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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.

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