Atomistic Computer Simulations. A Practical Guide
John Wiley and Sons Ltd, March 2013, Pages: 361
This introductory "how to" title enables readers to understand, plan, run, and analyze their own independent atomistic simulations, and decide which method to use and which questions to ask in their research project. It is written in a clear and precise language, focusing on a thorough understanding of the concepts behind the equations and how these are used in the simulations.
As a result, readers will learn how to design the computational model and which parameters of the simulations are essential, as well as being able to assess whether the results are correct, find and correct errors, and extract the relevant information from the results. Finally, they will know which information needs to be included in their publications.
This book includes checklists for planning projects, analyzing output files, and for troubleshooting, as well as pseudo keywords and case studies.
(The authors will provide an accompanying blog for the book with worked examples, and additional material and references.)
Preface XV
References XVI
Color Plates XVII
Part One The World at the Atomic Scale 1
1 Atoms, Molecules and Crystals 3
1.1 Length- and Timescales 3
1.2 Electrons in an Atom 5
1.3 Local Environment of an Atom 8
1.3.1 Electrons 8
1.3.2 Local Arrangement of Atoms 11
1.4 Most Favorable Arrangement of Atoms 12
1.4.1 The Concept of Total Energy 12
1.4.2 Beyond the Total Energy 13
1.4.3 The Most Stable Configuration 15
References 16
2 Bonding 17
2.1 Electronic Ground State 18
2.2 Types of Bonds 18
2.2.1 Covalent Bonding 21
2.2.2 Ionic Bonding 22
2.2.3 Metallic Bonding 24
2.2.4 Hydrogen Bonding 25
2.2.5 Dispersion Bonding 25
2.3 Bond Breaking and Creation 26
2.4 Distortion of Bonds 27
References 29
3 Chemical Reactions 31
3.1 Chemical Equations 31
3.2 Reaction Mechanisms 32
3.3 Energetics of Chemical Reactions 33
3.4 Every (Valence) Electron Counts 37
3.5 The Energy Zoo 38
References 39
4 What Exactly is Calculated? 41
4.1 What Can Be Calculated? 41
4.2 What Actually Happens? 43
4.3 Models and Simulation Cells 44
4.4 Energies 47
4.5 Terms 48
4.6 Liquid Iron: An Example 50
References 53
Part Two Introducing Equations to Describe the System 55
5 Total Energy Minimization 57
5.1 The Essential Nature of Minimization 58
5.2 Minimization Algorithms 59
5.2.1 Steepest Descents 61
5.2.2 Conjugate Gradients 62
5.2.3 Quasi-Newton Methods 62
5.2.4 Alternatives 63
5.2.5 Exploring Landscapes 64
5.2.6 Scaling and Computational Cost 66
5.3 Optimize with Success 67
5.3.1 Initial Configuration 67
5.3.2 Initial Forces, Choice of Algorithm and Parameters 68
5.3.3 Fixing Atoms 69
5.3.4 Scaling with System Size 70
5.4 Transition States 71
5.5 Pseudokeywords 72
References 73
6 Molecular Dynamics and Monte Carlo 75
6.1 Equations of Motion 76
6.2 Time and Timescales 77
6.3 System Preparation and Equilibration 79
6.4 Conserving Temperature, Pressure, Volume or Other Variables 81
6.5 Free Energies 83
6.6 Monte Carlo Approaches 84
6.7 Pseudokeywords for an MD Simulation 86
References 87
Part Three Describing Interactions Between Atoms 89
7 Calculating Energies and Forces 91
7.1 Forcefields 92
7.1.1 Reliability and Transferability 95
7.2 Electrostatics 97
7.3 Electronic and Atomic Motion 98
7.3.1 The Born–Oppenheimer Approximation 99
7.3.2 Approximating the Electronic Many-Body Problem 100
7.4 Electronic Excitations 100
References 103
8 Electronic Structure Methods 105
8.1 Hartree–Fock 106
8.2 Going Beyond Hartree–Fock 109
8.3 Density Functional Theory 111
8.4 Beyond DFT 114
8.5 Basis Sets 116
8.6 Semiempirical Methods 119
8.7 Comparing Methods 121
References 124
9 Density Functional Theory in Detail 127
9.1 Independent Electrons 127
9.2 Exchange-Correlation Functionals 128
9.3 Representing the Electrons: Basis Sets 130
9.3.1 Plane Waves 131
9.3.2 Atomic-Like Orbitals 132
9.4 Electron–Nuclear Interaction 133
9.4.1 Pseudopotentials 133
9.4.2 PAW 136
9.4.3 Using All Electrons 136
9.5 Solving the Electronic Ground State 136
9.5.1 Charge Mixing and Electrostatics 137
9.5.2 Metals and Occupancy 139
9.6 Boundary Conditions and Reciprocal Space 139
9.7 Difficult Problems 141
9.8 Pseudokeywords 142
References 143
Part Four Setting Up and Running the Calculation 145
10 Planning a Project 147
10.1 Questions to Consider 147
10.1.1 Research Questions 148
10.1.2 Simulation Questions 149
10.2 Planning Simulations 151
10.2.1 Making it Simple 151
10.2.2 Planning and Adapting the Sequence of Calculations 151
10.3 Being Realistic: Available Resources for the Project 153
10.4 Creating Models 155
10.5 Choosing a Method 156
10.5.1 Molecular Mechanics and Forcefields 156
10.5.2 Semiempirical Methods 158
10.5.3 DFT 159
10.5.4 Post-HF 160
10.5.5 Post-DFT 161
10.6 Writing About the Simulation 162
10.7 Checklists 163
References 164
11 Coordinates and Simulation Cell 165
11.1 Isolated Molecules 166
11.1.1 Cartesian Coordinates 166
11.1.2 Molecular Symmetry 167
11.1.3 Internal Coordinates 169
11.2 Periodic Systems 170
11.2.1 Fractional Coordinates 171
11.2.2 Crystallography and Symmetry in Periodic Systems 172
11.2.3 Supercells 175
11.2.4 Understanding Crystallographic Notation: Space Groups 175
11.2.5 Understanding Crystallographic Notation: Atomic Coordinates 176
11.3 Systems with Lower Periodicity 180
11.3.1 Surfaces in Crystallography 180
11.3.2 Grain Boundaries and Dislocations 182
11.3.3 Modeling Surfaces, Wires and Isolated Molecules 182
11.4 Quality of Crystallographic Data 186
11.5 Structure of Proteins 187
11.6 Pseudokeywords 188
11.7 Checklist 189
References 190
12 The Nuts and Bolts 193
12.1 A Single-Point Simulation 193
12.2 Structure Optimization 194
12.3 Transition State Search 195
12.4 Simulation Cell Optimization 197
12.5 Molecular Dynamics 199
12.6 Vibrational Analysis 200
12.6.1 Simulation of Anharmonic Vibrational Spectra 201
12.6.2 Normal Mode Analysis 202
12.6.3 Harmonic or Anharmonic? 204
12.7 The Atomistic Model 205
12.7.1 Small Beginnings 205
12.7.2 Periodic Images and Duplicate Atoms 205
12.7.3 Crossing (Periodic) Boundaries 206
12.7.4 Hydrogen Atoms in Proteins 207
12.7.5 Solvating a Protein 209
12.8 How Converged is Converged? 209
12.9 Checklists 210
References 211
13 Tests 213
13.1 What is the Correct Number? 213
13.2 Test Systems 214
13.3 Cluster Models and Isolated Systems 215
13.4 Simulation Cells and Supercells of Periodic Systems 216
13.5 Slab Models of Surfaces 216
13.6 Molecular Dynamics Simulations 217
13.7 Vibrational Analysis by Finite Differences 218
13.8 Electronic-Structure Simulations 219
13.8.1 Basis Sets 219
13.8.2 Pseudopotentials and Projector-Augmented Waves 220
13.8.3 K-Points in Periodic Systems 220
13.9 Integration and FFT Grids 221
13.10 Checklists 222
References 223
Part Five Analyzing Results 225
14 Looking at Output Files 227
14.1 DeterminingWhat Happened 227
14.1.1 Has it Crashed? 227
14.2 Why Did it Stop? 229
14.2.1 Why it Did Not Converge? 230
14.3 Do the Results Make Sense? 233
14.4 Is the Result Correct? 234
14.5 Checklist 234
References 234
15 What to do with All the Numbers 235
15.1 Energies 236
15.1.1 Stability 236
15.1.2 Relative Energies: Adsorption, Binding etc. 239
15.1.3 Free Energies 242
15.2 Structural Data 242
15.2.1 Bond Lengths and Angles 243
15.2.2 Distributions 243
15.2.3 Atomic Transport 244
15.2.4 Elastic Constants 246
15.3 Normal Mode Analysis 246
15.3.1 Irreducible Representations 246
15.3.2 Selection Rules from Irreducible Representations 250
15.3.3 Fundamentals, Overtones, and Combination Bands 250
15.4 Other Numbers 251
References 252
16 Visualization 253
16.1 The Importance Of Visualizing Data 253
16.2 Sanity Checks 253
16.3 Is There a Bond? 254
16.4 Atom Representations 254
16.5 Plotting Properties 256
16.5.1 Looking at Charge Density 256
16.5.2 Density of States 256
16.6 Looking at Vibrations 257
16.7 Conveying Information 258
16.7.1 Selecting the Important Bits 258
16.7.2 From Three to Two Dimensions 258
16.7.3 How to Make Things Look Different 260
16.8 Technical Pitfalls Of Image Preparation 264
16.8.1 JPEG, GIF, PNG, TIFF: Raster Graphics Images 264
16.8.2 Manipulating Raster Graphics Images 265
16.8.3 How to Get a 3D Scene into a 2D Image that Can Be Saved 266
16.9 Ways and Means 266
References 268
17 Electronic Structure Analysis 269
17.1 Energy Levels and Band Structure 269
17.2 Wavefunctions and Atoms 271
17.3 Localized Functions 273
17.4 Density of States, Projected DOS 274
17.5 STM and CITS 276
17.5.1 Tersoff–Hamann 277
17.5.2 Bardeen 278
17.6 Other Spectroscopies: Optical, X-Ray, NMR, EPR 278
References 280
18 Comparison to Experiment 283
18.1 Why It Is Important 284
18.2 What Can and Cannot Be Directly Compared 285
18.2.1 Energies 285
18.2.2 Structural Data 286
18.2.3 Spectroscopy 288
18.2.4 Vibrational Spectroscopy 290
18.2.5 Scanning Probes 291
18.2.6 Barriers 292
18.3 How to Determine Whether There is Agreement with Experiment 293
18.4 Case Studies 295
18.4.1 Proton Pumping in Cytochrome c Oxidase 295
18.4.2 Bismuth Nanolines on Silicon 300
References 304
Appendix A UNIX 307
A.1 What’s in a Name 307
A.2 On the Command Line 308
A.3 Getting Around 309
A.4 Working with Data 309
A.5 Running Programs 311
A.6 Remote Work 312
A.7 Managing Data 313
A.8 Making Life Easier by Storing Preferences 314
A.9 Be Careful What You Wish For 315
Appendix B Scientific Computing 317
B.1 Compiling 317
B.2 High Performance Computing 319
B.3 MPI and mpirun 320
B.3.1 How to Run an MPI Job 321
B.3.2 Scaling 321
B.3.3 How to Kill a Parallel Job 321
B.4 Job Schedulers and Batch Jobs 322
B.4.1 How to Queue 322
B.4.2 Submitting and Monitoring 323
B.5 File Systems and File Storage 324
B.6 Getting Help 324
Index 325
Dr. Veronika Br?zdov? obtained her PhD from Humboldt University Berlin in 2005 with Professor J. Sauer. She is currently a Postdoctoral Research Fellow at the London Centre for Nanotechnology, University College London. Her research is focused on computational simulations of solid state surfaces and interfaces, using mainly density functional theory. She has been collaborating closely with experimental groups. She is also an experienced programmer, particularly in Fortran 90 and the Message Passing Interface. She has supervised many undergraduate students taking their first steps. in computational physics.. . Dr. David R. Bowler received his D.Phil. from Oxford University in 1997. He has been a Reader in Physics at UCL since 2005, and held a Royal Society University Research Fellowship from 2002-2010. He is a PI in the London Centre for Nanotechnology and the London-wide Thomas Young Centre. He has driven the development of the massively-parallel linear scaling density functional theory code, Conquest, and collaborates extensively with experimental groups on the growth and properties of nanostructures on semiconductor surfaces..
Customers who bought this item also bought
All rights reserved. © Copyright 2013 Research and Markets WWW4
Terms and Conditions Privacy Policy Publishers Employment Opportunities Site Map Link to us Webmaster Affiliate Network
