0 Up votes0 Down votes

0 views45 pagesRocky DEM

Jun 12, 2019

© © All Rights Reserved

PDF, TXT or read online from Scribd

Rocky DEM

© All Rights Reserved

0 views

Rocky DEM

© All Rights Reserved

- 67-surah-al-mulk
- Resultant and Equilibrant Forces Experiment No. 4
- energycasestudies 1
- Intro 2 MD Simulation
- copy of chemistry poster period 6 1
- testebanner.pdf
- Johnson Liu ACS Poster
- andreussi2017.pdf
- Nichele Et Al. - 2017 - Accurate Calculation of Near-critical Heat Capacities CP and CV of Argon Using Molecular Dynamics-Annotated
- 22
- geo diske
- F.Sc Part-1 Physics Notes Ch04
- DYNAMICS (Accelerates Constantly)
- Affiliates_2003_Sen.pdf
- Rectangular Combined Footing
- H83RED Exam Feedback Form 2011-2012
- Condensed Matter Physics - Wikipedia, The Free Encyclopedia
- erratas
- F56 Lesson Plan
- Ansient Analysis of a Variable Speed Rotary Compressor

You are on page 1of 45

Javier Junquera

Born-Oppenheimer dynamics

mn >> me electronic

decoupling

nuclear

Extracting information from the Potential

Energy Surface (PES)

-MD

-We move on the PES

-We move over the PES

- Local vs global minima

- Good Sampling is required!!

- PES is harmonic close to minima

Molecular Dynamics

•Follows the time evolution of a system

•Solve Newton’s equations of motion:

! 2 ~

F~ (t)

= rE

~ = m~a(t) = m d r(t)

! dt2

•Treats electrons quantum mechanically

•Treats nuclei classically

•Hydrogen may raise issues:

- tunneling

(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.

!

• This is OK only if system is ergodic.

!

!

• Ergodic 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.

!

!

• In other words, Ergodic hypothesis: each state consistent with our knowledge

is equally “likely”.

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

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

!

• Are systems in nature really ergodic? Not always!

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

harmonic crystals (in principle).

Different aspects of ergodicity

unique equilibrium state (microcanonical state)

!

• Trajectories wander irregularly through the energy surface

eventually sampling all of accesible phase space.

to initial conditions). Lyapunov exponent.

!

Ergodic behavior makes possible the use of

statistical methods on MD of small system. Small

round-off errors and other mathematical

approximations may not matter.

Molecular Dynamics

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.

!

• Small errors (precision) or minimal differences in the initial conditions lead to

completely different trajectories (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).

!

• Conservation of energy IS important!!. We can allow errors in the total energy

conservation of the order of 0.01 kT.

!

• CPU time is completely dominated by the calculation of the forces. Therefore,

it is preferable to choose algorithms that require few evaluations of the

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

Standard method to solve ordinary differential equations:

the finite difference approach

information at a time

to a sufficient degree of accuracy

h=δt

t0 t1 t2 tn-1 tn tn+1 tN

Notes:

of solution, but will be significantly smaller than the

typical time taken for a molecule to travel its own length

General step of a stepwise Molecular Dynamics simulation

using the current values of these quantities

from the new positions

new accelerations

parameters, ready for the accumulation of time averages, before

returning to the first point for the next step

Desirable qualities for a successful simulation algorithm

Since the most time consuming part is the evaluation of the force, the

raw speed of the integration algorithm is not so important

It should permit the use of long time step

Far more important to employ a long time step. In this way, a given

period of simulation time can be covered in a modest number of steps

It should duplicate the classical trajectory as closely as possible

momentum, and be time reversible

Involve the storage of only a few coordinates, velocitites,…

Energy conservation is degraded as time step is increased

ECONOMY

ACCURACY

while preserving acceptable energy conservation

Parameters that determine the size of

molecules, and for rapidly varying potential functions

The Verlet algorithm method of integrating the

equations of motion: description of the algorithm

Direct solution of the second-order equations

- the positions

- the accelerations

- the positions from the previous step

The Verlet algorithm method of integrating

the equations of motion: some remarks

Remark 1

The velocities are not needed to compute the trajectories, but they are useful

for estimating the kinetic energy (and the total energy).

They can be computed a posteriori using

[ can only be computed once is known]

Remark 2

The velocities are subject to errors of the order of

The Verlet algorithm method of integrating

the equations of motion: some remarks

Remark 3

The Verlet algorithm is properly centered: and

play symmetrical roles.

The Verlet algorithm is time reversible

Remark 4

rather than in two stages as in the predictor-corrector algorithm.

The Verlet algorithm method of integrating

the equations of motion: overall scheme

compute the forces (and

therefore the accelerations at t)

algorithm equations to compute

the new positions

the forces (and therefore the

accelerations at )

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

Nose-Hoover thermostat

• Introduce a friction force ζ(t)

SYSTEM

!

!

dp T Reservoir

= F(q, t) − ζ (t ) p(t)

dt

Dynamics of friction coefficient to get canonical ensemble.

dζ 1 2 3N Feedback makes

Q = ∑ mivi − k BT K.E.=3/2kT

dt 2 2

Hints

the system, better high energy frequency

Which Ensemble should we use?

! Canonical

• Good trajectories.

• Time reversible (up to numerical Same sampling !

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.

!

• NPE (Parrinello- • NPT (Nose-

Rahman) Parrinello-Rahman)

• Phase transitions • Phase transitions under P

systems under 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

• MD.TypeOfRun Anneal

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

Phonons and MD

1. MD simulations (NVE)

2. Fourier transform of

Velocity-Velocity autocorrelation function.

1. Anharmonic effects: ω(T)

2. Expensive, but information available for MD

simulations.

How to run a Molecular Dynamic in Siesta: the

Verlet algorithm (NVE-microcanonical ensemble)

Computing the instantaneous temperature,

kinetic energy and total energy

How to run a Molecular Dynamic in Siesta: the

Verlet algorithm (NVE-microcanonical ensemble)

Maxwell-Boltzmann

Output of a Molecular Dynamic in Siesta:

the Verlet algorithm (NVE-microcanonical ensemble)

SystemLabel.MDE

Conserved quantity

Output of a Molecular Dynamic in Siesta:

(and lattice vectors and their time derivatives if the

dynamics implies variable cell).

(unformatted; post-process with iomd.F)

SystemLabel.MDE shorter description of the run, with energy,

temperature, etc. per time step

SystemLabel.ANI (contains the coordinates of every Molecular

Dynamics step in xyz format)

Remember to delete previous ones if you are not interested on them

Check conservation of energy

Length of time step: 3 fs

$ gnuplot

$ gnuplot> plot "md_verlet.MDE" using 1:3 with lines, "md_verlet.MDE" using 1:4

with lines

Compare:

Total energy

with

KS energy

$ gnuplot> set output “energy.ps”

$ gnuplot> replot

Check conservation of energy

Length of time step: 1 fs

$ gnuplot

$ gnuplot> plot "md_verlet.MDE" using 1:3 with lines, "md_verlet.MDE" using 1:4

with lines

Compare:

Total energy

with

KS energy

$ gnuplot> set output “energy.ps”

$ gnuplot> replot

Check conservation of energy

Length of time step: 0.5 fs

$ gnuplot

$ gnuplot> plot "md_verlet.MDE" using 1:3 with lines, "md_verlet.MDE" using 1:4

with lines

Compare:

Total energy

with

KS energy

$ gnuplot> set output “energy.ps”

$ gnuplot> replot

Check conservation of energy

Length of time step: 0.1 fs

$ gnuplot

$ gnuplot> plot "md_verlet.MDE" using 1:3 with lines, "md_verlet.MDE" using 1:4

with lines

Compare:

Total energy

with

KS energy

$ gnuplot> set output “energy.ps”

$ gnuplot> replot

Check conservation of energy

Full solvation: Ab Initio Molecular Dynamics

X. Shen,Y. A. Small, J. Wang,

P. B. Allen, M.V. Fernandez-Serra,

M. S. Hybertsen, and J. T. Muckerman,

J. Phys. Chem. C 114, 13695 (2010).

!

J. Wang, L, Pedroza, A. Poissier, and

M. Fernandez-Serra, JPCB (2012).

24 GaN surface sites

94 Water molecules

240 GaN atoms

MD Method: DFT (PBE)

Package: SIESTA

!

AIMD Equilibration: 2ps

AIMD production: 10ps

Dissociation occurred in first 1 ps;

initially undissociated.

Early history of GaN/liquid water interface equilibration:

dissociation of water seen in AIMD run

OH– quickly, then fluctuate slightly.

H+ quickly, then hardly fluctuate.

GaN/Aqueous Interface: H-bond network

Proton diffusion

bution function P(δ,RO

δ=ROa H -ROb H of a giv

oxygen atoms distance

ROO and Ob are defined in F

“Diﬀs-b ”, (b) “Diﬀs-s ” a

tion, the P(δ,ROO ) dist

shown on the same sca

free-energy profile alon

be obtained from ∆F=

Surface-Surface diffusion

Symmetric Distribution

at delta~0 there is non zero probability:

centrosymmetric complexes of the Zundel

(H5O2)+ type. Barrier ~ 40 meV

bulk-bulk diffusion

Symmetric Distribution

at delta~0 there is non zero probability:

centro-symmetric complexes of the Zundel

(H5O2)+ type. Barrier ~ 20 meV

Surface-bulk diffusion

Zundel complex

at delta~0 there is ~ 0 probability:

Barrier out ~ 75 meV.

Barrier in ~ 55 meV

Ref? the standard-state deprotonation free energy ∆G(0)

proton

Deprotonation

from a surface water

free energy barrier Band pKa

to a

The deprotonation free energy bar

via −log 10 exp(−β∆G (0)

at the! GaN

), where β is 1/k

1010/Aqueous

T and

interf

proton from a surface water to a bu

#

R

The pK can dRA(R)exp[−β∆F (R)] a

be derived from

" cut

(0)

∆G = −kB T ln C0a

at the GaN ? 1010/Aqueous

Ref the standard-state

0 interface

deproton

(1)

Thehere C pK

0

via

a =

denotescan−log

1.0 Mbe

10 derived

exp(−β∆G

concentration, R

(0)

from

is ),

the a

where

reaction sim

?

Ref the standard-state deprotonatio ! "

Rcut

(0)

via −log10 ∆G exp(−β∆G

(0)

= −kB T ln ),Cwhere 0

β dR is

Once H+ leave the surface, the barriers to diffuse within the bulk0liquid region

∗

To whom correspondence should be addressed:

are smaller than those to return to the surface.

! This agrees with the large

maria.fernandez-serra@stonybrook.edu

acidity obtained.

" Rcut

K. (0)

Maeda, K. Teramura, D. Lu, T. Takata, N. Saito, Y. In-

∆G = −k T ln C

here

oue, and K. C

Domen, denotes

B0Nature 01.0

440, 295 M concentra

(2006). dRA(R

K. Maeda, K. Teramura, N. Saito, N. Saito,

0 Y. Inoue, and

K. Domen, Bull. Chem. Soc. Jpn 80, 1004 (2007).

PHONONS FROM MOLECULAR DYNAMICS

Fourier Transform

Vibrational Spectrum

stretching, anti-stretching and

2*bending modes

surface OH- s

- 67-surah-al-mulkUploaded byHaider Ali
- Resultant and Equilibrant Forces Experiment No. 4Uploaded byKevin Turingan
- energycasestudies 1Uploaded byapi-471228436
- Intro 2 MD SimulationUploaded byachsanuddin
- copy of chemistry poster period 6 1Uploaded byapi-357217799
- testebanner.pdfUploaded byJames Hodge
- Johnson Liu ACS PosterUploaded byJohnson Liu
- andreussi2017.pdfUploaded byEder Ruiz Hernandez
- Nichele Et Al. - 2017 - Accurate Calculation of Near-critical Heat Capacities CP and CV of Argon Using Molecular Dynamics-AnnotatedUploaded byJakler Nichele
- 22Uploaded byGuadalupe Valladares
- geo diskeUploaded byCrishan Karunapala
- F.Sc Part-1 Physics Notes Ch04Uploaded bySaher
- DYNAMICS (Accelerates Constantly)Uploaded by103jak
- Affiliates_2003_Sen.pdfUploaded bySalam AlNabulsi
- Rectangular Combined FootingUploaded bybollasudarshan
- H83RED Exam Feedback Form 2011-2012Uploaded byDevina Irene
- Condensed Matter Physics - Wikipedia, The Free EncyclopediaUploaded bydonodoni0008
- erratasUploaded byAnonymous l6OMyp4w
- F56 Lesson PlanUploaded byThamil Valluvan
- Ansient Analysis of a Variable Speed Rotary CompressorUploaded byNguyen Danh Tuyen
- 2D TransformationsUploaded byvirendrakushwah
- StaticsSlidesUploaded bygilla2010
- Chapter 15 Retaining Walls and Braced CutsUploaded byLester Cabungcal
- CEG 883 Design Sheet1Uploaded byInemesit Ekop
- Steel Designer's Manual, 6th Edition, 2003 R20070821FUploaded bysaad7159
- Design of StructuresUploaded byMuhammad Farooq Zia
- Math182Spring2014Notes.pdfUploaded byambreen mehmood
- Viscometer Model 35Uploaded byAji Sentosa Pramono
- Exp 4Uploaded bysachinkurhekar
- Spontaneity of Chemical Processes and Equilibria Are Imprtant Topics That Are Covered in Detail in Every Introductory Chemistry TexbookUploaded byAleidy Marquez Jimenez

- FuelCell_NafionUploaded bySrashmi
- Resume - Srivalli MS - Mechanical Engineer - 2016-Sep-16Uploaded bySrashmi
- 14.Nanoscale Density functional theory.pdfUploaded bySrashmi
- RegistrationForm FatigueDurabilityIndia2019 WebUploaded bySrashmi
- Flownex_ModulesBrochureUploaded bySrashmi
- Turbine-brochure_FNXUploaded bySrashmi
- Flownex_AcademicBrochureUploaded bySrashmi
- Data_Brochure_Digital_Rev1Uploaded bySrashmi
- Control_Brochure_rev1Uploaded bySrashmi
- NURETH14-599Uploaded bySrashmi
- Safety Brochure Digital(s)Uploaded bySanthosh Lingappa
- Solid Mechanics - Theory and Practical SessionsUploaded byFaizan
- CMTFEA002 ContactMechanics Theory&PracticalUploaded bySrashmi
- Workshop Course OnSolidMechanics 2019Uploaded bySrashmi
- Multiscale MolecularDynamics CertificationCourse WebUploaded bySrashmi
- Rubber Fatigue DurabilityUploaded bySrashmi
- Rubber Compounding for Durability InformationUploaded bySrashmi
- Rubber DurabilityUploaded bySrashmi
- 3DTransVidia 2012 BrochureUploaded bySrashmi
- HVAC ApplicationsUploaded bySrashmi
- AFDEXUploaded bySrashmi
- 3.Mechanics.pdfUploaded bySrashmi
- ANSYS Solutions Spring05Uploaded bySrashmi
- ANSYS Solutions Winter05Uploaded bySrashmi
- Acoustics Analysis of SpeakerUploaded bySrashmi
- Granuleworks v1 Catalog Eng 2Uploaded bySrashmi
- WaterSloshing EnglishUploaded bySrashmi

- Models, databases, and simulation tools needed for the realization of integrated computational materials engineeriing 2011 ASM International.pdfUploaded byLuisGuzman
- DM-basicsUploaded byStephania Vásquez Rodriguez
- Groenhof 2013 Meth Mol BiolUploaded byGianlucaTirimbò
- DFT4beginners.pdfUploaded byKallen Stadfeld
- Intro 2 Molecular Dynamics Simulation by MP AllenUploaded byachsanuddin
- class dual inhibitors against Alzheimer’s disease.pdfUploaded byDr. Kaushal Kishor Sharma
- cv rklindsey 122315Uploaded byapi-295850343
- principles of multiscale modelling.pdfUploaded byjahid
- Qgui ManualUploaded byy
- MartinTobiasKlein-2000-JChemPhysUploaded bykensaii
- Molecular DynamicsUploaded byStephania Vásquez Rodriguez
- Nanotechnology Application Guide - Accelrys Inc., 2004-MTUploaded byIqbal Safi
- Kimia Komputasi B_zevano c. Sibarani_1506740654)Uploaded byZevano C. Sibarani
- Computational ChemistryUploaded byshadow_anchor
- New Nanotechnology DevelopmentsUploaded byHector Rojas
- Flow TheoryUploaded bybala_murali
- Vmd TutorialUploaded byMichell De Oliveira Almeida
- Chemical Sensors: Simulation and Modeling Volume 4: Optical SensorsUploaded byMomentum Press
- 12 - Modeling and Simulation of Nuclear Fuel Recycling SystemsUploaded byacetilen
- Emlg 2016 ProgrammeUploaded byDimitris Chaniotakis
- VMD ManualUploaded byGani Priambodo
- Kalyani Materials2Uploaded bySouparno Adhikary
- Amber12.pdfUploaded bySupuranIonel
- Qmmm Free EnergyUploaded byinterestingese
- Nucleation and Growth of Nanoparticles in the Atmosphere.pdfUploaded byAna Gabriela
- hyperChemUploaded byKarlina Noordiningsih
- 10.1016@j.commatsci.2018.03.060Uploaded byFrancisco Torres
- Application of Artificial Intelligence (AI) for Solving Global Optimization Problems in PhysicsUploaded byVaughan Png
- Jansen KMC Introduction 2008Uploaded byhkmydreams
- Amber 15Uploaded byFCiências

## Much more than documents.

Discover everything Scribd has to offer, including books and audiobooks from major publishers.

Cancel anytime.