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首页LAMMPS模拟器用户手册:大规模原子/分子并行模拟
LAMMPS模拟器用户手册:大规模原子/分子并行模拟
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"LAMMPS-Manual"
LAMMPS(Large-scale Atomic/Molecular Massively Parallel Simulator)是一款大型原子/分子大规模并行模拟器,专为处理大量粒子的科学计算而设计。它由美国桑迪亚国家实验室开发,并遵循GNU General Public License进行开源分发。该软件主要用于模拟各种物理系统的动力学行为,包括材料科学、化学、生物学、地质学等领域的问题。
LAMMPS的特点主要包括以下几个方面:
1. **通用特性**:LAMMPS支持多种粒子类型和模型,可以模拟不同的力场,如EAM、REAXFF、CHARMM等。它能够创建、删除或移动粒子,处理不同类型的ensemble(如NVE、NVT、NPT等)、约束和边界条件。此外,LAMMPS包含各种数值积分器,用于求解牛顿运动方程,以及丰富的诊断工具和输出选项。
2. **特殊功能**:LAMMPS支持多复制模型,可用于模拟大尺度系统或进行并行计算。预处理和后处理功能使得用户能够方便地导入和导出数据,进行系统设置和结果分析。还有许多针对特定应用的扩展功能,如分子动力学模拟、蒙特卡洛方法、界面动力学等。
3. **非功能特性**:LAMMPS不包括图形用户界面,用户主要通过命令行界面和输入脚本来操作。尽管如此,它提供了强大的脚本语言,允许用户定义复杂的模拟流程。
4. **获取和使用LAMMPS**:LAMMPS的分发包括源代码和其他必要的文件,用户可以根据需求选择构建不同的可执行版本或库。构建过程可以通过Makefile或Python脚本完成,根据个人或系统需求选择是否包含额外的包。运行LAMMPS时,用户需要指定命令行选项,控制模拟参数,并理解其屏幕输出。
5. **命令和输入脚本**:LAMMPS使用输入脚本来定义模拟的各个部分,包括初始化系统、定义力场、设置时间步长、选择积分器、添加约束、运行模拟和收集数据。输入脚本中的命令由LAMMPS解析执行,用户可以通过阅读手册学习各种命令的使用方法。
6. **社区支持**:由于LAMMPS的开源性质,它有一个活跃的用户社区和开发者团队,不断更新和改进软件,添加新的功能和力场。用户可以通过文档、邮件列表、论坛等途径获取帮助和分享经验。
LAMMPS是一个功能强大的并行模拟工具,它提供的灵活性和可扩展性使其成为科学研究和工程应用的重要选择。用户需要熟悉其输入脚本语法和命令,以充分利用其功能进行复杂系统的模拟研究。
Table of Contents
pair_style lj/long/coul/long/opt command...................................................................................1065
pair_style lj/long/tip4p/long command.......................................................................................1065
pair_style lj/sf command.............................................................................................................1069
pair_style lj/sf/omp command.....................................................................................................1069
pair_style lj/smooth command....................................................................................................1071
pair_style lj/smooth/cuda command............................................................................................1071
pair_style lj/smooth/omp command............................................................................................1071
pair_style lj/smooth/linear command..........................................................................................1073
pair_style lj/smooth/linear/omp command..................................................................................1073
pair_style lubricate command.....................................................................................................1075
pair_style lubricate/omp command.............................................................................................1075
pair_style lubricate/poly command.............................................................................................1075
pair_style lubricate/poly/omp command.....................................................................................1075
pair_style lubricateU command...................................................................................................1079
pair_style lubricateU/poly command..........................................................................................1079
pair_style nb3b/harmonic command...........................................................................................1083
pair_style nb3b/harmonic/omp command...................................................................................1083
pair_style meam command..........................................................................................................1085
pair_style meam/spline................................................................................................................1091
pair_style meam/spline/omp........................................................................................................1091
pair_style meam/sw/spline..........................................................................................................1094
pair_style meam/sw/spline/omp..................................................................................................1094
pair_style mie/cut command.......................................................................................................1097
pair_style mie/cut/gpu command................................................................................................1097
pair_style morse command..........................................................................................................1099
pair_style morse/cuda command.................................................................................................1099
pair_style morse/gpu command...................................................................................................1099
pair_style morse/omp command.................................................................................................1099
pair_style morse/opt command...................................................................................................1099
pair_style nm/cut command........................................................................................................1101
pair_style nm/cut/coul/cut command..........................................................................................1101
pair_style nm/cut/coul/long command........................................................................................1101
pair_style nm/cut/omp command................................................................................................1101
pair_style nm/cut/coul/cut/omp command..................................................................................1101
pair_style nm/cut/coul/long/omp command................................................................................1101
pair_style none command............................................................................................................1104
pair_style peri/pmb command.....................................................................................................1105
pair_style peri/pmb/omp command.............................................................................................1105
pair_style peri/lps command.......................................................................................................1105
pair_style peri/lps/omp command...............................................................................................1105
pair_style peri/ves command.......................................................................................................1105
pair_style peri/eps command.......................................................................................................1105
pair_style reax/c command..........................................................................................................1109
pair_style reax command.............................................................................................................1114
pair_style resquared command....................................................................................................1118
pair_style resquared/gpu command.............................................................................................1118
pair_style resquared/omp command............................................................................................1118
pair_style lj/sdk command...........................................................................................................1122
LAMMPS-ICMS Users Manual
xv
Table of Contents
pair_style lj/sdk/gpu command...................................................................................................1122
pair_style lj/sdk/omp command..................................................................................................1122
pair_style lj/sdk/coul/long command..........................................................................................1122
pair_style lj/sdk/coul/long/gpu command...................................................................................1122
pair_style lj/sdk/coul/long/omp command..................................................................................1122
pair_style soft command.............................................................................................................1125
pair_style soft/gpu command......................................................................................................1125
pair_style soft/omp command.....................................................................................................1125
pair_style sph/heatconduction command....................................................................................1128
pair_style sph/idealgas command................................................................................................1129
pair_style sph/lj command...........................................................................................................1131
pair_style sph/rhosum command.................................................................................................1133
pair_style sph/taitwater command...............................................................................................1134
pair_style sph/taitwater/morris command...................................................................................1136
pair_style command....................................................................................................................1138
pair_style sw command...............................................................................................................1142
pair_style sw/cuda command......................................................................................................1142
pair_style sw/gpu command........................................................................................................1142
pair_style sw/omp command.......................................................................................................1142
pair_style table command............................................................................................................1146
pair_style table/gpu command.....................................................................................................1146
pair_style table/omp command...................................................................................................1146
pair_style tersoff command.........................................................................................................1150
pair_style tersoff/table command................................................................................................1150
pair_style tersoff/cuda.................................................................................................................1150
pair_style tersoff/omp..................................................................................................................1150
pair_style tersoff/table/omp command........................................................................................1150
pair_style tersoff/mod command.................................................................................................1156
pair_style tersoff/mod/omp command.........................................................................................1156
pair_style tersoff/zbl command...................................................................................................1161
pair_style tersoff/zbl/omp command...........................................................................................1161
pair_style tri/lj command.............................................................................................................1167
pair_style tri/lj/omp command....................................................................................................1167
pair_write command....................................................................................................................1169
pair_style yukawa command.......................................................................................................1171
pair_style yukawa/gpu command................................................................................................1171
pair_style yukawa/omp command...............................................................................................1171
pair_style yukawa/colloid command...........................................................................................1173
pair_style yukawa/colloid/gpu command....................................................................................1173
pair_style yukawa/colloid/omp command...................................................................................1173
pair_style zbl command...............................................................................................................1176
pair_style zbl/omp command......................................................................................................1176
bond_style class2 command........................................................................................................1178
bond_style class2/omp command................................................................................................1178
bond_coeff command..................................................................................................................1180
bond_style fene/expand command..............................................................................................1182
bond_style fene/expand/omp command......................................................................................1182
bond_style fene command...........................................................................................................1184
LAMMPS-ICMS Users Manual
xvi
Table of Contents
bond_style fene/omp command...................................................................................................1184
bond_style harmonic command...................................................................................................1186
bond_style harmonic/omp command..........................................................................................1186
bond_style harmonic/shift command..........................................................................................1188
bond_style harmonic/shift/omp command..................................................................................1188
bond_style harmonic/shift/cut command....................................................................................1190
bond_style harmonic/shift/cut/omp command............................................................................1190
bond_style hybrid command.......................................................................................................1192
bond_style morse command........................................................................................................1194
bond_style morse/omp command................................................................................................1194
bond_style none command..........................................................................................................1196
bond_style nonlinear command...................................................................................................1197
bond_style nonlinear/omp command..........................................................................................1197
bond_style quartic command.......................................................................................................1199
bond_style quartic/omp command..............................................................................................1199
bond_style table command..........................................................................................................1201
bond_style table/omp command..................................................................................................1201
angle_style charmm command....................................................................................................1204
angle_style charmm/omp command............................................................................................1204
angle_style class2 command.......................................................................................................1206
angle_style class2/omp command...............................................................................................1206
angle_coeff command.................................................................................................................1209
angle_style cosine command.......................................................................................................1211
angle_style cosine/omp command...............................................................................................1211
angle_style cosine/delta command..............................................................................................1213
angle_style cosine/delta/omp command......................................................................................1213
angle_style cosine/periodic command.........................................................................................1215
angle_style cosine/periodic/omp command................................................................................1215
angle_style cosine/shift command...............................................................................................1217
angle_style cosine/shift/omp command......................................................................................1217
angle_style cosine/shift/exp command........................................................................................1219
angle_style cosine/shift/exp/omp command...............................................................................1219
angle_style cosine/squared command.........................................................................................1221
angle_style cosine/squared/omp command.................................................................................1221
angle_style dipole command.......................................................................................................1223
angle_style dipole/omp command...............................................................................................1223
angle_style fourier command......................................................................................................1226
angle_style fourier/omp command..............................................................................................1226
angle_style fourier/simple command..........................................................................................1228
angle_style fourier/simple/omp command..................................................................................1228
angle_style harmonic command..................................................................................................1230
angle_style harmonic/omp command..........................................................................................1230
angle_style hybrid command.......................................................................................................1232
angle_style none command.........................................................................................................1234
angle_style quartic command......................................................................................................1235
angle_style quartic/omp command..............................................................................................1235
angle_style sdk command...........................................................................................................1237
angle_style table command.........................................................................................................1238
LAMMPS-ICMS Users Manual
xvii
Table of Contents
angle_style table/omp command.................................................................................................1238
dihedral_style charmm command...............................................................................................1241
dihedral_style charmm/omp command.......................................................................................1241
dihedral_style class2 command...................................................................................................1243
dihedral_style class2/omp command...........................................................................................1243
dihedral_coeff command.............................................................................................................1247
dihedral_style cosine/shift/exp command...................................................................................1249
dihedral_style cosine/shift/exp/omp command...........................................................................1249
dihedral_style fourier command..................................................................................................1251
dihedral_style fourier/omp command.........................................................................................1251
dihedral_style harmonic command.............................................................................................1253
dihedral_style harmonic/omp command.....................................................................................1253
dihedral_style helix command.....................................................................................................1255
dihedral_style helix/omp command............................................................................................1255
dihedral_style hybrid command..................................................................................................1257
dihedral_style multi/harmonic command....................................................................................1259
dihedral_style multi/harmonic/omp command............................................................................1259
dihedral_style nharmonic command...........................................................................................1261
dihedral_style nharmonic/omp command...................................................................................1261
dihedral_style none command.....................................................................................................1263
dihedral_style opls command......................................................................................................1264
dihedral_style opls/omp command..............................................................................................1264
dihedral_style quadratic command..............................................................................................1266
dihedral_style quadratic/omp command.....................................................................................1266
dihedral_style table command.....................................................................................................1268
dihedral_style table/omp command.............................................................................................1268
improper_style class2 command.................................................................................................1271
improper_style class2/omp command.........................................................................................1271
improper_coeff command...........................................................................................................1274
improper_style cossq command..................................................................................................1276
improper_style cossq/omp command..........................................................................................1276
improper_style cvff command.....................................................................................................1278
improper_style cvff/omp command............................................................................................1278
improper_style fourier command................................................................................................1280
improper_style fourier/omp command........................................................................................1280
improper_style harmonic command............................................................................................1282
improper_style harmonic/omp command....................................................................................1282
improper_style hybrid command.................................................................................................1284
improper_style none command...................................................................................................1285
improper_style ring command.....................................................................................................1286
improper_style ring/omp command............................................................................................1286
improper_style umbrella command.............................................................................................1288
improper_style umbrella/omp command.....................................................................................1288
LAMMPS-ICMS Users Manual
xviii
LAMMPS-ICMS Documentation
14 Feb 2014 version
Version info:
The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated
continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this
page of the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and
including that version date. The version date is printed to the screen and logfile every time you run LAMMPS.
It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and
at the top of the first page of the manual (this page).
LAMMPS-ICMS is an experimental variant of LAMMPS with additional features made available for testing
before they will be submitted for inclusion into the official LAMMPS tree. The source code is based on the
official LAMMPS svn repository mirror at the Institute for Computational Molecular Science at Temple
University and generally kept up-to-date as much as possible. Sometimes, e.g. when additional development
work is needed to adapt the upstream changes into LAMMPS-ICMS it can take longer until synchronization;
and occasionally, e.g. in case of the rewrite of the multi-threading support, the development will be halted
except for important bugfixes until all features of LAMMPS-ICMS fully compatible with the upstream
version or replaced by alternate implementations.
If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most
current version of upstream LAMMPS, but may be missing some new features in LAMMPS-ICMS.
•
If you browse the HTML doc pages included in your tarball, they describe the version you have,
however, not all new features in LAMMPS-ICMS are documented immediately.
•
The PDF file on the WWW site or in the tarball is updated about once per month. This is because it is
large, and we don't want it to be part of every patch.
•
There is also a Developer.pdf file in the doc directory, which describes the internal structure and
algorithms of LAMMPS.
•
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator.
LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel
computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public
License (GPL).
The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be
contacted at sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at http://lammps.sandia.gov
has more information about the code and its uses.
The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this
manual or have suggestions for useful information to add, please send an email to the developers so we can
improve the LAMMPS documentation.
Once you are familiar with LAMMPS, you may want to bookmark this page at
Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands.
PDF file of the entire manual, generated by htmldoc
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