Ma bibliothèque

Demande

Ajouter à Mes listes

Ajouter à Mon panier

Affichage MARC

Retour en feuilletage

Modifier recherche

Plus comme

Limiter la recherche aux exemplaires disponibles

19645 résultats trouvés.trié(s) par pertinence | date | Titre .

Notice précédente Notice suivante

Ressources

Autres Ressources

Plus d' Information

* Search MOBIUS *

Auteur Français

Titre Atomistic computer simulations [electronic resource] : a practical guide / Veronika Br©Łzdov©Ł and David R. Bowler.

Adresse Bibliographique

Weinheim : Wiley-VCH, ℗♭2013.

Se connecter à
Click here to view online version; access limited to Brown University users

Table des matières
	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.	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 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

Exemplaires

Localisation	Cote	Statut
Innovative University Library	QC171.2 .B73 2013	AVAILABLE

Description	1 online resource.
Content Type	text txt rdacontent.
Type De Document	computer c rdamedia.
Carrier Type	online resource cr rdacarrier.
Bibliography	Includes bibliographical references and index.
Reproduction	Electronic reproduction. Hoboken, N.J. Available via World Wide Web.
Source Of Description	Print version record.
Local Note	Multiple user access license.
Sujet	Atoms -- Computer simulation.
	Molecular dynamics -- Computer simulation.
Autre Auteur	Bowler, D. R. (David R.)
	Wiley InterScience (Online service)
Publié Avec	Print version: Br©Łzdov©Ł, Veronika. Atomistic computer simulations. Weinheim : Wiley-VCH, ℗♭2013 9783527410699 3527410694.
ISBN	9783527671816
	3527671811
	9783527671847
	3527671846
	9781299448711
	1299448712

Permalien