Atomistic computer simulations: a practical guide
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| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Weinheim
Wiley-VCH
2013
|
| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XXIX, 331 S. Ill., graph. Darst. |
| ISBN: | 9783527410699 9783527671847 3527410694 |
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| 245 | 1 | 0 | |a Atomistic computer simulations |b a practical guide |c Veronika Brázdová and David R. Bowler |
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2013 | |
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IMAGE 1
CONTENTS
PREFACE X V
REFERENCES X V I
COLOR PLATES X V I I
PART O N E THE WORLD A T T H E ATOMIC SCALE 1
1 ATOMS, MOLECULES AND CRYSTALS 3
1.1 LENGTH- A N D TIMESCALES 3
1.2 ELECTRONS I N A N ATOM 5
1.3 LOCAL ENVIRONMENT O F A N ATOM 8
1.3.1 ELECTRONS 8
1.3.2 LOCAL ARRANGEMENT O F ATOMS 11 1.4 MOST FAVORABLE ARRANGEMENT O F
ATOMS 12
1.4.1 THE CONCEPT O F TOTAL ENERGY 12
1.4.2 BEYOND THE TOTAL ENERGY 13
1.4.3 T H E MOST STABLE CONFIGURATION 15 REFERENCES 16
2 BONDING 17
2.1 ELECTRONIC GROUND STATE 18
2.2 TYPES O F 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 A N D CREATION 26
2.4 DISTORTION O F BONDS 2 7
REFERENCES 29
3 CHEMICAL REACTIONS 31
3.1 CHEMICAL EQUATIONS 31
3.2 REACTION MECHANISMS 32
3.3 ENERGETICS O F CHEMICAL REACTIONS 33
HTTP://D-NB.INFO/1026137284
IMAGE 2
VIII | CONTENTS
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 A N D SIMULATION CELLS 44
4.4 ENERGIES 4 7
4.5 TERMS 48
4.6 LIQUID IRON: A N EXAMPLE 50
REFERENCES 53
PART TWO INTRODUCING EQUATIONS TO DESCRIBE T H E SYSTEM 5 5
5 TOTAL ENERGY MINIMIZATION 5 7
5.1 T H E ESSENTIAL NATURE O F 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 A N D COMPUTATIONAL COST 66 5.3 OPTIMIZE WITH SUCCESS 67
5.3.1 INITIAL CONFIGURATION 67
5.3.2 INITIAL FORCES, CHOICE O F ALGORITHM A N D 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 O F MOTION 76
6.2 TIME A N D TIMESCALES 77
6.3 SYSTEM PREPARATION A N D 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 A N 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 A N D TRANSFERABILITY 95
IMAGE 3
CONTENTS | I X
7.2 ELECTROSTATICS 97
7.3 ELECTRONIC A N D 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 A N D ELECTROSTATICS 137 9.5.2 METALS A N D
OCCUPANCY 139
9.6 BOUNDARY CONDITIONS A N D RECIPROCAL SPACE 139 9.7 DIFFICULT
PROBLEMS 141
9.8 PSEUDOKEYWORDS 142
REFERENCES 143
PART FOUR SETTING UP AND RUNNING T H E 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 A N D ADAPTING THE SEQUENCE O F CALCULATIONS 151 10.3
BEING REALISTIC: AVAILABLE RESOURCES FOR THE PROJECT 153 10.4 CREATING
MODELS 155
10.5 CHOOSING A METHOD 156
IMAGE 4
X | CONTENTS
10.5.1 MOLECULAR MECHANICS A N D 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 269 11.2 PERIODIC SYSTEMS 170
11.2.1 FRACTIONAL COORDINATES 171 11.2.2 CRYSTALLOGRAPHY A N D SYMMETRY
I N 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 I N CRYSTALLOGRAPHY
180
11.3.2 GRAIN BOUNDARIES A N D DISLOCATIONS 182 11.3.3 MODELING SURFACES,
WIRES A N D ISOLATED MOLECULES 182 11.4 QUALITY O F CRYSTALLOGRAPHIC
DATA 186 11.5 STRUCTURE O F 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 O F 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 A N D DUPLICATE ATOMS
205 12.7.3 CROSSING (PERIODIC) BOUNDARIES 206 12.7.4 HYDROGEN ATOMS I N
PROTEINS 207
IMAGE 5
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 A N D ISOLATED SYSTEMS 215 13.4 SIMULATION CELLS A N
D SUPERCELLS O F PERIODIC SYSTEMS 216 13.5 SLAB MODELS O F 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 A N D PROJECTOR-AUGMENTED WAVES 220 13.8.3
K-POINTS I N PERIODIC SYSTEMS 220 13.9 INTEGRATION A N D FFT GRIDS 221
13.10 CHECKLISTS 222
REFERENCES 223
PART FIVE ANALYZING RESULTS 225
14 LOOKING A T OUTPUT FILES 227
14.1 DETERMINING WHAT 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 T H E 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 A N D 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, A N D
COMBINATION BANDS 250
IMAGE 6
XII | CONTENTS
15.4 OTHER NUMBERS 251
REFERENCES 252
16 VISUALIZATION 253
16.1 T H E IMPORTANCE O F 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 O F 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 O F 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 A N D MEANS 266
REFERENCES 268
17 ELECTRONIC STRUCTURE ANALYSIS 269
17.1 ENERGY LEVELS A N D BAND STRUCTURE 269
17.2 WAVEFUNCTIONS A N D ATOMS 271
17.3 LOCALIZED FUNCTIONS 273
17.4 DENSITY O F STATES, PROJECTED DOS 274
17.5 STM A N D 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
I S COMPARISON T O EXPERIMENT 283
18.1 WHY IT IS IMPORTANT 284
18.2 W H A T CAN A N D 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 I N CYTOCHROME C OXIDASE 295
IMAGE 7
CONTENTS | X I I I
18.4.2 BISMUTH NANOLINES O N SILICON 300
REFERENCES 304
APPENDIX A UNIX 307 A . L WHAT'S I N A NAME 307
A.2 O N THE C O M M A N D 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.L COMPILING 317
B.2 HIGH PERFORMANCE COMPUTING 319
B.3 MPI A N D M P I R U N 320
B.3.1 HOW TO RUN A N MPI JOB 321
B.3.2 SCALING 321
B.3.3 HOW TO KILL A PARALLEL JOB 321
B.4 JOB SCHEDULERS A N D BATCH JOBS 322
B.4.1 HOW TO QUEUE 322
B.4.2 SUBMITTING A N D MONITORING 323 B.5 FILE SYSTEMS A N D FILE
STORAGE 324
B.6 GETTING HELP 324
INDEX 325 |
| any_adam_object | 1 |
| author | Brázdová, Veronika 1975- Bowler, David R. |
| author_GND | (DE-588)131475703 |
| author_facet | Brázdová, Veronika 1975- Bowler, David R. |
| author_role | aut aut |
| author_sort | Brázdová, Veronika 1975- |
| author_variant | v b vb d r b dr drb |
| building | Verbundindex |
| bvnumber | BV040898178 |
| classification_rvk | SK 955 ST 340 VC 6300 |
| classification_tum | CHE 026f |
| ctrlnum | (OCoLC)840752725 (DE-599)DNB1026137284 |
| dewey-full | 539.70285 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 539 - Modern physics |
| dewey-raw | 539.70285 |
| dewey-search | 539.70285 |
| dewey-sort | 3539.70285 |
| dewey-tens | 530 - Physics |
| discipline | Chemie / Pharmazie Physik Informatik Chemie Mathematik |
| format | Book |
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| id | DE-604.BV040898178 |
| illustrated | Illustrated |
| indexdate | 2024-08-21T00:37:49Z |
| institution | BVB |
| isbn | 9783527410699 9783527671847 3527410694 |
| language | English |
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| oclc_num | 840752725 |
| open_access_boolean | |
| owner | DE-11 DE-91G DE-BY-TUM DE-703 DE-634 DE-355 DE-BY-UBR DE-29T |
| owner_facet | DE-11 DE-91G DE-BY-TUM DE-703 DE-634 DE-355 DE-BY-UBR DE-29T |
| physical | XXIX, 331 S. Ill., graph. Darst. |
| publishDate | 2013 |
| publishDateSearch | 2013 |
| publishDateSort | 2013 |
| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Brázdová, Veronika 1975- Verfasser (DE-588)131475703 aut Atomistic computer simulations a practical guide Veronika Brázdová and David R. Bowler Weinheim Wiley-VCH 2013 XXIX, 331 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Mesoskopisches System (DE-588)4280799-2 gnd rswk-swf Atomphysik (DE-588)4003423-9 gnd rswk-swf Computersimulation (DE-588)4148259-1 gnd rswk-swf Mesoskopisches System (DE-588)4280799-2 s Atomphysik (DE-588)4003423-9 s Computersimulation (DE-588)4148259-1 s DE-604 Bowler, David R. Verfasser aut X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=4126135&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025877706&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Brázdová, Veronika 1975- Bowler, David R. Atomistic computer simulations a practical guide Mesoskopisches System (DE-588)4280799-2 gnd Atomphysik (DE-588)4003423-9 gnd Computersimulation (DE-588)4148259-1 gnd |
| subject_GND | (DE-588)4280799-2 (DE-588)4003423-9 (DE-588)4148259-1 |
| title | Atomistic computer simulations a practical guide |
| title_auth | Atomistic computer simulations a practical guide |
| title_exact_search | Atomistic computer simulations a practical guide |
| title_full | Atomistic computer simulations a practical guide Veronika Brázdová and David R. Bowler |
| title_fullStr | Atomistic computer simulations a practical guide Veronika Brázdová and David R. Bowler |
| title_full_unstemmed | Atomistic computer simulations a practical guide Veronika Brázdová and David R. Bowler |
| title_short | Atomistic computer simulations |
| title_sort | atomistic computer simulations a practical guide |
| title_sub | a practical guide |
| topic | Mesoskopisches System (DE-588)4280799-2 gnd Atomphysik (DE-588)4003423-9 gnd Computersimulation (DE-588)4148259-1 gnd |
| topic_facet | Mesoskopisches System Atomphysik Computersimulation |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=4126135&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025877706&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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