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Frenkel D., Smit B. — Understanding Molecular Simulation: from algorithms to applications
Frenkel D., Smit B. — Understanding Molecular Simulation: from algorithms to applications



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Название: Understanding Molecular Simulation: from algorithms to applications

Авторы: Frenkel D., Smit B.

Аннотация:

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.


Язык: en

Рубрика: Математика/Численные методы/Моделирование физических процессов/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Издание: second edition

Год издания: 2002

Количество страниц: 638

Добавлена в каталог: 21.02.2005

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID
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Предметный указатель
Harmonic oscillator, trajectories      156 158
Harris, J.      271 272 331
Harvey, A.H.      223
Hasslacher, B.      476
Hautman,J.      317
Haymet, A.D.J.      236
Hcp, free energy      261
heat capacity      58 85
Heermann, D.W.      6 398
Hegger,R.      283
Heinbruch,U.      178
Hellekalek, P.      588
Helmholtz free energy      116
Helmholtz free energy, definition      12
Helmholtz free energy, elastic constants      520
Helmholtz free energy, excess      116
Helmholtz free energy, ideal gas      116
Henderson, D.      236 243 318
Hendriks, E.M.      222
Henkelman, G.      463
Henry coefficient      280
Hermann, D.W.      125 217
Heyes,D.M.      316 317
Hilbers, PA.J.      362 403
Histogram reweighting technique      395
Histogram reweighting technique, example      394
Hiwatari, Y.      167
Hockney, R.W.      6 75 292 310 311 314 550
Hoefsloot, H.C.J.      471 474
Holm,C      311 312 314
Holmes, S.      55
Holt,A.C.      522 523
Hoogerbrugge, P.J.      466 469
Hoover, W.G.      6 63 147 152 156 159 235 236 242 243 256 261 510 516 522 523
Hoye,J.S.      222
Huse,D.A.      261 263
Hut, P.      306
Hydrodynamics, example      474
Hyper-parallel tempering      395
Hyperdynamics      464
Ideal chain      276 337 366
Ideal chain, chemical potential      368
Iedema,PD.      474
Ilario,G.      585
Impey,R.W      523
Importance-sampling scheme      24
Initialization, algorithm      66
Interfacial tension      472
Internal potential energy      276
Interstitial, concentration      263
Ion, example      460
Irving, J.H.      472
Ising model, finite-size effects      219
Ising, exercise      137
Isobaric-isothermal ensemble, case study      122 123
Isobaric-isothermal ensemble, Monte Carlo technique      115
Isobaric-isothermal ensemble, schematic sketch      117
Isotension-isothermal ensemble, Monte Carlo technique      125
Jackson, G.      136 209
Jacobian      490
Jacobian, elastic constant      521
Jacobson, J.D.      6 235 237
Jacucci,G.      529
Jarzynski, C.      196
Jarzynski’s identity      196
Joannopoulos, J.D.      501
Johnson, J.K.      52 53 54 55 57 123 133 145 146 213 231
Johnson, K.W.      236 243
Jonsson, H.      462 463
Jorgensen, W.L.      372 373
June,R.L.      135
Kalikmanov, V.I.      222
Kalos,M.H.      6 30
Kantor,Y.      523
Kapral,R.      466 478
Karaborni, S.      362 368 372 373 374
Karasawa, N.      306 315
Karavias, F.      135
Kennedy, A.      398
Kerkhof, P.J.A.M.      582
Kirkpatrick, S.      389
Kirkwood g factor      302
Kirkwood — Buff      472
Kirkwood,J.G.      170 472
Kirkwood’s coupling parameter method      170
Klein, M.L.      106 157 159 317 423 424 427 503 523 535 536 537 538 543 544 584 585
Kleinman, L.      501
Koelman, J.M.V.A.      466 469
Kofke, D.A.      168 202 225 229 231 233 234 236 237 238 239 241
Kolafa,J.A.      304 389
Koonin, S.E.      6
Koper,G.J.M.      117
Koutras,N.K.      223
Kramer, H.A.      445
Kranendonk, W.G.T.      43 171 227
Kremer, K.      280 281 283 331
Krishna, R.      351 352 362 370 383
Kron,A.K.      4
Kumar, S.K.      270 350 374
Ladd, A.J.C.      98 167 171 236 243 244 245 246 258 260 261 262 466 477 522
Lagrangian      481
Lagrangian strain tensor      519
Lagrangian, example      485
Laird, B.B.      236
Landau, D.P      6 167
Laso,M.      271 331 372
Lattice Boltzmann method      476
Lattice gas cellular automata      476
Lattice-coupling-expansion method      246
Lattice-switch Monte Carlo      262
Law of rectilinear diameters      217
Leap Frog algorithm      75
Lebowitz, J.L.      84 111 178
Lee,H.      311 313 314
Lee,M.A.      306 310 315
Leighton, R.B.      481
Lekkerkerker, H.N.W.      171 234
Lennard — Jones chains, case study      340 382
Lennard — Jones chains, equation of state      340 342
Lennard — Jones chains, recoil growth      382
Lennard — Jones, algorithm force calculation      68
Lennard — Jones, Andersen thermostat      142
Lennard — Jones, case study      51 54 56 98 100 101 122 123 133 142 153 175 181 211
Lennard — Jones, chemical potential      133 175 177 181 182
Lennard — Jones, diffusion      100—102
Lennard — Jones, energies      99
Lennard — Jones, equation of state      51 53 55 57 122 123 133 146
Lennard — Jones, example      394
Lennard — Jones, exercise      60 105
Lennard — Jones, finite-size effects      220
Lennard — Jones, force      69
Lennard — Jones, Gibbs ensemble      214
Lennard — Jones, mean-squared displacement      102 147 155
Lennard — Jones, molecular dynamics      98 100
Lennard — Jones, Nose — Hoover thermostat      153
Lennard — Jones, phase diagram      38 214
Lennard — Jones, phase equilibria      123
Lennard — Jones, radial distribution function      101
Lennard — Jones, statistical error, calculation of      100
Lennard — Jones, truncated and shifted potential      98
Lennard — Jones, truncation of the potential, effect of      38
Lennard — Jones, vapor-liquid coexistence      124
Lennard — Jones, velocity autocorrelation function      102
Lennard — Jones, velocity distribution      145 154
LeSar, R.A.      171 243 244 245 246
Levesque,D.      222 292
Levy,R.M.      316
Limcharoen, P.      134
Linear response theory      509
Linear response theory, dissipation      513
Linear response theory, dynamic      511
Linear response theory, static      509
Linked lists      550
Linked lists, algorithm      551—553
Liouville formulation, multiple time step      424
Liouville formulation, Nose — Hoover algorithm      536
Liouville operator      78
Liouville theorem, non-Hamiltonian system      496
Liu, Yi      156 495 497 507
Lofti, A.      213
Long-range interactions      36
Long-range interactions, example      314
Lowe, C.P.      312 467 477
Lowen, H.      422
Loyens, L.D.J.C.      361
Lustig,R.      176
Luty, B.A.      315
Lutz,C.      551
Lyapunov instability      81
Lyubartsev, A.P      389
Macedonia, M.D.      345
MacGowan, D.      135
Machlup,S.      84
Mackie,A.D.      473 474
Madden, PA.      171 422 423
Madden, T.J.      474 475
Maddox,M.W.      135
Madura, J.D.      372 373
Maesen, T.L.M.      368
Maginn,E.J.      281 282 345
Malevanets, A.      466 478
MandeLM.J.      35
Manousiouthakis, VI.      42
MarchLM.      427 428
Marinari, E.      389
Markov chain      29
Marsh, C.A.      469 473
Martin del Rio, E.      220 223
Martin, M.G.      352 353 362 374 383
Martsinovski, A.A.      389
Martyna, G.J.      77 106 156 157 159 160 398 409 424 427 428 495 497 503 507 535 536 537 538 543 544 584 585
Massobrio, C.      176 178 226
Masters, A.J.      469
Matrix, antisymmetric      490
Matrix, Jacobian      490
Matrix, symplectic      491
Matrix, transposed      491
Matsuda,H.      236 243
Mau,S.-C.      261 263
Mavrantzas, V.G.      353 358 360
Maxwell — Boltzmann distribution      66
McCabe,C.      374
McCormick, A V.      135
McDonald, I.R.      3 4 84 90 111 116 119 178 195 509 582
McNamara, G.R      476 477
Mean-squared displacement, algorithm      91 95
Mehlig, B.      398
Meijer, E.J.      171 234 243 244 245 246
Meirovitch, H.      287 375
Meiss,J.D.      494
Meller,J.      84
Mesoscale dynamics      476
Mesoscopic model      465
Methane, adsorption isotherm      135
Methane, example      134
Metropolis scheme, schematic sketch      28
Metropolis, N.      4 24 27 32 174
Meyer, M.      6 63 421
Mezei,M.      128 133 221
Microcanonical ensemble, Monte Carlo technique      114
Microcanonical ensemble, partition function      492
Miiller,M.      270
Miiser,M.H.      443
Milgram, M.      4
Miller, M.A.      55
Miller, W.H.      442
Mills, G.      462
Minimum image convention      39
Mobility      513
Model fluid, $\mathrm{Br_2-Cl_2-BrCl}$      231
Model fluid, alkanes      372
Model fluid, block copolymers      474
Model fluid, dipolar hard-sphere fluid      222
Model fluid, hard spheres      237 256 261
Model fluid, ideal chains      345
Model fluid, ions in water      460
Model fluid, Lennard — Jones      51 54 56 98 100 101 122 123 133 142 153 175 181 211 394
Model fluid, Lennard — Jones chains      340
Model fluid, Lennard — Jones dumbbell      427
Model fluid, methane      134
Model fluid, point dipoles      330
Model fluid, polymers      396
Model fluid, restricted primitive model      221
Model fluid, soft spheres      235
Model fluid, Stockmayer fluid      170 222
Model fluid, water      329
Molecular dynamics, algorithm (NVE)      65 66 70
Molecular dynamics, algorithm (NVT)      143 144
Molecular dynamics, boundary conditions      32
Molecular dynamics, case study      98 100 101
Molecular dynamics, exercise      105 161
Molecular dynamics, initialization      40
Molecular dynamics, Lennard — Jones      98 100 101
Molecular dynamics, NPT ensemble      158
Molecular dynamics, NVE ensemble      64
Molecular dynamics, NVT ensemble      140 147 155
Molecular dynamics, potential, truncation of      35
Mon,K.K.      218 219 270
Mondello,M.      374
Monson,P.A.      241
Monte Carlo integration, exercise      59
Monte Carlo technique, algorithm $(\mu VT)$      131 132
Monte Carlo technique, algorithm (fixed center of mass)      251
Monte Carlo technique, algorithm (Gibbs)      209 210 212
Monte Carlo technique, algorithm (NPT)      121 122
Monte Carlo technique, algorithm (NVT)      33
Monte Carlo technique, boundary conditions      32
Monte Carlo technique, canonical ensemble      112
Monte Carlo technique, canonical ensemble: justification of algorithm      114
Monte Carlo technique, case study      51 54 56 122 123 133 211 256
Monte Carlo technique, configurational-bias Monte Carlo (lattice)      334 335
Monte Carlo technique, efficiency      119
Monte Carlo technique, grand-canonical ensemble      126
Monte Carlo technique, initialization      40
Monte Carlo technique, isobaric-isothermal ensemble      115
Monte Carlo technique, isotension-isothermal ensemble      125
Monte Carlo technique, justification      112
Monte Carlo technique, Metropolis scheme      28
Monte Carlo technique, microcanonical ensemble      114
Monte Carlo technique, orientational bias      325
Monte Carlo technique, path ensemble      454
Monte Carlo technique, potential, truncation of      35
Monte Carlo technique, random sampling      24
Monte Carlo, dynamic      31
Monte Carlo, end-bridging      357
Monte Carlo, exercise      59—61 136 137 161
Monte Carlo, rebridging      357
Mooij, G.C.A.M.      234 270 271 282 331 341 372 374 573
Moore, J.D.      374
Morriss,G.P.      6 141
Mountain, R.D.      47 223
Mouritsen, O.G.      6 167
Mousseau, N.      463
Mulder, B.M.      171
Multicanonical method      262
Multiple time step, algorithm      426
Multiple time step, case study      427
Multiple time step, Liouville formulation      424
Mundy,CJ.      495
Myers, A.L.      135
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