LEADER 00000cam a22037813a 4500
003 NhCcYBP
005 20151001093036.0
006 m o d
007 cr |n|||||||||
008 130426s2013 gw a ob 001 0 eng d
010 ybp99085402
020 9783527671816
020 3527671811
020 9783527671847
020 3527671846
020 9781299448711
020 1299448712
037 476121|bMIL
040 NhCcYBP|cNhCcYBP|dNhCcYME
050 4 QC171.2|b.B73 2013
100 1 Br©Łzdov©Ł, Veronika.
245 10 Atomistic computer simulations|h[electronic resource] :|ba
practical guide /|cVeronika Br©Łzdov©Ł and David R.
Bowler.
260 Weinheim :|bWiley-VCH,|c℗♭2013.
300 1 online resource.
336 text|btxt|2rdacontent.
337 computer|bc|2rdamedia.
338 online resource|bcr|2rdacarrier.
504 Includes bibliographical references and index.
533 Electronic reproduction.|bHoboken, N.J.|nAvailable via
World Wide Web.
588 0 Print version record.
590 Multiple user access license.
650 0 Atoms|xComputer simulation.
650 0 Molecular dynamics|xComputer simulation.
700 1 Bowler, D. R.|q(David R.)
710 2 Wiley InterScience (Online service)
776 08 |iPrint version:|aBr©Łzdov©Ł, Veronika.|tAtomistic
computer simulations.|dWeinheim : Wiley-VCH, ℗♭2013
|z9783527410699|z3527410694.
856 40 |uhttps://login.revproxy.brown.edu/login?URL=http://
onlinelibrary.wiley.com/book/10.1002/9783527671816|zClick
here to view online version; access limited to Brown
University users
907 .b76519247|b02-25-16|c09-30-15
910 RDA ENRICHED
910 ybp
910 Backstage
910 TOC
910 BROWNu
940 |les001
970 01 |tPreface|pXV
970 11 |tReferences|pXVI
970 01 |tColor Plates|pXVII
970 01 |tPart One The World at the Atomic Scale|p1
970 11 |l1.|tAtoms, Molecules and Crystals|p3
970 11 |l1.1.|tLength- and Timescales|p3
970 11 |l1.2.|tElectrons in an Atom|p5
970 11 |l1.3.|tLocal Environment of an Atom|p8
970 11 |l1.3.1.|tElectrons|p8
970 11 |l1.3.2.|tLocal Arrangement of Atoms|p11
970 11 |l1.4.|tMost Favorable Arrangement of Atoms|p12
970 11 |l1.4.1.|tThe Concept of Total Energy|p12
970 11 |l1.4.2.|tBeyond the Total Energy|p13
970 11 |l1.4.3.|tThe Most Stable Configuration|p15
970 11 |tReferences|p16
970 11 |l2.|tBonding|p17
970 11 |l2.1.|tElectronic Ground State|p18
970 11 |l2.2.|tTypes of Bonds|p18
970 11 |l2.2.1.|tCovalent Bonding|p21
970 11 |l2.2.2.|tIonic Bonding|p22
970 11 |l2.2.3.|tMetallic Bonding|p24
970 11 |l2.2.4.|tHydrogen Bonding|p25
970 11 |l2.2.5.|tDispersion Bonding|p25
970 11 |l2.3.|tBond Breaking and Creation|p26
970 11 |l2.4.|tDistortion of Bonds|p27
970 11 |tReferences|p29
970 11 |l3.|tChemical Reactions|p31
970 11 |l3.1.|tChemical Equations|p31
970 11 |l3.2.|tReaction Mechanisms|p32
970 11 |l3.3.|tEnergetics of Chemical Reactions|p33
970 11 |l3.4.|tEvery (Valence) Electron Counts|p37
970 11 |l3.5.|tThe Energy Zoo|p38
970 11 |tReferences|p39
970 11 |l4.|tWhat Exactly is Calculated?|p41
970 11 |l4.1.|tWhat Can Be Calculated?|p41
970 11 |l4.2.|tWhat Actually Happens?|p43
970 11 |l4.3.|tModels and Simulation Cells|p44
970 11 |l4.4.|tEnergies|p47
970 11 |l4.5.|tTerms|p48
970 11 |l4.6.|tLiquid Iron: An Example|p50
970 11 |tReferences|p53
970 01 |tPart Two Introducing Equations to Describe the System
|p55
970 11 |l5.|tTotal Energy Minimization|p57
970 11 |l5.1.|tThe Essential Nature of Minimization|p58
970 11 |l5.2.|tMinimization Algorithms|p59
970 11 |l5.2.1.|tSteepest Descents|p61
970 11 |l5.2.2.|tConjugate Gradients|p62
970 11 |l5.2.3.|tQuasi-Newton Methods|p62
970 11 |l5.2.4.|tAlternatives|p63
970 11 |l5.2.5.|tExploring Landscapes|p64
970 11 |l5.2.6.|tScaling and Computational Cost|p66
970 11 |l5.3.|tOptimize with Success|p67
970 11 |l5.3.1.|tInitial Configuration|p67
970 11 |l5.3.2.|tInitial Forces, Choice of Algorithm and
Parameters|p68
970 11 |l5.3.3.|tFixing Atoms|p69
970 11 |l5.3.4.|tScaling with System Size|p70
970 11 |l5.4.|tTransition States|p71
970 11 |l5.5.|tPseudokeywords|p72
970 11 |tReferences|p73
970 11 |l6.|tMolecular Dynamics and Monte Carlo|p75
970 11 |l6.1.|tEquations of Motion|p76
970 11 |l6.2.|tTime and Timescales|p77
970 11 |l6.3.|tSystem Preparation and Equilibration|p79
970 11 |l6.4.|tConserving Temperature, Pressure, Volume or Other
Variables|p81
970 11 |l6.5.|tFree Energies|p83
970 11 |l6.6.|tMonte Carlo Approaches|p84
970 11 |l6.7.|tPseudokeywords for an MD Simulation|p86
970 11 |tReferences|p87
970 01 |tPart Three Describing Interactions Between Atoms|p89
970 11 |l7.|tCalculating Energies and Forces|p91
970 11 |l7.1.|tForcefields|p92
970 11 |l7.1.1.|tReliability and Transferability|p95
970 11 |l7.2.|tElectrostatics|p97
970 11 |l7.3.|tElectronic and Atomic Motion|p98
970 11 |l7.3.1.|tThe Born-Oppenheimer Approximation|p99
970 11 |l7.3.2.|tApproximating the Electronic Many-Body Problem
|p100
970 11 |l7.4.|tElectronic Excitations|p100
970 11 |tReferences|p103
970 11 |l8.|tElectronic Structure Methods|p105
970 11 |l8.1.|tHartree-Fock|p106
970 11 |l8.2.|tGoing Beyond Hartree-Fock|p109
970 11 |l8.3.|tDensity Functional Theory|p111
970 11 |l8.4.|tBeyond DFT|p114
970 11 |l8.5.|tBasis Sets|p116
970 11 |l8.6.|tSemiempirical Methods|p119
970 11 |l8.7.|tComparing Methods|p121
970 11 |tReferences|p124
970 11 |l9.|tDensity Functional Theory in Detail|p127
970 11 |l9.1.|tIndependent Electrons|p127
970 11 |l9.2.|tExchange-Correlation Functionals|p128
970 11 |l9.3.|tRepresenting the Electrons: Basis Sets|p130
970 11 |l9.3.1.|tPlane Waves|p131
970 11 |l9.3.2.|tAtomic-Like Orbitals|p132
970 11 |l9.4.|tElectron-Nuclear Interaction|p133
970 11 |l9.4.1.|tPseudopotentials|p133
970 11 |l9.4.2.|tPAW|p136
970 11 |l9.4.3.|tUsing All Electrons|p136
970 11 |l9.5.|tSolving the Electronic Ground State|p136
970 11 |l9.5.1.|tCharge Mixing and Electrostatics|p137
970 11 |l9.5.2.|tMetals and Occupancy|p139
970 11 |l9.6.|tBoundary Conditions and Reciprocal Space|p139
970 11 |l9.7.|tDifficult Problems|p141
970 11 |l9.8.|tPseudokeywords|p142
970 11 |tReferences|p143
970 01 |tPart Four Setting Up and Running the Calculation|p145
970 11 |l10.|tPlanning a Project|p147
970 11 |l10.1.|tQuestions to Consider|p147
970 11 |l10.1.1.|tResearch Questions|p148
970 11 |l10.1.2.|tSimulation Questions|p149
970 11 |l10.2.|tPlanning Simulations|p151
970 11 |l10.2.1.|tMaking it Simple|p151
970 11 |l10.2.2.|tPlanning and Adapting the Sequence of
Calculations|p151
970 11 |l10.3.|tBeing Realistic: Available Resources for the
Project|p153
970 11 |l10.4.|tCreating Models|p155
970 11 |l10.5.|tChoosing a Method|p156
970 11 |l10.5.1.|tMolecular Mechanics and Forcefields|p156
970 11 |l10.5.2.|tSemiempirical Methods|p158
970 11 |l10.5.3.|tDFT|p159
970 11 |l10.5.4.|tPost-HF|p160
970 11 |l10.5.5.|tPost-DFT|p161
970 11 |l10.6.|tWriting About the Simulation|p162
970 11 |l10.7.|tChecklists|p163
970 11 |tReferences|p164
970 11 |l11.|tCoordinates and Simulation Cell|p165
970 11 |l11.1.|tIsolated Molecules|p166
970 11 |l11.1.1.|tCartesian Coordinates|p166
970 11 |l11.1.2.|tMolecular Symmetry|p167
970 11 |l11.1.3.|tInternal Coordinates|p169
970 11 |l11.2.|tPeriodic Systems|p170
970 11 |l11.2.1.|tFractional Coordinates|p171
970 11 |l11.2.2.|tCrystallography and Symmetry in Periodic
Systems|p172
970 11 |l11.2.3.|tSupercells|p175
970 11 |l11.2.4.|tUnderstanding Crystallographic Notation: Space
Groups|p175
970 11 |l11.2.5.|tUnderstanding Crystallographic Notation: Atomic
Coordinates|p176
970 11 |l11.3.|tSystems with Lower Periodicity|p180
970 11 |l11.3.1.|tSurfaces in Crystallography|p180
970 11 |l11.3.2.|tGrain Boundaries and Dislocations|p182
970 11 |l11.3.3.|tModeling Surfaces, Wires and Isolated Molecules
|p182
970 11 |l11.4.|tQuality of Crystallographic Data|p186
970 11 |l11.5.|tStructure of Proteins|p187
970 11 |l11.6.|tPseudokeywords|p188
970 11 |l11.7.|tChecklist|p189
970 11 |tReferences|p190
970 11 |l12.|tThe Nuts and Bolts|p193
970 11 |l12.1.|tA Single-Point Simulation|p193
970 11 |l12.2.|tStructure Optimization|p194
970 11 |l12.3.|tTransition State Search|p195
970 11 |l12.4.|tSimulation Cell Optimization|p197
970 11 |l12.5.|tMolecular Dynamics|p199
970 11 |l12.6.|tVibrational Analysis|p200
970 11 |l12.6.1.|tSimulation of Anharmonic Vibrational Spectra
|p201
970 11 |l12.6.2.|tNormal Mode Analysis|p202
970 11 |l12.6.3.|tHarmonic or Anharmonic?|p204
970 11 |l12.7.|tThe Atomistic Model|p205
970 11 |l12.7.1.|tSmall Beginnings|p205
970 11 |l12.7.2.|tPeriodic Images and Duplicate Atoms|p205
970 11 |l12.7.3.|tCrossing (Periodic) Boundaries|p206
970 11 |l12.7.4.|tHydrogen Atoms in Proteins|p207
970 11 |l12.7.5.|tSolvating a Protein|p209
970 11 |l12.8.|tHow Converged is Converged?|p209
970 11 |l12.9.|tChecklists|p210
970 11 |tReferences|p211
970 11 |l13.|tTests|p213
970 11 |l13.1.|tWhat is the Correct Number?|p213
970 11 |l13.2.|tTest Systems|p214
970 11 |l13.3.|tCluster Models and Isolated Systems|p215
970 11 |l13.4.|tSimulation Cells and Supercells of Periodic
Systems|p216
970 11 |l13.5.|tSlab Models of Surfaces|p216
970 11 |l13.6.|tMolecular Dynamics Simulations|p217
970 11 |l13.7.|tVibrational Analysis by Finite Differences|p218
970 11 |l13.8.|tElectronic-Structure Simulations|p219
970 11 |l13.8.1.|tBasis Sets|p219
970 11 |l13.8.2.|tPseudopotentials and Projector-Augmented Waves
|p220
970 11 |l13.8.3.|tK-Points in Periodic Systems|p220
970 11 |l13.9.|tIntegration and FFT Grids|p221
970 11 |l13.10.|tChecklists|p222
970 11 |tReferences|p223
970 01 |tPart Five Analyzing Results|p225
970 11 |l14.|tLooking at Output Files|p227
970 11 |l14.1.|tDetermining What Happened|p227
970 11 |l14.1.1.|tHas it Crashed?|p227
970 11 |l14.2.|tWhy Did it Stop?|p229
970 11 |l14.2.1.|tWhy it Did Not Converge?|p230
970 11 |l14.3.|tDo the Results Make Sense?|p233
970 11 |l14.4.|tIs the Result Correct?|p234
970 11 |l14.5.|tChecklist|p234
970 11 |tReferences|p234
970 11 |l15.|tWhat to do with All the Numbers|p235
970 11 |l15.1.|tEnergies|p236
970 11 |l15.1.1.|tStability|p236
970 11 |l15.1.2.|tRelative Energies: Adsorption, Binding etc.
|p239
970 11 |l15.1.3.|tFree Energies|p242
970 11 |l15.2.|tStructural Data|p242
970 11 |l15.2.1.|tBond Lengths and Angles|p243
970 11 |l15.2.2.|tDistributions|p243
970 11 |l15.2.3.|tAtomic Transport|p244
970 11 |l15.2.4.|tElastic Constants|p246
970 11 |l15.3.|tNormal Mode Analysis|p246
970 11 |l15.3.1.|tIrreducible Representations|p246
970 11 |l15.3.2.|tSelection Rules from Irreducible
Representations|p250
970 11 |l15.3.3.|tFundamentals, Overtones, and Combination Bands
|p250
970 11 |l15.4.|tOther Numbers|p251
970 11 |tReferences|p252
970 11 |l16.|tVisualization|p253
970 11 |l16.1.|tThe Importance Of Visualizing Data|p253
970 11 |l16.2.|tSanity Checks|p253
970 11 |l16.3.|tIs There a Bond?|p254
970 11 |l16.4.|tAtom Representations|p254
970 11 |l16.5.|tPlotting Properties|p256
970 11 |l16.5.1.|tLooking at Charge Density|p256
970 11 |l16.5.2.|tDensity of States|p256
970 11 |l16.6.|tLooking at Vibrations|p257
970 11 |l16.7.|tConveying Information|p258
970 11 |l16.7.1.|tSelecting the Important Bits|p258
970 11 |l16.7.2.|tFrom Three to Two Dimensions|p258
970 11 |l16.7.3.|tHow to Make Things Look Different|p260
970 11 |l16.8.|tTechnical Pitfalls Of Image Preparation|p264
970 11 |l16.8.1.|tJPEG, GIF, PNG, TIFF: Raster Graphics Images
|p264
970 11 |l16.8.2.|tManipulating Raster Graphics Images|p265
970 11 |l16.8.3.|tHow to Get a 3D Scene into a 2D Image that Can
Be Saved|p266
970 11 |l16.9.|tWays and Means|p266
970 11 |tReferences|p268
970 11 |l17.|tElectronic Structure Analysis|p269
970 11 |l17.1.|tEnergy Levels and Band Structure|p269
970 11 |l17.2.|tWavefunctions and Atoms|p271
970 11 |l17.3.|tLocalized Functions|p273
970 11 |l17.4.|tDensity of States, Projected DOS|p274
970 11 |l17.5.|tSTM and CITS|p276
970 11 |l17.5.1.|tTersoff-Hamann|p277
970 11 |l17.5.2.|tBardeen|p278
970 11 |l17.6.|tOther Spectroscopies: Optical, X-Ray, NMR, EPR
|p278
970 11 |tReferences|p280
970 11 |l18.|tComparison to Experiment|p283
970 11 |l18.1.|tWhy It Is Important|p284
970 11 |l18.2.|tWhat Can and Cannot Be Directly Compared|p285
970 11 |l18.2.1.|tEnergies|p285
970 11 |l18.2.2.|tStructural Data|p286
970 11 |l18.2.3.|tSpectroscopy|p288
970 11 |l18.2.4.|tVibrational Spectroscopy|p290
970 11 |l18.2.5.|tScanning Probes|p291
970 11 |l18.2.6.|tBarriers|p292
970 11 |l18.3.|tHow to Determine Whether There is Agreement with
Experiment|p293
970 11 |l18.4.|tCase Studies|p295
970 11 |l18.4.1.|tProton Pumping in Cytochrome c Oxidase|p295
970 11 |l18.4.2.|tBismuth Nanolines on Silicon|p300
970 11 |tReferences|p304
970 01 |tAppendix A UNIX|p307
970 11 |lA.1.|tWhat's in a Name|p307
970 11 |lA.2.|tOn the Command Line|p308
970 11 |lA.3.|tGetting Around|p309
970 11 |lA.4.|tWorking with Data|p309
970 11 |lA.5.|tRunning Programs|p311
970 11 |lA.6.|tRemote Work|p312
970 11 |lA.7.|tManaging Data|p313
970 11 |lA.8.|tMaking Life Easier by Storing Preferences|p314
970 11 |lA.9.|tBe Careful What You Wish For|p315
970 01 |tAppendix B Scientific Computing|p317
970 11 |lB.1.|tCompiling|p317
970 11 |lB.2.|tHigh Performance Computing|p319
970 11 |lB.3.|tMPI and mpirun|p320
970 11 |lB.3.1.|tHow to Run an MPI Job|p321
970 11 |lB.3.2.|tScaling|p321
970 11 |lB.3.3.|tHow to Kill a Parallel Job|p321
970 11 |lB.4.|tJob Schedulers and Batch Jobs|p322
970 11 |lB.4.1.|tHow to Queue|p322
970 11 |lB.4.2.|tSubmitting and Monitoring|p323
970 11 |lB.5.|tFile Systems and File Storage|p324
970 11 |lB.6.|tGetting Help|p324
970 01 |tIndex|p325
996 |uhttp://library.brown.edu/bookplates/
fund.php?account=054149|zPurchased on the Harvey A.
Heffner Book Fund
998 es001|b09-30-15|cm|da|e|feng|ggw |h0|i1
998 es001|b09-30-15|cm|da|feng|ggw |h0|i1
