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Computational
Materials
Science
AN INTRODUCTION
SECOND EDITION
Computational
Materials
Science
AN INTRODUCTION
SECOND EDITION

June Gunn Lee

Boca Raton London New York

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Taylor & Francis Group, an informa business
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Library of Congress Cataloging‑in‑Publication Data

Names: Lee, June Gunn, author.

Title: Computational materials science : an introduction / June Gunn Lee.
Description: Second edition. | Boca Raton : CRC Press, Taylor & Francis,
2017. | Includes bibliographical references and index.
Identifiers: LCCN 2016025825 | ISBN 9781498749732 (alk. paper)
Subjects: LCSH: Materials--Mathematical models. | Materials--Data processing.
| Molecular dynamics--Mathematics.
Classification: LCC TA404.23 .L44 2017 | DDC 620.1/10113--dc23
LC record available at https://lccn.loc.gov/2016025825

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 Dedication
to Hak Nam, Susan and Ray, Sandra and Dongho,
Gia, Joseph, James, and Gina
Contents
Preface ...............................................................................................................xix
Author ............................................................................................................ xxiii

Chapter 1 Introduction.................................................................................. 1
1.1 Computational materials science .......................................................... 1
1.1.1 Human beings versus matter................................................... 1
1.1.2 Computational materials science ............................................ 3
1.1.2.1 Goals ........................................................................... 3
1.1.2.2 Our approach............................................................. 3
1.2 Methods in computational materials science ...................................... 4
1.2.1 Basic procedures of computational materials science .......... 5
1.2.2 Finite element analysis.............................................................. 5
1.2.3 Monte Carlo method ................................................................. 6
1.2.4 Molecular dynamics .................................................................. 7
1.2.5 First-principles methods (ab initio methods) .......................... 7
1.2.6 Remarks ...................................................................................... 7
1.3 Computers ................................................................................................ 8
Reference ............................................................................................................. 9

Chapter 2 Molecular dynamics ................................................................. 11

2.1 Introduction ............................................................................................ 12
2.1.1 Atomic model in MD............................................................... 12
2.1.2 Classical mechanics ................................................................. 13
2.1.3 Molecular dynamics ................................................................ 14
2.2 Potentials ................................................................................................. 15
2.2.1 Pair potentials .......................................................................... 17
2.2.2 Embedded atom method potentials...................................... 19
2.2.3 Tersoff potential ....................................................................... 22
2.2.4 Potentials for ionic solids ........................................................ 23
2.2.5 Reactive force field potentials ................................................ 24

vii
viii Contents

2.3 Solutions for Newton’s equations of motion...................................... 24

2.3.1 N-atom system.......................................................................... 24
2.3.2 Verlet algorithm ....................................................................... 26
2.3.3 Velocity Verlet algorithm ........................................................ 27
2.3.4 Predictor–corrector algorithm ............................................... 27
2.4 Initialization ........................................................................................... 29
2.4.1 Pre-setups ................................................................................. 29
2.4.1.1 Potential cutoff ........................................................ 29
2.4.1.2 Periodic boundary conditions ............................... 31
2.4.1.3 Neighbor lists .......................................................... 32
2.4.2 Initialization ............................................................................. 32
2.4.2.1 Number of atoms (system size) ............................. 33
2.4.2.2 Initial positions and velocities .............................. 33
2.4.2.3 Timestep ................................................................... 33
2.4.2.4 Total simulation time ............................................. 34
2.4.2.5 Type of ensemble .................................................... 34
2.5 Integration/equilibration ...................................................................... 36
2.5.1 Temperature and pressure control ........................................ 36
2.5.2 Minimization in a static MD run .......................................... 37
2.5.2.1 Steepest-descent method ....................................... 37
2.5.2.2 Conjugate gradients method ................................. 38
2.6 Data production ..................................................................................... 38
2.6.1 Run analysis ............................................................................. 38
2.6.1.1 Conservation of energy .......................................... 38
2.6.1.2 Confirmation of global minimum ........................ 39
2.6.1.3 Time averages under the ergodic hypothesis ..... 39
2.6.1.4 Errors ........................................................................ 40
2.6.2 Energies .................................................................................... 40
2.6.3 Structural properties ............................................................... 41
2.6.3.1 Equilibrium lattice constant, cohesive energy .... 41
2.6.3.2 Bulk modulus .......................................................... 41
2.6.3.3 Thermal expansion coefficient .............................. 42
2.6.3.4 Radial distribution function.................................. 42
2.6.4 Mean-square displacement .................................................... 43
2.6.5 Energetics, thermodynamic properties, and others ........... 44
Homework ........................................................................................................ 44
References.......................................................................................................... 45
Further reading................................................................................................. 46

Chapter 3 MD exercises with XMD and LAMMPS ............................. 47

3.1 Potential curve of Al.............................................................................. 47
3.1.1 Input files .................................................................................. 48
3.1.1.1 Run file ..................................................................... 48
3.1.1.2 Potential file ............................................................. 49
Contents ix

3.1.2 Run ........................................................................................ 50

3.1.3 Results ................................................................................... 50
3.1.3.1 Potential energy curve ....................................... 51
3.2 Melting of Ni cluster............................................................................ 52
3.2.1 Run file ................................................................................. 52
3.2.2 Results ................................................................................... 53
3.2.2.1 Visualization with MDL ChimeSP6 ................. 54
3.3 Sintering of Ni nanoparticles ............................................................. 55
3.3.1 Input file ............................................................................... 55
3.3.2 Results ................................................................................... 57
3.4 Speed distribution of Ar gas: A computer experiment .................. 58
3.4.1 Input file ............................................................................... 60
3.4.2 Results ................................................................................... 61
3.5 SiC deposition on Si(001) ..................................................................... 62
3.5.1 Input file ............................................................................... 62
3.5.2 Results ................................................................................... 65
3.6 Yield mechanism of an Au nanowire ............................................... 66
3.6.1 Input file ............................................................................... 67
3.6.2 Results ................................................................................... 68
3.6.2.1 Snapshots ............................................................. 68
3.6.3 Conclusions .......................................................................... 69
3.7 Nanodroplet of water wrapped by a graphene nanoribbon ......... 69
3.7.1 Input files .............................................................................. 69
3.7.1.1 Positions file (data.C–H2O) ................................ 70
3.7.1.2 Input file .............................................................. 71
3.7.2 Results ................................................................................... 72
3.7.3 Conclusions .......................................................................... 73
3.8 Carbon nanotube tension ................................................................... 74
3.8.1 Introduction ......................................................................... 74
3.8.2 Input file ............................................................................... 75
3.8.3 readdata.CNT ....................................................................... 76
3.8.4 CH.old.airebo ....................................................................... 77
3.8.5 Results ................................................................................... 78
3.9 Si-tension ............................................................................................... 79
3.9.1 Introduction ......................................................................... 79
3.9.2 Input file ............................................................................... 79
3.9.3 Results ................................................................................... 82
3.10 Si–CNT composite under tension...................................................... 83
3.10.1 Introduction ......................................................................... 83
3.10.2 Potentials .............................................................................. 85
3.10.3 Input files .............................................................................. 85
3.10.4 Run ........................................................................................ 89
3.10.5 Results .................................................................................. 89
3.10.6 Conclusions .......................................................................... 90
x Contents

3.11 ZrO2-Y2O3-MSD .................................................................................... 91

3.11.1 Introduction .......................................................................... 91
3.11.2 Input files .............................................................................. 92
3.11.3 Run ........................................................................................ 94
3.11.4 Results ................................................................................... 94
Homework ........................................................................................................ 95
References.......................................................................................................... 96

Chapter 4 First-principles methods .......................................................... 99

4.1 Quantum mechanics: The beginning ............................................. 100
4.1.1 Niels Bohr and the quantum nature of electrons .......... 101
4.1.2 De Broglie and the dual nature of electrons .................. 103
4.1.3 Schrödinger and the wave equation ............................... 104
4.1.4 Heisenberg and the uncertain nature of electrons ........ 105
4.1.5 Remarks............................................................................... 106
4.2 Schrödinger wave equation .............................................................. 107
4.2.1 Simplifying the problem................................................... 107
4.2.1.1 Forget about gravity, relativity, and time ...... 107
4.2.1.2 Forget about nuclei and spin........................... 108
4.2.1.3 Forget about the excited states ........................ 109
4.2.1.4 Use of atomic units ........................................... 109
4.2.2 Time-independent electronic wave equation ................ 109
4.2.3 Energy operator: Hamiltonian H  .....................................110
4.2.4 Waves and wave function................................................. 112
4.2.4.1 Plane wave ..........................................................113
4.2.4.2 Standing wave....................................................114
4.2.4.3 Superposition principle of waves ....................114
4.2.4.4 Indistinguishability of electrons .....................115
4.2.5 Energy E ...............................................................................115
4.2.6 Solutions of Schrödinger wave equation: An
electron in a well .................................................................116
4.2.6.1 An electron in a one-dimensional infinite
well ......................................................................116
4.2.6.2 An electron in a one-dimensional well
with a finite potential ........................................119
4.2.6.3 Hydrogen atom ..................................................119
4.2.6.4 Degenerate states .............................................. 120
4.3 Early first-principles calculations .................................................... 120
4.3.1 n-electron problem ............................................................ 120
4.3.2 Hartree method: One-electron model ............................ 121
4.3.3 Hartree–Fock method ....................................................... 122
4.3.3.1 Expression for Ψ(r ) ........................................... 122
4.3.3.2 Orthonormality of wave functions ................ 123
4.3.3.3 Expression for E ................................................ 124
Contents xi

4.3.3.4 Calculation for E ................................................... 126

4.3.3.5 Variational approach to the search for the
ground-state energy ............................................. 127
4.3.3.6 Self-consistent procedure..................................... 127
4.3.3.7 Remarks .................................................................. 128
Homework ...................................................................................................... 128
References........................................................................................................ 129
Further reading............................................................................................... 129

Chapter 5 Density functional theory ..................................................... 131

5.1 Introduction .......................................................................................... 132
5.1.1 Electron density ..................................................................... 133
5.1.1.1 Electron density in DFT ....................................... 135
5.1.2 Hohenberg–Kohn theorems ................................................. 135
5.1.2.1 Electron density as central player....................... 135
5.1.2.2 Search for the ground-state energy .................... 136
5.2 Kohn–Sham approach ......................................................................... 138
5.2.1 One-electron representations............................................... 138
5.2.2 One-electron system replacing n-electron system ............ 139
5.3 Kohn–Sham equations ........................................................................ 140
5.3.1 Energy terms ...........................................................................141
5.3.1.1 Kinetic energy ........................................................141
5.3.1.2 External energy ..................................................... 142
5.3.1.3 Hartree energy ...................................................... 142
5.3.1.4 Exchange-correlation energy .............................. 143
5.3.1.5 Magnitudes of each energy term ........................ 144
5.3.2 Functional derivatives........................................................... 145
5.3.3 Kohn–Sham equations .......................................................... 147
5.3.3.1 KS orbitals .............................................................. 148
5.3.3.2 KS eigenvalues....................................................... 149
5.4 Exchange-correlation functionals ..................................................... 149
5.4.1 Exchange-correlation hole .................................................... 150
5.4.1.1 Exchange hole ........................................................ 151
5.4.1.2 Correlation hole ..................................................... 152
5.4.1.3 Exchange-correlation hole ................................... 152
5.4.2 Local density approximation ............................................... 153
5.4.2.1 Homogeneous electron gas ................................. 154
5.4.2.2 Exchange energy ................................................... 154
5.4.2.3 Correlation energy ................................................ 154
5.4.2.4 XC energy ............................................................... 155
5.4.2.5 Remarks .................................................................. 156
5.4.3 Generalized gradient approximation ................................. 156
5.4.3.1 PW91 ....................................................................... 158
5.4.3.2 PBE .......................................................................... 158
xii Contents

5.4.4 Other XC functionals ............................................................ 159

5.4.5 Remarks .................................................................................. 160
5.4.5.1 General trends of GGA ........................................ 160
5.4.5.2 Limitations of GGA: Strongly correlated
systems ....................................................................161
5.4.5.3 Limitations of GGA: Band gap
underestimation .....................................................161
5.5 Solving Kohn–Sham equations ..........................................................162
5.5.1 Introduction .............................................................................162
5.5.1.1 Self-consistency ......................................................162
5.5.1.2 Variational principle ............................................. 163
5.5.1.3 Constraints ............................................................. 163
5.5.2 Direct diagonalization .......................................................... 164
5.5.3 Iterative diagonalization ....................................................... 164
5.5.3.1 Total energy and other properties ...................... 165
5.6 DFT extensions and limitations ......................................................... 166
5.6.1 DFT extensions ....................................................................... 166
5.6.1.1 Spin-polarized DFT ...............................................167
5.6.1.2 DFT with fractional occupancies .........................167
5.6.1.3 DFT for excited states ............................................167
5.6.1.4 Finite-temperature DFT ....................................... 168
5.6.1.5 Time-dependent DFT ........................................... 168
5.6.1.6 Linear scaling of DFT ........................................... 169
5.6.2 DFT limitations ...................................................................... 169
Homework ...................................................................................................... 170
References........................................................................................................ 171
Further reading............................................................................................... 172

Chapter 6 Treating solids ......................................................................... 173

6.1 Pseudopotential approach ...................................................................174
6.1.1 Freezing the core electrons................................................... 175
6.1.1.1 Core electrons ........................................................ 175
6.1.1.2 Valence electrons................................................... 175
6.1.1.3 Frozen-core approximation ..................................176
6.1.2 Pseudizing the valence electrons .........................................176
6.1.2.1 Pseudizing procedure .......................................... 177
6.1.2.2 Benefits ................................................................... 178
6.1.3 Various pseudopotentials ..................................................... 179
6.1.3.1 Norm-conserving PPs .......................................... 179
6.1.3.2 Ultrasoft PPs .......................................................... 179
6.1.3.3 PAW potentials ...................................................... 180
6.2 Reducing the calculation size ............................................................ 181
6.2.1 Supercell approach under periodic
boundary conditions ............................................................ 182
Contents xiii

6.2.2 First Brillouin zone and irreducible Brillouin zone.......... 183

6.2.2.1 Reciprocal lattice ................................................... 183
6.2.2.2 The first Brillouin zone ........................................ 186
6.2.2.3 Irreducible Brillouin zone.................................... 186
6.2.3 k-points ................................................................................... 187
6.2.3.1 k-point sampling ................................................... 188
6.2.3.2 Monkhorst–Pack method..................................... 189
6.2.3.3 Γ-point .................................................................... 189
6.3 Bloch theorem ...................................................................................... 189
6.3.1 Electrons in solid ................................................................... 190
6.3.2 Bloch expression with periodic function ........................... 190
6.3.3 Bloch expression with Fourier expansions ........................ 192
6.3.3.1 Fourier expansions ............................................... 192
6.3.3.2 Fast Fourier transformation ................................ 193
6.3.3.3 Matrix expression for the KS equations ............ 193
6.4 Plane wave expansions ....................................................................... 195
6.4.1 Basis set .................................................................................. 195
6.4.1.1 Local basis set ........................................................ 195
6.4.1.2 Plane wave basis set ............................................. 195
6.4.2 Plane wave expansions for KS quantities .......................... 196
6.4.2.1 Charge density ...................................................... 196
6.4.2.2 Kinetic energy ....................................................... 198
6.4.2.3 Effective potential ................................................. 198
6.4.2.4 KS equations .......................................................... 198
6.4.3 KS orbitals and bands ........................................................... 199
6.4.3.1 Band structure of free electron ........................... 200
6.4.3.2 Band structure of electrons in solids ................. 200
6.4.3.3 Density of states .................................................... 202
6.5 Some practical topics ........................................................................... 203
6.5.1 Energy cutoff .......................................................................... 203
6.5.1.1 Cutoff energy ......................................................... 203
6.5.2 Smearing ................................................................................. 204
6.5.2.1 Gaussian smearing ............................................... 205
6.5.2.2 Fermi smearing ..................................................... 205
6.5.2.3 Methfessel–Paxton smearing .............................. 205
6.5.2.4 Tetrahedron method with Blöchl corrections....... 206
6.6 Practical algorithms for DFT runs..................................................... 206
6.6.1 Electronic minimizations ..................................................... 206
6.6.1.1 Direct diagonalization ......................................... 207
6.6.1.2 Iterative Davidson method .................................. 207
6.6.1.3 RMM-DIIS method ............................................... 207
6.6.2 Ionic minimizations .............................................................. 209
6.6.2.1 Hellmann–Feynman forces ................................. 209
6.6.2.2 Minimization methods ........................................ 210
xiv Contents

6.6.3 Born–Oppenheimer molecular dynamics ......................... 210

6.6.4 Car–Parrinello molecular dynamics ....................................211
6.6.4.1 CPMD for electronic minimization.....................211
6.6.4.2 CPMD for ionic minimization ............................ 212
6.6.5 Multiscale methods ............................................................... 213
6.6.5.1 Crack propagation in silicon ............................... 213
Homework .......................................................................................................214
References.........................................................................................................214
Further reading............................................................................................... 215

Chapter 7 DFT exercises with Quantum Espresso ............................. 217

7.1 Quantum espresso............................................................................... 217
7.1.1 General features ..................................................................... 217
7.1.2 Installation ............................................................................. 218
7.2 Si2 ........................................................................................................... 218
7.2.1 Introduction ............................................................................ 218
7.2.2 Si2.in ........................................................................................ 218
7.2.3 Si.pbe-rrkj.UPF ....................................................................... 220
7.2.4 Run .......................................................................................... 221
7.2.5 Si2.out ..................................................................................... 221
7.3 Si2-convergence test ............................................................................ 223
7.3.1 Introduction ............................................................................ 223
7.3.2 Si2-conE.in ............................................................................. 223
7.3.3 Results ..................................................................................... 223
7.3.4 Further runs ........................................................................... 224
7.4 Si2-band ................................................................................................. 227
7.4.1 Introduction ............................................................................ 227
7.4.2 Si2-scf ...................................................................................... 227
7.4.3 Si2-bands ................................................................................. 228
7.4.4 Results and discussion .......................................................... 229
7.5 Si7-vacancy............................................................................................ 230
7.5.1 Introduction ............................................................................ 230
7.5.2 Si8-scf ...................................................................................... 231
7.5.3 Si7v-relax ................................................................................ 232
7.6 Si7-vacancy diffusion .......................................................................... 235
7.6.1 Introduction ............................................................................ 235
7.6.2 Calculation method ............................................................... 235
7.6.3 Step 1: First image .................................................................. 236
7.6.4 Step 2: Last image .................................................................. 236
7.6.5 Step 3: Si7v.NEB20.in ............................................................. 237
Homework ...................................................................................................... 241
References........................................................................................................ 242
Contents xv

Chapter 8 DFT exercises with VASP ...................................................... 243

8.1 VASP ...................................................................................................... 245
8.1.1 General features of VASP ..................................................... 245
8.1.2 Flow of VASP .......................................................................... 245
8.1.2.1 Ten things you should not do in a VASP run........ 246
8.2 Pt-atom .................................................................................................. 247
8.2.1 Input files ............................................................................. 247
8.2.1.1 INCAR .................................................................... 247
8.2.1.2 KPOINTS................................................................ 248
8.2.1.3 POSCAR ................................................................. 248
8.2.1.4 POTCAR ................................................................. 249
8.2.2 Run .......................................................................................... 249
8.2.3 Results .................................................................................... 250
8.2.3.1 OSZICAR................................................................ 250
8.2.3.2 OUTCAR ................................................................ 251
8.2.3.3 Continuous run ..................................................... 251
8.3 Pt-FCC.................................................................................................... 252
8.3.1 Input files ................................................................................ 252
8.3.1.1 INCAR .................................................................... 252
8.3.1.2 KPOINTS................................................................ 254
8.3.1.3 POSCAR ................................................................. 254
8.3.2 Run .......................................................................................... 255
8.3.2.1 run.vasp .................................................................. 255
8.3.2.2 nohup.out ............................................................... 255
8.3.3 Results ..................................................................................... 256
8.3.3.1 CONTCAR ............................................................. 256
8.3.3.2 OUTCAR ................................................................ 257
8.4 Convergence tests ................................................................................ 257
8.4.1 Encut convergence ................................................................. 257
8.4.1.1 Shell script run.lattice........................................... 258
8.4.1.2 Run .......................................................................... 259
8.4.1.3 Results .................................................................... 259
8.4.2 k-points convergence ............................................................. 261
8.5 Pt-bulk ................................................................................................... 262
8.5.1 Cohesive energy of solid Pt .................................................. 262
8.5.1.1 Cohesive energy .................................................... 264
8.5.2 Vacancy formation energy of Pt .......................................... 265
8.5.2.1 Vacancy formation energy ................................... 265
8.5.2.2 CHGCAR plot ........................................................ 266
8.6 Pt(111)-surface ....................................................................................... 268
8.6.1 Pt(111)-slab .............................................................................. 268
8.6.1.1 INCAR .................................................................... 268
8.6.1.2 KPOINTS................................................................ 269
xvi Contents

8.6.1.3 POSCAR ............................................................... 269

8.6.1.4 Results................................................................... 271
8.6.2 Adsorption energy................................................................. 272
8.6.2.1 POSCAR ............................................................... 272
8.6.2.2 POTCAR ............................................................... 274
8.6.2.3 Results................................................................... 274
8.6.3 Work function and dipole correction .................................. 275
8.6.3.1 Work function ...................................................... 275
8.6.3.2 Results................................................................... 276
8.7 Nudged elastic band method ............................................................. 277
8.7.1 Principle of NEB method ...................................................... 278
8.7.2 Procedure of the NEB method ............................................. 278
8.7.2.1 Initial and final states ......................................... 278
8.7.2.2 Initial band ........................................................... 279
8.7.2.3 Nudging the band ............................................... 279
8.7.2.4 Force calculation.................................................. 279
8.7.2.5 NEB method with climb..................................... 279
8.7.3 Pt(111)-O-NEB ........................................................................ 280
8.7.3.1 Pt(111)-slab-O-HCP ............................................. 280
8.7.3.2 Run NEB with VTST scripts .............................. 281
8.7.3.3 Results................................................................... 282
8.8 Pt(111)-catalyst ..................................................................................... 284
8.8.1 Catalyst ................................................................................... 284
8.8.2 Density of states ..................................................................... 285
8.8.3 Pt(111)-slab-O-DOS................................................................ 285
8.8.3.1 Static run............................................................... 285
8.8.3.2 DOS run ................................................................ 285
8.8.3.3 Results................................................................... 286
8.9 Band structure of silicon ..................................................................... 287
8.9.1 Static run for Si ....................................................................... 288
8.9.2 Run for band structure of Si ................................................. 290
8.9.2.1 INCAR .................................................................. 290
8.9.2.2 KPOINTS .............................................................. 290
8.9.2.3 EIGENVAL ........................................................... 291
8.10 Phonon calculation for silicon............................................................ 293
8.10.1 Input files ................................................................................ 293
8.10.2 Phonon calculations .............................................................. 294
8.10.2.1 INPHON............................................................... 295
Homework ...................................................................................................... 297
References........................................................................................................ 297
Contents xvii

Chapter 9 DFT exercises with MedeA-VASP ....................................... 299

9.1 MedeA-VASP ........................................................................................ 299
9.1.1 General features ..................................................................... 299
9.2 Si2-band-HSE06.................................................................................... 300
9.2.1 Introduction ............................................................................ 300
9.2.2 Run steps ................................................................................ 301
9.2.3 Results ..................................................................................... 302
9.3 Si16-phonon .......................................................................................... 304
9.3.1 Introduction ............................................................................ 304
9.3.2 Ionic relaxation for supercell with displacements ............ 304
9.3.3 Results ..................................................................................... 304
9.4 W12C9-Co28-interface ......................................................................... 307
9.4.1 Introduction ............................................................................ 307
9.4.2 Surface models for WC and Co............................................ 308
9.4.3 Interface model for WC–Co .................................................. 308
9.4.4 Results .................................................................................... 309
9.5 Mg4(Mo6S8)3-barrier energy .................................................................311
9.5.1 Introduction .............................................................................311
9.5.2 NEB run ...................................................................................314
9.5.3 Results ......................................................................................314
9.6 Si14-H2-ab initio MD .............................................................................314
9.6.1 Introduction .............................................................................314
9.6.2 Run steps ..................................................................................316
9.6.3 Results ..................................................................................... 317
References.........................................................................................................318

Appendix A: List of symbols and abbreviations ....................................... 319

Appendix B: Linux basic commands .......................................................... 323
Appendix C: Convenient scripts .................................................................. 325
Appendix D: The Greek alphabet ................................................................ 337
Appendix E: SI prefixes ................................................................................. 339
Appendix F: Atomic units............................................................................. 341
Index ................................................................................................................ 343
Preface
No longer underestimated, computational science has emerged as a pow-
erful partner to experimental and theoretical studies. Accelerated by the
ever-growing power of computers and new computational methods, it
is one of the fastest growing fields in science these days. Its predictive
power in atomic and subatomic scales benefits all disciplines of science,
and materials science is definitely one of them. Note that, for example,
materials under extreme conditions such as high temperature or pressure,
high radiation, on a very small scale, can be rather easily examined via the
keyboard in computational materials science.
Computational science has been a familiar subject in physics and
chemistry, but in the materials field it was considered of secondary
importance. It is now in the mainstream, and we have to catch up with
the knowledge accumulated in the subject, which strongly involves phys-
ics and mathematics. Here, we are forced to deal with an obvious ques-
tion: how much catch-up will be enough to cover the major topics and to
perform computational works as materials researchers? Dealing with the
entire field might be most desirable, but many certainly prefer to cover
only the essential and necessary parts and would rather be involved in
actual computational works. That is what this book is all about.
As listed in the “Further Readings” sections in several chapters, a
number of excellent and successful books are already available in this
field. However, they are largely physics- or chemistry-oriented, full
of theories, algorisms, and equations. It is quite difficult, if not impos-
sible, for materials students to follow all those topics in detail. This book
intends to do some sorting and trimming of the subject, so that many are
able to venture into the field without too much difficulty. Thus, this book
is exclusively devoted to students who would like to venture into compu-
tational science and to use it as a tool for solving materials problems. Once
this book is completed, one may go further to the more advanced books as
listed in “Further Readings.”
A materials system may be described at three different levels: the elec-
tronic structure level of nuclei and electrons, the atomistic or molecular
level, and the finite element level of coupled structural elements. In this

xix
xx Preface

book, we will deal with only the first two levels of the materials system
and their computational treatments with molecular dynamics (MD) and
first-principles methods, which are most relevant and essential in materi-
als science and engineering. With these tools, we simply try to bring a
very small part of nature on computer as a system, and apply the known
rules of nature to solve a certain problem at hands, especially on materials.
This book is organized into nine chapters, starting with Chapter 1,
which gives a general overview of computational science. Chapter 2 intro-
duces MD methods based on classical mechanics: Its implementation
into actual calculations follows in Chapter 3 with run examples of XMD
and LAMMPS, respectively. Chapter 4 introduces first-principles meth-
ods based on quantum mechanics on a brief introductory level. Here,
various illustrations and appropriate analogies will be presented to assist
students to understand this tough subject. Chapter 5 is dedicated solely
to the density functional theory (DFT) in detail, because this is the very
first-principles method that can handle materials practically.
Chapter 6 exclusively deals with solids and reveals how bulk materi-
als can be represented with a handful of k-points. The chapter also pro-
vides how each orbital of electron leads to particular properties of solids
such as total energy, band structure, and band gap. Finally, Chapters 7
through 9 implement the DFT into actual calculations with various codes
such as Quantum Espresso, VASP, and MedeA-VASP, respectively. They
cover from an atom to solids, and from simple GGA to GGA+U and hybrid
methods. Chapter 9 specifically deals with advanced topics in DFT count-
ing dispersion, +U, DFT with hybrid XC potentials, and ab initio MD by
using a convenient GUI program, MedeA-VASP.
Note that methods once considered as “too expensive” are now prac-
tical enough to treat materials, owing to the ever-increasing power of
computers. Various postprocessing programs such as VESTA, VMD, and
VTST will be exercised through the runs.
For using this book as a textbook in the classroom, here are some tips
and suggestions for a course outline:

• The contents are so arranged that one semester will be enough to

cover this book.
• Lectures and run exercises may be conducted simultaneously, for
example, Chapter 2 with Chapter 3, and Chapters 5 and 6 with
Chapters 7 through 9.
• Most exercises with XMD (Chapter 3), LAMMPS (Chapter 3), and
Quantum Espresso (Chapter 7) are so arranged that they can be car-
ried out on student’s notebook computers or PCs in a reasonable time.
• Most exercises with VASP (Chapter 8) can be carried out on any
mini-supercom with more than eight CPUs via remote access from
Preface xxi

the classroom. However, only starting the run during class and pro-
viding the results at the next class will be an excellent option.
• The exercises with MedeA-VASP (Chapter 9) can be carried out on
any mini-supercom with more than eight CPUs via remote access
from the classroom. Again, only starting the run during class and
providing the results at the next class will be an excellent option.

Writing a book is a variational process. One minimizes mistakes itera-

tively, but it never goes down to the ground-state (zero mistake). Erratum
will be posted under http://www.amazon.com/June-Gunn-Lee/e/
B005N2XON0/ref=ntt_dp_epwbk_0.
Some final remarks concerning the preparation of this book:

• Analogies and illustrations used in this book may have been exag-
gerated to emphasize certain points.
• Figures used in this book often show the general features, neglect-
ing the details or exact numbers.

During the course of writing this book, I have been privileged to have
much support. I am particularly grateful to three of my colleagues at the
Computational Science Center, Korea Institute of Science and Technology
(KIST): Dr. Kwang-Ryoel Lee, Dr. Seung-Cheol Lee, and Dr. Jung-Hae
Choi. Without their support and advice, this book would not have been
possible. I am indebted to all my friends who kindly provided examples
and scripts for this book: Professor Ho-Seok Nam (Kookmin University,
Seoul), Professor Aloysius Soon (Yonsei University, Seoul), Dr. Sang-Pil
Kim (Samsung Electronics, Suwon), Dr. Jinwoo Park (Sejong University,
Seoul), Na-Young Park (KIST, Seoul), Dr. Joo-Whi Lee (Kyoto University,
Kyoto), Byung-Hyun Kim (Samsung Electronics, Suwon), Dr. Jung-Ho
Shin (Humboldt-Universität zu Berlin, Berlin), Professor Yeong-Cheol Kim
(KoreaTech, Cheonan, Korea), and Dr. Ji-Su Kim (KoreaTech, Cheonan,
Korea).

MATLAB® is a registered trademark of The MathWorks, Inc. For product

information, please contact:

The MathWorks, Inc.

3 Apple Hill Drive
Natick, MA 01760-2098 USA
Tel: +1 508 647 7000
Fax: +1 508 647 7001
E-mail: info@mathworks.com
Web: www.mathworks.com
Author
June Gunn Lee is an emeritus research fellow at the Computational
Science Center, Korea Institute of Science and Technology (KIST), Seoul,
where he served for 28 years. He has also lectured at various universi-
ties in Korea for over 20 years. He has published about 70 papers both on
engineering ceramics and computational materials science. Dr. Lee is a
graduate of Hanyang University, Seoul, and acquired his PhD in materials
science and engineering from the University of Utah. He has been involved
in computational materials science ever since he was a visiting professor
at Rutgers University, New Jersey, in 1993. Currently, he is lecturing at
University of Seoul, Seoul.

xxiii
chapter one

Introduction
It is amazing how much computing power has progressed since the
invention of the Chinese abacus: from slide rule to mechanical calcula-
tor, vacuum-tube computer, punch-card computer, personal computer,
supercomputer, and cluster-supercomputer (Figure 1.1). Calculation speed
has increased roughly 1010 times in the span of about 50 years and is still
growing. Its immense impact on every sector of society is astonishing.
In this chapter, the significance of computational science in materials is
addressed, and a brief description of the various methods is presented.
The last section will provide remarks on the development of computers.

1.1 Computational materials science

1.1.1 Human beings versus matter
We may say that we are all alike since all of us talk, work, play, and eat
in a very similar manner. While this is true, our individual behaviors
are so versatile as a result of different feelings, emotions, ideologies, phi-
losophies, religions, and cultures that no individuals actually behave
in exactly the same way. Despite scientific studies on human behaviors
and mental processes, it is very difficult to predict events that involve
humans. The numerous upsets in battle and sports aside, we cannot even
tell whether the person next to us will stand up or remain seated in the
very next moment.
On the contrary, atoms and their constituting electrons and nuclei (the
main characters at the arena of computational materials science) always
follow specific rules without exceptions. If an exception is observed, it is
more likely that it is a mistake due to a human error. Unlike humans,
an electron never kills itself or other electrons because of love. The same
goes for nuclei, atoms, molecules, and materials. They simply follow the
known laws of nature, which are mainly classical and quantum mechan-
ics in terms of electromagnetic force (Figure 1.2). Therefore, we can foresee
practically all forms of phenomena encountered in materials by tracing
down the interactions between them.

1
2 Computational Materials Science

Figure 1.1 Developments of computing power: from Chinese abacus to

cluster-supercomputer.

Electromagnetic
force

Figure 1.2 Complexity involved in human events and simplicity associated with
matters.
Chapter one: Introduction 3

1.1.2 Computational materials science

1.1.2.1 Goals
In computational materials science, we aim to understand various prop-
erties and phenomena of materials and achieve designing and making
better materials for society. This goal is realized by modeling materi-
als with computers that are programmed with theories and algorithms
based on physics, mathematics, chemistry, material science, and com-
puter science. For example, the sintering behavior of a metal or a ceramic
can be normally studied with the usual sintering furnace in a laboratory.
However, it can be done on a computer by using molecular dynamics
(MD) on atomic scale. By changing various input conditions, the entire
spectra of data can be generated efficiently and accurately if the runs are
set up properly.
In many cases, a computational approach may become the only way to
handle materials under extreme and hostile conditions that can never be
reached in a laboratory: under high pressures, at high temperatures, and
in the presence of toxic substances or nuclear radiation. For example, the
materials under nuclear fusion environments are of great concern these
days. The various damages occurring in fusion materials by neutron irra-
diation can be simulated without worrying about expensive equipment
and danger of radiation.
Let us look at another example that has great impact on our daily lives.
Every day we use a cell phone, smart phone, smart pad, TV, computer,
and so on, which employ IC chips usually made of silicon. Using com-
putational materials science, we can design better materials and develop
faster, smaller, and lighter IC chips. To summarize, there is no doubt that
computational materials science will change the paradigm of materi-
als research. It will change “lab experiments” with heavy equipment to
“keyboard science” on computers. Currently, computational materials
science is no longer a specialized topic. It has become familiar and rou-
tine such as analyzing XRD curves and examining SEM or TEM images.
Furthermore, most people recognize that computational materials science
is not just an optional topic but an essential one. It is not surprising to hear
scientists say “computation first, then experiment” or “material design by
computation.”

1.1.2.2 Our approach

I wrote the following comparison as an illustration in my book (Lee 2003)
published in 2003, but allow me to restate it. For a materials scientist, com-
putational science is a convenient tool such as a car (Figure 1.3). In order
to operate a car, it is not necessary to understand how the engine block
is cast with molten metal or how the combustion energy transfers from
engine to wheels as the mechanical energy of rotation. We only need to
4 Computational Materials Science

Figure 1.3 Driving on the roads of computational materials science.

know how to use the accelerator, brakes, and steering wheel, as well as be
aware of a few traffic rules.
Then, we check the car for maintenance if we notice anything wrong.
Similarly, we use computational methods with well-proven codes, run
it, obtain data, and check the results with experts if we find something
amiss. It is not necessary to understand all the theories, algorithms, and
equations in detail. It is also not necessary to understand the codes or pro-
grams down to the bits and bytes. This knowledge is reserved for other
professionals such as physicists and chemists.
However, it is undeniable that there are still certain basics to be fully
comprehended even for materials people. Otherwise, there will be limita-
tions not only to our understanding but also to our performance on actual
simulations. This book intends to cover the essential basics and to pro-
vide assistance to materials people with many useful illustrations, figures,
quotes, and, most of all, step-by-step examples. This will help readers to
be on track during a simulation process without losing the connection
between the particles involved and the underlying concepts. Then this
will lead to a more meaningful interpretation of the results.

1.2 Methods in computational materials science

Do you want to calculate it, or do you want it to be
accurate?
John C. Slater (1900–1976)

In this section, the basic procedures and methods in computational mate-

rials science are briefly introduced.
Exploring the Variety of Random
Documents with Different Content
 214 Osiris and the Egyptian Resurrection plumes, and
mounted on a staff "^, just as W, the backbone of Osiris, was the
religious symbol of the city of Busiris ; each was the symbol of
slaughter, or sacrifice, and to each, or before each, sacrifice had to
be made. Details of the early history of Busiris and Abydos are not
forthcoming, but it is tolerably certain that the worship of Osiris was
the most important feature in the life of these cities at all periods of
their existence, and that among all the observances connected with
his cult, the sacrificing of human beings was not the least frequent,
and not the least important. We have now to consider some of the
proofs found in Egyptian texts that human sacrifice was regarded as
a necessary concomitant of burials of the followers of Osiris, and the
evidence on the same point which is deduced from Egyptian
archaeology. Every one is familiar with the little figures, found in
such large numbers in our museums, which are made in the form of
a mummy and are commonly called " Shabtiu," or " Ushabtiu."' The
Shabti, or Shauabti,^ is a figure made of stone, alabaster, wood,
faience, etc., and is found in tombs from the Vlth dynasty to the
Roman Period. In the Vlth dynasty the Shabti appears to have been
uninscribed ; in the Xllth it frequently bears the name and titles of
the person for whom it was made, and with whom it was buried ;
and in the XVII Ith and following dynasties, in addition to the name
and titles of the deceased, it bears a text which is identical with the
Vlth Chapter of the Book of the Dead. Its earliest form is that of a
mummy with no hands showing, later it has its hands crossed over
the breast,^ later each hand holds the emblem of life,* still later
each hand holds a hoe \ ,^ and ^ See the Shabti figure of Amasis I
in the British Museum (No. 32,191). * See the Shabti figure of
Amen-hetep II in the British Museum (No. 35,365). '' See the Shabti
figure of Seti I in the British Museum No. 22,818).
 Osiris and Human Sacrifice 215 A Meroitic queen spearing
captives. From a pyramid chapel at Meroe.
 2i6 Osiris and the Egyptian Resurrection last of all a basket
is thrown over the shoulder.-^ The text, which is cut or written on
figures from the Xllth dynasty onwards, explains quite clearly the
purpose which the figures were intended to serve, for in it the figure
is called upon, in the name of the deceased person written upon it,
to perform whatsoever labours he might be adjudged to do in the
Other World. These labours consisted in tilling and planting and
watering the fields, and in bringing sand from the East to the West,
and in doing whatsoever had to be done in connection with
agriculture in the Other World. Now, the earliest figures of this class
are uninscribed, and the custom of burying mummy-figures of this
kind with the dead seems to be senseless unless we accept the view
which we owe first of all to Professor Maspero, viz., that they
represent the slaves who were buried, alive or dead, with their
masters, in order that their spirits might serve the spirits of their
masters in the Other World, just as their bodies had ministered to
their masters' bodies in this world. This view is undoubtedly correct,
and agrees with all that we know about African funeral murders.
When, however, we come to apply this view to the ushabtiu figures
which have names and a formula cut upon them, certain difficulties
appear in the way, for it seems as if they were made for an entirely
different purpose. The early uninscribed figures were intended to do
work of every kind for their master, in fact, to make themselves
generally useful in the Other World. The inscribed figures were
intended, as we learn from the formula, to do agricultural work
chiefly, and it is clear that they were destined to perform celestial
corvde work in the kingdom of Osiris. The purposes of all of these
figures was to do work for the dead, but why particular kinds of
work are specified on those which have names cut upon them it is
hard to say. Some think that the early and late figures represent two
distinct beliefs, i.e., in the first case, that whatsoever a man needed
to have done in the Other World would be done as a matter of
course by servants, or slaves, and in the second case, that
whatsoever he needed to have done ' See the figures of the XXVIth
dynasty.
 Osiris and Human Sacrifice 217 A Meroitic queen spearing
captives. From a pyramid at Meroe.
 2i8 Osiris and the Egyptian Resurrection would have to be
done by himself.^ To avoid this unpleasant possibility, ushabtiu
figures were invented. This view does not, it seems to me, explain
the difficulty, for it was obvious to the Egyptian of all periods that if
he had no one to do work for him in the Other World he would have
to do it himself; and, believing this, he took steps to provide
ushabtiu figures, which in the early times were without inscriptions,
and in the later times had names and a formula cut or written on
them. The explanation of the appearance of the name and the
formula is, I believe, to be sought for in connection with the
development of the cult of Osiris during and after the Xllth dynasty.
It is possible that men began to think that the spirit of an
unprincipled chief or king in the Other World might lay claim to, or
annex, the services of the spirit-slaves belonging to other people,
and do this to such a degree that certain spirits would have no spirit-
slaves left to minister to their wants. Whether ushabtiu bore names
or not makes no difference to the fact that they represented slaves,
but if an Egyptian gave a figure his own name, a spirit-slave so
represented would bear that name, and no spirit-chief could then
annex the services of that spirit-slave and plead ignorance of his
identity and of his master's name if called upon to explain. It
appears to be certain that the naming of the figure in some way
assured the services of a spirit-slave to the man whose name it bore.
The application of the formula, or Vlth Chapter of the Book of the
Dead, to the shabti figure represents, I believe, the adoption of the
old African custom of funeral murder into the cult of Osiris. This cult,
as we have already seen, abolished cannibalism, or at least the
eating of Egyptian human flesh by the Egyptians, and as Osiris
introduced the eating of grain and cereals in its stead, it was meet
that his followers should be proficient in the arts of agriculture. But
no Egyptian ever loved digging or top-dressing the ground, or the
toil of the shddtif, for its own sake, and if the shabti figure could be
made to serve in the capacity of a farmlabourer, by cutting upon it
the magical formula, the ^ A.Z., Band XXXII, p. ii6. On the so-called
"servant figures," see A.Z., Band XXXV, p. 119.
 Osiris and Human Sacrifice 219 A Meroitic queen
slaughtering prisoners of war. From a bas-relief at Nagaa.
 220 Osiris and the Egyptian Resurrection demands of the
cuU of Osiris would be fulfilled, and the high-class Egyptian might
reasonably hope to enjoy absolute idleness in the Other World, as
his fathers had done before him. A pious follower of Osiris like Seti I
took great care to provide himself with a large corvde party, for
seven hundred ushabtiu, at least, inscribed with the Vlth Chapter of
the Book of the Dead, were found in his tomb. In later times, when
the ushabtiu were placed in boxes, it seems that some people had
buried with them one shabti figure for each day in the year. This was
probably the case with the officials Amen-hetep and Ankh-f-en-
Khensu, for of the former 149 ushabtiu, and of the latter 171
ushabtiu are preserved in the British Museum.^ When the boxes
were first found each was full, and each contained very many more
figures. Another proof that human beings were sacrificed at funerals
of the followers of Osiris is furnished by Chapter LI I of the Book of
the Dead. In this Chapter, which was written with the view of
providing the deceased with food, he is made to say : " Let me
direct " my fields in Tetu (Busiris), and my crops in Anu "
(Heliopolis), let me live on bread made of white grain, " and beer
made of red grain (barley), may there be given " to me the victims
of my father and mother as guardians " of my door." The word I
have here rendered " victims " is abtu \ \'^\> "^ ^ J) ' • Formerly I
translated it by " ancestors,'' and compared it with the Hebrew word
for " fathers,"^ but it seems that it is rather to be connected with
the idea of " smiting," " slaughtering," etc., an idea which is
suggested by the determinative \v . The word, no doubt, means
sacrifices,^ and the other determinatives, VW J) , indicate clearly
that they were men and women, and the deceased 1 See Third
Egyptian Room (Wall-case 115), Nos. 35,289, 35,290. ' nils.
Compare tr J c. V^ .^ 0 , " slaughters " (Papyrus of Nu, Chapter
CXLVI, § XVI).
 Osiris and Human Sacrifice 221 A Meroitic queen
slaughtering prisoners of war. From a bas-relief at Nagaa.
 222 Osiris and the Egyptian Resurrection seems to wish
that victims may be sacrificed to him, even as they were for his
father and mother. A tradition extant in the XlXth dynasty, and
illustrated in the Book Am-Tuat (Division VII), also proves that the
Egyptians believed human sacrifices to have been made when Osiris
himself was buried. The illustrations on the tomb of Seti I represent
the tombs of Tem, Khepera, Ra, and Osiris. At each end we see a
human head, and these, as Professor Maspero suggested many
years ago, represent those of the victims who were buried in the
foundations of the grave. The custom of resting the coffin, where a
coffin is used at all, on human heads, is common in many parts of
the Sfidin.i In Ashanti several persons are invariably put to death
after an earthquake, as a sacrifice to Sasabonsum, and houses
which are rebuilt or repaired after an earthquake are sprinkled or
moistened with human blood. In 1 88 1 an earthquake shock threw
down a portion of the wall of the king's residence in Coomassie, and
the priests declared it to be the act of Sasabonsum. Fifty girls were
slain, and the wall was rebuilt of mud moistened with the blood of
these virgins. Slaves often are sacrificed when a building is begun, to
make it stable, and the foundations are sprinkled with their blood.
The idea that human blood is necessary to make a foundation secure
is very widespread.^ A direct proof that human sacrifices were
offered to Osiris under the New Empire is afforded by the tomb of
Mentu-her-khepesh-f,^ from which the following illustrations are
taken. Here, in the first cut, we see three men drawing a sledge, on
which, kneeling with his face downwards, is a man, who is described
as the " Tekenu," I . In the second cut we see a "kher-heb" priest, 1
Compare, " The heads of the victims slain are usually placed at the
bottom of the grave, and on them the coffin rests." — Ellis,
Tshispeaking Peoples, p. 1 64. ^ Ibid., p. 36. ^ v\ Y 2^.=^ . See
Maspero, Mimoires Miss. Archiologique, torn. V, Paris, 1894, p. 435
ff.
Osiris and Human Sacrifice 223
 224 Osiris and the Egyptian Resurrection a "smer" priest, a
" sem " priest, a "royal kinsman," and an Ut official, presenting a
table of offerings to the Tet, symbol of Osiris, and the Ram of
Mendes, where the backbone (tet) of Osiris was found. In the third
cut we see, beginning on the right, two men bringing a sledge. Next
we see the sledge cast into a grave-pit, or pit of slaughter, kheb ® J
, and then two men, who are arrayed as mummies, lying flat
supported on their hands, which are free from the bandages, and on
their toes. The inscription shows that they are " Anti, from the land
of Sti," i.e., Nubians, or Sudani folk. We next see each of these
seated on the ground, with his grave garment stripped from him,
and two men, one on each side of him, engaged in strangling him. It
is, of course, possible to argue that the strangling of two of the Anu,
or Anti, folk here represented is only a symbolic act, and that these
men did not lose their lives at all. When, however, we remember
that the festival of sacrificing the Anu began under the Ancient
Empire, and that sacrifices of the Anu, or Anti, were offered up by
Usertsen III in the Xllth dynasty, and by Thothmes III in the XVIIIth
dynasty, and that other kings religiously followed their example, we
can only conclude that the sacrifice of the two Anti represented in
these cuts actually took place. Apart from the political importance of
the ceremony of sacrificing the Anti, which has been well described
elsewhere,^ the Egyptians were accustomed to strangle human
victims at funerals, and of this fact there is abundant evidence. Thus
in the Xlth dynasty tombs of the priestesses at Der al-Bahart Mr. H.
R. Hall, in 1905, found the body of a woman who had been
strangled, and the priestess Amenit, whose body may now be seen
in the Egyptian Museum in Cairo, was also strangled.^ And the
women who are now lying on the floor of the sarcophagus chamber
of Amen-hetep II either committed suicide on the death 1 Naville,
Les Anu (in Recueil, torn. XXXII) ; and Capart, La Fete de Frapper Us
Anou (in Revue de P Histoire des Religions, torn. XLIII, 1901). ^
King and Hall, Egypt and Western Asia, p. 329.
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