Professional Documents
Culture Documents
6 Spin-Orbit Calculations 33
6.1 Example 1: Ge with ECP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
6.2 Example 2: Hg with ECP . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
7 Dispersion Calculations 36
2
8 Running Band Structure and PDOS Jobs 37
8.1 The Usual Case: PDOS and BS Simultaneously . . . . . . . . . . . . . . . . 37
8.2 PDOS Only . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
8.2.1 Input Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
8.2.2 PDOS Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
8.3 Band Structure Only . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
8.3.1 Example Input File . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
8.3.2 Output Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
8.4 Obtaining BS/PDOS Later . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
8.5 Detailed Description of BS/PDOS IOps . . . . . . . . . . . . . . . . . . . . . 42
9 Symmetry 43
9.1 A Sample band.inp File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
9.2 Determining the SG for 3-D Systems . . . . . . . . . . . . . . . . . . . . . . 45
9.3 2-D Slabs/Films . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
9.4 1-D Monolayers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3
12.3.3 Module List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
12.3.4 Module Unload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
12.3.5 Modules & Submission . . . . . . . . . . . . . . . . . . . . . . . . . . 61
12.4 G09 Modules Available on STIC . . . . . . . . . . . . . . . . . . . . . . . . . 62
12.4.1 Applications Modules on STIC . . . . . . . . . . . . . . . . . . . . . 63
12.5 Modules Available on Group Workstations . . . . . . . . . . . . . . . . . . . 64
13 Scripts 65
13.1 PBS Submission Scripts (Rice-Specific) . . . . . . . . . . . . . . . . . . . . . 66
13.1.1 STIC Serial Job PBS Submission Script . . . . . . . . . . . . . . . . 66
13.1.2 STIC Parallel (Linda) Job PBS Submission Script . . . . . . . . . . . 67
13.1.3 DaVinci Parallel (Linda) Job PBS Submission Script . . . . . . . . . 68
13.1.4 BioU Serial Job PBS Submission Script . . . . . . . . . . . . . . . . . 69
13.2 PDOS Vertical Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
13.3 PDOS Horizontal Template . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
13.4 Band Structure: gpband Default . . . . . . . . . . . . . . . . . . . . . . . . 72
13.5 Band Structure: Modified AlSb (HISS) gpt File . . . . . . . . . . . . . . . . 73
13.6 BS and PDOS Multiplot Example . . . . . . . . . . . . . . . . . . . . . . . . 74
13.6.1 Header and Multiplot Set-Up . . . . . . . . . . . . . . . . . . . . . . 74
13.6.2 Band Structure Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
13.6.3 Band Structure Plot–II . . . . . . . . . . . . . . . . . . . . . . . . . . 76
13.6.4 The Rotated PDOS Plot-I . . . . . . . . . . . . . . . . . . . . . . . . 77
13.6.5 The Rotated PDOS Plot-II . . . . . . . . . . . . . . . . . . . . . . . 78
14 PBC Functionals 80
14.1 Scuseria Functionals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
14.2 Just-For-Solids Functionals . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
14.3 (Semi)Local Functionals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
14.4 Global Hybrids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
14.5 Functional Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
4
16 Backing Up Your Data 90
16.1 Using rsync: Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5
1 Conventions Used in this Document
• Input and Output files for/from a G09 job, when discussed in the text, will be in
green.
• Internal links to sections or files within this pdf file will be in a darker, navy blue.
• Directory paths on GUSCUS or any other machine will appear in, violet2.
• sgu1 is an imaginary Scuseria Group User with an ID in the style that Rice uses, which
is typically 3 initials from your name followed by a number. sgu1 appears in several
examples...
1.1 Examples
Generally, the EXAMPLES will be in monospace font and indented, e.g.
3. Scripts (PBS, etc.) if small enough, will be included in Section 13 of this document
or accessible locally by SCP from guscus:/projects/guscus/Manuals/scripts/.
4. Small Basis Sets for illustrative purposes will be included in Section 15. Links or
paths to a database, if one exists, will also be listed in this section. Note that the basis
sets are generally not small since we are not limited to H, He, Li and Be in the 21st
century.
All of these files should be immediately useable via cut-N-paste from this document. Acrobat
Reader should allow this, Evince does not always work. If not, there will always be some
template, somewhere. (But Acrobat works pretty much most of the time.)
6
Sec. 1: Conventions Used in this Document
The unmodified (HSE03) input files and basis sets from this paper are located at online.
Simply replace the route line below in those *.com files, with the recommended route in
Sections 3.2.2-3.2.3).
%chk= file.chk
#p HSEh1PBE/GenECP Int(Grid=UltraFine) Pop=Regular FMM=(print)
IOp1=timestamp IOp(5/13=1,5/33=1)
SCF=(NoVarAcc,NoIncFock,Tight)
7
2 Using the ICSD: Starting Structures
The ICSD Web database is located at icsd.fiz-karlsruhe.de. For Rice users free access is
available via IP address at icsd.fiz-karlsruhe.de.ezproxy.rice.edu.
• The red rectangle in the center shows you how you are logged in. If it does not show that
you are logged in through Rice then you have access to the full database. You cannot access
the full database at home, or remotely, since the license is via IP address.)
• The orange arrow to the right indicates how you can log in, and personalize your account.
This feature allows you to save your searches, which is very handy.
• The yellow rectangle to the right shows you all of the options available for the different
searches. Chemistry is the most frequently used option.
• NOTE: The contents of the center section change, depending upon the chosen option, while
the choices to the far left and right remain the same.
8
Sec. 2: Using the ICSD: Starting Structures
Figure 1: The ICSD page once you have logged in and are ready to begin a search.
Once you have clicked on “Chemistry” you will be provided with an empty form, as in
Figure 2.
1. Type in the element/compound/alloy/system you are interested in the line marked by
thered arrow This example is for bcc Cr.
2. Enter the number of elements in the system.orange arrow. (In this case “1”.)
3. Hit “Run Query” on the left. green arrow.
Figure 2: The ICSD page once you have logged in and are ready to begin a search.
Notice that the lower right of Figure 2 has saved searches, indicated by the blue arrow in
the lower left corner. You can save your searches and recall them as necessary.
9
Sec. 2: Using the ICSD: Starting Structures
The various crystal structures for your system available in the database then appear, as in
the Cr example discussed and in Figure 3, below.
1. It is better to use the most recent and/or highest quality structures, but in this example,
the “High Quality Data only” option does not reduce the number of structures. (See
the red arrow to the far left.)
2. The ICSD generally reports only the Hermann-Mauguin notation (HMN) to report the
symmetry elements in the space groups. See the orange arrow to the left. (The space
group in HMN and as number(s) are in the *.cif files.)
• The 4th column has the Structure Type, which is also listed in the band.inp file
names. So, since, we know we want bcc-Cr and it is a metal like W (Tungsten)
select the Im3̄m structure.
• - BUT - what if you do not know that much? Refer to Section ?? for more
information on determining symmetry in various dimensions.
3. Simply select the structure(s) with the space group(s) you need. See the Green arrow.
4. Click “Export Selected Data” at the top, right, as indicated by the blue arrow.
10
Sec. 2: Using the ICSD: Starting Structures
Figure 3: Some of the many crystal structures available for Cr on the ICSD.
Note that if the “Show Detailed View” button is clicked once the structure has been
selected (purple arrow of Figure 3), that significantly more information about the structure
appears, as shown in Figure 4.
1. The structure is a Jmol animation with free rotation in and out of the ICSD win-
dow/tab.
2. The Experimental section summarizes what can be found in the articles of the Bibli-
ography section.
3. The Warnings and Comments may be helpful in determining the quality of the structure
4. Once satisfied, click the Export CIF File button. (Circled in red.)
11
Sec. 2: Using the ICSD: Starting Structures
1. Enter the name of the cif file(s) in the form (circled in red.)
2. Click either “Single CIF FIle” or Multiple CIF Files to export. (red arrows.)
• In the Cr example, there will be only one file saved, with the name Cr_bcc.cif
• If multiple files are selected, they are saved as a zip file, with the filenames
Cr_bccX.cif , with X= 1, 2, 3, ... once they are extracted.
12
Sec. 2: Using the ICSD: Starting Structures
3. Notice that there are two other formats: *.csv and *.xls, if tabulated data is desired.
Figure 5: The Export Selected Data page for Cr cif file ID #44731.
NOTE:
GaussView can read *.cif files as is,
so once they are downloaded, you are ready to go!
13
Sec. 2: Using the ICSD: Starting Structures
;
The absorption and refraction corrections and the lattice constants of
chromium
;
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary ’Zhurnal Eksperimental’noi i Teoreticheskoi Fiziki’ 1964 47 476 479
ZETFA7
loop_
_publ_author_name
’Straumanis, M.E.’
’Weng, C.-C.’
_cell_length_a 2.88494(7)
_cell_length_b 2.88494
_cell_length_c 2.88494
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 90.
_cell_volume 24.01
_cell_formula_units_Z 2
_symmetry_space_group_name_H-M ’I m -3 m’
_symmetry_Int_Tables_number 229
14
Sec. 2: Using the ICSD: Starting Structures
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz (TRUNCATED)
1 ’z, y, -x’
2 ’y, x, -z’
3 ’x, z, -y’
4 ’z, x, -y’
5 ’y, z, -x’
6 ’x, y, -z’
7 ’z, -y, x’
8 ’y, -x, z’
9 ’x, -z, y’
10 ’z, -x, y’
11 ’y, -z, x’
12 ’x, -y, z’
13 ’-z, y, x’
14 ’-y, x, z’
15 ’-x, z, y’
16 ’-z, x, y’
17 ’-y, z, x’
18 ’-x, y, z’
19 ’-z, -y, -x’
20 ’-y, -x, -z’
. . .
15
Sec. 2: Using the ICSD: Starting Structures
4. Go to the directory you want and select the cif file you want
5. The file name should appear in parentheses in the first box e.g., “BaTiO3.cif”
6. Click the blue Open button to the left and GaussView will open the structure
7. A new window will open with the crystal structure inside the box defined by the lattice
parameters. (See the right image of Figure 7.)
• Note that the lower left corner contains information about the number of atoms, and
electrons as well as the charge and multiplicity.
• The information to the right will change upon selection of atoms or bonds.
Figure 7: GaussView for cif files. Left: The window to select and open a cif file in your
directory. Right: The periodic system with cell axes and atoms constructed from the cif
file by GaussView.
16
Sec. 2: Using the ICSD: Starting Structures
1. On the menu bar, select CALCULATE → Gaussian Calculation Setup... (See Figure 8.)
2. If you have already save a calculation scheme, you may do this, instead.
4. All requisite keywords/IOps discussed in Section 3 are input via the Additional Keywords
line.
5. Paths to basis sets or ECPs can be added via the Add. Input tab to the far right.
6. Store the file first by hitting the Retain button at the bottom (5th ) from the left.
7. Save it as a *.gjf file by going to the main window under FIle → Save.
17
3 PBC Input Files
The example below contains the minimal input file you will need for running
a PBC job. Copying the route and using it should ensure that any small test
PBC job will run reasonably smoothly.
CdS-Wurzite (hexagonal) using basis set from JJ Sowa xtal Solid State
Sciences 2005 7 73 78
0 1
Cd 0.00000000 2.38820939 0.00000000
S 0.00000000 2.38820939 2.53193200
Cd 2.06825000 1.19410469 3.35800000
S 2.06825000 1.19410469 5.88993200
Tv 4.13650000 0.00000000 0.00000000
Tv -2.06825000 3.58231408 0.00000000
Tv 0.00000000 0.00000000 6.71600000
@/projects/guscus/basis/cd-heyd.gbs/N
@/projects/guscus/basis/s-mHeyd2005.gbs/N
1. Link 0 commands: checkpoint file specification (%mem etc., added in *.pbs files)
2. The route
18
Sec. 3: PBC Input Files
• HSEh1PBE is the HSE06h version of HSE – the most current and accurate “flavor” of
HSE. USE THIS FOR HSE.
• Frequently used functionals are SVWN5, PBE, TPSS, PBEsol, and HISS.
• All other functionals, the appropriate keywords and/or IOps are tabulated in the Func-
tionals section, Section 14.
• References for the various functionals are also in Section 14 or may be found locally as
bib file at guscus:/projects/guscus/Manuals/functionals.bib.
3. GenECP – Basis set specification: read in a basis set and and an ECP
• To make valid energy comparisons among two or more jobs, the same grid must be used
and the Ultrafine grid is generally better for PBC calculations...
• Note that there are numerous ways to specify this grid: consult the G09 Keyword page
to see the other variations. (G09 input is essentially free-format, so case usually DOES
NOT matter.)
• Absolutely necessary for computing Band Structure and PDOS: leaving it out will result
in much distress. Section 8.1.
19
Sec. 3: PBC Input Files
• Using the Pop=FULL option will result in an... overly large file.
• Odds are, you will use these at some point: put them in your template and be glad
later.
7. Other important PBC IOps: (Check the G09 IOps Page for more details. These are all
Overlay 5 → Direct link to Overlay 5)
8. The SCF settings are key for both energy calculations and optimizations. Again,this is the
minimal route for a PBC job. See the specific keyword pages for more details.
• NoVarAcc – Do not use the default of modest integral accuracy early in direct SCF,
switching to full accuracy later on.
• NoIncFock – Prevents the use of incremental Fock matrix formation, and it is the
default for conventional SCF
• Tight – SCF=Tight, should be default: SCF details.
– Note that "tight" varies by Gaussian version for PBC, so explicitly stating this is
a safety measure.
– If in doubt, check your output file.
– There is a definite difference between HSE03 and HSE06.
• Cannot exceed five (5) lines and must be preceded and followed by a blank line.
• Do not use @ # ! - _ \ or any control characters (especially Ctrl-G)
• Use for “notes” e.g., recording the name, symmetry, ICSD ID and lattice parameters of
the compound, etc..
• Charge is the number to the left, multiplicity the number to the right.
20
Sec. 3: PBC Input Files
• For a neutral singlet, will usually see 0 1, but be aware of an older notation using
commas: 0,1
• The/N prevents the basis set from being printed at the beginning if the output file
• Alternatively, the basis set and/or ECP can be added to the end of the file, as in
molecular calculations
6. There are cases where additional specifications may be added to a file. For examples, review
the sample input files in Sections 4, 5, and 6.
This example, with the complete input file (including both basis sets)
and the corresponding output file is provided locally at:
guscus:/projects/guscus/Manuals/examples/CdS-wu/.
21
Sec. 3: PBC Input Files
Note that both the lattice parameters *and* the atomic positions
are relaxed within a gaussian PBC optimization.
%chk=CdS-wu_x.chk
#p HSEh1pbe/GenEcp Int(Grid=UltraFine) Pop=Regular FMM=(Print)
IOp1=timestamp IOpp(5/13=1,5/33=1,5/181=10,5/184=186)
SCF=(NoVarAcc,NoIncFock,Tight) Opt Guess=(Read,Fock)
4. The *chk files can become very, very large (hundreds of MB or even a tens of GB)
• If running a big job, back up the *chk file periodically. A corrupted checkpoint file
is an extremely sad thing
• The STIC/DaVinci/BlueBioU file systems can and *will* corrupt checkpoint files – such
is the price of cutting-edge computing.
22
Sec. 3: PBC Input Files
The best way to apply constraints in these geometry optimizations would be to use the keyword
Opt=ModRedundant, symbolic Z-matrices would not work well for PBC optimizations.
The trick in applying constraints to PBC geometry optimizations is to get the correct
numbering right. Note that the translation vectors count for the purpose of atom numbering even
though they are obviously not atoms and thus their numbers cannot be used directly to apply a
constraint. So, for example, if one wants to freeze the length of a translation vector, the constraint
would be to freeze the interatomic distance between an atom in the origin cell and the same atom
in the contiguous cell along the direction of the translation vector of interest.
In a 3-D periodic calculation, there are 8 cells to consider, the origin cell (O) and seven contiguous
cells (one along each one of the three translation vector, T1, T2 and T3, plus the four contiguous
cells along the diagonals, T1+T2, T1+T3, T2+T3, and T1+T2+T3). The following shows how
these cells are ordered for atom numbering purposes:
where N is the number of entries in the input file, that is the number of "real" atoms plus the three
translation vectors.
For instance, in the input file you sent here, you have 12 atoms plus the three translation vectors,
that makes N=15. If you were to freeze the length of the first translation vector (T1), you could
freeze, for instance, the interatomic distance between atom 1 (in cell O) and atom 61 (same atom
but in cell T1).
In your case, I see that you would like to constrain the lengths of T1 and T2 to be the same, not just
freeze the length. Unfortunately, the redundant internal set does not allow to impose the identity
condition between two coordinates. However, for this particular case, it would still be possible to
do what you are trying here.
In order to keep the lengths of T1 and T2 equal during the optimization, you could freeze the angle
between an atom in cell T1, the same atom in cell O, and the same atom in cell T1+T2. This angle
23
Sec. 3: PBC Input Files
should bisect the angle between T1-O-T2. So, given that your translation vectors form an angle
of 90 degrees, the T1-O-T1+T2 angle should be frozen to be 45.0 degrees, exactly at the bisection
(which implies that the two translation vectors will be equal in length). Below is an example of how
to do this for your input file.
0 5
V 1.27880629 4.44482660 -0.22374016
O 0.27860530 0.95052300 0.87756065
O 1.81959437 3.32683050 0.96076224
V 3.48744003 2.18167660 1.19205909
V 2.73205066 0.08147340 3.77512190
V 0.52341693 2.34462340 2.35932265
O 4.48764102 3.21367300 0.09075828
O 3.73225165 3.57577700 2.67382109
O -0.47678407 1.31262700 3.46062345
O 2.94665196 1.06368050 0.00755669
O 2.19126259 1.19946950 2.59061950
O 1.06420500 3.46261950 3.54382505
Tv 4.55460000 0.00000000 0.00000000
Tv 0.00000000 4.55460000 0.00000000
Tv 0.00000000 0.00000000 5.70280000
@v_towler.bas
@o_towler.bas
24
Sec. 3: PBC Input Files
3.5 Restarts
For both energy calculations and optimizations, adding Restart is sufficient, i.e.,
See also Section 3.4 for instructions on how to run constrained geometry optimizations
25
4 Antiferromagnetic Guess Calculations
The "Antiferromagnetic Guess" or "Spin-Flip" code for PBCS "flips" the spin
density for a given set of atoms. It is useful for generating AFM (antiferromag-
netic) guesses from FM (ferromagnetic) calculations.
4.1 Input
If the AFM guess is turned on, a list of atoms whose spin densities are to be flipped should be
specified after a blank line from the input file. This is best accomplished by running a two-part
calculation using Link 1. (See Section 4.2 for more details.)
1. The first part of the input file should be the "unflipped" system
3. Add –Link1–
4. The new route will include Guess=(Read,Fock), IOp(5/150=1) and NoSymm. The
NoSymm keyword prevents the reorientation and causes all computations to be performed
in the input orientation.
26
Sec. 4: Antiferromagnetic Guess Calculations
In the following example, the comments are actually *in* the G09 input file.
%chk=H.chk
#p PBEPBE/cc-pvtz
0,3
H 0.0000 0.000 0.0000
H 0.0000 0.000 1.1000
TV 0.0000 0.000 2.2000
--Link1--
%chk=H.chk
#p PBEPBE/cc-pvtz Guess={Read,Fock} IOp(5/150=1) NoSymm
0,1
H 0.0000 0.000 0.0000
H 0.0000 0.000 1.1000
TV 0.0000 0.000 2.2000
followed by the list of atoms and basis sets involved in the spin flipping.
The input and output files – with comments – are located locally at:
guscus:/projects/guscus/Manuals/AFMGuess/Example1-H.
27
Sec. 4: Antiferromagnetic Guess Calculations
%chk=Cr.chk
#p PBEPBE/LANL2DZ
PBE Cr
0,3
Cr 0.0000 0.000 0.0000
Cr 0.0000 0.000 2.4000
TV 0.0000 0.000 4.8000
--Link1--
%chk=Cr.chk
#p PBEPBE/LANL2DZ guess=read IOp(5/150=1)
PBE Cr
!
! **** note that total spin multiplicity here is 1.
!
0,1
Cr 0.0000 0.000 0.0000
Cr 0.0000 0.000 2.4000
TV 0.0000 0.000 4.8000
2nd line: Converged SCF energy corresponding to that of the singlet arising post spin-flip.
A sample version of the input and output with comments is located locally at:
guscus:/projects/guscus/Manuals/AFMGuess/Example2-Cr.
28
Sec. 4: Antiferromagnetic Guess Calculations
%chk=LTO.chk
#p UPBEpbe/GEN pseudo=read Int=Grid=Ultrafine
iop(5/13=1,5/33=1,3/18=1,3/65=-25) GFInput pop=regular SCF=tight
0,5
La,0,3.0649514287,-2.2692554128,-1.580103775
Ti,0,0.27940315,-2.4932384439,-3.5559414972
O,0,-2.2052614311,0.2766559378,-1.5802918116
O,0,1.4815133703,-0.890960693,-3.3214858263
La,0,-2.5045921227,2.8229404289,2.3702238711
La,0,0.2660765836,0.0554120936,2.3713792713
La,0,0.2942660209,0.4982535617,-1.5812458804
Ti,0,0.2793469199,-2.490041081,0.3961952352
Ti,0,-2.5196374746,0.2743011984,-3.5568557237
Ti,0,-2.5197041276,0.2775004992,0.3952969214
O,0,2.7656449004,0.277038938,2.3704292974
O,0,0.5937990896,-2.4894430993,2.3716929806
O,0,-0.0334301204,3.0431335943,-1.5815593191
O,0,-0.922206137,1.443200864,0.6296615465
O,0,-1.3188302628,-1.3219594526,4.112984379
O,0,1.8777073771,1.8772833843,0.1591920659
O,0,-0.9211487908,1.4446548897,4.1116294151
O,0,1.4825626149,-0.8895175017,0.1604564175
O,0,1.8791897066,1.8756333904,-3.322861073
O,0,-1.3173586107,-1.3236264087,0.6309382415
TV,0,5.5997593459,-0.0013274988,-0.0004424492
TV,0,0.0016897946,5.5337445538,-0.0022507369
TV,0,-0.0001024768,0.0064109731,7.9042794351
! used basis sets @2_mod_SVP_Ti.gbs, SVP_O.gbs, 2_SVP_La.gbs get from Fadwa El-Mellouhi
! fadwa.el_mellouhi@qatar.tamu.edu
%--------------------------------------------------
%chk=LTO.chk
#p UPBEpbe/GEN pseudo=read Int=Grid=Ultrafine
Guess(Read,Fock) IOp(5/13=1,5/33=1,3/18=1,3/65=-25,5/150=1) GFInput pop=regular SCF=tight
AntiFerromagnetic state will be obtained from the previous run by activating the IOP 5/150=1 indicating
to flip spin for the Ti atoms. Atoms 8 and 9 will have spin DOWN while 2 and 10 will keep spin UP.
0,1
La,0,3.0649514287,-2.2692554128,-1.580103775
Ti,0,0.27940315,-2.4932384439,-3.5559414972
O,0,-2.2052614311,0.2766559378,-1.5802918116
O,0,1.4815133703,-0.890960693,-3.3214858263
La,0,-2.5045921227,2.8229404289,2.3702238711
La,0,0.2660765836,0.0554120936,2.3713792713
La,0,0.2942660209,0.4982535617,-1.5812458804
Ti,0,0.2793469199,-2.490041081,0.3961952352
Ti,0,-2.5196374746,0.2743011984,-3.5568557237
Ti,0,-2.5197041276,0.2775004992,0.3952969214
O,0,2.7656449004,0.277038938,2.3704292974
O,0,0.5937990896,-2.4894430993,2.3716929806
O,0,-0.0334301204,3.0431335943,-1.5815593191
O,0,-0.922206137,1.443200864,0.6296615465
O,0,-1.3188302628,-1.3219594526,4.112984379
O,0,1.8777073771,1.8772833843,0.1591920659
O,0,-0.9211487908,1.4446548897,4.1116294151
O,0,1.4825626149,-0.8895175017,0.1604564175
O,0,1.8791897066,1.8756333904,-3.322861073
O,0,-1.3173586107,-1.3236264087,0.6309382415
TV,0,5.5997593459,-0.0013274988,-0.0004424492
TV,0,0.0016897946,5.5337445538,-0.0022507369
TV,0,-0.0001024768,0.0064109731,7.9042794351
Local versions of the input and output files (with comments) are located at:
guscus:/projects/guscus/Manuals/AFMGuess/Example3-LTO.
29
5 Variable Magnetic Moment Calculations
The Variable Magnetic Moment (VMM) code is similar to that of the AFM Guess.
For version G09-b1-pbc-2.3 the IOps are:
5.1 Input
1. The first part of the input file should be the "unflipped" system
4. Add –Link1–
5.2 Output
For final energy information:
30
Sec. 5: Variable Magnetic Moment Calculations
NOTE: The reference data is taken from Dr. Juan Peralta’s calculations run
with GDV-F.02. At the time of this writing, we used G09-B1. Please exercise
caution if using older or newer versions. Files are accessible locally at:
guscus:/projects/guscus/Manuals/VMM/Example1-Pd
%chk=Pd.ccpvtzpp.SVWN5.5.V06.chk
#p USVWN5/Gen Pseudo=read 5D 7F IOp1=timestamp
SCF=(Conver=8,MaxCycle=300,CDIIS,NoIncFock,NoVarAcc)
iop(5/33=1,5/13=1) PBC(NCellMin=120)
0,5
Pd .000000 .00000 .000000
Pd 0.000 0.000 3.000
Tv 0.0 0.0 6.0000
0,5
Pd .000000 .00000 .000000
Pd 0.000 0.000 3.000
Tv 0.0 0.0 6.000
31
Sec. 5: Variable Magnetic Moment Calculations
In the following example, the comments are actually *in* the G09 input file.
32
6 Spin-Orbit Calculations
The key is to use a gdv version that has Spin-Orbit Coupling implemented and to use IOp(3/117=1).
As of April 1, 2012, G09-B1 and gdv-H11 may be used with confidence, although gdv-H13 has
been tested.
%subst l302 ..
%KJob l302
#p USVWN5/Gen Pseudo=Read 5d 7F IOp1=tstamp gfprint
iop(3/117=1) NosSmm
--Link1--
%subst l502 ..
#p USVWN5/Gen Pseudo=Read 5d 7F IOp1=tstamp
SCF(maxcycle=60,conver=5)
PBC(cellrange=60,NKPoint=1000)
IOp(5/193=1)
IOp(5/155=3)
33
Sec. 6: Spin-Orbit Calculations
The output file provides the magnitude of the coupling via the cmd line: grep − A300 SCF D00
34
Sec. 6: Spin-Orbit Calculations
%subst l302 ..
%KJob l302
#p NoSymm UHF/Gen Pseudo=read 5d 7F SCF=NoVarAcc test
IOp(3/117=1)
0 1
Hg 0.0000 0.0000 0.0000
35
7 Dispersion Calculations
How to run Irek’s 2- and 3-body code based
36
8 Running Band Structure and PDOS Jobs
Generally, it is easier to run PDOS and band structure calculations at the same
time – if it becomes apparent that one part of the data is not needed, the
extraneous output can always be deleted. Nevertheless, be aware that band
structure and PDOS data tend to complement each other much of the time.
For the example route below, both PDOS and band data will be computed for the HSE single point
energy calculation of a monolayer of MoS2 .[1]
%chk=monohse.chk
#p HSEh1PBE/GenECP Int(Grid=UltraFine) pop=regular FMM=print
IOp1=timestamp iop(5/13=1,5/33=1)
SCF=(NoVarAcc,NoIncFock,Tight)
IOp(5/181=10,5/184=194)
NOTE:
1. Both band structure and projected densities of states data will be produced at the end of this
SPE calculation.
• If this had been an optimization, band structure data would appear at the end of each
opt cycle.
• Some PDOS data files appear during an energy calculation (see Section 8.2 but all files
do not appear until the job completes.
2. The IOp 5/181=10 indicates that G09 should calculate the PDOS.
3. The IOp 5/184=194 indicates that the k-path and labels for space group 194 (hexagonal)
have been provided in the band.inp file.
• The band.inp files are described in Section 9.1 and located locally at
guscus:/projects/guscus/Manuals/binps/.
• A band.inp file with the correct symmetry (see Section 9 must be copied, renamed and
placed in the same directory as your job.
4. The monolayer is a 2-D system, so a modified band.inp file was used for this calculation.
5. Ensure that your pbs or other submission file has the following line at the very end:
37
Sec. 8: Running Band Structure and PDOS Jobs
1. G09 input and output files: *.gjf and *.out (See Section 3.)
5. A multiplot gnuplot file both.gpt that produces the plot. (See Section 13.6.)
All relevant files to reproduce the plot in Figure 10 may be copied from:
guscus:/projects/guscus/Manuals/examples/MoS2mono
See Section 10 for explicit details on using Gnuplot for BS/PDOS plots.
12 12
Ss
Sp
10 Sd 10
Mos
Mop
8 Mod 8
Total
6 6
4 4
Energy (eV)
2 2
MoS2 Monolayer SPE
0 EF
HSE Gap 2.33 eV (D)
−2 −2
−4 −4
−6 −6
−8 −8
Γ M K Γ 1 2 3 4 5 6
K−Path PDOS (states/eV/unit cell)
Figure 10: An example of BS and PDOS as plotted using multiplot. The data is from the
HSE SP calc of an MoS2 monolayer, with a calculated direct band gap Eg of 2.33 eV. (See
#386, Appl. Phys. Lett. 99, 261908 (2011).)
38
Sec. 8: Running Band Structure and PDOS Jobs
2.5
Sis
Fermi level
Si (dia) Sip
HSE OPT Sid
2 Total
Eg = 1.22 eV (I)
PDOS (states/eV/unit cell)
0.5
0
-10 -8 -6 -4 -2 0 2 4 6 8 10
Energy (eV)
Figure 11: HSE opt of Si (dia) – horizontal. Figure 12: HSE opt of Si (dia) – vertical.
39
Sec. 8: Running Band Structure and PDOS Jobs
%chk=AlSb_x.chk
#p HSEh1PBE/GenECP Int(Grid=Ultrafine) fmm=(print) pop=regular
IOp1=timestamp iop(5/13=1,5/33=1) SCF=(NoVarAcc,NoIncFock,Tight)
IOp(5/181=200,5/184=227)
1. The number of the space group for your system needs to be input as the 5/184 argument in
the route of the input file. e.g., IOp(5/184=227) indicates an FCC system with space group
number 227.
3. The band.inp file, containing the appropriate K-path and coordinates for the Brillouin zone
for that space group must also be copied from the /binps directory (where ever it is) into the
running directory of your job and re-namedband.inp.
5. If the band.inp file is not present, the band structure code will choke, as the default is to
look for a band.inp file that will have the coordinates and K-path for the specified space
group.
1. band.dat This contains everything you need to plot band structure. The last 6 lines of the
file (tail -6 band.dat) provide the number of electrons, the HOCO and LUCO values, the
indirect gap (after scaling) and mGap1/MGap1.
2. bandk.dat This is in the work-up, but it is not as large as band.dat and is not necessary
once a gnuplot file has been set up.
40
Sec. 8: Running Band Structure and PDOS Jobs
%chk=AlN_x.chk
#p HSEh1PBE/ChkBas Geom=AllCheck Guess=(Read,Fock)
IOp1=timestamp iop(5/13=1,5/33=1)
IOp(5/181=10,5/184=227,5/14=20)
ChkBas reads the basis set information from the *chk file
Geom=AllCheck takes the title, charge, multiplicity and coordinates from the *chk file.
IOp 5/14=20 uses the BS data from the already computed real-space Fock matrix.
These 4 lines are sufficient to produce, in this case, both PDOS and BS for a FCC system in space
group 227.
• To turn off PDOS, which should usually run automatically as it is in most *pbs scripts, (See
Section 13) change the PDOS IOp to IOp(5/181=200).
• This “restart” is much faster than re-doing a full energy calculation, but is generally not
instant unless it is PDOS only.
• This usually works, but if the *chk file was corrupted or there was not band.inp file in place
for the restart from an good *chk file, all sorts of weirdness will ensue.
41
Sec. 8: Running Band Structure and PDOS Jobs
42
9 Symmetry
Formally, the “space group number” refers to the unique numbers (1-230) assigned to all space group
types, as defined by the International Union of Crystallography.
• Groups within the same crystal system or point group have consecutive numbers, otherwise,
the numbering is arbitrary.
• Not all space groups are represented by known compounds.
NOTE:
There are numerous systems to designate symmetry, so familiarity with the more
common systems will prove helpful when information other than SG is provided.
43
Sec. 9: Symmetry
KLABELS:
GM 0 0 0
K 3/8 3/8 3/4
L 1/2 1/2 1/2
U 5/8 1/4 5/8
W 1/2 1/4 3/4
X 1/2 0 1/2
KPATH: GM X W K GM L U W L K|U X
IMPORTANT:
• This external band.inp file is necessary because the internal library cannot always correctly
identify the symmetry, especially for space groups lower than 200. (The band structure code
looks for the band.inp file by default.)
• More importantly, band.inp files allow the path to be changed as necessary to match the
literature or, in the case of optimizations where the symmetry has changed, re-run the job
with the correct space group and path
• Again, the band.inp template files are in the /binps directory on guscusgw and
are named (1) according to space group and lattice and/or (2) labeled to indicate
any modifications or use in publications.
• Notice that fractions or decimal representations can be used, e.g., 1/2 or 0.5 for the coordi-
nates.
44
Sec. 9: Symmetry
The space group of crystal structure is usually included in the *.cif (or, less frequently *.pdf ) file
downloaded from a database, e.g., the ICSD or the AMS.
The space groups are numbers ranging from 1-230, as is seen to the far left column of Figure 13, which
contains also the “short symbols” to the far right, another commonly used symmetry designation.
1. The literature – the computational or experimental methods section(s) will include mention
the SG, or at least the “short symbol” designations.
2. The Energy Materials site maintained by Curtarolo’s group at Duke provides an online con-
verter at ACONVASP Online.
3. Similarly, the Aflow Library is a searchable database of band structures and related properties,
containing:
6. The Bilbao Crystallographic Server has numerous utilities that are updated, periodically, e.g.,
8. Materials-specfic GUIs such as Materials Studio, Vesta, XcrysDen, etc., that will determine
symmetry and convert to any of a number of primitive cell types.
45
Sec. 9: Symmetry
Figure 13: Table of Space Groups in 3-D. The SGs used as the argument for IOp 5/184
are located in the far left column, as numbers 1-230. The other common system, the “In-
ternational Short System” designations, are an abbreviated version of Hermman-Mauguin
notation and form the column to the far right. Other systems such as the Pearson for Struck-
turbericht designations are as not universally applicable, and are thus not as widely used.
(From: en.wikipedia.org/wiki/Space_group)
46
Sec. 9: Symmetry
Figure 14: 2D-Brillouin Zones. (a) Square, with lattice constant a, (b) Rectangular, with
lattice contants α1 , α2 , and, (c) Hexagonal with lattice constant a. (Taken from: Economou,
2010, Ref. [2])
1. The literature
2. Non-Gaussview software
47
10 Plotting BS and PDOS
10.1 A Basic PDOS Plot
Density of states plots are generally *MUCH* easier to work-up than BS data: simply use the
pdos.dat, pdos.legend.txt files generated by your job output and a *.gpt template file.
The pdos.dat file for am MgInS2 LSDA OPT looks like this:
# E/eV 0 Mg S a 0 Mg P a 0 In S a 0 In P a 0 In D a 0 S S a 0 S P a 0 S D a Total a
-42.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
-41.9800 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
-41.9600 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
-41.9400 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
-41.9200 0.0000 0.0006 0.0000 0.0000 0.0000 0.0000 -0.0000 0.0000 0.0006
-41.9000 0.0000 0.0026 0.0000 0.0000 0.0000 0.0000 -0.0000 0.0000 0.0026
-41.8800 0.0000 0.0097 0.0000 0.0000 0.0000 0.0000 -0.0000 0.0000 0.0097
-41.8600 0.0000 0.0335 0.0000 0.0000 0.0000 0.0000 -0.0000 0.0000 0.0334
-41.8400 0.0000 0.1067 -0.0000 -0.0000 0.0000 0.0000 -0.0001 0.0000 0.1066
-41.8200 0.0000 0.3143 -0.0000 -0.0000 0.0000 0.0001 -0.0004 0.0000 0.3139
-41.8000 0.0000 0.8543 -0.0000 -0.0000 0.0000 0.0001 -0.0011 0.0000 0.8534
-41.7800 0.0000 2.1437 -0.0000 -0.0000 0.0000 0.0004 -0.0027 0.0000 2.1413
-41.7600 0.0000 4.9656 -0.0000 -0.0000 -0.0000 0.0009 -0.0063 0.0000 4.9601
-41.7400 -0.0000 10.6178 -0.0001 -0.0001 -0.0000 0.0018 -0.0136 0.0001 10.6060
-41.7200 -0.0000 20.9583 -0.0001 -0.0002 -0.0000 0.0036 -0.0268 0.0002 20.9350
-41.7000 -0.0000 38.1885 -0.0003 -0.0003 -0.0000 0.0066 -0.0488 0.0003 38.1460
-41.6800 -0.0000 64.2341 -0.0004 -0.0005 -0.0000 0.0111 -0.0821 0.0005 64.1627
-41.6600 -0.0000 99.7368 -0.0007 -0.0008 -0.0000 0.0172 -0.1274 0.0007 99.6258
-41.6400 -0.0000 142.9556 -0.0009 -0.0011 -0.0000 0.0246 -0.1827 0.0011 142.7966
-41.6200 -0.0000 189.1489 -0.0012 -0.0014 -0.0000 0.0326 -0.2417 0.0014 188.9385
. . .
1 E(eV)
2 0 Mg S a
3 0 Mg P a
4 0 InS a
5 0 In P a
6 0 In D a
7 0 S S a
8 0 S P a
9 0 S D a
10 Total a
where the different orbitals for each atom are listed followed by the Total electron density. This
helps you determine the color scheme of your gnuplot output.
48
Sec. 10: Plotting BS and PDOS
1. Replace the argument for stub with the name of your PDOS *.dat file:
e.g., stub = ’MgInSlda’ → stub = ’YourPDOS’
2. Adjust the color scheme according the the pdos.legend.txt file, which will determine the
legend/key. (This is illustrated in the last eight (8) lines in the example below.)
reset # Avoids ugliness in Gnuplot if something went wrong in the previous compilation
HOCO = 0
LUCO = 4.1252
set arrow 1 from HOCO, graph 0 to HOCO, graph 1 nohead lc rgbcolor "dark-red" lw 1.5
set label 1 ’Fermi level’ at HOCO, graph 1 right rotate offset character 1, character -1
fa(x) = x
fb(x) = 0
plot 0 w l lt 0 notitle, \
stub . ’dat’ using 1:(fa($10)) w l ls 1 title ’Total’, \
stub . ’dat’ using 1:(fa($2)) w l ls 2 title ’Mg_s’ , \
stub . ’dat’ using 1:(fa($3)) w l ls 3 title ’Mg_p’ , \
stub . ’dat’ using 1:(fa($4)) w l ls 5 title ’In_s’ , \
stub . ’dat’ using 1:(fa($5)) w l ls 6 title ’In_p’ , \
stub . ’dat’ using 1:(fa($6)) w l ls 7 title ’In_d’ , \
stub . ’dat’ using 1:(fa($7)) w l ls 8 title ’S_s’, \
stub . ’dat’ using 1:(fa($8)) w l ls 9 title ’S_p’, \
stub . ’dat’ using 1:(fa($9)) w l ls 10 title ’S_d’
49
Sec. 10: Plotting BS and PDOS
• The files that are processed include band.dat bandk.dat and the *.out, hence the
admonition to run gpband in the job’s working directory.
• Note the numerous annotations within the script, describing the program and how the
band*.dat files are arranged.
• Of the many options, gpband nameoffile.dat seems to work the best, but feel
free to explore.
3. Copy the gnuplot and *.dat files to your desktop to plot the data. (There is no Gnuplot on
most Rice clusters.)
4. gpband prepares a basic gp file that runs to produce eps output – see Figure 15.
• The default color scheme is most likely not what will be used in the final plot.
• The lowest gap is generally plotted, but may be adjusted for aesthetic reasons.
• Labels, I-bars, additional lines and comments must be added by hand.
20
Figure 15: The band struc-
10 ture for AlSb optimized using
HISS. The command gpband
0 band.dat produced a Gnuplot
file, band-p.gp, ran it and cre-
Energy (eV)
50
Sec. 10: Plotting BS and PDOS
set arrow 11 \
Arrow for Fermi Level/VBM
from graph 0, first E(HOCO) \
to graph 1, first E(HOCO) nohead lt 19
set arrow 12 \
from graph 0, first E(LUCO) \
Arrow for CBM
to graph 1, first E(LUCO) nohead lt 20
51
Sec. 10: Plotting BS and PDOS
• The scale of the y-axis is now from -7 to 10, so it is easier to see the “camel-back” structure
of AlSb.
• The Fermi Level E = 0 is now labeled and the energy denoted as a horizontal black line
• The favored, indirect transition from Γ to somewhere near X is marked by both an arrow
and a green I-bar.
• The slightly higher in energy direct gap is marked only with an I-bar.
• Structure analysis, e.g., locating points on the bands that are not along the high-symmetry
k-lines for energy comparisons. Mining the data in the band*.dat files will be discussed in
Section 10.4.
10
6
Figure 16: The band struc-
4 ture for AlSb optimized
using HISS. The predicted
Energy (eV)
K X W K K L U W K|U X
All files necessary to produce this plot and that of Figure 15 are locally
available at guscus:/projects/guscus/Manuals/examples/AlSb-HISS.
The full gp files are also listed in Sections 10.3.4 and 13.5.
52
Sec. 10: Plotting BS and PDOS
1. an indirect gap between one k-point and a point in between two others
53
11 Increasing the Accuracy and Efficiency of PBC Jobs
For Starters: Read the Gaussian 09 manual entries for Molecule Specifications and the keywords:
PBC and FMM. (The input file information in Section 3 has more information for PBC.
Perhaps an FMM section would be useful...)
What not to do: If you want to put your computer system on its knees, try B3LYP with a diffuse
basis set on your favorite 3D system, e.g., diamond.
1. The near-field portion of the FMM without symmetry included will be very costly.
2. Symmetry is not implemented, yet, but we are working on it and even when it is, doping
and disorder lower the symmetry, anyway.
3. The HFx (Hartree Fock exchange) portion with diffuse basis functions (bfs), a full-range
1/r potential, and default cutoffs will take forever, and it is almost guaranteed that a
single iteration will exceed your patience.
Hybrids: Any with full (global) or long-range 1/r potential are significantly more expensive (10-
20x or even more) than short-range hybrids like HSE that were designed with solids in mind.
Be extremely careful if you want to do a PBC full or long-range hybrid.
Dimensionality: 3D calculations are more expensive than 2D, which are, in turn, much more
expensive than 1D. If you are not familiar with the PBC code and how to tune up its options,
we recommend that you start playing in 1D and move your way up to 2D/3D slowly.
Diffuse bfs: They may be needed in some specific cases and for some specific properties but in
general, it is a good idea to carefully analyze whether your chosen MOLECULAR basis set
(i.e., a basis set that was developed for atoms/molecules and usually contain fairly diffuse bfs
to describe atomic tails) is really needed for your PERIODIC system, which does not have
any density tail (well... it does if you are doing 1D or 2D, but not in 3D).
Linear dependencies: Our PBC code does not suffer from linear dependencies, i.e., if you use
a dense basis on a dense system and you end up with product bfs that are almost linearly
dependent (overlap matrix eigenvalue at some k-point below a certain threshold), the code
will remove the offending linear combination. However, there may be cases where the overall
accuracy is affected because of
1. Aggressive thresholds
2. A sloppy (or not accurate enough) xc quadrature grid, or,
3. A sloppy (or not accurate enough) Brillouin zone (k-point) integration grid.
In these cases, the SCF will die with some error message (with the cause not
trivially identifiable form the error message) being a combination of the above.
54
Sec. 11: Increasing the Accuracy and Efficiency of PBC Jobs
bf Exponents: As a practical matter, bfs with exponents smaller than 0.10-0.15 are problematic
and usually not needed. Removing them (i.e., adapting a molecular basis for an efficient
periodic calculation) is not required in our code (our numerics are usually robust enough to
deal with them) but it will surely make your calculations much faster and your life
much easier on thresholds.
Metals: Tread very carefully if your system is metallic. Metal calculations are tricky and costly.
1. Integration in k-point space is arduous. There are several options that can be tried
here if one has convergence problems in the SCF. A radical solution is to start from a
finite temperature calculation at ca. 1000 K and then try to cool off the system some
or converge ILT (or similar) from there.
2. Most PW calculations on metals are done at finite temperature, otherwise convergence
is rather difficult to achieve even with PW codes.
3. Diffuse and polarization functions are generally important for metals. Your cpu time will
go up because to achieve convergence you will need a larger basis than for semiconductors
or insulators and lots of k-points.¡
Semiconductors and Insulators: If you feel that your calculations are slow, there is plenty of
room of improvement by playing with many of the accuracy thresholds (explained in detail in
Izmaylov’s piece). The record for this type improvement may be the InAs case finely-tuned
by Ed Brothers: he was able to achieve a 20x speed-up by tuning thresholds (from default
values) with a minimal loss of accuracy for the band gap (less than 0.01 eV)
Density Fitting Gaussian provides the density fitting approximation for pure DFT calculations.
The desired fitting basis set is specified as a third component of the model chemistry, as in
this example:
#p BLYP/6-31G(d)/Auto
Note that the slashes are required when a density fitting basis set is specified. See the Basis
Sets entry in the Gaussian manual for more information.
CPU Time Monitor your cpu time with flags like #p and IOp1=timestamp, which will increase
cpu time printing and allow you to spot portions that are particularly expensive and amenable
to improvement by fine-tuning thresholds. See Section 3.
55
Sec. 11: Increasing the Accuracy and Efficiency of PBC Jobs
• NMtPBC is determined for k = 0. Unfortunately, the convergence of the Bloch sums with the
numberof cells depends on k for the Bloch sum form currently used in Gaussian. This is
usually not a problem; however, for diffuse functions, this may become a huge problem. The
number of cells may increase toward k = ±π. While the number of cells is enough at k = 0,
it may not be enough as k = ±π, and Gaussian will die with the error:
If this happens the only way around it is to increase the number of cells by forcing a larger
range: PBC=(CellRange=N). See the PBC keyword page. -OR- use less-diffuse basis
functions, since the calculations become prohibitively expensive with diffuse functions anyway.
• Due to the same problem of the form of the Bloch functions, the norms of the Bloch functions
become exponentially small when the exponents become small (norm ca. exp(−k 2 /a). The
norms are also k-dependent, so even if the near linear dependencies are eliminated at k = 0,
the norms of the Bloch functions may still be too small at other values of k. This condition
leads to warnings from subroutine ZFrmV2 of the form:
The only solution to this problem is to prune the diffuse basis functions (especially the p-type).
Gaussian removes the culprits, (see Section ?? but when this happens the basis functions are
too diffuse and is usually associated with the previous problem (not enough cells included in
PBC) or Gaussian dies with an error of the following type:
-------------------- ATTENTION--------------------
Total charge is not ZERO --- -0.002902253251
-------------------- ATTENTION--------------------
There is a problem with the total charge.
• There is also a problem with 5d/6d basis sets. See the Basis Sets entry in the Gaussian Õ09
manual. This problem can be exacerbated for periodic calculations, especially when using
a 5d basis set as a 6done, thus having an extra s-type function that can be nearly linear
dependent with the existing s-type functions. This is true the other way, too: a 6d basis set
may assume to have an extra s-type functions from the d-type shells.
• The rule of thumb for diffuse functions: the smallest exponent for s-type functions should be
larger than about αmin = 2/d2 , where d is the smallest distance between two atoms. The
exponent input in Gaussian is in Bohr −2 , so use d in Bohr.
56
Sec. 11: Increasing the Accuracy and Efficiency of PBC Jobs
11.3.1 Description
The PBC keyword allows you to specify options for Periodic Boundary Conditions jobs.
Note: PBC is turned on simply by including translation vectors in the input structure, and this
keyword is used only to control how PBC calculations are performed.
If you do not need any of these options, you do not have to include the keyword PBC to perform
a PBC calculation.
11.3.2 Options
GammaOnly Do just the Γ point (k = 0) rather than full k-integration.
• By default, if exact exchange is included, then this is twice the number of cells used for
overlap-related quantities and XC quadrature.
11.3.3 Availability
HF and DFT energy and optimizations. Not valid with SCRF or Charge. For periodic systems of
any reasonable size, acceptable performance may only be feasible by using a pure DFT functional
in combination with density fitting.
57
12 Submitting Jobs at Rice
The module system is employed on Scuseria Group workstations as well as on the shared com-
putational resources at Rice: BlueBioU, DaVinci and STIC. (An older machine, SUG@R is also
available, but is is non-ideal for PBC jobs.) A “condo” of Scuseria-Group-Only nodes exists on each
of the Rice clusters. Normally, it is more efficient to use the guscus condo (see Section 13), but
change the queue name to “common,” for access to the public nodes.
SUG@R - Shared University Grid @ Rice An older Intel Xeon compute cluster.
For general information, see the Getting Started documentation.
58
Sec. 12: Submitting Jobs at Rice
The following is the procedure for STIC, but the procedure works the same on all Rice computers.
1. Login via ssh
2. Source the .bashrc file containing the Gaussian paths in it: source /projects/guscus/.bashrc
3. cd to shared.scratch, e.g., cd /shared.scratch/sgu1
4. Type “module avail” to see what modules are available (See Section 12.3.1) for the output.)
-OR-
5. Type “module list” to confirm which modules are already loaded. (See Section 12.3.3)
6. Type “module load gdv-h11-hiss-and-pbc.2.3” to load the module for PBC calculations
(See Section 12.3.2.)
7. Check to see that the module loaded successfully by typing “module list” (See Section 12.3.3)
8. Run the script to create the *.pbs file (See Section 13 for the necessary scripts.)
9. Type ’qsub *.pbs’ to submit your job
10. Type ’qstat’ to see that your job was submitted and is in the queue you want it to be in...
STIC.RICE.EDU
****************IMPORTANT*******************
********************************************
59
Sec. 12: Submitting Jobs at Rice
The gaussian-related codes are listed in the top section, which includes G09, all usable gdv versions
and the Portland Group compilers. The bottom section lists various applications that may be of
use, like matlab.
• The g09- series are actual g09 versions, not development versions of the gaussian code.
• The most stable for PBC, with the most features and options is gdv-h11-hiss-and-pbc.2.3.
USE THIS unless otherwise instructed.
• gdv-h11-sol has PBEsol incorporated in it, but no PBC features like BS, PDOS, AFM,
VMM, SO or Dispersion.
60
Sec. 12: Submitting Jobs at Rice
61
Sec. 12: Submitting Jobs at Rice
Table 2: Gaussian Modules Currently Available (as of March 27, 2012) on STIC
[1] This version will eventually also include PBEsol, Irek’s dispersion code, any new Bulik
functionals and any other code that is to be used by many, PBC or not. This will be the version
that will be kept current.
62
Sec. 12: Submitting Jobs at Rice
Table 3: Applications Modules Currently Available on STIC (As of March 27, 2012), sorted
according to potential interest to the Scuseria Group.
63
Sec. 12: Submitting Jobs at Rice
64
13 Scripts
The scripts provided herein are optimized for quick cut-N-paste.
Alternatively, local users may copy them from:
guscus:/projects/guscus/Manuals/scripts
Questions, comments or better implementations are welcome.
Please feel free to contact Melissa Lucero.
Note: The script content may vary slightly as the OS for each cluster is
updated and or with new gdv/G09 versions. If in doubt, please feel free to
contact Irek W. Bulik or Melissa J. Lucero.
Last Modified March 29, 2012
65
Sec. 13: Scripts
if [ $# -eq 0 ]; then
cat <<EOF
USAGE:
${0##*/} Input NNodes WallTime_in_days
EOF
exit 1
fi
Inp=$1
if [ -z "$2" ]; then
echo "Wall Time Not Specified"
exit 1
fi
WALLTIME=$(( 24 * $2 )):00:00
InpBase=${Inp%.*}
InpBase=$InpBase
GAUSS_SCRDIR=/shared.scratch/\$USER/tmp/\$PBS_JOBID
export GAUSS_SCRDIR
\${GAUSS_MEMDEF:=2415919104}
cd \$PBS_O_WORKDIR
exec &>$InpBase.err
df -h
uname -a
printenv
EOF
66
Sec. 13: Scripts
if [ $# -eq 0 ]; then
cat <<EOF
USAGE:
${0##*/} Input NNodes WallTime_in_days
EOF
exit 1
fi
Inp=$1
NNodes=$3
if [ -z "$2" ]; then
echo "Wall Time Not Specified"
exit 1
fi
if [ -z "$NNodes" ]; then
echo "Number Of Nodes Not Specified"
exit 1
fi
WALLTIME=$(( 24 * $2 )):00:00
InpBase=${Inp%.*}
SubFile=$InpBase.pbs #Prepare submission script
InpBase=$InpBase
exec &>$InpBase.err
df -h
uname -a
printenv
LINDA_WORKERS=\$(cat \$PBS_NODEFILE |sort -u |tr ’\n’ ’,’ |sed ’s/,$//’)
time \$GAU <<EOGJF >"\$InpBase.out"
%nprocsh=6
%mem=23500mb
%LindaWorkers=\$LINDA_WORKERS
EOFPBS
cat $Inp >> $SubFile
echo "EOGJF" >> $SubFile
cat << EOF >> $SubFile
echo \$?
EOF
67
Sec. 13: Scripts
if [ $# -eq 0 ]; then
cat <<EOF
USAGE:
${0##*/} INPut NNODES
EOF
exit 1
fi
INP=$1
NNODES=$2
if [ -z "$NNODES" ]; then
echo "Number Of Nodes Not Specified"
exit 1
fi
INPBASE=${INP%.*}
INPBASE=$INPBASE
TIMEFORMAT="TIMING: %3R %3U %3S" # Format for bash time builtin
GAUSS_SCRDIR=/scratch/\$USER/tmp/\$PBS_JOBID
export GAUSS_SCRDIR
: \${GAUSS_MEMDEF:=2415919104}
cd \$PBS_O_WORKDIR
exec &>$INPBASE.err
df -h
uname -a
printenv
68
Sec. 13: Scripts
Inp=$1
#WALLTIME=$(( 24 * $2 )):00:00
InpBase=${Inp%.*}
SubFile=$InpBase.pbs #Prepare submission script
InpBase=$InpBase
cd \$PBS_O_WORKDIR
exec &>$InpBase.err
df -h
uname -a
printenv
time \$GAU <<EOGJF >"\$InpBase.out"
%mem=23500mb
EOFPBS
69
Sec. 13: Scripts
reset
set term postscript portrait enhanced dashed lw 2.0 color ’Times-Roman’ 20
set ytics 2.0 # THIS IS BASED ON A SMALL UNIT CELL, ADJUST AS NECESSARY
set xtics 0.5
# ARROWS
# The gray baseline along the y-axis
set arrow 1 from 0, graph 0 to 0, graph 1 nohead lc rgb ’dark-gray’ lw 1.0
set key at 2.40,9.50 right # X-coord of Upper Left Corner and Y-coord of Upper Right Corner
# PLOT THE DATA -- FIRST LINE IS DASHED BLACK LINE FOR FERMI LEVEL
plot 0 w l lt 2 lw 2.0 lc rgb ’black’ not,\
data using 2:1 w l ls 2 t ’Q_{/Helvetica-oblique s}’,\
data using 3:1 w l ls 3 t ’Q_{/Helvetica-oblique p}’,\
data using 4:1 w l ls 4 t ’Q_{/Helvetica-oblique d}’,\
data using 5:1 w l ls 1 t ’Total’
70
Sec. 13: Scripts
reset
set term postscript eps enhanced dashed dl 2.0 color ’Times-Roman’ 20
# PLOT RANGES
set lmargin 5.5
Si (dia) Sip
set style line 6 lt 4 lw 1.0 lc rgbcolor ’forest-green’ HSE OPT Sid
2 Total
set style line 7 lt 1 lw 1.0 lc rgbcolor ’gold’ Eg = 1.22 eV (I)
PDOS (states/eV/unit cell)
71
Sec. 13: Scripts
#! /usr/bin/gnuplot
reset
set encoding iso_8859_1
set terminal postscript eps enhanced color dl 2 "Times-Roman,18"
set output ’band.eps’
set macros
unset key
unset colorbox
set xlabel "k path"
set ylabel "Energy (eV)" offset 1.5,0
data = ’band.dat’
x1_GM = 0.000000
x2_X = 0.862114
x3_W = 1.293143
x4_K = 1.597934
x5_GM = 2.512322
x6_L = 3.258914
x7_U = 3.786839
x8_W = 4.091633
x9_K = 4.396424
x10_X = 4.701213
set xtics ( "{/Symbol G}" x1_GM, "X" x2_X, "W" x3_W, "K" x4_K, "{/Symbol G}" x5_GM, "L" x6_L, "U" x7_U, "W" x8_W, "K | U" x9_K, "X" x10_X )
E0 = 10.371738
cHOCO = 10
HOCO = 10.371738
cLUCO = 11
LUCO = 12.420518
EF = 10.371738
mGap = 3.058369
MGap = 8.405779
iGap = 2.048780
set arrow 11 \
from graph 0, first E(HOCO) to graph 1, first E(HOCO) nohead lt 19
set arrow 12 \
from graph 0, first E(LUCO) to graph 1, first E(LUCO) nohead lt 20
plot \
data using 1:(E($19)) t "27" with l ls 18, \
data using 1:(E($18)) t "26" with l ls 17, \
data using 1:(E($17)) t "25" with l ls 16, \
data using 1:(E($16)) t "24" with l ls 15, \
data using 1:(E($15)) t "23" with l ls 14, \
data using 1:(E($14)) t "22" with l ls 13, \
data using 1:(E($13)) t "21" with l ls 12, \
data using 1:(E($12)) t "20" with l ls 11, \
data using 1:(E($11)) t "19" with l ls 10, \
data using 1:(E($10)) t "18" with l ls 9, \
data using 1:(E($9)) t "17" with l ls 8, \
data using 1:(E($8)) t "16" with l ls 7, \
data using 1:(E($7)) t "15" with l ls 6, \
data using 1:(E($6)) t "14" with l ls 5, \
data using 1:(E($5)) t "13" with l ls 4, \
data using 1:(E($4)) t "12" with l ls 3, \
data using 1:(E($3)) t "11" with l ls 2, \
data using 1:(E($2)) t "10" with l ls 1
72
Sec. 13: Scripts
x1_GM = 0.000000
x2_X = 0.862114
x3_W = 1.293143
x4_K = 1.597934
x5_GM = 2.512322
x6_L = 3.258914
x7_U = 3.786839
x8_W = 4.091633
x9_K = 4.396424
x10_X = 4.701213
set xtics ( "{/Symbol G}" x1_GM, "X" x2_X, "W" x3_W, "K" x4_K, "{/Symbol G}" x5_GM, "L" x6_L, "U" x7_U, "W" x8_W, "K | U" x9_K, "X" x10_X )
E0 = 10.371738
cHOCO = 10
HOCO = 10.371738
cLUCO = 11
LUCO = 12.420518
EF = 10.371738
mGap = 3.058369
MGap = 8.405779
iGap = 2.048780
UCO2 = 12.700369
# LINE STYLES
set style line 1 lt 4 lw 0.7 lc rgbcolor ’dark-turquoise’ #k-point Vertical LINESS
set style line 2 lt 1 lw 1.0 lc rgbcolor ’black’ # BORING BANDS thin black line
set style line 3 lt 1 lw 2.5 lc rgbcolor ’black’ # BANDS OF INTEREST thicker black line c
set style line 4 lt 1 lw 2.5 lc rgbcolor ’red’ # VB Max ......................
set style line 5 lt 1 lw 2.5 lc rgbcolor ’blue’ # CB Min -----------------
plot 0 w l lt -1 not,\
E(LUCO) w l lt 2 lc rgbcolor "orange" not, \
data using 1:(E($19)) t "27" with l ls 5, \
data using 1:(E($18)) t "26" with l ls 5, \
data using 1:(E($17)) t "25" with l ls 5, \
data using 1:(E($16)) t "24" with l ls 5, \
data using 1:(E($15)) t "23" with l ls 5, \
data using 1:(E($14)) t "22" with l ls 5, \
data using 1:(E($13)) t "21" with l ls 5, \
data using 1:(E($12)) t "20" with l ls 5, \
data using 1:(E($11)) t "19" with l ls 5, \
data using 1:(E($10)) t "18-occ" with l ls 4, \
data using 1:(E($9)) t "17-occ" with l ls 4, \
data using 1:(E($8)) t "16-occ" with l ls 4, \
data using 1:(E($7)) t "15-occ" with l ls 4, \
data using 1:(E($6)) t "14-occ" with l ls 4, \
data using 1:(E($5)) t "13-occ" with l ls 4, \
data using 1:(E($4)) t "12-occ" with l ls 4, \
data using 1:(E($3)) t "11-occ" with l ls 4, \
data using 1:(E($2)) t "10-occ" with l ls 4
73
Sec. 13: Scripts
This gnuplot script is modified gpband output → gpband will *not* pro-
duce this file. Note that the length of this template necessitates that it be
broken into sections. Simply concatenate the parts discussed in the follow-
ing pages to obtain a working script or scp the full version located at gus-
cus:/projects/guscus/Manuals/scripts/both.gpt
# TERMINAL SET-UP
reset
set encoding iso_8859_1
set terminal postscript eps enhanced lw 2 color "Times-Roman,16"
unset key
unset colorbox
# SET MULTIPLOT
# --> 1 ROW, 2 COLUMNS, NO TITLE
74
Sec. 13: Scripts
x1_GM = 0.000000
x2_M = 0.969907
x3_K = 1.529883
x4_GM = 2.649834
set xtics ( "{/Symbol G}" x1_GM, "M" x2_M, "K" x3_K, "{/Symbol G}" x4_GM )
# LINE STYLES & EXTRA COLORS FOR LABELING VARIOUS BANDS WHEN NECESSARY
# -----> Note, there are more in the actual gpt file on guscus...
75
Sec. 13: Scripts
76
Sec. 13: Scripts
pdosdata = ’pdos.dat’
unset xlabel
unset ylabel
set xlabel ’PDOS (states/eV/unit cell)’
unset ytics
unset xtics
set xrange [*:*] # Use until you know your system, overwritten by line below.
set xrange [-0.1:6] # Adjust as is necessary
set xtics 1,1,6
set key
unset arrow
unset label
# I-BAR
set arrow 1 from 2,E(HOCO) to 2,E(LUCO) heads size .3,90 ls 10 lw 2 front
# ARROW
set arrow 2 from 2,0 to 2,E(LUCO) heads lw 0.8 front
77
Sec. 13: Scripts
78
Sec. 13: Scripts
79
14 PBC Functionals
14.1 Scuseria Functionals
Table 5: Functionals developed in the Scuseria Group sorted according to type. Note that
availability is variable. SR=Short -range, MR=Middle-range, and LR=Long-range.
Keyword and/or IOp Acronym(s) Citation(s) Availability/Notes
Global Hybrids
TPSSh TPSSh [5, 6] G09-B1 and higher
SR Screened Hybrids
HSEh1HSE HSE, HSE06H [7, 8, 9] Use this *always*
HSE1PBE HSE, HSE06 [8, 9]
HSE2PBE HSE03 [10]
MR Screened Hybrids
3/74=-61 HISS, HISSb [11] Use this!
G09-B, gdv-h11 (PBC)
3/74=-56 HISS, HISSb [11] Use this gdv-h1 (PBC)
3/74=-62 HISS-a [12] Don’t use; gdv-h11 (PBC)
3/74=-57 HISS-a [12] Don’t use; gdv-h1 (PBC)
LR Screened Hybrids
LC-wPBE LC-ωPBE [13] G09-B1 and higher
Semilocal
PBEPBE + 3/74=5050 PBEsol [14, 15] gdv-h11-sol; no PBC, yet...
TPSSTPSS TPSS [16]
Table 6: Functionals developed explicitly for solids, discussed and compared in the literature,
but not necessarily implemented widely. (Not an exhaustive list.)
Keyword and/or IOp Acronym(s) Citation(s) Availability/Notes
— AMO5 [17] Not available
— HSEsol [18] Not available
— HTBS [19] Not available
— MBJLDA [20] Not available
PBEPBE + 3/74=5050 PBEsol [14, 15] gdv-h11-sol; no PBC, yet...
80
Sec. 14: PBC Functionals
Table 7: Functionals commonly encountered by the solid state theoretician that are known
not to work well, but continue to be used, anyway. Arranged roughly according to the rungs
of the functional Jacob’s Ladder.[21]
Keyword and/or IOp Acronym(s) Citation(s) Availability/Notes
SVWN5 LSDA [22] G09-B1 and higher
“...use the LSDA with SVWN5”
LSDA LSDA, LDA [23] Never use
M06L M06L [24]
PBEPBE PBE [25, 26] Use this rather than PW91
PW91 PW91 [27] Less-clean version of PBE
PW92 PW92 [28] Not sure what this is
TPSSTPSS TPSS [16]
revTPSS revTPSS [29, 30, 31] Jian-Min says “eh.”
WC WC [32] Not sure about any of this
Table 8: Global hybrid functionals that have been applied to the extended systems. Note:
expect to expend extensive amounts of CPU time.
Keyword and/or IOp Acronym(s) Citation(s) Availability/Notes
B3LYP B3LYP [33] G09-B1 and higher
PBEh1PBE PBEh,PBE0 [34, 35] PBE hybrid → HSE
M06 M06 [36] Truhlar Suite
M06HF M06HF [37] Variation of above
M062X M062X [38] Variation of above
TPSSh TPSSh [5, 6] Not sure which
81
15 Basis Sets for Extended Systems
The format for PBC basis sets is the same as that for molecular basis sets. See the G09 Basis Set
and Gen/GenECP pages for more details. Generally, the basis sets will be called externally via
Gen/GenECP(or Pseudo=Read) or by specifying the path to the basis set preceded by an @
and terminated with a /N to prevent writing to the output file. (As in Section 3) The anatomy of
a G09 basis set file is as follows:
1. The shell descriptor line contains: the shell type, the number of primitive gaus-
sians, and the scale factor.
82
Sec. 15: Basis Sets for Extended Systems
WHY?
Molecular basis sets typically contain one or more few diffuse basis functions (bfs) in order
to properly describe atomic tails.
• A periodic system in 3-D does not need these tails, which will slow down your jobs.
(They slow the Coulomb near field of the fast multipole method.)[39]
• There are are some tails in lower dimensions, but these calculations are not as sensitive.
• See also Sections 11.1 and 11.2 and References [40, 41, 42] for additional, more detailed
discussion.
The Gaussian Basis Set FAQ prepared by Mike Towler provides a nice
introduction to the use of gaussian basis sets in PBC calculations.
A copy is also kept at: gusucs:/projects/guscus/Manuals/Towler.pdf
CAUTION:
→ A basis set properly optimized for previous PBC calculations may not
work as well when applied to a different system.
To address this potential issue:
1. Find an LSDA or GGA planewave calculation with PDOS or band gap data for the
system of interest
2. Run the LSDA/GGA calculation with the modified PBC gaussian basis set in G09
• If they are similar, (within 3-5 eV) then the modified PBC basis set is sufficient.
• If the gap is too large, and the basis sets for two or more atoms were modified,
the PDOS will usually indicate which basis set should be re-adjusted.
4. Keep in mind that the reference planewave calculation must be of reasonable quality.
In the case of no decent standard, common sense and experience must be employed.
For illustrative purposes, the next two sections include annotated examples of
PBC-optimized basis sets with and without effective core potentials (ECPs),
followed by a step-by-step example for chlorine.
83
Sec. 15: Basis Sets for Extended Systems
**** ****
Si 0 S 0
S 6 1.00 S 6 1.00
69379.2300000 0.0007570 69379.2300 0.757000000E-03
10354.9400000 0.0059320 10354.9400 0.593200000E-02
2333.8796000 0.0310880 2333.87960 0.310880000E-01
657.1429500 0.1249670 657.142950 0.124967000
214.3011300 0.3868970 214.301130 0.386897000
77.6291680 0.5548880 77.6291680 0.554888000
S 3 1.00 S 3 1.00
77.6291680 0.1778810 77.6291680 0.177881000
30.6308070 0.6277650 30.6308070 0.627765000
12.8012950 0.2476230 12.8012950 0.247623000
S 1 1.00 S 1 1.00
3.9268660 1.0000000 3.92686600 1.00000000
S 1 1.00 S 1 1.00
1.4523430 1.0000000 1.45234300 1.00000000
S 1 1.00 S 1 1.00
0.2562340 1.0000000 0.256234000 1.00000000
S 1 1.00 S 1 1.00
0.0942790 1.0000000 0.120000000 1.00000000
P 4 1.00 P 4 1.00
335.4831900 0.0088660 335.483190 0.886600000E-02
78.9003660 0.0682990 78.9003660 0.682990000E-01
24.9881500 0.2909580 24.9881500 0.290958000
9.2197110 0.7321170 9.21971100 0.732117000
P 2 1.00 P 2 1.00
3.6211400 0.6198790 3.62114000 0.619879000
1.4513100 0.4391480 1.45131000 0.439148000
P 1 1.00 P 1 1.00
0.5049770 1.0000000 0.504977000 1.00000000
P 1 1.00 P 1 1.00
0.1863170 1.0000000 <---- reset to 0.25 0.250000000 1.00000000
P 1 1.00 P 1 1.00
0.0654320 1.0000000 <---- reset to 0.12 0.120000000 1.00000000
D 1 1.00 D 1 1.00
0.4500000 1.0000000 0.450000000 1.00000000
**** ****
C 0 C 0
S 6 1.00 S 6 1.00
4563.2400000 0.00196665 4563.24000 0.196665000E-02
682.0240000 0.0152306 682.024000 0.152306000E-01
154.9730000 0.0761269 154.973000 0.761269000E-01
44.4553000 0.2608010 44.4553000 0.260801000
13.0290000 0.6164620 13.0290000 0.616462000
1.8277300 0.2210060 1.82773000 0.221006000
SP 3 1.00 SP 3 1.00
20.9642000 0.1146600 0.0402487 20.9642000 0.114660000 0.402487000E-01
4.8033100 0.9199990 0.2375940 4.80331000 0.919999000 0.237594000
1.4593300 -0.00303068 0.8158540 1.45933000 -0.303068000E-02 0.815854000
SP 1 1.00 SP 1 1.00
0.4834560 1.0000000 1.0000000 0.483456000 1.00000000 1.00000000
SP 1 1.00 SP 1 1.00
0.1455850 1.0000000 1.0000000 0.145585000 1.00000000 1.00000000
D 1 1.00 D 1 1.00
0.6260000 1.0000000 0.626000000 1.00000000
**** ****
84
Sec. 15: Basis Sets for Extended Systems
As 0
As 0
S 6 1.00
S 8 1.00
2542.81000 0.113700000E-02
2542.8100000 0.0011370
381.169000 0.605500000E-02
381.1690000 0.0060550
40.2342000 0.841250000E-01
40.2342000 0.0841250
16.1217000 -0.405285000
16.1217000 -0.4052850
3.20189000 0.712926000
3.2018900 0.7129260
1.42096000 0.473376000
1.4209600 0.4733760
S 6 1.00
0.3214430 0.0180130 <-------- deleted
2542.81000 -0.390000000E-03
0.1167350 -0.0037200 <-------- deleted
381.169000 -0.219000000E-02
S 8 1.00 <-------- Goes from 8 to 6 bc of deletions
40.2342000 -0.268530000E-01
2542.8100000 -0.0003900
16.1217000 0.136878000
381.1690000 -0.0021900
3.20189000 -0.320457000
40.2342000 -0.0268530
1.42096000 -0.337391000
16.1217000 0.1368780
S 1 1.00
3.2018900 -0.3204570
0.321443000 1.00000000
1.4209600 -0.3373910
S 1 1.00
0.3214430 0.6763840 <-------- deleted
0.120000000 1.00000000
0.1167350 0.5349800 <-------- deleted
P 6 1.00
S 1 1.00
99.5349000 0.385700000E-02
0.3214430 1.0000000
24.1195000 -0.851010000E-01
S 1 1.00
5.84196000 0.404762000
0.1167350 1.0000000 <-------- set to 0.12
2.56010000 0.531478000
S 1 1.00
1.09308000 0.184012000
0.0370000 1.0000000 <-------- deleted
0.318424000 0.576400000E-02
P 7 1.00 <-------- Goes from 7 to 6 bc of deletion
P 6 1.00
99.5349000 0.0038570
99.5349000 -0.772000000E-03
24.1195000 -0.0851010
24.1195000 0.199410000E-01
5.8419600 0.4047620
5.84196000 -0.107210000
2.5601000 0.5314780
2.56010000 -0.172259000
1.0930800 0.1840120
1.09308000 0.876100000E-02
0.3184240 0.0057640
0.318424000 0.569744000
0.1009720 -0.0003520 <-------- deleted
P 1 1.00
P 7 1.00 <-------- Goes from 7 to 6 bc of deletion
0.120000000 1.00000000
99.5349000 -0.0007720
D 6 1.00
24.1195000 0.0199410
113.509000 0.119800000E-01
5.8419600 -0.1072100
36.8872000 0.795440000E-01
2.5601000 -0.1722590
13.6893000 0.236755000
1.0930800 0.0087610
5.38964000 0.401534000
0.3184240 0.5697440
2.08046000 0.406686000
0.1009720 0.5356530 <-------- deleted
0.737568000 0.173162000
P 1 1.00
D 1 1.00
0.1009720 1.0000000 <-------- set to 0.12
0.307800000 1.00000000
P 1 1.00
****
0.0308000 1.0000000
D 7 1.00 <-------- Goes from 7 to 6 bc of deletion
AS 0
113.5090000 0.0119800
AS-ECP 4 10
36.8872000 0.0795440
G POTENTIAL
13.6893000 0.2367550
1
5.3896400 0.4015340
2 1.00000000 0.00000000
2.0804600 0.4066860
S-G POTENTIAL
0.7375680 0.1731620
2
0.3078000 0.0087300 <-------- deleted
2 28.72512200 370.11402500
D 1 1.00
2 6.76768100 9.34929600
0.3078000 1.0000000
P-G POTENTIAL
D 1 1.00
4
0.1000000 1.0000000 <-------- deleted
2 45.33106400 99.14210300
****
2 44.76741500 198.30788000
2 19.53909000 28.38307300
2 18.97347100 56.87146400
D-G POTENTIAL
6
2 51.05715200 -18.48514500
2 50.15134000 -28.11353000
2 16.10893600 -1.22389500
2 14.67222300 -1.34576500
2 3.85192700 0.10175700
2 3.81350200 0.17033800
F-G POTENTIAL
2
2 11.94058400 -0.77523000
2 17.76116000 -2.15725900
85
Sec. 15: Basis Sets for Extended Systems
General Procedure:
On the left is the original 6-311++G(3df) basis set for chlorine: all exponents with values of
0.15 have been marked with arrows. (Note that in Section 15.2.3, 0.12 is the minimum.) In the
column to the right, the values of the 2 marked exponents have been changed to 0.15.
ORIGINAL Cl 6-311++G(3df ) basis set from the EMSL 1st MODIFICATION Cl 6-311++G(3df ) basis set
Cl 0 Cl 0
S 6 1.00 S 6 1.00
105819.0000000 0.0007380 105819.0000000 0.0007380
15872.0000000 0.0057180 15872.0000000 0.0057180
3619.6500000 0.0294950 3619.6500000 0.0294950
1030.8000000 0.1172860 1030.8000000 0.1172860
339.9080000 0.3629490 339.9080000 0.3629490
124.5380000 0.5841490 124.5380000 0.5841490
S 3 1.00 S 3 1.00
124.5380000 0.1341770 124.5380000 0.1341770
49.5135000 0.6242500 49.5135000 0.6242500
20.8056000 0.2917560 20.8056000 0.2917560
S 1 1.00 S 1 1.00
6.5834600 1.0000000 6.5834600 1.0000000
S 1 1.00 S 1 1.00
2.5646800 1.0000000 2.5646800 1.0000000
S 1 1.00 S 1 1.00
0.5597630 1.0000000 0.5597630 1.0000000
S 1 1.00 S 1 1.00
0.1832730 1.0000000 0.1832730 1.0000000
P 5 1.00 P 5 1.00
589.7760000 0.0023910 589.7760000 0.0023910
139.8490000 0.0185040 139.8490000 0.0185040
45.1413000 0.0813770 45.1413000 0.0813770
16.8733000 0.2215520 16.8733000 0.2215520
6.7411000 0.7725690 6.7411000 0.7725690
P 2 1.00 P 2 1.00
6.7411000 -1.5722440 6.7411000 -1.5722440
2.7715200 0.9923890 2.7715200 0.9923890
P 1 1.00 P 1 1.00
1.0238700 1.0000000 1.0238700 1.0000000
P 1 1.00 P 1 1.00
0.3813680 1.0000000 0.3813680 1.0000000
P 1 1.00 P 1 1.00
0.1094370 1.0000000 <---------------------------------------> 0.1500000 1.0000000
SP 1 1.00 SP 1 1.00
0.0483000 1.0000000 1.0000000 <----------------------> 0.1500000 1.0000000 1.0000000
D 1 1.00 D 1 1.00
3.0000000 1.0000000 3.0000000 1.0000000
D 1 1.00 D 1 1.00
0.7500000 1.0000000 0.7500000 1.0000000
D 1 1.00 D 1 1.00
0.1875000 1.0000000 0.1875000 1.0000000
F 1 1.00 F 1 1.00
0.7000000 1.0000000 0.7000000 1.0000000
**** ****
86
Sec. 15: Basis Sets for Extended Systems
• The 1st modification (left column) results in a basis set with P (Sim1) and SP (Sim2) functions
with values of 0.15.
• Since they are virtually the same, pull out the SP function. (Marked *** YANKED *** in
the right column.)
• Notice a similar logic was used for the As basis set in Section 15.2.3.
Cl 0
Cl 0
S 6 1.00
S 6 1.00
105819.0000000 0.0007380
105819.0000000 0.0007380
15872.0000000 0.0057180
15872.0000000 0.0057180
3619.6500000 0.0294950
3619.6500000 0.0294950
1030.8000000 0.1172860
1030.8000000 0.1172860
339.9080000 0.3629490
339.9080000 0.3629490
124.5380000 0.5841490
124.5380000 0.5841490
S 3 1.00
S 3 1.00
124.5380000 0.1341770
124.5380000 0.1341770
49.5135000 0.6242500
49.5135000 0.6242500
20.8056000 0.2917560
20.8056000 0.2917560
S 1 1.00
S 1 1.00
6.5834600 1.0000000
6.5834600 1.0000000
S 1 1.00
S 1 1.00
2.5646800 1.0000000
2.5646800 1.0000000
S 1 1.00
S 1 1.00
0.5597630 1.0000000
0.5597630 1.0000000
S 1 1.00
S 1 1.00
0.1832730 1.0000000 <------------------ Sim3 --------------------->
0.1832730 1.0000000
P 5 1.00
P 5 1.00
589.7760000 0.0023910
589.7760000 0.0023910
139.8490000 0.0185040
139.8490000 0.0185040
45.1413000 0.0813770
45.1413000 0.0813770
16.8733000 0.2215520
16.8733000 0.2215520
6.7411000 0.7725690
6.7411000 0.7725690
P 2 1.00
P 2 1.00
6.7411000 -1.5722440
6.7411000 -1.5722440
2.7715200 0.9923890
2.7715200 0.9923890
P 1 1.00
P 1 1.00
1.0238700 1.0000000
1.0238700 1.0000000
P 1 1.00
P 1 1.00
0.3813680 1.0000000
0.3813680 1.0000000
P 1 1.00
P 1 1.00
0.1500000 1.0000000 <----------------- Sim1 ---------------------->
0.1500000 1.0000000
SP 1 1.00 <----------------- Sim2 ---------------->
# SP 1 1.00 (*** YANKED ***)
0.1500000 1.0000000 1.0000000 <------ Sim2 ------>
# 0.1500000 1.0000000 1.0000000 (*** YANKED ***)
D 1 1.00
D 1 1.00
3.0000000 1.0000000
3.0000000 1.0000000
D 1 1.00
D 1 1.00
0.7500000 1.0000000
0.7500000 1.0000000
D 1 1.00
D 1 1.00
0.1875000 1.0000000
0.1875000 1.0000000
F 1 1.00
F 1 1.00
0.7000000 1.0000000
0.7000000 1.0000000
****
****
87
Sec. 15: Basis Sets for Extended Systems
15.3.1 Example: Ge
The process for acquiring the Ge 6-311G* basis set for use in gaussian is illustrated in Figure 18.
Specifically:
Notice that information about the basis set chosen appears in the bottom section (purple rectangle).
Figure 18: The process for acquiring the Ge 6-311G* basis set in gaussian format.
88
Sec. 15: Basis Sets for Extended Systems
Sc_864-11G*_harrison_2006 ! Sc_864-11G*_harrison_2006
! N. M. Harrison, B. Montanari, Ling Ge, 2006, unpublished.
21 6 ! It is being used for Sc@C82 and Sc@C82@SWNT
0 0 8 2. 1. ! (single-wall carbon nanotube).
208000. 0.000225 Sc 0
29700. 0.001927 S 8 1.0
6280.0 0.011094 208000.0000000000 2.2500000000E-04
1642.0 0.04997 29700.0000000000 1.9270000000E-03
494.64 0.17014 6280.0000000000 1.1094000000E-02
170.62 0.3688 1642.0000000000 4.9970000000E-02
66.62 0.4029 494.6400000000 1.7014000000E-01
27.72 0.1449 170.6200000000 3.6880000000E-01
0 1 6 8. 1. 66.6200000000 4.0290000000E-01
499.4 -0.00558 0.00851 27.7200000000 1.4490000000E-01
118.53 -0.0738 0.06021 SP 6 1.0
39.01 -0.1160 0.2129 499.4000000000 -5.5800000000E-03 8.5100000000E-03
15.20 0.2493 0.3847 118.5300000000 -7.3800000000E-02 6.0210000000E-02
6.511 0.6985 0.4028 39.0100000000 -1.1600000000E-01 2.1290000000E-01
1.998 0.323 0.183 15.2000000000 2.4930000000E-01 3.8470000000E-01
0 1 4 8. 1. 6.5110000000 6.9850000000E-01 4.0280000000E-01
25.09 0.0016 -0.0331 1.9980000000 3.2300000000E-01 1.8300000000E-01
9.62 -0.1360 -0.0713 SP 4 1.0
3.979 -0.7059 0.1465 25.0900000000 1.6000000000E-03 -3.3100000000E-02
1.612 1.018 1.452 9.6200000000 -1.3600000000E-01 -7.1300000000E-02
0 1 1 2. 1. 3.9790000000 -7.0590000000E-01 1.4650000000E-01
0.780 1. 1. 1.6120000000 1.0180000000 1.4520000000
0 1 1 0. 1. SP 1 1.0
0.390 1. 1. 0.7800000000 1.0 1.0
0 3 3 1. 1. SP 1 1.0
3.940 0.160 0.3900000000 1.0 1.0
1.072 0.313 D 3 1.0
0.394 0.406 3.9400000000 1.6000000000E-01
1.0720000000 3.1300000000E-01
N. M. Harrison, B. Montanari, Ling Ge, 2006, unpublished. 0.3940000000 4.0600000000E-01
It is being used for Sc@C82 and Sc@C82@SWNT ****
(single-wall carbon nanotube).
The Sc_864-11G*_harrison_2006 Crystal basis set *.cry on the left was converted to a gaussian-
formatted *.gbs file using the gbsutil script written by Cris Diaconu.
Download the original Sc.cry file at the link above, or copy it locally, along
with the Sc.gbs file from: guscus:/projects/guscus/Manuals/examples/.
The gbsutil script is too long to include in Section 13, so a copy is available
at guscus:/projects/guscus/Manuals/scripts/gbsutil.
89
16 Backing Up Your Data
Given that the state-of-the-art filesystems can crash and there are monthly purges of /shared.scratch/
on all Rice clusters (See Section 12) it is a good idea to back up all data you might want. Especially
since PBC jobs tend to run long, the gjf , out, chk and all BS and PDOS dat files may be of import
later. The easiest and fasted way to accomplish routine backups is via the rsync command: rsync
-aHVhu, where
(2) Alternatively, an exclude file may be used. This is useful to prevent backing up all *err files,
pdos.d directories, large chk files for unfinished jobs and anything else not needing to be saved.
90
Sec. 16: Backing Up Your Data
The output from adding the --̇exclude-from /users/sgu1/xclud option to the rsync command
to back up a STIC directory with subdirectories AlAs-wu2PBE, CdSe-wu, GaN-wu, InP-B3LYP
and MgO is shown below.
[sgu1@guscus STIC]$ rsync -aHvhu --exclude-from /users/sgu1/xclud sgu1@stic:/shared.scratch/sgu1/
sgu1@stic’s password:
receiving file list ... done
AlAs-wu2PBE/
AlAs-wu2PBE_x.out
AlAs-wuPBE/band.dat
AlAs-wu2PBE/bandk.dat
AlAs-wu2PBE/pdos.legend.txt
CdSe-wu/
CdSe-wu/OPT/
CdSe-wu/OPT/CdSe-wu_o.out
CdSe-wu/OPT/band.dat
CdSe-wu/OPT/bandk.dat
CdSe-wu/OPT/pdos.dat
CdSe-wu/OPT/pdos.eps
CdSe-wu/OPT/pdos.gpt
CdSe-wu/OPT/pdos.png
CdSe-wu/OPT/pdos.legend.txt
GaN-wu/LSDA/XTAL/
GaN-wu/LSDA/XTAL/README
GaN-wu/LSDA/OPT/GaN-w2-LSDAo.chk.bz2
GaN-wu/LSDA/OPT/GaN-w2-LSDAo.out
GaN-wu/LSDA/OPT/band.dat
GaN-wu/LSDA/OPT/bandk.dat
InP-B3LYP/
InP-B3LYP/InP-z-B3LYPx.chk.bz2
InP-B3LYP/InP-z-B3LYPx.gjf
InP-B3LYP/InP-z-B3LYPx.out
InP-B3LYP/InP-z-B3LYPx.pbs
InP-B3LYP/band.dat
InP-B3LYP/bandk.dat
InP-B3LYP/pdos.dat
InP-B3LYP/pdos.legend.txt
MgO/
MgO/HSE/XTAL/
MgOHSE/XTAL/deleteme
MgO/HSE/OPT/
MgO/HSE/OPT/MgO-rs_o.chk.bz2
MgO/HSE/OPT/MgO-rs_o.gjf
MgO/HSE/OPT/MgO-rs_o.out
MgO/HSE/OPT/MgO-rs_o.pbs
MgO/HSE/OPT/pdos.dat
MgO/HSE/OPT/pdos.legend.txt
MgO/TPSS/
MgO/TPSS/MgO-TPSSx.chk.bz2
MgO/TPSS/MgO-TPSSx.gjf
MgO/TPSS/MgO-TPSSx.out
MgO/TPSS/Readme-2-this-is-weird
Si-TPSS/Si-d-TPSSx.out
Notice that none of the files or directories specified in the xclud file on the previous page are down-
loaded, while non-gaussian-generated files including text (README, deleteme, etc.), image
(eps, png), Gnuplot (gpt), and BS/PDOS dat files are all copied recursively.
rsync cmds as aliases are very convenient, e.g., in the .bashrc file:
alias stics=’rsync -aHvhu --̇exclude-from /users/sgu1/xclud sgu1@stic:/shared.scratch/sgu1/ ./’
91
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