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MOLECULAR DYNAMICS SIMULATION

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MOLECULAR DYNAMICS SIMULATION FUNDAMENTALS AND APPLICATIONS

KUN ZHOU School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore

BO LIU School of Mechanical and Vehicle Engineering, Hunan University, China

Elsevier Radarweg 29, PO Box 211, 1000 AE Amsterdam, Netherlands The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States Copyright © 2022 Elsevier Inc. All rights reserved.

No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions.

This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein).

Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary.

Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility.

To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein.

British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress ISBN: 978-0-12-816419-8 For Information on all Elsevier publications visit our website at https://www.elsevier.com/books-and-journals

Publisher: Matthew Deans Acquisitions Editor: Brian Guerin Editorial Project Manager: Emily Thomson Production Project Manager: Nirmala Arumugam Cover Designer: Christian J. Bilbow Typeset by MPS Limited, Chennai, India

Contents

List of symbols Preface

vii xxv

1. Fundamentals of classical molecular dynamics simulation

1

1.1 Introduction 1.2 Fundamentals of molecular dynamics simulation 1.3 Hardware and software for MD simulation References

1 10 37 40

2. Potential energy functions

41

2.1 The Born Oppenheimer assumption 2.2 Potential energy functions for different materials References

41 50 63

3. Control techniques of molecular dynamics simulation

67

3.1 Types of constraints in molecular dynamics simulation 3.2 Thermodynamic ensembles 3.3 Temperature control 3.4 Pressure control 3.5 Boundary conditions 3.6 Rigid bond constraints References

67 68 70 83 90 93 95

4. Advanced ab initio molecular dynamics and coarse-grained molecular dynamics

97

4.1 Motivations for the development of advanced molecular dynamics simulation methods 4.2 Ab initio molecular dynamics 4.3 Coarse-grained molecular dynamics References

97 99 109 126

5. Application of molecular dynamics simulation in mechanical problems

129

5.1 Role of molecular dynamics simulation in modeling the mechanical properties of materials

129

v

vi

Contents

5.2 Tensile, compressive, and shear tests 5.3 Nanoindentation and nanoscratching tests 5.4 Tribological behaviors 5.5 Interfacial effects in nanocomposites 5.6 Defect effects References

130 143 149 161 167 178

6. Application of molecular dynamics simulation in thermal problems

183

6.1 Demand for understanding the thermal properties of nanomaterials 6.2 Molecular dynamics simulation methods for thermal conductivity calculation 6.3 Molecular dynamics simulation of interfacial thermal transport 6.4 Thermal rectification effects References

183 185 205 228 233

7. Application of molecular dynamics simulation in mass transport problems

237

7.1 Fluids in nanoconfinement 7.2 Nanofiltration with porous thin films 7.3 Liquid vapor phase transition References

237 274 291 311

8. Application of molecular dynamics simulation in other problems

315

8.1 Reactive molecular dynamics simulations 8.2 Irradiation processes 8.3 Material crystallization References

315 326 334 336

Index

339

List of symbols a

Side length of a cubic simulation box Mean nearest-neighbor separation

a

Acceleration vector (the second-order time derivative of a position vector) Edge vector of a unit cell

apre

Predicted acceleration vector

acor

Corrected acceleration vector

aGE

Lattice constant of graphene (2.46 Å)

aSE

Lattice constant of silicene (3.98 Å)

A

A physical quantity A material-dependent constant Amplitude of surface roughness Contact area Cross-section area Surface area

AIn

Area of the interface between a graphene monolayer and a silicene monolayer

A(RN)

Configurational component of the Helmholtz free energy

hAi

True mean value of a physical quantity A

hAiblk

Time-averaged value of a physical quantity A obtained in a block period of an MD simulation

hAisim

Time-averaged value of a physical quantity A obtained from an MD simulation

AðRNn ; tÞ

Amplitude factor of a nuclear wave function

bij

Bond order in the REBO potential

b

Third-order time derivative of a position vector Edge vector of a unit cell

B

A physical quantity

Bijk

A constant that denotes interaction strength

vii

viii

List of symbols

BOij

Bond order between the ith and the jth atom

c

A fitting parameter

c

Edge vector of a unit cell

cIi

Linear coefficient for the mapping function of the coordinates of the Ith coarse-grained sites

c(t)

Autocorrelation function of hydrogen bonding

C

A material-dependent constant

CGE

Constant volume heat capacity of a graphene nanosheet

CSE

Constant volume heat capacity of a silicene nanosheet

CV

Isochoric heat capacity

d

Mean grain size Thickness of a nanochannel

D

Diffusion constant of a gaseous or liquid system Diameter of the nanowire Interlayer distance A material-dependent constant

Dc

Diffusion coefficient

D0

Dimer binding energy in the Tersoff potential energy function

De

Potential energy well depth of the Morse potential energy function

D(ω)

Phonon density of states

e

Elementary electron charge (1.60217662 3 10219 C)

ePot i

Potential energy of the atom i

E, Ea

Electric field intensity

E0

Original energy of a wave packet

E

Electric field strength vector

Ei

Electric field vector at the position ri

ΔE

Interfacial bonding strength of a nanocomposite

Ea

Adsorption energy Activation energy

Eangle

Potential energy related to the bending of a bond angle in the ReaxFF force field

Eavg

Average kinetic energy of a group of atoms

Ebond

Potential energy associated with the bonding between two atoms in the ReaxFF force field

List of symbols

ix

Ecoh

Cohesive energy of the interface

Ecut

Highest kinetic energy pertaining to an expansion of a wave function in terms of an electronic orbital set

ECoul

Potential energy corresponding to electrostatic interactions

E~ e ðt0 Þ

Phase factor of the complete wave function of an atomic system

Egap

Energy difference between the lowest unoccupied orbital and the highest occupied orbital

EH-bond

Cohesive energy due to hydrogen bonding

Ematrix

Energy of the matrix of a nanocomposite

Enanofillers

Energy of the nanofillers of a nanocomposite

Eover

Energy penalty term that prevents the overcoordination of atoms in the ReaxFF force field

Erep

Potential energy of an atom interacting with a repulsive wall

Est

Spring potential energy function

Especific

System-specific energy terms in the ReaxFF force field

Esystem

Total energy of a molecular system in the ReaxFF force field

Etot

Total energy of the nanocomposite

Etr

Transmitted energy of a wave packet

Etors

Potential energy related to the twist of a dihedral bond angle in the ReaxFF force field

EvdW

Potential energy corresponding to nonbonding van der Waals interactions in the ReaxFF force field

f

Number of degrees of freedom of an MD system

f

Resultant atomistic force acting on an atom

fA(rij)

Attractive atomic interaction function of the Tersoff potential

fc(rij)

Cutoff function for nearest-neighbor interactions

fd

Driving force

fFVF

Free volume fraction

fij

Interatomic force imposed by the jth atom in the wall on the ith atom in the fluid

fi(r 2 ri)

Radial distribution of the remaining charge outside the core of the ith atom

fiw

Force exerted on the ith fluid particle by the channel wall

fp

Force arising from the pressure difference at the boundary of the “pump” region

x

List of symbols

fR(rij)

Repulsive atomic interactions of the Tersoff potential

fw

fz

Force exerted on a channel wall by the fluid particles Net electrostatic force averaged over all the water molecules

Fi(R )

Force acting on the ith particle

FI

Force acting on the Ith coarse-grained site

Fij

Force imposed on the atom i due to its interaction with atom j

Fijk

Force on the atom i due to the three-body interactions among atoms i, j, and k

Fj(ijk)

Three-body force term for the calculation of heat flux

F[ni(ri)]

Function of the local electron density ni(ri) at the atomic site ri

g

Gradient of the potential energy

g(r)

Radial distribution function

g(θijk)

Bond angle distribution function of the Tersoff potential energy function

gref MN ðRÞ

Target radial distribution function

gkMN ðRÞ

Paired radial distribution function for the effective potential obtained from the kth IBI iteration step

gμVT MN ðRIJ Þ

Radial distribution function in the μVT ensemble

G

Interfacial thermal conductance

G+

Interfacial thermal conductance of the system corresponding to the forward heat flux direction

G2

Interfacial thermal conductance of the system corresponding to the opposite heat flux direction

G

Metric tensor given by G=hhT, with h=(a, b, c)T

GN MN

Kirkwood-Buff integral in the thermodynamic limit

GkMN ðRÞ

Plateau value of the running Kirkwood Buff integral after the kth IBI iteration step

Gref MN ðRÞ

Plateau value of the running Kirkwood Buff integral calculated from the reference all-atom system

GV MN

Kirkwood Buff integral of the radial distribution function between species M and N

h̄

Reduced Planck constant (1.054572 3 10234 J s21)

h

A matrix defined by the edge vectors a, b, and c of a unit cell

H

Separation distance

N

Hamiltonian of a simple one-dimensional harmonic oscillator

List of symbols

H

Hessian matrix of potential energy

Hij

Strength of the steric repulsion for the two-body term of the Vashishta potential energy function

He

Partial Hamiltonian

H2

Interlayer distance between the two graphene layers in each electrode

H(R , P )

Hamiltonian of an atomic system

H2;adi ðp2 ; x2 Þ

Hamiltonian of particle 2 in an adiabatic two-particle system

J

Heat flux vector

+

Heat flux in the forward direction (from silicene to graphene)

N

J

xi

2

N

J

Heat flux in the reserve direction (from graphene to silicene)

Jx(y,t)

Momentum of the flux density

Jμ

Component of the heat flux vector J in the μ direction

k

Force constant in the harmonic function

ks

Spring constant of an oscillator Spring constant of a simple one-dimensional harmonic oscillator

k0

Wavenumber

k0

Wave vector

kB

Boltzmann constant (1.380649 3 10223 J K21)

kbi

Material-dependent constants that determine the interaction strength of bond stretching

kθi

Material-dependent constants that determine the interaction strength of bond angle bending

kχ

Force constant

K

Evaporation constant

K2

Kinetic energy of particle 2

K(t)

Instantaneous kinetic energy

Kfict

Fictitious electronic “kinetic energy”

Kn

Knudsen number

Kst

Stochastic kinetic energy defined in the Bussi Donadio Parrinello thermostat

l

Length of the MFP of the phonons

l

Set of variationally determined parameters

lb

Intrinsic length of the phonon MFP of the bulk material

li,0

Reference value of bond length

xii

List of symbols

li

Bond length

ly

Length of the simulation box in the y-direction

L

Length of an MD simulation system

L

Second-order tensor or matrix of the deformation rate

Lp

Period length

m

Mass of a simple one-dimensional harmonic oscillator

me

Mass of an electron (9.109 383 3 10231 kg)

mi

Mass of the ith atom or particle Mass of the ith nucleus

mw

Fictitious mass of the wall

minx1 Vðx1 ; x2 Þ

The lowest energy state of the system

M

Mass of a nucleus Fictitious mass having the extra degree of freedom Q

MI

Mass of the Ith nucleus

n MN R ðr Þ

Mapping function of the coordinates between the sites of a coarse-grained system and the corresponding atoms in a reference all-atom system

n MN P ðp Þ

Mapping function of the momenta between the sites of a coarsegrained system and the corresponding atoms in a reference allatom system

M RI ðrn Þ

Mapping function of the position of the Ith site in a coarsegrained system

M PI ðpn Þ

Mapping function of the momenta of the Ith site in a coarsegrained system

n

Empirical fitting parameter Local electron density Adjusting parameter in the Tersoff potential energy function

ne

Phonon occupation number

n(r’)

Electron density distribution

nb

Number of blocks for the block average method

nk

Number of atoms in the kth slab

nt

Total number of configurations sampled during the entire course of an all-atom MD simulation

N

Number of atoms Average number of water molecules in a nanochannel

List of symbols

xiii

Na

Number of atoms

NA

Avogadro constant (6.022140 3 1023 mol21)

Nc

Number of atoms in a cell

Ne

Number of electrons

Nf

Number of atoms in the “pump” region

Ni, nei

Number of neighbors of the atom i

Nm

Number of molecules

Nn

Number of nuclei

Ns

Number of atoms on the box surface

Nt

Total atom number

Ntransfer

Total number of velocity exchange events that occur over time t

Nw

Number of atoms in the constraint wall

N0

Half of the total number of C atoms in a graphene nanosheet

N1

Number of H atoms on one side of a graphene nanosheet

minx1 Vðx1 ; x2 Þ

Minimized potential energy Vðx1 ; x2 Þ with respect to x1 for a fixed value of x2

p

Momentum vector of an atom Dipole moment of a water molecule

pi

Momentum vector of the ith atom

pbo

Empirical parameter

p

elc

Momentum vectors of the electrons

p

n

Momentum vectors of the atoms

n o Collection of the momentum vectors p1 ; . . .; pNe of an MD simulation system containing Ne electrons

pNe pnul

Momentum vectors of the nuclei

pp ðp Þ

Probability density of the atomic momenta of an all-atom system described by momentum vectors pn ¼ p1 ; . . .; pn

prp ðrn ; pn Þ

Probability density of the dynamic states of an all-atom system described by position vectors rn ¼ fr1 ; . . .; rn g and momentum

vectors pn ¼ p1 ; . . .; pn

pr ðrn Þ

Probability density of the atomic positions of an all-atom system described by position vectors rn ¼ fr1 ; . . .; rn g

p(t)

Instantaneous momentum of a 1D oscillator

p0

Initial momentum of a 1D oscillator

n

xiv

List of symbols

pðθjik ; θ0jik Þ

Function for the bending of the bond angle of the Vashishta potential

P

Pressure

Pα

Total momentum of an MD system in the α-direction, with α being x, y, or z

Padi ðx2 Þ

Probability distribution function of x2 in the adiabatic limit

Padi ðxÞ

Probability distribution function of x in the adiabatic limit

Pext

External pressure

Pf

Pressure exerted on the fluctuating wall

Pin

Inlet pressure

P

Nn

Collection of the momentum vectors P1 ; . . .; PNn of an MD simulation system containing Nn atoms

PN

Generalized spatial momenta of all the particles in an MD simulation system

PP ðPN Þ

Probability density of the site momenta of a coarse-grained system described by momentum vectors PN ¼ fP1 ; . . .; PN g

P(q)

Normalized probability distribution of a specific degree of freedom q

pR ðRN Þ

Reference probability density of a coarse-grained system determined by its corresponding all-atom trajectories

PRP ðRN ; PN Þ

Probability density of the dynamic states of a coarse-grained system described by position vectors RN ¼ fR1 ; . . .; RN g and momentum vectors PN ¼ fP1 ; . . .; PN g

PR ðRN Þ

Probability density of the site positions of a coarse-grained system described by position vectors RN ¼ fR1 ; . . .; RN g

P(t)

Instantaneous pressure

P(x)

Gaussian distribution of a random variable x

Pout

Outlet pressure

q

Charge of a particle

qi

Partial charge of the ith atom

Q

A physical quantity Charge possessed by a core in the shell model Fictitious mass for the additional degree of freedom introduced in the Nosé Hoover thermostat Fictitious degree of freedom introduced in the Andersen barostat Water flux

List of symbols

QHP N

xv

Estimated flow rate based on the HP equation N

Q(R ,P )

A physical quantity of an MD system described by the generalized spatial coordinates RN and spatial momenta PN

Q0

Estimation of a quantity Q for a bulk material

r

Distance between two atoms

r_

The first-order derivative of the position vector with respect to time

r€

The second-order derivative of the position vector with respect to time

r0

Distance corresponding to the minimum potential energy Equilibrium distance Equilibrium bond lengths

rcm

Position of the center of mass

rcut

Cutoff distance for a potential energy function

elc

r

Position vectors of the electrons

ri

Position vector of the ith atom

~r i ðΔtÞ

Position of the ith atom without considering the bond constraint between the atoms i and j

ri,c

Position of the ith core for the shell model

r ij

Displacement vector from the atom i to atom j

rij

Distance between the atoms i and j

ri,s

Position of the ith shell for the shell model

ri,α

Component of ri in the α-direction

ri(t)

Time-dependent position of the ith atom

rm

Empirical parameter for the LJ potential function

rnei

Neighbor list distance defined for the Verlet neighbor list method

Collection of the position vectors r1 ; . . .; rNe of an MD simulation system containing Ne electrons

r Ne rn

Spatial coordinates of the n atoms in the detailed atomistic system

rn,i

Configuration of the ith all-atom MD simulation system

nul

r

Position vectors of the nuclei

r4s

Decay length of the two-body term of the Vashishta potential

rN

Radius of the inner boundary of the ambient region

xvi

List of symbols

Rc

Critical distance of an atom within which its closest neighbors can interact with it

RI

Ideal gas constant (8.314462 J K21 mol21)

RIJ

Relative position vector of the Ith and Jth coarse-grained site

RI

Position of the Ith coarse-grained site

RMSD

Mean square displacement

R

Generalized spatial coordinates of all the particles in an MD simulation system

N

ΔRN R

Nn

Atomic displacement

Collection of the position vectors R1 ; . . .; RNn of an MD simulation system containing Nn atoms

Ry

Rydberg constant (1 Ry=13.605693 eV)

s

An enhancement factor A fictitious degree of freedom

si

A row vector with the components (li ,mi , and ni )

s(k)

Smap rn

Direction vector

Srel

Relative entropy

Average entropy resulting from the degeneracies caused by configuration mapping

SðR ; tÞ

Phase factor for the nuclear wave function

t

Time

Nn

Δt

Time step

Δt

The maximum value of the AIMD timestep

tsignal

Time at which the HFACF possesses a magnitude equivalent to that of W

T

Temperature

ΔT

Temperature difference

rT

Temperature gradient

Tc

Critical temperature

Td

High threshold displacement energy

Telec

“Fictitious” temperature of the electrons

Tf

Tilt factor that denotes the angle between the xz-plane and the yz-plane

Tf0

Initial tilt factor at t=t0 that denotes the angle between the xzplane and the yz-plane

max

List of symbols

xvii

TG

Temperature of the graphene monolayer

TG0

Initial temperature of the graphene monolayer

Ti

Total nuclear charge of the ith atom

ΔTIn

Temperature drop at an interface

TMD

Calculated temperature based on MD simulation

Tnucl

Temperature of the nuclei

TN2m (zk)

Instantaneous temperature of the kth slab at the (N 2 m)th time step

Tr(.)

Trace of a matrix

TS

Temperature of the silicene monolayer

TS0

Initial temperature of the silicene monolayer

T(t)

Tðzk Þ M

Instantaneous temperature

@T=@z

ui

Temperature of the kth slab averaged over the final M time steps of the simulation Averaged value of the temperature gradient in the z-direction over time Displacement vector of the ith atom

u_ i

Time derivative of the displacement vector of the atom i n

u(r )

Atomistic interaction potential energy

Ubond-bending

Bond bending potential component

U

Buck

Buckingham potential

Ucross

Cross potential function terms for the couplings among bond stretching, bond angle bending, and bond torsion

UCG

Effective potentials of the CGMD model

U

Coul

Potential energy due to Coulombic interactions

U

ES

Potential energy due to electrostatic interactions

, Uel

ΔU KBI ðRÞ U

Morse

KBI IBI ramp correction term Morse potential function

0 ðRÞ UMN

Initial guess of the nonbonded two-body potential of a CGMD model

UMN(R)

Nonbonded two-body potential of a CGMD model

k UMN ðRÞ

Effective potential obtained from the kth IBI iteration step

Unb

Potential energy due to nonbonded van der Waal interaction in the MM force field

ΔUP ðRÞ

Linear pressure correction term

xviii

List of symbols

U(RN)

Potential energy function

N

U’(R )

Gradient of U(RN)

URigid ðRN Þ

Potential energy of an MD simulation system with a rigid bond constraint imposed

U SR(rij)

Potential energy due to the repulsion of the electron shells

tot

U

Potential energy function

Uχ

Out-of-plane bending interactions that are closely related to the bond torsion term

U2(rij)

Two-body term of the Vashishta potential

U3(rij, rik, rjk)

Three-body term of the Vashishta potential

v

Velocity of an atom Rotational frequency

v

Average velocity of the water molecules in the nanochannel

vC

Velocity of the center of mass of all the particles in the heat source or the heat sink

vcom

Velocity of the center of mass of the atoms in a strip

vi,α

Component of the velocity of the ith atom in the α-direction

vi

Velocity vector of the ith atom

vij

Relative velocity of the two points (or atoms) i and j

vj(t)

Velocity of the atom j at time t

vmax

Maximum value of the advection velocity

hvmax i

Time average of the highest atomic velocity

vp

Group velocity of the phonons Velocity of the incident wave

vs

Velocity of the surface wave on the solid

vx

x-component of the local average stream velocity

V

Volume of a system

V(x1, x2)

Potential of a simple one-dimensional chain model consisting the two particles 1 and 2

V(r)

Electron nuclei interaction potential energy

V(rij)

Two-body potential that accounts for the interactions among the nuclei

V2(rij)

Two-body potential energy function

V3(ri, ri, rk)

Three-body potential energy function

List of symbols

xix

VeE ðRNn Þ

Effective potential energy contributed by the electrons

Vfree

Total free volume

Voccupy

Total volume occupied by the nanofillers and the matrix of the composite

Vvacuum

Sum of the free volumes that exceed a critical size

VH(r)

Hartree potential energy

Vm

Volume of the composite

Vne ðr ; R Þ

Operator for the total potential energy of the nuclei and electrons

Vn

Energy barriers for bond torsion

Ne

Nn

V

REBO

REBO term of the AIREBO potential energy function

V

LJ

Lennard Jones potential energy function

V

Torsion

Potential energy contributed by bond rotations for the AIREBO potential energy function

Vw

Potential energy contributed by the interaction between the ith particle and the wall

W(τ)

Amplitude of the autocorrelation function

wA

Wave amplitude of a wave packet

0

x

Initial position of a 1D oscillator

x1;adi ðx1 ð0Þ; v1 ð0Þ; x2 ð0Þ; tÞ

Value of x1 at time t when x1 evolves adiabatically under the initial conditions of x1(0) and v1(0) with x2 being fixed at its initial value

x(t)

Instantaneous position of a 1D oscillator at time t

xi(t0)

Coordinate of atom i at t=t0 in the x-direction

yi

y-component of the position of the center of mass of water molecule

yi(t0)

Coordinate of the atom i at t=t0 in the y-direction

Z

Effective configuration partition function

ZI

Atomic number of the Ith nucleus

Z1 ðx2 ; β 1 Þ

Effective configuration partition function of x2

Zi,eff

Effective nuclear charge of the ith ion

zi

Coordinate of the ith atom in the direction of heat transport

zk

Position of the center of the kth slab of atoms

z0

Center of the wave packet

zðrn;i Þ

Partition functions of the ith all-atom configuration rn;i

xx

List of symbols

zðRN;i Þ

Partition functions of the ith coarse-grained configuration RN;i

αi

Electronic polarizability of the ith ion Angles at the core of the nanowire for the ith wedge

ρ

ρ y; t

A material-dependent constant Mass density at the position y and time t

ρ(RN, PN)

Probability density distribution of the phases of an MD system described by the generalized spatial coordinates RN and spatial momenta PN

ρi

Electron density at the site of the ith atom

ρij(rij)

Electron density of the jth atom at the site of the ith atom

ρN

Number density of the atoms in an MD system

ρN

Number density of coarse-grained particles of the N type

θ

General angle Misorientation angle Rayleigh angle

θD

Debye temperature of the system

θi

Bond angle

θi,0

Reference value of θi

θijk

Angle between two successive bond vectors

θ0jik

Equilibrium bond angle

hθi

Time-averaged dipole orientation angle of the water molecules

ε

Depth of the potential energy well Scaling factor in the SW potential energy function Effective spring constant of a simple harmonic spring potential energy function Rectification ratio

εAB

Potential energy well depth of the Lennard Jones potential for the two atom types A and B

εcoh

Cohesive energy density

εi

Eigenvalues of the unoccupied orbitals

εPot i

Potential energy term of the site energy

εi(k0)

Polarization parameter

εi(t)

Site energy of the ith atom at time t

εfw

Potential energy well (or binding energy) of the LJ potential

List of symbols

εj

Eigenvalues of the occupied orbitals

ε_ i

Atomic strain rate tensor

ε_ xy

Shear strain rate

ε0

Vacuum dielectric constant (8.854 3 10 12 F m21)

Δε

Amount of heat input into the heat source

ξ

Width of the wave packet

ξi

Material-dependent constant

xxi

Noise term in the Langevin equation that imposes a stochastic force on the ith atom ζ

Effective coordination number of the atoms for the Tersoff potential energy function Thermal relaxation time Velocity rescaling factor

ζ ij

Effective coordination number of the atoms

ςi

Scaled coordinate vector for the Andersen barostat

πi

Momentum that conjugates the scaled coordinate vector for the Andersen barostat

Π

Momentum that conjugates the degree of freedom Q in the Andersen barostat

ηi

Coefficient that determines the magnitude of the stochastic force imposed on the ith atom for the Langevin thermostat

ηij

Exponent of the steric repulsion for the Vashishta potential energy function

μ

Mean of a Gaussian distribution Reduced mass of the atom for the Morse potential Fictitious mass parameter (in the unit of eV s2)

υ

Constant that denotes the nonzero collision frequency for the Andersen thermostat

δαβ

Kronecker delta

σ

Critical separation distance for a negative potential energy Standard deviation of a Gaussian distribution Zero-crossing distances of the LJ potential

σAB

Zero-crossing distance of the Lennard Jones potential for the two atom types A and B

σ2

Variance of the Gaussian distribution

σ

virial

(r)

Virial stress of a volume element

xxii λ

List of symbols

Positive coefficient for the steepest descent method Thermal conductivity Time-dependent Lagrange multiplier

λ

+

2

Thermal conductivity in the forward direction

λ

Thermal conductivity in the opposite direction

λμv

Component of the thermal conductivity tensor λ

λ

Thermal conductivity tensor

λGE

Thermal conductivity of the graphene sheet

λH

Thermal conductivity of the hybrid graphene/silicene monolayer

λk

Lagrange multipliers for bond constraints

λ(k)

A coefficient

λSE

Thermal conductivity of the silicene sheet

λ0

Predefined value of λ(k)

λ3

Cutoff parameter in the Tersoff potential energy function

λmax N

Upper limit of bulk thermal conductivity

Λ

de Broglie thermal wave length

Λij

Lagrange multipliers introduced to dynamically satisfy the D E condition ψi jψj ¼ δij

γ

Fitting constant for the SW potential energy function

γi

Positive atomic friction coefficient

φ

A general angle

φ0

Torsion angles at points of minimum potential energy

ω

Vibrational frequency of a bond Frequency of motion of a particle Strength of a wedge disclination Angular frequency Phonon frequency

ωc

Critical disclination strength

ωD

Debye frequency that corresponds to the highest phonon frequency allowed in the Debye model

ωe

Vibrational frequency of the electrons

ωmax e

Highest possible electronic frequency

ωmin e

Lowest possible electronic frequency

List of symbols

ωn

xxiii

Vibration frequency of the nuclei

ωmax n

Highest phonon mode frequency

ΞðR Þ

Wave function of the nuclei in a system

ΦðrNe ;RNn Þ

Wave function of the electrons in a system

ΦðrNe ; RNn ; tÞ

Time-dependent wave function that depends on both the nuclear and electronic degrees of freedom

Φ(ri 2 rj)

Pure two-body potential for modeling nuclei

ΦiRc

Set of atoms within a sphere of radius Rc with the atom i at its center

ΨðRNn ; rNe Þ

Total wave function of an atomic system

ΨðrNe ; tÞ

Time-dependent wave function of the electrons in a system

χðR ; tÞ

Time-dependent wave function of the nuclei in a system

Ψ

Wave function

Ψi

One-particle orbital subjected to the orthonormal constraint

Ψ0

Potential energy of electrons at the ground state

Ψ1

Potential energy of electrons at the first excited state

α

Electronic polarizability of an ion

β

Adjusting parameter in the Tersoff potential energy function

Nn

Nn

Isothermal compressibility of a material χ

Dihedral angle Nuclear wave function

χ

2

τb

Objective residual function Time steps for the block average method Intrinsic relaxation time of the corresponding single-crystal bulk material

τg

Relaxation time under the effect of grain boundary scattering

τs

Relaxation time under the effect of surface scattering

τ im

Relaxation time in the presence of impurities

τm

Upper integral limit in the Green Kubo expression

τ m;max

Largest numerically meaningful upper limit for the integral in the Green Kubo expression

τP

Coupling parameter that determines how closely a system is coupled with a barostat

τT

Coupling parameter of the Berendsen thermostat

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List of symbols

Δτ

Time interval between two successive collisions for a given atom

Σ

Reciprocal coincidence site density

γ

Atomic friction coefficient of the Langevin thermostat Interfacial adhesion energy

h?i

Average of a physical quantity over all the possible phases of an MD system

hji

Inner product of two functions

Ω

A volume element System volume

Ωi

Volume surrounding the atom i

n;i Ωmap ðM N R ðr ÞÞ

Degree of degeneracy of RN;i

Γ

Transmission coefficient

Dyadic product of two vectors

Preface Molecular dynamics (MD) simulation is a powerful computational method for modeling matter on the atomistic scale. It provides detailed information regarding the interactions and movements of the constituent atoms or molecules of a system and allows for the prediction and understanding of its macroscopic properties, thereby complementing physical experiments. Since this method was first applied to model the phase transition of a simple hard-sphere system in 1957, it has undergone extensive development to become a robust, established, and widely adopted tool for the scientific community. Moreover, with the advent of increasingly powerful computers and advanced numerical algorithms, MD simulation is frequently employed nowadays to solve highly complex problems in areas of cutting-edge research, which include nanomaterial development, polymer science, metallurgy, seawater desalination, pharmacy, organic chemistry, catalytic development, and tribology.

A deep understanding of the fundamental principles of MD simulation is indispensable for its utilization. Its theoretical foundation is multidisciplinary in nature and entails key concepts from several subjects, including classical mechanics, molecular mechanics, statistical mechanics, quantum mechanics, and condensed matter physics. Therefore, understanding the rudiments of MD simulation constitutes a daunting task for novice researchers. This book introduces and encapsulates the core principles of MD simulation while emphasizing their significance in the general workflow of the simulation processes. For more experienced practitioners, advanced MD simulation techniques developed in recent years are reviewed along with substantial case studies. The case studies selected feature the wide applicability of MD simulation and include diverse research topics spanning mechanical, thermal, mass transport, and chemical reaction problems.

Chapters 1 4 are devoted to the fundamentals of MD simulation as well as recently developed simulation algorithms. Researchers unfamiliar with MD simulation are encouraged to peruse these four chapters sequentially to attain a solid understanding of these principles. For more experienced practitioners, these chapters serve as a concise handbook in which the theoretical foundations of key concepts and the physical meanings of important simulation parameters are revealed.

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