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LAMMPS（大型分子多粒子模拟）是一种广泛使用的分子动力学模拟软件，适用于研究各种物质系统的结构和动力学性质，包括固体、液体、软物质、生物分子等。该软件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。 LAMMPS用户手册是该软件的核心文档，提供了详细的使用指南和功能介绍。2015年8月发布的版本是当时最新的官方手册，包含了自软件发布以来的最新更新和改进。手册通常会包含版本信息，以便用户了解其正在使用的软件的精确状态和功能。 在“1. Introduction”部分，手册首先解释了LAMMPS是什么。LAMMPS代表大型分子多粒子模拟器，它是一个设计用于模拟大系统（数千到数百万粒子）的高性能计算程序，支持多种计算模型，如经典分子动力学、蒙特卡洛、粗粒化模拟等。这一部分还概述了LAMMPS的主要特点，如灵活的输入脚本语言、多种相互作用势、支持并行计算以及与外部分析工具的接口。 接着，“1.2 LAMMPS features”详细列出了LAMMPS的特性，包括支持多种力场（如EAM、REAXFF、CHARMM等），粒子间作用力的广泛选择，如Lennard-Jones、Coulomb、 Buckingham势等。此外，LAMMPS还具有强大的时间步进控制，可以进行温度、压力控制的NVT、NPT模拟，以及复杂的边界条件处理能力。 “1.3 LAMMPS non-features”则指出LAMMPS不包括的功能，例如量子力学模拟、有限元分析或连续介质模拟。这帮助用户明确LAMMPS的适用范围。 “1.4 Open source distribution”强调了LAMMPS的开源性质，用户可以自由下载、修改和分发代码，促进社区协作和软件的持续发展。 在“1.5 Acknowledgments and citations”中，手册通常会感谢贡献者和资助机构，并提供了适当的引用指南，以便用户在发表研究成果时正确地引用LAMMPS。 “2. Getting Started”部分为新用户提供入门指导，包括了如何获取LAMMPS源代码、如何编译和构建LAMMPS，以及如何安装可选的附加包，这些包扩展了LAMMPS的基本功能，比如增强的分子动力学算法、新的力场或特定领域的应用。 手册的其余部分深入探讨了LAMMPS的使用，包括输入文件结构、设置参数、运行模拟、输出数据解析以及各种模拟技术的详细说明。对于每个功能，都有清晰的示例和解释，使得用户能够快速理解和应用LAMMPS进行科学研究。 LAMMPS手册是学习和使用LAMMPS进行分子模拟的宝贵资源，无论你是新手还是经验丰富的用户，都能从中找到所需的信息和支持。
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LAMMPS Users Manual
10 Aug 2015 version
http://lammps.sandia.gov - Sandia National Laboratories
Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.
Table of Contents
LAMMPS Documentation.............................................................................................................................1
10 Aug 2015 version...............................................................................................................................1
Version info:.....................................................................................................................................1
1. Introduction.........................................................................................................................................4
1.1 What is LAMMPS......................................................................................................................4
1.2 LAMMPS features......................................................................................................................5
1.3 LAMMPS non-features...............................................................................................................8
1.4 Open source distribution.............................................................................................................9
1.5 Acknowledgments and citations...............................................................................................10
2. Getting Started...................................................................................................................................12
2.1 What's in the LAMMPS distribution........................................................................................12
2.2 Making LAMMPS....................................................................................................................13
2.3 Making LAMMPS with optional packages..............................................................................20
2.4 Building LAMMPS via the Make.py script..............................................................................25
2.5 Building LAMMPS as a library................................................................................................27
2.6 Running LAMMPS...................................................................................................................28
2.7 Command-line options..............................................................................................................30
2.8 LAMMPS screen output...........................................................................................................36
2.9 Tips for users of previous LAMMPS versions.........................................................................37
3. Commands.........................................................................................................................................39
3.1 LAMMPS input script...............................................................................................................39
3.2 Parsing rules..............................................................................................................................40
3.3 Input script structure.................................................................................................................41
3.4 Commands listed by category...................................................................................................42
3.5 Individual commands................................................................................................................43
Fix styles.........................................................................................................................................44
Compute styles................................................................................................................................45
Pair_style potentials........................................................................................................................45
Bond_style potentials......................................................................................................................47
Angle_style potentials.....................................................................................................................47
Dihedral_style potentials................................................................................................................47
Improper_style potentials................................................................................................................48
Kspace solvers................................................................................................................................48
4. Packages............................................................................................................................................49
4.1 Standard packages.....................................................................................................................49
4.2 User packages...........................................................................................................................51
USER-ATC package.......................................................................................................................52
USER-AWPMD package................................................................................................................53
USER-CG-CMM package..............................................................................................................53
USER-COLVARS package............................................................................................................53
USER-CUDA package....................................................................................................................54
USER-DIFFRACTION package....................................................................................................54
USER-DRUDE package.................................................................................................................55
USER-EFF package........................................................................................................................55
USER-FEP package........................................................................................................................56
USER-INTEL package...................................................................................................................56
USER-LB package..........................................................................................................................56
USER-MISC package.....................................................................................................................56
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Table of Contents
USER-MOLFILE package..............................................................................................................57
USER-OMP package......................................................................................................................57
USER-PHONON package..............................................................................................................57
USER-QMMM package.................................................................................................................57
USER-QTB package.......................................................................................................................58
USER-REAXC package.................................................................................................................58
USER-SMD package......................................................................................................................59
USER-SPH package........................................................................................................................59
5. Accelerating LAMMPS performance................................................................................................60
5.1 Measuring performance............................................................................................................60
5.2 General strategies......................................................................................................................61
5.3 Packages with optimized styles................................................................................................62
5.4 Comparison of various accelerator packages............................................................................64
6. How-to discussions............................................................................................................................66
6.1 Restarting a simulation.............................................................................................................66
6.2 2d simulations...........................................................................................................................68
6.3 CHARMM, AMBER, and DREIDING force fields.................................................................68
6.4 Running multiple simulations from one input script................................................................69
6.5 Multi-replica simulations..........................................................................................................71
6.6 Granular models........................................................................................................................71
6.7 TIP3P water model...................................................................................................................72
6.8 TIP4P water model...................................................................................................................73
6.9 SPC water model.......................................................................................................................75
6.10 Coupling LAMMPS to other codes........................................................................................75
6.11 Visualizing LAMMPS snapshots............................................................................................76
6.12 Triclinic (non-orthogonal) simulation boxes..........................................................................77
6.13 NEMD simulations.................................................................................................................81
6.14 Finite-size spherical and aspherical particles..........................................................................81
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)....................................85
6.16 Thermostatting, barostatting, and computing temperature.....................................................89
6.17 Walls.......................................................................................................................................91
6.18 Elastic constants......................................................................................................................92
6.19 Library interface to LAMMPS................................................................................................93
6.20 Calculating thermal conductivity............................................................................................94
6.21 Calculating viscosity...............................................................................................................95
6.22 Calculating a diffusion coefficient..........................................................................................96
6.23 Using chunks to calculate system properties..........................................................................97
6.24 Setting parameters for the kspace_style pppm/disp command...............................................99
6.25 Polarizable models................................................................................................................100
6.26 Adiabatic core/shell model...................................................................................................101
6.27 Drude induced dipoles..........................................................................................................104
7. Example problems...........................................................................................................................106
8. Performance & scalability...............................................................................................................108
9. Additional tools...............................................................................................................................109
amber2lmp tool.............................................................................................................................110
binary2txt tool...............................................................................................................................110
ch2lmp tool...................................................................................................................................110
chain tool.......................................................................................................................................110
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Table of Contents
colvars tools..................................................................................................................................110
createatoms tool............................................................................................................................111
data2xmovie tool...........................................................................................................................111
eam database tool..........................................................................................................................111
eam generate tool..........................................................................................................................111
eff tool...........................................................................................................................................112
emacs tool.....................................................................................................................................112
fep tool..........................................................................................................................................112
i-pi tool..........................................................................................................................................112
ipp tool..........................................................................................................................................112
kate tool.........................................................................................................................................112
lmp2arc tool..................................................................................................................................113
lmp2cfg tool..................................................................................................................................113
lmp2vmd tool................................................................................................................................113
matlab tool....................................................................................................................................113
micelle2d tool................................................................................................................................113
moltemplate tool...........................................................................................................................113
msi2lmp tool.................................................................................................................................114
phonon tool...................................................................................................................................114
polymer bonding tool....................................................................................................................114
pymol_asphere tool.......................................................................................................................114
python tool....................................................................................................................................114
reax tool........................................................................................................................................115
restart2data tool.............................................................................................................................115
vim tool.........................................................................................................................................115
xmgrace tool..................................................................................................................................116
xmovie tool...................................................................................................................................116
10. Modifying & extending LAMMPS...............................................................................................117
10.1 Atom styles...........................................................................................................................118
10.2 Bond, angle, dihedral, improper potentials...........................................................................120
10.3 Compute styles......................................................................................................................120
10.4 Dump styles..........................................................................................................................121
10.5 Dump custom output options................................................................................................121
10.6 Fix styles...............................................................................................................................121
10.7 Input script commands..........................................................................................................123
10.8 Kspace computations............................................................................................................124
10.9 Minimization styles...............................................................................................................124
10.10 Pairwise potentials..............................................................................................................124
10.11 Region styles.......................................................................................................................125
10.11 Body styles..........................................................................................................................125
10.13 Thermodynamic output options..........................................................................................125
10.14 Variable options..................................................................................................................126
10.15 Submitting new features for inclusion in LAMMPS..........................................................126
11. Python interface to LAMMPS.......................................................................................................129
11.1 Overview of running LAMMPS from Python......................................................................129
11.2 Overview of using Python from a LAMMPS script.............................................................130
11.3 Building LAMMPS as a shared library................................................................................131
11.4 Installing the Python wrapper into Python............................................................................131
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Table of Contents
11.5 Extending Python with MPI to run in parallel......................................................................132
11.6 Testing the Python-LAMMPS interface...............................................................................134
11.7 Using LAMMPS from Python..............................................................................................135
11.8 Example Python scripts that use LAMMPS.........................................................................139
12. Errors.............................................................................................................................................141
12.1 Common problems................................................................................................................141
12.2 Reporting bugs......................................................................................................................142
12.3 Error & warning messages....................................................................................................142
Errors:...........................................................................................................................................143
Warnings:......................................................................................................................................238
13. Future and history..........................................................................................................................247
13.1 Coming attractions................................................................................................................247
13.2 Past versions..........................................................................................................................247
5.3.1 USER-CUDA package.........................................................................................................249
5.3.2 GPU package.......................................................................................................................253
5.3.3 USER-INTEL package........................................................................................................257
5.3.4 KOKKOS package...............................................................................................................262
5.3.5 USER-OMP package...........................................................................................................270
5.3.6 OPT package........................................................................................................................273
angle_style charmm command............................................................................................................275
angle_style charmm/kk command.......................................................................................................275
angle_style charmm/omp command....................................................................................................275
angle_style class2 command...............................................................................................................277
angle_style class2/omp command.......................................................................................................277
angle_coeff command.........................................................................................................................279
angle_style cosine command...............................................................................................................281
angle_style cosine/omp command.......................................................................................................281
angle_style cosine/delta command......................................................................................................283
angle_style cosine/delta/omp command..............................................................................................283
angle_style cosine/periodic command.................................................................................................285
angle_style cosine/periodic/omp command........................................................................................285
angle_style cosine/shift command.......................................................................................................287
angle_style cosine/shift/omp command..............................................................................................287
angle_style cosine/shift/exp command................................................................................................289
angle_style cosine/shift/exp/omp command........................................................................................289
angle_style cosine/squared command.................................................................................................291
angle_style cosine/squared/omp command.........................................................................................291
angle_style dipole command...............................................................................................................293
angle_style dipole/omp command.......................................................................................................293
angle_style fourier command..............................................................................................................295
angle_style fourier/omp command......................................................................................................295
angle_style fourier/simple command..................................................................................................297
angle_style fourier/simple/omp command..........................................................................................297
angle_style harmonic command..........................................................................................................299
angle_style harmonic/kk command.....................................................................................................299
angle_style harmonic/omp command..................................................................................................299
angle_style hybrid command...............................................................................................................301
angle_style none command.................................................................................................................303
LAMMPS Users Manual
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