSD(TQ) methods [see K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18-35 (2000), idem., ibid. 113, 5644-5652 (2000), and P. Piecuch and K. Kowalski, in J. Leszczynski (Ed.), Computational Chemistry: Reviews of Current Trends, Vol. 5, World Scientific, Singapore, 2000, pp. 1-104], and the most recent (Fall 2005), rigorously size extensive formulation of CR-CCSD(T), termed CR-CC(2,3) or CR-CCSD(T)L [see P. Piecuch and M.

Further Information

4-82

Wloch, J. Chem. Phys. 123, 224105-1 - 224105-10 (2005) and P. Piecuch, M. Wloch, J.R. Gour, and A. Kinal, Chem. Phys. Lett. 418, 467-474 (2006)]. All of these approaches are based on the more general formalism of the method of moments of coupled-cluster equations (MMCC; biorthogonal MMCC in the case of CR-CC(2,3)), developed by the Piecuch group at Michigan State University. They remove or considerably reduce the pervasive failing of the conventional CCSD[T], CCSD(T), and CCSD(TQ) approximations at larger internuclear separations and for diradical systems, while preserving the ease of use and the relatively low cost of the single-reference methods of the CCSD(T) or CCSD(TQ) type. In analogy to the CCSD[T], CCSD(T), and CCSD(TQ) methods, the R-CCSD[T], R-CCSD(T), RCCSD(TQ)-n,x (n=1,2;x=a,b), CR-CCSD[T], CR-CCSD(T), CRCC(2,3), and CR-CCSD(TQ),x (x=a,b) approaches are based on an idea of improving the CCSD results by adding a posteriori noniterative corrections to CCSD energies. These corrections employ the generalized moments of CCSD equations (projections of the Schroedinger equation for the CCSD wave function on the triply (T) or triply and quadruply (TQ) excited determinants) and are designed by extracting the leading terms that define the theoretical difference between the CCSD and full CI energies. The CRCCSD[T], CR-CCSD(T), and CR-CC(2,3) approaches are capable of eliminating the unphysical humps on the potential energy surfaces involving single bond breaking produced by the conventional CCSD[T] and CCSD(T) methods. They also significantly improve the poor description of diradical species (for example, diradical transition states and intermediates) by the CCSD[T] and CCSD(T) methods. What is important in practical applications, the CR-CCSD(T) and CRCC(2,3) approaches are capable of providing a good balance between the dynamical and nondynamical correlation effects when the diradical and closed-shell structures have to be examined together. The rigorously size extensive CR-CC(2,3) method is particularly effective in this regard, although the older and somewhat less expensive CR-CCSD(T) approach is very useful as well. The R-CCSD[T] and R-CCSD(T) approaches may improve the CCSD[T] and CCSD(T) results at intermediate internuclear separations, but they usually fail at larger distances. The CR-CCSD[T], CR-CCSD(T), and CR-CC(2,3) methods are better in this regard, since they often provide a very good description of single bond breaking at all internuclear separations. This includes various cases of unimolecular dissociations and exchange and bond insertion chemical reactions, in which single bonds break and form. We DO NOT recommend applying the CRCCSD[T], CR-CCSD(T), and CR-CC(2,3) approaches to multiple

Further Information

4-83

bond breaking, although some types of multiple bond stretching can be described by these methods very well if the relevant stretches of chemical bonds are not too large. In general, however, multiple bond dissociations require using the higher-order methods, such as the completely renormalized CCSD(TQ) and CCSDT(Q) approaches (the CRCCSD(TQ) methods are available in GAMESS), the so-called MMCC(2,6) method, and the more recent generalized and quadratic MMCC methods, if the single-reference approach is preferred, or the multi-reference CC methods of the stateuniversal and state-specific type (some of the most promising approaches in these categories, including activespace and state-universal CC methods, will be included in GAMESS in the future). In particular, the CR-CCSD(TQ) approaches available in GAMESS are reasonably accurate in situations involving double bond dissociations and a simultaneous stretching or breaking of two single bonds. They may work reasonably well even when the triple bond stretching or breaking is examined, but the results for more complicated cases of bond breaking are not as good as those that one can obtain with the best multi-reference approaches. A detailed description of the R-CCSD[T], RCCSD(T), CR-CCSD[T], CR-CCSD(T), CR-CC(2,3), R-CCSD(TQ), and CR-CCSD(TQ) approaches and other MMCC methods can be found in several papers by Piecuch and coworkers listed at the very end of the "Coupled-Cluster Theory" section. Unlike the newest CR-CC(2,3) approximation, the somewhat older R-CCSD[T], R-CCSD(T), CR-CCSD[T], CR-CCSD(T), RCCSD(TQ), and CR-CCSD(TQ) methods are not strictly size extensive, i.e. there are unlinked terms in the MBPT (manybody perturbation theory) expansions of the renormalized and completely renormalized [T], (T), and (TQ) corrections to CCSD energies. This has little or no effect on bond breaking (on the contrary, the CR-CCSD[T], CR-CCSD(T), and CR-CCSD(TQ) potential surfaces are MUCH better than potential energy surfaces obtained in the standard and size extensive CCSD[T], CCSD(T), and CCSD(TQ) calculations), but lack of strict size extensivity may have an effect on the results of calculations for larger and extended systems. A lot depends on the values of T2 amplitudes and the chemical problem of interest. If the T2 amplitudes are small, then the overlap denominator expressions which define the renormalized [T], (T), and (TQ) corrections of the RCCSD[T], R-CCSD(T), CR-CCSD[T], CR-CCSD(T), R-CCSD(TQ), and CR-CCSD(TQ) methods are close to 1, in which case there is no major problem. If the T2 amplitudes are large, then these denominators may become significantly greater than 1. This behavior of the R-CCSD[T], R-CCSD(T), CR-CCSD[T], CR-

Further Information

4-84

CCSD(T), R-CCSD(TQ), and CR-CCSD(TQ) denominator expressions is extremely useful for improving the results for bond breaking, since the denominators defining the renormalized [T], (T), and (TQ) corrections damp the unphysical values of the standard [T], (T), and (TQ) corrections at larger internuclear separations or when the wave function gains a significant multi-reference character. The same applies to diradical species, where the standard [T], (T), and (TQ) corrections produce unphysical results and need damping that the renormalized methods provide. However, for larger many-electron systems (with 50 correlated electrons or more), the denominators defining the renormalized [T], (T), and (TQ) corrections may "overdamp" the [T], (T), and (TQ) energy corrections. On the other hand, the renormalized [T], (T), and (TQ) energy corrections are constructed using the cluster amplitudes resulting from the size extensive CCSD calculations. Moreover, it is often the case that the number of correlated electrons used in CC calculations for larger molecules (and only these electrons are used in constructing the renormalized [T], (T), and (TQ) corrections to CCSD energies) is much smaller than the total number of electrons. Thus, the consequences of the lack of strict size extensivity of the R-CCSD[T], RCCSD(T), CR-CCSD[T], CR-CCSD(T), R-CCSD(TQ), and CRCCSD(TQ) methods do not have to be serious for larger systems, particularly when one examines, for example, the relative energies of stationary points along the reaction pathways relative to the relevant reactants (see comments below). A number of interesting chemical problems involving smaller and medium size polyatomic diradical systems, including, for example, the Cope rearrangement of 1,5-hexadiene, the cycloaddition of cyclopentyne to ethylene, the isomerizations of bicyclopentene and tricyclopentane into cyclopentadiene, the thermal stereomutations of cyclopropane, and the relative energetics of dicopper systems relevant to molecular oxygen activation by copper metalloenzymes, where the standard CCSD(T) approach and, in some cases, the low-order multireference perturbation theory methods encounter serious difficulties, have been successfully examined with the CRCCSD(T) approach, demonstrating that problems of size extensivity in CR-CCSD(T) calculations are of no major significance in molecules of these sizes. But one may have to be more careful when chemical systems have more than 50 correlated electrons. Extensive numerical tests indicate that lack of strict size extensivity has little (fraction of a millihartree or so) effect on the results of the CRCCSD[T], CR-CCSD(T), and CR-CCSD(TQ) calculations for

Further Information

4-85

smaller systems. For larger systems, such as the glycine dimer described by the 6-31G basis set, the departure from rigorous size extensivity, as measured by forming the difference of the sum of the energies of isolated glycine molecules from the energy of the dimer consisting of glycine molecules at very large (200 bohr) distance, is ca. 3 millihartree (2 kcal/mol). The violation of strict size extensivity by the CR-CCSD(T) methods has been estimated at approximately 0.5 % of the total correlation energy (changes in the correlation energy if the relative energies along reaction pathways are examined), which is often a small price to pay considering the significant improvements that the renormalized CC methods offer for potential energy surfaces and diradicals and the ease with which the CR-CC calculations can be performed. IMPORTANT PRACTICAL ADVICE: In studies of reaction pathways with the CR-CCSD(T) approach, where reactants and products are connected by one or more transition states and intermediates and where there are two or more reactants, we STRONGLY RECOMMEND that the user of CR-CCSD(T) proceeds in a manner similar to multireference CI calculations. Thus, we advise to calculate the energies of transition states, intermediates, and products relative to reactants, using the total CR-CCSD(T) energy of a noninteracting complex formed by reactants (reactants separated by a large distance, say, 200 Angs.) as the reference energy of reactants rather than the sum of the CR-CCSD(T) energies of isolated reactants. This reduces the possible size extensivity errors in the CR-CCSD(T) calculations for larger systems to a minimum, since all species along a reaction pathway (including reactants, transition states, intermediates, and products) are treated then in the same, well balanced, manner. Similar remarks apply to the CR-CCSD(TQ) (and all R-CC) calculations. None of the above has to be done when the CR-CC(2,3) approach is employed, since CR-CC(2,3) is size extensive and the CRCC(2,3) energy of A+B equals the sum of CR-CC(2,3) energies of A and B. The rigorously size extensive modifications of the CRCC methods have recently (2005) been developed, using the idea of locally renormalized methods, such as LR-CCSD(T), which lead to size extensive results when localized orbitals are employed, and, in an alternative formulation, the idea of exploiting the left CC states combined with the so-called biorthogonal MMCC theory. The latter development seems particularly attractive. The resulting CR-CC(2,3) method, also called CR-CCSD(T)L, which combines the best features of CCSD(T) and CR-CCSD(T) and which we already mentioned above, satisfies the following criteria: (i) is

Further Information

4-86

at least as accurate as (sometimes more accurate than) CCSD(T) for nondegenerate ground states, (ii) provides highly accurate results for single-bond breaking and diradicals with the noniterative No**3 * Nu**4 steps similar to those of CCSD(T) and CR-CCSD(T),(iii) is more accurate than the CR-CCSD(T), LR-CCSD(T), and other noniterative triples CC approaches, such as CCSD(2)T, which all aim at eliminating the failures of CCSD(T) in the diradical/bond breaking regions, and (iv) is rigorously size extensive without localizing orbitals. The criterion (ii) of a highly accurate description at the triples level of CC theory is defined here by the accuracy provided by the full CCSDT approach, which is almost exact in studies of diradicals and single-bond breaking, but also limited to very small systems with up to 2-3 light atoms due to very expensive iterative No**3 * Nu**5 steps that it uses. As demonstrated, for example, in recent studies of the relative energetics of the Cu2O2 systems with up to six ammonia ligands and thermal stereomutations of cyclopropane involving the trimethylene diradical as a transition state, CR-CC(2,3) has a wide range of applicability that includes larger polyatomic systems with up to 10-20 light and a few transition metal atoms. At the same time, CR-CC(2,3) provides a size extensive, highly accurate, and well balanced description of dynamical and nondynamical correlation effects in studies of single bond breaking and diradicals, particularly when the molecular systems involving a varying degree of diradical character along the relevant reaction pathways are examined. For all these reasons, the CR-CC(2,3) approach has been recently included in GAMESS. The CR-CC(2,3) method (invoked by typing CCTYP=CR-CCL in the input) seems to represent the most accurate non-iterative triples CC approximation formulated to date. Since the construction of the triples corrections to CCSD energies in CR-CC(2,3) calculations requires the determination of the left CCSD eigenstates, the CCPRP variable from $CCINP is automatically set at .TRUE. when variable CCTYP in $CONTRL is set at CR-CCL. As a result, by running the CR-CC(2,3) calculations, the user of GAMESS obtains a great deal of useful information in addition to excellent energetics (excellent as long as multiple bonds are not broken). This information includes the first-order reduced density matrices (printed in the PUNCH file), natural occupation numbers, and a variety of one-electron properties (e.g., electrostatic multipole moments) calculated at the CCSD level of theory. The ground-state CR-EOMCCSD(T) energies (cf. the next

Further Information subsection), corresponding to CCTYP=CR-EOM calculations with NSTATE(1)=0,0,0,0,0,0,0,0, are printed as well.

4-87

The CR-CC(2,3) approach has several variants, labeled with an additional letter, A-D (D means a full treatment of the perturbative denominators that are used to define triple excitation components, based on the diagonal matrix elements of the triples-triples block of the CCSD similarity transformed Hamiltonian; A means the crudest treatment of these denominators through bare orbital energies). Of all printed CR-CC(2,3) energies, the CRCC(2,3),D value, which corresponds to the most complete variant of CR-CC(2,3), is the most accurate one and we STRONGLY RECOMMEND to use it in high accuracy calculations of molecular energetics. Because of the way the CRCC(2,3),D approach is presently implemented in GAMESS, it is safer, for now, to use the simplified CR-CC(2,3),A or CR-CC(2,3),B models in numerical derivative calculations if there are orbital degeneracies (the aforementioned CCSD(2)T approach is equivalent to the CR-CC(2,3),A approximation). Because of some small simplifications in the present computer implementation of the CR-CC(2,3),D method, the CRCC(2,3),D energies may slightly depend on the choice of molecular coordinate system if there are orbital degeneracies. Although changes in the most accurate CRCC(2,3),D energies for systems with orbital degeneracies due to changes of the coordinate system are minimal (0.1 millihartree or less), it is safer to calculate numerical CR-CC(2,3) derivatives for systems with orbital degeneracies using the CR-CC(2,3),A or CR-CC(2,3),B approximations. For this reason, the CR-CC(2,3),A energy is automatically passed to the numerical derivative calculations with GAMESS if they are requested by the user, with the most complete CR-CC(2,3),D approach providing the most accurate energetics. We should emphasize, however, that the above technical issues are only limited to systems with orbital degeneracies. When there are no orbital degeneracies (which is the case when the highest molecular symmetry group is an Abelian group), the present implementation of the CR-CC(2,3),D approach in GAMESS leads to perfectly invariant energies. The issue of a slight (0.1 millihartree or less) dependence of the CR-CC(2,3),D (also CR-CC(2,3),C) energies on the choice of molecular coordinate system when orbital degeneracies are present is only temporary and will be eliminated in the future releases of GAMESS via a suitable modification of the CRCC(2,3) code.

Further Information

4-88

Since CR-CC methods can find use in applications involving bond breaking and reaction pathways, one has to make sure that the underlying solution of the CCSD equations, on which the completely renormalized [T], (T), (2,3), and (TQ) corrections are based, represents the same physical solution as those defining other regions of a given molecular potential energy surface. This remark is quite important, since, for example, diradical regions of potential energy surface are characterized by larger cluster amplitudes and one has to make sure that the properly converged values of these amplitudes are obtained. GAMESS is equipped with a good algorithm for converging CCSD equations and a restart option discussed in a later part of this document that facilitate converging larger cluster amplitudes in difficult cases. The user is encouraged to examine various interesting elements of the CC input and output. In addition to CC energies, GAMESS prints the largest T1 and T2 cluster amplitudes obtained in the CCSD calculations, the T1 diagnostic, norms of T1 and T2 vectors, and the R-CCSD[T], R-CCSD(T), and R-CCSD(TQ) denominators that define the renormalized and completely renormalized triples and quadruples corrections. For example, bond breaking and diradical cases are characterized by larger cluster amplitudes (particularly, T2) and a significant increase in the values of the R-CCSD[T], R-CCSD(T), and CR-CCSD(TQ) denominators, which damp unphysical triples and quadruples corrections of the standard CCSD[T], CCSD(T), and CCSD(TQ) approximations, compared to closed-shell regions of potential energy surface. As already mentioned, the CRCC(2,3) calculations provide user with one-particle reduced density matrices, natural occupation numbers, and a number of one-electron properties, calculated at the CCSD level, in addition to the highly accurate CR-CC(2,3) and some other CR-CC energies.

available computations (excited states)

The equation of motion coupled cluster (EOMCC) method and the closely related response CC and symmetry-adapted cluster configuration interaction (SAC-CI) approaches provide very useful extensions of the ground-state CC theory to excited states. In the EOMCC theory, the excited states |PsiK> are obtained by applying the excitation operator R = R0 + R1 + R2 + ...,

Further Information

4-89

where R0, R1, R2, etc. are the reference, singly excited (1-particle-1-hole), doubly excited (2-particle-2-hole), etc. components of R, to the CC ground state |Psi0>. Thus, the EOMCC expression for the excited state |PsiK> is |PsiK> = R |Psi0> = R exp(T) |Phi> = (R0+R1+R2+...) exp(T1+T2+...) |Phi> . In practice, the standard EOMCC calculations are performed by diagonalizing the CC similarity transformed Hamiltonian H-bar = exp(-T) H exp(T) in the space of excited determinants included in the cluster operator T and the excitation operator R. For example, the basic EOMCCSD calculations defined by the truncation schemes T=T1+T2 and R=R0+R1+R2 are performed by diagonalizing exp(-T1-T2) H exp(T1+T2) in the space of singly and doubly excited determinants defining the CCSD (T=T1+T2) approximation. The direct result of such diagonalization are the vertical excitation energies omegaK = EK - E0 (EK and E0 and the excited- and ground- state energies, respectively). The EOMCC methods have several advantages. The most expensive steps of the basic EOMCCSD calculations scale only as No**2 * Nu**4 and yet the accuracy of the EOMCCSD results for excited states dominated by one-electron transitions (single excitations or singles or 1-particle-1hole excitations) is very good. The errors in the EOMCCSD calculations for such states are often on the order of 0.10.3 eV, which is acceptable in many applications. The EOMCCSD approximation and other standard EOMCC methods have an ease of application that is not matched by the multireference techniques, since formally the EOMCC theory is a single-reference formalism. Thus, the EOMCC methods are particularly well suited for calculations where active orbital spaces required in CASSCF-related calculations become very large or difficult to identify. Given sufficient computational resources, the EOMCCSD calculations for systems involving up to 10-20 light or a few heavy atoms are nowadays (meaning year 2004 and on) routine. The EOMCCSD method works reasonably well for excited states dominated by singles, but it fails to describe states dominated by two-electron transitions (doubles) and potential energy surfaces along bond breaking coordinates. These failures can be remedied by the CREOMCCSD(T) approximations described below. The EOMCC programs incorporated in GAMESS enable user to perform standard EOMCCSD calculations employing the RHF

Further Information

4-90

reference determinant. They also enable to improve the EOMCCSD results by adding the state-selective noniterative corrections due to triples to the ground and excited-state CCSD/EOMCCSD energies via the completely renormalized EOMCCSD(T) (CR-EOMCCSD(T)) approaches developed by the Piecuch group. The CR-EOMCCSD(T) approaches represent extensions of the ground-state CR-CCSD(T) method to excited states. In particular, in analogy to the CR-CCSD(T) approximation, the excited-state CR-EOMCCSD(T) approaches are based on the formalism of the method of moments of coupled-cluster equations (MMCC). Moreover, the CREOMCCSD(T) methods preserve the relatively low computer costs and ease of use of the ground-state CCSD(T) calculations. The most expensive noniterative steps of the CR-EOMCCSD(T) approach scale as No**3 * Nu**4. The CREOMCCSD(T) option (CCTYP=CR-EOM) is a unique feature of GAMESS. At this time, the applicability of the EOMCCSD and CR-EOMCCSD(T) codes in GAMESS is limited to singlet states. The main advantage of the MMCC-based CR-EOMCCSD(T) approximations, in addition to their "black-box" character and relatively low computer costs, is their high (0.1 eV or so) accuracy in the calculations of excited states dominated by double excitations and excited-state potential energy surfaces along bond breaking coordinates, for which the standard EOMCCSD method fails (producing errors on the order of 1 eV or even bigger). In this regard, the CREOMCCSD(T) methods are quite similar to the CR-CCSD(T) approach, which is capable of describing ground-state potential energy surfaces involving single bond breaking. As a matter of fact, when limited to the ground-state problem, the CR-EOMCCSD(T) approximations become essentially identical to the CR-CCSD(T) method. There are, however, small differences and the CR-EOMCCSD(T) energies of the ground state are slightly different than the CRCCSD(T) energies discussed in the earlier section. This is due to the fact that the original CR-CCSD(T) approximation has been designed for the ground states only, whereas the CR-EOMCCSD(T) approaches apply to ground and excited states and this required small modifications in the ground-state energy equations. A few different variants of the CR-EOMCCSD(T) method, termed the CR-EOMCCSD(T),IX, CR-EOMCCSD(T),IIX, and CREOMCCSD(T),III approaches (X=A,B,C,D) have been proposed and included in GAMESS. Types I, II, and III refer to three different ways of defining the approximate wave functions |PsiK> that are used to construct the CREOMCCSD(T) triples corrections to EOMCCSD energies in the

Further Information

4-91

underlying MMCC formalism. Types I and II use perturbative expressions for |PsiK> in terms of cluster components T1 and T2 and excitation components R0, R1, and R2. Type III uses additional CISD (CI singles and doubles) calculations in designing the wave functions |PsiK> that enter the CREOMCCSD(T) triples corrections. Thus, user should be aware of the fact that CR-EOMCCSD(T),III calculations involve the single-reference CISD calculations, in addition to the CCSD, EOMCCSD, and (T) steps common to all CR-EOMCCSD(T) methods. This increases the CPU timings of the CREOMCCSD(T),III calculations, when compared to CREOMCCSD(T),IX and CR-EOMCCSD(T),IIX (X=A-D) approaches. Additional letters A-D that label the CR-EOMCCSD(T),I and CR-EOMCCSD(T),II approximations refer to different ways of treating perturbative denominators in evaluating the (T) triples corrections (D means full treatment of these denominators, based on the diagonal matrix elements of the triples-triples block of the CCSD similarity transformed Hamiltonian, A means the crudest treatment through bare orbital energies). The user interested in further details is referred to a 2004 paper by Kowalski and Piecuch (J. Chem. Phys. 120, 1715-1738 (2004)). Our experience to date indicates that the CREOMCCSD(T),ID and CR-EOMCCSD(T),III methods are the most accurate ones when it comes to the calculations of excited states dominated by double excitations and excited-state potential energy surfaces along bond breaking coordinates, at least for moderate bond stretches. The CR-EOMCCSD(T),ID and CR-EOMCCSD(T),III methods are particularly good when examining the total energies of excited states (for example, as functions of nuclear geometries). If the user is only interested in vertical excitation energies rather than total energies, the good balance between ground and excited states, particularly when excited states are dominated by doubles, can be achieved by considering mixed approximations, such as CR-EOMCCSD(T),ID/IB. The ID/IB acronym means that the excitation energy is obtained by subtracting the CR-EOMCCSD(T),IB ground-state energy from the CR-EOMCCSD(T),ID energy of excited state. Other mixed approaches (IID/IB, etc.) are obtained in a similar way. The ID/IB results are particularly good when the excited states have significant doubly excited character. The fact that the CR-EOMCCSD(T),ID results for excited states are usually better than the CR-EOMCCSD(T),IA,IB,IC results is related to a better treatment of perturbative denominators in evaluating the (T) triples corrections in the CREOMCCSD(T),ID approximation.

Further Information

4-92

In addition to the total CR-EOMCCSD(T),IX, CREOMCCSD(T),IIX (X=A-D), and CR-EOMCCSD(T),III energies and vertical excitation energies based on the idea of mixing different approximations for excited and ground states (the ID/IA, IID/IA, ID/IB, and IID/IB excitation energies), GAMESS prints the so-called DELTA-CR-EOMCCSD(T) values (the del(IA), del(IB), del(IC), del(ID), del(IIA), del(IIB), del(IIC), del(IID), and del(III) energies). These are the vertical excitation energies obtained by directly correcting the EOMCCSD excitation energies rather than the total CCSD/EOMCCSD energies by triples corrections. For example, del(ID) refers to the vertical excitation energy obtained by subtracting the CCSD ground-state energy from the excited-state CR-EOMCCSD(T),ID energy. The DELTA-CREOMCCSD(T) values may be somewhat worse than the pure CREOMCCSD(T) (e.g., CR-EOMCCSD(T),ID) or CR-EOMCCSD(T),III) or mixed CR-EOMCCSD(T) (e.g., CR-EOMCCSD(T),ID/IB)) values of vertical excitation energies for states dominated by doubles, but they may provide a reasonable balance between ground and excited states and somewhat bigger improvements for vertical excitation energies corresponding to states dominated by singles. The DELTA-CR-EOMCCSD(T) methods provide a reasonably good balance between improvements in the results for excited states dominated by singles and improvements in the results for excited states dominated by doubles, but one should treat this remark with caution. In addition to the above CR-EOMCCSD(T) results, GAMESS also prints the so-called (T)/R excitation energies. These are the analogs of the EOMCCSD(T~) excitation energies proposed by Watts and Bartlett, obtained by using the right eigenvectors of the CCSD similarity transformed and righthand moments of EOMCCSD equations rather than the left eigenstates of EOMCCSD and left-hand analogs of the EOMCCSD moments (see K. Kowalski and P. Piecuch, J. Chem. Phys. 120, 1715-1738 (2004) for details). Just like the EOMCCSD(T~) method of Watts and Bartlett, the (T)/R approach is based on the idea of directly correcting the EOMCCSD vertical excitation energies by triples. In analogy to the EOMCCSD(T~) method, the (T)/R corrections improve the EOMCCSD results for states dominated by singles, but they may fail to produce reasonable results for states dominated by doubles and for excited-state potential energy surfaces along bond breaking coordinates. The CR-EOMCCSD(T) methods are considerably more robust in this regard. In performing the CR-EOMCCSD(T) calculations, user should realize that the EOMCCSD method can provide a wrong

Further Information

4-93

state ordering if low-lying doubly excited states are mixed up with singly excited states in the electronic spectrum. This may require calculating a larger number of EOMCCSD states before correcting them for triples. An example of this situation has been described in K. Kowalski and P. Piecuch, J. Chem. Phys. 120, 1715-1738 (2004). The EOMCCSD method provides an incorrect ordering of the singlet A1 states of ozone, so that one must use the third excited EOMCCSD state of the singlet A1 (1A1) symmetry (the fourth 1A1 state total, using the CCSD/EOMCCSD energy ordering of ground and excited states) to calculate the noniterative CR-EOMCCSD(T) triples correction that describes the first excited singlet A1 (the second 1A1) state. Without calculating several states of each symmetry at the EOMCCSD level prior to CR-EOMCCSD(T) calculations, one would risk losing information about some important lowlying doubly excited states. Because of the inherent limitations of the EOMCCSD approximation, complicated doubly excited states resulting from the EOMCCSD calculations may be shifted to high energies, mixing with the singly excited states that are accurately described by the EOMCCSD method. After correcting the EOMCCSD energies for the effect of triples, these doubly excited states may become low-lying states. This is exactly what we observe in the case of ozone and other cases of severe quasidegeneracies. The issues of size extensivity in the EOMCCSD and CREOMCCSD(T) calculations are highly complex and much beyond the scope of this writing. Briefly, none of the EOMCC methods are rigorously size extensive and yet all EOMCC methods are very useful in great many applications. The EOMCCSD approach is size intensive for excited states dominated by singles and the EOMCCSD energies correctly separate when the one-electron charge-transfer excitations are considered. Thus, the EOMCCSD approach correctly describes the dissociation of a singly excited system (AB)* into the A* + B, A + B*, (A+) + (B-), and (A-) + (B+) fragments (* designates a one-electron excitation). We must remember, however, that the above separability properties of the EOMCCSD energies are no longer true if the reference determinant |Phi> does not separate correctly (for example, the RHF determinant does not correctly separate if the AB -> A+B fragmentation involves the dissociation of the closed-shell system AB into open-shell fragments A and B). As in the case of the ground-state CR-CCSD(T) approach, the CR-EOMCCSD(T) methods slightly violate the rigorous size extensivity/intensivity (at the level of 1-2 millihartree for systems with up to 30-50 correlated electrons), but at

Further Information

4-94

the same time the CR-EOMCCSD(T) approaches significantly improve a poor description of excited states with significant double excitation components by the EOMCCSD method. As a result, lack of strict size extensivity of the CR-EOMCCSD(T) theories is of relatively minor significance in applications for systems with up to at least 50 correlated electrons [see M. Wloch, J.R. Gour, K. Kowalski, and P. Piecuch, J. Chem. Phys. 122, 214107-1 - 214107-15 (2005) for a thorough discussion of the complicated extensivity issues in EOMCCSD and CR-EOMCCSD(T) calculations]. The user is encouraged to examine various interesting elements of the EOMCC input and output. In addition to EOMCC energies, GAMESS prints the largest R1 and R2 excitation amplitudes and the so-called reduced excitation level (REL) diagnostic, which provides information about the character of a given excited state (REL close to 1 means singly excited, REL close to 2 means doubly excited). GAMESS also prints the R0 value (the coefficient at the reference in the EOMCCSD wave function). If a molecule has symmetry and R0 equals 0, user immediately learns the excited state has a different symmetry than the ground state. GAMESS provides full information about irreps of the calculated excited states.

density matrices and properties

One of the major advantages of EOMCC methods, including EOMCCSD, is a relatively straightforward access to reduced density matrices and molecular properties that these methods offer. This is done by considering the left eigenstates of the similarity transformed Hamiltonian H-bar = exp(-T) H exp(T) mentioned in the earlier sections. The similarity transformed Hamiltonian H-bar is not hermitian, so that, in addition to the right eigenstates R|Phi>, which define the "ket" CC or EOMCC wave functions discussed in the previous section, we can also define the left eigenstates of H-bar, <Phi|L, which determine the "bra" CC or EOMCC wave functions, <PsiK| = <Phi| L exp(-T) = <Phi|(L0+L1+L2+...)exp(-T1-T2-...), where L0=1 for the ground state and 0 for excited states and where L1, L2, etc. are the one-body, two-body, etc. deexcitation operators, respectively. In the ground-state case, we often write

Further Information <Psi0| = <Phi|(1+Lambda) exp(-T) = <Phi|(1+Lambda1+Lambda2+...)exp(-T1-T2-...),

4-95

where Lambda1, Lambda2, etc. are the one-body, two-body, etc. components of the deexcitation Lambda operator of the analytic gradient CC theory. The left eigenstates of H-bar, <Phi|L, and the right eigenstates R|Phi> form a biorthonormal set. We can use these eigenstates to calculate expectation values and transition matrix elements of quantum-mechanical operators (observables), involving the CC and EOMCC ground and excited states, as follows: <PsiK| W |PsiM> = <Phi|L(K) W-bar R(M) |Phi>, where W-bar = exp(-T) W exp(T) is a similarity transformed form of the observable W we are interested in and where we added labels K and M to operators L and R to indicate the CC/EOMCC electronic states they are associated with. The operator W could be, for example, a dipole or quadrupole moment. It could also be a product of creation and annihilation operators, which we could use to calculate the reduced density matrices. For example, if the operator W = (ap-dagger) aq, where ap-dagger and aq are the creation and annihilation operators associated with the spinorbitals p and q, respectively, we can calculate the CC or EOMCC one-body reduced density matrix in the electronic state K, Gamma(qp,K), as Gamma(qp,K) = <Phi|L(K) {exp(-T)[(ap-dagger)aq]exp(T)} R(K) |Phi>. For the corresponding transition density matrix involving two different states K and M, say ground and excited states or some other combination, we can write Gamma(qp,KM) = <Phi|L(K) {exp(-T)[(ap-dagger)aq]exp(T)} R(M) |Phi>. By having access to reduced density matrices, we can calculate various properties analytically. For example, by calculating the one-body reduced density matrices of ground and excited states and the corresponding transition density matrices, we can determine all one-electron properties and the corresponding transition matrix elements involving oneelectron properties using a single mathematical expression: <PsiK| W |PsiM> = Sum_pq <p|w|q> Gamma(qp,KM),

Further Information

4-96

where <p|w|q> are matrix elements of the one-body property operator W in a basis set of molecular spin-orbitals used in the calculations. The calculation of reduced density matrices provides the most convenient way of calculating CC and EOMCC properties of ground and excited states. In addition, by having reduced density matrices, one can calculate CC and EOMCC electron densities, rhoK(x) = Sum_pq Gamma(qp,K) (phi_q(x))* phi_p(x), where phi_p(x) and phi_q(x) are molecular spin-orbitals and x represents the electronic (spatial and spin) coordinates. By diagonalizing Gamma(qp,K), one can determine the natural occupation numbers and natural orbitals for the CC or EOMCC state |PsiK>. The above strategy of handling molecular properties analytically by determining one-body reduced density matrices was implemented in the CC/EOMCC programs incorporated in GAMESS. At this time, the calculations of reduced density matrices and selected properties are possible at the CCSD (ground states) and EOMCCSD (ground and excited states) levels of theory (T=T1+T2, R=R1+R2, L=L0+L1+L2). Currently, in the main output the program prints the CCSD and EOMCCSD electric multipole (dipole, quadrupole, etc.) moments and several other one-electron properties that one can extract from the CCSD/EOMCCSD density matrices, the EOMCCSD transition dipole moments and the corresponding dipole and oscillator strengths, and the natural occupation numbers characterizing the CCSD/EOMCCSD wave functions. In addition, the complete CCSD/EOMCCSD onebody reduced density matrices and transition density matrices in the RHF molecular orbital basis and the CCSD and EOMCCSD natural orbital occupation numbers are printed in the PUNCH output file. The eigenvalues of the density matrix (natural occupation numbers) are ordered such that the corresponding eigenvectors (CCSD or EOMCCSD natural orbitals) have the largest overlaps with the consecutive ground-state RHF MOs. Thus, the first eigenvalue of the density matrix corresponds to the CCSD or EOMCCSD natural orbital that has the largest overlap with the RHF MO 1, the second with RHF MO 2, etc. This ordering is particularly useful for analyzing excited states, since in this way one can easily recognize orbital excitations that define a given excited state. One has to keep in mind that the reduced density matrices originating from CC and EOMCC calculations are not symmetric. Thus, if we, for example, want to calculate the

Further Information

4-97

dipole strength between states K and M for the x component of the dipole mu_x, |<PsiK | mu_x | PsiM>|**2, we must write |<PsiK | mu_x | PsiM>|**2 = <PsiK | mu_x | PsiM><PsiM | mu_x | PsiK>, where each matrix element in the above expression is evaluated using the expression for <PsiK| W |PsiM> shown above. A similar remark applies to the corresponding component of the oscillator strength, (2/3)*|EK-EM|*|<PsiK| mu_x|PsiM>|**2, which we have to write as (2/3)*|EK-EM|*<PsiK|mu_x|PsiM><PsiM|mu_x|PsiK>. In other words, both matrix elements <PsiK | mu_x | PsiM> and <PsiM | mu_x | PsiK> have to be evaluated, since they are not identical. This is reflected in the GAMESS output, where the user can see quantities such as the left and right transition dipole moments. From the above description, it follows that in order to calculate reduced density matrices and properties using CC and EOMCC methods, one has to determine the left as well as the right eigenstates of the similarity transformed Hamiltonian H-bar. For the ground state, this is done by solving the linear system of equations for the deexcitation operator Lambda (in the CCSD case, the one- and two-body components Lambda1 and Lambda2). For excited states, we can proceed in several different ways. We can solve the linear system of equations for the amplitudes defining the EOMCC deexcitation operator L, after determining the corresponding EOMCC excitation operator R and excitation energy omega (recommended option, default in GAMESS), or we can solve for the L and R amplitudes simultaneously in the process of diagonalizing the similarity transformed Hamiltonian. These different ways of solving the EOMCC problem are discussed in section "Eigensolvers for excitedstate calculations." As already mentioned, the left eigenstates of the similarity transformed Hamiltonian of the CCSD approach are also used to construct the triples corrections to CCSD energies defining the rigorously size extensive completely renormalized CR-CC(2,3) approximation. This is why the user gets an immediate access to electrostatic multipole moments and other one-electron properties calculated at the CCSD level, when running the CR-CC(2,3) calculations.

Further Information

4-98

excited state example

! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! excited states of methylidyne cation...CH+ Basis set and geometry come from a FCI study by J.Olsen, A.M.Sanchez de Meras, H.J.Aa.Jensen, P.Jorgensen Chem. Phys. Lett. 154, 380-386(1989). EOMCC methods give: STATE EOMCCSD ID/IA IID/IA ID/IB IID/IB FCI B1 (1Pi) 3.261 3.226 3.226 3.225 3.224 3.230 A1 (1Delta) 7.888 6.988 6.963 6.987 6.962 6.964 A1 (1Sigma+) 9.109 8.656 8.638 8.654 8.637 8.549 A1 (1Sigma+) 13.580 13.525 13.526 13.524 13.525 13.525 B1 (1Pi) 14.454 14.229 14.221 14.228 14.219 14.127 A1 (1Sigma+) 17.316 17.232 17.220 17.231 17.219 17.217 A2 (1Delta) 17.689 16.820 16.790 16.819 16.789 16.833 Note the improvements in the EOMCCSD results by the CR-EOMCCSD(T) appproaches (e.g., ID/IB) for the Sigma+ state at 8.549 eV and both Delta states. The ground state CCSD dipole is z=-0.645, and the right/left transition moment to the first pi state is x=0.297 and 0.320, with oscillator strength 0.0076

$contrl scftyp=rhf cctyp=cr-eom runtyp=energy icharg=1 units=bohr $end $system mwords=5 $end $ccinp ncore=0 $end $eominp nstate(1)=4,2,2,0 minit=1 noact=3 nuact=7 ccprpe=.true. $end $data CH+ at R=2.13713...basis set from CPL 154, 380 (1989) Cnv 2 Carbon S 1 2 3 4 5 6 S 1 S S S P 1 2 6.0 6 0.0 0.0 0.16558134

4231.610 0.002029 634.882 0.015535 146.097 0.075411 42.4974 0.257121 14.1892 0.596555 1.9666 0.242517 ; 1 5.1477 1.0 1 ; 1 0.4962 1.0 1 ; 1 0.1533 1.0 1 ; 1 0.0150 1.0 4 18.1557 0.018534 3.9864 0.115442

Further Information 3 4 1.1429 0.3594 1 ; 1 0.1146 1 ; 1 0.011 1 ; 1 0.75 0.386206 0.640089 1.0 1.0 1.0

4-99

P P D

Hydrogen 1.0 0.0 0.0 -1.97154866 S 3 1 1.924060D+01 3.282800D-02 2 2.899200D+00 2.312080D-01 3 6.534000D-01 8.172380D-01 S 1 ; 1 1.776D-01 1.0 S 1 ; 1 2.5D-02 1.0 P 1 ; 1 1.0 1.0 $end

resource requirements
User can perform LCCD, CCD, and CCSD calculations, that is without calculating the [T], (T), (2,3), and (TQ) corrections, or calculate the entire set of the standard and renormalized [T], (T), (2,3), and (TQ) ground-state corrections, in addition to the CCSD energies. User can also perform the EOMCCSD calculations of excited states and stop at EOMCCSD or continue to obtain some or all CREOMCCSD(T) triples corrections (cf. the values of input variable CCTYP in $CONTRL and $EOMINP group). Finally, user can perform the calculations of ground-state properties at the CCSD level or calculate ground- and excited-state properties. It is also possible to combine some of the above calculations. For example, one can calculate the CCSD and EOMCCSD properties and obtain triples corrections to the calculated CCSD and EOMCCSD energies from a single input (see the example above). The CR-CC(2,3) calculation produces the MBPT(2) and CCSD energies, and CCSD oneelectron properties and density matrices, in addition to the CR-CC(2,3) and some other CR-CC triples corrections to the CCSD energies, again all from a single input (CCTYP=CRCCL). The most expensive steps in CC/EOMCC calculations scale as follows: LCCD, CCD, CCSD, EOMCCSD No**2 times Nu**4 (iterative) CCSD[T], CCSD(T), R-CCSD[T], R-CCSD(T), CR-CCSD[T], CR-CCSD(T), CR-CC(2,3) (#1), CR-EOMCCSD(T) (#2) No**3 times Nu**4 (non-iterative) plus No**2 times Nu**4 (iterative)

Further Information

4-100

CCSD(TQ), R-CCSD(TQ), CR-CCSD(TQ) No**2 times Nu**5 or Nu**6 (#3) (non-iterative) plus No**3 times Nu**4 (non-iterative) plus No**2 times Nu**4 (iterative) ---(#1) In addition to the usual No**2 times Nu**4 iterative CCSD steps and No**3 times Nu**4 non-iterative steps needed to determine the (2,3) triples correction, the CR-CC(2,3) calculations require extra No**2 times Nu**4 iterative steps needed to obtain the left CCSD state, which enters the CR-CC(2,3) triples correction formula. (#2) In addition to the No**2 times Nu**4 iterative CCSD and EOMCCSD steps and No**3 times Nu**4 non-iterative (T) steps that are common to all CR-EOMCCSD(T) models, the CR-EOMCCSD(T),III method requires the iterative No**2 times Nu**4 steps of CISD. The CR-EOMCCSD(T),IX and CR-EOMCCSD(T),IIX (X=A-D) methods do not require these additional CISD calculations. (#3) To reduce the cost, the program will automatically choose between the No**2 times Nu**5 and Nu**6 algorithms in the (Q) part, depending on the ratio of Nu to No. ---The cost of calculating the standard CCSD[T] and CCSD(T) energies and the cost of calculating the R-CCSD[T] and RCCSD(T) energies are essentially the same. The cost of calculating the triples corrections of the CR-CCSD[T] and CR-CCSD(T) approaches is essentially twice the cost of calculating the standard CCSD[T] and CCSD(T) corrections. Similar relationships hold between the costs of the CCSD(TQ), R-CCSD(TQ), and CR-CCSD(TQ) calculations. The cost of calculating the triples corrections of the CRCC(2,3),X (X=A-D) approaches is also twice the cost of calculating the CCSD[T] and CCSD(T) triples corrections, but additional No**2 times Nu**4 iterative steps are required to generate the left CCSD state after converging the CCSD equations in order to calculate the final CRCC(2,3) energies. Although the noniterative triples corrections may be seen to grow as the seventh power of the system size, they often require less time than the sixth power iterations of the CCSD step, while providing a great increase in accuracy. Similar remarks apply to the CREOMCCSD(T) calculations: The cost of the CR-EOMCCSD(T) calculation for a single electronic state, in its noniterative triples part, is twice the cost of computing

Further Information

4-101

the standard (T) corrections of CCSD(T). The total CPU time of the CR-EOMCCSD(T) calculations scales linearly with the number of calculated states. In spite of the formal N**6 scaling, the calculations of the CCSD/EOMCCSD properties per single electronic state are considerably less expensive than the CCSD calculations for two reasons. First of all, the process of obtaining the left eigenstates of the similarity transformed Hamiltonian H-bar can reuse the intermediates (matrix elements of H-bar) which are obtained in the prior CCSD calculations. Second, converging left eigenstates of H-bar is usually much quicker than converging the CCSD equations when one obtains the left eigenstates of H-bar by solving the linear system of equations for the L deexcitation amplitudes after determining the R excitation amplitudes and excitation energies. This means that computing properties at the CCSD/EOMCCSD level is not very expensive once the CCSD and EOMCCSD right eigenvectors are obtained. Similar remarks apply to the CR-CC(2,3) calculations, which require the left CCSD eigenstates in addition to the CCSD T1 and T2 amplitudes: The determination of the left CCSD states that are needed to determine the non-iterative triples corrections of the CR-CC(2,3) approach makes the entire CCSD part of the CR-CC(2,3) calculation only somewhat more expensive than the regular CCSD iterations needed to obtain T1 and T2 clusters. The CCSD(TQ), R-CCSD(TQ), and CRCCSD(TQ) calculations are more expensive than the CCSD(T) calculations, in spite of the fact that all of these methods use non-iterative N**7 steps. This is related to the fact that the No**2 times Nu**5 steps of the (TQ) methods are more expensive than the No**3 times Nu**4 steps of the (T) approaches. On the other hand, the CCSD(TQ), RCCSD(TQ), and CR-CCSD(TQ) methods are much less expensive than the iterative ways of obtaining the information about quadruply excited clusters. This is a result of an efficient use of diagram factorization in coding the CCSD(TQ), R-CCSD(TQ), and CR-CCSD(TQ) methods, which leads to a reduction of the N**9-type steps in the original (Q) expressions to N**7 steps. Rough estimates of the memory required are: CCSD 4 No**2 times Nu**2 + No times Nu**3

CCSD[T], CCSD(T), R-CCSD[T], R-CCSD(T) 4 No**2 times Nu**2 + No times Nu**3 CR-CCSD[T], CR-CCSD(T) No**2 times Nu**2 + 2 * No times Nu**3 (faster algorithm)

Further Information

4-102

4 No**2 times Nu**2 + No times Nu**3 (slower, less memory) CR-CC(2,3) The most expensive routine requires 3 * No * Nu**3 + 3 * Nu**3 + 5 * No**2 *Nu**2 words CCSD(TQ),b, R-CCSD(TQ)-n,x (n=1,2;x=a,b), CR-CCSD(TQ),x (x=a,b) 2 * No times Nu**3 + No**2 times Nu**2 + Nu**3, preceded and followed by steps that require memories, such as, for example, 3 * Nu**3 + 5 * No**2 * Nu**2 EOMCCSD No times Nu**3 + 4 No**2 times Nu**2 (MEOM=0,1) if MEOM=2, add to this (4 times number of roots + 2) times No**2 times Nu**2 CR-EOMCCSD(T),IX, 2 * No times Nu**3 + 3 No**2 times Nu**2 CR-EOMCCSD(T),IIX(X=A-D) [MTRIP=1 in $EOMINP] CR-EOMCCSD(T) 3 * No times Nu**3 + 5 No**2 times Nu**2 all variants (faster algorithm) [MTRIP=2 in $EOMINP] CR-EOMCCSD(T),III 2 * No times Nu**3 + 5 No**2 times Nu**2 [MTRIP=3 in $EOMINP] CR-EOMCCSD(T) 2 * No times Nu**3 + 5 No**2 times Nu**2 all variants (slower algorithm) [MTRIP=4 in $EOMINP] The program automatically selects the algorithm for the CRCCSD[T] and CR-CCSD(T) calculations, depending on the amount of available memory. A similar remark applies to the EOMCCSD calculations, where some additional reductions of memory requirements are possible if memory is low. The above estimates are rough. The time required for calculating the CR-CCSD[T] and CRCCSD(T) triples corrections is only twice the time used to calculate the standard CCSD[T] and CCSD(T) corrections. Thus, by just doubling the CPU time for the noniterative triples corrections and by selecting CCTYP=CR-CC, we gain access to all six noniterative triples corrections (the CCSD[T], CCSD(T), R-CCSD[T], R-CCSD(T), CR-CCSD[T], and CRCCSD(T) energies) plus, of course, to the MBPT(2) and CCSD energies. At the same time, the CR-CCSD[T] and CR-CCSD(T) results for stretched nuclear geometries and diradicals are better than the results of the conventional CCSD[T] and CCSD(T) calculations. In some cases, choosing CCTYP=R-CC might be reasonable, too. The choice CCTYP=R-CC gives five different energies (CCSD, CCSD[T], CCSD(T), R-CCSD[T], and

Further Information

4-103

R-CCSD(T)) for the price of three (CCSD, CCSD[T], and CCSD(T)) as the there is no extra time needed for the Rtheories compared to the standard ones. If we ignore the iterative CCSD steps and additional iterative steps needed to determine the left CCSD state, the time required for calculating the size extensive CR-CC(2,3) triples corrections is also only twice the time of calculating the CCSD[T] and CCSD(T) corrections. There is an additional bonus though: The CR-CC(2,3) calculations automatically produce a variety of CCSD one-electron properties at no extra cost. Similar remarks apply to quadruples and excited state calculations, although in the latter case a lot depends on user's expectations. If user is only interested in excited states dominated by singles and if accuracies on the order of 0.1-0.3 eV (sometimes better, sometimes worse) are acceptable, EOMCCSD is a good choice. However, it may be worth improving the EOMCCSD results by performing the CR-EOMCCSD(T) calculations, which often lower the errors in calculated excited states to 0.1 eV or less without making the calculations a lot more expensive (the CR-EOMCCSD(T) corrections are noniterative, so that the CPU time needed to calculate them may be comparable to the time spent in all EOMCCSD iterations). If there is a risk of encountering low-lying states having significant doubly excited contributions or multi-reference character, choosing CREOMCCSD(T) is a necessity, since errors obtained in EOMCCSD calculations for states dominated by doubles can easily be on the order of 1 eV. The CCSD(T) approach is often fine for closed-shell molecules, but there are cases, such as the vibrational frequencies of ozone and properties of other multiply bonded systems, where inclusion of quadruples is necessary. The CR-CCSD(T) approach is very useful in cases involving single bond breaking and diradicals, but CR-CC(2,3) and CR-CCSD(TQ) should be better. In addition, the CR-CC(2,3) method provides rigorously size extensive results. In cases of multiple bond dissociations, CR-CCSD(TQ) is a better alternative. The program is organized such that choosing a CR-CCSD(TQ) option (CCTYP=CR-CC(Q)) produces all energies obtained with CCTYP=CR-CCSD(T) and all CCSD(TQ), R-CCSD(TQ), and CRCCSD(TQ) energies. By selecting CCTYP=CCSD(TQ), the user can obtain the CCSD(TQ) and R-CCSD(TQ) energies, in addition to the CCSD, CCSD[T], CCSD(T), R-CCSD[T], and RCCSD(T) energies. We encourage the user to read papers, such as P.Piecuch, S.A.Kucharski, K.Kowalski, M.Musial Comput. Phys. Comm., 149, 71-96(2002); K. Kowalski and P. Piecuch,

Further Information

4-104

J. Chem. Phys., 120, 1715-1738 (2004); M. Wloch, J.R. Gour, K. Kowalski, and P. Piecuch, J. Chem. Phys. 122, 214107 (2005); K. Kowalski, P. Piecuch, M. Wloch, S.A. Kucharski, M. Musial, and M.W. Schmidt, in preparation, where time and memory requirements for various types of CC and EOMCC calculations are described in considerable detail.

restarts in ground-state calculations

The CC code incorporated in GAMESS is quite good in converging the CCSD equations with the default guess for cluster amplitudes. The code is designed to converge in relatively few iterations for significantly stretched nuclear geometries, where it is not unusual to obtain large cluster amplitudes whose absolute values are close to 1. This is accomplished by combining the standard Jacobi algorithm with the DIIS extrapolation method of Pulay. The maximum number of amplitude vectors used in the DIIS extrapolation procedure is defined by the input variable MXDIIS. The default for MXDIIS is as follows: MXDIIS = 5, for 5 < No*Nu, MXDIIS = 3, for 2 < No*Nu < 6, MXDIIS = 0, for No*Nu < 3. Thus, in the vast majority of cases, the default value of MXDIIS is 5. However, for very small problems, when the DIIS expansion subspace leads to singular systems of linear equations, it is necessary to reduce the value of MXDIIS to 2-4 (we chose 3) or switch off DIIS altogether (which is the case when MXDIIS = 0). It may, of course, happen that the solver for the CCSD equations does not converge, in spite of increasing the maximum number of iterations (input variable MAXCC; the default value is 30) and in spite of changing the default value of MXDIIS. In order to facilitate the calculations in all such cases, we included the restart option in the CC codes incorporated in GAMESS. Thus, user can restart a CCSD (or (L)CCD) calculation from the restart file created by an earlier CC calculation. In order to use the restart option, user must save the disk file CCREST (unit 70) from the previous CC run (cf. the GAMESS script rungms) and make sure that this file is copied to scratch directory where the restarted calculation is carried out. A restart is invoked by entering a nonzero value for IREST, which should be the number of the last iteration completed, and must be

Further Information

4-105

some value greater than or equal 3. Examples of using the restart option include the following situations: o The CCSD program did not converge in MAXCC iterations, but there is a chance to converge it if the value of MAXCC is increased. User restarts the calculation with the increased value of MAXCC. o User ran a CCSD calculation, obtaining the converged CCSD energy, but later decided to run CR-CCSD(T) or CR-CC(2,3) calculation. Instead of running the entire CCSD --> CRCCSD(T) or CCSD --> CR-CC(2,3) task again, user restarts the calculation after changing the value of input variable CCTYP to CR-CC (the CR-CCSD(T) case) or CR-CCL (the CR-CC(2,3) case) and entering IREST to reuse the previous CCSD amplitudes, proceeding at once to the noniterative triples corrections (left CCSD calculations and triples corrections in the CR-CC(2,3) case). o The CCSD program diverged for some geometry with a significantly stretched bond. User performs an extra calculation for a different nuclear geometry, for which it is easier to converge the CCSD equations, and restarts the calculation from the restart file generated by an extra calculation. This technique of restarting the CC calculations from the cluster amplitudes obtained for a neighboring nuclear geometry is particularly useful for scanning PESs and for calculating energy derivatives by numerical differentiation. There also are situations where restart of the groundstate CCSD calculations is useful for excited-state and property calculations: o User ran a CCSD, CCSD(T), or CR-CCSD(T) calculation, obtaining the converged CC energies for the ground state, but later decided to run an excited-state EOMCCSD or CR-EOMCCSD(T) calculations. Instead of running the entire CCSD --> EOMCCSD or CCSD --> CR-EOMCCSD(T) task, user restarts the calculation after changing the value of input variable CCTYP to EOM-CCSD or CR-EOM, selecting excited-state options in $EOMINP, and entering IREST greater or equal to 3 to reuse the previously converged CCSD amplitudes, proceeding at once to the excited-state (EOMCCSD or CR-EOMCCSD(T)) calculations. o User ran an EOMCCSD excited-state calculation, obtaining the converged CCSD amplitudes, but later discovered (by analyzing R1 and R2 amplitudes and REL values)

Further Information

4-106

that some states are dominated by doubles, so that the EOMCCSD results need to be improved by the CR-EOMCCSD(T) triples corrections. Instead of running the entire CCSD --> CR-EOMCCSD(T) task, user restarts the calculation after changing the value of input variable CCTYP from EOM-CCSD to CR-EOM, and entering IREST greater or equal to 3 to reuse the previously converged CCSD amplitudes, proceeding at once to the EOMCCSD and CR-EOMCCSD(T) calculations. o User ran a CR-CCSD(T) calculation, obtaining the converged ground-state energies, but later decided to run CCSD and EOMCCSD properties. Instead of running the CCSD --> EOMCCSD task again, user restarts the calculation after changing the value of input variable CCTYP to EOM-CCSD, adding CCPRPE=.TRUE. and the desired values of NSTATE in $EOMINP, and entering IREST to reuse the previously converged CCSD amplitudes, proceeding at once to CCSD and EOMCCSD properties.

initial guesses in excited-state calculations

The EOMCCSD calculation is an iterative procedure which needs initial guesses for the excited states of interest. The popular initial guess for the EOMCCSD calculations is obtained by performing the CIS calculations (diagonalizing the Hamiltonian in a space of singles only). This is acceptable for states dominated by singles, but user may encounter severe convergence difficulties or even miss some states entirely if the calculated states have significant doubly excited character. One possible philosophy is not to worry about it and use the CIS initial guess only, since EOMCCSD fails to describe states with large doubly excited components. This is not the philosophy of the EOMCC programs in GAMESS. GAMESS is equipped with the CREOMCCSD(T) triples corrections to EOMCCSD energies, which are capable of reducing the large errors in the EOMCCSD results for states dominated by two-electron transitions, on the order of 1 eV, to 0.1 eV or even less. Thus, the ability to capture states with significant doubly excited contributions is an important element of the EOMCC GAMESS codes. Excited states with significant contributions from double excitations can easily be found by using the EOMCCSd (little d) initial guesses provided by GAMESS. In the EOMCCSd calculations (and analogous CISd calculations used to initiate the CISD calculations for the CR-EOMCCSD(T),III

Further Information

4-107

method), the initial guesses for the calculated excited states are defined using all single excitations (letter S in EOMCCSd and CISd) and a small subset of double excitations (the little d in EOMCCSd and CISd) defined by active orbitals or orbital range specified by the user. The inclusion of a small set of active double excitations in addition to all singles in the initial guess greatly facilitates finding excited states characterized by relatively large doubly excited amplitudes. GAMESS input offers a choice between the CIS and EOMCCSd/CISd initial guesses. The use of EOMCCSd/CISd initial guesses is highly recommended. This is accomplished by setting the input variable MINIT at 1 and by selecting the orbital range (active orbitals to define "little doubles" d) through the numbers of active occupied and active unoccupied orbitals (variables NOACT and NUACT, respectively) or an array of active orbitals called MOACT.

eigensolvers for excited-state calculations

The basic eigensolver for the EOMCCSD calculations is the Hirao and Nakatsuji's generalization of the Davidson diagonalization algorithm to non-Hermitian problems (the similarity transformed Hamiltonian H-bar is non-Hermitian). GAMESS offers the following three choices of EOMCCSD eigensolvers for the right eigenvalue problem (R amplitudes and energies only): o the true multi-root eigensolver based on the Hirao and Nakatsuji's algorithm, in which all states are calculated at once using a united iterative space (variable MEOM=2). o the single-root eigensolver, in which one calculates one state at a time, but the iterative subspace corresponding to all calculated roots remains united (variable MEOM=0). o the single-root eigensolver, in which one calculates one state at a time and each calculated root has a separate iterative subspace (variable MEOM=1). The latter option (MEOM=1) leads to the fastest algorithm, but there is a risk (often worth taking) that some states will be converged more than once. The true multi-root eigensolver (MEOM=2) is probably the safest, but it is also the most expensive solver and there are some risks associated with using it too. When MEOM=2, there is a risk that one root, which is difficult to converge, may cause the entire multi-root procedure fail in spite of the fact that all other roots participating in the calculation

Further Information

4-108

converged. The EOMCCSD program in GAMESS is prepared to handle this problem by saving individual roots that converged during multi-root iterations in case the entire procedure fails because of one or more roots which are difficult to converge. In this way, at least some roots are saved for the subsequent CR-EOMCCSD(T) calculations. The middle option (MEOM=0) seems to offer the best compromise. MEOM=0 is a single-root eigensolver, so there are no risks associated with loosing some states during multi-root calculations. At the same time, the use of the united iterative subspace for all calculated roots helps to eliminate the problem of MEOM=1 of obtaining the same root more than once. The single-root eigensolver with a united iterative subspace (MEOM=0) is recommended (and used as a default), although other ways of converging the right EOMCCSD equations (MEOM=1,2) are very useful too. As pointed out earlier, in order to calculate reduced density matrices and properties using CCSD and EOMCCSD methods, one has to determine the left as well as the right eigenstates of the non-Hermitian similarity transformed Hamiltonian H-bar. For the ground state, this is done by solving the linear system of equations for the deexcitation operator Lambda (in the CCSD case, the one- and two-body components Lambda1 and Lambda2). For the amplitudes defining the L1 and L2 components of the excited-state operator L, one can proceed in several different ways and these different ways are reflected in the EOMCCSD algorithm incorporated in GAMESS. One can, for example, solve the linear system of equations for the amplitudes defining the EOMCCSD deexcitation operator L=L1+L2, after determining the corresponding excitation operator R=R1+R2 and excitation energy omega. This is a highly recommended option, which is also a default in GAMESS. This option is executed with any choice of MEOM=0,1,2 and when the user selects CPRPE=.TRUE. In case of unlikely difficulties with obtaining the L1 and L2 components, one can solve for the EOMCCSD values of the L1,L2 and R1,R2 amplitudes and excitation energies simultaneously in the process of diagonalizing the similarity transformed Hamiltonian H-bar completely in a single sequence of iterations. This approach is reflected by the following two additional choices of the input variable MEOM: o MEOM=3, one root at a time, separate iterative space for each computed root, left and right eigenvectors of the similarity transformed Hamiltonian and energies (like MEOM=1, but both left and right eigenvectors are iterated). o MEOM=4, one root at a time, united iterative spaces

Further Information

4-109

for all calculated roots, left and right eigenvectors of the similarity transformed Hamiltonian and energies (like MEOM=0, but both left and right eigenvectors are iterated). In both cases, the user has to select CCPRPE=.TRUE. in order for these two choices of MEOM to work.

references and citations required in publications

Any publication describing the results of CC calculations obtained using GAMESS should give reference to the relevant papers. Depending on the specific CCTYP value, these are: CCTYP = LCCD, CCD, CCSD, CCSD(T) P. Piecuch, S.A. Kucharski, K. Kowalski, and M. Musial Comput. Phys. Commun. 149, 71-96 (2002). CCTYP = R-CC, CR-CC, CCSD(TQ), CR-CC(Q) P. Piecuch, S.A. Kucharski, K. Kowalski, and M. Musial Comput. Phys. Commun. 149, 71-96 (2002); K. Kowalski and P. Piecuch J. Chem. Phys. 113, 18-35 (2000); K. Kowalski and P. Piecuch J. Chem. Phys. 113, 5644-5652 (2000). CCTYP = CR-CCL P. Piecuch, S.A. Kucharski, K. Kowalski, and M. Musial Comput. Phys. Commun. 149, 71-96 (2002); P. Piecuch and M. Wloch J. Chem. Phys. 123, 224105/1-10 (2005). CCTYP = EOM-CCSD, CR-EOM P. Piecuch, S.A. Kucharski, K. Kowalski, and M. Musial Comput. Phys. Commun. 149, 71-96 (2002); K. Kowalski and P. Piecuch, J. Chem. Phys. 120, 1715-1738 (2004); M. Wloch, J.R. Gour, K. Kowalski, and P. Piecuch, J. Chem. Phys. 122, 214107-1 - 214107-15 (2005). CCTYP = CR-EOML P. Piecuch, J. R. Gour, and M. Wloch Int. J. Quantum Chem. 109, 3268-3304(2009) and the first two papers cited for CR-EOM just above CCTYP J. R. J. J. R. = IP-EOM2, EA-EOM2 Gour, P. Piecuch, M. Wloch Chem. Phys. 123, 134113/1-14(2005) Gour, P. Piecuch

Further Information J. Chem. Phys. 125, 234107/1-17(2006)

4-110

In addition, the explicit use of CCPRP=.TRUE. in $CCINP and/or the use of CCPRPE=.TRUE. in $EOMINP should reference M. Wloch, J.R. Gour, K. Kowalski, and P. Piecuch, J. Chem. Phys. 122, 214107/1-15 (2005). --The rest of this section is a list of references to the original formulation of various areas in Coupled-Cluster Theory relevant to methods available in GAMESS: Electronic structure: J. Cizek, J. Chem. Phys. 45, 4256 (1966). J. Cizek, Adv. Chem. Phys. 14, 35 (1969). J. Cizek, J. Paldus, Int.J.Quantum Chem. 5, 359 (1971). Nuclear theory (examples): F. Coester, Nucl. Phys. 7, 421 (1958). F. Coester, H. Kuemmel, Nucl. Phys. 17, 477 (1960). K. Kowalski, D.J. Dean, M. Hjorth-Jensen, T. Papenbrock, P. Piecuch, Phys. Rev. Lett. 92, 132501 (2004). D.J. Dean, J.R. Gour, G. Hagen, M. Hjorth-Jensen, K. Kowalski, T. Papenbrock, P. Piecuch, M. Wloch, Nucl. Phys. A. 752, 299 (2005). M. Wloch, D.J. Dean, J.R. Gour, P. Piecuch, M. HjorthJensen, T. Papenbrock, K. Kowalski, Eur. Phys. J. A 25 (Suppl. 1), 485 (2005). M. Wloch, J.R. Gour, P. Piecuch, D.J. Dean, M. HjorthJensen, T. Papenbrock, J. Phys. G: Nucl. Phys. 31, S1291 (2005). M. Wloch, D.J. Dean, J.R. Gour, M. Hjorth-Jensen, K. Kowalski, T. Papenbrock, P. Piecuch, Phys. Rev. Lett. 94, 212501 (2005). P. Piecuch, M. Wloch, J.R. Gour, D.J. Dean, M. HjorthJensen, T. Papenbrock, in V. Zelevinsky (Ed.), Nuclei and Mesoscopic Physics, AIP Conference Proceedings, Vol. 777 (AIP Press, 2005), p. 28. D.J. Dean, M. Hjorth-Jensen, K. Kowalski, T. Papenbrock, M. Wloch, and P. Piecuch, in Key Topics in Nuclear Structure, Proceedings of the 8th International Spring Seminar on Nuclear Physics, edited by A. Covello (World Scientific, Singapore, 2005), p. 147. Coupled-Cluster Method with Doubles (CCD) J. Cizek, J. Chem. Phys. 45, 4256 (1966). J. Cizek, Adv. Chem. Phys. 14, 35 (1969). J. Cizek, J. Paldus, Int.J.Quantum Chem. 5, 359 (1971).

Further Information J.A. Pople, R. Krishnan, H.B. Schlegel, J.S. Binkley, Int. J. Quantum Chem. Symp. 14, 545 (1978). R.J. Bartlett and G.D. Purvis, Int. J. Quantum Chem. Symp. 14, 561 (1978). J. Paldus, J. Chem. Phys. 67, 303 (1977) [orthogonally spin-adapted formulation].

4-111

Linearized Coupled-Cluster Method with Doubles (LCCD; cf., also, D-MBPT(infinity), CEPA(0)) J. Cizek, J. Chem. Phys. 45, 4256 (1966). J. Cizek, Adv. Chem. Phys. 14, 35 (1969). R.J. Bartlett, I. Shavitt, Chem.Phys.Lett.50, 190 (1977) 57, 157 (1978) [Erratum]. R. Ahlrichs, Comp. Phys. Commun. 17, 31 (1979). Coupled-Cluster Method with Singles and Doubles (CCSD) G.D.Purvis III, R.J.Bartlett, J.Chem.Phys. 76, 1910 (1982) [spin-orbital formulation]. P. Piecuch, J. Paldus, Int.J.Quantum Chem. 36, 429 (1989). [orthogonally spin-adapted formulation]. G.E.Scuseria, A.C.Scheiner, T.J.Lee, J.E.Rice, H.F.Schaefer III, J. Chem. Phys. 86, 2881 (1987) [non-orthogonally spin-adapted formulation]. G.E. Scuseria, C.L. Janssen, H.F.Schaefer III J. Chem. Phys. 89, 7382 (1988) [non-orthogonally spin-adapted formulation]. T.J. Lee and J.E. Rice, Chem. Phys. Lett. 150, 406 (1988) [non-orthogonally spin-adapted formulation]. Coupled-Cluster Method with Singles and Doubles and Noniterative Triples, CCSD[T] = CCSD+T(CCSD) M. Urban, J. Noga, S. J. Cole, and R. J. Bartlett, J. Chem. Phys. 83, 4041 (1985). P. Piecuch and J. Paldus, Theor. Chim. Acta 78, 65 (1990) [orthogonally spin-adapted formulation]. P. Piecuch, S. Zarrabian, J. Paldus, and J. Cizek, Phys. Rev. B 42, 3351-3379 (1990) [orthogonally spin-adapted formulation]. P. Piecuch, R. Tobola, and J. Paldus, Int. J. Quantum Chem. 55, 133-146 (1995) [orthogonally spin-adapted formulation]. Coupled-Cluster Method with Singles and Doubles and Noniterative Triples, CCSD(T) K. Raghavachari, G. W. Trucks, J. A. Pople, M. Head-Gordon, Chem. Phys. Lett. 157, 479 (1989). Equation of Motion Coupled-Cluster Method, Response CC/Time Dependent CC Approaches, SAC-CI (Original Ideas), -

Further Information

4-112

H. Monkhorst, Int. J. Quantum Chem. Symp. 11, 421 (1977). K. Emrich, Nucl. Phys. A 351, 379 (1981). H. Sekino and R.J. Bartlett, Int. J. Quantum Chem. Symp. 18, 255 (1984). E. Daalgard and H. Monkhorst, Phys. Rev. A 28, 1217 (1983). M. Takahashi and J. Paldus, J. Chem. Phys. 85, 1486 (1986). H. Koch and P. Jorgensen, J. Chem. Phys. 93, 3333 (1990). H. Nakatsuji, K. Hirao, Chem. Phys. Lett. 47, 569 (1977). H. Nakatsuji, K. Hirao, J.Chem.Phys. 68, 2053, 4279 (1978). Equation of Motion Coupled-Cluster Method with Singles and Doubles, EOMCCSD J. Geertsen, M. Rittby, and R.J. Bartlett, Chem. Phys. Lett. 164, 57 (1989). J.F. Stanton and R.J. Bartlett, J. Chem. Phys. 98, 7029 (1993). Method of Moments of Coupled-Cluster Equations and Renormalized and Completely Renormalized Coupled-Cluster Methods (Overviews) P. Piecuch, K. Kowalski, I.S.O. Pimienta, S.A. Kucharski, in M.R. Hoffmann, K.G. Dyall (Eds.), Low-Lying Potential Energy Surfaces, ACS Symposium Series, Vol. 828, Am. Chem. Society, Washington, D.C., 2002, p. 31 [ground and excited states]. P. Piecuch, K. Kowalski, I.S.O. Pimienta, M.J. McGuire, Int. Rev. Phys. Chem. 21, 527 (2002) [ground and excited states]. P. Piecuch, I.S.O. Pimienta, P.-F. Fan, K. Kowalski, in J. Maruani, R. Lefebvre, E. Brandas (Eds.), Progress in Theoretical Chemistry and Physics, Vol. 12, Advanced Topics in Theoretical Chemical Physics, Kluwer, Dordrecht, 2003, p. 119 [ground states]. P. Piecuch, K. Kowalski, I.S.O. Pimienta, P.-D. Fan, M. Lodriguito, M.J. McGuire, S.A. Kucharski, T. Kus, M. Musial, Theor. Chem. Acc. 112, 349 (2004) [ground and excited states]. P. Piecuch, M. Wloch, M. Lodriguito, and J.R. Gour, in S. Wilson, J.-P. Julien, J. Maruani, E. Brandas, and G. Delgado-Barrio (Eds.), Progress in Theoretical Chemistry and Physics, Vol. 15, Recent Advances in the Theory of Chemical and Physical Systems, Springer, Berlin, 2006, p. XX, in press [excited states]. P. Piecuch, I.S.O. Pimienta, P.-D. Fan, and K. Kowalski, in A.K. Wilson (Ed.), Recent Progress in Electron Correlation Methodology, ACS Symposium Series, Vol. XXX, Am. Chem. Society, Washington, D.C., 2006, p. XX

Further Information [in press; ground states]. P.-D. Fan and P. Piecuch, Adv. Quantum Chem., in press (2006).

4-113

Renormalized and Completely Renormalized Coupled-Cluster Methods, Method of Moments of Coupled-Cluster Equations (Initial Original Papers, Ground States) P. Piecuch, K. Kowalski, in J. Leszczynski (Ed.), Computational Chemistry: Reviews of Current Trends, Vol. 5, World Scientific, Singapore, 2000, p. 1. K. Kowalski, P. Piecuch, J. Chem. Phys. 113, 18 (2000). K. Kowalski, P. Piecuch, J. Chem. Phys. 113, 5644 (2000). Biorthogonal Method of Moments of Coupled-Cluster Equations and Size Extensive Completely Renormalized Coupled-Cluster Singles, Doubles, and Non-iterative Triples Approach (CRCC(2,3)=CR-CCSD(T)L; Initial Original Papers) P. Piecuch and M. Wloch, J. Chem. Phys. 123, 224105(2005). P. Piecuch, M. Wloch, J.R. Gour, and A. Kinal, Chem. Phys. Lett. 418, 467-474 (2006). Renormalized and Completely Renormalized Coupled-Cluster Methods, Method of Moments of Coupled-Cluster Equations (Other Original Papers, Higher-Order Methods, Ground-State Benchmarks) K. Kowalski, P. Piecuch, Chem. Phys. Lett. 344, 165 (2001). P. Piecuch, S.A. Kucharski, K. Kowalski, Chem. Phys. Lett. 344, 176 (2001). P. Piecuch, S.A. Kucharski, V. Spirko, K. Kowalski, J.Chem.Phys. 115, 5796 (2001). P. Piecuch, K. Kowalski, and I.S.O. Pimienta, Int. J. Mol. Sci. 3, 475 (2002). M.J. McGuire, K. Kowalski, P. Piecuch, J. Chem. Phys. 117, 3617 (2002). P. Piecuch, S.A. Kucharski, K. Kowalski, M. Musial, Comput. Phys. Comm., 149, 71 (2002). I.S.O. Pimienta, K. Kowalski, and P. Piecuch, J. Chem. Phys. 119, 2951 (2003). S. Hirata, P.-D. Fan, A.A. Auer, M. Nooijen, P. Piecuch, J. Chem. Phys. 121, 12197 (2004). K. Kowalski and P. Piecuch, J. Chem. Phys. 122, 074107 (2005). P.-D. Fan, K. Kowalski, and P. Piecuch, Mol. Phys. 103, 2191 (2005). Completely Renormalized Coupled-Cluster Methods, Examples of Large-Scale Applications to Ground-State Properties I. Ozkan, A. Kinal, M. Balci,

Further Information

4-114

J.Phys.Chem. A 108, 507 (2004). R.L. DeKock, M.J. McGuire, P. Piecuch, W.D. Allen, H.F. Schaefer III, K. Kowalski, S.A. Kucharski, M. Musial, A.R. Bonner, S.A. Spronk, D.B Lawson, S.L. Laursen, J. Phys. Chem. A 108, 2893 (2004). M.J. McGuire, P. Piecuch, K. Kowalski, S.A. Kucharski, M. Musial, J. Phys. Chem. A 108, 8878 (2004). M.J. McGuire, P. Piecuch J. Am. Chem. Soc. 127, 2608 (2005). A. Kinal, P. Piecuch, J. Phys. Chem. A 110, 367 (2006). C.J. Cramer, M. Wloch, P. Piecuch, C. Puzzarini, and L. Gagliardi, J. Phys. Chem. A 110, 1991 (2006). Completely Renormalized Equation of Motion Coupled-Cluster Methods, Method of Moments of Coupled-Cluster Equations for Ground and Excited States (Original Papers) K. Kowalski P. Piecuch, J. Chem. Phys. 115, 2966 (2001). K. Kowalski P. Piecuch, J. Chem. Phys. 116, 7411 (2002). K. Kowalski P. Piecuch, J. Chem. Phys. 120, 1715 (2004). M. Wloch, J.R. Gour, K. Kowalski, and P. Piecuch, J. Chem. Phys. 122, 214107 (2005). Also, multi-reference and other externally corrected MMCC methods including ground and excited states, K. Kowalski and P. Piecuch, J. Molec. Struct.: THEOCHEM 547, 191 (2001). K. Kowalski and P. Piecuch, Mol. Phys. 102}, 2425 (2004). M.D. Lodriguito, K. Kowalski, M. Wloch, and P. Piecuch J. Mol. Struct: THEOCHEM, in press (2006). Completely Renormalized Equation of Motion Coupled-Cluster Methods, Method of Moments of Coupled-Cluster Equations for Ground and Excited States (Selected Benchmarks and Applications) C.D. Sherrill, P. Piecuch, J.Chem.Phys. 122, 124104 (2005) R.K. Chaudhuri, K.F. Freed, G. Hose, P. Piecuch, K. Kowalski, M. Wloch, S. Chattopadhyay, D. Mukherjee, Z. Rolik, A. Szabados, G. Toth, and P.R. Surjan, J. Chem. Phys. 122, 134105-1 (2005). K. Kowalski, S. Hirata, M. Wloch, P. Piecuch, and T.L. Windus, J. Chem. Phys. 123, 074319 (2005). S. Nangia, D.G. Truhlar, M.J. McGuire, and P. Piecuch J. Phys. Chem. A 109, 11643 (2005). P. Piecuch, S. Hirata, K. Kowalski, P.-D. Fan, and T.L. Windus, Int. J. Quantum Chem. 106, 79 (2006). M. Wloch, M.D. Lodriguito, P. Piecuch, and J.R. Gour Mol. Phys., in press (2006). S. Coussan, Y. Ferro, A. Trivella, P. Roubin, R. Wieczorek,

Further Information

4-115

C. Manca, P. Piecuch, K. Kowalski, M. Wloch, S.A. Kucharski, and M. Musial, J. Phys. Chem. A, in press (2006). Completely Renormalized Coupled-Cluster and Equation of Motion Coupled-Cluster Methods, GAMESS Implementations P. Piecuch, S.A. Kucharski, K. Kowalski, M. Musial, Comput. Phys. Comm., 149, 71 (2002). K. Kowalski and P. Piecuch J. Chem. Phys. 120, 1715 (2004). M. Wloch, J.R. Gour, K. Kowalski, and P. Piecuch, J. Chem. Phys. 122, 214107 (2005). P. Piecuch and M. Wloch, J. Chem. Phys. 123, 224105 (2005). K. Kowalski, P. Piecuch, M. Wloch,S.A. Kucharski, M. Musial, and M.W. Schmidt, in preparation. T1 diagnostic: T.J.Lee, P.R.Taylor Int.J.Quantum Chem., S23, 199207(1989). It is often assumed that T1>0.02 indicates that CCSD may not be correct for a system which is not very single reference in nature. (T) corrections tolerate greater singles amplitudes. However, T1 diagnostic is in many cases misleading, since one can easily have small (or even vanishing) T1 cluster amplitudes due to symmetry and a significant configurational quasi-degeneracy and multireference character. In general, in typical multi-reference situations, such as bond stretching and diradicals, one observes a significant increase of T2 cluster amplitudes. The larger values of T2 amplitudes are a clear signature of a multi-reference character of the wave function. The CRCCSD(T), CR-CCSD(TQ), and CR-CC(2,3) methods tolerate significant increases of T2 amplitudes in cases of singlebond breaking and diradicals. CCSD(T) and CCSD(TQ) approaches cannot do this, when the spin-adapted RHF references are employed. Written by Piotr Piecuch, Michigan State University (updated March 18, 2006)

Further Information

4-116

Density Functional Theory

There are actually two DFT programs in GAMESS, one using the typical grid quadrature for integration of functionals, and one using resolution of the identity to avoid the need or grids. The default METHOD=GRID program is discussed below, following a short description of METHOD=GRIDFREE. The final section is references to various functionals, and other topics of interest.

DFTTYP keywords
Let's begin with a translation table to NWchem's input: GAMESS NWchem's XC keyword Slater slater Gill gill96 SVWN slater vwn_5 Becke becke88 BVWN becke88 vwn_5 BLYP becke88 lyp B97 becke97 B97-1,B97-2,B97-3 becke97-1, becke-2, becke-3 HCTH93,HCTH120,HCTH147,HCTH407 hcth,hcth120,hcth147,hcth407 B98 becke98 B3LYP HFexch 0.20 slater 0.80 \ becke88 nonlocal 0.72 \ lyp 0.81 vwn_5 0.19 B3LYP1 b3lyp or, if you like to type: HFexch 0.20 slater 0.80 \ becke88 nonlocal 0.72 \ lyp 0.81 vwn_1_rpa 0.19 X3LYP HFexch 0.218 slater 0.782 \ becke88 nonlocal 0.542 \ xperdew91 nonlocal 0.167 \ lyp 0.871 vwn_1_rpa 0.129 PW91 xperdew91 perdew91 B3PW91 HFexch 0.20 slater 0.80 \ becke88 nonlocal 0.72 \ perdew91 0.81 pw91lda 1.00 PBE xpbe96 cpbe96 PBE0 pbe0 revPBE revpbe cpbe96

Further Information VS98 M06 PKZB TPSS TPSSh vs98 m06 (and similarly for M05-2X, etc.) xpkzb99 cpkzb99 xtpss03 cptss03 xctpssh

4-117

Note that B3LYP in GAMESS is based in part on the VWN5 electron gas correlation functional. Since there are five formulae with two possible parameterizations mentioned in the VWN paper about local correlation, other programs may use other choices, and therefore generate different B3LYP energies. For example, NWChem's manual says it uses the "VWN 1 functional with RPA parameters as opposed to the prescribed Monte Carlo parameters" as its default. Should you wish to use this VWN1 formula in a B3LYP hybrid, simply choose "DFTTYP=B3LYP1".

grid-free DFT
The grid-free code is a research tool into the use of the resolution of the identity to simplify evaluation of integrals over functionals, rather than quadrature grids. This trades the use of finite grids and their associated errors for the use of a finite basis set used to expand the identity, with an associated truncation error. The present choice of auxiliary basis sets was obtained by tests on small 2nd row molecules like NH3 and N2, and hence the built in bases for the 3rd row are not as well developed. Auxiliary bases for the remaining elements do not exist at the present time. The grid-free Becke/6-31G(d) energy at a C1 AM1 geometry for ethanol is -154.084592, while the result from a run using the "army grade grid" is -154.105052. So, the error using the AUX3 RI basis is about 5 milliHartree per 2nd row atom (the H's must account for some of the error too). The energy values are probably OK, the differences noted should by and large cancel when comparing different geometries. The grid-free gradient code contains some numerical inaccuracies, possibly due to the manner in which the RI is implemented for the gradient. Computed gradients consequently may not be very reliable. For example, a Becke/6-31G(d) geometry optimization of water started from the EXAM08 geometry behaves as: FINAL E= -76.0439853638, RMS GRADIENT = .0200293 FINAL E= -76.0413274662, RMS GRADIENT = .0231574 FINAL E= -76.0455283912, RMS GRADIENT = .0045887

Further Information

4-118

FINAL E= -76.0457360477, RMS GRADIENT = .0009356 FINAL E= -76.0457239113, RMS GRADIENT = .0001222 FINAL E= -76.0457216186, RMS GRADIENT = .0000577 FINAL E= -76.0457202264, RMS GRADIENT = .0000018 FINAL E= -76.0457202253, RMS GRADIENT = .0000001 Examination shows that the point on the PES where the gradient is zero is not where the energy is lowest, in fact the 4th geometry is the lowest encountered. The behavior for Becke/6-31G(d) ethanol is as follows: FINAL E= -154.0845920132, RMS GRADIENT = .0135540 FINAL E= -154.0933138447, RMS GRADIENT = .0052778 FINAL E= -154.0885472996, RMS GRADIENT = .0009306 FINAL E= -154.0886268185, RMS GRADIENT = .0002043 FINAL E= -154.0886352947, RMS GRADIENT = .0000795 FINAL E= -154.0885599794, RMS GRADIENT = .0000342 FINAL E= -154.0885514829, RMS GRADIENT = .0000679 FINAL E= -154.0884955093, RMS GRADIENT = .0000205 FINAL E= -154.0886438244, RMS GRADIENT = .0000330 FINAL E= -154.0886596883, RMS GRADIENT = .0000325 FINAL E= -154.0886094081, RMS GRADIENT = .0000120 FINAL E= -154.0886054003, RMS GRADIENT = .0000109 FINAL E= -154.0885939751, RMS GRADIENT = .0000152 FINAL E= -154.0886711482, RMS GRADIENT = .0000439 FINAL E= -154.0886972557, RMS GRADIENT = .0000230 with similar fluctuations through a total of 50 steps without locating a zero gradient. Note that the second energy above is substantially below all later points, so geometry optimizations with the grid-free DFT gradient code are at this time unsatisfactory.

DFT with grids

METHOD=GRID (the default for DFT) produces good energy and gradient quantities. Its energy errors should usually be less than 10 microHartree/atom, using the default grid. The default grid was changed on April 11, 2008 to use Lebedev angular grids. This changes all results obtained prior to that date using the original polar coordinate angular grid. The old grids can still be used, $dft nrad=96 nthe=12 nphi=24 $end $tddft nrad=24 nthe=8 nphi=16 $end in case you need to reproduce numbers from older versions. Since April 2008, the default is $dft nrad=96 nleb=302 $end $tddft nrad=48 nleb=110 $end

Further Information

4-119

The new grid settings produce root mean square gradient vectors accurate to about 0.00010, which matches the default value for OPTTOL in $STATPT. The "standard gridone" contains many fewer points, $dft sg1=.true. $end $tddft sg1=.true. $end However, SG1 will produce nuclear gradients accurate only to about 5 times OPTTOL, namely 0.00050 or so. SG1 is a very fast grid, and will provide substantial speedups if SG1 is used for the early steps of geometry optimizations. Rather high quality results, meaning an OPTTOL near 0.00001 can be used, may be obtained by $dft nrad=96 nleb=590 $end Very accurate (converged) results come from using the "army grade" grid, $dft nrad=96 nleb=1202 $end Turn to the next page to see numerical results.

A numerical demonstration of grid accuracies can be obtained from ethanol, DFTTYP=BECKE: energy RMS grad. CPU sg1=.true. -154.105070 0.010837 11 nrad=96 nthe=12 nphi=24 -154.104863 0.010724 56 nrad=96 nleb=302 -154.105042 0.010704 58 nrad=96 nleb=590 -154.105051 0.0107349 108 nrad=96 nleb=1202 -154.105052 0.0107353 214 Note that the energies are a function of the grid size, just as they are a function of the basis used, so you must only compare runs that use the same grid size (and of course the same basis set). The default grid (and the 590 point grid) will give nuclear gradients which are accurate enough to lead to satisfactory geometry optimizations. This means that DFT frequencies obtained by numerical differentiation should also be OK. RUNTYP=ENERGY, GRADIENT, HESSIAN, and their chemical combinations for OPTIMIZE, SADPOINT, IRC, DRC, VSCF, RAMAN, and FFIELD should all work. The grid DFT program uses symmetry during the numerical quadrature in two ways. First, the integration runs only over grid points placed around the symmetry unique atoms. Your run should be done in the full non-Abelian group, so that grid points as well as the usual integrals and the SCF steps can exploit full molecular symmetry. Symmetry is turned off during any TD-DFT stages, since excited states often have different symmetry than the ground state, but will be used in the ground state DFT.

Further Information

4-120

Secondly, for polar coordinate angular grids only, "octant symmetry" is implemented using an appropriate Abelian subgroup of the full group. The grid evaluation automatically uses an appropriate subgroup to reduce the number of grid points for atoms that lie on symmetry axes or planes. For example, in Cs, atoms lying in the xy plane will be integrated only over the upper hemisphere of their grid points. Octant symmetry is not used for any of these: a) if a non-standard axis orientation is input in $DATA b) if the angular grid size (NTHE,NTHE0,NPHI,NPI0) is not a multiple of the octant symmetry factors, such as NTHE=15 in C2v. The permissible values depend on the group, but NTHE a multiple of 2 and NPHI a multiple of 4 is generally safe.

Time Dependent Density Functional Theory (TD-DFT)

Two review articles are available, "Single-Reference ab Initio Methods for the Calculation of Excited States of Large Molecules" A.Dreuw, M.Head-Gordon Chem.Rev. 105, 4009-4037(2005) "Excited states from time-dependent density functional theory" P.Elliott, F.Furche, K.Burke Rev.Comp.Chem. 26, 91-166(2009) The following article is very informative: S.Hirata, M.Head-Gordon Chem.Phys.Lett. 314, 291-299(1999) It also explains the Tamm/Dancoff approximation which connects TD-DFT to CIS. TD-DFT requires higher functional derivatives of the exchange correlation energy with respect to the density: 2nd derivatives to do TD-DFT excitation energies, and 3rd derivatives to do TD-DFT nuclear gradients. Consequently, some of the functionals permit only excitation energies. To use metaGGAs in TD-DFT, the above functional derivatives involve a non-trivial differentiation of the kinetic energy tau's density dependence. The latter is the subject of a forthcoming paper, F.Zahariev, S.Sok, M.S.Gordon (to be submitted)

Further Information The TD-DFT nuclear gradient implementation in GAMESS is M.Chiba, T.Tsuneda, K.Hirao J.Chem.Phys. 124, 144106/1-11 (2006) and the long-range correction (useful in Rydberg and/or charge transfer states is Y.Tawada, T.Tsuneda, S.Yanagisawa, Y.Yanai, K.Hirao J.Chem.Phys. 120, 8425-8433(2004) See also K.A.Nguyen, P.N.Day, R.Pachter Int.J.Quantum Chem. 110, 2247-2255(2010) The "lambda diagnostic" is described by M.J.G.Peach, P.Benfield, T.Helgaker, D.J.Tozer J.Chem.Phys. 128, 044118/1-8(2008) This is a procedure for separating valence states from charge transfer and Rydberg states.

4-121

Note that it is possible to do TD-HF excitation energies, by requesting TDDFT=EXCITE, but leaving DFTTYP=NONE. Solvation effects can be added by PCM or EFP or both, with nuclear gradients. PCM + TD-DFT gradient: Y.Wang, H.Li J.Chem.Phys. 133, 034108/1-11(2010) EFP1 + TD-DFT energy: S.Yoo, F.Zahariev, S.Sok, M.S.Gordon J.Chem.Phys. 129, 144112/1-8(2008) EFP1 + TD-DFT gradient: N.Minezawa, N.De Silva, F.Zahariev, M.S.Gordon J.Chem.Phys. 134, 05411(2011) POL5P + TD-DFT gradient (similar polarizable solvent): D.Si, H.Li J.Chem.Phys. 133, 144112(2010) * * * * * In some cases, a more balanced description of the states might be obtained if the orbitals are optimized for a reference with unpaired electrons. This is possible with spin-flip methods, see TDDFT=SPNFLP. For example, in C2H4, one might optimize the orbitals for the triplet state (pi)1(pi*)1, but be interested in the energies of the three singlets and one triplet states N=(pi)2, T=(pi)1(pi*)1, V=(pi)1(pi*)1, and Z=(pi*)2. Using the T state as the reference optimizes the shape of both pi and pi*, since both are occupied. Flipping one of the two unpaired alpha spins in the T reference will access all four valence states (recall that a triplet state with Ms=0 is perfectly OK, namely ab+ba). For more information, see Y.Shao, M.Head-Gordon, A.I.Krylov

Further Information

4-122

J.Chem.Phys. 118,4807(2003) F.Wang, T.Ziegler J.Chem.Phys. 121, 12191(2004) J.Chem.Phys. 122, 074109(2005) O.Vahtras, Z.Rinkevicius J.Chem.Phys. 126, 114101(2007) Z.Rinkevicius, H.Agren Chem.Phys.Lett. 491, 132(2010) Z.Rinkevicius, O.Vahtras, H.Agren J.Chem.Phys. 113, 114101(2010 M.Huix-Rotllant, B.Natarajan, A.Ipatov, C.M.Wawire, T.Deutsch, M.E.Casida Phys.Chem.Chem.Phys. 12, 12811(2010) The penalty constrained optimization procedure was used to find ethylene's conical intersections by N.Minezawa, M.S.Gordon J.Phys.Chem.A 113, 12749(2009)

references for DFT

An excellent overview of DFT can be found in Chapter 6 of Frank Jensen's book. Two other monographs are "Density Functional Theory of Atoms and Molecules" R.G.Parr, W.Yang Oxford Scientific, 1989 "A Chemist's Guide to Density Functional Theory" W.Koch, M.C.Holthausen Wiley-VCH, 2001 If you would like to understand the "theory" of Density Functional Theory, see Kieron Burke's online book "The ABC of DFT", at http://dft.uci.edu/dftbook.html. You may also enjoy "Fourteen easy lessons in Density Functional Theory", by John Perdew and Adrienn Ruzsinszky, Int. J. Quantum Chem., in press 2010. A delightful and thought provoking paper on the relationship of DFT to conventional quantum mechanics using wavefunctions: P.M.W.Gill Aust.J.Chem. 54, 661-662(2001) A paper comparing DFT's approach to correlation to traditional quantum chemistry methods: E.J.Baerends, O.V.Gritsenko J.Phys.Chem.A 101, 5383-5403(1997) Some philosophy about designing functionals at each rung of DFT's "Jacob's ladder": J.P.Perdew, A.Ruzsinszky, J.Tao, V.N.Staroverov, G.E.Scuseria, G.I.Csonka J.Chem.Phys. 123, 062201/1-9(2005)

Further Information On hybridization: J.P.Perdew, M.Ernzerhof, K.Burke J.Chem.Phys. 105, 9982-9985(1996) G.I.Csonka, J.P.Perdew, A.Ruzsinszky J.Chem.Theory Comput. 6, 3688-3703(2010) Some reading on the grid-free approach to density functional theory is: Y.C.Zheng, J.Almlof Chem.Phys.Lett. 214, 397-401(1996) Y.C.Zheng, J.Almlof J.Mol.Struct.(Theochem) 288, 277(1996) K.Glaesemann, M.S.Gordon J.Chem.Phys. 108, 9959-9969(1998) K.Glaesemann, M.S.Gordon J.Chem.Phys. 110, 6580-6582(1999) K.Glaesemann, M.S.Gordon J.Chem.Phys. 112, 10738-10745(2000)

4-123

References about gridding: A.D.Becke J.Chem.Phys. 88, 2547-2553(1988) C.W.Murray, N.C.Handy, G.L.Laming Mol.Phys. 78, 997-1014(1993) P.M.W.Gill, B.G.Johnson, J.A.Pople Chem.Phys.Lett. 209, 506-512(1993) A.A.Jarecki, E.R.Davidson Chem.Phys.Lett. 300, 44-52(1999) R.Lindh, P.-A.Malmqvist, L.Gagliardi Theoret.Chem.Acc. 106, 178-187(2001) S.-H.Chien, P.M.W.Gill J.Comput.Chem. 27, 730-739(2006) J.Grafenstein, D.Izotov, D.Cremer J.Chem.Phys. 127, 164113/1-7(2007) Gill's 1993 paper is the reference for SG1=.TRUE. Handy's 1993 paper is a reference for polar coordinates. Lebedev grids may be referenced as V.I.Lebedev, D.N.Laikov Doklady Math. 59, 477-481(1999) GAMESS uses Christoph van Wuellen's FORTRAN translation of these grids, originally coded in C by Laikov (www.ccl.net). --- exchange functionals Slater exchange: J.C.Slater Phys.Rev. 81, 385-390(1951) XALPHA is Slater with alpha=0.70 BECKE (often called B88) exchange:

Further Information A.D.Becke Phys.Rev. A38, 3098-3100(1988)

4-124

GILL (often called G96) exchange: P.M.W.Gill Mol.Phys. 89, 433-445(1996) OPTX exchange: N.C.Handy, A.J.Cohen Mol.Phys. 99, 403-412(2001) J.Chem.Phys. 86, 1425-1428(1987)

Depristo/Kress exchange: A.E.DePristo, J.E.Kress

--- correlation functionals VWN local correlation: S.H.Vosko, L.Wilk, M.Nusair Can.J.Phys. 58, 1200-1211(1980) This paper has five formulae in it, and since the 5th is a good quality fit, it states "since formula 5 is easiest to implement in LSDA calculations, we recommend its use". PZ81 correlation: J.P.Perdew, A.Zunger P86 GGA correlation: Phys.Rev.B 23, 5048-5079(1981)

J.P.Perdew Phys.Rev.B 33, 8822(1986)

PW local correlation (used in PW91): J.P.Perdew, Y.Wang Phys.Rev.B 45, 13244-13249(1992) LYP correlation: C.Lee, W.Yang, R.G.Parr Phys.Rev. B37, 785-789(1988) For practical purposes this is always used in a transformed way, involving the square of the density gradient: B.Miehlich, A.Savin, H.Stoll, H.Preuss Chem.Phys.Lett. 157, 200-206(1989) OP (One-parameter Progressive) correlation: T.Tsuneda, K.Hirao Chem.Phys.Lett. 268, 510-520(1997) T.Tsuneda, T.Suzumura, K.Hirao J.Chem.Phys. 110, 10664-10678(1999) --- exchange/correlation functionals PW91 exchange/correlation: J.P.Perdew, J.A.Chevray, S.H.Vosko, K.A.Jackson, M.R.Pederson, D.J.Singh, C.Fiolhais Phys.Rev. B46, 6671-6687(1992) EDF1 - empirical density functional #1, a tweaked BLYP

Further Information developed for use with 6-31+G(d) basis sets, R.D.Adamson, P.M.W.Gill, J.A.Pople Chem.Phys.Lett. 284, 6-11(1998)

4-125

MOHLYP - metal optimized OPTX exchange, half LYP correlation N.E.Schultz, Y.Zhao, D.G.Truhlar J.Phys.Chem.A 109, 11127-11143(2005) See also comp.chem.umn.edu/info/MOHLYP_reference.pdf for information about the related functional MOHLYP2. PBE exchange/correlation functional: J.P.Perdew, K.Burke, M.Ernzerhof Phys.Rev.Lett. 77, 3865-8(1996); Err. 78,1396(1997) revPBE (revised PBE exchange, but see RPBE below): Y.Zhang, W.Yang Phys.Rev.Lett. 80, 890(1998) RPBE (a different revision of PBE exchange): B.Hammer, L.B.Hansen, J.K.Norskov Phys.Rev.B 59, 7413-7421(1999) This revision retains the same increase in accuracy for atomization energies that revPBE affords, while rigorously preserving the correct Lieb-Oxford limit, unlike revPBE. PBEsol (modified PBE parameters, for solid properties): J.P.Perdew, A.Ruzsinszky, G.I.Csonka, O.A.Vydrov, G.E.Scuseria, L.A.Constantin, Z.Zhou, K.Burke Phys.Rev.Lett. 100, 136406/1-7(2008) Dispersion corrections: Local Response Dispersion (LRD) T.Sato, H.Nakai J.Chem.Phys. 131, 224104/1-12(2009) T.Sato, H.Nakai J.Chem.Phys. 132, 194101/1-9(2010) empirical dispersion correction (DC): This is developed in three successive versions by Grimme 1: S.Grimme J.Comput.Chem. 25, 1463-1473(2004) 2: S.Grimme J.Comput.Chem. 27, 1787-1799(2006) 3: S.Grimme, J.Antony, S.Ehrlich, H.Krieg J.Chem.Phys. 132, 154104/1-19(2010) which are applied to different functionals with different parameterizations of the correction. Setting DC=.TRUE. thus converts functionals such as BLYP/B3LYP/PBE/BP86/TPSS to BLYP-D, B3LYP-D, and so forth. See the papers for more details.

Further Information

4-126

A functional where the input keyword contains already the -D, namely B97-D, consists of a revamping of the B97 functional to remove its hybridization with HF exchange and reparameterization, as well as adding the dispersion correction: S.Grimme J.Comput.Chem. 27, 1787-1799(2006) A somewhat different form for the dispersion correction is used in the wB97-D functional. Selection of DFTTYP=B97-D or wB97-D does not require setting DC on. The next two occur in the grid-free program only, various WIGNER exchange/correlation functionals: Q.Zhao, R.G.Parr Phys.Rev. A46, 5320-5323(1992) CAMA/CAMB exchange/correlation functionals: G.J.Laming, V.Termath, N.C.Handy J.Chem.Phys. 99. 8765-8773(1993) --- hybrids with HF exchange B3PW91 hybrid: A.D.Becke J.Chem.Phys. 98, 5648-5642(1993) B3LYP hybrid: A.D.Becke J.Chem.Phys. 98, 5648-5642(1993) P.J.Stephens, F.J.Devlin, C.F.Chablowski, M.J.Frisch J.Phys.Chem. 98, 11623-11627(1994) R.H.Hertwig, W.Koch Chem.Phys.Lett. 268, 345-351(1997) The first paper is actually on B3PW91 hybridization, and optimizes the mixing of five functionals with PW91 as the correlation GGA. The second paper then proposed use of LYP in place of PW91, without reoptimizing the mixing ratios of the hybrid. The final paper discusses the controversy surrounding which VWN functional is used in the hybrid. GAMESS uses VWN5 in its B3LYP hybrid, but see also B3LYP1 to use the RPA parameterized VWN1 formula. B97 hybrid: A.D.Becke J.Chem.Phys. 107, 8554-8560(1997)

B97-1 hybrid, a reparameterization of B97: F.A.Hamprecht, A.J.Cohen, D.J.Tozer, N.C.Handy J.Chem.Phys. 109, 6264-6271(1998) B97-2 hybrid, a reparameterization of B97: P.J.Wilson, T.J.Bradley, D.J.Tozer J.Chem.Phys. 115, 9233-9242(2001)

Further Information B97-3 hybrid, a reparameterization of B97: T.W.Keal, D.J.Tozer J.Chem.Phys. 123, 121103-1/4(2005) B97-K and BMK hybrids, K=kinetics: A.D.Boese, J.M.L.Martin J.Chem.Phys. 123, 3405-3416(2004)

4-127

HCTH93, HCTH120, HCTH147, and HCTH407 use training sets with the indicated number of atoms and molecules used to adjust the B97 functional: HCTH93 is defined in the B97-1 paper. HCTH120 and HCTH147: A.D.Boese, N.L.Doltsinis, N.C.Handy, M.Sprik J.Chem.Phys. 112, 1670-1678(2000) HCTH407: A.D.Boese, N.C.Handy J.Chem.Phys. 114, 5497-5503(2001) B98, Becke's reparameterization of B97: A.D. Becke J.Chem.Phys. 108, 9624-9631(1998) ...bringing to an end "the B97 family". X3LYP hybrid: X.Xu, Q.Zhang, R.P.Muller, W.A.Goddard J.Chem.Phys. 122, 014105/1-14(2005) PBE0 hybrid: C.Adamo, V.Barone J.Chem.Phys. 110, 6158-6170(1999)

in the grid free program only, HALF exchange: This is programmed as 50% HF plus 50% B88 exchange. BHHLYP exchange/correlation: This is 50% HF plus 50% B88, with LYP correlation. Note: neither is the HALF-AND-HALF exchange/correlation: A.D.Becke J.Chem.Phys. 98, 1372-1377(1993) which he defined as 50% HF + 50% SVWN. --- meta-GGA functionals These are pure DFT meta-GGAs, unless the description explicitly says it is a hybrid!

Further Information PKZB (a prototype of the TPSS family): J.P.Perdew, S.Kurth, A.Zupan, P.Blaha Phys.Rev.Lett. 82, 2544-2547(1999) tHCTH and tHCTHhyb=15% HF exchange: A.D.Boese, N.C.Handy J.Chem.Phys. 116, 9559-9569(2002) TPSS: J.P.Perdew, J.Tao, V.N.Staroverov, G.E.Scuseria Phys.Rev.Lett. 91, 146401/1-4(2003) J.P.Perdew, J.Tao, V.N.Staroverov, G.E.Scuseria J.Chem.Phys. 120, 6898-6911(2004)

4-128

TPSSm, a modified TPSS improving atomization energies: J.P.Perdew, A.Ruzsinszky, J.Tao, G.I.Csonka, G.E.Scuseria Phys.Rev.A 76, 042506/1-6(2007) TPSSh, a 10% hybrid using TPSS: V.N.Staroverov, G.E.Scuseria, J.Tao, J.P.Perdew J.Chem.Phys. 119, 12129-12137(2003), erratum is J.Chem.Phys. 121, 11507(2004) revTPSS, "workhorse functional for CMP and QC" J.P.Perdew, A.Ruzsinsky, G.I.Csonka, L.A.Constantin, J.Sun Phys.Rev.Lett. 103, 026403/1-4(2009) VS98 (whose form is the prototype of the M06 family): T.V.Voorhis, G.E.Scuseria J.Chem.Phys. 109, 400-410(1998) U.Minnesota hybrid meta-GGA family: M05: Y.Zhao, N.E.Schultz, D.G.Truhlar J.Chem.Phys. 123, 161103/1-4(2005) M05-2X: Y.Zhao, D.G.Truhlar J.Comput.Chem.Theory Comput. 2, 1009-1018(2006) M06: Y.Zhao, D.G.Truhlar Theoret.Chem.Acc. 120,215-241(2008) M06-2X: ibid M06-HF: Y.Zhao, D.G.Truhlar J.Phys.Chem.A 110, 13126-13130(2006) M06-L: Y.Zhao, D.G.Truhlar J.Chem.Phys. 125, 194101/1-18(2006) SOGGA: Y.Zhao, D.G.Truhlar J.Chem.Phys. 128, 184109/1-8(2008) M08-HX and M08-SO: Y.Zhao, D.G.Truhlar J.Chem.Theory Comput. 4, 1849-1868(2008) For reviews, please see the paper for M06, and also Y.Zhao, D.G.Truhlar Acc.Chem.Res. 41, 157-167(2008)

Further Information These contain recommendations for choosing the one most appropriate to your problem. ---- long-range corrected functionals: LC-BLYP, LC-BOP, LC-BVWN: Y.Tawada, T.Tsuneda, S.Yanagisawa, Y.Yanai, K.Hirao J.Chem.Phys. 120, 8425-8433(2004) CAM-B3LYP: T.Yanai, D.P.Tew, N.C.Handy Chem.Phys.Lett. 393, 51-57(2004) wB97, wB97X, wB97X-D: J.-D. Chai, M.Head-Gordon J.Chem.Phys. 128, 084106/1-15(2004) J.-D. Chai, M.Head-Gordon Phys.Chem.Chem.Phys. 10, 6615-6620(2008)

4-129

A review on the topic of long range corrections, which are also called 'range separated hybrids', is D.Jacquemin, E.A.Perpete, G.E.Scuseria, I.Ciofini, C.Adamo J.Chem.Theory Comput. 4, 123-135(2008) ---- "double-hybrid" ---The B2PLYP family is a mixture of B88 and HF exchange, and a mixture of LYP and MP2 correlation: B2-PLYP: S.Grimme J.Chem.Phys. 124, 034108/1-15(2006) B2G-PLYP: A.Karton, A.Tarnopolsky, J.F.Lamere, G.C.Schatz, J.M.L.Martin J.Phys.Chem. A 112, 12868(2008) B2K-PLYP, B2T-PLYP: A.Tarnopolsky, A.Karton, R.Sertchook, D.Vuzman, J.M.L.Martin J.Phys.Chem. A 112, 3(2008) Double hybrids which are also "long range corrected" (and whose parameters depend on the basis set): wB97X-2, wB97X-2L: J.-D. Chai, M.Head-Gordon J.Chem.Phys. 131, 174105/1-13(2009) * * * * * Some of the recent functional additions to GAMESS were made using code from the "density functional repository",

http://www.cse.clrc.ac.uk/qcg/dft

Further Information

4-130

We thank Huub van Dam for his assistance with this, and particularly for providing the VWN1 functional. The Minnesota functionals are based on subroutines provided by the Truhlar group at the University of Minnesota. Some functionals, and particularly their high derivatives needed by TDDFT, were created by MAXIMA's algebraic manipulation, along the lines described by P.Salek, A.Hesselmann J.Comput.Chem. 28, 2569-2575(2007) * * * * * The paper of Johnson, Gill, and Pople listed below has a useful summary of formulae, and details about a gradient implementation. A paper on 1st and 2nd derivatives of DFT with respect to nuclear coordinates and applied fields is A.Komornicki, G.Fitzgerald J.Chem.Phys. 98, 1398-1421(1993) and see also P.Deglmann, F.Furche, R.Ahlrichs Chem.Phys.Lett. 362, 511-518(2002). A few of the many papers assessing the accuracy of DFT: B.Miehlich, A.Savin, H.Stoll, H.Preuss Chem.Phys.Lett. 157, 200-206(1989) B.G.Johnson, P.M.W.Gill, J.A.Pople J.Chem.Phys. 98, 5612-5626(1993) N.Oliphant, R.J.Bartlett J.Chem.Phys. 100, 6550-6561(1994) L.A.Curtiss, K.Raghavachari, P.C.Redfern, J.A.Pople J.Chem.Phys. 106, 1063-1079(1997) E.R.Davidson Int.J.Quantum Chem. 69, 241-245(1998) B.J.Lynch, D.G.Truhlar J.Phys.Chem.A 105, 2936-2941(2001) R.A.Pascal J.Phys.Chem.A 105, 9040-9048(2001) A.D.Boese, J.M.L.Martin, N.C.Handy J.Chem.Phys. 119, 3005-3014(2003) Y.Zhao, D.G.Truhlar, J.Phys.Chem.A 109, 5656-5667(2005) K.E.Riley, B.T.Op't Holt, K.M.Merz J.Chem.Theory Comput. 3, 407-433(2007) S.F.Sousa, P.A.Fernandes, M.J.Ramos J.Phys.Chem.A 111, 10439-10452(2007) Boese et al. include basis set comparisons, as well as functional comparisons. The final paper is a review of reviews, and encourages you to think past B3LYP, which after all dates from 1993! Of course there are assessments in many of the functional papers as well.

Further Information

4-131

On the accuracy of DFT for large molecule thermochemistry: L.A.Curtiss, K.Ragavachari, P.C.Redfern, J.A.Pople J.Chem.Phys. 112, 7374-7383(2000) P.C.Redfern, P.Zapol, L.A.Curtiss, K.Ragavachari J.Phys.Chem.A 104, 5850-5854(2000) Spin contamination in DFT: 1. It is empirically observed that the <S**2> values for unrestricted DFT are smaller than for unrestricted HF. 2. GAMESS computes the <S**2> quantity in an approximate way, namely it pretend that the Kohn-Shan orbitals can be used to form a determinant (WRONG, WRONG, WRONG, there is no wavefunction in DFT!!!) and then uses the same formula that UHF uses to evaluate that determinant's spin expectation value. See G.J.Laming, N.C.Handy, R.D.Amos Mol.Phys. 80, 1121-1134(1993) J.Baker, A.Scheiner, J.Andzelm Chem.Phys.Lett. 216, 380-388(1993) C.Adamo, V.Barone, A.Fortunelli J.Chem.Phys. 98, 8648-8652(1994) J.A.Pople, P.M.W.Gill, N.C.Handy Int.J.Quantum Chem. 56, 303-305(1995) J.Wang, A.D.Becke, V.H.Smith J.Chem.Phys. 102, 3477-3480(1995) J.M.Wittbrodt, H.B.Schlegel J.Chem.Phys. 105, 6574-6577(1996) J.Grafenstein, D.Cremer Mol.Phys. 99, 981-989(2001) and commentary in Koch & Holthausen, pp 52-54. Orbital energies: The discussion on page 49-50 of Koch and Holthausen shows that although the highest occupied orbital's eigenvalue should be the ionization potential for exact Kohn-Sham calculations, the functionals we actually have greatly underestimate IP values. The 5th reference below shows how inclusion of HF exchange helps this, and provides a linear correction formula for IPs. The first two papers below connect the HOMO eigenvalue to the IP, and the third shows that while the band gap is underestimated by existing functionals, the gap's center is correctly predicted. However, the 5th paper shows that DFT is actually pretty hopeless at predicting these gaps. The 4th paper uses SCF

Further Information

4-132

densities to generate exchange-correlation potentials that actually give fairly good IP values: J.F.Janak Phys.Rev.B 18, 7165-7168(1978) M.Levy, J.P.Perdew, V.Sahni Phys.Rev.A 30, 2745-2748(1984) J.P.Perdew, M.Levy Phys.Rev.Lett. 51, 1884-1887(1983) A.Nagy, M.Levy Chem.Phys.Lett. 296, 313-315(1998) G.Zhang, C.B.Musgrave J.Phys.Chem.A 111, 1554-1561(2007)

Further Information

4-133

Summary of excited state methods

This is not a "how to" section, as the actual calculations will be carried out by means described elsewhere in the chapter. Instead, a summary of methods that can treat excited states is given. The simplest possibility is SCFTYP. For example, a closed shell molecule's first triplet state can always be treated by SCFTYP=ROHF MULT=3. Assuming there is some symmetry present, the GVB program may be able to do excited singlets variationally, provided they are of a different space symmetry than the ground state. The MCSCF program gives a general entree into excited states, since upper roots of a Hamiltonian are always variational: see for example NSTATE and WSTATE and IROOT in $DET. CI calculations also give a simple entry into excitated states. There are a variety of programs, selected by CITYP in $CONTRL. Note in particular CITYP=CIS, programmed for closed shell ground states, with gradient capability for singlet excited states, and the calculation of triplet state energies. The other CI programs can generate very flexible wavefunctions for the evaluation of the excitation energy, and property values. Note that the GUGA program will do nuclear gradients provided the reference is RHF. The TD-DFT method treats singly excited states, including correlation effects, and is a popular alternative to CIS. The program allows for excitation energies from a UHF reference, but is much more powerful for RHF references: nuclear gradients and/or properties may be computed. Use of a "long range corrected" or "range separated" functional (the two terms are synonymous) is often thought to be important when treating charge transfer or Rydberg states: see the LC=.TRUE. flag or CAMB3LYP. Equation of Motion (EOM) coupled cluster can give accurate estimates of excitation energies. There are no gradients, and properties exist only for EOM-CCSD, but triples corrections to the energy are available. See $EOMINP for more details. Most of the runs will predict oscillator strengths, or Einstein coefficients, or similar data regarding the electronic transition moments. Full prediction of UV-vis spectra is not possible without Franck-Condon information.

Further Information

4-134

Excited states frequently come close together, and crossings between them are of great interest. See RUNTYP=TRANSITION for spin-orbit coupling, responsible for InterSystem Crossing (ISC) between states of different multiplicity. See RUNTYP=NACME for the non-adiabatic coupling matrix elements that cause Internal Conversion (IC) between states of the same spin multiplicity. It is possible to search for the lowest energy on the crossing seam between two surfaces, provided those surfaces have different spins, or different space symmetries (or both), see RUNTYP=MEX. Solvent effects (EFP and/or PCM) can easily be incorporated when using SCFTYP to generate the states, and nuclear gradients are available. It is now possible to assess solvent effects on TD-DFT excitation energies from closed shell references, using either EFP or PCM. Excited states often possess Rydberg character, so diffuse functions in the basis set are likely to be important.

Further Information

4-135

Geometry Searches and Internal Coordinates

Stationary points are places on the potential energy surface with a zero gradient vector (first derivative of the energy with respect to nuclear coordinates). These include minima (whether relative or global), better known to chemists as reactants, products, and intermediates; as well as transition states (also known as saddle points). The two types of stationary points have a precise mathematical definition, depending on the curvature of the potential energy surface at these points. If all of the eigenvalues of the hessian matrix (second derivative of the energy with respect to nuclear coordinates) are positive, the stationary point is a minimum. If there is one, and only one, negative curvature, the stationary point is a transition state. Points with more than one negative curvature do exist, but are not important in chemistry. Because vibrational frequencies are basically the square roots of the curvatures, a minimum has all real frequencies, and a saddle point has one imaginary vibrational "frequency". GAMESS locates minima by geometry optimization, as RUNTYP=OPTIMIZE, and transition states by saddle point searches, as RUNTYP=SADPOINT. In many ways these are similar, and in fact nearly identical FORTRAN code is used for both. The term "geometry search" is used here to describe features which are common to both procedures. The input to control both RUNTYPs is found in the $STATPT group. As will be noted in the symmetry section below, an OPTIMIZE run does not always find a minimum, and a SADPOINT run may not find a transtion state, even though the gradient is brought to zero. You can prove you have located a minimum or saddle point only by examining the local curvatures of the potential energy surface. This can be done by following the geometry search with a RUNTYP=HESSIAN job, which should be a matter of routine.

quasi-Newton Searches
Geometry searches are most effectively done by what is called a quasi-Newton-Raphson procedure. These methods assume a quadratic potential surface, and require the

Further Information

4-136

exact gradient vector and an approximation to the hessian. It is the approximate nature of the hessian that makes the method "quasi". The rate of convergence of the geometry search depends on how quadratic the real surface is, and the quality of the hessian. The latter is something you have control over, and is discussed in the next section. GAMESS contains different implementations of quasiNewton procedures for finding stationary points, namely METHOD=NR, RFO, QA, and the seldom used SCHLEGEL. They differ primarily in how the step size and direction are controlled, and how the Hessian is updated. The CONOPT method is a way of forcing a geometry away from a minimum towards a TS. It is not a quasi-Newton method, and is described at the very end of this section. The NR method employs a straight Newton-Raphson step. There is no step size control, the algorithm will simply try to locate the nearest stationary point, which may be a minimum, a TS, or any higher order saddle point. NR is not intended for general use, but is used by GAMESS in connection with some of the other methods after they have homed in on a stationary point, and by Gradient Extremal runs where location of higher order saddle points is common. NR requires a very good estimate of the geometry in order to converge on the desired stationary point. The RFO and QA methods are two different versions of the so-called augmented Hessian techniques. They both employ Hessian shift parameter(s) in order to control the step length and direction. In the RFO method, the shift parameter is determined by approximating the PES with a Rational Function, instead of a second order Taylor expansion. For a RUNTYP=SADPOINT, the TS direction is treated separately, giving two shift parameters. This is known as a Partitioned Rational Function Optimization (P-RFO). The shift parameter(s) ensure that the augmented Hessian has the correct eigenvalue structure, all positive for a minimum search, and one negative eigenvalue for a TS search. The (P)-RFO step can have any length, but if it exceeds DXMAX, the step is simply scaled down. In the QA (Quadratic Approximation) method, the shift parameter is determined by the requirement that the step size should equal DXMAX. There is only one shift parameter for both minima and TS searches. Again the augmented Hessian will have the correct structure. There

Further Information

4-137

is another way of describing the same algorithm, namely as a minimization on the "image" potential. The latter is known as TRIM (Trust Radius Image Minimization). The working equation is identical in these two methods. When the RFO steplength is close to DXMAX, there is little difference between the RFO and QA methods. However, the RFO step may in some cases exceed DXMAX significantly, and a simple scaling of the step will usually not produce the best direction. The QA step is the best step on the hypersphere with radius DXMAX. For this reason QA is the default algorithm. Near a stationary point the straight NR algorithm is the most efficient. The RFO and QA may be viewed as methods for guiding the search in the "correct" direction when starting far from the stationary point. Once the stationary point is approached, the RFO and QA methods switch to NR, automatically, when the NR steplength drops below 0.10 or DXMAX, whichever is the smallest. The QA method works so well that we use it exclusively, and so the SCHLEGEL method will probably be omitted from some future version of GAMESS. You should read the papers mentioned below in order to understand how these methods are designed to work. The first 3 papers describe the RFO and TRIM/QA algorithms. A good but slightly dated summary of search procedures is given by Bell and Crighton, and see also the review by Schlegel. Most of the FORTRAN code for geometry searches, and some of the discussion in this section was written by Frank Jensen of the University of Aarhus, whose paper compares many of the algorithms implemented in GAMESS: 1. J.Baker J.Comput.Chem. 7, 385-395(1986) 2. T.Helgaker Chem.Phys.Lett. 182, 503-510(1991) 3. P.Culot, G.Dive, V.H.Nguyen, J.M.Ghuysen Theoret.Chim.Acta 82, 189-205(1992) 4. H.B.Schlegel J.Comput.Chem. 3, 214-218(1982) 5. S.Bell, J.S.Crighton J.Chem.Phys. 80, 2464-2475(1984). 6. H.B.Schlegel Advances in Chemical Physics (Ab Initio Methods in Quantum Chemistry, Part I), volume 67, K.P.Lawley, Ed. Wiley, New York, 1987, pp 249-286. 7. F.Jensen J.Chem.Phys. 102, 6706-6718(1995).

Further Information

4-138

the nuclear Hessian

Although quasi-Newton methods require only an approximation to the true hessian, the quality of this matrix has a great affect on convergence of the geometry search. There is a procedure contained within GAMESS for guessing a positive definite hessian matrix, HESS=GUESS. If you are using Cartesian coordinates, the guess hessian is based on pairwise atom stretches. The guess is more sophisticated when internal coordinates are defined, as empirical rules will be used to estimate stretching and bending force constants. Other angular force constants are set to 1/4. The guess often works well for minima, but cannot possibly find transition states (because it is positive definite). Therefore, GUESS may not be selected for SADPOINT runs. Two options for providing a more accurate hessian are HESS=READ and CALC. For the latter, the true hessian is obtained by direct calculation at the initial geometry, and then the geometry search begins, all in one run. The READ option allows you to feed in the hessian in a $HESS group, as obtained by a RUNTYP=HESSIAN job. The second procedure is actually preferable, as you get a chance to see the frequencies. Then, if the local curvatures look good, you can commit to the geometry search. Be sure to include a $GRAD group (if the exact gradient is available) in the HESS=READ job so that GAMESS can take its first step immediately. Note also that you can compute the hessian at a lower basis set and/or wavefunction level, and read it into a higher level geometry search. In fact, the $HESS group could be obtained at the semiempirical level. This trick works because the hessian is 3Nx3N for N atoms, no matter what atomic basis is used. The gradient from the lower level is of course worthless, as the geometry search must work with the exact gradient of the wavefunction and basis set in current use. Discard the $GRAD group from the lower level calculation! You often get what you pay for. HESS=GUESS is free, but may lead to significantly more steps in the geometry search. The other two options are more expensive at the beginning, but may pay back by rapid convergence to the stationary point.

Further Information

4-139

The hessian update frequently improves the hessian for a few steps (especially for HESS=GUESS), but then breaks down. The symptoms are a nice lowering of the energy or the RMS gradient for maybe 10 steps, followed by crazy steps. You can help by putting the best coordinates into $DATA, and resubmitting, to make a fresh determination of the hessian. The default hessian update for OPTIMIZE runs is BFGS, which is likely to remain positive definite. The POWELL update is the default for SADPOINT runs, since the hessian can develop a negative curvature as the search progresses. The POWELL update is also used by the METHOD=NR and CONOPT since the Hessian may have any number of negative eigenvalues in these cases. The MSP update is a mixture of Murtagh-Sargent and Powell, suggested by Josep Bofill, (J.Comput.Chem., 15, 1-11, 1994). It sometimes works slightly better than Powell, so you may want to try it.

coordinate choices
Optimization in cartesian coordinates has a reputation of converging slowly. This is largely due to the fact that translations and rotations are usually left in the problem. Numerical problems caused by the small eigenvalues associated with these degrees of freedom are the source of this poor convergence. The methods in GAMESS project the hessian matrix to eliminate these degrees of freedom, which should not cause a problem. Nonetheless, Cartesian coordinates are in general the most slowly convergent coordinate system. The use of internal coordinates (see NZVAR in $CONTRL as well as $ZMAT) also eliminates the six rotational and translational degrees of freedom. Also, when internal coordinates are used, the GUESS hessian is able to use empirical information about bond stretches and bends. On the other hand, there are many possible choices for the internal coordinates, and some of these may lead to much poorer convergence of the geometry search than others. Particularly poorly chosen coordinates may not even correspond to a quadratic surface, thereby ending all hope that a quasi-Newton method will converge. Internal coordinates are frequently strongly coupled. Because of this, Jerry Boatz has called them "infernal coordinates"! A very common example to illustrate this might be a bond length in a ring, and the angle on the

Further Information

4-140

opposite side of the ring. Clearly, changing one changes the other simultaneously. A more mathematical definition of "coupled" is to say that there is a large off-diagonal element in the hessian. In this case convergence may be unsatisfactory, especially with a diagonal GUESS hessian, where a "good" set of internals is one with a diagonally dominant hessian. Of course, if you provide an accurately computed hessian, it will have large off-diagonal values where those are truly present. Even so, convergence may be poor if the coordinates are coupled through large 3rd or higher derivatives. The best coordinates are therefore those which are the most "quadratic". One very popular set of internal coordinates is the usual "model builder" Z-matrix input, where for N atoms, one uses N-1 bond lengths, N-2 bond angles, and N-3 bond torsions. The popularity of this choice is based on its ease of use in specifying the initial molecular geometry. Typically, however, it is the worst possible choice of internal coordinates, and in the case of rings, is not even as good as Cartesian coordinates. However, GAMESS does not require this particular mix of the common types. GAMESS' only requirement is that you use a total of 3N-6 coordinates, chosen from these 3 basic types, or several more exotic possibilities. (Of course, we mean 3N-5 throughout for linear molecules). These additional types of internal coordinates include linear bends for 3 collinear atoms, out of plane bends, and so on. There is no reason at all why you should place yourself in a straightjacket of N-1 bonds, N-2 angles, and N-3 torsions. If the molecule has symmetry, be sure to use internals which are symmetrically related. For example, the most effective choice of coordinates for the atoms in a four membered ring is to define all four sides, any one of the internal angles, and a dihedral defining the ring pucker. For a six membered ring, the best coordinates seem to be 6 sides, 3 angles, and 3 torsions. The angles should be every other internal angle, so that the molecule can "breathe" freely. The torsions should be arranged so that the central bond of each is placed on alternating bonds of the ring, as if they were pi bonds in Kekule benzene. For a five membered ring, we suggest all 5 sides, 2 internal angles, again alternating every other one, and 2 dihedrals to fill in. The internal angles of necessity skip two atoms where the ring closes. Larger rings should generalize on the idea

Further Information

4-141

of using all sides but only alternating angles. If there are fused rings, start with angles on the fused bond, and alternate angles as you go around from this position. Rings and more especially fused rings can be tricky. For these systems, especially, we suggest the Cadillac of internal coordinates, the "natural internal coordinates" of Peter Pulay. For a description of these, see P.Pulay, G.Fogarosi, F.Pang, J.E.Boggs, J.Am.Chem.Soc. 101, 2550-2560 (1979). G.Fogarasi, X.Zhou, P.W.Taylor, P.Pulay J.Am.Chem.Soc. 114, 8191-8201 (1992). These are linear combinations of local coordinates, except in the case of rings. The examples given in these two papers are very thorough. An illustration of these types of coordinates is given in the example job EXAM25.INP, distributed with GAMESS. This is a nonsense molecule, designed to show many kinds of functional groups. It is defined using standard bond distances with a classical Z-matrix input, and the angles in the ring are adjusted so that the starting value of the unclosed OO bond is also a standard value. Using Cartesian coordinates is easiest, but takes a very large number of steps to converge. This however, is better than using the classical Z-matrix internals given in $DATA, which is accomplished by setting NZVAR to the correct 3N-6 value. The geometry search changes the OO bond length to a very short value on the 1st step, and the SCF fails to converge. (Note that if you have used dummy atoms in the $DATA input, you cannot simply enter NZVAR to optimize in internal coordinates, instead you must give a $ZMAT which involves only real atoms). The third choice of internal coordinates is the best set which can be made from the simple coordinates. It follows the advice given above for five membered rings, and because it includes the OO bond, has no trouble with crashing this bond. It takes 20 steps to converge, so the trouble of generating this $ZMAT is certainly worth it compared to the use of Cartesians. Natural internal coordinates are defined in the final group of input. The coordinates are set up first for the ring, including two linear combinations of all angles and all torsions withing the ring. After this the methyl is

Further Information

4-142

hooked to the ring as if it were a NH group, using the usual terminal methyl hydrogen definitions. The H is hooked to this same ring carbon as if it were a methine. The NH and the CH2 within the ring follow Pulay's rules exactly. The amount of input is much greater than a normal Z-matrix. For example, 46 internal coordinates are given, which are then placed in 3N-6=33 linear combinations. Note that natural internals tend to be rich in bends, and short on torsions. The energy results for the three coordinate systems which converge are as follows: NSERCH Cart 0 -48.6594935049 1 -48.6800538676 2 -48.6822702585 3 -48.6858299354 4 -48.6881499412 5 -48.6890226067 6 -48.6898261650 7 -48.6901936624 8 -48.6905304889 9 -48.6908626791 10 -48.6914279465 11 -48.6921521142 12 -48.6931136707 13 -48.6940437619 14 -48.6949546487 15 -48.6961698826 16 -48.6973813002 17 -48.6984850655 18 -48.6991553826 19 -48.6996239136 20 -48.7002269303 21 -48.7005379631 22 -48.7008387759 ... 50 -48.7022519950 good Z-mat -48.6594935049 -48.6806631261 -48.6510215698 -48.6882945647 -48.6849667085 -48.6911899936 -48.6878047907 -48.6930608185 -48.6940607117 -48.6949137185 -48.6963767038 -48.6986608776 -48.7007305310 -48.7016095285 -48.7021531692 -48.7022080183 -48.7022454522 -48.7022492840 -48.7022503853 -48.7022507037 -48.7022508393 nat. int. -48.6594935049 -48.6838361406 -48.6874045449 -48.6932811528 -48.6946836332 -48.6959800274 -48.6973821465 -48.6987652146 -48.6996366016 -48.7006656309 -48.7017273728 -48.7021504975 -48.7022405019 -48.7022548935 -48.7022569328 -48.7022570260 -48.7022570662

from which you can see that the natural internals are actually the best set. The $ZMAT exhibits upward burps in the energy at step 2, 4, and 6, so that for the same number of steps, these coordinates are always at a higher energy than the natural internals. The initial hessian generated for these three columns contains 0, 33, and 46 force constants. This assists the natural internals, but is not the major reason for

Further Information

4-143

its superior performance. The computed hessian at the final geometry of this molecule, when transformed into the natural internal coordinates is almost diagonal. This almost complete uncoupling of coordinates is what makes the natural internals perform so well. The conclusion is of course that not all coordinate systems are equal, and natural internals are the best. As another example, we have run the ATCHCP molecule, which is a popular geometry optimization test, due to its two fused rings: H.B.Schlegel, Int.J.Quantum Chem., Symp. 26, 253-264(1992) T.H.Fischer and J.Almlof, J.Phys.Chem. 96, 9768-9774(1992) J.Baker, J.Comput.Chem. 14, 1085-1100(1993) Here we have compared the same coordinate types, using a guess hessian, or a computed hessian. The latter set of runs is a test of the coordinates only, as the initial hessian information is identical. The results show clearly the superiority of the natural internals, which like the previous example, give an energy decrease on every step: Cartesians good Z-matrix natural internals HESS=GUESS 65 32 24 HESS=READ 41 steps 23 13

A final example is phosphinoazasilatrane, with three rings fused on a common SiN bond, in which 112 steps in Cartesian space became 32 steps in natural internals. The moral is: "A little brain time can save a lot of CPU time." In late 1998, a new kind of internal coordinate method was included into GAMESS. This is the delocalized internal coordinate (DLC) of J.Baker, A. Kessi, B.Delley J.Chem.Phys. 105, 192-212(1996) although as is the usual case, the implementation is not exactly the same. Bonds are kept as independent coordinates, while angles are placed in linear combination by the DLC process. There are some interesting options for applying constraints, and other options to assist the automatic DLC generation code by either adding or deleting coordinates. It is simple to use DLCs in their most basic form: $contrl nzvar=xx $end $zmat dlc=.true. auto=.true. $end Our initial experience is that the quality of DLCs is

Further Information

4-144

not as good as explicitly constructed natural internals, which benefit from human chemical knowledge, but are almost always better than carefully crafted $ZMATs using only the primitive internal coordinates (although we have seen a few exceptions). Once we have more numerical experience with the use of DLC's, we will come back and revise the above discussion of coordinate choices. In the meantime, they are quite simple to choose, so give them a go.

the role of symmetry

At the end of a succesful geometry search, you will have a set of coordinates where the gradient of the energy is zero. However your newly discovered stationary point is not necessarily a minimum or saddle point! This apparent mystery is due to the fact that the gradient vector transforms under the totally symmetric representation of the molecular point group. As a direct consequence, a geometry search is point group conserving. (For a proof of these statements, see J.W.McIver and A.Komornicki, Chem.Phys.Lett., 10,303-306(1971)). In simpler terms, the molecule will remain in whatever point group you select in $DATA, even if the true minimum is in some lower point group. Since a geometry search only explores totally symmetric degrees of freedom, the only way to learn about the curvatures for all degrees of freedom is RUNTYP=HESSIAN. As an example, consider disilene, the silicon analog of ethene. It is natural to assume that this molecule is planar like ethene, and an OPTIMIZE run in D2h symmetry will readily locate a stationary point. However, as a calculation of the hessian will readily show, this structure is a transition state (one imaginary frequency), and the molecule is really trans-bent (C2h). A careful worker will always characterize a stationary point as either a minimum, a transition state, or some higher order stationary point (which is not of great interest!) by performing a RUNTYP=HESSIAN. The point group conserving properties of a geometry search can be annoying, as in the preceeding example, or advantageous. For example, assume you wish to locate the transition state for rotation about the double bond in ethene. A little thought will soon reveal that ethene is D2h, the 90 degrees twisted structure is D2d, and structures in between are D2. Since the saddle point is

Further Information

4-145

actually higher symmetry than the rest of the rotational surface, you can locate it by RUNTYP=OPTIMIZE within D2d symmetry. You can readily find this stationary point with the diagonal guess hessian! In fact, if you attempt to do a RUNTYP=SADPOINT within D2d symmetry, there will be no totally symmetric modes with negative curvatures, and it is unlikely that the geometry search will be very well behaved. Although a geometry search cannot lower the symmetry, the gain of symmetry is quite possible. For example, if you initiate a water molecule optimization with a trial structure which has unequal bond lengths, the geometry search will come to a structure that is indeed C2v (to within OPTTOL, anyway). However, GAMESS leaves it up to you to realize that a gain of symmetry has occurred. In general, Mother Nature usually chooses more symmetrical structures over less symmetrical structures. Therefore you are probably better served to assume the higher symmetry, perform the geometry search, and then check the stationary point's curvatures. The alternative is to start with artificially lower symmetry and see if your system regains higher symmetry. The problem with this approach is that you don't necessarily know which subgroup is appropriate, and you lose the great speedups GAMESS can obtain from proper use of symmetry. It is good to note here that "lower symmetry" does not mean simply changing the name of the point group and entering more atoms in $DATA, instead the nuclear coordinates themselves must actually be of lower symmetry.

practical matters
Geometry searches do not bring the gradient exactly to zero. Instead they stop when the largest component of the gradient is below the value of OPTTOL, which defaults to a reasonable 0.0001. Analytic hessians usually have residual frequencies below 10 cm**-1 with this degree of optimization. The sloppiest value you probably ever want to try is 0.0005. If a geometry search runs out of time, or exceeds NSTEP, it can be restarted. For RUNTYP=OPTIMIZE, restart with the coordinates having the lowest total energy (do a string search on "FINAL"). For RUNTYP=SADPOINT, restart with the coordinates having the smallest gradient

Further Information (do a string search on "RMS", which means root mean square). These are not necessarily at the last geometry!

4-146

The "restart" should actually be a normal run, that is you should not try to use the restart options in $CONTRL (which may not work anyway). A geometry search can be restarted by extracting the desired coordinates for $DATA from the printout, and by extracting the corresponding $GRAD group from the PUNCH file. If the $GRAD group is supplied, the program is able to save the time it would ordinarily take to compute the wavefunction and gradient at the initial point, which can be a substantial savings. There is no input to trigger reading of a $GRAD group: if found, it is read and used. Be careful that your $GRAD group actually corresponds to the coordinates in $DATA, as GAMESS has no check for this. Sometimes when you are fairly close to the minimum, an OPTIMIZE run will take a first step which raises the energy, with subsequent steps improving the energy and perhaps finding the minimum. The erratic first step is caused by the GUESS hessian. It may help to limit the size of this wrong first step, by reducing its radius, DXMAX. Conversely, if you are far from the minimum, sometimes you can decrease the number of steps by increasing DXMAX. When using internals, the program uses an iterative process to convert the internal coordinate change into Cartesian space. In some cases, a small change in the internals will produce a large change in Cartesians, and thus produce a warning message on the output. If these warnings appear only in the beginning, there is probably no problem, but if they persist you can probably devise a better set of coordinates. You may in fact have one of the two problems described in the next paragraph. In some cases (hopefully very few) the iterations to find the Cartesian displacement may not converge, producing a second kind of warning message. The fix for this may very well be a new set of internal coordinates as well, or adjustment of ITBMAT in $STATPT. There are two examples of poorly behaved internal coordinates which can give serious problems. The first of these is three angles around a central atom, when this atom becomes planar (sum of the angles nears 360). The other is a dihedral where three of the atoms are nearly linear, causing the dihedral to flip between 0 and 180. Avoid these two situations if you want your geometry

Further Information search to be convergent.

4-147

Sometimes it is handy to constrain the geometry search by freezing one or more coordinates, via the IFREEZ array. For example, constrained optimizations may be useful while trying to determine what area of a potential energy surface contains a saddle point. If you try to freeze coordinates with an automatically generated $ZMAT, you need to know that the order of the coordinates defined in $DATA is y y y y y x x x x r1 r2 r4 r7

x a3 x a5 x a8

x w6 x w9

and so on, where y and x are whatever atoms and molecular connectivity you happen to be using.

saddle points
Finding minima is relatively easy. There are large tables of bond lengths and angles, so guessing starting geometries is pretty straightforward. Very nasty cases may require computation of an exact hessian, but the location of most minima is straightforward. In contrast, finding saddle points is a black art. The diagonal guess hessian will never work, so you must provide a computed one. The hessian should be computed at your best guess as to what the transition state (T.S.) should be. It is safer to do this in two steps as outlined above, rather than HESS=CALC. This lets you verify you have guessed a structure with one and only one negative curvature. Guessing a good trial structure is the hardest part of a RUNTYP=SADPOINT! This point is worth iterating. Even with sophisticated step size control such as is offered by the QA/TRIM or RFO methods, it is in general very difficult to move correctly from a region with incorrect curvatures towards a saddle point. Even procedures such as CONOPT or RUNTYP=GRADEXTR will not replace your own chemical intuition about where saddle points may be located. The RUNTYP=HESSIAN's normal coordinate analysis is rigorously valid only at stationary points on the surface. This means the frequencies from the hessian at your trial

Further Information

4-148

geometry are untrustworthy, in particular the six "zero" frequencies corresponding to translational and rotational (T&R) degrees of freedom will usually be 300-500 cm**-1, and possibly imaginary. The Sayvetz conditions on the printout will help you distinguish the T&R "contaminants" from the real vibrational modes. If you have defined a $ZMAT, the PURIFY option within $STATPT will help zap out these T&R contaminants). If the hessian at your assumed geometry does not have one and only one imaginary frequency (taking into account that the "zero" frequencies can sometimes be 300i!), then it will probably be difficult to find the saddle point. Instead you need to compute a hessian at a better guess for the initial geometry, or read about mode following below. If you need to restart your run, do so with the coordinates which have the smallest RMS gradient. Note that the energy does not necessarily have to decrease in a SADPOINT run, in contrast to an OPTIMIZE run. It is often necessary to do several restarts, involving recomputation of the hessian, before actually locating the saddle point. Assuming you do find the T.S., it is always a good idea to recompute the hessian at this structure. As described in the discussion of symmetry, only totally symmetric vibrational modes are probed in a geometry search. Thus it is fairly common to find that at your "T.S." there is a second imaginary frequency, which corresponds to a non-totally symmetric vibration. This means you haven't found the correct T.S., and are back to the drawing board. The proper procedure is to lower the point group symmetry by distorting along the symmetry breaking "extra" imaginary mode, by a reasonable amount. Don't be overly timid in the amount of distortion, or the next run will come back to the invalid structure. The real trick here is to find a good guess for the transition structure. The closer you are, the better. It is often difficult to guess these structures. One way around this is to compute a linear least motion (LLM) path. This connects the reactant structure to the product structure by linearly varying each coordinate. If you generate about ten structures intermediate to reactants and products, and compute the energy at each point, you will in general find that the energy first goes up, and then down. The maximum energy structure is a "good" guess for the true T.S. structure. Actually, the success of

Further Information this method depends on how curved the reaction path is. A particularly good paper on the symmetry which a saddle point (and reaction path) can possess is by P.Pechukas, J.Chem.Phys. 64, 1516-1521(1976)

4-149

mode following
In certain circumstances, METHOD=RFO and QA can walk from a region of all positive curvatures (i.e. near a minimum) to a transition state. The criteria for whether this will work is that the mode being followed should be only weakly coupled to other close-lying Hessian modes. Especially, the coupling to lower modes should be almost zero. In practise this means that the mode being followed should be the lowest of a given symmetry, or spatially far away from lower modes (for example, rotation of methyl groups at different ends of the molecule). It is certainly possible to follow also modes which do not obey these criteria, but the resulting walk (and possibly TS location) will be extremely sensitive to small details such as the stepsize. This sensitivity also explain why TS searches often fail, even when starting in a region where the Hessian has the required one negative eigenvalue. If the TS mode is strongly coupled to other modes, the direction of the mode is incorrect, and the maximization of the energy along that direction is not really what you want (but what you get). Mode following is really not a substitute for the ability to intuit regions of the PES with a single local negative curvature. When you start near a minimum, it matters a great deal which side of the minima you start from, as the direction of the search depends on the sign of the gradient. We strongly urge that you read before trying to use IFOLOW, namely the papers by Frank Jensen and Jon Baker mentioned above, and see also Figure 3 of C.J.Tsai, K.D.Jordan, J.Phys.Chem. 97, 11227-11237 (1993) which is quite illuminating on the sensitivity of mode following to the initial geometry point. Note that GAMESS retains all degrees of freedom in its hessian, and thus there is no reason to suppose the lowest mode is totally symmetric. Remember to lower the symmetry in the input deck if you want to follow non-symmetric modes. You can get a printout of the modes in internal

Further Information coordinate space by a EXETYP=CHECK run, which will help you decide on the value of IFOLOW. * * *

4-150

CONOPT is a different sort of saddle point search procedure. Here a certain "CONstrained OPTimization" may be considered as another mode following method. The idea is to start from a minimum, and then perform a series of optimizations on hyperspheres of increasingly larger radii. The initial step is taken along one of the Hessian modes, chosen by IFOLOW, and the geometry is optimized subject to the constraint that the distance to the minimum is constant. The convergence criteria for the gradient norm perpendicular to the constraint is taken as 10*OPTTOL, and the corresponding steplength as 100*OPTTOL. After such a hypersphere optimization has converged, a step is taken along the line connecting the two previous optimized points to get an estimate of the next hypersphere geometry. The stepsize is DXMAX, and the radius of hyperspheres is thus increased by an amount close (but not equal) to DXMAX. Once the pure NR step size falls below DXMAX/2 or 0.10 (whichever is the largest) the algorithm switches to a straight NR iterate to (hopefully) converge on the stationary point. The current implementation always conducts the search in cartesian coordinates, but internal coordinates may be printed by the usual specification of NZVAR and ZMAT. At present there is no restart option programmed. CONOPT is based on the following papers, but the actual implementation is the modified equations presented in Frank Jensen's paper mentioned above. Y. Abashkin, N. Russo, J.Chem.Phys. 100, 4477-4483(1994). Y. Abashkin, N. Russo, M. Toscano, Int.J.Quant.Chem. 52, 695-704(1994). There is little experience on how this method works in practice, experiment with it at your own risk!

Further Information

4-151

Intrinisic Reaction Coordinate Methods

The Intrinsic Reaction Coordinate (IRC) is defined as the minimum energy path connecting the reactants to products via the transition state. In practice, the IRC is found by first locating the transition state for the reaction. The IRC is then found in halves, going forward and backwards from the saddle point, down the steepest descent path in mass weighted Cartesian coordinates. This is accomplished by numerical integration of the IRC equations, by a variety of methods to be described below. The IRC is becoming an important part of polyatomic dynamics research, as it is hoped that only knowledge of the PES in the vicinity of the IRC is needed for prediction of reaction rates, at least at threshhold energies. The IRC has a number of uses for electronic structure purposes as well. These include the proof that a certain transition structure does indeed connect a particular set of reactants and products, as the structure and imaginary frequency normal mode at the saddle point do not always unambiguously identify the reactants and products. The study of the electronic and geometric structure along the IRC is also of interest. For example, one can obtain localized orbitals along the path to determine when bonds break or form. The accuracy to which the IRC is determined is dictated by the use one intends for it. Dynamical calculations require a very accurate determination of the path, as derivative information (second derivatives of the PES at various IRC points, and path curvature) is required later. Thus, a sophisticated integration method (such as GS2), and small step sizes (STRIDE=0.05, 0.01, or even smaller) may be needed. In addition to this, care should be taken to locate the transition state carefully (perhaps decreasing OPTTOL by a factor of 10, to OPTTOL=1D-5), and in the initiation of the IRC run. The latter might require a hessian matrix obtained by double differencing, certainly the hessian should be PROJCT'd or PURIFY'd. Note also that EVIB must be chosen carefully, as decribed below. On the other hand, identification of reactants and products allows for much larger step sizes, and cruder integration methods. In this type of IRC one might want to be careful in leaving the saddle point (perhaps STRIDE should be reduced to 0.10 or 0.05 for the first few steps away from the transition state), but once a few points have

Further Information

4-152

been taken, larger step sizes can be employed. In general, the defaults in the $IRC group are set up for this latter, cruder quality IRC. The STRIDE value for the GS2 method can usually be safely larger than for other methods, no matter what your interest in accuracy is. The next few paragraphs describe the various integrators, but note that GS2 is superior to the others. The simplest method of determining an IRC is linear gradient following, PACE=LINEAR. This method is also known as Euler's method. If you are employing PACE=LINEAR, you can select "stabilization" of the reaction path by the Ishida, Morokuma, Komornicki method. This type of corrector has no apparent mathematical basis, but works rather well since the bisector usually intersects the reaction path at right angles (for small step sizes). The ELBOW variable allows for a method intermediate to LINEAR and stabilized LINEAR, in that the stabilization will be skipped if the gradients at the original IRC point, and at the result of a linear prediction step form an angle greater than ELBOW. Set ELBOW=180 to always perform the stabilization. A closely related method is PACE=QUAD, which fits a quadratic polynomial to the gradient at the current and immediately previous IRC point to predict the next point. This pace has the same computational requirement as LINEAR, and is slightly more accurate due to the reuse of the old gradient. However, stabilization is not possible for this pace, thus a stabilized LINEAR path is usually more accurate than QUAD. Two rather more sophisticated methods for integrating the IRC equations are the fourth order Adams-Moulton predictor-corrector (PACE=AMPC4) and fourth order RungeKutta (PACE=RK4). AMPC4 takes a step towards the next IRC point (prediction), and based on the gradient found at this point (in the near vincinity of the next IRC point) obtains a modified step to the desired IRC point (correction). AMPC4 uses variable step sizes, based on the input STRIDE. RK4 takes several steps part way toward the next IRC point, and uses the gradient at these points to predict the next IRC point. RK4 is one of the most accurate integration method implemented in GAMESS, and is also the most time consuming. The Gonzalez-Schlegel 2nd order method (PACE=GS2) finds the next IRC point by a constrained optimization on the

Further Information

4-153

surface of a hypersphere, centered at a point 1/2 STRIDE along the gradient vector leading from the previous IRC point. By construction, the reaction path between two successive IRC points is a circle tangent to the two gradient vectors. The algorithm is much more robust for large steps than the other methods, so it has been chosen as the default method. Thus, the default for STRIDE is too large for the other methods. The number of energy and gradients need to find the next point varies with the difficulty of the constrained optimization, but is normally not very many points. Taking more than 2-3 steps in this constrained optimization is indicative of reaction path curvature, and thus it may help to reduce the step size. Use a small GCUT (same value as OPTTOL) when trying to integrate an IRC very accurately, to be sure the hypersphere optimizations are well converged. Be sure to provide the updated hessian from the previous run when restarting PACE=GS2. The number of wavefunction evaluations, and energy gradients needed to jump from one point on the IRC to the next point are summarized in the following table: PACE ---LINEAR stabilized LINEAR QUAD AMPC4 RK4 GS2 # energies ---------1 3 1 2 4 2-4 # gradients ----------1 2 1 (+ reuse of historical gradient) (see note)

2 4 2-4 (equal numbers)

Note that the AMPC4 method sometimes does more than one correction step, with each such correction adding one more energy and gradient to the calculation. You get what you pay for in IRC calculations: the more energies and gradients which are used, the more accurate the path found. A description of these methods, as well as some others that were found to be not as good is geven by Kim Baldridge and Lisa Pederson, Pi Mu Epsilon J., 9, 513-521 (1993). * * * All methods are initiated by jumping from the saddle point, parallel to the normal mode (CMODE) which has an imaginary frequency. The jump taken is designed to lower

Further Information

4-154

the energy by an amount EVIB. The actual distance taken is thus a function of the imaginary frequency, as a smaller FREQ will produce a larger initial jump. You can simply provide a $HESS group instead of CMODE and FREQ, which involves less typing. To find out the actual step taken for a given EVIB, use EXETYP=CHECK. The direction of the jump (towards reactants or products) is governed by FORWRD. Note that if you have decided to use small step sizes, you must employ a smaller EVIB to ensure a small first step. The GS2 method begins by following the normal mode by one half of STRIDE, and then performing a hypersphere minimization about that point, so EVIB is irrelevant to this PACE. The only method which proves that a properly converged IRC has been obtained is to regenerate the IRC with a smaller step size, and check that the IRC is unchanged. Again, note that the care with which an IRC must be obtained is highly dependent on what use it is intended for. Some key IRC references are: K.Ishida, K.Morokuma, A.Komornicki J.Chem.Phys. 66, 2153-2156 (1977) K.Muller Angew.Chem., Int.Ed.Engl. 19, 1-13 (1980) M.W.Schmidt, M.S.Gordon, M.Dupuis J.Am.Chem.Soc. 107, 2585-2589 (1985) B.C.Garrett, M.J.Redmon, R.Steckler, D.G.Truhlar, K.K.Baldridge, D.Bartol, M.W.Schmidt, M.S.Gordon J.Phys.Chem. 92, 1476-1488(1988) K.K.Baldridge, M.S.Gordon, R.Steckler, D.G.Truhlar J.Phys.Chem. 93, 5107-5119(1989) C.Gonzales, H.B.Schlegel J.Chem.Phys. 90, 2154-2161(1989) The IRC discussion closes with some practical tips: The $IRC group has a confusing array of variables, but fortunately very little thought need be given to most of them. An IRC run is restarted by moving the coordinates of the next predicted IRC point into $DATA, and inserting the new $IRC group into your input file. You must select the desired value for NPOINT. Thus, only the first job which initiates the IRC requires much thought about $IRC. The symmetry specified in the $DATA deck should be the symmetry of the reaction path. If a saddle point happens to have higher symmetry, use only the lower symmetry in the

Further Information

4-155

$DATA deck when initiating the IRC. The reaction path will have a lower symmetry than the saddle point whenever the normal mode with imaginary frequency is not totally symmetric. Be careful that the order and orientation of the atoms corresponds to that used in the run which generated the hessian matrix. If you wish to follow an IRC for a different isotope, use the $MASS group. If you wish to follow the IRC in regular Cartesian coordinates, just enter unit masses for each atom. Note that CMODE and FREQ are a function of the atomic masses, so either regenerate FREQ and CMODE, or more simply, provide the correct $HESS group.

Further Information

4-156

Gradient Extremals
This section of the manual, as well as the source code to trace gradient extremals was written by Frank Jensen of the University of Aarhus. A Gradient Extremal (GE) curve consists of points where the gradient norm on a constant energy surface is stationary. This is equivalent to the condition that the gradient is an eigenvector of the Hessian. Such GE curves radiate along all normal modes from a stationary point, and the GE leaving along the lowest normal mode from a minimum is the gentlest ascent curve. This is not the same as the IRC curve connecting a minimum and a TS, but may in some cases be close. GEs may be divided into three groups: those leading to dissociation, those leading to atoms colliding, and those which connect stationary points. The latter class allows a determination of many (all?) stationary points on a PES by tracing out all the GEs. Following GEs is thus a semi-systematic way of mapping out stationary points. The disadvantages are: i) There are many (but finitely many!) GEs for a large molecule. ii) Following GEs is computationally expensive. iii) There is no control over what type of stationary point (if any) a GE will lead to. Normally one is only interested in minima and TSs, but many higher order saddle points will also be found. Furthermore, it appears that it is necessary to follow GEs radiating also from TSs and second (and possibly also higher) order saddle point to find all the TSs. A rather complete map of the extremals for the H2CO potential surface is available in a paper which explains the points just raised in greater detail: K.Bondensgaard, F.Jensen, J.Chem.Phys. 104, 8025-8031(1996). An earlier paper gives some of the properties of GEs: D.K.Hoffman, R.S.Nord, K.Ruedenberg, Theor. Chim. Acta 69, 265-279(1986). There are two GE algorithms in GAMESS, one due to Sun and Ruedenberg (METHOD=SR), which has been extended to include the capability of locating bifurcation points and

Further Information

4-157

turning points, and another due to Jorgensen, Jensen, and Helgaker (METHOD=JJH): J. Sun, K. Ruedenberg, J.Chem.Phys. 98, 9707-9714(1993) P. Jorgensen, H. J. Aa. Jensen, T. Helgaker Theor. Chim. Acta 73, 55 (1988). The Sun and Ruedenberg method consist of a predictor step taken along the tangent to the GE curve, followed by one or more corrector steps to bring the geometry back to the GE. Construction of the GE tangent and the corrector step requires elements of the third derivative of the energy, which is obtained by a numerical differentiation of two Hessians. This puts some limitations on which systems the GE algorithm can be used for. First, the numerical differentiation of the Hessian to produce third derivatives means that the Hessian should be calculated by analytical methods, thus only those types of wavefunctions where this is possible can be used. Second, each predictor/corrector step requires at least two Hessians, but often more. Maybe 20-50 such steps are necessary for tracing a GE from one stationary point to the next. A systematic study of all the GE radiating from a stationary point increases the work by a factor of ~2*(3N-6). One should thus be prepared to invest at least hundreds, and more likely thousands, of Hessian calculations. In other words, small systems, small basis sets, and simple wavefunctions. The Jorgensen, Jensen, and Helgaker method consists of taking a step in the direction of the chosen Hessian eigenvector, and then a pure NR step in the perpendicular modes. This requires (only) one Hessian calculation for each step. It is not suitable for following GEs where the GE tangent forms a large angle with the gradient, and it is incapable of locating GE bifurcations. Although experience is limited at present, the JJH method does not appear to be suitable for following GEs in general (at least not in the current implementation). Experiment with it at your own risk! The flow of the SR algorithm is as follows: A predictor geometry is produced, either by jumping away from a stationary point, or from a step in the tangent direction from the previous point on the GE. At the predictor geometry, we need the gradient, the Hessian, and the third derivative in the gradient direction. Depending on HSDFDB, this can be done in two ways. If .TRUE. the gradient is calculated, and two Hessians are calculated at

Further Information

4-158

SNUMH distance to each side in the gradient direction. The Hessian at the geometry is formed as the average of the two displaced Hessians. This corresponds to a doublesided differentiation, and is the numerical most stable method for getting the partial third derivative matrix. If HSDFDB = .FALSE., the gradient and Hessian are calculated at the current geometry, and one additional Hessian is calculated at SNUMH distance in the gradient direction. This corresponds to a single-sided differentiation. In both cases, two full Hessian calculations are necessary, but HSDFDB = .TRUE. require one additional wavefunction and gradient calculation. This is usually a fairly small price compared to two Hessians, and the numerically better double-sided differentiation has therefore been made the default. Once the gradient, Hessian, and third derivative is available, the corrector step and the new GE tangent are constructed. If the corrector step is below a threshold, a new predictor step is taken along the tangent vector. If the corrector step is larger than the threshold, the correction step is taken, and a new micro iteration is performed. DELCOR thus determines how closely the GE will be followed, and DPRED determine how closely the GE path will be sampled. The construction of the GE tangent and corrector step involve solution of a set of linear equations, which in matrix notation can be written as Ax=B. The A-matrix is also the second derivative of the gradient norm on the constant energy surface. After each corrector step, various things are printed to monitor the behavior: The projection of the gradient along the Hessian eigenvalues (the gradient is parallel to an eigenvector on the GE), the projection of the GE tangent along the Hessian eigenvectors, and the overlap of the Hessian eigenvectors with the mode being followed from the previous (optimzed) geometry. The sign of these overlaps are not significant, they just refer to an arbitrary phase of the Hessian eigenvectors. After the micro iterations has converged, the Hessian eigenvector curvatures are also displayed, this is an indication of the coupling between the normal modes. The number of negative eigenvalues in the A-matrix is denoted the GE index. If it changes, one of the eigenvalues must have passed through zero. Such points may either be GE bifurcations (where two GEs cross) or may just be "turning

Further Information

4-159

points", normally when the GE switches from going uphill in energy to downhill, or vice versa. The distinction is made based on the B-element corresponding to the A-matrix eigenvalue = 0. If the B-element = 0, it is a bifurcation, otherwise it is a turning point. If the GE index changes, a linear interpolation is performed between the last two points to locate the point where the A-matrix is singular, and the corresponding B-element is determined. The linear interpolation points will in general be off the GE, and thus the evaluation of whether the B-element is 0 is not always easy. The program additionally evaluates the two limiting vectors which are solutions to the linear sets of equations, these are also used for testing whether the singular point is a bifurcation point or turning point. Very close to a GE bifurcation, the corrector step become numerically unstable, but this is rarely a problem in practice. It is a priori expected that GE bifurcation will occur only in symmetric systems, and the crossing GE will break the symmetry. Equivalently, a crossing GE may be encountered when a symmetry element is formed, however such crossings are much harder to detect since the GE index does not change, as one of the A-matrix eigenvalues merely touches zero. The program prints an message if the absolute value of an A-matrix eigenvalue reaches a minimum near zero, as such points may indicate the passage of a bifurcation where a higher symmetry GE crosses. Run a movie of the geometries to see if a more symmetric structure is passed during the run. An estimate of the possible crossing GE direction is made at all points where the A-matrix is singular, and two perturbed geometries in the + and - direction are written out. These may be used as predictor geometries for following a crossing GE. If the singular geometry is a turning point, the + and - geometries are just predictor geometries on the GE being followed. In any case, a new predictor step can be taken to trace a different GE from the newly discovered singular point, using the direction determined by interpolation from the two end point tangents (the GE tangent cannot be uniquely determined at a bifurcation point). It is not possible to determine what the sign of IFOLOW should be when starting off along a crossing GE at a bifurcation, one will have to try a step to see if it returns to the bifurcation point or not.

Further Information

4-160

In order to determine whether the GE index change it is necessary to keep track of the order of the A-matrix eigenvalues. The overlap between successive eigenvectors are shown as "Alpha mode overlaps". Things to watch out for: 1) The numerical differentiation to get third derivatives requires more accuracy than usual. The SCF convergence should be at least 100 times smaller than SNUMH, and preferably better. With the default SNUMH of 10**(-4) the SCF convergence should be at least 10**(-6). Since the last few SCF cycles are inexpensive, it is a good idea to tighten the SCF convergence as much as possible, to maybe 10**(-8) or better. You may also want to increase the integral accuracy by reducing the cutoffs (ITOL and ICUT) and possibly also try more accurate integrals (INTTYP=HONDO). The CUTOFF in $TRNSFM may also be reduced to produce more accurate Hessians. Don't attempt to use a value for SNUMH below 10**(-6), as you simply can't get enough accuracy. Since experience is limited at present, it is recommended that some tests runs are made to learn the sensitivity of these factors for your system. 2) GEs can be followed in both directions, uphill or downhill. When stating from a stationary point, the direction is implicitly given as away from the stationary point. When starting from a non-stationary point, the "+" and "-" directions (as chosen by the sign of IFOLOW) refers to the gradient direction. The "+" direction is along the gradient (energy increases) and "-" is opposite to the gradient (energy decreases). 3) A switch from one GE to another may be seen when two GE come close together. This is especially troublesome near bifurcation points where two GEs actually cross. In such cases a switch to a GE with -higher- symmetry may occur without any indication that this has happened, except possibly that a very large GE curvature suddenly shows up. Avoid running the calculation with less symmetry than the system actually has, as this increases the likelihood that such switches occuring. Fix: alter DPRED to avoid having the predictor step close to the crossing GE. 4) "Off track" error message: The Hessian eigenvector which is parallel to the gradient is not the same as the one with the largest overlap to the previous Hessian mode. This usually indicate that a GE switch

Further Information

4-161

has occured (note that a switch may occur without this error message), or a wrong value for IFOLOW when starting from a non-stationary point. Fix: check IFOLOW, if it is correct then reduce DPRED, and possibly also DELCOR. 5) Low overlaps of A-matrix eigenvectors. Small overlaps may give wrong assignment, and wrong conclusions about GE index change. Fix: reduce DPRED. 6) The interpolation for locating a point where one of the A-matrix eigenvalues is zero fail to converge. Fix: reduce DPRED (and possibly also DELCOR) to get a shorther (and better) interpolation line. 7) The GE index changes by more than 1. A GE switch may have occured, or more than one GE index change is located between the last and current point. Fix: reduce DPRED to sample the GE path more closely. 8) If SNRMAX is too large the algorithm may try to locate stationary points which are not actually on the GE being followed. Since GEs often pass quite near a stationary point, SNRMAX should only be increased above the default 0.10 after some consideration.

Further Information

4-162

Continuum Solvation Methods

In a very thorough 1994 review of continuum solvation models, Tomasi and Persico divide the possible approaches to the treatment of solvent effects into four categories: a) virial equations of state, correlation functions b) Monte Carlo or molecular dynamics simulations c) continuum treatments d) molecular treatments The Effective Fragment Potential method, documented in the following section of this chapter, falls into the latter category, as each EFP solvent molecule is modeled as a distinct object (discrete solvation). This section describes the four continuum models which are implemented in the standard version of GAMESS, and a fifth model which can be interfaced. Continuum models typically form a cavity of some sort containing the solute molecule, while the solvent outside the cavity is thought of as a continuous medium and is categorized by a limited amount of physical data, such as the dielectric constant. The electric field of the charged particles comprising the solute interact with this background medium, producing a polarization in it, which in turn feeds back upon the solute's wavefunction.

Self Consistent Reaction Field (SCRF)

A simple continuum model is the Onsager cavity model, often called the Self-Consistent Reaction Field, or SCRF model. This represents the charge distribution of the solute in terms of a multipole expansion. SCRF usually uses an idealized cavity (spherical or ellipsoidal) to allow an analytic solution to the interaction energy between the solute multipole and the multipole which this induces in the continuum. This method is implemented in GAMESS in the simplest possible fashion: i) a spherical cavity is used ii) the molecular electrostatic potential of the solute is represented as a dipole only, except a monopole is also included for an ionic solute. The input for this implementation of the Kirkwood-Onsager model is provided in $SCRF. Some references on the SCRF method are 1. J.G.Kirkwood J.Chem.Phys. 2, 351 (1934)

Further Information

4-163

2. L.Onsager J.Am.Chem.Soc. 58, 1486 (1936) 3. O.Tapia, O.Goscinski Mol.Phys. 29, 1653 (1975) 4. M.M.Karelson, A.R.Katritzky, M.C.Zerner Int.J.Quantum Chem., Symp. 20, 521-527 (1986) 5. K.V.Mikkelsen, H.Agren, H.J.Aa.Jensen, T.Helgaker J.Chem.Phys. 89, 3086-3095 (1988) 6. M.W.Wong, M.J.Frisch, K.B.Wiberg J.Am.Chem.Soc. 113, 4776-4782 (1991) 7. M.Szafran, M.M.Karelson, A.R.Katritzky, J.Koput, M.C.Zerner J.Comput.Chem. 14, 371-377 (1993) 8. M.Karelson, T.Tamm, M.C.Zerner J.Phys.Chem. 97, 11901-11907 (1993) The method is very sensitive to the choice of the solute RADIUS, but not very sensitive to the particular DIELEC of polar solvents. The plots in reference 7 illustrate these points very nicely. The SCRF implementation in GAMESS is Zerner's Method A, described in the same reference. The total solute energy includes the Born term, if the solute is an ion. Another limitation is that a solute's electrostatic potential is not likely to be fit well as a dipole moment only, for example see Table VI of reference 5 which illustrates the importance of higher multipoles. Finally, the restriction to a spherical cavity may not be very representative of the solute's true shape. However, in the special case of a roundish molecule, and a large dipole which is geometry sensitive, the SCRF model may include sufficient physics to be meaningful: M.W.Schmidt, T.L.Windus, M.S.Gordon J.Am.Chem.Soc. 117, 7480-7486(1995). Most cases should choose PCM (next section) over SCRF!!!

Polarizable Continuum Model (PCM)

A much more sophisticated continuum method, named the Polarizable Continuum Model, is also available. The PCM method places a solute in a cavity formed by a union of spheres centered on each atom. PCM includes a more exact treatment of the electrostatic interaction of the solute with the surrounding medium, on the cavity's surface. The computational procedure divides this surface into many small tesserae, each having a different "apparent surface charge", reflecting the solute's and other tesserae's electric field at each. These surface charges are the PCM model's "solvation effect" and make contributions to the energy and to the gradient of the solute.

Further Information

4-164

Typically the cavity is defined as a union of atomic spheres, which should be roughly 1.2 times the atomic van der Waals radii. A technical difficulty caused by the penetration of the solute's charge density outside this cavity is dealt with by a renormalization. The solvent is characterized by its dielectric constant, surface tension, size, density, and so on. Procedures are provided not only for the computation of the electrostatic interaction of the solute with the apparent surface charges, but also for the cavitation energy, and for the dispersion and repulsion contributions to the solvation free energy. Methodology for solving the Poisson equation to obtain the "apparent surface charges" has progressed from D-PCM to IEF-PCM to C-PCM over time, with the latter preferred. Iterative solvers require far less computer resources than direct solvers. Advancements have also been made in schemes to divide the surface cavity into tiny tesserae. As of fall 2008, the FIXPVA tessellation, which has smooth switching functions for tesserae near sphere boundaries, together with iterative C-PCM, gives very satisfactory geometry optimizations for molecules of 100 atoms. The FIXPVA tessellation was extended to work for cavitation (ICAV), dispersion (IDP), and repulsion (IREP) options in fall 2009, and dispersion/repulsion (IDISP) in spring 2010. Other procedures remain, and make the input seem complex, but their use is discouraged. Thus $PCM SOLVNT=WATER $END chooses iterative C-PCM (IEF=-10) and FIXPVA tessellation (METHOD=4 in $TESCAV) to do basic electrostatics in an accurate fashion. The main input group is $PCM, with $PCMCAV providing auxiliary cavity information. If any of the optional energy computations are requested in $PCM, the additional input groups $IEFPCM, $NEWCAV, $DISBS, or $DISREP may be required. It is useful to summarize the various cavities used by PCM, since as many as three cavities may be used: the basic cavity for electrostatics, cavity for cavitation energy, if ICAV=1, cavity for dispersion/repulsion, if IDISP=1. The first and second share the same radii (see RADII in $PCMCAV), which are scaled by ALPHA=1.2 for electrostatics, but are used unscaled for cavitation. The dispersion cavity is defined in $DISREP with a separate set of atomic radii, and even solvent molecule radii! Only the electrostatics cavity can use any of the GEPOL-GB, GEPOL-AS

Further Information

4-165

or recommended FIXPVA tessellation, while the other two use only the original GEPOL-GB. Radii are an important part of the PCM parameterization. Their values can have a significant impact on the quality of the results. This is particularly true if the solute is charged, and thus has a large electrostatic interaction with the continuum. John Emsley's book "The Elements" is a useful source of van der Waals and other radii. PCM is at heart a means of treating the electrostatic interactions between the solute's wavefunction and a dielectric model for the bulk solvent. The former is represented as an electron density from whatever quantum mechanical treatment is used for the solute, and the latter is a set of surface charges on the finite elements of the cavity (tessellation). This leaves out other important contributions to the solvation energy! These include the energy needed to make a hole in the solvent (cavitation energy), dispersion or repulsive interactions between the solute and solvent, and in the SMD model (see below) solvent structure changes such as would occur in the first solvation shell. Some empirical formulae for such "CDS" corrections are provided as keywords ICAV, IDISP, IREP/IDP, which may not work with all wavefunctions, and may not be compatible with gradients. The SMD model gives an alternative set of such "CDS" corrections, which are compatible with nuclear gradients: see SMD=.TRUE. in $PCM. A more detailed description of SMD is given in the paper cited below. The SMD solvent parameters is described (as of 2010) in http://comp.chem.umn.edu/solvation/mnsddb.pdf This gives numerical parameters, all built into GAMESS, as the various SOLX values, for SOLVNT= ACETACID CLPROPAN PHOPH EGME E2PENTEN ACETONE OCLTOLUE DPROAMIN MEACETAT PENTACET ACETNTRL M-CRESOL DODECAN MEBNZATE PENTAMIN ACETPHEN O-CRESOL MEG MEBUTATE PFB ANILINE CYCHEXAN ETSH MEFORMAT BENZALCL ANISOLE CYCHEXON ETHANOL MIBK PROPANAL BENZALDH CYCPENTN ETOAC MEPROPYL PROPACID BENZENE CYCPNTOL ETOME ISOBUTOL PROPANOL BENZNTRL CYCPNTON EB TERBUTOL PROPNOL2 BENZYLCL DECLNCIS PHENETOL NMEANILN PROPNTRL BRISOBUT DECLNTRA C6H5F MECYCHEX PROPENOL BRBENZEN DECLNMIX FOCTANE NMFMIXTR PROPACET BRETHANE DECANE FORMAMID ISOHEXAN PROPAMIN BROMFORM DECANOL FORMACID MEPYRID2 PYRIDINE

Further Information

4-166

BROCTANE EDB12 HEPTANE MEPYRID3 C2CL4 BRPENTAN DIBRMETN HEPTANOL MEPYRID4 THF BRPROPA2 BUTYLETH HEPTNON2 C6H5NO2 SULFOLAN BRPROPAN ODICLBNZ HEPTNON4 C2H5NO2 TETRALIN BUTANAL EDC12 HEXADECN CH3NO2 THIOPHEN BUTACID C12DCE HEXANE NTRPROP1 PHSH BUTANOL T12DCE HEXNACID NTRPROP2 TOLUENE BUTANOL2 DCM HEXANOL ONTRTOLU TBP BUTANONE ETHER HEXANON2 NONANE TCA111 BUTANTRL ET2S HEXENE NONANOL TCA112 BUTILE DIETAMIN HEXYNE NONANONE TCE NBA MI C6H5I OCTANE ET3N NBUTBENZ DIPE IOBUTANE OCTANOL TFE222 SBUTBENZ DMDS C2H5I OCTANON2 TMBEN124 TBUTBENZ DMSO IOHEXDEC PENTDECN ISOCTANE CS2 DMA CH3I PENTANAL UNDECANE CARBNTET CISDMCHX IOPENTAN NPENTANE M-XYLENE CLBENZEN DMF IOPROPAN PENTACID O-XYLENE SECBUTCL DMEPEN24 CUMENE PENTANOL P-XYLENE CHCL3 DMEPYR24 P-CYMENE PENTNON2 XYLENEMX CLHEXANE DMEPYR26 MESITYLN PENTNON3 CLPENTAN DIOXANE METHANOL PENTENE and provides a translation table to full chemical names, if you can't guess from the input choices given above. The translations can also be found in the source code. Two important things to note about SMD are: a) the atomic radii are changed, so although the algorithms for electrostatics are those of standard PCM, the numerical results for the electrostatics do change. b) SMD's parameterization was developed for IEF-PCM using GEPOL tessellation with a fine grid: IEF=-3 and MTHALL=2, NTSALL=240. However it is considered acceptable to use SMD's parameters, unchanged, with C-PCM and with the FIXPVA tessellation, at default coarseness. Hence, input such as $pcm solvnt=dmso smd=.true. $end is enough to carry out a SMD-style C-PCM treatment in DMSO. c) The CDS correction involves cavitation, dispersion, and as a collective "solvent structure contribution" estimates for partial hydrogen bonding, repulsion, and deviation of the dielectric constant from its bulk value. d) See also SMVLE in the more sophisticated SS(V)PE continuum model's description. Solvation of course affects the non-linear optical properties of molecules. The PCM implementation extends RUNTYP=TDHF to include solvent effects. Both static and frequency dependent hyperpolarizabilities can be found. Besides the standard PCM electrostatic contribution, the

Further Information

4-167

IREP and IDP keywords can be used to determine the effects of repulsion and dispersion on the polarizabilities. The implementation of the PCM model in GAMESS has received considerable attention from Hui Li and Jan Jensen at the University of Iowa, Iowa State University, and University of Nebraska. This includes new iterative techniques to solving the surface charge problem, new tessellations that provide for numerically stable nuclear gradients, the implementation of C-PCM equations, the extension of PCM to all SCFTYPs and TDDFT, development of an interface with the EFP model (quo vadis), and heterogenous dielectric. Dmitri Fedorov at AIST has interfaced PCM to the FMO method (quo vadis), and reduced storage requirements. Due to its sophistication, users of the PCM model are strongly encouraged to read the primary literature: Of particular relevance to PCM in GAMESS: 1) "Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface" H.Li, C.S.Pomelli, J.H.Jensen Theoret.Chim.Acta 109, 71-84(2003) 2) "Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation" H.Li, J.H.Jensen J.Comput.Chem. 25, 1449-1462(2004) 3) "The polarizable continuum model interfaced with the Fragment Molecular Orbital method" D.G.Fedorov, K.Kitaura, H.Li, J.H.Jensen, M.S.Gordon J.Comput.Chem. 27, 976-985(2006) 4) "Energy gradients in combined Fragment Molecular Orbital and Polarizable Continuum Model (FMO/PCM)" H.Li, D.G.Fedorov, T.Nagata, K.Kitaura, J.H.Jensen, M.S.Gordon J.Comput.Chem. 31, 778-790(2010) 5) "Continuous and smooth potential energy surface for conductor-like screening solvation model using fixed points with variable area" P.Su, H.Li J.Chem.Phys. 130, 074109/1-13(2009) 6) "Heterogenous conductorlike solvation model" D.Si, H.Li J.Chem.Phys. 131, 044123/1-8(1009) 7) "Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients" H.Li J.Chem.Phys. 131, 184103/1-8(2009)

Further Information

4-168

8) "Smooth potential energy surface for cavitation, dispersion, and repulsion free energies in polarizable continuum model" Y.Wang, H.Li J.Chem.Phys. 131, 206101/1-2(2009) 9) "Excited state geometry of photoactive yellow protein chromophore: a combined conductorlike polarizable continuum model and time-dependent density functional study" Y.Wang, H.Li J.Chem.Phys. 133, 034108/1-11(2010) Paper number 7 is about the treatment of QM systems with the solvation models EFP and/or C-PCM. SMD and its CDS cavitation/dispersion/solvent structure corrections are described in "Universal solution model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions" A.V.Marenich, C.J.Cramer, D.G.Truhlar J.Phys.Chem.B 113, 6378-6396(2009) General papers on PCM: 10) S.Miertus, E.Scrocco, J.Tomasi Chem.Phys. 55, 117-129(1981) 11) J.Tomasi, M.Persico Chem.Rev. 94, 2027-2094(1994) 12) R.Cammi, J.Tomasi J.Comput.Chem. 16, 1449-1458(1995) 13) J.Tomasi, B.Mennucci, R.Cammi Chem.Rev. 105, 2999-3093(2005) The GEPOL-GB method for cavity construction: 14) J.L.Pascual-Ahuir, E.Silla, J.Tomasi, R.Bonaccorsi J.Comput.Chem. 8, 778-787(1987) Charge renormalization (see also ref. 12): 15) B.Mennucci, J.Tomasi J.Chem.Phys. 106, 5151-5158(1997) Derivatives with respect to nuclear coordinates: (energy gradient and hessian) See also paper 2 and 3. 16) R.Cammi, J.Tomasi J.Chem.Phys. 100, 7495-7502(1994) 17) R.Cammi, J.Tomasi J.Chem.Phys. 101, 3888-3897(1995) 18) M.Cossi, B.Mennucci, R.Cammi J.Comput.Chem. 17, 57-73(1996) Derivatives with respect to applied electric fields: (polarizabilities and hyperpolarizabilities) 19) R.Cammi, J.Tomasi Int.J.Quantum Chem. Symp. 29, 465-474(1995) 20) R.Cammi, M.Cossi, J.Tomasi J.Chem.Phys. 104, 4611-4620(1996) 21) R.Cammi, M.Cossi, B.Mennucci, J.Tomasi

Further Information J.Chem.Phys. 105, 10556-10564(1996) 22) B. Mennucci, C. Amovilli, J. Tomasi Chem.Phys.Lett. 286, 221-225(1998) Cavitation energy: 23) R.A.Pierotti Chem.Rev. 76, 717-726(1976) 24) J.Langlet, P.Claverie, J.Caillet, A.Pullman J.Phys.Chem. 92, 1617-1631(1988)

4-169

Dispersion and repulsion energies: 25) F.Floris, J.Tomasi J.Comput.Chem. 10, 616-627(1989) 26) C.Amovilli, B.Mennucci J.Phys.Chem.B 101, 1051-1057(1997) Integral Equation Formalism PCM. The first of these deals with anisotropies, the last 2 with nuclear gradients. 27) E.Cances, B.Mennucci, J.Tomasi J.Chem.Phys. 107, 3032-3041(1997) 28) B.Mennucci, E.Cances, J.Tomasi J.Phys.Chem.B 101, 10506-17(1997) 29) B.Mennucci, R.Cammi, J.Tomasi J.Chem.Phys. 109, 2798-2807(1998) 30) J.Tomasi, B.Mennucci, E.Cances J.Mol.Struct.(THEOCHEM) 464, 211-226(1999) 31) E.Cances, B.Mennucci J.Chem.Phys. 109, 249-259(1998) 32) E.Cances, B.Mennucci, J.Tomasi J.Chem.Phys. 109, 260-266(1998) Conductor PCM (C-PCM): 33) V.Barone, M.Cossi J.Phys.Chem.A 102, 1995-2001(1998) 34) M.Cossi, N.Rega, G.Scalmani, V.Barone J.Comput.Chem. 24, 669-681(2003) C-PCM with TD-DFT: 35) M.Cossi, V.Barone J.Chem.Phys. 115, 4708-4717(2001) See also paper #8 above for the coding in GAMESS. At the present time, the PCM model in GAMESS has the following limitations: a) Any SCFTYP may be used (RHF to MCSCF). MP2 or DFT may be used with any of the RHF, UHF, and ROHF gradient programs. Closed shell TD-DFT excited state gradients may also be used. CI and Coupled Cluster programs are not available. b) semi-empirical methods may not be used. c) the only other solvent method that may be used at used with PCM is the EFP model. d) point group symmetry is switched off internally

Further Information

4-170

during PCM. e) The PCM model runs in parallel for IEF=3, -3, 10, or -10 and for all 5 wavefunctions (energy or gradient), but not for RUNTYP=TDHF jobs. f) D-PCM stores electric field integrals at normals to the surface elements on disk. IEF-PCM and C-PCM using the explicit solver (+3 and +10) store electric potential integrals at normals to the surface on disk. This is true even for direct AO integral runs, and the file sizes may be considerable (basis set size squared times the number of tesserae). IEF-PCM and C-PCM with the iterative solvers do not store the potential integrals, when IDIRCT=1 in the $PCMITR group (this is the default) g) nuclear derivatives are limited to gradients, although theory for hessians is given in paper 17. * * * The only PCM method prior to Oct. 2000 was D-PCM, which can be recovered by selecting IEF=0 and ICOMP=2 in $PCM. The default PCM method between Oct. 2000 and May 2004 was IEF-PCM, recoverable by IEF=-3 (but 3 for non-gradient runs) and ICOMP=0. As of May 2004, the default PCM method was changed to C-PCM (IEF=-10, ICOMP=0). The extension of PCM to all SCFTYPs as of May 2004 involved a correction to the MCSCF PCM operator, so that it would reproduce RHF results when run on one determinant, meaning that it is impossible to reproduce prior MCSCF PCM calculations. The cavity definition was GEPOL-GB (MTHALL=1 in $TESCAV) prior to May 2004, GEPOL-AS (MTHALL=2) from then until September 2008, and FIXPVA (MTHALL=4) to the present time. The option for generation of 'extra spheres' (RET in $PCM) was changed from 0.2 to 100.0, to suppress these, in June 2003. * * * In general, use of PCM electrostatics is very simple, as may be seen from exam31.inp supplied with the program. The calculation shown next illustrates the use of some of the older PCM options. Since methane is non-polar, its internal energy change and the direct PCM electrostatic interaction is smaller than the cavitation, repulsion, and dispersion corrections. Note that the use of ICAV, IREP, and IDP are currently incompatible with gradients, so a

Further Information

4-171

reasonable calculation sequence might be to perform the geometry optimization with PCM electrostatics turned on, then perform an additional calculation to include the other solvent effects, adding extra functions to improve the dispersion correction. ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! calculation of CH4 (metano), in PCM water. This input reproduces the data in Table 2, line 6, of C.Amovilli, B.Mennucci J.Phys.Chem.B 101, 1051-7(1997) To do this, we must use many original PCM options. The gas phase FINAL energy is The FINAL energy in PCM water is -40.2075980292 -40.2048210283

(lit.)

FREE ENERGY IN SOLVENT = -25234.89 KCAL/MOL INTERNAL ENERGY IN SOLVENT = -25230.64 KCAL/MOL DELTA INTERNAL ENERGY = .01 KCAL/MOL ( 0.0) ELECTROSTATIC INTERACTION = -.22 KCAL/MOL (-0.2) PIEROTTI CAVITATION ENERGY = 5.98 KCAL/MOL ( 6.0) DISPERSION FREE ENERGY = -6.00 KCAL/MOL (-6.0) REPULSION FREE ENERGY = 1.98 KCAL/MOL ( 2.0) TOTAL INTERACTION = 1.73 KCAL/MOL ( 1.8) TOTAL FREE ENERGY IN SOLVENT= -25228.91 KCAL/MOL

$contrl scftyp=rhf runtyp=energy $end $guess guess=huckel $end $system mwords=2 $end ! the "W1 basis" input here exactly matches HONDO's DZP $DATA CH4...gas phase geometry...in PCM water Td Carbon 6. DZV D 1 ; 1 0.75 1.0 Hydrogen 1. 0.6258579976 0.6258579976 0.6258579976 DZV 0 1.20 1.15 ! inner and outer scale factors P 1 ; 1 1.00 1.0 ! ! ! ! ! ! ! $END The reference cited used a value for H2O's solvent radius that differs from the built in value (RSOLV). The IEF, ICOMP, MTHALL, and RET keywords are set to duplicate the original code's published results, namely D-PCM and GEPOL-GB. This run doesn't put in any "extra spheres" but we try that option (RET) like it originally would have.

Further Information $PCM

4-172

SOLVNT=WATER RSOLV=1.35 RET=0.2 IEF=0 ICOMP=2 IDISP=0 IREP=1 IDP=1 ICAV=1 $end $TESCAV MTHALL=1 $END $NEWCAV IPTYPE=2 ITSNUM=540 $END ! dispersion "W2 basis" uses exponents which are ! 1/3 of smallest exponent in "W1 basis" of $DATA. $DISBS NADD=11 NKTYP(1)=0,1,2, 0,1, 0,1, 0,1, 0,1 XYZE(1)=0.0,0.0,0.0, 0.0511 0.0,0.0,0.0, 0.0382 0.0,0.0,0.0, 0.25 1.1817023, 1.1817023, 1.1817023, 0.05435467 1.1817023, 1.1817023, 1.1817023, 0.33333333 -1.1817023, 1.1817023,-1.1817023, 0.05435467 -1.1817023, 1.1817023,-1.1817023, 0.33333333 1.1817023,-1.1817023,-1.1817023, 0.05435467 1.1817023,-1.1817023,-1.1817023, 0.33333333 -1.1817023,-1.1817023, 1.1817023, 0.05435467 -1.1817023,-1.1817023, 1.1817023, 0.33333333 $end

SVPE and SS(V)PE.

The Surface Volume Polarization for Electrostatics (SVPE), and an approximation to SVPE called the Surface and Simulation of Volume Polarization for Electrostatics (SS(V)PE) are continuum solvation models. Compared to other continuum models, SVPE and SS(V)PE pay careful attention to the problems of escaped charge, the shape of the surface cavity, and to integration of the Poisson equation for surface charges. The original references for what is now called the SVPE (surface and volume polarization for electrostatics) method are the theory paper: "Charge penetration in Dielectric Models of Solvation" D.M.Chipman, J.Chem.Phys. 106, 10194-10206 (1997) and the two implementation papers: "Volume Polarization in Reaction Field Theory" C.-G.Zhan, J.Bentley, D.M.Chipman J.Chem.Phys. 108, 177-192 (1998) and "New Formulation and Implementation for Volume Polarization in Dielectric Continuum Theory" D.M.Chipman, J.Chem.Phys. 124, 224111-1/10 (2006) which should be cited in any publications that utilize the SVPE code.

Further Information

4-173

The original reference for the SS(V)PE (surface and simulation of volume polarization for electrostatics) method is: "Reaction Field Treatment of Charge Penetration" D.M.Chipman, J.Chem.Phys. 112, 5558-5565 (2000) which should be cited in any publications that utilize the SS(V)PE code. Further information on the performance of SVPE and of SS(V)PE can be found in: "Comparison of Solvent Reaction Field Representations" D.M.Chipman, Theor.Chem.Acc. 107, 80-89 (2002). Details of the SS(V)PE convergence behavior and programming strategy are in: "Implementation of Solvent Reaction Fields for Electronic Structure" D.M.Chipman, M.Dupuis, Theor.Chem.Acc. 107, 90-102 (2002). The SMVLE option (solvation model with volume and local electrostatics) is described in "Free energies of solvation with surface, volume, and local electrostatic effects and atomic surface tensions to represent the first solvation shell" J.Liu, C.P.Kelly, A.C.Goren, A.V.Marenich, C.J.Cramer, D.G.Truhlar, C.-G. Zhan J.Chem.Theory Comput. 6, 1109-1117(2010). The SVPE and SS(V)PE models are like PCM and COSMO in that they treat solvent as a continuum dielectric residing outside a molecular-shaped cavity, determining the apparent charges that represent the polarized dielectric by solving Poisson's equation. The main difference between SVPE and SS(V)PE is in treatment of volume polarization effects that arise because of the tail of the electronic wave function that penetrates outside the cavity, sometimes referred to as the "escaped charge." SVPE treats volume polarization effects explicitly by including apparent charges in the volume outside the cavity as well as on the cavity surface. With a sufficient number of grid points, SVPE can then provide an exact treatment of charge penetration effects. SS(V)PE, like PCM and COSMO, is an approximate treatment that only uses apparent charges located on the cavity surface. The SS(V)PE equation is particularly designed to simulate as well as possible the influence of the missing volume charges. For more information on the similarities and differences of the SVPE and SS(V)PE models with other continuum methods, see the paper "Comparison of Solvent Reaction Field Representations" cited just above.

Further Information

4-174

In addition, the cavity construction and Poisson solver used in this implementation of SVPE and SS(V)PE also receive careful numerical treatment. For example, the cavity may be chosen to be an isodensity contour surface, and the Lebedev grids for the Poisson solver can be chosen very densely. The Lebedev grids used for surface integration are taken from the Fortran translation by C. van Wuellen of the original C programs developed by D. Laikov. They were obtained from the CCL web site www.ccl.net/cca/software/SOURCES/FORTRAN/Lebedev-LaikovGrids. A recent leading reference is V. I. Lebedev and D. N. Laikov, Dokl. Math. 59, 477-481 (1999). All these grids have octahedral symmetry and so are naturally adapted for any solute having an Abelian point group. The larger and/or the less spherical the solute may be, the more surface points are needed to get satisfactory precision in the results. Further experience will be required to develop detailed recommendations for this parameter. Values as small as 110 are usually sufficient for simple diatomics and triatomics. The default value of 1202 has been found adequate to obtain the energy to within 0.1 kcal/mol for solutes the size of monosubstituted benzenes. The SVPE method uses additional layers of points outside the cavity. Typically just two layers are sufficient to converge the direct volume polarization contribution to better than 0.1 kcal/mol. The SVPE and SS(V)PE codes both report the amount of solute charge penetrating outside the cavity as calculated by Gauss' Law. The SVPE code additionally reports the same quantity as alternatively calculated from the explicit volume charges, and any substantial discrepancy between these two determinations indicates that more volume polarization layers should have been included for better precision. The energy contribution from the outermost volume polarization layer is also reported. If it is significant then again more layers should have been included. However, these tests are only diagnostic. Passing them does not guarantee that enough layers are included. The SVPE and SS(V)PE models treat the electrostatic interaction between a quantum solute and a classical dielectric continuum solvent. No treatment is yet implemented for cavitation, dispersion, or any of a variety of other specific solvation effects. Note that corrections for these latter effects that might be reported by other programs are generally not transferable. The reason is that they are usually parameterized to improve the ultimate

Further Information

4-175

agreement with experiment. In addition to providing corrections for the physical effects advertised, they therefore also inherently include contributions that help to make up for any deficiencies in the electrostatic description. Consequently, they are appropriate only for use with the particular electrostatic model in which they were originally developed. Analytic nuclear gradients are not yet available for the SVPE or SS(V)PE energy, but numerical differentiation will permit optimization of small solute molecules. Wavefunctions may be any of the SCF type: RHF, UHF, ROHF, GVB, and MCSCF, or the DFT analogs of some of these. In the MCSCF implementation, no initial wavefunction is available so the solvation code does not kick in until the second iteration. We close with a SVPE example. The gas phase energy, obtained with no $SVP group, is -207.988975, and the run just below gives the SVPE energy -208.006282. The free energy of solvation, -10.860 kcal/mole, is the difference of these, and is quoted at the right side of the 3rd line from the bottom of Table 2 in the paper cited. The "REACTION FIELD FREE ENERGY" for SVPE is -12.905 kcal/mole, which is only part of the solvation free energy. There is also a contribution due to the SCRF procedure polarizing the wave function from its gas phase value, causing the solute internal energy in dielectric to differ from that in gas. Evaluating this latter contribution is what requires the separate gas phase calculation. Changing the number of layers (NVLPL) to zero produces the SS(V)PE approximation to SVPE, E= -208.006208. ! ! ! ! SVPE solvation test...acetamide reproduce data in Table 2 of the paper on SVPE, D.M.Chipman J.Chem.Phys. 124, 224111/1-10(2006)

$contrl scftyp=rhf runtyp=energy $end $system mwords=4 $end $basis gbasis=n31 ngauss=6 ndfunc=1 npfunc=1 $end $guess guess=moread norb=16 $end $scf nconv=8 $end $svp nvlpl=3 rhoiso=0.001 dielst=78.304 nptleb=1202 $end $data CH3CONH2 cgz geometry RHF/6-31G(d,p) C1 C 6.0 1.361261 -0.309588 -0.000262 C 6.0 -0.079357 0.152773 -0.005665 H 1.0 1.602076 -0.751515 0.962042

Further Information H H O N H H 1.0 1.0 8.0 7.0 1.0 1.0 1.537200 2.002415 -0.387955 -1.002151 -1.961646 -0.752774 -1.056768 0.542830 1.310027 -0.840834 -0.589397 -1.798630 -0.767127 -0.168045 0.002284 -0.011928 0.038911 0.035006

4-176

$end gas phase vectors, E(RHF)= -207.9889751769 $VEC 1 1 1.18951670E-06 1.74015997E-05 ...snipped... $END

Conductor-like screening model (COSMO)

The COSMO (conductor-like screening model) represents a different approach for carrying out polarized continuum calculations. COSMO was originally developed by Andreas Klamt, with extensions to ab initio computation in GAMESS by Kim Baldridge. In the COSMO method, the surrounding medium is modeled as a conductor rather than as a dielectric in order to establish the initial boundary conditions. The assumption that the surrounding medium is well modeled as a conductor simplifies the electrostatic computations and corrections may be made a posteriori for dielectric behavior. The original model of Klamt was introduced using a molecular shaped cavity, which had open parts along the crevices of intersecting atomic spheres. While having considerable technical advantages, this approximation causes artifacts in the context of the more generalized theory, so the current method for cavity construction includes a closure of the cavity to eliminate crevices or pockets. Two methodologies are implemented for treatment of the outlying charge errors (OCE). The default is the wellestablished double cavity procedure using a second, larger cavity around the first one, and calculates OCE through the difference between the potential on the inner and the outer cavity. The second involves the calculation of distributed multipoles up to hexadecapoles to represent the entire charge distribution of the molecule within the cavity. The COSMO model accounts only for the electrostatic interactions between solvent and solute. Klamt has

Further Information

4-177

proposed a novel statistical scheme to compute the full solvation free energy for neutral solutes, COSMO-RS, which is formulated for GAMESS by Peverati, Potier and Baldridge, and is available as external plugin to the COSMOtherm program by COSMOlogic GmbH&Co. The iterative inclusion of non-electrostatic effects is also possible right after a COSMO-RS calculation. The DCOSMO-RS approach was implemented in GAMESS by Peverati, Potier, and Baldridge, and more information is available on Baldridge website at: http://ocikbws.uzh.ch/gamess/ The simplicity of the COSMO model allows computation of gradients, allowing optimization within the context of the solvent. The method is programmed for RHF and UHF, all corresponding kinds of DFT (including DFT-D), and the corresponding MP2, energy and gradient. Some references on the COSMO model are: A.Klamt, G.Schuurman J.Chem.Soc.Perkin Trans 2, 799-805(1993) A.Klamt J.Phys.Chem. 99, 2224-2235(1995) K.Baldridge, A.Klamt J.Chem.Phys. 106, 6622-6633 (1997) V.Jonas, K.Baldridge J.Chem.Phys. 113, 7511-7518 (2000) L.Gregerson, K.Baldridge Helv.Chim.Acta 86, 4112-4132 (2003) R.Peverati, Y.Potier, K.Baldridge TO BE PUBLISHED SOON Additional references on the COSMO-RS model, with explanation of the methodology and program can be found: A.Klamt, F.Eckert, W.Arlt Annu.Rev.Chem.Biomol.Eng. 1, (2010)

Further Information

4-178

The Effective Fragment Potential Method

The basic idea behind the effective fragment potential (EFP) method is to replace the chemically inert part of a system by EFPs, while performing a regular ab initio calculation on the chemically active part. Here "inert" means that no covalent bond breaking process occurs. This "spectator region" consists of one or more "fragments", which interact with the ab initio "active region" through non-bonded interactions, and so of course these EFP interactions affect the ab initio wavefunction. The EFP particles can be closed shell or open shell (high spin ROHF) based potentials. The "active region" can use nearly every kind of wavefunction available in GAMESS. A simple example of an active region might be a solute molecule, with a surrounding spectator region of solvent molecules represented by fragments. Each discrete solvent molecule is represented by a single fragment potential, in marked contrast to continuum models for solvation. The quantum mechanical part of the system is entered in the $DATA group, along with an appropriate basis. The EFPs defining the fragments are input by means of a $EFRAG group, and one or more $FRAGNAME groups describing each fragment's EFP. These groups define non-bonded interactions between the ab initio system and the fragments, and also between the fragments. The former interactions enter via one-electron operators in the ab initio Hamiltonian, while the latter interactions are treated by analytic functions. The only electrons explicitly treated (with basis functions used to expand occupied orbitals) are those in the active region, so there are no new two electron terms. Thus the use of EFPs leads to significant time savings, compared to full ab initio calculations on the same system. There are two types of EFP available in GAMESS, EFP1 and EFP2. EFP1, the original method, employs a fitted repulsive potential. EFP1 is primarily used to model water molecules to study aqueous solvation effects, at the RHF/DZP or DFT/DZP (specifically, B3LYP) levels, see references 1-3 and 26, respectively. EFP2 is a more general method that is applicable to any species, including water, and its repulsive potential is obtained from first principles. EFP2 has been extended to include other effects as well, such as charge transfer and dispersion.

Further Information

4-179

EFP2 forms the basis of the covalent EFP method described below for modeling enzymes, see reference 14. Parallelization of the EFP1 and EFP2 models is described in reference 32. MD simulations with EFP are described in reference 31. The ab initio/EFP1, or pure EFP system can be wrapped in a Polarizable Continuum Model, see references 23, 43, and 50.

terms in an EFP
The non-bonded interactions currently implemented are: 1) Coulomb interaction. The charge distribution of the fragments is represented by an arbitrary number of charges, dipoles, quadrupoles, and octopoles, which interact with the ab initio hamiltonian as well as with multipoles on other fragments (see reference 2 and 18). It is possible to use a screening term that accounts for the charge penetration (reference 17 and 42). This screening term is automatically included for EFP1. Typically the multipole expansion points are located on atomic nuclei and at bond midpoints. 2) Dipole polarizability. An arbitrary number of dipole polarizability tensors can be used to calculate the induced dipole on a fragment due to the electric field of the ab initio system as well as all the other fragments. These induced dipoles interact with the ab initio system as well as the other EFPs, in turn changing their electric fields. All induced dipoles are therefore iterated to selfconsistency. Typically the polarizability tensors are located at the centroid of charge of each localized orbital of a fragment. See reference 41. 3) Repulsive potential. Two different forms are used in EFP1: one for ab initio-EFP repulsion and one for EFP-EFP repulsion. The form of the potentials is empirical, and consists of distributed Gaussian or exponential functions, respectively. The primary contribution to the repulsion is the quantum mechanical exchange repulsion, but the fitting technique used to develop this term also includes the effects of charge transfer. Typically these fitted potentials are located on each atomic nucleus within the fragment (see reference 3). In EFP2, polarization energies

Further Information

4-180

can also be augmented by screening terms, analogous to the electrostatic screening, to prevent "polarization collapse" (MS in preparation) For EFP2, the third term is divided into separate analytic formulae for different physical interactions: a) exchange repulsion b) dispersion c) charge transfer A summary of EFP2, and its contrast to EFP1 can be found in reference 18 and 44. The repulsive potential for EFP2 is based on an overlap expansion using localized molecular orbitals, as described in references 5, 6, and 9. Dispersion energy is described in reference 34, and charge transfer in reference 39 (which supercedes reference 22's formulae). EFP2 potentials have no fitted parameters, and can be automatically generated during a RUNTYP=MAKEFP job, as described below.

constructing an EFP1
RUNTYP=MOROKUMA assists in the decomposition of intermolecular interaction energies into electrostatic, polarization, charge transfer, and exchange repulsion contributions. This is very useful in developing EFPs since potential problems can be attributed to a particular term by comparison to these energy components for a particular system. A molecular multipole expansion can be obtained using $ELMOM. A distributed multipole expansion can be obtained by either a Mulliken-like partitioning of the density (using $STONE) or by using localized molecular orbitals ($LOCAL: DIPDCM and QADDCM). The dipole polarizability tensor can be obtained during a Hessian run ($CPHF), and a distributed LMO polarizability expression is also available ($LOCAL: POLDCM). In EFP1, the repulsive potential is derived by fitting the difference between ab initio computed intermolecular interaction energies, and the form used for Coulomb and polarizability interactions. This difference is obtained at a large number of different interaction geometries, and is then fitted. Thus, the repulsive term is implicitly a function of the choices made in representing the Coulomb

Further Information

4-181

and polarizability terms. Note that GAMESS currently does not provide a way to obtain these EFP1 repulsive potential. Since a user cannot generate all of the EFP1 terms necessary to define a new $FRAGNAME group using GAMESS, in practice the usage of EFP1 is limited to the internally stored H2ORHF or H2ODFT potentials mentioned below.

constructing an EFP2
As noted above, the repulsive potential for EFP2 is derived from a localized orbital overlap expansion. It is generally recommended that one use at least a double zeta plus diffuse plus polarization basis set, e.g. 6-31++G(d,p) to generate the EFP2 repulsive potential. However, it has been observed that 6-31G(d) works reasonably well due to a fortuitous cancellation of errors. The EFP2 potential for any molecule can be generated as follows: (a) Choose a basis set and geometry for the molecule of interest. The geometry is ordinarily optimized at your choice of Hartree-Fock/MP2/CCSD(T), with your chosen basis set, but this is not a requirement. It is good to recall, however, that EFP internal geometries are fixed, so it is important to give some thought to the chosen geometry. (b) Perform a RUNTYP=MAKEFP run for the chosen molecule using the chosen geometry in $DATA and the chosen basis set in $BASIS. This will generate the entire EFP2 potential in the run's .efp file. The only user-defined variable that must be filled in is changing the FRAGNAME's group name, to $C2H5OH or $DMSO, etc. This step can use RHF or ROHF to describe the electronic structure of the system. (c) Transfer the entire fragment potential for the molecule to any input file in which this fragment is to be used. Since the internal geometry of an EFP is fixed, one need only specify the first three atoms of any fragment in order to position them in $EFRAG. Coordinates of any other atoms in the rigid fragment will be automatically determined by the program. If the EFP contains less than three atoms, you can still generate a fragment potential. After a normal MAKEFP run, add dummy atoms (e.g. in the X and/or Y directions) with zero nuclear charges, and add corresponding dummy bond midpoints too. Carefully insert zero entries in the multipole sections, and in the electrostatic screening

Further Information

4-182

sections, for each such dummy point, but don't add data to any other kind of EFP term such as polarizability. This trick gives the necessary 3 points for use in $EFRAG groups to specify "rotational" positions of fragments.

current limitations
1. For EFP1, the energy and energy gradient are programmed, which permits RUNTYP=ENERGY, GRADIENT, and numerical HESSIAN. The necessary programing to use the EFP gradients to move on the potential surface are programmed for RUNTYP=OPTIMIZE, SADPOINT, IRC, and VSCF, but the other gradient based potential surface explorations such as DRC are not yet available. Finally, RUNTYP=PROP is also permissible. For EFP2, the gradient terms for ab initio-EFP interactions have not yet been coded, so geometry optimizations are only sensible for a COORD=FRAGONLY run; that is, a run in which only EFP2 fragments are present. 2. The ab initio part of the system must be treated with RHF, ROHF, UHF, the open shell SCF wavefunctions permitted by the GVB code, or MCSCF. DFT analogs of RHF, ROHF, and UHF may also be used. Correlated methods such as MP2 and CI should not be used. 3. EFPs can move relative to the ab initio system and relative to each other, but the internal structure of an EFP is frozen. 4. The boundary between the ab initio system and EFP1's must not be placed across a chemical bond. However, see the discussion below regarding covalent bonds. 5. Calculations must be done in C1 symmetry at present. 6. Reorientation of the fragments and ab initio system is not well coordinated. If you are giving Cartesian coordinates for the fragments (COORD=CART in $EFRAG), be sure to use $CONTRL's COORD=UNIQUE option so that the ab initio molecule is not reoriented. 7. If you need IR intensities, you have to use NVIB=2. The potential surface is usually very soft for EFP motions, and double differenced Hessians should usually be obtained.

Further Information

4-183

practical hints for using EFPs

At the present time, we have only two internally stored EFP potentials suitable for general use. These model water, using the fragment name H2ORHF or H2ODFT. The H2ORHF numerical parameters are improved values over the values which were presented and used in reference 2, and they also include the improved EFP-EFP repulsive term defined in reference 3. The H2ORHF water EFP was derived from RHF/DH(d,p) computations on the water dimer system. When you use it, therefore, the ab initio part of your system should be treated at the SCF level, using a basis set of the same quality (ideally DH(d,p), but probably other DZP sets such as 6-31G(d,p) will give good results as well). Use of better basis sets than DZP with this water EFP has not been tested. Similarly, H2ODFT was developed using B3LYP/DZP water wavefunctions, so this should be used (rather than H2ORHF) if you are using DFT to treat the solute. Since H2ODFT water parameters are obtained from a correlated calculation, they can also be used when the solute is treated by MP2. As noted, effective fragments have frozen internal geometries, and therefore only translate and rotate with respect to the ab initio region. An EFP's frozen coordinates are positioned to the desired location(s) in $EFRAG as follows: a) the corresponding points are found in $FRAGNAME. b) Point -1- in $EFRAG and its FRAGNAME equivalent are made to coincide. c) The vector connecting -1- and -2- is aligned with the corresponding vector connecting FRAGNAME points. d) The plane defined by -1-, -2-, and -3- is made to coincide with the corresponding FRAGNAME plane. Therefore the 3 points in $EFRAG define only the relative position of the EFP, and not its internal structure. So, if the "internal structure" given by points in $EFRAG differs from the true values in $FRAGNAME, then the order in which the points are given in $EFRAG can affect the positioning of the fragment. It may be easier to input water EFPs if you use the Z-matrix style to define them, because then you can ensure you use the actual frozen geometry in your $EFRAG. Note that the H2ORHF EFP uses the frozen geometry r(OH)=0.9438636, a(HOH)=106.70327, and the names of its 3 fragment points are ZO1, ZH2, ZH3. * * *

Further Information

4-184

Building a large cluster of EFP particles by hand can be tedious. The RUNTYP=GLOBOP program described below has an option for constructing dense clusters. The method tries to place particles near the origin, but not colliding with other EFP particles already placed there, so that the clusters grow outwards from the center. Here are some ideas: a) place 100 water molecules, all with the same coords in $EFRAG. This will build up a droplet of water with particles close together, but not on top of each other, with various orientations. b) place 16 waters (same coords, all first) followed by 16 methanols (also sharing their same coords, after all waters). A 50-50 mixture of 32 molecules will be created, if you choose the default of picking the particles randomly from the initial list of 32. c) to solvate a solute, create a dummy $FRAGNAME group for the solute that is to be modeled as ab initio, so the GLOBOP run thinks the solute is an EFP. Its potential can consist of just monopoles with zero charges. Place the solute first in $EFRAG, with as many solute particles as you like after it. Of course the latter can all have the same coordinates. Pick the option to preserve the order of particles, so the solute is kept at the center of the cluster. After the check run gives you coordinates, move the solute from $EFRAG to $DATA. Example, allowing the random cluster to have 20 geometry optimization steps: $contrl runtyp=globop coord=fragonly $end $globop rndini=.true. riord=rand mcmin=.true. $end $statpt nstep=20 $end $efrag coord=cart FRAGNAME=WATER O1 -2.8091763203009 -2.1942725073400 -0.2722207394107 H2 -2.3676165499399 -1.6856118830379 -0.9334073942601 H3 -2.1441965467625 -2.5006167998896 0.3234583094693 ...repeat this 15 more times... FRAGNAME=MeOH O1 4.9515153249 .4286994611 1.3368662306 H2 5.3392575544 .1717424606 3.0555957053 C3 6.2191743799 2.5592349960 .4064662379 H4 5.7024200977 2.7548960076 -1.5604873643 H5 5.6658856694 4.2696553371 1.4008542042 H6 8.2588049857 2.3458272252 .5282762681 ...repeat 15 more times... $end $water

Further Information

4-185

...give a full EFP2 potential for water... $end $meoh ...give a full EFP2 potential for methanol... $end Note that this run does not proceed into a full Monte Carlo simulation. You can start Monte Carlo (or simulated annealing) by placing the randomized structure into $EFRAG, and of course provide relevant $GLOBOP inputs rather than RNDINI=.TRUE. * * * The translations and rotations of EFPs with respect to the ab initio system and one another are automatically quite soft degrees of freedom. After all, the EFP model is meant to handle weak interactions! Therefore the satisfactory location of structures on these flat surfaces will require use of a tight convergence on the gradient: OPTTOL=0.00001 in the $STATPT group. The effect of a bulk continuum surrounding the solute plus EFP waters can be obtained by using the PCM model, see reference 23 and 43. To do this, simply add a $PCM group to your input, in addition to the $EFRAG. The simultaneous use of EFP and PCM allows for gradients, so geometry optimization can be performed.

global optimization
If there are a large number of effective fragments, it is difficult to locate the lowest energy structures by hand. Typically these are numerous, and one would like to have a number of them, not just the very lowest energy. The RUNTYP of GLOBOP contains a Monte Carlo procedure to generate a random set of starting structures to look for those with the lowest energy at a single temperature. If desired, a simulated annealing protocol to cool the temperature may be used. These two procedures may be combined with a local minimum search, at some or all of the randomly generated structures. The local minimum search is controlled by the usual geometry optimizer, namely $STATPT input, and thus permits the optimization of any ab initio atoms. The Monte Carlo procedure by default uses a Metropolis algorithm to move just one of the effective fragments. If desired, the method of Parks to move all fragments at once

Further Information may be tried, by changing ALPHA from zero and setting BOLTWT=AVESTEP instead of STANDARD.

4-186

The present program was used to optimize the structure of water clusters. Let us consider the case of the twelve water cluster, for which the following ten structures were published by Day, Pachter, Gordon, and Merrill: 1. (D2d)2 -0.170209 6. (D2d)(C2) -0.167796 2. (D2d)(S4) -0.169933 7. S6 -0.167761 3. (S4)2 -0.169724 8. cage b -0.167307 4. D3 -0.168289 9. cage a -0.167284 5. (C1c)(Cs) -0.167930 10. (C1c)(C1c) -0.167261 A test input using Metropolis style Monte Carlo to examine 300 geometries at each temperature value, using simulated annealing cooling from 200 to 50 degrees, and with local minimization every 10 structures was run ten times. Each run sampled about 7000 geometries. One simulation found structure 2, while two of the runs found structure 3. The other seven runs located structures with energy values in the range -0.163 to -0.164. In all cases the runs began with the same initial geometry, but produced different results due to the random number generation used in the Monte Carlo. Clearly one must try a lot of simulations to be confident about having found most of the low energy structures. In particular, it is good to try more than one initial structure, unlike what was done in this test. If there is an ab initio molecule in your system, it is probably impractical to carry out a simulated annealing protocol. However, a single temperature Monte Carlo calculation may be feasible. In particular, you may wish to avoid the local minimization steps, and instead manually examine the structures from the Monte Carlo steps in order to choose a few for full geometry optimization. Note that SMODIF input can allow the ab initio part of the system to participate in the Monte Carlo jumps. However, this should be done with caution. Monte Carlo references: N.Metropolis, A.Rosenbluth, A.Teller J.Chem.Phys. 21, 1087(1953). G.T.Parks Nucl.Technol. 89, 233(1990). Monte Carlo with local minimization: Z.Li, H.A.Scheraga Proc.Nat.Acad.Sci. USA 84, 6611(1987). Simulated annealing reference: S.Kirkpatrick, C.D.Gelatt, M.P.Vecci Science 220, 671(1983).

Further Information

4-187

The present program is described in reference 15. It is pattened on the work of D.J.Wales, M.P.Hodges Chem.Phys.Lett. 286, 65-72 (1998).

QM/MM across covalent bonds

Recent work by Visvaldas Kairys and Jan Jensen has made it possible to extend the EFP methodology beyond the simple solute/solvent case described above. When there is a covalent bond between the portion of the system to be modeled by quantum mechanics, and the portion which is to be treated by EFP multipole and polarizability terms, an additional layer is needed in the model. The covalent linkage is not so simple as the interactions between closed shell solute and solvent molecules. The "buffer zone" between the quantum mechanics and the EFP consists of frozen nuclei, and frozen localized orbitals, so that the quantum mechanical region sees a orbital representation of the closest particles, and multipoles etc. beyond that. Since the orbitals in the buffer zone are frozen, it need extend only over a few atoms in order to keep the orbitals in the fully optimized quantum region within that region. The general outline of this kind of computation is as follows: a) a full quantum mechanics computation on a system containing the quantum region, the buffer region, and a few atoms into the EFP region, to obtain the frozen localized orbitals in the buffer zone. This is called the "truncation run". b) a full quantum mechanics computation on a system with all quantum region atoms removed, and with the frozen localized orbitals in the buffer zone. The necessary multipole and polarizability data to construct the EFP that will describes the EFP region will be extracted from the wavefunction. This is called the "MAKEFP run". It is possible to use several such runs if the total EFP region is quite large. c) The intended QM/MM run(s), after combining the information from these first two types of runs. As an example, consider a protonated lysine residue which one might want to consider quantum mechanically in a protein whose larger parts are to be treated with an EFP. The protonated lysine is NH2

Further Information + / H3N(CH2)(CH2)(CH2)--(CH2)(CH) \ COOH

4-188

The bonds which you see drawn show how the molecule is partitioned between the quantum mechanical side chain, a CH2CH group in the buffer zone, and eventually two different EFPs may be substituted in the area of the NH2 and COOH groups to form the protein backbone. The "truncation run" will be on the entire system as you see it, with the 13 atoms in the side chain first in $DATA, the 5 atoms in the buffer zone next in $DATA, and the simplified EFP region at the end. This run will compute the full quantum wavefunction by RUNTYP=ENERGY, followed by the calculation of localized orbitals, and then truncation of the localized orbitals that are found in the buffer zone so that they contain no contribution from AOs outside the buffer zone. The key input groups for this run are $contrl $truncn doproj=.true. plain=.true. natab=13 natbf=5 $end This will generate a total of 6 localized molecular orbitals in the buffer zone (one CC, three CH, two 1s inner shells), expanded in terms of atomic orbitals located only on those atoms. The truncation run prepares template input files for the next run, including adjustments of nuclear charges at boundaries, etc. The "MAKEFP" run drops all 13 atoms in the quantum region, and uses the frozen orbitals just prepared to obtain a wavefunction for the EFP region. The carbon atom in the buffer zone that is connected to the now absent QM region will have its nuclear charge changed from 6 to 5 to account for a missing electron. The key input for this RUNTYP=MAKEFP job is the six orbitals in $VEC, plus the groups $guess guess=huckel insorb=6 $end $mofrz frz=.true. ifrz(1)=1,2,3,4,5,6 $end $stone QMMMbuf $end which will cause the wavefunction optimization for the remaining atoms to optimize orbitals only in the NH2 and COOH pieces. After this wavefunction is found, the run extracts the EFP information needed for the QM/MM third

Further Information run(s). This means running the Stone analysis for distributed multipoles, and obtaining a polarizability tensor for each localized orbital in the EFP region.

4-189

The QM/MM run might be RUNTYP=OPTIMIZE, etc. depending on what you want to do with the quantum atoms, and its $DATA group will contain both the 13 fully optimized atoms, and the 5 buffer atoms, and a basis set will exist on both sets of atoms. The carbon atom in the buffer zone that borders the EFP region will have its nuclear charge set to 4 since now two bonding electrons to the EFP region are lost. $VEC input will provide the six frozen orbitals in the buffer zone. The EFP atoms are defined in a fragment potential group. The QM/MM run could use RHF or ROHF wavefunctions, to geometry optimize the locations of the quantum atoms (but not of course the frozen buffer zone or the EFP piece). It could remove the proton to compute the proton affinity at that terminal nitrogen, hunt for transition states, and so on. Presently the gradient for GVB and MCSCF is not quite right, so their use is discouraged. Input to control the QM/MM preparation is $TRUNCN and $MOFRZ groups. There are a number of other parameters in various groups, namely QMMMBUF in $STONE, MOIDON and POLNUM in $LOCAL, NBUFFMO in $EFRAG, and INSORB in $GUESS that are relevant to this kind of computation. For RUNTYP=MAKEFP, the biggest choices are LOCAL=RUEDENBRG vs. BOYS, and POLNUM in $LOCAL, otherwise this is pretty much a standard RUNTYP=ENERGY input file. Source code distributions of GAMESS contain a directory named ~/gamess/tools/efp, which has various tools for EFP manipulation in it, described in file readme.1st. A full input file for the protonated lysine molecule is included, with instructions about how to proceed to the next steps. Tips on more specialized input possibilities are appended to the file readme.1st.

Simpler potentials
Since the EFP model's electrostatics is a set of distributed multipoles (monopole to octopole) and distributed polarizabilities (dipole), it is possible to generate some water potentials found in the literature by setting many EFP terms to zero. It is also necessary to provide a Lennard-Jones 6-12 repulsive potential, and then

Further Information

4-190

make a choice to follow the EFP1 type formula for QM/EFP repulsion. Accordingly, EFP1 type calculations can be made with the following water potentials, FRAGNAME=SPC, SPCE, TIP5P, TIP5PE, or POL5P The Wikipedia page http://en.wikipedia.org/wiki/Water_model defines the first four of these, which are not polarizable potentials. The same web site references the primary literature, so that is not repeated here. POL5P is a polarizable potential, with parameters given by D.Si and H.Li J.Chem.Phys. 133, 144112/1-8(2010)

references
The first paper is more descriptive, while the second presents a very detailed derivation of the EFP1 method. Reference 18 is an overview article on EFP2. Reference 44 is the most recent review. The model development papers are: 1, 2, 3, 5, 6, 9, 14, 17, 18, 22, 23, 26, 31, 32, 34, 39, 41, 42, 43, 44, 46, 50, 51, 55, 57. 1. "Effective fragment method for modeling intermolecular hydrogen bonding effects on quantum mechanical calculations" J.H.Jensen, P.N.Day, M.S.Gordon, H.Basch, D.Cohen, D.R.Garmer, M.Krauss, W.J.Stevens in "Modeling the Hydrogen Bond" (D.A. Smith, ed.) ACS Symposium Series 569, 1994, pp 139-151. 2. "An effective fragment method for modeling solvent effects in quantum mechanical calculations". P.N.Day, J.H.Jensen, M.S.Gordon, S.P.Webb, W.J.Stevens, M.Krauss, D.Garmer, H.Basch, D.Cohen J.Chem.Phys. 105, 1968-1986(1996). 3. "The effective fragment model for solvation: internal rotation in formamide" W.Chen, M.S.Gordon, J.Chem.Phys., 105, 11081-90(1996) 4. "Transphosphorylation catalyzed by ribonuclease A: Computational study using ab initio EFPs" B.D.Wladkowski, M. Krauss, W.J.Stevens J.Am.Chem.Soc. 117, 10537-10545(1995) 5. "Modeling intermolecular exchange integrals between nonorthogonal orbitals" J.H.Jensen J.Chem.Phys. 104, 7795-7796(1996) 6. "An approximate formula for the intermolecular Pauli repulsion between closed shell molecules" J.H.Jensen, M.S.Gordon Mol.Phys. 89, 1313-1325(1996) 7. "A study of aqueous glutamic acid using the effective

Further Information

4-191

fragment potential model" P.N.Day, R.Pachter J.Chem.Phys. 107, 2990-9(1997) 8. "Solvation and the excited states of formamide" M.Krauss, S.P.Webb J.Chem.Phys. 107, 5771-5(1997) 9. "An approximate formula for the intermolecular Pauli repulsion between closed shell molecules. Application to the effective fragment potential method" J.H.Jensen, M.S.Gordon J.Chem.Phys. 108, 4772-4782(1998) 10. "Study of small water clusters using the effective fragment potential method" G.N.Merrill, M.S.Gordon J.Phys.Chem.A 102, 2650-7(1998) 11. "Solvation of the Menshutkin Reaction: A Rigourous test of the Effective Fragement Model" S.P.Webb, M.S.Gordon J.Phys.Chem.A 103, 1265-73(1999) 12. "Evaluation of the charge penetration energy between nonorthogonal molecular orbitals using the Spherical Gaussian Overlap approximation" V.Kairys, J.H.Jensen Chem.Phys.Lett. 315, 140-144(1999) 13. "Solvation of Sodium Chloride: EFP study of NaCl(H2O)n" C.P.Petersen, M.S.Gordon J.Phys.Chem.A 103, 4162-6(1999) 14. "QM/MM boundaries across covalent bonds: frozen LMO based approach for the Effective Fragment Potential method" V.Kairys, J.H.Jensen J.Phys.Chem.A 104, 6656-65(2000) 15. "A study of water clusters using the effective fragment potential and Monte Carlo simulated annealing" P.N.Day, R.Pachter, M.S.Gordon, G.N.Merrill J.Chem.Phys. 112, 2063-73(2000) 16. "A combined discrete/continuum solvation model: Application to glycine" P.Bandyopadhyay, M.S.Gordon J.Chem.Phys. 113, 1104-9(2000) 17. "Evaluation of charge penetration between distributed multipolar expansions" M.A.Freitag, M.S.Gordon, J.H.Jensen, W.J.Stevens J.Chem.Phys. 112, 7300-7306(2000) 18. "The Effective Fragment Potential Method: a QM-based MM approach to modeling environmental effects in chemistry" M.S.Gordon, M.A.Freitag, P.Bandyopadhyay, J.H.Jensen, V.Kairys, W.J.Stevens J.Phys.Chem.A 105, 293-307(2001) 19. "Accurate Intraprotein Electrostatics derived from first principles: EFP study of proton affinities of lysine 55 and tyrosine 20 in Turkey Ovomucoid" R.M.Minikis, V.Kairys, J.H.Jensen J.Phys.Chem.A 105, 3829-3837(2001) 20. "Active site structure & mechanism of Human Glyoxalase"

Further Information 21.

4-192

22.

23.

24.

25. 26. 27.

28.

29.

30.

31. 32.

33.

U.Richter, M.Krauss J.Am.Chem.Soc. 123, 6973-6982(2001) "Solvent effect on the global and atomic DFT-based reactivity descriptors using the EFP model. Solvation of ammonia." R.Balawender, B.Safi, P.Geerlings J.Phys.Chem.A 105, 6703-6710(2001) "Intermolecular exchange-induction and charge transfer: Derivation of approximate formulas using nonorthogonal localized molecular orbitals." J.H.Jensen J.Chem.Phys. 114, 8775-8783(2001) "An integrated effective fragment-polarizable continuum approach to solvation: Theory & application to glycine" P.Bandyopadhyay, M.S.Gordon, B.Mennucci, J.Tomasi J.Chem.Phys. 116, 5023-5032(2002) "The prediction of protein pKa's using QM/MM: the pKa of Lysine 55 in turkey ovomucoid third domain" H.Li, A.W.Hains, J.E.Everts, A.D.Robertson, J.H.Jensen J.Phys.Chem.B 106, 3486-3494(2002) "Computational studies of aliphatic amine basicity" D.C.Caskey, R.Damrauer, D.McGoff J.Org.Chem. 67, 5098-5105(2002) "Density Functional Theory based Effective Fragment Potential" I.Adamovic, M.A.Freitag, M.S.Gordon J.Chem.Phys. 118, 6725-6732(2003) "Intraprotein electrostatics derived from first principles: Divid-and-conquer approaches for QM/MM calculations" P.A.Molina, H.Li, J.H.Jensen J.Comput.Chem. 24, 1971-1979(2003) "Formation of alkali metal/alkaline earth cation water clusters, M(H2O)1-6, M=Li+, K+, Mg+2, Ca+2: an effective fragment potential caase study" G.N.Merrill, S.P.Webb, D.B.Bivin J.Phys.Chem.A 107, 386-396(2003) "Anion-water clusters A-(H2O)1-6, A=OH, F, SH, Cl, and Br. An effective fragment potential test case" G.N.Merrill, S.P.Webb J.Phys.Chem.A 107,7852-7860(2003) "The application of the Effective Fragment Potential to molecular anion solvation: a study of ten oxyanionwater clusters, A-(H2O)1-4" G.N.Merrill, S.P.Webb J.Phys.Chem.A 108, 833-839(2004) "The effective fragment potential: small clusters and radial distribution functions" H.M.Netzloff, M.S.Gordon J.Chem.Phys. 121, 2711-4(2004) "Fast fragments: the development of a parallel effective fragment potential method" H.M.Netzloff, M.S.Gordon J.Comput.Chem. 25, 1926-36(2004) "Theoretical investigations of acetylcholine (Ach) and acetylthiocholine (ATCh) using ab initio and effective

Further Information

4-193

34.

35.

36. 37. 38.

39. 40.

41.

42.

43.

44.

45.

fragment potential methods" J.Song, M.S.Gordon, C.A.Deakyne, W.Zheng J.Phys.Chem.A 108, 11419-11432(2004) "Dynamic polarizability, dispersion coefficient C6, and dispersion energy in the effective fragment potential method" I.Adamovic, M.S.Gordon Mol.Phys. 103, 379-387(2005) "Solvent effects on the SN2 reaction: Application of the density functional theory-based effective fragment potential method" I.Adamovic, M.S.Gordon J.Phys.Chem.A 109, 1629-36(2005) "Theoretical study of the solvation of fluorine and chlorine anions by water" D.D.Kemp, M.S.Gordon J.Phys.Chem.A 109, 7688-99(2005) "Modeling styrene-styrene interactions" I.Adamovic, H.Li, M.H.Lamm, M.S.Gordon J.Phys.Chem.A 110, 519-525(2006) "Methanol-water mixtures: a microsolvation study using the Effective Fragment Potential method" I.Adamovic, M.S.Gordon J.Phys.Chem.A 110, 10267-10273(2006) "Charge transfer interaction in the effective fragment potential method" H.Li, M.S.Gordon, J.H.Jensen J.Chem.Phys. 124, 214108/1-16(2006) "Incremental solvation of nonionized and zwitterionic glycine" C.M.Aikens, M.S.Gordon J.Am.Chem.Soc. 128, 12835-12850(2006) "Gradients of the polarization energy in the Effective Fragment Potential method" H.Li, H.M.Netzloff, M.S.Gordon J.Chem.Phys. 125, 194103/1-9(2006) "Electrostatic energy in the Effective Fragment Potential method: Theory and application to benzene dimer" L.V.Slipchenko, M.S.Gordon J.Comput.Chem. 28, 276-291(2007) "Polarization energy gradients in combined Quantum Mechanics, Effective Fragment Potential, and Polarizable Continuum Model Calculations" H.Li, M.S.Gordon J.Chem.Phys. 126, 124112/1-10(2007) "The Effective Fragment Potential: a general method for predicting intermolecular interactions" M.S.Gordon, L.V.Slipchenko, H.Li, J.H.Jensen Annual Reports in Computational Chemistry, Volume 3, pp 177-193 (2007). "An Interpretation of the Enhancement of the Water Dipole Moment Due to the Presence of Other Water Molecules"

Further Information

4-194

46.

47.

48.

49.

50.

51.

52. 53. 54.

55.

56. 57.

D.D.Kemp, M.S.Gordon J.Phys.Chem.A 112, 4885-4894(2008) "Solvent effects on optical properties of molecules: a combined time-dependent density functional/effective fragment potential approach" S.Yoo, F.Zahariev, S.Sok, M.S.Gordon J.Chem.Phys. 129, 144112/1-8(2008) "Modeling pi-pi interactions with the effective fragment potential method: The benzene dimer and substituents" T.Smith, L.V.Slipchenko, M.S.Gordon J.Phys.Chem.A 112, 5286-5294(2008) "Water-benzene interactions: An effective fragment potential and correlated quantum chemistry study" L.V.Slipchenko, M.S.Gordon J.Phys.Chem.A 113, 2092-2102(2009) "Ab initio QM/MM excited-state molecular dynamics study of Coumarin 151 in water solution" D.Kina, P.Arora, A.Nakayama, T.Noro, M.S.Gordon, T.Taketsugu Int.J.Quantum Chem. 109, 2308-2318(2009) "Damping functions in the effective fragment potential method L.V.Slipchenko, M.S.Gordon Mol.Phys. 197, 999-1016 (2009) "A combined effective fragment potential-fragment molecular orbital method. 1. the energy expression" T.Nagata, D.G.Fedorov, K.Kitaura, M.S.Gordon J.Chem.Phys. 131, 024101/1-12(2009) "Alanine: then there was water" J.M.Mullin, M.S.Gordon J.Phys.Chem.B 113, 8657-8669(2009) "Water and Alanine: from puddles(32) to ponds(49)" J.M.Mullin, M.S.Gordon J.Phys.Chem.B 113, 14413-14420(2009) "Structure of large nitrate-water clusters at ambient temperatures: simulations with effective fragment potentials and force fields with implications for atmospheric chemistry" Y.Miller, J.L.Thoman, D.D.Kemp, B.J.Finlayson-Pitts, M.S.Gordon, D.J.Tobias, R.B.Gerber J.Phys.Chem.A 113, 12805-12814(2009) "Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients" H.Li J.Chem.Phys. 131, 184103/1-8(2009) "Aqueous solvation of bihalide anions" D.D.Kemp, M.S.Gordon J.Phys.Chem.A 114, 1298-1303(2010) "Exchange repulsion between effective fragment

Further Information potentials and ab initio molecules" D.D.Kemp, J.M.Rintelman, M.S.Gordon, J.H.Jensen Theoret.Chem.Acc. 125, 481-491(2010).

4-195

Further Information

4-196

The Fragment Molecular Orbital method

coded by D.G. Fedorov, M.Chiba, T. Nagata and K. Kitaura at Research Institute for Computational Sciences (RICS) National Institute of Advanced Industrial Science and Technology (AIST) AIST Tsukuba Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan. with code contributions by: C. Steinmann (U. Copenhagen). The method was proposed by Professor Kitaura and coworkers in 1999, based on the Energy Decomposition Analysis (EDA, sometimes called the Morokuma-Kitaura energy decomposition). The FMO method is completely independent of and bears no relation to: 1. Frontier molecular orbitals (FMO), 2. Fragment molecular orbitals (FMO). The latter name is often used for the process of construction of full molecular orbitals by combining MO diagrams for parts of a molecule, ala Roald Hoffmann. The effective fragment molecular orbital method (EFMO) is closely related to but also bears significant difference to FMO, and discussed below. The FMO program was interfaced with GAMESS and follows general GAMESS guidelines for code distribution and usage. The users of the FMO program are requested to cite the FMO3-RHF paper as the basic FMO reference, D.G. Fedorov, K. Kitaura, J. Chem. Phys. 120, 6832-6840(2004) and other papers as appropriate (see below). The basic idea of the method is to acknowledge the fact the exchange and self-consistency are local in most molecules (and clusters and molecular crystals), which permits treating remote parts with Coulomb operators only, ignoring the exchange. This idea further evolves into doing molecular calculations, piecewise, with Coulomb fields due to the remaining parts. In practice one divides the molecule into fragments and performs n-mer calculations of these in the Coulomb field of other fragments (n=1,2,3). There are no empirical parameters, and the only departure from ab initio rigor is the subjective fragmentation. It has been observed that if performed physically reasonably, the fragmentation scheme alters the results very little. What changes the accuracy the most is the fragment size,

Further Information

4-197

which also determines the computational efficiency of the method. The first question is how to get started. The easiest way to prepare an FMO input file for GAMESS is to use free GUI software Facio, developed by M. Suenaga at Kyushu University. It can do molecular modeling, automatic fragmentation of peptides, nucleotides and saccharides and create GAMESS/FMO input files. http://www1.bbiq.jp/zzzfelis/Facio.html Alternatively, if you prefer command line interface, and your molecule is a protein found in the PDB (http://www.rcsb.org/pdb), you can simply use the fragmentation program "fmoutil" that is provided with GAMESS in tools/fmo, or at the FMO home page http://staff.aist.go.jp/d.g.fedorov/fmo/main.html for the latest version. If you have a cluster of identical molecules, you can perform fragmentation with just one keyword ($FMO nacut=). Computationally, it is always better to partition in a geometrical way (close parts together), so that the distance-based approximations are more efficient. The accuracy depends mainly upon the locality of the density distribution, and the appropriateness of partitioning it into fragments. There is no simple connexion between the geometrical proximity of fragmentation and accuracy. Supposing you know how to fragment, you should choose a basis set and fragment size. We recommend 2 amino acid residues or 2-4 water molecules per fragment for final energetics (or, even better, three-body with 1 molecule or residue per fragment). For geometry optimizations one may be able to use 1 res/mol per fragment, especially if gradient convergence to about 0.001 is desired. Note that although it was claimed that FMO gradient is analytic (Chem. Phys. Lett., 336 (2001), 163.) it is not so. Neither theory nor program for fully analytic gradient has been developed, to the best of our knowledge up to this day (December 21, 2006). The gradient implementation is nearly analytic, meaning three small terms are missing, one which can now be included using MODGRD=8+2. The magnitude of these small terms depends upon the fragment size (larger fragments have smaller errors). It has been our experience that in proteins with 1 residue per fragment one gets 1e3...1e-4 error in the gradient, and with 2 residues per fragment it is about 1e-4...1e-5. If you experience energy rising during geometry optimizations, you can consider two countermeasures:

Further Information

4-198

1. increase approximation thresholds, e.g. RESPPC from 2.0->2.5, RESDIM from 2.0 -> 2.5. 2. increase fragment size (e.g. by merging very small fragments with their neighbors). Finally a word of caution: optimizing systems with charged fragments in the absence of solvent is frequently not a good idea: oppositely charged fragments will most likely seek each other, unless there is some conformational barrier. One thing you should clearly understand about gradients is that if you compare FMO gradients with full molecule ab initio gradients, there are two sources of errors: a) error of the analytic FMO gradient compared to ab initio. b) error of a "nearly analytic" FMO gradient compared to the analytic FMO gradient. Since the analytic FMO gradient is not available, these two are not separable at the moment. If FMO gradients were fully analytic, geometry optimization and dynamics would have run perfectly, irrespective of error a). For basis sets you should use general guidelines and your experience developed for ab initio methods. There is a file provided (HMOs.txt) that contains hybrid molecular orbitals (HMO) used to divide the MO space along fragmentation points at covalent bonds. If your basis set is not there you need to construct your own set of HMOs. See the example file makeLMO.inp for this purpose. Next you choose a wave function type. At present one can use RHF, DFT, MP2, CC, and MCSCF (all except MCSCF support the 3-body expansion). Geometry optimization can be performed with all of these methods, except CC. Note that presence of $FMO turns FMO on.

Surfaces and solids

Until 2008, for treating covalently connected fragments, FMO had fully relaxed electron density of the detached bonds. This method is now known as FMO/HOP (HOP=hybrid orbital projection operator). It allows for a full polarization of the system and is thus well suited to very polar systems, such as proteins with charged residues. In 2008, an alternative fragmentation was suggested, based on adaptive frozen orbitals (AFO), FMO/AFO. In it, the electron density for each detached bond is first computed

Further Information

4-199

in the automatically generated small model system (with the bond intact), and in the FMO fragment calculations this electron density is frozen. It was found that FMO/AFO works quite well for surfaces and solids, where there is a dense network of bonds to be detached in order to define fragments (and the detached bonds interact quite strongly). In addition, by restricting the polarization, FMO/AFO was found to give a more balanced properties for large basis sets (triple-zeta with polarization or larger), or in comparing different isomers. However, for proteins with charged residues the original FMO/HOP scheme has a better accuracy (except large basis sets). At this point, FMO/AFO was applied to zeolites only, and some more experience is needed to give more practical advice to applications. FMO/AFO is turned on by a nonzero rafo(1) parameter (rafo array provides the thresholds to build model systems).

FMO variants
In 2007, Dahlke et al. introduced the Electrostatically Embedded Many-Body Expansion method (see E. E. Dahlke and D. G. Truhlar, J. Chem. Theory Comput. 4, 1-6 (2008) for more recent work). This method is essentially FMO with the RESPPC approximation (point charges for the electrostatic field) applied to all fragments, with the further provision that these charges may be defined at will (whereas RESPPC uses Mulliken charges), and they are kept frozen (not optimized, as in FMO). Next, Kamiya et al. suggested a fast electron correlation method (M. Kamiya, S. Hirata, M. Valiev, J. Chem. Phys. 128, 074103 (2008)), where again FMO with the RESPPC approximation to all fragments is applied with the further provision that the charges are derived from the electrostatic potential (so called ESP charges), and BSSE correction is added. The Dahlke's method was generalized in GAMESS with the introduction of an arbitrary hybrid approach, in which some fragments may have fixed and some variationally optimized charges. This implementation was employed in FMO-TDDFT calculations of solid state quinacridone (see Ref. 16 below) by using DFT/PBC frozen charges. The present energy only implementation is mostly intended for such cases as that (i.e., TDDFT), and some more work is needed to finish it for general calculations. To turn this on, set RESPPC=-1 and define NOPFRG for frozen charge fragments to 64, set frozen charges in ATCHRG. Another FMO-like method is EFMO, see its own subsection below. EFMO itself is related to several methods (PMISP: P. Soederhjelm, U. Ryde, J. Phys. Chem. A 2009, 113, 617627;

Further Information another is G. J. O. Beran, J. Chem. Phys. 2009, 130, 164115).

4-200

Effective fragment molecular orbital method (EFMO)

EFMO has been formulated by combining the physical models in EFP and FMO, namely, in EFMO, fragments are computed without the ESP (of FMO), and the polarization is estimated using EFP models of fragment polarizabilities, which are computed on the fly, so this can be thought of as automatically generated potentials in EFP. Consequently, close dimers are computed quantum-mechanically (without ESP) and far dimers are computed using the electrostatic multipole models of EFP. At present, only vacuum closedshell RHF and DFT are supported, for energy and gradient; and only molecular clusters can be computed (no systems with detached bonds). From the user point of view, EFMO functionality is very intensively borrowed from FMO, and the calculation setup is almost identical. Most additional physical models such as PCM are not supported in EFMO. EFMO should not be confused with FMO/EFP. The latter uses FMO for some fragments and EFP for others. EFMO uses the same model (EFMO), which is neither FMO nor EFP. For approximations, EFMO at present has only RESDIM. EFMO references are: 1. Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods. C. Steinmann, D. G. Fedorov, J. H. Jensen, J. Phys. Chem. A 114, 8705-8712 (2010).

Guidelines for approximations with FMO3

Three sets are suggested, for various accuracies: low: resppc=2.5 resdim=2.5 ritrim(1)=0.001,-1,1.25 medium: resppc=2.5 resdim=3.25 ritrim(1)=1.25,-1,2.0 high: resppc=2.5 resdim=4.0 ritrim(1)=2,2,2 For correlated runs, add one more value to ritrim, equal to the third element (i.e., 1.25 or 2.0). Note that gradient runs do not support nonzero RESDIM and thus use RESDIM=0 if gradient is to be computed. The "low" level of accuracy for FMO3 has an error versus full ab initio similar to FMO2, except for extended basis sets (6-311G** etc) where it is substantially better than FMO2. Thus the low level is only recommended for those large basis sets, and if a better level cannot be afforded. The medium level is recommended for production FMO3 runs; the high level is

Further Information

4-201

mostly for accuracy evaluation in FMO development. The cost is roughly: 3(low), 6(medium), 12(high). This means that FMO3 with the medium level takes roughly six times longer than FMO2. Some of the default tolerances were changed as of January 2009, when FMO 3.2 was included in GAMESS. In general, stricter parameters are now enforced when using FMO3, which of course is intended to produce more accurate results. If you wish to reproduce earlier results with the new code, use the input to revert to the earlier values: former -> FMO2 or FMO3 (as of 1/2009) RESPPC: 2.0 2.0 2.50 RESDIM: 2.0 2.0 3.25 RCORSD: 2.0 2.0 3.25 RITRIM: 2.0,2.0,2.0,2.0 -> 1.25,-1.0,2.0,2.0 (FMO3 only) MODESP: 1 0 1 MODGRD: 0 10 0 and two other settings which are not strictly speaking FMO keywords may change FMO results: MTHALL: 2 -> 4 (FMO/PCM only, see $TESCAV) DFT grid: spherical -> Lebedev (FMO-DFT only, see $DFT) Note that FMO2 energies printed during a FMO3 run will differ from those in a FMO2 run, due to the different tolerances used.

How to perform FMO-MCSCF calculations

Assuming that you are reasonably acquainted with ab initio MCSCF, only FMO-specific points are highlighted. The active space (the number of orbitals/electrons) is specified for the MCSCF fragment. The number of core/virtual orbitals for MCSCF dimers will be automatically computed. The most important issue is the initial orbitals for the MCSCF monomer. Just as for ab initio MCSCF, you should exercise chemical knowledge and provide appropriate orbitals. There are two basic ways to input MCSCF initial orbitals: A) through the FMO monomer density binary file B) by providing a text $VEC group. The former way is briefly described in INPUT.DOC (see orbital conversion). The latter way is really identical to ab initio MCSCF, except the orbitals should be prepared for the fragment (so in many cases you would have to get them from an FMO calculation). Once you have the orbitals, put them into $VEC1, and use the IJVEC option in $FMOPRP (e.g., if your MCSCF fragment is number 5, you would use $VEC1 and ijvec(1)=5,0). For two-layer MCSCF the following conditions apply. Usually one cannot simply use F40

Further Information

4-202

restart, because its contents will be overwritten with RHF orbitals and this will mess up your carefully chosen MCSCF orbitals. Therefore, two ways exist. One is to modify A) above by reordering the orbitals with something like $guess guess=skip norder=1 iorder(28)=29,30,31,32,28 $end Then the lower RHF layer will converge RHF orbitals that you reorder with iorder in the same run (add 512 to nguess in $FMO). This requires you know how to reorder before running the job so it is not always convenient. Probably the best way to run two-layer MCSCF is verbatim B) above, so just provide MCSCF monomer orbitals in $VEC1. Finally, it may happen that some MCSCF dimer will not converge. Beside the usual MCSCF tricks to gain convergence as the last resort you may be able to prepare good initial dimer orbitals, put them into $VEC2 ($VEC3 etc) and read them with ijvec. SOSCF is the preferred converger in FMO, and the other one (FULLNR) has not been modified to eradicate the artefacts of convergence (due to detached bonds). In the bad cases you can try running one or two monomer SCF iterations with FULLNR, stop the job and use its orbitals in F40 to do a restart with SOSCF. We also found useful to set CASDII=0.005 and nofo=10 in some cases running FOCAS longer to get better orbitals for SOSCF.

How to perform multilayer runs

For some fragments you may like to specify a different level of electron correlation and/or basis set. In a typical case, you would use high level for the reaction center and a lower level for the remaining part of the system. The set up for multilayer runs is very similar to the unilayer case. You only have to specify to what layer each fragment belongs and for each layer define DFTTYP, MPLEVL, SCFTYP as well as a basis set. If detached bonds are present, appropriate HMOs should be defined. See the paragraph above for multilayer MCSCF. Currently geometry optimizations of multilayer runs require adding 128 to NGUESS, if basis sets in layers differ from each other.

How to mix basis sets in FMO

You can mix basis sets in both uni and multilayer cases. The difference between a 2-layer run with one basis set per layer and a 1-layer run with 2-basis sets is significant: in the former case the lower level densities are converged with all fragments computed at the lower level. In the latter case, the fragments are converged simultaneously,

Further Information

4-203

each with its own basis set. In addition, dimer corrections between layers will be computed differently: with the lower basis set in the former case and with mixed basis set in the latter. The latter approach may result in unphysical polarization, so mixing basis sets is mainly intended to add diffuse functions to anionic (e.g., carboxyl) groups, not as a substitute for two-layer runs.

How to perform FMO/PCM calculations

Solvent effects can be taken into account with PCM. PCM in FMO is very similar to regular PCM. There is one basic difference: in FMO/PCM the total electron density that determines the electrostatic interaction is computed using the FMO density expansion up to n-body terms. The cavity is constructed surrounding the whole molecule, and the whole cavity is used in each individual m-mer calculation. There are several levels of accuracy (determined by the "n" above), and the recommended level is FMO/PCM[1(2)], specified by: $pcm ief=-10 icomp=2 icav=1 idisp=1 ifmo=2 $end $fmoprp npcmit=2 $end $tescav ntsall=240 $end $pcmcav radii=suahf $end Many PCM options can be used as in the regular PCM. The following restrictions apply: IEF may be only -3 or -10, IDP must be 0. No FMO/PCM gradients are available. Multilayer FMO runs are supported. Restarts are only limited to IREST=2, and in this case PCM charges (the ASCs) are not recycled. However, the initial guess for the charges is fairly reasonable, so IREST=2 may be useful although reading the ASCs may be implemented in future. Note for advanced users. IFMO < NBODY runs are permitted. They are denoted by FMOm/PCM[n], where m=NBODY and n=IFMO. In FMOm/PCM[n], the ASCs are computed with n-body level. The difference between FMO2/PCM[1] and FMO2/PCM[1(2)] is that in the former the ASCs are computed at the 1-body level, whereas for the former at the 2-body level, but without self-consistency (which would be FMO2/PCM[2]). Probably, FMO3/PCM[2] should be regarded as the most accurate and still affordable (with a few thousand nodes) method. However, FMO3/PCM[1(2)] (specified with NBODY=3, IFMO=2 and NPCMIT=2) is much cheaper and slightly less

Further Information accurate than FMO3/PCM[2]. FMO3/PCM[3] is the most accurate and expensive level of all.

4-204

How to perform FMO/EFP calculations

Solvent effects can also be taken into account with the Effective Fragment Potential model. The presence of both $FMO and $EFRAG groups selects FMO/EFP calculations. See the $EFRAG group and the $FMO group for details. In the FMO/EFP method, the Quantum Mechanical part of the calculation in the usual EFP method is replaced by the FMO method, which may save time for large molecules such as proteins. In the present version, only FMOn/EFP1 (water solvent only) is available for RHF, DFT and MP2. One can use the MC global optimization technique for FMO/EFP by RUNTYP=GLOBOP. Of course, the group DDI (GDDI) parallelization technique for the FMO method can be used.

Geometry optimizations for FMO

The standard optimizers in GAMESS are now well parallelized, and thus recommended to be used with FMO up to the limit hardwired in GAMESS (2000 atoms). In practice, if more than about 1000 atoms are present, numeric Hessian updates often result in the improper curvature and optimization stops. One can either do a restart, or use RUNTYP=OPTFMO (which does not diagonalize the Hessian). RUNTYP=OPTIMIZE applies to Cartesian coordinates only. Other types have not been tested and should be assumed to be not usable with FMO. If your system has more than 2000 atoms you can consider RUNTYP=OPTFMO, which can now use Hessian updates and provides reasonable way to optimize although it is not as good as the standard means in RUNTYP=OPTIMIZE. Recently, there was gradient improvement, enabled with MODGRD (=2+8).

Pair interaction energy decomposition analysis (PIEDA)

PIEDA can be performed for the PL0 and PL states. The PL0 state is the electronic state in which fragments are polarised by the environment in its free (noninteracting) state. The simplest example is that in a water cluster, each molecule is computed in the electrostatic field

Further Information

4-205

exerted by the electron densities of free water molecules. The PL state is the FMO converged monomer state, that is, the state in which fragments are polarised by the selfconsistently converged environment. Namely, following the FMO prescription, fragments are recomputed in the external field, until the latter converges. Using the PL0 state requires a series of separate runs; and it also relies on a "free state" which can be defined in many ways for molecules with detached covalent bonds. What should be done to do the PL0 state analysis? 1. run FMO0. This computes the free state for each fragment, and those electron densities are stored on file 30 (to be renamed file 40 and reused in step 3). 2. compute BDA energies (if detached bonds are present), using sample files in tools/fmo/pieda. This corrects for artifacts of bond detaching, and involves running a model system like H3C-CH3, to amend for C-C bond detaching. 3. Using results of (1) and (2), one can do the PL0 analysis. In addition to pasting the data from the two punch files in steps 1,2 and the density file in step 1 should be provided. What should be done to do the PL state analysis? The PL state itself does not need either the free state or PL0 results. However, if the PL0 results are available, coupling terms can be computed, and in this case IPIEDA is set to 2; otherwise to 1. So the easiest and frequently sufficient way to run PIEDA is to set IPIEDA=1 and do not provide any data from preceding calculations. The result of a PIEDA calculation is a set of pair interaction energies (interfragment interaction energies), decomposed into electrostatic, exchange-repulsion, charge transfer and dispersion contributions. Finally, PIEDA (especially for the PL state) can be thought of as FMO-EDA, EDA being the Kitaura-Morokuma decomposition (RUNTYP=MOROKUMA). In fact, PIEDA (for the PL state) in the case of just two fragments of standalone molecules is entirely equivalent to EDA, which can be easily verified, by running the full PIEDA analysis (ipieda=2). Note that PIEDA can be run as direct SCF, whereas EDA cannot be, and for large fragments PIEDA code can be used to perform EDA. Also, EDA in GAMESS has no explicit dispersion.

Further Information

4-206

Excited states
At present, one can use CI, MCSCF, or TDDFT to compute excited states in FMO. MCSCF is discussed separately above, so here only TDDFT and CI are explained. They are enabled by setting the IEXCIT option (EXCIT(1) defines the excited state's fragment ID). Two levels are implemented for TDDFT (FMO1-TDDFT and FMO2TDDFT). In the former, only monomer TDDFT calculations are performed, whereas the latter adds pair corrections from TDDFT dimers. PCM may be used for solvent effects with TDDFT (PCM[1] is usually sufficient). CI can only be done for CIS at the monomer level (nbody=1), FMO1-CIS. The set-up for CI is similar to that for TDDFT.

Selective FMO
Sometimes, one is interested only in some pair interactions, for example, between ligand and protein, or the opposite, only pair interactions within ligand. This saves a lot of CPU time by omitting all other pair calculations, but does not give the total properties. To use this feature, define MOLFRG and MODMOL. RUNTYP=ENERGY only is implemented.

Frozen domains
To accelerate geometry optimisations, one can specify that the electronic state of the first layer in a 2-layer FMO can be computed at the initial geometry and consequently be frozen. One can define the polarizable buffer (equal to layer 2) and frozen domain (layer 1). Fragments in the polarizable buffer which contain the atoms active in geometry optimisation form the active domain. The fragments in the active domain should have a nonzero separation from the frozen domain. In FMO/FD all dimers in the polarizable buffer are computed; in FMO/FDD only those dimers which have at least one monomer in the active domain are computed. FMO/FD and FNI/FDD are only implemented for RUNTYP=OPTIMIZE. MODFD and IACTAT in $FMO specify FMO/FD(D) atop of the usual multilayer FMO setup with some atoms frozen in geometry optimization by the standard means (i.e., IACTAT in $STATPT). Note that in FMO/FD(D) the Hessian as used in RUNTYP=OPTIMIZE is formed only for the

Further Information

4-207

atoms in the second layer, so this upper layer should not have more than the GAMESS limit (currently, 2000 atoms).

Analyzing and visualizing the results

Annotated outputs provided in tools/fmo have matching mathematical formulae added onto the outputs, for easier reading. Facio (http://www1.bbiq.jp/zzzfelis/Facio.html) can plot various FMO properties such as interaction energies, using interactive GUI viewers. To plot orbitals for an n-mer, set NPUNCH=2 in $SCF and PLTORB=.T.. There are several ways to produce cube files with electron densities. They are described in detail in tools/fmo/fmocube/README. To plot pair interaction maps, use tools/fmo/fmograbres to generate CSV files from GAMESS output, which can be easily read into Gnuplot or Excel.

Parallelization of FMO runs with GDDI

The FMO method has been developed within a 2-level hierarchical parallelization scheme, group DDI (GDDI), allowing massively parallel calculations. Different groups of processors handle the various monomer, dimer, and maybe trimer computations. The processor groups should be sized so that GAMESS' innate scaling is fairly good, and the fragments should be mapped onto the processor groups in an intelligent fashion. This is a very important and seemingly difficult issue. It is very common to be able to speed up parallel runs at least several times just by using GDDI better. First of all, do not use plain DDI and always employ GDDI when running FMO calculations. Next, learn that you can and should divide nodes into groups to achieve better performance. The very basic rule of thumb is to try to have several times fewer groups than jobs. Since the number of monomers and dimers is different, group division should reflect that fact. Ergo, find a small parallel computer with 8-32 nodes and experiment changing just two numbers: ngrfmo(1)=N1,N2 and see how performance changes for your particular system.

Limitations of the FMO method in GAMESS

Further Information

4-208

1. dimensions: in general none, except that geometry optimizations use the standard GAMESS engine which means you are limited to 2000 atoms. This can be changed by changing the source and recompiling GAMESS (see elsewhere). 2. Almost none of the "SCF extensions" in GAMESS can be used with FMO. This means, in particular, no ECPs, no CHARMM, no SIMOMM, etc. Anything that is not a plain basis set, with atoms given only by those legally entered in $FMOXYZ, will not work. The only "SCF extensions" supported are the PCM and EFP solvent models, and MCP type pseudopotentials. Not every illegal combination is trapped, caveat emptor! 3. RUNTYP is limited to ENERGY, GRADIENT, OPTIMIZE, OPTFMO, FMO0, and GLOBOP only! Do not even try other ones. 4. For the three-body FMO expansion ($FMO NBODY=3). RESDIM may be used with RUNTYP=ENERGY. Three-body FMO-MCSCF is not implemented. 5. No semiempirical methods may be used. What will work the same way as ab initio: The various SCF convergers, all DFT functionals, in-core integrals, direct SCF.

Restarts with the FMO method

RUNTYP=ENERGY can be restarted from anywhere before trimers. To restart monomer SCF, copy file F40 with monomer densities to the grandmaster node. To restart dimers, provide file F40 and monomer energies ($FMOENM). Optionally, some dimer energies can be supplied ($FMOEND) to skip computation of corresponding dimers. RUNTYP=GRADIENT can be easily restarted from monomer SCF (which really means it is a restart of RUNTYP=ENERGY, since gradient is computed at the end of this step). Provide file F40. There is another restart option (1024 in $FMOPRP irest=), supporting full gradient restart, requiring, however, that you set this option in the original run (whose results you use to restart). To use this option, you would also need to keep (or save and restore) F38 files on each node (they are different). RUNTYP=OPTIMIZE can be restarted from anywhere within the first RUNTYP=GRADIENT run (q.v.). In addition, by replacing FMOXYZ group, one can restart at a different geometry.

Further Information

4-209

RUNTYP=OPTFMO can be restarted by providing a new set of coordinates in $FMOXYZ and, optionally, by transferring $OPTRST from the punch into the input file.

Note on accuracy
The FMO method is aimed at computation of large molecules. This means that the total energy is large, for example, a 6646 atom molecule has a total energy of -165,676 Hartrees. If one uses the standard accuracy of roughly 1e-9 (that should be taken relatively), one gets an error as much as 0.001 hartree, in a single calculation. FMO involves many ab initio single point calculations of fragments and their n-mers, thus it can be expected that numeric accuracy is 12 orders lower than that given by 1e-9. Therefore, it is compulsory that accuracy should be raised, which is done by default. The following default parameters are reset by FMO: ICUT/$CONTRL (9->12), ITOL/$CONTRL(20->24), CONV/$SCF(1e-5 -> 1e-7), CUTOFF/$MP2 (1e-9->1e-12), CUTTRF/$TRANS(1e-9->1e-10). CVGTOL/$DET,$GUGDIA (1e-5 -> 1e-6) This to some extent slows down the calculation (perhaps on the order of 10-15%). It is suggested that you maintain this accuracy for all final energetics. However, you may be able to drop the accuracy a bit for the initial part of geometry optimization if you are willing to do manual work of adjusting accuracy in the input. It is recommended to keep high accuracy at the flat surfaces (the final part of optimizations) though. For DFT the numeric grid's accuracy may be increased in accordance with the molecule size, e.g. extending the default grid of 96*12*24 to 96*20*40. However, some tests indicate that energy differences are quite insensitive to this increase.

FMO References
I. Basic FMO papers A book chapter contains an introduction to FMO basics: Theoretical development of the fragment molecular orbital (FMO) method, D. G. Fedorov, K. Kitaura, in "Modern methods for theoretical physical chemistry of biopolymers", E. B. Starikov, J. P. Lewis, S. Tanaka,

Further Information Eds., pp 3-38, Elsevier, Amsterdam, 2006.

4-210

There is now a full FMO book (11 chapters), which contains an introduction to FMO aimed at general application chemists, and a wealth of practical advice on doing FMO calculations: The Fragment Molecular Orbital Method: Practical Applications to Large Molecular System, D. G. Fedorov, K. Kitaura, Eds., CRC Press, Boca Raton, FL, 2009. An FMO review is published as a Feature Article: D. G. Fedorov, K. Kitaura J. Phys. Chem. A 111, 6904-6914(2007). A very concise and detailed mathematical formulation of FMO including various extensions and property calculations is published as Mathematical formulation of the fragment molecular orbital method. T. Nagata, D. G. Fedorov, K. Kitaura. In "Linear-Scaling Techniques in Computational Chemistry and Physics". R. Zalesny, M. G. Papadopoulos, P. G. Mezey, J. Leszczynski, Eds., pp. 17-64, Springer, New York, 2011. 1. Fragment molecular orbital method: an approximate computational method for large molecules" K. Kitaura, E. Ikeo, T. Asada, T. Nakano, M. Uebayasi Chem. Phys. Lett., 313, 701(1999). 2. Fragment molecular orbital method: application to polypeptides T. Nakano, T. Kaminuma, T. Sato, Y. Akiyama, M. Uebayasi, K. Kitaura Chem.Phys.Lett. 318, 614(2000). 3. Fragment molecular orbital method: analytical energy gradients K. Kitaura, S.-I. Sugiki, T. Nakano, Y. Komeiji, M. Uebayasi, Chem. Phys. Lett., 336, 163(2001). 4. Fragment molecular orbital method: use of approximate electrostatic potential T. Nakano, T. Kaminuma, T. Sato, K. Fukuzawa, Y. Akiyama, M. Uebayasi, K. Kitaura Chem. Phys. Lett., 351, 475(2002). 5. The extension of the fragment molecular orbital method with the many-particle Green's function, K. Yasuda, D. Yamaki, J. Chem. Phys. 125, 154101(2006). 6. The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method.

Further Information D. G. Fedorov, K. Kitaura J. Chem. Phys. 131, 171106(2009). II. FMO in GAMESS

4-211

1. A new hierarchical parallelization scheme: generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO). D. G. Fedorov, R. M. Olson, K. Kitaura, M. S. Gordon, S. Koseki J. Comput. Chem. 25, 872-880(2004). 2. The importance of three-body terms in the fragment molecular orbital method. D. G. Fedorov and K. Kitaura J. Chem. Phys. 120, 6832-6840(2004). 3. On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory D. G. Fedorov and K. Kitaura Chem. Phys. Lett. 389, 129-134(2004). 4. Second order Moeller-Plesset perturbation theory based upon the fragment molecular orbital method. D. G. Fedorov and K. Kitaura J. Chem. Phys. 121, 2483-2490(2004). 5. Multiconfiguration self-consistent-field theory based upon the fragment molecular orbital method. D. G. Fedorov and K. Kitaura J. Chem. Phys. 122, 054108/1-10(2005). 6. Multilayer Formulation of the Fragment Molecular Orbital Method (FMO). D. G. Fedorov, T. Ishida, K. Kitaura J. Phys. Chem. A. 109, 2638-2646(2005). 7. Coupled-cluster theory based upon the Fragment Molecular Orbital method. D. G. Fedorov, K. Kitaura J. Chem. Phys. 123, 134103/1-11 (2005) 8. The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). D. G. Fedorov, K. Kitaura, H. Li, J. H. Jensen, M. S. Gordon, J. Comput. Chem., 27, 976-985(2006) 9. The three-body fragment molecular orbital method for accurate calculations of large systems, D. G. Fedorov, K. Kitaura Chem. Phys. Lett. 433, 182-187(2006). 10. Pair interaction energy decomposition analysis, D. G. Fedorov, K. Kitaura J. Comp. Chem. 28, 222-237(2007). 11. On the accuracy of the three-body fragment molecular orbital method (FMO) applied to Moeller-Plesset perturbation theory, D. G. Fedorov, K. Ishimura, T. Ishida, K. Kitaura,

Further Information

4-212

P. Pulay, S. Nagase J. Comput. Chem., 28, 1476-1484 (2007). 12. The Fragment Molecular Orbital method for geometry optimizations of polypeptides and proteins, D.G.Fedorov, T. Ishida, M. Uebayasi, K. Kitaura J.Phys.Chem.A, 111, 2722-2732(2007). 13. Time-dependent density functional theory with the multilayer fragment molecular orbital method M. Chiba, D. G. Fedorov, K. Kitaura Chem. Phys. Lett. 444, 346-350 (2007). 14. Time-dependent density functional theory based upon the fragment molecular orbital method M. Chiba, D. G. Fedorov, K. Kitaura J. Chem. Phys. 127, 104108(2007). 15. Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory. M. Chiba, D. G. Fedorov, K. Kitaura J. Comput. Chem. 29, 2667-2676 (2008). 16. Theoretical Analysis of the Intermolecular Interaction Effects on the Excitation Energy of Organic Pigments: Solid State Quinacridone. H. Fukunaga, D.G.Fedorov, M. Chiba, K. Nii, K. Kitaura J. Phys. Chem. A 112, 10887-10894 (2008). 17. Covalent Bond Fragmentation Suitable To Describe Solids in the Fragment Molecular Orbital Method. D. G. Fedorov, J. H. Jensen, R. C. Deka, K. Kitaura J. Phys. Chem. A 112, 11808-11816 (2008). 18. Excited state geometry optimizations by time-dependent density functional theory based on the fragment molecular orbital method. M. Chiba, D. G. Fedorov, T. Nagata, K. Kitaura Chem. Phys. Lett. 474, 227-232 (2009). 19. Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method. T. Nagata, D. G. Fedorov, K. Kitaura, Chem. Phys. Lett. 475, 124-131 (2009). 20. A combined effective fragment potential - fragment molecular orbital method. I. The energy expression and initial applications. T. Nagata, D. G. Fedorov, K. Kitaura, M. S. Gordon, J. Chem. Phys. 131, 024101 (2009). 21. Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method. D. G. Fedorov, P. V. Avramov, J.H. Jensen, K. Kitaura, Chem. Phys. Lett. 477, 169-175 (2009). 22. Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis.

Further Information

4-213

T. Ikegami, T. Ishida, D. G. Fedorov, K. Kitaura, Y. Inadomi, H. Umeda, M. Yokokawa, S. Sekiguchi, J. Comp. Chem. 31, 447-454 (2010). 23. Open-Shell Formulation of the Fragment Molecular Orbital Method. S. R. Pruitt, D. G. Fedorov, K. Kitaura, M. S. Gordon J. Chem. Theor. Comp. 6, 1-5 (2010) 24. Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation. H. Li, D. G. Fedorov, T. Nagata, K. Kitaura, J. H. Jensen, M. S. Gordon J. Comput. Chem. 31, 778-790 (2010). 25. Nuclear-Electronic Orbital Method within the Fragment Molecular Orbital Approach. B. Auer, M. V. Pak, S. Hammes-Schiffer, J. Phys. Chem. C 114, 5582-5588 (2010). 26. Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method. T. Nagata, D. G. Fedorov, K. Kitaura, Chem. Phys. Lett. 492, 302-308 (2010). 27. Systematic Study of the Embedding Potential Description in the Fragment Molecular Orbital Method. D. G. Fedorov, L. V. Slipchenko, K. Kitaura, J. Phys. Chem. A 114, 8742-8753 (2010). 28. A combined effective fragment potential - fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin. T. Nagata, D. G. Fedorov, T. Sawada, K. Kitaura, M. S. Gordon, J. Chem. Phys. 134, 034110 (2011). 29. Geometry optimization of the active site of a large system with the fragment molecular orbital method. D. G. Fedorov, Y. Alexeev, K. Kitaura, J. Phys. Chem. Lett. 2, 282-288 (2011). 30. Fully analytic energy gradient in the fragment molecular orbital method. T. Nagata, K. Brorsen, D. G. Fedorov, K. Kitaura, M. S. Gordon, J. Chem. Phys. 134, 124115(2011). Other FMO references including applications can be found at: http://staff.aist.go.jp/d.g.fedorov/fmo/main.html EFMO references are given in its own subsection.

Further Information

4-214

MOPAC Calculations within GAMESS

Parts of MOPAC 6.0 have been included in GAMESS giving access to four semiempirical wavefunctions: MNDO, AM1, PM3, and RM1. RM1 is the most recent parameterization, replacing AM1 data for H, C-F, P-Cl, Br, and I. See G.

Bruno Rocha, R. Oliveira Freire, A. Mayall Simas, and J. J. P. Stewart, J. Comput. Chem. 27, 1101-1111(2006).
These wavefunctions are quantum mechanical in nature but neglect most two electron integrals, a deficiency that is (hopefully) compensated for by introduction of empirical parameters. The quantum mechanical nature of semiempirical theory makes it quite compatible with the ab initio methodology in GAMESS. As a result, very little of MOPAC 6.0 actually is incorporated into GAMESS. The part that did make it in is the code that evaluates 1) 2) 3) 4) the the the the one- and two-electron integrals, two-electron part of the Fock matrix, cartesian energy derivatives, and ZDO atomic charges and molecular dipole.

Everything else is actually GAMESS: coordinate input (including point group symmetry), the SCF convergence procedures, the matrix diagonalizer, the geometry searcher, the numerical hessian driver, and so on. Most of the output will look like an ab initio output. It is extremely simple to perform one of these calculations. All you need to do is specify GBASIS=MNDO, AM1, or PM3 in the $BASIS group. Note that this not only picks a particular Slater orbital basis, it also selects a particular "hamiltonian", namely a particular parameter set. MNDO, AM1, and PM3 will not work with every option in GAMESS. Currently the semiempirical wavefunctions support SCFTYP=RHF, UHF, and ROHF in any combination with RUNTYP=ENERGY, GRADIENT, OPTIMIZE, SADPOINT, HESSIAN, and IRC. Note that all hessian runs are numerical finite differencing. The MOPAC CI and half electron methods are not supported. Because the majority of the implementation is GAMESS rather than MOPAC you will notice a few improvments. Dynamic memory allocation is used, so that GAMESS uses far

Further Information

4-215

less memory for a given size of molecule. The starting orbitals for SCF calculations are generated by a Huckel initial guess routine. Spin restricted (high spin) ROHF can be performed. Converged SCF orbitals will be labeled by their symmetry type. Numerical hessians will make use of point group symmetry, so that only the symmetry unique atoms need to be displaced. Infrared intensities will be calculated at the end of hessian runs. We have not at present used the block diagonalizer during intermediate SCF iterations, so that the run time for a single geometry point in GAMESS is usually longer than in MOPAC. However, the geometry optimizer in GAMESS can frequently optimize the structure in fewer steps than the procedure in MOPAC. Orbitals and hessians are punched out for convenient reuse in subsequent calculations. Your molecular orbitals can be drawn with the PLTORB graphics program, which has been taught about s and p STO basis sets. However, because of the STO basis set used in semiempirical runs, the various property calculations coded for Gaussian basis sets are unavailable. This means $ELMOM, $ELPOT, etc. properties are unavailable. Likewise the solvation models do not work with semi-empirical runs. Note that MOPAC6 did not include d STO functions, and it is therefore quite impossible to run transition metals. To reduce CPU time, only the EXTRAP convergence accelerator is used by the SCF procdures. For difficult cases, the DIIS, RSTRCT, and/or SHIFT options will work, but may add significantly to the run time. With the Huckel guess, most calculations will converge acceptably without these special options. MOPAC parameters exist for the following elements. The printout when you run will give you specific references for each kind of atom. The quote on alkali's below means that these elements are treated as "sparkles", rather than as atoms with genuine basis functions. For MNDO: H Li Na' K' Rb' * H * * * ... * ... * ... B Al Zn * * * Hg * For AM1: H C Si Ge Sn Pb N P * * * O F S Cl * Br * I For PM3:

Further Information * * B C N P * * * O F Li Be Na Mg K Ca ... Rb' * ... * * ... * C N P F Na Mg Cl K Ca ... Br Rb' * ... I * * ... For RM1: H

4-216 O S

Al Si Zn * Hg * Ge * Sn * *

S Cl * Br * I

Al Si

Zn Ga Ge As Se Cd In Sn Sb Te Hg Tl Pb Bi

(AM1 will be used for any other atoms RM1.) C N P O F S Cl Br I

Semiempirical calculations are very fast. One of the motives for the MOPAC implementation within GAMESS is to take advantage of this speed. Semiempirical models can rapidly provide reasonable starting geometries for ab initio optimizations. Semiempirical hessian matrices are obtained at virtually no computational cost, and may help dramatically with an ab initio geometry optimization. Simply use HESS=READ in $STATPT to use a MOPAC $HESS group in an ab initio run. It is important to exercise caution as semiempirical methods can be dead wrong! The reasons for this are bad parameters (in certain chemical situations), and the underlying minimal basis set. A good question to ask before using MNDO, AM1 or PM3 is "how well is my system modeled with an ab initio minimal basis sets, such as STO-3G?" If the answer is "not very well" there is a good chance that a semiempirical description is equally poor.

Further Information

4-217

Molecular Properties and Conversion Factors

These two papers are of general interest: A.D.Buckingham, J.Chem.Phys. 30, 1580-1585(1959). D.Neumann, J.W.Moskowitz J.Chem.Phys. 49, 2056-2070(1968). The first deals with multipoles, and the second with other properties such as electrostatic potentials. All units are derived from the atomic units for distance and the monopole electric charge, as given below. distance monopole dipole quadrupole octopole electric potential electric field - 1 au = 5.291771E-09 cm - 1 au = 4.803242E-10 esu 1 esu = sqrt(g-cm**3)/sec - 1 au = 2.541766E-18 esu-cm 1 Debye = 1.0E-18 esu-cm - 1 au = 1.345044E-26 esu-cm**2 1 Buckingham = 1.0E-26 esu-cm**2 - 1 au = 7.117668E-35 esu-cm**3 - 1 au = 9.076814E-02 esu/cm - 1 au = 1.715270E+07 esu/cm**2 1 esu/cm**2 = 1 dyne/esu

electric field gradient- 1 au = 3.241390E+15 esu/cm**3 The atomic unit for electron density is electron/bohr**3 for the total density, and 1/bohr**3 for an orbital density. The atomic unit for spin density is excess alpha spins per unit volume, h/4*pi*bohr**3. Only the expectation value is computed, with no constants premultiplying it. IR intensities are printed in Debye**2/amu-Angstrom**2. These can be converted into intensities as defined by Wilson, Decius, and Cross's equation 7.9.25, in km/mole, by multiplying by 42.255. If you prefer 1/atm-cm**2, use a conversion factor of 171.65 instead. A good reference for deciphering these units is A.Komornicki, R.L.Jaffe J.Chem.Phys. 1979, 71, 2150-2155. A reference showing how IR intensities change with basis improvements at the HF

Further Information level is Y.Yamaguchi, M.Frisch, J.Gaw, H.F.Schaefer, J.S.Binkley, J.Chem.Phys. 1986, 84, 2262-2278.

4-218

Raman activities in A**4/amu multiply by 6.0220E-09 for units of cm**4/g. One of the many sources explaining how activity relates to intensity is D.Michalska, R.Wysokinski Chem.Phys.Lett. 403, 211-217(2005)

Polarizabilities
Static polarizabilities are named alpha, beta, and gamma; and are called the polarizability, hyperpolarizability, and second hyperpolarizability. They are the 2nd, 3rd, and 4th derivatives of the energy with respect to applied uniform electric fields, with the 1st derivative being the dipole moment! It might be worth mentioning that a uniform field can be applied using $EFIELD, if you wish to develop custom usages, but $EFIELD is not to be given for any kind of run discussed below. The general approach to computing static polarizabilities is numerical differentiation, namely RUNTYP=FFIELD, which should work for any energy method provided by GAMESS. A sequence of computations with fields applied in the x, y, and/or z directions will generate the tensors. See $FFCALC for details. Analytic computation of all three tensors is available for SCFTYP=RHF only, see RUNTYP=TDHF and $TDHF. If you need to know just the alpha polarizability, see POLAR in $CPHF during any analytic hessian job. A break down of the static alpha polarizability in terms of contributions from individual localized orbitals can be obtained by setting POLDCM=.TRUE. in $LOCAL. Calculation will be by analytic means, unless POLNUM in that group is selected. This option is available only for SCFTYP=RHF. The keyword LOCHYP in $FFCALC gives a similar analysis for all three static polarizabilities, determined by numerical differentiation. Polarizabilities in a static electric field differ from those in an oscillating field such as a laser produces. For RHF cases only, a variety of frequency dependent polarizabilities alpha, beta, and gamma can be generated, depending on the experiment. A particularly easy one to describe is 'second harmonic generation', governed by a beta tensor describing the absorption of two photons and the emission of one at doubled frequency. See RUNTYP=TDHF,

Further Information

4-219

and papers listed under $TDHF, for many other non-linear optical experiments. Nuclear derivatives of the dipole moment and the various polarizabilities are also of interest. For example, knowledge of the derivative of the dipole with respect to nuclear coordinates yields the IR intensity. Similarly, the nuclear derivative of the static alpha polarizability gives Raman intensities: see RUNTYP=RAMAN. Analytic of 1st or 2nd nuclear derivatives of static or frequency dependent polarizabilities are available for SCFTYP=RHF only, see RUNTYP=TDHFX and $TDHFX, giving rise to experimental observations such as resonance Raman and hyper-Raman. Finally, instead of considering polarizabilities as a function of real frequencies, they can be considered to be dependent on the imaginary frequency. The imaginary frequency dependent alpha polarizability can be computed analytically for SCFTYP=RHF only, using POLDYN=.TRUE. in $LOCAL. Integration of this quantity over the imaginary frequency domain can be used to extract C6 dispersion constants. Polarizabilities are tensor quantities. There are a number of different ways to define them, and various formulae to extract "scalar" and "vector" quantites from the tensors. A good reference for learning how to compare the output of a theoretical program to experiment is A.Willetts, J.E.Rice, D.M.Burland, D.P.Shelton J.Chem.Phys. 97, 7590-7599(1992)

Further Information

4-220

Localized Molecular Orbitals

Three different orbital localization methods are implemented in GAMESS. The energy and dipole based methods normally produce similar results, but see M.W.Schmidt, S.Yabushita, M.S.Gordon in J.Chem.Phys., 1984, 88, 382-389 for an interesting exception. You can find references to the three methods at the beginning of this chapter. The method due to Edmiston and Ruedenberg works by maximizing the sum of the orbitals' two electron self repulsion integrals. Most people who think about the different localization criteria end up concluding that this one seems superior. The method requires the two electron integrals, transformed into the molecular orbital basis. Because only the integrals involving the orbitals to be localized are needed, the integral transformation is actually not very time consuming. The Boys method maximizes the sum of the distances between the orbital centroids, that is the difference in the orbital dipole moments. The population method due to Pipek and Mezey maximizes a certain sum of gross atomic Mulliken populations. This procedure will not mix sigma and pi bonds, so you will not get localized banana bonds. Hence it is rather easy to find cases where this method give different results than the Ruedenberg or Boys approach. GAMESS will localize orbitals for any kind of RHF, UHF, ROHF, or MCSCF wavefunctions. The localizations will automatically restrict any rotation that would cause the energy of the wavefunction to be changed (the total wavefunction is left invariant). As discussed below, localizations for GVB or CI functions are not permitted. The default is to freeze core orbitals. The localized valence orbitals are scarcely changed if the core orbitals are included, and it is usually convenient to leave them out. Therefore, the default localizations are: RHF functions localize all doubly occupied valence orbitals. UHF functions localize all valence alpha, and then all valence beta orbitals. ROHF functions localize all valence doubly occupied orbitals, and all singly occupied orbitals, but do not mix these two orbital spaces. MCSCF functions

Further Information

4-221

localize all valence MCC type orbitals, and localize all active orbitals, but do not mix these two orbital spaces. To recover the invariant MCSCF function, you must be using a FORS=.TRUE. wavefunction, and you must set GROUP=C1 in $DRT, since the localized orbitals possess no symmetry. In general, GVB functions are invariant only to localizations of the NCO doubly occupied orbitals. Any pairs must be written in natural form, so pair orbitals cannot be localized. The open shells may be degenerate, so in general these should not be mixed. If for some reason you feel you must localize the doubly occupied space, do a RUNTYP=PROP job. Feed in the GVB orbitals, but tell the program it is SCFTYP=RHF, and enter a negative ICHARG so that GAMESS thinks all orbitals occupied in the GVB are occupied in this fictitous RHF. Use NINA or NOUTA to localize the desired doubly occupied orbitals. Orbital localization is not permitted for CI, because we cannot imagine why you would want to do that anyway. Boys localization of the core orbitals in molecules having elements from the third or higher row almost never succeeds. Boys localization including the core for second row atoms will often work, since there is only one inner shell on these. The Ruedenberg method should work for any element, although including core orbitals in the integral transformation is more expensive. The easiest way to do localization is in the run which generates the wavefunction, by selecting LOCAL=xxx in the $CONTRL group. However, localization may be conveniently done at any time after determination of the wavefunction, by executing a RUNTYP=PROP job. This will require only $CONTRL, $BASIS/$DATA, $GUESS (pick MOREAD), the converged $VEC, possibly $SCF or $DRT to define your wavefunction, and optionally some $LOCAL input. There is an option to restrict all rotations that would mix orbitals of different symmetries. SYMLOC=.TRUE. yields only partially localized orbitals, but these still possess symmetry. They are therefore very useful as starting orbitals for MCSCF or GVB-PP calculations. Because they still have symmetry, these partially localized orbitals run as efficiently as the canonical orbitals. Because it is much easier for a user to pick out the bonds which are to be correlated, a significant number of iterations can be saved, and convergence to false solutions is less likely. * * *

Further Information

4-222

The most important reason for localizing orbitals is to analyze the wavefunction. A simple example is to look at shapes of the orbitals with the MacMolPlt program. Or, you might read the localized orbitals in during a RUNTYP=PROP job to examine their Mulliken populations. Localized orbitals are a particularly interesting way to analyze MCSCF computations. The localized orbitals may be oriented on each atom (see option ORIENT in $LOCAL) to direct the orbitals on each atom towards their neighbors for maximal bonding, and then print a bond order analysis. The orientation procedure is newly programmed by J.Ivanic and K.Ruedenberg, to deal with the situation of more than one localized orbital occuring on any given atom. Some examples of this type of analysis are D.F.Feller, M.W.Schmidt, K.Ruedenberg J.Am.Chem.Soc. 104, 960-967 (1982) T.R.Cundari, M.S.Gordon J.Am.Chem.Soc. 113, 5231-5243 (1991) N.Matsunaga, T.R.Cundari, M.W.Schmidt, M.S.Gordon Theoret.Chim.Acta 83, 57-68 (1992). In addition, the energy of your molecule can be partitioned over the localized orbitals so that you may be able to understand the origin of barriers, etc. This analysis can be made for the SCF energy, and also the MP2 correction to the SCF energy, which requires two separate runs. An explanation of the method, and application to hydrogen bonding may be found in J.H.Jensen, M.S.Gordon, J.Phys.Chem. 99, 8091-8107(1995). Analysis of the SCF energy is based on the localized charge distribution (LCD) model: W.England and M.S.Gordon, J.Am.Chem.Soc. 93, 4649-4657 (1971). This is implemented for RHF and ROHF wavefunctions, and it requires use of the Ruedenberg localization method, since it needs the two electron integrals to correctly compute energy sums. All orbitals must be included in the localization, even the cores, so that the total energy is reproduced. The LCD requires both electronic and nuclear charges to be partitioned. The orbital localization automatically accomplishes the former, but division of the nuclear charge may require some assistance from you. The program attempts to correctly partition the nuclear charge, if you select the MOIDON option, according to the following: a Mulliken type analysis of the localized orbitals is made. This determines if an orbital is a core, lone pair, or

Further Information

4-223

bonding MO. Two protons are assigned to the nucleus to which any core or lone pair belongs. One proton is assigned to each of the two nuclei in a bond. When all localized orbitals have been assigned in this manner, the total number of protons which have been assigned to each nucleus should equal the true nuclear charge. Many interesting systems (three center bonds, backbonding, aromatic delocalization, and all charged species) may require you to assist the automatic assignment of nuclear charge. First, note that MOIDON reorders the localized orbitals into a consistent order: first comes any core and lone pair orbitals on the 1st atom, then any bonds from atom 1 to atoms 2, 3, ..., then any core and lone pairs on atom 2, then any bonds from atom 2 to 3, 4, ..., and so on. Let us consider a simple case where MOIDON fails, the ion NH4+. Assuming the nitrogen is the 1st atom, MOIDON generates NNUCMO=1,2,2,2,2 MOIJ=1,1,1,1,1 2,3,4,5 ZIJ=2.0,1.0,1.0,1.0,1.0, 1.0,1.0,1.0,1.0 The columns (which are LMOs) are allowed to span up to 5 rows (the nuclei), in situations with multicenter bonds. MOIJ shows the Mulliken analysis thinks there are four NH bonds following the nitrogen core. ZIJ shows that since each such bond assigns one proton to nitrogen, the total charge of N is +6. This is incorrect of course, as indeed will always happen to some nucleus in a charged molecule. In order for the energy analysis to correctly reproduce the total energy, we must ensure that the charge of nitrogen is +7. The least arbitrary way to do this is to increase the nitrogen charge assigned to each NH bond by 1/4. Since in our case NNUCMO and MOIJ and much of ZIJ are correct, we need only override a small part of them with $LOCAL input: IJMO(1)=1,2, 1,3, 1,4, 1,5 ZIJ(1)=1.25, 1.25, 1.25, 1.25 which changes the charge of the first atom of orbitals 2 through 5 to 5/4, changing ZIJ to ZIJ=2.0,1.25,1.25,1.25,1.25, 1.0, 1.0, 1.0, 1.0 The purpose of the IJMO sparse matrix pointer is to let you give only the changed parts of ZIJ and/or MOIJ. Another way to resolve the problem with NH4+ is to change one of the 4 equivalent bond pairs into a "proton". A "proton" orbital AH treats the LMO as if it were a

Further Information

4-224

lone pair on A, and so assigns +2 to nucleus A. Use of a "proton" also generates an imaginary orbital, with zero electron occupancy. For example, if we make atom 2 in NH4+ a "proton", by IPROT(1)=2 NNUCMO(2)=1 IJMO(1)=1,2,2,2 MOIJ(1)=1,0 ZIJ(1)=2.0,0.0 the automatic decomposition of the nuclear charges will be NNUCMO=1,1,2,2,2,1 MOIJ=1,1,1,1,1,2 3,4,5 ZIJ=2.0,2.0,1.0,1.0,1.0,1.0 1.0,1.0,1.0 The 6th column is just a proton, and the decomposition will not give any electronic energy associated with this "orbital", since it is vacant. Note that the two ways we have disected the nuclear charges for NH4+ will both yield the correct total energy, but will give very different individual orbital components. Most people will feel that the first assignment is the least arbitrary, since it treats all four NH bonds equivalently. However you assign the nuclear charges, you must ensure that the sum of all nuclear charges is correct. This is most easily verified by checking that the energy sum equals the total SCF energy of your system. As another example, H3PO is studied in EXAM26.INP. Here the MOIDON analysis decides the three equivalent orbitals on oxygen are O lone pairs, assigning +2 to the oxygen nucleus for each orbital. This gives Z(O)=9, and Z(P)=14. The least arbitrary way to reduce Z(O) and increase Z(P) is to recognize that there is some backbonding in these "lone pairs" to P, and instead assign the nuclear charge of these three orbitals by 1/3 to P, 5/3 to O. Because you may have to make several runs, looking carefully at the localized orbital output before the correct nuclear assignments are made, there is an option to skip directly to the decomposition when the orbital localization has already been done. Use $CONTRL RUNTYP=PROP $GUESS GUESS=MOREAD NORB= $VEC containing the localized orbitals! $TWOEI The latter group contains the necessary Coulomb and exchange integrals, which are punched by the first localization, and permits the decomposition to begin

Further Information immediately. SCF level dipoles can also be analyzed using the DIPDCM flag in $LOCAL. The theory of the dipole analysis is given in the third paper of the LCD sequence. The following list includes application of the LCD analysis to many problems of chemical interest: W.England, M.S.Gordon W.England, M.S.Gordon M.S.Gordon, W.England M.S.Gordon, W.England M.S.Gordon, W.England M.S.Gordon W.England, M.S.Gordon,

4-225

J.Am.Chem.Soc. 93, 4649-4657 (1971) J.Am.Chem.Soc. 94, 4818-4823 (1972) J.Am.Chem.Soc. 94, 5168-5178 (1972) Chem.Phys.Lett. 15, 59-64 (1972) J.Am.Chem.Soc. 95, 1753-1760 (1973) J.Mol.Struct. 23, 399 (1974) K.Ruedenberg, Theoret.Chim.Acta 37, 177-216 (1975) J.H.Jensen, M.S.Gordon, J.Phys.Chem. 99, 8091-8107(1995) J.H.Jensen, M.S.Gordon, J.Am.Chem.Soc. 117, 8159-8170(1995) M.S.Gordon, J.H.Jensen, Acc.Chem.Res. 29, 536-543(1996) * * * It is also possible to analyze the MP2 correlation correction in terms of localized orbitals, for the RHF case. The method is that of G.Peterssen and M.L.Al-Laham, J.Chem.Phys., 94, 6081-6090 (1991). Any type of localized orbital may be used, and because the MP2 calculation typically omits cores, the $LOCAL group will normally include only valence orbitals in the localization. As mentioned already, the analysis of the MP2 correction must be done in a separate run from the SCF analysis, which must include cores in order to sum up to the total SCF energy. * * * Typically, the results are most easily interpreted by looking at "the bigger picture" than at "the details". Plots of kinetic and potential energy, normally as a function of some coordinate such as distance along an IRC, are the most revealing. Once you determine, for example, that the most significant contribution to the total energy is the kinetic energy, you may wish to look further into the minutia, such as the kinetic energies of individual localized orbitals, or groups of LMOs corresponding to an entire functional group.

Further Information

4-226

Transition Moments and Spin-Orbit Coupling

A review of various ways of computing spin-orbit coupling: D.G.Fedorov, S.Koseki, M.W.Schmidt, M.S.Gordon, Int.Rev.Phys.Chem. 22, 551-592(2003) GAMESS can compute transition moments and oscillator strengths for the radiative transitions between states written in terms of CI wavefunctions (GUGA only). The moments are computed using both the "length form" and the "velocity form". In a.u., where h-bar=m=1, we start from [A,q] = -i dA/dp For A=H, dH/dp=p, and p= -i d/dq, [H,q] = -i p = -d/dq. For non-degenerate states, <a|[H,q]|b> = <a|-d/dq|b> (Ea-Eb)<a|q|b> = - <a|d/dq|b> This relates the dipole to the velocity form, <a|q|b> = -1/(Ea-Eb) <a|d/dq|b> but the CI states will give different numbers for each side, since the states aren't exact eigenfunctions. Transition moment computation is OPERAT=DM in $TRANST. For transition moments, the CI is necessarily performed on states of the same multiplicity. All other operators are various spin-orbit coupling options. There are two kinds of calculations possible, which we will call SO-CI and SO-MCQDPT. Note that there is a hyphen in "spin-orbit CI" to avoid confusion with "second order CI" in the sense of the SOCI keyword in $DRT input. For SO-CI, the initial states may be any CI wavefunction that the GUGA package can generate. For SO-MCQDPT the initial states for spin-orbit coupling are of CAS type, and the operator mixing them corresponds to MCQDPT generalised for spin-dependent operators (with certain approximations). GAMESS can compute the "microscopic Breit-Pauli spin-orbit operator", which includes both a one and two electron operator. The full Breit-Pauli operator can be computed exactly (OPERAT=HSO2), or approximated in two ways: complete elimination of the 2e- term, whose absence can be approximately accounted for by means of effective nuclear charges (HSO1), or by inclusion of only the coreactive 2e- terms which typically account for 90% or more of the two electron term, while saving most of the 2eterms' CPU cost (HSO2P).

Further Information

4-227

Spin-orbit runs can be done for general spins, for more than two different spin multiplicities at once, for general active spaces. At times, when the spatial wavefunction is degenerate, a spin-orbit run may involve only one spin multiplicity, e.g. a triplet-pi state in a linear molecule. The most common case is two different spins. It is also possible to obtain the dipole transition moments between the final spin-mixed wavefunctions, which of course do not any longer have a rigourous S quantum no. When the run is SO-MCQDPT, the transition moment are first computed only between CAS states, and then combined with the spinmixed SO-MCQDPT coefficients. Compared to older versions, the basis set has been fully generalized to allow any s, p, d, f, g, or L functions.

states
For transition moments, the states are generated by CI calculations using the GUGA package. These states are the final states, and the results are just the transition moments between these states. The states are defined by $DRTx input groups. For SO-CI, the energy of the CI states forms the diagonal of a spin-orbit Hamiltonian, as in the state basis the spin-free Hamiltonian is of course diagonal. Addition of the Pauli-Breit operator does not change the diagonal, but does add H-so elements off diagonal. For SO-MCQDPT, the spin-free MCQDPT matrix elements are expanded into matrices corresponding to all Ms values for a pair of multiplicities. These matrices are block-diagonal before the addition of spin-orbit coupling terms, coupling Ms values. The diagonalization of this spin-orbit Hamiltonian gives new energy levels, and spin-mixed final states. Optionally, the transition dipoles between the final states can be computed. The input requirements are $DRTx or $MCQDx groups which define the original pure spin states. We will call the initial states CAS-CI, since most of the time they will be MCSCF states. There may be cases such as the Na example below where SCF orbitals are used, or other cases where a FOCI or SOCI wavefunction might be used for the initial states. Please keep in mind that the term does not imply the states must be MCSCF states, just that they commonly are. In the above, x may vary from 1 to 64. The reason for allowing such a large range is to permit the use of Abelian

Further Information

4-228

point group symmetry during the generation of the initial states. The best explanation will be an example, but the number of these input groups depends on both the number of orbital sets input, and how much symmetry is present. The next two subsections discuss these points.

orbitals
The orbitals for transition moments or for SO-CI can be one common set of orbitals used by all CI states. If one set of orbitals is used, the transition moment or spinorbit coupling can be found for any type of GUGA CI wavefunction. Alternatively, two sets of orbitals (obtained by separate MCSCF orbital optimizations) can be used. Two or more separate CIs will be carried out. The two MO sets must share a common set of frozen core orbitals, and the CI must be of the complete active space type. These restrictions are needed to leave the CI wavefunctions invariant under the necessary rotation to corresponding orbitals. The non-orthogonal procedure implemented is a GUGA driven equivalent to the method of Lengsfield, et al. Note that the FOCI and SOCI methods described by these workers are not available in GAMESS. If you would like to use separate orbitals during the CI, they may be generated with the FCORE option in $MCSCF. Typically you would optimize the ground state completely, then use these MCSCF orbitals in an optimization of the excited state, under the constraint of FCORE=.TRUE. For SO-MCQDPT calculations, only one set of orbitals may be input to describe all CAS-CI states. Typically that orbital set will be obtained by state-averaged MCSCF, see WSTATE in $DET/$DRT, and also in the $MCQDx input. Note that although the RUNTYP=TRANSITN driver is tied to the GUGA CI package, there is no reason the orbitals cannot be obtained using the determinant CI package. In fact, for the case of spin-orbit coupling, you might want to utilize the ability to state average over several spins, see PURES in $DET. If there is no molecular symmetry present, transition moment calculations will provide $DRT1 if there is one set of orbitals, otherwise $DRT1 defines the CI based on $VEC1 and $DRT2 the CI based on $VEC2. Also for the case of no symmetry, a spin-orbit job should enter one $DRTx or $MCQDx for every spin multiplicity, and all states of the same multiplicity have to be generated from $VEC1 or $VEC2,

Further Information according to IVEX input.

4-229

symmetry
The CAS-CI states are most efficiently generated using symmetry, since states of different symmetry have zero Hamiltonian matrix elements. It is probably more efficient to do four CI calculations in the group C2v on A1, A2, B1, and B2 symmetry, than one CI with a combined Hamiltonian in C1 symmetry (unless the active space is very small), and similar remarks apply to the SO-MCQDPT case. In order to avoid repeatedly saying $DRTx or $MCQDx, the following few paragraphs say $DRTx only. Again supposing the group is C2v, and you are interested in singlet-triplet coupling. After some preliminary CI calculations, you might know that the lowest 8 states are two 1-a1, 1-b1, two 1-b2, one 3-a1, and two 3b2 states. In this case your input would consist of five $DRTx, of which you can give the three singlets in any order but these must preceed the two triplet input groups to follow the rule of increasing multiplicity. Clearly it is not possible to write a formula for how many $DRTx there will be, this depends not only on the point group, but also the chemistry of the situation. If you are using two sets of orbitals, the generation of the corresponding orbitals for the two sets will permute the active orbitals in an unpredictable way. Use STSYM to define the desired state symmetry, rather than relying on the orbital order. It is easy and safer to be explicit about the spatial orbital symmetry. The users are encouraged to specify full symmetry in their $DATA input even though they may choose to set the symmetry in $DRTx to C1. The CI states will be labelled in the group given in $DATA. The use of non-Abelian symmetry is limited by the absence of non-Abelian CI or MCQDPT. In this case the users can choose between setting full nonAbelian symmetry in $DATA and C1 in $DRT or else an Abelian subgroup in both $DATA and $DRT. The latter choice appears to be most efficient at present. An example of SO-MCQDPT illustrating how the carbon atom of Kh symmetry (full rotation-reflection group) can be entered in D2h, Kh's highest Abelian group. The run time is considerably longer in C1 symmetry.

Further Information

4-230

As another example, consider an organic molecule with a singly excited state, where that state might be coupled to low or high spin, and where these two states might be close enough to have a strong spin-orbit coupling. If it happens that the S1 and S0 states possess different symmetry, a very reaasonable calculation would be to treat the S1 and T1 state with the same $VEC2 orbitals, leaving the ground state described by $VEC1. After doing an MCSCF on the S0 ground state for $VEC1, you could do a state-averaged MCSCF for $VEC2 optimized for T1 and S1 simultaneously, using PURES. The spin orbit job would obtain its initial states from three GUGA CI computations, S0 from $VEC1 and $DRT1, S1 from $VEC2 and $DRT2, and T1 from $VEC2 and $DRT3. Your $TRANST would be NUMCI=3, IROOTS(1)=1,1,1, IVEX(1)=1,2,2. Note that the second IROOTS value is 1 because S1 was presumed to have a different symmetry than S0, so STSYM in $DRT1 and $DRT2 will differ. The calculation just outlined cannot be done if S0 and S1 have the same spatial symmetry, as IROOTS(1)=1,2,1 to obtain S1 during the second CI will bring in an additional S0 state (one expressed in terms of the $VEC2, at slightly higher energy). This problem is the origin of the statement several paragraphs above that a system with no symmetry will have one $DRTx for every spin multiplicity included. For transition moments, which do not diagonalize a matrix containing these duplicated states, it is OK to proceed, provided you ignore all transition moments between the same states obtained in the two different CIs.

spin orbit details

Spin-orbit coupling is always performed in a quasidegenerate perturbative manner. Typically the states close in energy are included into the spin-orbit coupling matrix. "Close" has a easily understandable meaning, since in the limit of small coupling the quasi-degenerate treatment is reduced to a second order perturbative treatment, that is, the affect of a state upon the state of primary interest is given by the square of the spin-orbit coupling matrix element divided by the difference of the adibatic energies. This is useful to keep in mind when deciding how many CI states to include in the matrix. The states that are included are treated in a fashion that is equivalent to infinite order perturbation theory (exact) whereas the states that are not included make no contribution. The choice between HSO2 and HSO2FF is very often in

Further Information

4-231

favour of the former. HSO2 computes the matrix elements in CSF basis and then contracts them with CI coefficients, whereas HSO2FF uses a generalized density in AO basis computed for each pair of states, thus HSO2 is much more efficient in case of multiple states given in IROOTS. HSO2FF takes less memory for integral storage, thus it can be superior in case of small active spaces and large basis sets, in part because it does not store 2e SOC integrals on disk and secondly, it does not redundantly treat the same pair of determinants if they appear in different CSFs. The numerical results with HSO2 and HSO2FF should be identical within machine and algorithmic accuracy. The spin-orbit operator contains a one electron term arising from Pauli's reduction of the hydrogenic Dirac equation to one-component form, and a two electron term added by Breit. The only practical limitation on the computation of the Breit term is that HSO2FF is limited to 10 active orbitals on 32 bit machines, and to about 26 active orbitals on 64 bit machines. The spin-orbit matrix elements vanish for |delta-S| > 1, but it is possible to include three or more spins in the computation. Since singlets interact with triplets, and triplets interact with pentuplets, inclusion of S=0,1,2 simultaneously lets you pick up the indirect interaction between singlets and pentuplets that the intermediate triplets afford. As an approximation, the nuclear charge appearing in the one electron term can be regarded as an empirical scale factor, compensating for the omission of the two electron operator. In addition, these effective charges are often used to compensate for missing nodes in valence orbitals of ECP runs, in which case the ZEFF are typically very far from the two nuclear charges. ZEFTYP selects some built in values obtained by S.Koseki et al, but if you have some favorite parameters, they can be read in as the ZEFF input array. Effective charges may be used for any OPERAT, but are most often used with HSO1. Various symmetries are used to avoid computing zero spin-orbit matrix elements. NOSYM in $TRANST allows some control over this: NOSYM=1 gives up point group symmetry completely, while 2 turns off additional symmetries such as spin selection rules. HSO1,2,2P compute all matrix elements in a group (i.e. between two $DRTx groups with fixed Ms(ket)-Ms(bra)) if at least one of them does not vanish by symmetry, and HSO2PP actually avoids computation for each pair of states if forbidden by symmetry. Setting NOSYM=2 will cause HSO2FF to consider the elements between

Further Information two singlets, which are always calculated for HSO1,2,2P when transition dipoles are requested as well.

4-232

SYMTOL has a dramatic effect on the run speed. This cutoff is applied to CSF coefficcients, their products, and these products times CSF orbital overlaps. The value permits a tradeoff of accuracy for run time, and since the error in the spin-orbit properties approaches SYMTOL mainly for SOCI functions, it may be useful to increase SYMTOL to save time for CAS or FOCI functions. Some experimenting will tell you what you can get away with. SYMTOL is also used during CI state symmetry assignment, for NOIRR=-1 in $DRT. In case if you do not provide enough storage for the form factors sorting then some extra disk space will be used; the extra disk space can be eliminated if you set SAVDSK=.TRUE. (the amount of savings depends on the active space and memory provided, it some cases it can decrease the disk space up to one order of magnitude). The form factors are in binary format, and so can be transfered between computers only if they have compatible binary files. There is a built-in check for consistency of a restart file DAFL30 with the current run parameters.

input nitty-gritty
The transition moment and spin-orbit coupling driver is a rather restricted path through the GUGA CI part of GAMESS. Note that $GUESS is not read, instead the MOs will be MOREAD in a $VEC1 and perhaps a $VEC2 group. It is not possible to reorder MOs. For SO-CI, 1) Give SCFTYP=NONE CITYP=GUGA MPLEVL=0. 2) $CIINP is not read. The CI is hardwired to consist of CI DRT generation, integral transformation/sorting, Hamiltonian generation, and diagonalization. This means $DRT1 (and maybe $DRT2,...), $TRANS, $CISORT, $GUGEM, and $GUGDIA input is read, and acted upon. 3) The density matrices are not generated, and so no properties (other than the transition moment or the spin-orbit coupling) are computed. 4) There is no restart capability provided, except for saving some form-factor information.

Further Information

4-233

5) $DRT1, $DRT2, $DRT3, ... must go from lowest to highest multiplicity. 6) IROOTS will determine the number of CI states in each CI for which the properties are calculated. Use NSTATE to specify the number of CI states for the CI Hamiltonian diagonalization. Sometimes the CI convergence is assisted by requesting more roots to be found in the diagonalization than you want to include in the property calculation. For SO-MCQDPT, the steps are 1) Give SCFTYP=NONE CITYP=NONE MPLEVL=2. 2) the number of roots in each MCQDPT is controlled by $TRANST's IROOTS, and each such calculation is defined by $MCQD1, $MCQD2, ... input. These must go from lowest multiplicity to highest.

references
The review already mentioned: "Spin-orbit coupling in molecules: chemistry beyond the adiabatic approximation". D.G.Fedorov, S.Koseki, M.W.Schmidt, M.S.Gordon, Int.Rev.Phys.Chem. 22, 551-592(2003) Reference for separate active orbital optimization: 1. B.H.Lengsfield, III, J.A.Jafri, D.H.Phillips, C.W.Bauschlicher, Jr. J.Chem.Phys. 74,6849-6856(1981) References for transition moments: 2a. H.C.Longuet-Higgins Proc.Roy.Soc.(London) A235, 537-543(1956) 2b. F.Weinhold, J.Chem.Phys. 54,1874-1881(1970) 3. C.W.Bauschlicher, S.R.Langhoff Theoret.Chim.Acta 79:93-103(1991) 4. "Intermediate Quantum Mechanics, 3rd Ed." Hans A. Bethe, Roman Jackiw Benjamin/Cummings Publishing, Menlo Park, CA (1986), chapters 10 and 11. 5. S.Koseki, M.S.Gordon J.Mol.Spectrosc. 123, 392-404(1987) References for Zeff spin-orbit coupling, and ZEFTYP values: 6. S.Koseki, M.W.Schmidt, M.S.Gordon J.Phys.Chem. 96, 10768-10772 (1992) 7. S.Koseki, M.S.Gordon, M.W.Schmidt, N.Matsunaga

Further Information J.Phys.Chem. 99, 12764-12772 (1995) 8. N.Matsunaga, S.Koseki, M.S.Gordon J.Chem.Phys. 104, 7988-7996 (1996) 9. S.Koseki, M.W.Schmidt, M.S.Gordon J.Phys.Chem.A 102, 10430-10435 (1998) 10. S.Koseki, D.G.Fedorov, M.W.Schmidt, M.S.Gordon J.Phys.Chem.A 105, 8262-8268 (2001) References for full Breit-Pauli spin-orbit coupling: 11. T.R.Furlani, H.F.King J.Chem.Phys. 82, 5577-5583 (1985) 12. H.F.King, T.R.Furlani J.Comput.Chem. 9, 771-778 (1988) 13. D.G.Fedorov, M.S.Gordon J.Chem.Phys. 112, 5611-5623 (2000) with the latter including information on the partial two electron operator method. Reference for SO-MCQDPT: 14. D.G.Fedorov, J.P.Finley

4-234

Phys.Rev.A 64, 042502 (2001)

Reference for Spin-Orbit with Model Core Potentials: 15. D.G.Fedorov, M.Klobukowski Chem.Phys.Lett. 360, 223-228(2002) Recent applications: 16. D.G.Fedorov, M.Evans, Y.Song, M.S.Gordon, C.Y.Ng J.Chem.Phys. 111, 6413-6421 (1999) 17. D.G.Fedorov, M.S.Gordon, Y.Song, C.Y.Ng J.Chem.Phys. 115, 7393-7400 (2001) 18. B.J.Duke J.Comput.Chem. 22, 1552-1556 (2001) 19. D.G.Fedorov, S.Koseki, M.W.Schmidt, M.S.Gordon K.Hirao and Y.Ishikawa (eds.) Recent Advances in Relativistic Molecular Theory, Vol. 5, (World Scientific, Singapore), 2004, pp 107-136. Reference for Spin-Orbit Natural Spinors: 20. T. Zeng, D. G. Fedorov, M. W. Schmidt, M. Klobukowski J. Chem. Phys. 134, 214107/1-9(2011) * * * Special thanks to Bob Cave and Dave Feller for their assistance in performing check spin-orbit coupling runs with the MELDF programs. Special thanks to Tom Furlani for contributing his 2e- spin-orbit code and answering many questions about its interface. Special thanks to Haruyuki Nakano for explaining the spin functions used in the MCQDPT package.

Further Information

4-235

examples
We end with 2 examples. Note that you must know what you are doing with term symbols, J quantum numbers, point group symmetry, and so on in order to make skillful use of this part of the program. Seeing your final degeneracies turn out like a text book says it should is beautiful! ! ! ! ! ! ! ! ! ! ! ! ! ! Compute the splitting of the famous sodium D line. Joseph von Fraunhofer (Denkschriften der Koeniglichen Akademie der Wissenschf. zu Muenchen, 5, 193(1814-1815)) observed the sun through good prisms, finding 700 lines, and named the brightest ones A, B, C... just in order. He was able to resolve the D line into two lines, which occur at 5895.940 and 5889.973 Angstroms. It would take a century to understand the D line is Na's 3s <-> 3p transition, and that spin-orbit coupling is what splits the D line into two. Charlotte Moore's Atomic Energy Levels, volume 1, gives the experimental 2-P interval as 17.1963, since the three relevent levels are at 2-S-1/2= 0.0, 2-P-1/2= 16,956.183, 2-P-3/2= 16,973.379.

1. generate ground state 2-S orbitals by conventional ROHF. the energy of the ground state is -161.8413919816 --- $contrl scftyp=rohf mult=2 $end --- $system kdiag=3 memory=300000 $end --- $guess guess=huckel $end 2. generate excited state 2-P orbitals, using a stateaveraged SCF wavefunction to ensure radial degeneracy of the 3p shell is preserved. The open shell SCF energy is -161.7682895801. The computation is both spin and space restricted open shell SCF on the 2-P Russell-Saunders term. Starting orbitals are reordered orbitals from step 1. --- $contrl scftyp=gvb mult=2 $end --- $system kdiag=3 memory=300000 $end --- $guess guess=moread norb=13 --norder=1 iorder(6)=7,8,9,6 $end --- $scf nco=5 nseto=1 no(1)=3 rstrct=.t. couple=.true. --f(1)= 1.0 0.16666666666667 --alpha(1)= 2.0 0.33333333333333 0.0 --beta(1)= -1.0 -0.16666666666667 0.0 $end 3. compute spin-orbit coupling in the 2-P term. The use of C1 symmetry in $DRT1 ensures that all three spatial CSFs are kept in the CI function. In the preliminary CI, the spin function is just the alpha spin doublet, and all three

Further Information

4-236

roots should be degenerate, and furthermore equal to the GVB energy at step 2. The spin-orbit coupling code uses both doublet spin functions with each of the three spatial wavefunctions, so the spin-orbit Hamiltonian is a 6x6 matrix. The two lowest roots of the full 6x6 spin-orbit Hamiltonian are the doubly degenerate 2-P-1/2 level, while the other four roots are the degenerate 2-P-3/2 level. $contrl scftyp=none cityp=guga runtyp=transitn mult=2 $end $system memory=2000000 $end $basis gbasis=n31 ngauss=6 $end $gugdia nstate=3 $end $transt operat=hso1 numvec=1 numci=1 nfzc=5 nocc=8 iroots=3 zeff=10.04 $end $drt1 group=c1 fors=.true. nfzc=5 nalp=1 nval=2 $end $data Na atom...2-P excited state...6-31G basis Dnh 2 Na 11.0 $end --- GVB ORBITALS --- GENERATED AT 7:46:08 CST 30-MAY-1996 Na atom...2-P excited state E(GVB)= -161.7682895801, E(NUC)= .0000000000, 5 ITERS $VEC1 1 1 9.97912679E-01 8.83038094E-03 0.00000000E+00... ... orbitals from step 2 go here ... 13 3-1.10674398E+00 0.00000000E+00 0.00000000E+00 $END As an example of both SO-MCQDPT, and the use of as much symmetry as possible, consider carbon. The CAS-CI uses an active space of 2s,2p,3s,3p orbitals, and the spin-orbit job includes all terms from the lowest configuration, 2s2,2p2. These terms are 3-P, 1-D, and 1-S. If you look at table 58 in Herzberg's book on electronic spectra, you will be able to see how the Kh spatial irreps P, D, S are partitioned into the D2h irreps input below. ! ! ! ! ! ! ! C SO-MRMP on all levels in the s**2,p**2 configuration. levels 1 2-4 5-9 10-14 CAS and MCQDPT .0000 .0000 cm-1 12.6879-12.8469 13.2721-13.2722 37.8469-37.8470 39.5638-39.5639 12169.1275 10251.7910 3-P-0 3-P-1 3-P-2 1-D-2

Further Information ! ! ! ! ! 15 19264.4221 21111.5130

4-237 1-S-0

The active space consists of (2s,2p,3s,3p) with 4 e-. D2h symmetry speeds up the calculation considerably, on the same computer D2h = 78 and C1 = 424 seconds. $contrl scftyp=none cityp=none mplevl=2 runtyp=transitn $end $system memory=5000000 $end

! ! below is input to run in C1 subgroup ! --- $transt operat=hso2 numvec=-2 numci=2 nfzc=1 nocc=9 --iroots(1)=6,3 parmp=3 --ivex(1)=1,1 $end --- $mrmp mrpt=mcqdpt rdvecs=.t. $end --- $MCQD1 nosym=1 nstate=6 mult=1 iforb=3 --nmofzc=1 nmodoc=0 nmoact=8 --wstate(1)=1,1,1,1,1,1 thrcon=1e-8 thrgen=1e-10 $END --- $MCQD2 nosym=1 nstate=3 mult=3 iforb=3 --nmofzc=1 nmodoc=0 nmoact=8 --wstate(1)=1,1,1 thrcon=1e-8 thrgen=1e-10 $END ! ! below is input to run in D2h subgroup ! $transt operat=hso2 numvec=-7 numci=7 nfzc=1 nocc=9 iroots(1)=3,1,1,1, 1,1,1 parmp=3 ivex(1)=1,1,1,1,1,1,1 $end $mrmp mrpt=mcqdpt rdvecs=.t. $end $MCQD1 nosym=-1 mult=1 iforb=3 nmofzc=1 nmodoc=0 nmoact=8 stsym=Ag wstate(1)=1,1,1 thrcon=1e-8 thrgen=1e-10 $END $MCQD2 nosym=-1 mult=1 iforb=3 nmofzc=1 nmodoc=0 nmoact=8 stsym=B1g wstate(1)=1 thrcon=1e-8 thrgen=1e-10 $END $MCQD3 nosym=-1 mult=1 iforb=3 nmofzc=1 nmodoc=0 nmoact=8 stsym=B2g wstate(1)=1 thrcon=1e-8 thrgen=1e-10 $END $MCQD4 nosym=-1 mult=1 iforb=3 nmofzc=1 nmodoc=0 nmoact=8 stsym=B3g wstate(1)=1 thrcon=1e-8 thrgen=1e-10 $END $MCQD5 nosym=-1 mult=3 iforb=3 nmofzc=1 nmodoc=0 nmoact=8 stsym=B1g wstate(1)=1 thrcon=1e-8 thrgen=1e-10 $END $MCQD6 nosym=-1 mult=3 iforb=3 nmofzc=1 nmodoc=0 nmoact=8 stsym=B2g wstate(1)=1 thrcon=1e-8 thrgen=1e-10 $END $MCQD7 nosym=-1 mult=3 iforb=3 nmofzc=1 nmodoc=0 nmoact=8 stsym=B3g wstate(1)=1 thrcon=1e-8 thrgen=1e-10 $END

Further Information

4-238

! ! input to prepare the 3-P ground state orbitals ! great care is taken to create symmetry equivalent p's ! --- $contrl scftyp=mcscf cityp=none mplevl=0 --runtyp=energy mult=3 $end --- $guess guess=moread norb=55 purify=.t. $end --- $mcscf cistep=guga fullnr=.t. $end --- $drt group=c1 fors=.true. --nmcc=1 ndoc=1 nalp=2 nval=5 $end --- $gugdia nstate=9 maxdia=1000 $end --- $gugdm2 wstate(1)=1,1,1 $end ! $data C...aug-cc-pvtz (10s,5p,2d,1f) -> [4s,3p,2d,1f] (1s,1p,1d,1f) Dnh 2 C 6.0 S 8 1 2 3 4 5 6 7 8 S 8 1 2 3 4 5 6 7 8 S 1 1 S 1 1 P 3 1 2 3 P 1 1 P 1 1

8236.000000 1235.000000 280.8000000 79.27000000 25.59000000 8.997000000 3.319000000 0.3643000000 8236.000000 1235.000000 280.8000000 79.27000000 25.59000000 8.997000000 3.319000000 0.3643000000 0.9059000000 0.1285000000 18.71000000 4.133000000 1.200000000 0.3827000000 0.1209000000

0.5310000000E-03 0.4108000000E-02 0.2108700000E-01 0.8185300000E-01 0.2348170000 0.4344010000 0.3461290000 -0.8983000000E-02 -0.1130000000E-03 -0.8780000000E-03 -0.4540000000E-02 -0.1813300000E-01 -0.5576000000E-01 -0.1268950000 -0.1703520000 0.5986840000 1.000000000 1.000000000 0.1403100000E-01 0.8686600000E-01 0.2902160000 1.000000000 1.000000000

Further Information D 1 D 1 F 1 S 1 P 1 D 1 F 1 1 1 1 1 1 1 1 0.268000000 1.00000000 0.356900000E-01 0.100000000 1.00000000 1.00000000 0.7610000000 0.440200000E-01 1.000000000 1.00000000 1.097000000 0.3180000000 1.000000000 1.000000000

4-239

$end --- OPTIMIZED MCSCF MO-S --- GENERATED 22-AUG-2000 E(MCSCF)= -37.7282408589, 11 ITERS $VEC1 1 1 9.75511467E-01 ...snipped... $END

Programmer's Reference (29 April 2011) ************************************** * * * Section 5 - Programmer's Reference * * * **************************************

5-1

This section describes features of GAMESS programming which are true for all machines. See the section 'hardware specifics' for information about specific machines. The contents of this section are: Installation overview ____________________________________________________ 2 Running Distributed Data Parallel GAMESS ________________________________ 5
parallelization history ________________________________________________________ 5 DDI compute and data server processes _________________________________________ 6 memory allocations and check jobs ____________________________________________ 11 representative performance examples __________________________________________ 13

Altering program limits _________________________________________________ 22 Names of source code modules ___________________________________________ 24 Programming Conventions ______________________________________________ 30 Parallel broadcast identifiers_____________________________________________ 33 Disk files used by GAMESS______________________________________________ 35
disk files in parallel runs_____________________________________________________ 41

Contents of the direct access file 'DICTNRY'________________________________ 43

Programmer's Reference

5-2

Installation overview
Very specific compiling directions are given in a file provided with the GAMESS distribution, namely ~/gamess/misc/readme.unix and this should be followed closely. The directions here are of a more general nature. Before starting the installation, you should also see the pages about your computer in the 'Hardware Specifics' section of this manual, and at the compiler version notes that are kept in the script 'comp'. There might be some special instructions for your machine. The first step in installing GAMESS should be to print the manual. If you are reading this, you've got that done! The second step would be to get the source code activator compiled and linked (note that the activator must be activated manually before it is compiled). Third, you should now compile all the quantum chemistry sources. Fourth, compile the DDI message passing library, and its process kickoff program. Fifth, link the GAMESS program. Finally, run all the short examples provided with GAMESS, and very carefully compare the key results shown in the 'sample input' section against your outputs. These "correct" results are from a IBM RS/6000, so there may be very tiny (last digit) precision differences for other machines. That's it! The rest of this section gives a little more detail about some of these steps. * * * * * GAMESS will run on essentially any machine with a FORTRAN 77 compiler. However, even given the F77 standard there are still a number of differences between various machines. For example, some chips still use 32 bit integers, as primitive as that may seem, while many chips allow for 64 bit processing (and hence very large run-time memory usage). It is also necessary to have a C compiler, as the message passing library is implemented entirely in that language. Although there are many types of computers, there is only one (1) version of GAMESS. This portability is made possible mainly by keeping machine dependencies to a minimum (that is, writing in

Programmer's Reference

5-3

FORTRAN77, not vendor specific language extensions). The unavoidable few statements which do depend on the hardware are commented out, for example, with "*I64" in columns 1-4. Before compiling GAMESS on a 64 bit machine, these four columns must be replaced by 4 blanks. The process of turning on a particular machine's specialized code is dubbed "activation". A semi-portable FORTRAN 77 program to activate the desired machine dependent lines is supplied with the GAMESS package as program ACTVTE. Before compiling ACTVTE on your machine, use your text editor to activate the very few machine dependent lines in ACTVTE before compiling it. Be careful not to change the DATA initialization! * * * * * The quantum chemistry source code of GAMESS is in the directory ~/gamess/source and consists almost entirely of unactivated FORTRAN source code, stored as *.src. There is a bit of C code in this directory to implement runtime memory allocation. The task of building an executable for GAMESS is: activate compile link *.SRC ---> *.FOR ---> *.OBJ ---> *.EXE source FORTRAN object executable code code code image where the intermediate files *.FOR and *.OBJ are discarded once the executable has been linked. It may seem odd at first to delete FORTRAN code, but this can always be reconstructed from the master source code using ACTVTE. The advantage of maintaining only one master version is obvious. Whenever any improvements are made, they are automatically in place for all the currently supported machines. There is no need to make the same changes in a plethora of other versions. * * * * * The Distributed Data Interface (DDI) is the message passing layer, supporting the parallel execution of GAMESS. It is stored in the directory tree ~/gamess/ddi It is necessary to compile this software, even if you don't intend to run on more than one processor. This directory contains a file readme.ddi with directions about compiling,

Programmer's Reference

5-4

and customizing your computer to enable the use of System V memory allocation routines. It also has information about some high end parallel computer systems. * * * * * The control language needed to activate, compile, and link GAMESS on your brand of computer involves several scripts, namely: COMP compiles a single quantum chemistry module. COMPALL compiles all quantum chemistry source modules. COMPDDI compiles the distributed data interface, and generates a process kickoff program, ddikick.x. LKED link-edit (links) together quantum chemistry object code, and the DDI library, to produce a binary executable gamess.x. RUNGMS runs a GAMESS job, in serial or parallel. RUNALL uses RUNGMS to run all the example jobs. There are files related to some utility programs: MBLDR.* model builder (internal to Cartesian) CARTIC.* Cartesian to internal coordinates CLENMO.* cleans up $VEC groups DK3.F prepare relativistic AO contractions. There are files related to two-D X-windows graphics, in: ~/gamess/graphics Better back-end graphics (3D as well as 2D) is available in the MacMolPlt program, now available for all popular desktop operating systems.

Programmer's Reference

5-5

Running Distributed Data Parallel GAMESS

GAMESS consists of many FORTRAN files implementing its quantum chemistry, and some C language files implementing the Distributed Data Interface (DDI). The directions for compiling DDI, configuring the system parameters to permit execution of DDI programs, and how to use the 'ddikick.x' program which "kicks off" GAMESS processes may be found in the file readme.ddi. If you are not the person installing the GAMESS software, you can skip reading that. Efficient use of GAMESS requires an understanding of three critical issues: The first is the difference between two types of memory (replicated MWORDS and distributed MEMDDI) and how these relate to the physical memory of the computer which you are using. Second, you must understand to some extent the degree to which each type of computation scales so that the proper number of CPUs is selected. Finally, many systems run -two- GAMESS processes on every processor, and if you read on you will find out why this is so. Since all code needed to implement the Distributed Data Interface (DDI) is provided with the GAMESS source code distribution, the program compiles and links ready for parallel execution on all machine types. Of course, you may choose to run on only one processor, in which case GAMESS will behave as if it is a sequential code, and the full functionality of the program is available.

parallelization history
We began to parallelize GAMESS in 1991 as part of the joint ARPA/Air Force piece of the Touchstone Delta project. Today, nearly all ab initio methods run in parallel, although some of these still have a step or two running sequentially only. Only the RHF+CI gradients have no parallel method coded. We have not parallelized the semiempirical MOPAC runs, and probably never will. Additional parallel work occurred as a result of a DoD CHSSI software initiative in 1996. This led to the DDI-based parallel RHF+MP2 gradient program, after development of the DDI programming toolkit itself. Since 2002, the DoE program SciDAC has sponsored additional parallelization. The DDI toolkit has been used since its 1999 introduction to add codes for UHF+MP2 gradient, ROHF+ZAPT2 energy, and MCSCF

Programmer's Reference

5-6

wavefunctions as well as their analytic Hessians or MCQDPT2 energy correction. In 1991, the parallel machine of choice was the Intel Hypercube although small clusters of workstations could also be used as a parallel computer. In order to have the best blend of portability and functionality, we chose in 1991 to use the TCGMSG message passing library rather than one of the early vendor's specialized libraries. As the major companies began to market parallel machines, and as MPI version 1 emerged as a standard, we began to use MPI on some equipment in 1996, while still using the very resilient TCGMSG library on everything else. However, in June 1999, we retired our old friend TCGMSG when the message passing library used by GAMESS changed to the Distributed Data Interface, or DDI. An SMP-optimized version of DDI was included with GAMESS in April 2004. Three people have been extremely influential upon the current parallel methodology. Theresa Windus, a graduate student in the early 1990s, created the first parallel versions. Graham Fletcher, a postdoc in the late 1990s, is responsible for the addition of distributed data programming concepts. Ryan Olson rewrote the DDI software in 2003-4 to support the modern SMP architectures well, and this was released in April 2004 as our standard message passing implementation.

DDI compute and data server processes

DDI contains the usual parallel programming calls, such as initialization/closure, point to point messages, and the collective operations global sum and broadcast. These simple parts of DDI support all parallel methods developed in GAMESS from 1991-1999, which were based on replicated storage rather than distributed data. However, DDI also contains additional routines to support distributed memory usage. DDI attempts to exploit the entire system in a scalable way. While our early work concentrated on exploiting the use of p processors and p disks, it required that all data in memory be replicated on every one of the p CPUs. The use of memory also becomes scalable only if the data is distributed across the aggregate memory of the parallel machine. The concept of distributed memory is contained in the Remote Memory Access portion of MPI version 2, but so far MPI-2 is not available from American computer vendors.

Programmer's Reference

5-7

The original concept of distributed memory was implemented in the Global Array toolkit of Pacific Northwest National Laboratory (see http://www.emsl.pnl.gov/pub/docs/global). Basically, the idea is to provide three subroutine calls to access memory on other processors (in the local or even remote nodes): PUT, GET, and ACCUMULATE. These give access to a class of memory which is assumed to be slower than local memory, but faster than disk: <--- fastest slowest ---> registers cache(s) local_memory remote_memory disks tapes <--- smallest biggest ---> Because DDI accesses memory on other CPUs by means of an explicit subroutine call, the programmer is aware that a message must be transmitted. This awareness of the access overhead should encourage algorithms that transfer many data items in a single message. Use of a subroutine call to reach remote memory is a recognition of the non-uniform memory access (NUMA) nature of parallel computers. In other words, the Distributed Data Interface (DDI) is an explicitly message passing implementation of global shared memory. In order to have one CPU pass data items to a second CPU when the second CPU needs them, without significant delay, the computing job on the first CPU must interrupt its computation briefly to furnish the data. This type of communication is referred to as "one sided messages" or "active messages" since the first CPU is an unwitting participant in the process, which is driven entirely by the requirements of the second CPU.

Programmer's Reference

5-8

The Cray T3E has a library named SHMEM to support this type of one sided messages (and good hardware support for this too) so, on the T3E, GAMESS runs as a single process per CPU. Its memory image looks like this: node 0 node 1 p=0 p=1 ----------------------------| GAMESS | | GAMESS | | quantum | | quantum | | chem code | | chem code | ----------------------------| DDI code | | DDI code | ----------------------------- input keywords: | replicated | | replicated | <-- MWORDS | data | | data | ----------------------------------------| | | | | | <-- MEMDDI | | distributed| | distributed | | | | data | | data | | | | | | | | | | | | | | | | | | | | | ----------------------------| ----------------------------------------where the box drawn around the distributed data is meant to imply that a large data array is residing in the memory of all processes (in this example, half on one and half on the other). Note that the input keyword MWORDS gives the amount of storage used to duplicate small matrices on every CPU, while MEMDDI gives the -total- distributed memory required by the job. Thus, if you are running on p CPUs, the memory that is used on any given CPU is total on any 1 CPU = MWORDS + MEMDDI/p Since MEMDDI is very large, its units are in millions of words. Since good execution speed requires that you not exceed the physical memory belonging to your CPUs, it is important to understand that when MEMDDI is large, you will need to choose a sufficiently large number of CPUs to keep the memory on each reasonable. To repeat, the DDI philosophy is to add more processors not just for their compute performance or extra disk space,

Programmer's Reference but also to aggregate a very large total memory. Bigger problems will require more CPUs to obtain sufficiently large total memories! We will give an example of how you can estimate the number of CPUs a little ways below.

5-9

If the GAMESS task running as process p=1 in the above example needs some values previously computed, it issues a call to DDI_GET. The DDI routines in process p=1 then figure out where this "patch" of data actually resides in the big rectangular distributed storage. Suppose this is on process p=0. The DDI routines in p=1 send a message to p=0 to interupt its computations, after which p=0 sends a bulk data message to process p=1's buffer. This buffer resides in part of the replicated storage of p=1, where computations can occur. Note that the quantum chemistry layer of process p=1 was sheltered from most of the details regarding which CPU owned the patch of data that process p=1 wanted to obtain. These details are managed by the DDI layer. Note that with the exception of DDI_ACC's addition of new terms into a distributed array, no arithmetic is done directly upon the distributed data. Instead, distributed data is accessed only by DDI_GET, DDI_PUT (its counterpart for storage of data items), and DDI_ACC (which accumulates new terms into the distributed data). DDI_GET and DDI_PUT can be thought of as analogous to FORTRAN READ and WRITE statements that transfer data between disk storage and local memory where computations may occur. It is the programmer's challenge to minimize the number of GET/PUT/ACC calls, and to design algorithms that maximize the chance that the patches of data are actually within the local CPU's portion of the distributed data.

Programmer's Reference Since the SHMEM library is available only on a few machines, all other platforms adopt the following memory model, which involves two- GAMESS processes running on every processor: node 0 p=0 --------------| GAMESS X| | quantum | | chem code | --------------| DDI code | --------------| replicated | | data | --------------node 1 p=1 --------------| GAMESS X| | quantum | | chem code | --------------| DDI code | --------------| replicated | | data | ---------------

5-10

compute processes

keyword: <-- MWORDS

p=2 p=3 ----------------------------| GAMESS | | GAMESS | | quantum | | quantum | | chem code | | chem code | ----------------------------| DDI code X| | DDI code X| --------------------------------------------------------------------| | | | | | | | distributed| | distributed | | | | data | | data | | | | | | | | | | | | | | | | | | | | | ----------------------------| -----------------------------------------

data servers

keyword: <-- MEMDDI

The first half of the processes do quantum chemistry, and the X indicates that they spend most of their time executing some sort of chemistry. Hence the name "compute process". Soon after execution, the second half of the processes call a DDI service routine which consists of an infinite loop to deal with GET, PUT, and ACC requests until such time as the job ends. The X shows that these "data servers" execute only DDI support code. (This makes the data server's quantum chemistry routines the equivalent of the human appendix). The whole problem of interupts is now in the hands of the operating system, as the data servers are distinct processes. To follow the same example as

Programmer's Reference

5-11

before, when the compute process p=1 needs data that turns out to reside on process 0, a request is sent to the data server p=2 to transfer information back to the compute process p=1. The compute process p=0 is completely unaware that such a transaction has occurred. The formula for the memory required by any single CPU is unchanged, if p is the total number of CPUs used, total on any 1 CPU = MWORDS + MEMDDI/p. As a technical matter, if you are running on a system where all processors are in the same node (the SGI Altix is an example), or if you are running on an IBM SP where LAPI assists in implementing one-sided messaging, then the data server processes are not started. The memory model in the illustration above is correct, if you just mentally omit the data server processes from it. In all cases, where the SHMEM library is not used, the distributed arrays are created by System V memory calls, shmget/shmat, and their associated semaphore routines. Your system may need to be reconfigured to allow allocation of large shared memory segments, see 'readme.ddi' for more details. The parallel CCSD and CCSD(T) programs add a third kind of memory to the mix: node-replicated. This is data (e.g. the doubles amplitudes) that is stored only once per node. Thus, this is more copies of the data than once per parallel job (fully distributed MEMDDI) but fewer than once per CPU (replicated MWORDS). A picture of the memory model for the CCSD(T) program can be found in the "readme.ddi" file, so is not duplicated here. There is presently no keyword for this type of memory, but the system limit on the total SystemV memory does apply. It is important to perform a check run when using CCSD(T) and carefully follow the printout of its memory requirements.

memory allocations and check jobs

At present, not all runs require distributed memory. For example, in an SCF computation (no hessian or MP2 to follow) the memory needed is on the order of the square of the basis set size, for such quantities as the orbital coefficients, density, Fock, overlap matrices, and so on. These are simply duplicated on every CPU in the MWORDS (or the older keyword MEMORY in $SYSTEM) region. In this case the data server processes still run, but are dormant because no distributed memory access is attempted.

Programmer's Reference

5-12

However, closed and open shell MP2 calculations, MCSCF wavefunctions, and their analytic hessian or MCQPDT energy correction do use distributed memory when run in parallel. Thus it is important to know how to obtain the correct value for MEMDDI in a check run, and how to compute how many CPUs are needed to do the run. Check runs (EXETYP=CHECK) need to run quickly, and the fastest turn around always comes on one CPU only. Runs which do not currently exploit MEMDDI distributed storage will formally allocate their MWORDS needs, and feel out their storage needs while skipping almost all of the real work. Since MWORDS is replicated, the amount that is needed on 1 CPU remains unchanged if you later do the true computation on more than 1 CPU. Check jobs which involve MEMDDI storage are a little bit trickier. As noted, we want to run on only 1 CPU to get fast turn around. However, MEMDDI is typically a large amount of memory, and this is unlikely to be available on a single CPU. The solution is that the check job will not actually allocate the MEMDDI storage, instead it just remembers what you gave as input and checks to see if this will be adequate. As someone once said, MEMDDI is a "fairy tale number" during a check job. So, you can input a big value like MEMDDI=25000 (25,000 million words is equal to 25,000 * 1,000,000 * 8 = 200 GBytes) and run this check job on a computer with only 1024 MB = 1 GB of memory per processor. Let us say that a closed shell MP2 check run for this case gives the output of SCALED *PER-NODE* MEMORY REQUIREMENT NODES DISTRIBUTED/MWORDS REPLICATED/WORDS TOTAL/MBYTES 1 952 7284508 7624 The real run requires MWORDS=8 MEMDDI=960. Note that we have just rounded up a bit from the 7.3 and 952 in this output, for safety. Of course, the actual computation will have to run on a large number of such processors, because you don't have 200 GB on your CPU, we are assuming 1024 MB (1 GB). Let us continue to compute how many processors are needed. We need to reserve some memory for the operating system (25 MB, say) and for the GAMESS program and local storage (let us say 50 MB, for GAMESS is a big program, and the compute processes should be swapped into memory). Thus our hypothetical 1024 MB processor has 950 MB available, assuming no one else is running. In units of words, this machine has 950/8 = 118 million words available for your run. We must choose the number of processors p to satisfy

Programmer's Reference needed <= available MWORDS + MEMDDI/p <= free physical memory 8 + 960/p <= 118 so solving for p, we learn this example requires p >= 9 compute processes. The answer for roughly 8 GB of distributed memory on 1 GB processors was not 8, because the O/S, GAMESS itself, and the MWORDS requirements together mean less than 1 GB could be contributed to the distributed total. More CPUs than 9 do not require changing MWORDS or MEMDDI, but will run faster than 9. Fewer CPUs than 9 do not have enough memory to run!

5-13

One more subtle point about CHECK runs with MEMDDI is that since you are running on 1 CPU only, the code does not know that you wish to run the parallel algorithm instead of the sequential algorithm. You must force the CHECK job into the parallel section of the program by $system parall=.true. $end There's no harm leaving this line in for the true runs, as any job with more than one compute process is parallel regardless of the input keyword PARALL. The check run for MCQDPT jobs will print three times a line like this MAXIMUM MEMDDI THAT CAN BE USED IN ... IS x MWORDS Typically the 2nd such step, transforming over all occupied and virtual canonical orbitals, will be the largest of the three requirements. Its size can be guesstimated before running, as (Nao*Nao+Nao)/2 * ((Nocc*Nocc+Nocc)/2 + Nocc*Nvirt) where Nocc = NMOFZC+NMODOC+NMOACT, Nvirt=NMOEXT, and Nao is the size of the atomic basis. Unlike the closed shell MP2 program, this section still does extensive I/O operations even when MEMDDI is used, so it may be useful to consider the three input keywords DOORD0, PARAIO, and DELSCR when running this code.

representative performance examples

This section describes the way in which the various quantum chemistry computations run in parallel, and shows some typical performance data. This should give you as the user some idea how many CPUs can be efficiently used for various SCFTYP and RUNTYP jobs The performance data you will see below were obtained on a 16 CPU Intel Pentium II Linux (Beowulf-type) cluster

Programmer's Reference

5-14

costing $49,000, of which $3,000 went into the switched Fast Ethernet component. 512 MB/CPU means this cluster has an aggregate memory of 8 GB. For more details, see http://www.msg.chem.iastate.edu/GAMESS/dist.pc.shtml. This is a low quality network, which exposes jobs with higher communication requirements, by noting when the wall time is much longer than the CPU. --The HF wavefunctions can be evaluated in parallel using either conventional disk storage of the integrals, or via direct recomputation of the integrals. Some experimenting will show which is more effective on your hardware. As an example of the scaling performance of RHF, ROHF, UHF, or GVB jobs that involve only computation of the energy or its gradient, we include here a timing table from the 16 CPU PC cluster. The molecule is luciferin, which together with the enzyme luciferase is involved in firefly light production. The chemical formula is C11N2S2O3H8, and RHF/6-31G(d) has 294 atomic orbitals. There's no molecular symmetry. The run is done as direct SCF, and the CPU timing data is 1e- ints Huckel guess 15 RHF iters properties 1e- gradient 2e- gradient total CPU total wall p=1 1.1 14 5995 6.0 9.7 1080 ---7106 7107 p=2 0.6 12 2982 6.6 4.7 541 ---3547 3562 p=4 0.4 11 1493 6.6 2.3 267 ---1780 1815 p=8 0.3 10 772 6.8 1.2 134 ---925 950 p=16 0.2 10 407 6.9 0.7 68 ---492 seconds 522 seconds

Note that direct SCF should run with the wall time very close to the CPU time as there is essentially no I/O and not that much communication (MEMDDI storage is not used by this kind of run). Running the same molecule as DFTTYP=B3LYP yields p=1 1e- ints 1.1 Huckel guess 14 23 DFT iters 14978 properties 6.6 1e- gradient 9.7 2e- grid grad 5232 2e- AO grad 1105 ---p=2 0.7 12 7441 6.4 4.7 2532 550 ---p=4 0.3 10 3681 6.5 2.3 1225 270 ---p=8 0.3 10 1876 7.0 1.3 595 136 ---p=16 0.2 9 961 6.5 0.7 303 69 ----

Programmer's Reference total CPU total wall 21347 10547 21348 10698 5197 5368 2626 2758 1349 1477

5-15

and finally if we run an RHF analytic hessian, using AO basis integrals, the result is 1e- ints Huckel guess 14 RHF iters properties 1e- grd+hss 2e- grd+hss CPHF total CPU total wall p=1 1.2 14 5639 6.4 40.9 21933 40433 ----68059 68102 p=2 0.6 12 2851 6.5 20.9 10859 20396 ----34146 34273 p=4 0.4 10 1419 6.6 11.9 5296 10016 ----16760 17430 p=8 0.3 10 742 7.0 7.7 2606 5185 ---8559 9059 p=16 0.2 10 390 6.7 5.8 1358 2749 ---4519 4978

CPU speedups for 1->16 processors for RHF gradient, DFT gradient, and RHF analytic hessian are 14.4, 15.8, and 15.1 times faster, respectively. The wall clock times are close to the CPU time, indicating very little communication is involved. If you are interested in an explanation of how the parallel SCF is implimented, see the main GAMESS paper, M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery J.Comput.Chem. 14, 1347-1363(1993) --The CIS energy and gradient code is also programmed to have the construction of Fock-like matrices as its computational kernel. Its scaling is therefore very similar to that just shown, for porphin C20N4H14, DH(d,p) basis, 430 AOs: p=1 p=2 p=4 p=8 p=16 setup 25 25 25 25 25 1e- ints 5.1 2.7 1.5 1.0 0.6 orb. guess 30 25 23 22 21 RHF iters 1647 850 452 251 152 RHF props 19 19 19 19 19 CIS energy 36320 18166 9098 4620 2398 CIS lagrang 6092 3094 1545 786 408 CPHF 20099 10183 5163 2688 1444 CIS density 2468 1261 632 324 170 CIS props 19 19 19 19 19 1e- grad 40.9 18.2 9.2 4.7 2.4 2e- grad 1644 849 423 223 122

Programmer's Reference ----total CPU 68424 total wall 68443 which is a speedup of 14.3 -------34526 17420 34606 17853 for 1->16. ---8994 9258

5-16 ---4791 4985

--For the next type of computation, we discuss the MP2 correction. For closed shell RHF + MP2 and unrestricted UHF + MP2, the gradient program runs in parallel using distributed memory, MEMDDI. In addition, the ROHF + MP2 energy correction for OSPT=ZAPT runs in parallel using distributed memory, but OSPT=RMP does not use MEMDDI in parallel jobs. All distributed memory parallel MP2 runs resemble RHF+MP2, which is therefore the only example given here. The example is a benzoquinone precursor to hongconin, a cardioprotective natural product. The formula is C11O4H10, and 6-31G(d) has 245 AOs. There are 39 valence orbitals included in the MP2 treatment, and 15 core orbitals. MEMDDI must be 156 million words, so the memory computation that was used above tells us that our 512 MB/CPU PC cluster must have at least three processors to aggregate the required MEMDDI. MOREAD was used to provide converged RHF orbitals, so only 3 RHF iterations are performed. The timing data are CPU and wall times (seconds) in the 1st/2nd lines: RHF iters MP2 step 2e- grad total CPU total wall p=3 241 243 5,953 7,366 1,429 1,492 ----7,637 9,116 p=4 181 184 4,399 5,669 1,135 1,183 ----5,727 7,053 3-->12 4.04 3.43 p=12 65 69 1,438 2,239 375 413 --1,890 2,658 4-->16 3.98 3.40 p=16 51 55 1,098 1,700 280 305 --1,440 2,077

CPU speedup wall speedup

The wall clock time will be closer to the CPU time if the quality of the network between the computer is improved (remember, this run used just switched Fast Ethernet). As noted, the number of CPUs is more influenced by a need to aggregate the necessary total MEMDDI, more than by concerns

Programmer's Reference

5-17

about scalability. MEMDDI is typically large for MP2 parallel runs, as it is proportional to the number of occupied orbitals squared times the number of AOs squared. For more details on the distributed data parallel MP2 program, see G.D.Fletcher, A.P.Rendell, P.Sherwood Mol.Phys. 91, 431-438(1997) G.D.Fletcher, M.W.Schmidt, M.S.Gordon Adv.Chem.Phys. 110, 267-294 (1999) G.D.Fletcher, M.W.Schmidt, B.M.Bode, M.S.Gordon Comput.Phys.Commun. 128, 190-200 (2000) --The next type of computation we will consider is analytic computation of the nuclear Hessian (force constant matrix). The performance of the RHF program, based on AO integrals, was given above, as its computational kernel (Fock-like builds) scales just as the SCF itself. However, for high spin ROHF, low spin open shell SCF and TCSCF (both done with GVB), the only option is MO basis integrals. The integral transformation is parallel according to T.L.Windus, M.W.Schmidt, M.S.Gordon Theoret.Chim.Acta 89, 77-88(1994). It distributes 'passes' over processors, so as to parallelize the transformation's CPU time but not the replicated memory, or the AO integral time. Finally the response equation step is hardly parallel at all. The test example is an intermediate in the ring opening of silacyclobutane, GVB-PP(1) or TCSCF, 180 AOs for 6311G(2d,2p): p=1 p=2 p=4 p=8 p=16 2e- ints 83 42 21 11 5 GVB iters 648 333 179 104 67 replicate 2en/a 81 81 81 82 transf. 476 254 123 67 51 1e- grd+hss 7 4 2 2 1 2e- grd+hss 4695 2295 1165 596 313 CP-TCSCF 344 339 331 312 325 ---------------total CPU 6256 3351 1904 1189 848 total wall 6532 3538 2072 1399 1108 Clearly, the final response equation (CPHF) step is a sequential bottleneck, as is the fact that the orbital hessian in this step is stored entirely on the disk space of CPU 0. Since the integral transformation is run in replicated MWORDS memory, rather than distributing this,

Programmer's Reference and since stored on very many than 3 or

5-18

it also needs a duplicated AO integral file be every CPU, the code is clearly not scalable to processors. Typically we would not request more 4 processors for an analytic ROHF or GVB hessian.

The final analytic hessian type is for MCSCF. The scalability of the MCSCF wavefunction will be given just below, but the response equation step for MCSCF is clearly quite scalable. The integral transformation for the response equation step uses distributed memory MEMDDI, and should scale like the MP2 program (documented above). The test case has 8e- in 8 orbitals, and the time reflect this, with most of the work involving the 4900 determinants. Total speedup for 4->16 is 4.11, due to luckier work distributing for 16 CPUs: MCSCF wfn DDI transf. 1e- grd+hss 2e- grd+hss CPMCHF RHS sides) CPMCHF iters total CPU total wall p=4 113.5 68.4 1.5 2024.9 878.8 115343.5 -------118430.8 119766.0 p=16 106.1 19.3 0.6 509.8 225.8 27885.9 -------28747.6 30746.4

(RHS=right hand

This code can clearly benefit from using many processors, with scalability of the MCSCF step itself almost moot. --Now lets turn to MCSCF energy/gradient runs. We will illustrate two convergers, SOSCF and then FULLNR. The former uses a 'pass' type of integral transformation (ala the GVB hessian job above), and runs in replicated memory only (no MEMDDI). The FULLNR converger is based on the MP2 program's distributed memory integral transformation, so it uses MEMDDI. In addition, the parallel implementation of the FULLNR step never forms the orbital hessian explicitly, doing Davidson style iterations to predict the new orbitals. Thus the memory demand is almost entirely MEMDDI. The example we choose is at a transition state for the water molecule assisted proton transfer in the first excited stat of 7-azaindole. The formula is C7N2H6(H2O), there are 190 active orbitals, and the active space is the

Programmer's Reference

5-19

10 pi electrons in 9 pi orbitals of the azaindole portion. There are 15,876 determinants used in the MCSCF calculation, and 5,292 CSFs in the perturbation calculation to follow. See Figure 6 of G.M.Chaban, M.S.Gordon J.Phys.Chem.A 103, 185-189(1999) if you are interested in this chemistry. The timing data for the SOSCF converger are p=1 dup. 2e- ints 327.6 transform. 285.1 det CI 39.3 2e- dens. 0.4 orb. update 39.2 iters 2-16 5340.0 1e- grad 5.3 2e- grad 695.6 -----total CPU 6,743 total wall 13,761 p=2 331.3 153.6 39.4 0.5 25.9 3153.5 2.3 354.9 -----4,071 8,289 p=4 326.4 88.4 38.9 0.5 17.4 2043.7 1.3 179.4 -----2,705 4,986 p=8 325.8 57.8 38.3 0.5 12.8 1513.6 0.7 93.2 -----2,052 3,429 p=16 326.5 47.3 38.1 0.5 11.0 1308.5 0.4 50.9 -----1,793 3,899

whereas the FULLNR convergers runs like this p=1 2e- DDI trans. 2547 det. CI 39 DM2 0.5 FULLNR 660 iters 2-9 24324 1e- grad 5.3 2e- grad 700 -----total CPU 28,288 total wall 28,290 p=2 1385 39 0.5 376 13440 2.3 352 -----15,605 20,719 p=4 698 38 0.5 194 6942 1.2 181 ---8,066 12,866 p=8 354 38 0.5 101 3669 0.7 95 ---4,268 8,292 p=16 173 38 0.5 51 1940 0.4 51 ---2,265 5,583

The first iteration is broken down into its primary steps from the integral transformation to the orbital update, inclusive. The SOSCF program is clearly faster, and should be used when the number of processors is modest (say up to 8), however the largest molecules will benefit from using more processors and the much more scalable FULLNR program. One should note that the CI calculation was more or less serial here. This data comes from before the ALDET and ORMAS codes were given a replicated memory parallization, so scaling in the CI step should now be OK, to say 8 or 16 CPUs. However, these two CI code's use of replicated memory in the CI step limits MCSCF scalability in the large active space limit.

Programmer's Reference

5-20

Now let's consider the second order pertubation correction for this example. As noted, it is an excited state, so the test corrects two states simultaneously (S0 and S1). The parallel multireference perturbation program is described in H.Umeda, S.Koseki, U.Nagashima, M.W.Schmidt J.Comput.Chem. 22, 1243-1251 (2001) The run is given the converged S1 orbitals, so that it can skip directly to the perturbation calculation: p=1 p=2 p=4 p=8 p=16 2e- ints 332 332 329 328 331 MCQDPT 87921 43864 22008 11082 5697 --------------------total CPU 88261 44205 22345 11418 6028 total wall 91508 45818 23556 12350 6852 This corresponds to a speedup for 1->16 of 14.6. --In summary, most ab initio computations will run in less time on more than one processor. However, some things can be run only on 1 CPU, namely semi-empirical runs RHF+CI gradient Coupled-Cluster calculations Some steps run with little or no speedup, forming sequential bottlenecks that limit scalability. They do not prevent jobs from running in parallel, but restrict the total number of processors that can be effectively used: ROHF/GVB hessians: solution of response equations MCSCF: Hamiltonian and 2e- density matrix (CI) energy localizations: the orbital localization step transition moments/spin-orbit: the final property step MCQDPT reference weight option Future versions of GAMESS will address these bottlenecks. A short summary of the useful number of CPUs (based on data like the above) would be RHF, ROHF, UHF, GVB energy/gradient, their DFT analogs, and CIS excited states 16-32+ MCSCF energy/gradient SOSCF 4-8 FULLNR 8-32+ analytic hessians RHF 16-32+ ROHF/GVB 4-8 MCSCF 64-128+ MPLEVL=2

Programmer's Reference RHF, UHF, ROHF OSPT=ZAPT ROHF OSPT=RMP energy MCSCF 8-256+ 8 16+

5-21

Programmer's Reference

5-22

Altering program limits

Almost all arrays in GAMESS are allocated dynamically, but some variables must be held in common as their use is ubiquitous. An example would be the common block /NSHEL/ which holds the ab initio atom's basis set. The following Unix script, which we call 'mung' (see Wikipedia entry for recursive acronyms), changes the PARAMETER statements that set various limitations: #!/bin/csh # # automatically change GAMESS' built-in dimensions # chdir /u1/mike/gamess/source # foreach FILE (*.src) set FILE=$FILE:r echo ===== redimensioning in $FILE ===== echo "C dd-mmm-yy - SELECT NEW DIMENSIONS" \ > $FILE.munged sed -e "/MXATM=2000/s//MXATM=500/" \ -e "/MXAO=8192/s//MXAO=2047/" \ -e "/MXGSH=30/s//MXGSH=30/" \ -e "/MXSH=5000/s//MXSH=1000/" \ -e "/MXGTOT=20000/s//MXGTOT=5000/" \ -e "/MXRT=100/s//MXRT=100/" \ -e "/MXFRG=1050/s//MXFRG=65/" \ -e "/MXDFG=5/s//MXDFG=1/" \ -e "/MXPT=2000/s//MXPT=100/" \ -e "/MXFGPT=12000/s//MXFGPT=2000/" \ -e "/MXSP=500/s//MXSP=100/" \ -e "/MXTS=20000/s//MXTS=2500/" \ -e "/MXABC=6000/s//MXABC=1/" \ $FILE.src >> $FILE.munged mv $FILE.munged $FILE.src end exit The script shows how to reduce memory, by decreasing the number of atoms and basis functions, and reducing the storage for the effective fragment and PCM solvent models. Of course, the 'mung' script can also be used to increase the dimensions!

Programmer's Reference

5-23

To fully turn off effective fragment storage, use MXFRG=4, MXDFG=1, MXPT=8, MXFGPT=4. To fully turn off PCM storage, use MXSP=1, MXTS=1. The parameters currently used for GAMESS imply about 75 MBytes of storage tied up in common blocks, which is not unreasonable, even in a laptop. Reducing the storage size makes sense mainly on microkernel type systems, without virtual memory managers. In this script, MXATM = max number MXAO = max number MXGSH = max number MXSH = max number MXGTOT= max number MXRT of of of of of ab initio atoms basis functions Gaussians per shell symmetry unique shells symmetry unique Gaussians

= max number of MCSCF/CI states max number of effective fragment potentials max number of different effective fragments max number of points in any one term of any EFP maximum storage for all EFPs, and is sized for a large number of EFPs with a small number of points (solvent applications), or a smaller number of EFPs with many points (biochemistry).

MXFRG = MXDFG = MXPT = MXFGPT=

MXSP MXTS

= max number of spheres (sfera) in PCM = max number of tesserae in PCM

MXABC = max number of A,B,C matrices in the COSMO algorithm. The default value of 6000 allows the construction of cavities for roughly 150 to 200 atoms.

Programmer's Reference

5-24

Names of source code modules

The source code for GAMESS is divided into a number of sections, called modules, each of which does related things, and is a handy size to edit. The following is a list of the different modules, what they do, and notes on their machine dependencies. module ------ALDECI ALGNCI BASCCN BASECP BASEXT BASG3L BASHUZ BASHZ2 BASKAR BASN21 BASN31 BASPCN BASSTO BLAS CCAUX CCDDI CCQAUX CCQUAD CCSDT CEEIS CHGPEN CISGRD COSMO COSPRT CPHF CPMCHF CPROHF DCCC DCGRD DCGUES DCINT2 DCLIB DCMP2 DCSCF DCTRAN DDILIB machine description dependency ---------------------------------Ames Lab determinant full CI code 1 Ames Lab determinant general CI code Dunning cc-pVxZ basis sets SBKJC and HW valence basis sets DH, MC, 6-311G extended basis sets G3Large basis sets Huzinaga MINI/MIDI basis sets to Xe Huzinaga MINI/MIDI basis sets Cs-Rn Karlsruhe (Ahlrichs) TZV basis sets N-21G basis sets N-31G basis sets Jensen polarization consistent basis sets STO-NG basis sets level 1 basic linear algebra subprograms auxiliary routines for CC calculations parallel CCSD(T) program auxiliaries for CCSD(TQ) program renormalized CCSD(TQ) corrections renormalized CCSD(T) program 1 corr. energy extrap. by intrinsic scaling screening for charge penetration of EFPs CI singles and its gradient 1 conductor-like screening model printing routine for COSMO coupled perturbed Hartree-Fock 1 multiconfigurational CPHF 1 open shell/TCSCF CPHF 1 divide and conquer coupled cluster divide and conquer gradients divide and conquer orbital guess divide and conquer AO integrals 1 divide and conquer library routines divide and conquer MP2 1 divide and conquer SCF divide and conquer integral transf. 1 message passing library interface code

Programmer's Reference DELOCL DEMRPT DFT DFTAUX DFTDIS DFTFUN DFTGRD DFTINT DFTXCA DFTXCB DFTXCC DFTXCD DFTXCE DFTXCF DFTXCG DGEEV DGESVD DMULTI DRC EAIPCC ECP ECPDER ECPLIB ECPPOT EFCHTR EFDRVR EFELEC EFGRD2 EFGRDA EFGRDB EFGRDC EFINP EFINTA EFINTB EFMO EFPAUL EFPCM EFPCOV EFPFMO EFTEI EIGEN ELGLIB ELGLOC ELGSCF EOMCC EWALD FFIELD FMO FMOESD delocalized coordinates determinant-based MCQDPT grid-free DFT drivers 1 grid-free DFT auxiliary basis integrals empirical dispersion correction to DFT grid-free DFT functionals grid DFT implementation grid-free DFT integrals 1 grid DFT functionals, hand coded grid DFT functionals, from repository grid DFT functionals for meta-GGA grid DFT functionals B97, etc grid DFT functionals for PKZB/TPSS family grid DFT functionals for CAMB3LYPdir grid DFT functional for revTPSS general matrix eigenvalue problem single value decomposition Amos' distributed multipole analysis dynamic reaction coordinate EA-EOM and IP-EOM method pseudopotential integrals pseudopotential derivative integrals initialization code for ECP HW and SBKJC internally stored potentials fragment charge transfer fragment only calculation drivers fragment-fragment interactions 2e- integrals for EFP numerical hessian ab initio/fragment gradient integrals " " " " " " " " " " effective fragment potential input ab initio/fragment integrals " " " " EFP + FMO interfacing effective fragment Pauli repulsion EFP/PCM interfacing EFP style QM/MM boundary code FMO and EFP interface QM/EFP 2e- integrals 1 Givens-Householder, Jacobi diagonalization elongation method utility routines elongation method orbital localization elongation method Hartree-Fock 1 equation of motion excited state CCSD Ewald summations for EFP model finite field polarizabilitie n-mer drivers for Fragment Molecular Orbital elestrostatic potential derivatives for FMO

5-25

Programmer's Reference FMOGRD FMOINT FMOIO FMOLIB FMOPBC FMOPRP FRFMT FSODCI G3 GAMESS GLOBOP GMCPT GRADEX GRD1 GRD2A GRD2B GRD2C GUESS GUGDGA GUGDGB GUGDM GUGDM2 GUGDRT GUGEM GUGSRT GVB HESS HSS1A HSS1B HSS2A HSS2B INPUTA INPUTB INPUTC INT1 INT2A INT2B INT2C INT2D INT2F INT2G INT2R INT2S INT2T INT2U INT2V INT2W INT2X IOLIB gradient routines for FMO integrals for FMO input/output and printing for FMO utilities for FMO periodic boundary conditions for FMO properties for FMO free format input scanner determinant based second order CI G3(MP2,CCSD(T)) thermochemistry main program, important driver routines Monte Carlo fragment global optimizer general MCQDPT multireference PT code 1 traces gradient extremals one electron gradient integrals two electron gradient integrals 1 specialized sp gradient integrals general spdfg gradient integrals initial orbital guess Davidson CI diagonalization 1 " " " 1 1 particle density matrix 2 particle density matrix 1 distinct row table generation GUGA method energy matrix formation 1 sort transformed integrals 1 generalized valence bond HF-SCF 1 hessian computation drivers one electron hessian integrals " " " " two electron hessian integrals 1 " " " " read geometry, basis, symmetry, etc. " " " " " " " " one electron integrals two electron integrals (Rys) 1 two electron integrals (s,p,L rot.axis) ERIC TEI code, and its s,p routines 11 ERIC special code for d TEI ERIC special code for f TEI ERIC special code for g TEI s,p,d,L rotated axis integral package s,p,d,L quadrature code s,p,d,L quadrature code s,p,d,L quadrature code s,p,d,L quadrature code s,p,d,L quadrature code s,p,d,L quadrature code input/output routines,etc. 2

5-26

Programmer's Reference IVOCAS LAGRAN LOCAL LOCCD LOCPOL LRD MCCAS MCJAC MCPGRD MCPINP MCPINT MCPL10 MCPL20 MCPL30 MCPL40 MCPL50 MCPL60 MCPL70 MCPL80 MCQDPT MCQDWT MCQUD MCSCF MCTWO MDEFP MEXING MLTFMO MM23 MOROKM MNSOL MP2 MP2DDI MP2GRD MP2GR2 MP2IMS MPCDAT MPCGRD MPCINT MPCMOL MPCMSC MTHLIB NAMEIO NEOSTB NMR ORDINT ORMAS1 PARLEY PCM PCMCAV improved virtual orbital CAS energy CI Lagrangian matrix various localization methods LCD SCF localization analysis LCD SCF polarizability analysis local response dispersion correction FOCAS/SOSCF MCSCF calculation JACOBI MCSCF calculation model core potential nuclear gradient model core potential input model core potential integrals model core potential library " " " " " " " " " " " " " " " " " " " " " " " " " " " " multireference perturbation theory weights for MR-perturbation theory QUAD MCSCF calculation FULLNR MCSCF calculation two electron terms for FULLNR MCSCF molecular dynamics using EFP particles minimum energy crossing point search multiscale solvation in FMO MMCC(2,3) corrections to EOMCCSD Morokuma energy decomposition U.Minnesota solution models 2nd order Moller-Plesset distributed data parallel MP2 CPHF and density for MP2 gradients disk based MP2 gradient program disk based MP2 energy program MOPAC parameterization MOPAC gradient MOPAC integrals MOPAC molecule setup miscellaneous MOPAC routines printout, matrix math utilities namelist I/O simulator dummy routines for NEO program nuclear magnetic resonance shifts sort atomic integrals occ. restricted multiple act. space CI communicate to other programs Polarizable Continuum Model setup PCM cavity creation 1 1 1 1 1

5-27

1 1 1 1

1 1 1

1 1

Programmer's Reference PCMCV2 PCMDER PCMDIS PCMIEF PCMPOL PCMVCH PRMAMM PRPEL PRPLIB PRPPOP QEIGEN QFMM QMFM QMMM QREL QUANPO RAMAN RHFUHF ROHFCC RXNCRD RYSPOL SCFLIB SCFMI SCRF SOBRT SOFFAC SOLIB SOZEFF STATPT SURF SVPCHG SVPINP SVPLEB SYMORB SYMSLC TDDEFP TDDFT TDDFUN TDDFXC TDDGRD TDDINT TDDXCA TDDXCC TDDXCD TDHF TDX TDXIO TDXITR TDXNI PCM cavity for gradients PCM gradients PCM dispersion energy PCM integral equation formalism PCM polarizabilities PCM repulsion and escaped charge atomic multipole moment expansion electrostatic properties miscellaneous properties population properties 128 bit precision RI for relativity 11 quantum fast multipole method additional QFMM code dummy routines for Tinker/SIMOMM program relativistic transformations Quantum Chem Polarizable force field Raman intensity RHF, UHF, and ROHF HF-SCF 1 open shell CC computations 1 intrinsic reaction coordinate roots for Rys polynomials HF-SCF utility routines, DIIS code molecular interaction SCF code self consistent reaction field full Breit-Pauli spin-orbit compling spin-orbit matrix element form factors spin-orbit library routines 1e- spin-orbit coupling terms geometry and transition state finder PES scanning surface volume polarization (SS(V)PE) input/output routines for SS(V)PE Lebedev grids for SS(V)PE integration orbital symmetry assignment " " " EFP solvent effects on TD-DFT time-dependent DFT excitations functionals for TD-DFT exchange-corr. grid pts. for TD-DFT gradient code for TD-DFT integral terms for TD-DFT 1 TD-DFT functional derivatives TD-DFT functional derivatives TD-DFT functional der. for metaGGA time-dependent Hartree-Fock polarzblity 1 extended time-dependent RHF input/output for extended TDHF iterative procedures in extended TDHF non-iterative tasks in extended TDHF

5-28

Programmer's Reference TDXPRP TRANS TRFDM2 TRNSTN TRUDGE UMPDDI UNPORT UTDDFT VBDUM VECTOR VIBANL VSCF VVOS ZAPDDI ZHEEV ZMATRX properties from extended TDHF partial integral transformation 1 two particle density backtransform 1 CI transition moments nongradient optimization distributed data parallel MP2 unportable, nasty code 3,4,5,6,7,8 unrestricted TD-DFT 1 dummy routines for VB programs vectorized version routines 10 normal coordinate analysis anharmonic frequencies valence virtual orbitals distrib. data ZAPT2 open shell PT gradient complex matrix diagonalization internal coordinates

5-29

UNIX versions use the C code ZUNIX.C for dynamic memory. The machine dependencies noted above are: 1) packing/unpacking 2) OPEN/CLOSE statments 3) machine specification 4) fix total dynamic memory 5) subroutine walkback 6) error handling calls 7) timing calls 8) LOGAND function 10) vector library calls 11) REAL*16 data type Note that the message passing support (DDI) for GAMESS is implemented in C (for most machines), and is stored in a separate subdirectory. Please see the ~/games/ddi tree for more information about the Distributed Data Interface's code and usage.

Programmer's Reference

5-30

Programming Conventions
The following "rules" should be adhered to in making changes in GAMESS. These rules are important in maintaining portability, and should be adhered to. The following rule is so important that it is not given a number, The Golden Rule: make sure your code not only has no compiler diagnostics (try as many compilers as possible), but that it also has no FTNCHEK diagnostics. The FTNCHEK program of Robert Moniot is a fantastic debugging tool, and results in the great portability of GAMESS. You can learn how to get FTNCHEK, and how to use it from the script ~/gamess/misc/checkgms Rule 1. If there is a way to do it that works on all computers, do it that way. Commenting out statements for the different types of computers should be your last resort. If it is necessary to add lines specific to your computer, PUT IN CODE FOR ALL OTHER SUPPORTED MACHINES. Even if you don't have access to all the types of supported hardware, you can look at the other machine specific examples found in GAMESS, or ask for help from someone who does understand the various machines. If a module does not already contain some machine specific statements (see the above list) be especially reluctant to introduce dependencies. Rule 2. Write a double precision program, and let the source activator handle any conversion to single precision, when that is necessary: a) Use IMPLICIT DOUBLE PRECISION(A-H,O-Z) specification statements throughout. Not REAL*8. Integer type should be just INTEGER, so that compiler flags can select 64 or 32 bit integers at compile time. b) All floating point constants should be entered as if they were in double precision, in a format that the souce code activator can recognize as being uniquely a number. Namely, the constants should contain a decimal point, a number after the decimal, and a signed, two digit exponent. A legal constant is 1.234D-02. Illegal examples are 1D+00, 5.0E+00, 3.0D-2. Check for illegals by grep "[0-9][DE][0-9]" *.src grep "[0-9][.]D" *.src

Programmer's Reference

5-31

grep "[0-9][.][0-9][DE][0-9]" *.src grep "[0-9][DE][+-][1-9][^0-9]" *.src c) Double precision BLAS names are used throughout, for example DDOT instead of SDOT, and DGEMM instead of SGEMM. The source code activator ACTVTE will automatically convert these double precision constructs into the correct single precision expressions for machines that have 64 rather than 32 bit words. Rule 3. FORTRAN 77 allows for generic functions. Thus the routine SQRT should be used in place of DSQRT, as this will automatically be given the correct precision by the compilers. Use ABS, COS, INT, etc. Your compiler manual will tell you all the generic names. Rule 4. Every routine in GAMESS begins with a card containing the name of the module and the routine. An example is "C*MODULE xxxxxx *DECK yyyyyy". The second star is in column 18. Here, xxxxxx is the name of the module, and yyyyyy is the name of the routine. This rule is designed to make it easier for a person completely unfamiliar with GAMESS to find routines. Rule 5. Whenever a change is made to a module, this should be recorded at the top of the module. The information required is the date, initials of the person making the change, and a terse summary of the change. Rule 6. No imbedded tabs, statements must lie between columns 7 and 72, etc. In other words, old style syntax. * * * The next few "rules" are not adhered to in all sections of GAMESS. Nonetheless they should be followed as much as possible, whether you are writing new code, or modifying an old section. Rule 7. Stick to the FORTRAN naming convention for integer (I-N) and floating point variables (A-H,O-Z). If you've ever worked with a program that didn't obey this, you'll understand why. Rule 8. Always use a dynamic memory allocation routine that calls the real routine. A good name for the memory

Programmer's Reference

5-32

routine is to replace the last letter of the real routine with the letter M for memory. Rule 9. All the usual good programming techniques, such as indented DO loops ending on CONTINUEs, IF-THEN-ELSE where this is clearer, 3 digit statement labels in ascending order, no three branch GO TO's, descriptive variable names, 4 digit FORMATs, etc, etc. The next set of rules relates to coding practices which are necessary for the parallel version of GAMESS to function sensibly. They must be followed without exception! Rule 10. All open, rewind, and close operations on sequential files must be performed with the subroutines SEQOPN, SEQREW, and SEQCLO respectively. You can find these routines in IOLIB, they are easy to use. SQREAD, SQWRIT, and various integral I/O routines like PREAD are used to process the contents of such files. The variable DSKWRK tells if you are processing a distributed file (one split between all compute processes, DSKWRK=.TRUE.) or a single file on the master process (DSKWRK=.FALSE., resulting in broadcasts of the data from the master to all other CPUs). Rule 11. All READ and WRITE statements for the formatted files 5, 6, 7 (variables IR, IW, IP, or named files INPUT, OUTPUT, PUNCH) must be performed only by the master task. Therefore, these statements must be enclosed in "IF (MASWRK) THEN" clauses. The MASWRK variable is found in the /PAR/ common block, and is true on the master process only. This avoids duplicate output from the other processes. Rule 12. All error termination is done by "CALL ABRT" rather than a STOP statement. Since this subroutine never returns, it is OK to follow it with a STOP statement, as compilers may not be happy without a STOP as the final executable statment in a routine. The purpose of calling ABRT is to make sure that all parallel tasks get shut down properly.

Programmer's Reference

5-33

Parallel broadcast identifiers

GAMESS uses DDI calls to pass messages between the parallel processes. Every message is identified by a unique number, hence the following list of how the numbers are used at present. If you need to add to these, look at the existing code and use the following numbers as guidelines to make your decision. All broadcast numbers must be between 1 and 32767. 20 100 200 210 220 225 230 250 275 325 350 400 425 450 475 500 800 900 910 920 980 1000 1030 1050 1200 1300 1495 1500 1505 1600 1605 1650 1700 1800 1850 1900 2000 199 204 214 224 265 310 329 354 424 449 474 499 599 830 : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : Parallel timing DICTNRY file reads Restart info from the DICTNRY file Pread PKread RAread SQread Nameio Free format $PROP group input $VEC group input $GRAD group input $HESS group input $DIPDR group input $VIB group input matrix utility routines Orbital symmetry ECP 1e- integrals 1e- integrals EFP and SCRF integrals property integrals SCF wavefunctions broadcasts in DFT Coulomb integrals MP2 localization reserved for Jim Shoemaker One-electron gradients EFP and SCRF gradients Two-electron gradients One-electron hessians Two-electron hessians integral transformation GUGA sorting GUGA CI diagonalization GUGA DM2 generation MCSCF

- 975 - 999 - 1025 - 1041 - 1215 - 1320 - 1499 1599 1602 1620 1665 1750

- 1865 - 1910 - 2010

Programmer's Reference 2100 2150 2300 2350 2120 2200 2309 2353 : : : : coupled perturbed HF MCSCF hessian spin-orbit jobs local response dispersion

5-34

Programmer's Reference

5-35

Disk files used by GAMESS

These files must be defined by your control language in order to execute GAMESS. For example, on UNIX the "name" field shown below should be set in the environment to the actual file name to be used. Most runs will open only a subset of the files shown below, with only files 5, 6, 7, and 10 used by every run. Files 1, 2, 3 (both), 4, 5, 6, 7, and 35 contain formatted data, while all others are binary (unformatted) files. Files ERICFMT, EXTBAS, and MCPPATH are used to read data into GAMESS. Files MAKEFP, TRAJECT, RESTART, and PUNCH are supplemental output files, containing more concise summaries than the log file for certain kinds of data. unit name ---- ---1 MAKEFP 2 3 3 3 4 35 ERICFMT MCPPATH EXTBAS GAMMA TRAJECT RESTART contents -------effective fragment potential from MAKEFP run Fm(t) interpolation table data, a data file named ericfmt.dat, supplied with GAMESS. a directory of model core potentials and associated basis sets, supplied with GAMESS external basis set library (user supplied) 3rd nuclear derivatives trajectory results for IRC, DRC, or MD runs. summary of results for RUNTYP=GLOBOP. restart data for numerical HESSIAN runs, numerical gradients, or for RUNTYP=VSCF. Used as a scratch unit during MAKEFP. Namelist input file. This MUST be a disk file, as GAMESS rewinds this file often. Print output (main log file). If not defined, UNIX systems will use the file "standard output" for this. Punch output. A copy of the $DATA deck, orbitals for every geometry calculated, hessian matrix, normal modes from FORCE, properties output, etc. etc. etc.

5 6

INPUT OUTPUT

PUNCH

Programmer's Reference 8 9 10 11 12 13 14 15 AOINTS MOINTS DICTNRY DRTFILE CIVECTR CASINTS CIINTS WORK15 Two e- integrals in AO basis Two e- integrals in MO basis

5-36

Master dictionary, for contents see below. Distinct row table file for -CI- or -MCSCFEigenvector file for -CI- or -MCSCFsemi-transformed ints for FOCAS/SOSCF MCSCF scratch file during spin-orbit coupling Sorted integrals for -CI- or -MCSCFGUGA loops for Hamiltonian diagonal; ordered two body density matrix for MCSCF; scratch storage during GUGA Davidson diag; Hessian update info during 2nd order SCF; [ij|ab] integrals during MP2 gradient density matrices during determinant CI GUGA loops for Hamiltonian off-diagonal; unordered GUGA DM2 matrix for MCSCF; orbital hessian during MCSCF; orbital hessian for analytic hessian CPHF; orbital hessian during MP2 gradient CPHF; two body density during MP2 gradient CSF data for state to state transition runs. derivative Fock matrices for analytic hess used during CP-MCHF response equations Sort file for various -MCSCF- or -CI- steps; also used by SCF level DIIS four center overlap ints for grid-free DFT mesh information for grid DFT shell J, K, and Fock matrices for -GVB-; Hessian update info during SOSCF MCSCF; orbital gradient and hessian for QUAD MCSCF sorted AO integrals; integral subsets during Morokuma analysis

16

WORK16

17 18 19 20 21 22 23

CSFSAVE FOCKDER WORK19 DASORT DFTINTS DFTGRID JKFILE

24

ORDINT

Programmer's Reference 25 26 27 26 27 26 27 27 28 29 30 EFPIND PCMDATA PCMINTS SVPWRK1 SVPWRK2 COSCAV COSDATA COSPOT MLTPL MLTPLT DAFL30 electric field integrals for EFP gradient and D-inverse data for PCM runs normal projections of PCM field gradients conjugate gradient solver for SV(P)SE conjugate gradient solver for SV(P)SE scratch file for COSMO's solvent cavity

5-37

output file to process by COSMO-RS program DCOSMO input file, from COSMO-RS program QMFM file, no longer used QMFM file, no longer used direct access file for FOCAS MCSCF's DIIS, direct access file for NEO's nuclear DIIS, direct access file for DC's DIIS. form factor sorting for Breit spin-orbit Lx 2e- integrals during spin-orbit Ly 2e- integrals during spin-orbit Lz 2e- integrals during spin-orbit RESC symmetrization of SO ints documented at the beginning of this list determinant list for general CI program hessian for FMO optimisations; gradient for FMO with restarts reserved for future use CSF list for SOC; fragment densities/orbitals for FMO aabb spinor [ia|jb] integrals during UMP2 bbaa spinor [ia|jb] integrals during UMP2

31 32 33 34 35 37 38 39 40 41 42

SOINTX SOINTY SOINTZ SORESC RESTART GCILIST HESSIAN QMMTEI SOCCDAT AABB41 BBAA42

Programmer's Reference 43 BBBB43 bbbb spinor [ia|jb] integrals during UMP2

5-38

files 50-63 are used for MCQDPT runs. files 50-54 are also used by CODE=IMS MP2 runs. unit name ---- ---50 MCQD50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 MCQD51 MCQD52 MCQD53 MCQD54 MCQD55 MCQD56 MCQD57 MCQD58 MCQD59 MCQD60 MCQD61 MCQD62 MCQD63 MCQD64 contents -------Direct access file for MCQDPT, its contents are documented in source code. One-body coupling constants <I/Eij/J> for CAS-CI and other routines One-body coupling constants for perturb. One-body coupling constants extracted from MCQD52 One-body coupling constants extracted further from MCQD52 Sorted 2e- AO integrals Half transformed 2e- integrals transformed 2e- integrals of (ii|ii) type transformed 2e- integrals of (ei|ii) type transformed 2e- integrals of (ei|ei) type 2e- integral in MO basis arranged for perturbation calculations One-body coupling constants between state and CSF <Alpha/Eij/J> Two-body coupling constants between state and CSF <Alpha/Eij,kl/J> canonical Fock orbitals (FORMATTED) Spin functions and orbital configuration functions (FORMATTED)

unit ---51 52 53 54 55 unit ---61 62 63

name contents ----------for RI-MP2 calculations only RIVMAT 2c-2e inverse matrix RIT2A 2nd index transformation data RIT3A 3rd index transformation data RIT2B 2nd index data for beta orbitals of UMP2 RIT3B 3rd index data for beta orbitals of UMP2 name contents ----------for RUNTYP=NMR only NMRINT1 derivative integrals for NMR NMRINT2 " " " " NMRINT3 " " " "

Programmer's Reference 64 65 66 67 68 67 68 69 70 71 72 70 71 72 74 75 77 78 79 80

5-39

NMRINT4 " " " " NMRINT5 " " " " NMRINT6 " " " " for RUNTYP=MAKEFP (or dynamic polarizability run) DCPHFH2 magnetic hessian in dynamic polarizability DCPHF21 magnetic hessian times electronic hessian for NEO runs, only (DAFL30 has nuclear DIIS) ELNUINT electron-nucleus AO integrals NUNUINT nucleus-nucleus AO integrals NUMOIN nucleus-nucleus MO integrals NUMOCAS nucleus-nucleus half transformed integrals NUELMO nucleus-electron MO integrals NUELCAS nucleus-electron half transformed integrals for elongation method, only ELGDOS elongation density of states ELGDAT elongation frozen/active region data ELGPAR elongation geometry optimization info ELGCUT elongation cutoff information ELGVEC elongation localized orbitals ELINTA elongation 2e- for cut-off part EGINTB elongation 2e- for next elongation EGTDHF elongation TDHF (future use) EGTEST elongation test file files 70-98 are used for closed shell Coupled-Cluster, all of these are direct access files.

unit ---70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86

name ---CCREST CCDIIS CCINTS CCT1AMP CCT2AMP CCT3AMP CCVM CCVE CCAUADS QUADSVO EOMSTAR EOMVEC1 EOMVEC2 EOMHC1 EOMHC2 EOMHHHH EOMPPPP

contents -------T1 and T2 amplitudes for restarting amplitude converger's scratch data MO integrals sorted by classes T1 amplitudes and some No*Nu intermediates for MMCC(2,3) T2 amplitudes and some No**2 times Nu**2 intermediates for MMCC(2,3) M3 moments No**3 times Nu - type main intermediate No times Nu**3 - type main intermediate Nu**3 times No intermediates for (TQ) No*Nu**2 times No intermediates for (TQ) initial vectors for EOMCCSD calculations iterative space for R1 components iterative space for R2 components singly excited components of H-bar*R doubly excited components of H-bar*R intermediate used by EOMCCSD intermediate used by EOMCCSD

Programmer's Reference 87 88 89 90 91 92 93 94 95 96 97 98 99 EOMRAMP EOMRTMP EOMDG12 MMPP MMHPP MMCIVEC MMCIVC1 MMCIITR EOMVL1 EOMVL2 EOMLVEC EOMHL1 EOMHL2 converged EOMCCSD right (R) amplitudes converged EOMCCSD amplitudes for MEOM=2 (if the max. no. of iterations exceeded) diagonal part of H-bar diagonal parts for triples-triples H-bar diagonal parts for triples-triples H-bar Converged CISD vectors Converged CISD vectors for mci=2 (if the max. no. of iterations exceeded) Iterative space in CISD calculations iterative space for L1 components iterative space for L2 components converged EOMCCSD left eigenvectors singly excited components of L*H-bar doubly excited components of L*H-bar

5-40

the next group of files (70-95) is for open shell CC: unit ---70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 name ---AMPROCC ITOPNCC FOCKMTX LAMB23 VHHAA VHHBB VHHAB VMAA VMBB VMAB VMBA VHPRAA VHPRBB VHPRAB VHPLAA VHPLBB VHPLAB VHPLBA VEAA VEBB VEAB VEBA VPPPP INTERM1 INTERM2 INTERM3 ITSPACE INSTART ITSPC3 contents -------restart info CCSD/Lambda eq./EA-EOM/IP-EOM working copy of the same information subsets of F-alpha and F-beta matrices data during CC(2,3) step [i,k|j,l]-[i,l|j,k] alpha/alpha [i,k|j,l]-[i,l|j,k] beta/beta [i,k|j,l] alpha/beta [j,l|k,a]-[j,a|k,l] alpha/alpha [j,l|k,a]-[j,a|k,l] beta/beta [j,l|k,a] alpha/beta [j,l|k,a] beta/alpha [a,j|c,l]-[a,l|c,j] alpha/alpha [a,j|c,l]-[a,l|c,j] beta/beta [a,j|b,l] alpha/beta [a,b|k,l]-[a,l|b,k] alpha/alpha [a,b|k,l]-[a,l|b,k] beta/beta [a,b|k,l] alpha/beta [a,b|k,l] beta/alpha [a,b|c,l]-[a,l|b,c] alpha/alpha [a,b|c,l]-[a,l|b,c] beta/beta [a,j|c,d] alpha/beta [a,j|c,d] beta/alpha all four virtual integrals one H-bar, some two H-bar, etc. some two H-bar, etc. remaining two H-bar intermediates iterative subspace data for EA-EOM/IP-EOM initial guesses for EA-EOM or IP-EOM runs triples iterative data for EA-EOM

Programmer's Reference

5-41

unit ----

name contents ----------files 201-239 may be used by RUNTYP=TDHFX 201 OLI201...running consecutively up to 239 OLI239 files 250-257 are used by divide-and-conquer runs file 30 is used for the DC-DIIS data 250 DCSUB subsystem atoms (central and buffer) 251 DCVEC subsystem orbitals 252 DCEIG subsystem eigenvalues 253 DCDM subsystem density matrices 254 DCDMO old subsystem density matrices 255 DCQ subsystem Q matrices 256 DCW subsystem orbital weights 257 DCEDM subsystem energy-weighted density matrices files 297-299 are used by hyperpolarizability analysis 297 LHYPWRK preordered LMOs 298 LHYPKW2 reassigned LMOs 299 BONDDPF bond dipoles with electric fields Unit 301 is used for direct access using an internally assigned filename during divide and conquer MP2 runs.

disk files in parallel runs

When a file is opened by the master compute process (which is rank 0), its name is that defined by the 'setenv'. On other processes (ranks 1 up to p-1, where p is the number of running processes), the rank 'nnn' is appended to the file name, turning the name xxx.Fyy into xxx.Fyy.nnn. The number of digits in nnn is adjusted according to the total number of processes started. Thus the common situation of a SMP node sharing a single disk for several processes, on up to the case of a machine like the Cray XT having only one disk partition for all nodes does not lead to file name conflicts. By the way, only the master process needs to read the environment to learn file names: these names are sent as network messages to the other processes. When DDI subgroups are not in use, the variable DSKWRK (in common /par/) defines the strategy. A large file like 2eAO integrals (AOINTS) is computed as several smaller files, which taken together have all the integrals. When all processes are supposed to process files private to each

Programmer's Reference

5-42

process, DSKWRK is .TRUE., and every process has a file, usually containing different values. For smaller data, such as CI vectors, where all processes want to store exactly the same data, only the master process needs to maintain the file. This situation is DSKWRK=.FALSE. When the data is to be recovered from disk, only the master process reads the disk, after which, the data is sent as a broadcast message to all other processes. The special file DICTNRY is always processed in this second way, so data recovered from it is the same (to the least significant bits) on every process. Another example of a file read by only one process is the run's INPUT file. If DDI subgroups are used, DSKWRK is ignored, and every process opens every file. These are often left empty, except on the master process in each subgroup. The input file (INPUT) is exempt from having the rank added to its name, so that a machine with a common file system can have all processes read from the same input file. If the groups have different disks, the INPUT must be copied to the master process of every group: a simple way to ensure that is to copy INPUT to every node's work disk. Similarly, the OUTPUT file (and a few other files like PUNCH) are written by every group master. If the run goes badly, these extra output files may be interesting, but most of the time the OUTPUT from the master of the first subgroup has enough information. The OUTPUT of non-group-masters is not very interesting. The DICTNRY file is also treated in a special way when running in groups, and that should be described here.

Programmer's Reference

5-43

Contents of the direct access file 'DICTNRY'

1. 2. 3. 4. 5-6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. int 38. 39. int 40. 41. 42. 43. 44. 45. 46. Atomic coordinates various energy quantities in /ENRGYS/ Gradient vector Hessian (force constant) matrix not used PTR - symmetry transformation for p orbitals DTR - symmetry transformation for d orbitals FTR - symmetry transformation for f orbitals GTR - symmetry transformation for g orbitals Bare nucleus Hamiltonian integrals Overlap integrals Kinetic energy integrals Alpha Fock matrix (current) Alpha orbitals Alpha density matrix Alpha energies or occupation numbers Beta Fock matrix (current) Beta orbitals Beta density matrix Beta energies or occupation numbers Error function interpolation table Old alpha Fock matrix Older alpha Fock matrix Oldest alpha Fock matrix Old beta Fock matrix Older beta Fock matrix Oldest beta Fock matrix Vib 0 gradient in FORCE (numerical hessian) Vib 0 alpha orbitals in FORCE Vib 0 beta orbitals in FORCE Vib 0 alpha density matrix in FORCE Vib 0 beta density matrix in FORCE dipole derivative tensor in FORCE. frozen core Fock operator RHF/UHF/ROHF Lagrangian (see 402-404) floating point part of common block /OPTGRD/ integer part of common block /OPTGRD/ ZMAT of input internal coords IZMAT of input internal coords B matrix of redundant internal coords pristine core Fock matrix in MO basis (see 87) Force constant matrix in internal coordinates. SALC transformation symmetry adapted Q matrix S matrix for symmetry coordinates

Programmer's Reference 47. int 48. 49. 50. 51. 52. 53. 54. 55. 56. 57. 58. 59. 60. 61. 62. 63. 64. 65. 66. 67. 68. 69. 70. 71. 72. 73. 74. 75. 76. 77. 78. 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. int 91. 92. int 93. 94.

5-44

ZMAT for symmetry internal coords IZMAT for symmetry internal coords B matrix B inverse matrix overlap matrix in Lowdin basis, temp Fock matrix storage for ROHF genuine MOPAC overlap matrix MOPAC repulsion integrals exchange integrals for screening orbital gradient during SOSCF MCSCF orbital displacement during SOSCF MCSCF orbital hessian during SOSCF MCSCF reserved for Pradipta Coulomb integrals in Ruedenberg localizations exchange integrals in Ruedenberg localizations temp MO storage for GVB and ROHF-MP2 temp density for GVB dS/dx matrix for hessians dS/dy matrix for hessians dS/dz matrix for hessians derivative hamiltonian for OS-TCSCF hessians partially formed EG and EH for hessians MCSCF first order density in MO basis alpha Lowdin populations beta Lowdin populations alpha orbitals during localization beta orbitals during localization alpha localization transformation beta localization transformation fitted EFP interfragment repulsion values model core potential information model core potential information "Erep derivative" matrix associated with F-a terms "Erep derivative" matrix associated with S-a terms EFP 1-e Fock matrix including induced dipole terms interfragment dispersion values MO-based Fock matrix without any EFP contributions LMO centroids of charge d/dx dipole velocity integrals d/dy dipole velocity integrals d/dz dipole velocity integrals unmodified h matrix during SCRF or EFP, AO basis PCM solvent operator contribution to Fock EFP multipole contribution to one e- Fock matrix ECP coefficients ECP labels ECP coefficients ECP labels bare nucleus Hamiltonian during FFIELD runs

Programmer's Reference 95. 96. 97. 98. 99. 100. x dipole integrals, in AO basis y dipole integrals, in AO basis z dipole integrals, in AO basis former coords for Schlegel geometry search former gradients for Schlegel geometry search dispersion contribution to EFP gradient

5-45

records 101-248 are used for NLO properties 101. 102. 103. 104. 105. 106. 107. 108. 109. 110. 111. 112. 113. 114. 115. 116. 117. 118. 119. 120. 121. 122. 123. 124. 125. 126. 127. 128. 129. 130. 131. 132. 133. 134. 135. 136. 137. 138. 139. 140. U'x(0) y z G'x(0) y z U'x(w) y z G'x(w) y z U'x(2w) y z G'x(2w) y z U'x(3w) y z G'x(3w) y z U''xx(0) xy xz yy yz zz G''xx(0) xy xz yy yz zz e''xx(0) xy xz yy 149. 150. 151. 152. 153. 154. 155. 156. 157. 158. 159. 160. 161. 162. 163. 164. 165. 166. 167. 168. 169. 170. 171. 172. 173. 174. 175. 176. 177. 178. 179. 180. 181. 182. 183. 184. 185. 186. 187. 188. U''xx(-2w;w,w) xy xz yy yz zz G''xx(-2w;w,w) xy xz yy yz zz e''xx(-2w;w,w) xy xz yy yz zz UM''xx(-2w;w,w) xy xz yy yz zz U''xx(-w;w,0) xy xz yz yy yz zx zy zz G''xx(-w;w,0) xy xz yz yy yz zx 200. 201. 202. 203. 204. 205. 206. 207. 208. 209. 210. 211. 212. 213. 214. 215. 216. 217. 218. 219. 220. 221. 222. 223. 224. 225. 226. 227. 228. 229. 230. 231. 232. 233. 234. 235. 236. 237. 238. 239. UM''xx(-w;w,0) xy xz yz yy yz zx zy zz U''xx(0;w,-w) xy xz yz yy yz zx zy zz G''xx(0;w,-w) xy xz yz yy yz zx zy zz e''xx(0;w,-w) xy xz yz yy yz zx zy zz UM''xx(0;w,-w) xy xz yz

Programmer's Reference 141. yz 142. zz 143. UM''xx(0) 144. xy 145. xz 146. yy 147. yz 148. zz 189. zy 190. zz 191. e''xx(-w;w,0) 192. xy 193. xz 194. yz 195. yy 196. yz 197. zx 198. zy 199. zz 240. 241. 242. 243. 244. yy yz zx zy zz

5-46

245. 246. 247. 249. 250. 251. 252. 253. 254. 255. 256. 257. 258. 259. 260-261. 262. 263. 264. 265. 266. 267. 268. 269. 270. 271. int 272. 273. 274. 275. 276. 277. 278. 279. 280. 281. 282. 283.

old NLO Fock matrix older NLO Fock matrix oldest NLO Fock matrix polarizability derivative tensor for Raman transition density matrix in AO basis static polarizability tensor alpha X dipole integrals in MO basis Y dipole integrals in MO basis Z dipole integrals in MO basis alpha MO symmetry labels beta MO symmetry labels not used Vnn gradient during MCSCF hessian core Hamiltonian from der.ints in MCSCF hessian reserved for Dan MO symmetry integers during determinant CI PCM nuclei/induced nuclear Charge operator PCM electron/induced nuclear Charge operator pristine alpha guess (MOREAD or Huckel+INSORB) EFP/PCM IFR sphere information fragment LMO expansions, for EFP Pauli fragment Fock operators, for EFP Pauli fragment CMO expansions, for EFP charge transfer not used orbital density matrix in divide and conquer subsystem data during divide and conquer old alpha Fock matrix for D&C Anderson-like DIIS old beta Fock matrix for D&C Anderson-like DIIS not used Vib 0 Q matrix in FORCE Vib 0 h integrals in FORCE Vib 0 S integrals in FORCE Vib 0 T integrals in FORCE Zero field LMOs during numerical polarizability Alpha zero field dens. during num. polarizability Beta zero field dens. during num. polarizability zero field Fock matrix. during num. polarizability

Programmer's Reference 284. 285. 286. 287. 290-299. 301. 302. 303. 304. 305. 306. 307. 308. 309. 311. 312. 313. 314. 315. 316. 317. 318. 319. 320. 321. 322. 323. 324. 325. 330. 331. 332. 333. 334. 335-339. 340. 341. 342. 343. 344. 345. 346. 347. 348. 349. 350. 351. 352. 353.

5-47

Fock eigenvalues for multireference PT density matrix or Fock matrix over LMOs oriented localized molecular orbitals density matrix of oriented LMOs not used Pocc during MP2 (RHF or ZAPT) or CIS grad Pvir during MP2 gradient (UMP2= 411-429) Wai during MP2 gradient Lagrangian Lai during MP2 gradient Wocc during MP2 gradient Wvir during MP2 gradient P(MP2/CIS)-P(RHF) during MP2 or CIS gradient SCF density during MP2 or CIS gradient energy weighted density in MP2 or CIS gradient Supermolecule h during Morokuma Supermolecule S during Morokuma Monomer 1 orbitals during Morokuma Monomer 2 orbitals during Morokuma combined monomer orbitals during Morokuma RHF density in CI grad; nonorthog. MOs in SCF-MI unzeroed Fock matrix when MOs are frozen MOREAD orbitals when MOs are frozen bare Hamiltonian without EFP contribution MCSCF active orbital density MCSCF DIIS error matrix MCSCF orbital rotation indices Hamiltonian matrix during QUAD MCSCF MO symmetry labels during MCSCF final uncanonicalized MCSCF orbitals CEL matrix during PCM VEF matrix during PCM QEFF matrix during PCM ELD matrix during PCM PVE tesselation info during PCM not used DFT alpha Fock matrix DFT beta Fock matrix DFT screening integrals DFT: V aux basis only DFT density gradient d/dx integrals DFT density gradient d/dy integrals DFT density gradient d/dz integrals DFT M[D] alpha density resolution in aux basis DFT M[D] beta density resolution in aux basis DFT orbital description overlap of true and auxiliary DFT basis previous iteration DFT alpha density previous iteration DFT beta density DFT screening matrix (true and aux basis)

Programmer's Reference 354. 355. 356. 357. 358-369. 370. 371. 370. 371. 372. 373. 374. 375. 376. 377. 378. 372. 373. 374. 375. 376. 377. 378. 379. 380. 381. 382. 383. 384. 385. int 386. 387. int 388. 389. 390. 391. 392. 393. 394. 395. 396-400. 401. 402. 403. 404. 405. 406. 407. 408.

5-48

DFT screening integrals (aux basis only) h in MO basis during DDI integral transformation alpha symmetry MO irrep numbers if UHF/ROHF beta symmetry MO irrep numbers if UHF/ROHF not used left transformation for pVp right transformation for pVp basis A (large component) during NESC basis B (small component) during NESC difference basis set A-B1 during NESC basis N (rel. normalized large component) basis B1 (small component) during NESC charges of non-relativistic atoms in NESC common nuclear charges for all NESC basis common coordinates for all NESC basis common exponent values for all NESC basis left transformation for V during RESC right transformation for V during RESC 2T, T is kinetic energy integrals during RESC pVp integrals during RESC V integrals during RESC Sd, overlap eigenvalues during RESC V, overlap eigenvectors during RESC Lz integrals reserved for Ly integrals. reserved for Lx integrals. X, AO orthogonalisation matrix during RESC Td, eigenvalues of 2T during RESC U, eigenvectors of kinetic energy during RESC exponents and contraction for the original basis shell integer arrays for the original basis exponents and contraction for uncontracted basis shell integer arrays for the uncontracted basis Transformation to contracted basis S integrals in the internally uncontracted basis charges of non-relativistic atoms in RESC copy of one e- integrals in MO basis in SO-MCQDPT Density average over all $MCQD groups in SO-MCQDPT overlap integrals in 128 bit precision kinetic ints in 128 bit precision, for relativity not used dynamic polarizability tensors GVB Lagrangian MCSCF Lagrangian GUGA CI Lagrangian (see 308 for CIS) not used MEX search state 1 alpha orbitals MEX search state 1 beta orbitals MEX search state 2 alpha orbitals

Programmer's Reference 409. 410. 411. 412. 413. 414. 415. 416. 417. 418. 419. 420. 421-429. 430. 440-469. 470. 471. 472. 473. 474. 475. 476. 477. 478-489. 490. 491. 492. 493. 494. 495. 496. 497. 498-500. 501. 502. 503. 504-510. 511. 512. 513. 514. 515. 516-950.

5-49

MEX search state 2 beta orbitals not used alpha Pocc during UMP2 gradient (see 301-309) alpha Pvir during UMP2 gradient alpha Wai during UMP2 gradient alpha Lagrangian Lai during UMP2 gradient alpha Wocc during UMP2 gradient alpha Wvir during UMP2 gradient alpha P(MP2/CIS)-P(RHF) during UMP2/USFTDDFT grad alpha SCF density during UMP2/USFTDDFT gradient alpha energy wghted density in UMP2/USFTDDFT grad not used same as 411-419, for beta orbitals not used reserved for NEO QUAMBO expansion matrix excitation vectors for FMO-TDDFT X+Y in MO basis during TD-DFT gradient X-Y in MO basis during TD-DFT gradient X+Y in AO basis during TD-DFT gradient X-Y in AO basis during TD-DFT gradient excited state density during TD-DFT gradient energy-weighted density in AO basis for TD-DFT not used transition Lagrangian right hand side during NACME gradients vectors during NACME NACME vectors during NACME difference gradient in conical intersection search derivative coupling vector in CI search mean energy gradient in CI search unused temp storage of gradient of 1st state in CI search not used A2 cavity data in COSMO A3 cavity data in COSMO AMTSAV cavity data in COSMO not used effective polarizability in LRD C6 coefficients in LRD C8 coefficients in LRD C10 coefficients in LRD atomic pair LRD energy not used

In order to correctly pass data between different machine types when running in parallel, it is required that a DAF record must contain only floating point values, or only integer values. No logical or Hollerith data may be stored. The final calling argument to DAWRIT and DAREAD

Programmer's Reference

5-50

must be 0 or 1 to indicate floating point or integer values are involved. The records containing integers are so marked in the list below. Physical record 1 (containing the DAF directory) is written whenever a new record is added to the file. This is invisible to the programmer. The numbers shown above are "logical record numbers", and are the only thing that the programmer need be concerned with.

Hardware Specifics (6 May 2010) ********************************** * * * Section 6 - Hardware Specifics * * * **********************************

6-1

This section of the manual contains pages dealing in a general way with dynamic memory allocation in GAMESS, the BLAS routines, and vectorization. The remaining portions of this section consist of specific suggestions for each type of machine. You should certainly read the section pertaining to your computer. It is a good idea to look at the rest of the machines as well, as you may get some ideas! The directions for executing GAMESS are given, along with hints and other tidbits. Any known problems with certain compiler versions are described in the control language files themselves, not here. The currently supported machines are all running Unix. The embedded versions for IBM mainframes and VAX/VMS have not been used in many years, and are no longer described here. There are binary versions for Windows available on our web site, but we do not supply a source code version for Windows (except that the Unix code will compile under the Cygwin Unix environment for Windows). Please note that with the OS X system, the Macintosh is considered to be a system running Unix, and is therefore well supported. Dynamic memory in GAMESS ____________________________________________ 2 BLAS routines _________________________________________________________ 4 Vectorization of GAMESS ________________________________________________ 5 Notes for specific machines _______________________________________________ 7

Hardware Specifics

6-2

Dynamic memory in GAMESS

GAMESS allocates its working memory from one large pool of memory. This pool consists of a single large array, which is partitioned into smaller arrays as GAMESS needs storage. When GAMESS is done with a piece of memory, that memory is freed for other uses. The units for memory are words, a term which GAMESS defines as the length used for floating point numbers, 64 bits, that is 8 bytes per word. GAMESS contains two memory allocation schemes. For some systems, a primitive implementation allocates a large array of a *FIXED SIZE* in a common named /FMCOM/. This is termed the "static" implementation, and the parameter MWORDS in $SYSTEM cannot request an amount larger than chosen at compile time. Wherever possible, a "dynamic" allocation of the memory is done, so that MWORDS can (in principle) request any amount. The memory management routines take care of the necessary details to fool the rest of the program into thinking the large memory pool exists in common /FMCOM/. Computer systems which have "static" memory allocation are IBM mainframes running VM or MVS to which we have no direct access for testing purposes. If your job requires a larger amount of memory than is available, your only recourse is to recompile UNPORT.SRC after choosing a larger value for MEMSIZ in SETFM. Computer which have "dynamic" memory allocation are all Unix systems and VMS. In principle, MWORDS can request any amount you want to use, without recompiling. In practice, your operating system will impose some limitation. As outlined below, common sense imposes a lower limit than your operating system will. By default, most systems allocate a small amount of memory: one million words. This amount is quite small by modern standards, and therefore exists on all machines. It is left up to you to increase this with your MWORDS input to what your machine has. EXETYP=CHECK runs will always tell you the amount of memory you need. Many computations in GAMESS implement out of memory algorithms, whenever the in memory algorithm can require an

Hardware Specifics

6-3

excessive amount. The in memory algorithms will perform very poorly when the work arrays reside in virtual memory rather than physical memory. This excessive page faulting activity can be avoided by letting GAMESS choose its out of core algorithms. These are programmed such that large amounts of numbers are transferred to and from disk at the same time, as opposed to page faulting for just a few values in that page. So, pick an amount for MWORDS that will reside in the physical memory of your system! MWORDS, multiplied by 8, is roughly the number of Mbytes and should not exceed more than about 90% of your installed memory (less if you are sharing the computer with other jobs!). The routines involved in memory allocation are VALFM, to determine the amount currently in use, GETFM to grab a block of memory, and RETFM to return it. Note that calls to RETFM must be in exactly inverse order of the calls to GETFM. SETFM is called once at the beginning of GAMESS to initialize, and BIGFM at the end prints a "high water mark" showing the maximum memory demand. GOTFM tells how much memory is not yet allocated.

Hardware Specifics

6-4

BLAS routines
The BLAS routines (Basic Linear Algebra Subprograms) are designed to perform primitive vector operations, such as dot products, or vector scaling. They are often found implemented in a system library, even on scalar machines. If this is the case, you should use the vendor's version! The BLAS are a simple way to achieve BOTH moderate vectorization AND portability. The BLAS are easy to implement in FORTRAN, and are provided in the file BLAS.SRC in case your computer does not have these routines in a library. The BLAS are defined in single and double precision, e.g. SDOT and DDOT. The very wonderful implementation of generic functions in FORTRAN 77 has not yet been extended to the BLAS. Accordingly, all BLAS calls in GAMESS use the double precision form, e.g. DDOT. The source code activator translates these double precision names to single precision, for machines such as Cray which run in single precision. If you have a specialized BLAS library on your machine, for example IBM's ESSL, Compaq's CXML, or Sun's Performance Library, using them can produce significant speedups in correlated calculations. The compiling scripts attempt to detect your library, but if they fail to do so, it is easy to use one: a) remove the compilation of 'blas' from 'compall', b) if the library includes level 3 BLAS, set the value of 'BLAS3' to true in 'comp', c) in 'lked', set the value of BLAS to a blank, and set libraries appropriately, e.g. to '-lessl'. Check the compilation log for mthlib.src, in particular, to be sure that your library is being found. It has a profound effect on the speed of MP2 and CC computations! The reference for the level 1 BLAS is C.L.Lawson, R.J.Hanson, D.R.Kincaid, F.T.Krogh ACM Trans. on Math. Software 5, 308-323(1979)

Hardware Specifics

6-5

Vectorization of GAMESS
As a result of a Joint Study Agreement between IBM and NDSU, GAMESS has been tuned for the IBM 3090 vector facility (VF), together with its high performance vector library known as the ESSL. This vectorization work took place from March to September of 1988, and resulted in a program which is significantly faster in scalar mode, as well as one which can take advantage (at least to some extent) of a vector processor's capabilities. Since our move to ISU we no longer have access to IBM mainframes, but support for the VF, as well as MVS and VM remains embedded within GAMESS. Several other types of vector computers are supported as well. Anyone who is using a current version of the program, even on scalar machines, owes IBM their thanks both for NDSU's having had access to a VF, and the programming time to do code improvements in the second phase of the JSA, from late 1988 to the end of 1990. Some of the vectorization consisted of rewriting loops in the most time consuming routines, so that a vectorizing compiler could perform automatic vectorization on these loops. This was done without directives, and so any vectorizing compiler should be able to recognize the same loops. In cases where your compiler allows you to separate scalar optimization from vectorization, you should choose not to vectorize the following sections: INT2A, GRD2A, GRD2B, and GUGEM. These sections have many very small loops, that will run faster in scalar mode. The remaining files will benefit, or at least not suffer from automatic compiler vectorization. The highest level of performance, obtained by vectorization at the matrix level (as opposed to the vector level operations represented by the BLAS) is contained in the file VECTOR.SRC. This file contains replacements for the scalar versions of routines by the same names that are contained in the other source code modules. VECTOR should be loaded after the object code from GAMESS.SRC, but before the object code in all the other files, so that the vector versions from VECTOR are the ones used.

Hardware Specifics

6-6

Most of the routines in VECTOR consist of calls to vendor specific libraries for very fast matrix operations, such as IBM's Engineering and Scientific Subroutine Library (ESSL). Look at the top of VECTOR.SRC to see what vector computers are supported currently. If you are trying to bring GAMESS up on some other vector machine, do not start with VECTOR. The remaining files (excepting BLAS, which are probably in a system library) represent a complete, working version of GAMESS. Once you have verified that all the regular code is running correctly, then you can adapt VECTOR to your machine for the maximum possible performance. Vector mode SCF runs in GAMESS on the IBM 3090 will proceed at about 90 percent of the scalar speed on these machines. Runs which compute an energy gradient may proceed slightly faster than this. MCSCF and CI runs which are dominated by the integral transformation step will run much better in vector mode, as the transformation step itself will run in about 1/4 time the scalar time on the IBM 3090 (this is near the theoretical capability of the 3090's VF). However, this is not the only time consuming step in an MCSCF run, so a more realistic expectation is for MCSCF runs to proceed at 0.3-0.6 times the scalar run. If very large CSF expansions are used (say 20,000 on up), however, the main bottleneck is the CI diagonalization and there will be negligible speedup in vector mode. Several stages in an analytic hessian calculation benefit significantly from vector processing. A more quantitative assessment of this can be reached from the following CPU times obtained on a IBM 3090-200E, with and without use of its vector facility: ROHF grad ------168 ( 1 ) 146 (0.87) RHF E -----164 ( 1 ) 143 (0.87) RHF hess ------917 ( 1 ) 513 (0.56) MCSCF E -----903 ( 1 ) 517 (0.57)

scalar vector

Hardware Specifics

6-7

Notes for specific machines

GAMESS will run on many kinds of UNIX computers. These systems runs the gamut from very BSD-like systems to very ATT-like systems, and even AIX. Our experience has been that all of these UNIX systems differ from each other. So, putting aside all the hype about "open systems", we divide the Unix world into four classes: Supported: Apple MAC under OS X, HP/Compaq/DEC AXP, HP PA-RISC, IBM RS/6000, 64 bit Intel/AMD chips such as the Xeon/Opteron/Itanium, and Sun ultraSPARC. These are the only types of computer we currently have at ISU, so these are the only systems we can be reasonably sure will work (at least on the hardware model and O/S release we are using). Both the source code and control language is correct for these. Acquainted: Cray XT, IBM SP, SGI Altix/ICE, and SGI MIPS. We don't have any of these systems at ISU, so we can't guarantee that these work. GAMESS has been run on each of these offsite, perhaps recently, but perhaps not. The source code for these systems is probably correct, but the control language may not be. Be sure to run all the test cases to verify that the current GAMESS still works on these brands. Jettisoned: Alliant, Apollo, Ardent, Celerity, Convex, Cray T3E, Cray vectors, DECstations, FPS model 500, Fujitsu AP and VPP, HP Exemplar, Hitachi SR, IBM AIX mainframes, Intel Paragon, Kendall Square, MIPS, NCube, and Thinking Machines. In most cases the company is out of business, or the number of machines in use has dropped to near zero. Of these, only the Celerity version's death should be mourned, as this was the original UNIX port of GAMESS, back in July 1986. Terra Incognita: everything else! You will have to decide on the contents of UNPORT, write the scripts, and generally use your head. * * * * * You should have a file called "readme.unix" at hand before you start to compile GAMESS. These directions should be followed carefully. Before you start, read the notes on your system below, and read the compiler clause

Hardware Specifics for your system in 'comp', as notes about problems with certain compiler versions are kept there.

6-8

Execution is by means of the 'rungms' script, and you can read a great deal more about its DDIKICK command in the installation guide 'readme.ddi'. Note in particular that execution of GAMESS now uses System V shared memory on many systems, and this will often require reconfiguring the system's limits on shared memory and semaphores, along with a reboot. Full details of this are in 'readme.ddi. Users may find examples of the scalability of parallel runs in the Programmer's Reference chapter of this manual. * * * * * *

AMD Opteron and other chips:

see "linux64" below.

AXP: These are scalar systems. This category means any AXP machines, whether labeled Digital or Compaq or HP on the front, with an O/S called OSF1, Digital Unix, or Tru64. It also includes systems running Linux, see below. The unique identifier is therefore the AXP chip, so the compiling target is 'axp64', rather than a company name. The compiling script invokes the f77 compiler, so read 'comp' if you have the f90 compiler instead. This version was changed to use native 64 bit integers in fall 1998. You can also run GAMESS on AXP Linux, by using the Tru64 Compaq compilers, which permit the Tru64 version to run. Do not use g77 which allocates 32 bit integers, as the system's malloc routine for dynamic memory allocation returns 64 bit addresses, which simply cannot be stored in 32 bit integers. The Compaq compilers can easily generate 64 bit integers, so obtain FORTRAN and C from http://h18000.www1.hp.com/products/software/alpha-tools Then compile and link using target 'compaq-axp'. Cray XT: a massively parallel platform, based on dual Opteron processor blades connected by Cray's 3D mesh, running a node O/S called "Compute Node Linux". The message passing involves a DDI running over MPI with a user selectable number of data servers. Unfortunately, the DDI is not fully integrated into our main code yet, and the scripting is a bit rough. Good support for these (XT3 through XT6) is expected by summer 2010.

Hardware Specifics Digital: See AXP above.

6-9

HP: Any Intel or PA-RISC series workstation or server. Help with this version has come from due to Fred Senese, Don Phillips, Tsuneo Hirano, and Zygmunt Krawczyk. Dave Mullally at HP has been involved in siting HP systems at ISU, presently Itanium2 based. So, we used 'hpux32' for many years, but are now running only the 'hpux64' version. The latter version can be considered to be carefully checked since it is in use at ISU, but please be a little more careful checking tests if you use 'hpux32'. IBM: "superscalar" RS/6000. There are two targets for IBM workstations, namely "ibm32" and "ibm64", neither of these should be used on a SP system. Parallelization is achieved using the TCP/IP socket calls found in AIX. IBM-SP: The SP parallel systems. This is a 64 bit implementation. The new DDI library will operate with LAPI support for one-sided messaging, and a special execution script for LoadLeveler is included. IBM Blue Gene: This target is "ibm-bg". The older BG/L has been outmoded by the BG/P, but we still have an "L" at ISU. These are massively parallel machine, using a 32 bit PowerPC, and a limited amount of node memory. The "L" uses DDI running over the ARMCI library, running in turn over MPI, so the "L" does not use data servers. The "P" uses a straightforward DDI to MPI interface, with data servers. The "L" port was done by Brian Smith of IBM and Brett Bode at ISU, included in GAMESS in June 2005, and changed to use ARMCI in 2007 by Andrey Asadchev of ISU. Nick Nystrom's initial port to the "P" system was polished up by Graham Fletcher at Argonne National Labs in 2010. Special notes, and various files to be used on this system are stored in the directory ~/gamess/machines/ibm-bg. Linux32: this means any kind of 32 bit chips, but typically is used only when "uname -p" replies "x86". Nearly every other chip is 64 bits, so see also Linux64 just below. This version is originally due to Pedro Vazquez in Brazil in 1993, and modified by Klaus-Peter Gulden in Germany. The usefulness of this version has matched the steady growth of interest in PC Unix, due to the improvement in CPU, memory, and disks, to workstation levels. We acquired a 266 MHz Pentium-II PC running RedHat Linux in August 1997, and found it performed flawlessly. In 1998 we obtained six 400 MHz Pentium-IIs for sequential use, and in 1999 a 16 PC cluster, running in parallel day

Hardware Specifics

6-10

in and day out. We have used RedHat 4.2, 5.1, 6.1, 7.1, and Fedora Core 1, prior to switching over exclusively to 64-bit Linux. This version is based on gfortran or g77, gcc, and the gcclib, so it should work for any kind of 32 bit Linux. This version uses 'sockets' for its message passing. The configuration script will suggest possible math library choices to you. By 2010, probably most Linux systems in existence are 64-bit capable, so the next version is more better! Linux64: this means any sort of 64 bit chip running an appropriate 64 bit Linux operating system. The most common "linux64" build is on AMD or Intel chips, where "uname -p" returns x86_64 or ia64. However, if you choose the 'gfortran' compiler, no processor-specific compiler flags are chosen, so this version should run on any 64-bit Linux system, e.g. AXP or SPARC. If you are running on Intel/AMD processors, the configuration script lets you choose various FORTRAN compilers: GNU's gfortran, Intel's ifort, Portland Group's pgf77, and Pathscale's pathf90. You can choose a variety of math libraries, such as Intel's MKL, AMD's ACML, or ATLAS. You can choose to use MPI if your machine has a good network for parallel computing, with the options for the MPI type specified in detail in the file, but sockets are an easy to use alternative to MPI. The choices for FORTRAN, math library, and MPI library can all be "mixed and matched". Except for 'gfortran', almost all this software has to be added to a standard Linux distribution. It is your responsibility to install what you want to use, to set up execution paths, to set up run time library paths (LD_LIBRARY_PATH), and so forth. The 'config' script will need to ask where these software packages are installed, since your system manager may have placed them almost anywhere. Macintosh OS X: This is for Apple running OS X, which is a genuine Unix system "under the hood". This version closely resembles the Linux version. Installation of Apple's XCODE (from the OS X distribution DVD) gives you a C compiler and a math library. You can obtain a FORTRAN compiler (gfortran for 64 bit or g77 for 32 bits) from the wonderful web site of Gourav Khanna: http://hpc.sourceforge.net Request target "mac32" if your OS X is 10.4, or "mac64" if your OS X is 10.5 or newer.

Hardware Specifics

6-11

NEC SX: vector system. This port was done by Janet Fredin at the NEC Systems Laboratory in Texas in 1993, and she periodically updates this version, including parallel usage, most recently in Oct. 2003. You should select both *UNX and *SNG when manually activating ACTVTE.CODE, and compile actvte by "f90 -ew -o actvte.x actvte.f". Silicon Graphics: The modern product line of this company is called Altix or Altix ICE. The operating system is Linux, the chips are 64 bit Intel processors, and the natural compiler and math library choices are Intel's ifort and MKL. The SGI software ProPack turns these commodity components into a supercomputer, and DDI should use the MPI library 'mpt' found in ProPack. Accordingly, the compiling target should be 'linux64', selecting ifort, MKL, and then mpt. Silicon Graphics: The ancient product line of this company use various MIPS chips such as R4x00, R5000, R12000, etc. There are very few of these machines left, so target's 'sgi32' and 'sgi64' should be regarded as "rusty". The 32 bit target uses sockets communications, while the 64 bit one will use an old SHMEM interface, that only partially implements DDI. Hence FMO and parallel CCSD(T) will not run on 'sgi64'. Sun: scalar system. This version is set up for the ultraSPARC or Opteron chips, running Solaris. The target for either chip is "sun64" as the scripts can automatically detect which one you are using, and adjust for that. Since Sun provided a ultraSPARC E450 system in 1998, two ultraSPARC3 Sunfire 280R systems in 2002, and a Opteron V40Z system in 2006, to the group at Iowa State, the Sun version is very reliable. Install the SunPerf math library from the compiler suite for maximum BLAS performance. Parallelization is accomplished using TCP/IP sockets and SystemV shared memory.