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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
Nadler,W.      286
Naghizadeh, J.      107
Najafabadi, R.      111 125
Nakanishi, K.      146
Nath,S.K.      374
Navas, V.      474
Neal,R.M.      55
Neighbor list      545
Neuhaus, T.      262
Neumann, M.      304
Newman, M.E.J.      6
Nezbeda, I.      389
Ng,K.-C.      222
Nicholson, D.      128 329
Nicolas, J.J.      52 54 213
Nielaba,P.      125 217 523
Nijmeijer, M.J.P.      472
Noid,D.W.      494
Norman, G.E.      111 128
Nose — Hoover chains, equations of motion      536
Nose — Hoover chains, harmonic oscillator      157
Nose — Hoover chains, Liouville formulation      536
Nose — Hoover chains, Trotter expansion      536
Nose — Hoover thermostat, algorithm      540—542
Nose — Hoover thermostat, case study      153
Nose — Hoover thermostat, diffusion      155
Nose — Hoover thermostat, harmonic oscillator      155
Nose — Hoover thermostat, Lennard — Jones      153
Nose,S.      141 147 152
NPT ensemble, exercise      136
Nudged elastic band      462
NVE simulations, diffusion      102
NVT ensemble, exercise      161
O1sen, O.H.      156
Ogawa, T.      236 243
Ogita, N.      236 243
Ogura, H.      236 243
Olender, R.      84
Onsager, L.      84
Orkoulas,G.      405
Orland,H.      283
Osborn,W.M.      477
Overlapping distribution, case study      181
Overlapping distribution, chain molecules      282
Overlapping distribution, chemical potential      179
Overlapping distribution, polymers      573
Overlapping distribution, Rosenbluth sampling      282
Pagonabarraga, I.      466 469
Panagiotopoulos, A.Z.      111 168 202 203 204 207 208 217 218 219 220 221 223 231 270 350 374 405 570
Pant, PV.K.      358 359 360
Parallel Monte Carlo      361
Parallel tempering, acceptance rule      390
Parallel tempering, case study      391
Parallel tempering, example      393 394 396 458
Parisi,G.      389
Parker, F.R.      34 52
Parrinello, M.      125 139 159 168 410 421
Parsonage, N.G.      128 134 329
Particle displacement, algorithm      33 251
Particle displacement, fixed center of mass      249
Particle exchange, algorithm      212
Particle insertion method      173
Particle insertion method, algorithm      175
Particle insertion method, case study      175
Partition function      12
Partition function, canonical ensemble      23 112
Partition function, configurational part      27
Partition function, Einstein crystal      244
Partition function, elastic constant      520
Partition function, Gibbs ensemble      204
Partition function, grand-canonical ensemble      129
Partition function, grand-canonical ensemble (mixture)      227
Partition function, isobaric-isothermal ensemble      118
Partition function, microcanonical ensemble      492
Partition function, Nose — Hoover      148
Partition function, NPT ensemble      118
Partition function, semigrand ensemble      229
Pasquarello, A.      422
Pasta, J.G.      4
PateyG.N      222 361
Path ensemble      452
Path ensemble, acceptance rule      455
Path ensemble, case study      456
Path ensemble, Monte Carlo technique      454
Path ensemble, shifting moves      456
Path ensemble, shooting moves      455
Paul,W.      270 551
Peczak, P.      374
Pedersen, L.      292 311 313 314
Pendleton, B.J.      398
Percus,J.K.      84 111 178
Perera,L.      311 313 314
Periodic boundary conditions      34
Periodic boundary conditions, schematic representation      34
Perram, J.W.      292 304 317 415
Peter, C.J.      223
Petersen, H.G.      98 103 304 313 314 315 415 530
Phase equilibria, $\mathrm{Br_2-Cl_2-BrCl}$      231
Phase equilibria, alkanes      372
Phase equilibria, case study      123 211 256
Phase equilibria, example      394
Phase equilibria, exercise      224
Phase equilibria, freezing soft spheres      235
Phase equilibria, Gibbs ensemble technique      203
Phase equilibria, Gibbs — Duhem integration      233
Phase equilibria, hard spheres      256
Phase equilibria, Lennard — Jones      123 211
Phase equilibria, semigrand ensemble      231
Phase equilibria, zero pressure      124
Phase space compressibility, dynamical system      496
Phenomenological rate equations      432
Photon gas, exercise      59
Pincus,P.G.      222
Poison, J.M.      256 260 261
Poisson’s equation      297
Polarization      422
Pollock, E.L.      311 315
Polydispersity, example      237
Polymers, block copolymers      474
Polymers, example      363 396
Pomeau, Y.      476
Pontikis,V.      6 63 421
Postma, J.P.M.      161 162 172
Potential energy, bonded      337
Potential energy, external      276
Potential energy, from radial distribution function      99
Potential energy, internal      276
Potential energy, nonbonded      337
Potential, truncation of      35
Potential, truncation of, minimum image convention      39
Potential, truncation of, simple truncation      37
Potential, truncation of, truncate and shift      39
Potoff,J.J.      374
Powles,J.G.      37
Praestgaard, E.      167
Pratt, L.R      450
Predictor corrector algorithm      73
Predictor-corrector algorithm      533
Press, W.H.      6 30 310 341 343 577 579 580
Pressure from radial distribution function      100
Pressure, trail volume method      200
Pressure, virial equation      84
Prins,J.A.      3
Probability density, canonical ensemble      113
Probability density, Gibbs ensemble      204
Probability density, grand-canonical ensemble      129
Probability density, isobaric-isothermal ensemble      118
Probability density, NPT ensemble      118
Procacci,P.      427 428
Pronk, S.      256 260 261 267
Pruned-enriched Rosenbluth method      285
Quinlan,G.D.      73
Quirke, N.      135 168 203 207 218 223 233 570
Radhkrishnan, R.      134
Radial distribution function, algorithm      86
Radial distribution function, potential energy      99
Radial distribution function, pressure      100
Rahman, A.      4 125 139 159 168 423 529
Random-number generators      30
Rapaport, D.C.      6
Rare events      431
Rare events, Bennet — Chandler approach      436
Rare events, case study      440 456
Rare events, diffusive barrier crossing      443
Rare events, transition path ensemble      450
Rare events, transition state theory      437
Rebridging Monte Carlo      357
RechtJ.R.      220
Recoil growth, acceptance rule      379
Recoil growth, algorithm      376
Recoil growth, case study      382
Recoil growth, Conformational-bias Monte Carlo, versus      374
Recoil growth, justification of the method      379
Recoil growth, Lennard — Jones chains      382
Recoil growth, super-detailed balance      380
Recursive sampling, chemical potential      283
Reduced units      40 58
Ree, F.H.      235 236 242 261
Reichl, L.E.      16 17 509 516
Reinhardt, W.P      55 171 172
Reiss,H.      117 267
Remle, D.K.      422
Renardus, M.K.R.      546 550
Restricted primitive model      221
Rice, O.K.      3
Rice, S.A.      107 271 272 331
Richards, E.      134
Ripoll,M.      474
Rokhlin,V.      292 306
Rosenbluth factor      324 332
Rosenbluth sampling      271
Rosenbluth sampling, chemical potential      275
Rosenbluth sampling, continuum model      276
Rosenbluth sampling, ensemble average      274
Rosenbluth sampling, lattice model      271
Rosenbluth sampling, overlapping distribution      282
Rosenbluth sampling, pruned-enriched      285
Rosenbluth, A.W.      4 24 27 32 174 271 272 324 331
Rosenbluth, M.N.      4 24 27 32 174 271 272 324 331
Ross,M.      236 243
Rovere,M.      125 217
Roweth,D.      398
Rowley, L.A.      128
Rowley, R.L.      318
Rowlinson, J.S.      135 217 472
Rudge,W.E.      551
Ruelle,D.      563 564
Ruiz-Montero, M.J.      439 447 450
Rull, L.F.      6 136 209 389
Rushbrooke, G.S.      222
Ryckaert, J.P.      6 50 51 253 414 427
Saboungi, M-L.      423
Saddle point      462
Saddle point, activation-relaxation technique      463
Saddle point, hyperdynamics      464
Saddle point, nudged elastic band      462
Saddle point, temperature-accelerated dynamics      464
Saeger,RB.      374
Safran,S.A.      222 223
Sagui,C.      312 316
Saha,P      81
Salsburg, Z.W.      53
Sands, M.      481
Scaling law      217
Scanning method      287
Schenter, G.K.      462
Schmidt, K.E.      306 310 315
Schneider, T.      167
Schouten, J.A.      245
Scriven,L.E.      221
Self-consistent histogram method, example      187 394
Self-diffusion coefficient      513
Self-diffusivity      106
Self-interaction      294
Semigrand ensemble      225 360
Semigrand ensemble, acceptance rule      230
Semigrand ensemble, example      231 237
Semigrand ensemble, partition function      229
Sengupta, S.      523
Sexton, J.C      77
Shadow orbit      73 83
SHAKE, constrained dynamics      427
Shear stress      519
Shear viscosity      90 519
Shelley, J.C.      222 361
Sheng,Y.-J.      374
Shevkunov, S.V.      389
Shifting moves, path ensemble      456
Shing, K.S.      176 179 226 389 575
Shing,K.      178 389
Shooting moves, path ensemble      455
Siepmann, J.I.      178 271 272 281 282 331 345 352 353 357 362 368 372 373 374 383
Sikkenk,J.H.      472
Sindzingre, P.      176 178 226
Sing,K.S.W.      368
Singer, K.      4 195
Single-occupancy cell method      242
Slattery, W.L.      236
Sliwinska-Bartkowiak, M.      134
Smit, B.      37 38 135 136 168 170 204 209 213 215 216 218 222 224 257 258 270 271 281 282 331 341 351 352 361 362 368 370 372 373 374 375 382 383 403 404 458 459 460 471 567 570 571
Smith, E.R      292 317 318
Smith, W.R.      231
Snook, I.K.      128
Snurr,R.Q.      135
Sorensen, M.R.      463 464
Soto,J.L.      135
Speedy, R.J.      256 257 266 267
Spohr,E.      317 318
Sprik,M.      423 424 523
Squire, D.R.      522 523
Stapleton, M.R.      168 203 207 218 221 223 233 570
Statistical error, block averages      529
Statistical error, calculation of      98
Statistical error, correlation functions      527
Statistical error, static properties      525
Statistical mechanics      9
Statistical mechanics, exercise      20—22
Statistical mechanics, Hamilton formalism      488
Steady-state velocity      513
Stegun, I.      260
Steinbach, PJ.      291
Stell,G.      222
Stillinger, F.H.      403
Stirling approximation      256
Stockmayer fluid      170
Stockmayer fluid, Gibbs ensemble      222
Stoll,E.      167
Straatsma, T.P      172
Streett,W.B.      52 54 213
Stringfellow, G.S.      236
Stroobants, A.      171
Stroud, H.J.F.      134
Succi,S.      476 477
Sumpter, B.Q.      494
Super-detailed balance      328 340 380
Surface tension      472
Suter, U.W.      271 331 372 398
Swendsen, R.H.      181 183 395 399
Swenson,C.J.      372 373
Swift, M.R.      477
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