0 views

Uploaded by Srashmi

- 62 1 60 Einstein Nanocrystal
- A Chronotopic Model of Mobility in Urban Spaces
- Systematic Synthesis of Functionally New Distillation Systems for Five Component Separations
- Optimization Plate Fin Heat Exchanger.pdf
- xuchuanliangIMF13-16-2008
- Barreira - Dynamical Systems - An Introduction.pdf
- Exam Review
- XenoView Manual
- UCSF OCPD 2017 Liberal Arts College (BAC)- Chemistry
- Chaos Cvitanovic
- 1506.06928v2
- Lab05.pdf
- D_Mia Ledyastuti.pdf
- Mathematical Ecology
- Adaptive Robust
- Paper_COB_2015_2449.pdf
- Hamiltonian Process
- j Me 751352061000
- OPTIM Report Bancora Venkateswaran
- 01177568

You are on page 1of 34

calculation of vibrational spectrum

Marivi Fernandez-Serra

CECAM

Born-Oppenheimer dynamics

electronic

decoupling

nuclear

Extracting information from the Potential

Energy Surface (PES)

-We move on the PES -We move over the PES

- Local vs global minima - Good Sampling is required!!

- PES is harmonic close to minima

Theory of geometry optimization

Gradients Hessian

Methods of optimization(I)

Ill conditioning:

convergence

Steepest descent: Move in the

direction of maximum

incline.

If all are equal

Methods of optimization(II)

- conjugate gradients (retains information)

directions are orthogonal to previous ones.

Methods of optimization(III)

- Newton-Raphson: An approximation of H at a position (Xk) is

calculated. Then finding the inverse of that Hessian (H-1), and solving the

equation P = -H-1*F(Xk) gives a good search direction P. Later, a line

search procedure has to determine just how much to go in that direction

(producing the scalar alpha). The new position is given by: Xk+1 = Xk +

alpha*P

Basic idea, update the Hessian along the minimization to fit:

BFGS

Optimization (and MD) general basic Step.

Optimization in SIESTA(1)

MD.TypeOfRun CG, Broyden

• Set maximum number of iterative steps:

MD.NumCGsteps 100

• Optionally set force tolerance:

MD.MaxForceTol 0.04 eV/Ang

• Optionally set maximum displacement:

MD.MaxCGDispl 0.2 Bohr

Optimizations in SIESTA(2)

• To allow unit cell to vary:

MD.VariableCell true

• Optionally set stress tolerance:

MD.MaxStressTol 1.0 Gpa

• Optionally set cell preconditioning:

MD.PreconditionVariableCell 5.0 Ang

• Set an applied pressure:

MD.TargetPressure 5.0 GPa

Advice on optimizations in SIESTA(I)

• Make sure that your MeshCutoff is high enough:

- Mesh leads to space rippling

- If oscillations are large convergence is slow

- May get trapped in wrong local minimum

Advice on Optimizations in SIESTA(II)

optimizations, very sensitive to mesh cuttof.

Fixed to Si Bulk

Advice on Optimizations in SIESTA(III)

separately different parts of the system).

Look at the evolution of relevant physics quantities

(band structure, Ef).

Fix the Zeolite,

Its relaxation is no

Longer relevant.

No constraints Ftube<0.04 eV/A

Fzeol>0.1 eV/A

Molecular Dynamics

•Follows the time evolution of a system

•Solve Newton’s equations of motion:

2

dE d x (t )

F (t ) = r = m a (t ) = m

dx dt 2

•Treats electrons quantum mechanically

•Treats nuclei classically

•Hydrogen may raise issues:

- tunnelling (overestimating Energy

barriers)

•Allows study of dynamic processes

•Annealing of complex materials

•Examines the influence of temperature

• Time averages Vs Statistical averages

Ergodicity

• In MD we want to replace a full sampling on the appropriate statistical

ensemble by a SINGLE very long trajectory.

• Ergodic Hypothesis:

Hypothesis a phase point for any isolated system passes in

succession through every point compatible with the energy of the

system before finally returning to its original position in phase space.

This journey takes a Poincare cycle.

hypothesis each state consistent with our

knowledge is equally “likely”.

– Implies the average value does not depend on initial conditions.

conditions

– <A>time= <A>ensemble , so <Atime> = (1/NMD) = t=1,N At is good

estimator.

– Non-ergodic examples are glasses, folding proteins (in practice)

and harmonic crystals (in principle).

Different aspects of ergodicity

• The system relaxes on a “reasonable” time scale towards a

unique equilibrium state (microcanonical state)

eventually sampling all of accesible phase space.

to initial conditions). Lyapunov exponent.

statistical methods on MD of small system. Small

round-off errors and other mathematical

approximations may not matter.

Particle in a smooth/rough circle

Haile: MD Simulations

Molecular Dynamics(I)

positions and velocities with time, solving Newton’s equations.

2

dE d x (t )

F (t ) = r = m a (t ) = m 2

dx dt

t t'

x (t ) = x (t0 )+ v (t0 ) (t t0 ) + dt' 1

F (t '')dt''

t0 t0 m

Molecular Dynamics(II)

• Initialize positions and momenta at t=0 (initial conditions in space and time)

– We need to make time discrete, instead of continuous!!!

• Estimate errors

Molecular Dynamics III

frequency motion

• Typical timestep is 1 fs (1 x 10-15 s)

• Typical simulation length = Depends on the system of study!!

(the more complex the PES the longer the simulation time)

• Is this timescale relevant to your process?

• Simulation has two parts:

- equilibration (redistribute energy)

System is equilibrated if averages of dynamical and

structural quantities do not change with time.

- production (record data)

• Results:

- diffusion coefficients

- Structural information (RDF’s,)

- free energies / phase transformations (very hard!)

• Is your result statistically significant?

Choosing the integrator

high derivatives, or are evaluated with limited precision.

to completely different trajectories (Ergodicity

(Ergodicity!).

!). Statistical averages are the

relevant quantities; they do not depend on the details of the trajectories (IF

the simulation is long enough!!!!).

• Because of this, and since potentials are not perfect (all potential models are

approximations to the real ones), one does not need too much accuracy in

the integration of the equations of motion (as long as errors are not too

large, and they do not affect fundamental properties such as conserved

quantities).

energy conservation of the order of 0.01 kT.

kT.

Therefore, it is preferable to choose algorithms that require few evaluations

of the forces, and do not need higher derivatives of the potential.

Verlet algorithm

The most commonly used algorithm:

r(t+h) = r(t) + v(t) h + 1/2 a(t) h2 + b(t) h3 + O(h4) (Taylor series expansion)

r(t-h) = r(t) - v(t) h + 1/2 a(t) h2 - b(t) h3 + O(h4)

• Trajectories are obtained from the first equation. Velocities are not necessary.

• Errors in trajectory: O(h4)

• Preserves time reversal symmetry.

• Excellent energy conservation.

• Modifications and alternative schemes exist (leapfrog, velocity Verlet),

Verlet), always

within the second order approximation

• Higher order algorithms: Gear

When do we use MD?

• Amorphous systems:

• Molecular Liquids (H2O,CO2)

• Glasses (Si, SiO2)

• Displacive Phase transitions (P and T

relevant).

• Study of kinetic effects.

• Diffusion at surfaces

• Thermal stability

Different ensembles, different Lagrangians,

different Conserved magnitudes.

• NVE (Verlet):

• NVT (Nose):

Microcanonical. Canonical

• Integrates Newtons equations of • System in thermal contact with a

motion, for N particles, in a fixed heat bath.

volume V. • Extended Lagrangian:

• Natural time evolution of the • N particles + Thermostat, mass

system: E is a constant of motion Q.

Rahman) (isobarical) Parrinello-Rahman)

• Extended Lagrangian • 2 Extended Lagrangians

• Cell vectors are dynamical • NVT+NPE.

variables with an associated

mass.

Nose-Hoover thermostat

• Introduce a friction force (t)

SYSTEM

dp T Reservoir

= F(q, t) (t ) p(t)

dt

Dynamics of friction coefficient to get canonical ensemble.

d 1 2 3N Feedback makes

Q = mivi k BT K.E.=3/2kT

dt 2 2

Hints

system, better high energy frequency

Which Ensemble should we use?

Canonical

• Good trajectories.

• Time reversible (up to Same sampling

numerical error) In the • Good T control

• Dynamical variables are well thermodynamic limit • Equilibrates the system.

defined.

• Initial X and V are relevant: • Choice for Structural

necessity of equilibration. sampling.

• Sensitive to Nose mass.

Rahman) Parrinello-Rahman)

• Phase transitions • Phase transitions under

systems under P and T

pressure. • 2 mass parameters,

• 1 mass parameter barostat and thermostat.

(Fluctuations!!

(barostat)

Molecular Dynamics in SIESTA(1)

• MD.TypeOfRun Verlet

NVE ensemble dynamics

• MD.TypeOfRun Nose

NVT dynamics with Nose thermostat

• MD.TypeOfRun ParrinelloRahman

NPE dynamics with P-R barostat

• MD.TypeOfRun NoseParrinelloRahman

NPT dynamics with thermostat/barostat Variable

• MD.TypeOfRun Anneal Cell

Anneals to specified p and T

Molecular Dynamics in SIESTA(2)

MD.InitialTimeStep 1

MD.FinalTimeStep 2000

• Setting the timestep:

MD.LengthTimeStep 1.0 fs

• Setting the temperature:

MD.InitialTemperature 298 K Maxwell-Boltzmann

MD.TargetTemperature 298 K

• Setting the pressure:

MD.TargetPressure 3.0 Gpa

• Thermostat / barostat parameters:

MD.NoseMass / MD.ParrinelloRahmanMass

Annealing in SIESTA

MD.Quench true

- zeros velocity when opposite to force

• MD annealing:

MD.AnnealOption Pressure

MD.AnnealOption Temperature

MD.AnnealOption TemperatureAndPressure

• Timescale for achieving target

MD.TauRelax 100.0 f

Vibrational spectrum: Phonons

Matrix (Harmonic approximation).

• Numerical evaluation of the second derivatives. (finite differences).

Harmonic

Approx. • Density Functional Perturbation Theory (Linear Response):

• Perturbation theory used to obtain analytically the Energy second derivatives within a

self consistent procedure.

• Link between time correlation functions and the response of the system to weak

Beyond perturbations.

Harmonic Approx.

Approx

Phonons in Siesta (I)

MD.TypeOfRun FC

Dynamical matrix: Vibra Suite (Vibrator)

Phonons in Siesta (II)

Phonons and MD

1. MD simulations (NVE)

2. Fourier transform of

Velocity-Velocity autocorrelation function.

1. Anharmonic effects: (T)

2. Expensive, but information available for MD

simulations.

- 62 1 60 Einstein NanocrystalUploaded byCassie Minor
- A Chronotopic Model of Mobility in Urban SpacesUploaded byZerattull
- Systematic Synthesis of Functionally New Distillation Systems for Five Component SeparationsUploaded byMassimilianø Erricø
- Optimization Plate Fin Heat Exchanger.pdfUploaded byEmilio José Berciano Rueda
- xuchuanliangIMF13-16-2008Uploaded byPavan Sandeep V V
- Barreira - Dynamical Systems - An Introduction.pdfUploaded bypedrohenrique1989
- Exam ReviewUploaded byAshwin Dollar
- XenoView ManualUploaded bysrokkam
- UCSF OCPD 2017 Liberal Arts College (BAC)- ChemistryUploaded byVishnu
- Chaos CvitanovicUploaded byfabianaristo
- 1506.06928v2Uploaded byKartikeya Singh
- Lab05.pdfUploaded byShweta Sridhar
- D_Mia Ledyastuti.pdfUploaded bykroidman
- Mathematical EcologyUploaded byTiffany Knapp
- Adaptive RobustUploaded byrdehghan66
- Paper_COB_2015_2449.pdfUploaded byAlex Brandão
- Hamiltonian ProcessUploaded byLe Tung
- j Me 751352061000Uploaded byluisparedes
- OPTIM Report Bancora VenkateswaranUploaded bySwaminath Venkateswaran
- 01177568Uploaded byLusi JeLita Sari
- Articulo Phenomena Transport.docUploaded bySergio Lesmes
- Before Optimization_ Design Space ExplorationUploaded bymivano
- 10[1].1.1.25.9085Uploaded bykcvara
- Hyman 1986 Order Complexity in Kuramoto SivashinskyUploaded byMhawan Setiyawan
- IA 0048- operations researchUploaded byJowin Jacob
- 1 - manual GenOpt.pdfUploaded byBazinga
- Kxu Chap02 SolutionUploaded byAkmal Gondal
- chap4Uploaded byडॉ. कनिष्क शर्मा
- A new reliability analysis method for uncertain structures with random and interval variablesUploaded byYoun Seok Choi
- All12aUploaded byChu Mạnh Tuấn

- HVAC ApplicationsUploaded bySrashmi
- 3DTransVidia 2012 BrochureUploaded bySrashmi
- 3DTransVidia 2012 BrochureUploaded bySrashmi
- ANSYS Solutions Winter05Uploaded bySrashmi
- ANSYS Solutions Spring05Uploaded bySrashmi
- Acoustics Analysis of SpeakerUploaded bySrashmi
- Granuleworks v1 Catalog Eng 2Uploaded bySrashmi
- 3.Mechanics.pdfUploaded bySrashmi
- FRANC3D_Overview_2003-1drwg3l.pdfUploaded bySrashmi
- Rubber DurabilityUploaded bySrashmi
- Academic BrochureUploaded bySrashmi
- AFDEXUploaded bySrashmi
- Three-dimensional Crack Growth Modelling of AUploaded bySrashmi
- Flownex_AcademicBrochureUploaded bySrashmi
- WaterSloshing EnglishUploaded bySrashmi
- Inagural Invitation FatigueDurabilityIndia2016Uploaded bySrashmi
- FatigueDurability India 2019 Brochure _Document DistributionUploaded bySrashmi
- FatigueDurability India 2019 Brochure _Document DistributionUploaded bySrashmi
- Flownex_HRSGBrochureUploaded bySrashmi
- Multi ScaleUploaded bySrashmi
- Flownex Turbomachinery 2017Uploaded bySrashmi
- Tutorial 21 Feedwater HeaterUploaded bySrashmi
- Characterizing Elastomer Course Info AnnArborUploaded bySrashmi
- Coal Applications 5Uploaded bySrashmi
- Fe-safe Ansys WorkbenchUploaded bySrashmi
- 9415-31442-1-PB.pdfUploaded bySrashmi
- End Uric AclUploaded bySrashmi
- Atlantic India Catalog Digital Edition CopiaUploaded byLuis León
- Libro (altro).pdfUploaded byStefano Bramante
- Brochure_Flownex Software Fired Heater Design.pdfUploaded bydatalogger123456

- Neural Computation Volume 4 issue 2 1992 [doi 10.1162%2Fneco.1992.4.2.141] Battiti, Roberto -- First- and Second-Order Methods for Learning- Between Steepest Descent and Newton's Method.pdfUploaded byEma Vidovik
- Scipy ReferenceUploaded byabydoun
- DeliveryOpenSourceModelBasedBayesian Gunning 030203Uploaded byThomas Rodriguez
- Shanno ConminUploaded byrogwar
- CMO Paper1Uploaded byAnkit Shrivastava
- LauraNovoa_HW6Uploaded byLaura Novoa
- scipyUploaded byAhmed Sajit
- Review of Optimization TechniquesUploaded byFrederic Nietzche
- YannNipsTutorialUploaded bySyariful Syafiq Shamsudin
- Optimization based on Gradient DescentUploaded byDiego Canedo
- 1606.04474v1Uploaded bysk3342001
- sqp+Uploaded byAlneo Lesag
- chap06_8up- OptimizationUploaded byagcore
- zhao08dmsUploaded byahmedtawab
- Rats GarchUploaded byvinayadhikari
- SAS the Neural ProcedureUploaded bylibredescarga
- Quasi Newton MethodsUploaded bym_k_amin
- Truncated Newton Raphson Methods for Quasi Continuum SimulationsUploaded by吴华
- Optimization with the Quasi-Newton MethodUploaded byLuis Vilchiz
- Sequential Quadratic ProgrammingUploaded byTaylor
- 2- Numerical OptimizationUploaded byBogdan Manea
- Optimization with QuantLibUploaded byMauricio Bedoya
- scipy-refUploaded byjammer999
- Tase Wire WarpingUploaded byAhmed Ramadan
- scipy-refUploaded byCharles Marcotte Girard
- Ma RssUploaded byroark47
- Quasi Newton MethodsUploaded byPoornima Narayanan
- scipy_reference.pdfUploaded byOmowaninuolaoluwa Fess
- Numerical OptimizationUploaded byMS
- Quasi NewtonUploaded bykslavnin