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LAMMPS-手册 2014
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LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator.
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LAMMPS-ICMS Users Manual
14 Feb 2014 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-ICMS Documentation............................................................................................................1
14 Feb 2014 version..........................................................................................................................1
Version info:...............................................................................................................................1
1. Introduction...................................................................................................................................4
1.1 What is LAMMPS................................................................................................................4
1.2 LAMMPS features................................................................................................................5
General features..........................................................................................................................5
Particle and model types.............................................................................................................5
Force fields.................................................................................................................................6
Atom creation.............................................................................................................................6
Ensembles, constraints, and boundary conditions......................................................................6
Integrators...................................................................................................................................7
Diagnostics..................................................................................................................................7
Output.........................................................................................................................................7
Multi-replica models...................................................................................................................7
Pre- and post-processing.............................................................................................................7
Specialized features....................................................................................................................7
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........................................................................19
2.4 Building LAMMPS via the Make.py script........................................................................22
2.5 Building LAMMPS as a library..........................................................................................23
2.6 Running LAMMPS.............................................................................................................25
2.7 Command-line options........................................................................................................26
2.8 LAMMPS screen output.....................................................................................................31
2.9 Tips for users of previous LAMMPS versions...................................................................32
3. Commands...................................................................................................................................34
3.1 LAMMPS input script........................................................................................................34
3.2 Parsing rules........................................................................................................................35
3.3 Input script structure...........................................................................................................36
3.4 Commands listed by category.............................................................................................37
3.5 Individual commands..........................................................................................................38
Fix styles...................................................................................................................................39
Compute styles..........................................................................................................................40
Pair_style potentials..................................................................................................................40
Bond_style potentials................................................................................................................42
Angle_style potentials...............................................................................................................43
Dihedral_style potentials..........................................................................................................43
Improper_style potentials.........................................................................................................44
Kspace solvers..........................................................................................................................44
4. Packages......................................................................................................................................45
4.1 Standard packages...............................................................................................................45
4.2 User packages.....................................................................................................................46
USER-MISC package...............................................................................................................48
LAMMPS-ICMS Users Manual
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Table of Contents
USER-ATC package.................................................................................................................48
USER-AWPMD package.........................................................................................................48
USER-COLVARS package......................................................................................................49
USER-CG-CMM package........................................................................................................49
USER-CUDA package.............................................................................................................50
USER-EFF package..................................................................................................................50
USER-OMP package................................................................................................................51
USER-REAXC package...........................................................................................................51
USER-SPH package.................................................................................................................51
5. Accelerating LAMMPS performance.........................................................................................53
5.1 Measuring performance......................................................................................................53
5.2 General strategies................................................................................................................54
5.3 Packages with optimized styles..........................................................................................55
5.4 OPT package.......................................................................................................................56
5.5 USER-OMP package..........................................................................................................56
5.6 GPU package......................................................................................................................58
5.7 USER-CUDA package.......................................................................................................60
5.8 Comparison of GPU and USER-CUDA packages.............................................................62
6. How-to discussions......................................................................................................................64
6.1 Restarting a simulation.......................................................................................................64
6.2 2d simulations.....................................................................................................................66
6.3 CHARMM, AMBER, and DREIDING force fields...........................................................66
6.4 Running multiple simulations from one input script..........................................................67
6.5 Multi-replica simulations....................................................................................................69
6.6 Granular models..................................................................................................................69
6.7 TIP3P water model.............................................................................................................70
6.8 TIP4P water model.............................................................................................................71
6.9 SPC water model................................................................................................................73
6.10 Coupling LAMMPS to other codes..................................................................................73
6.11 Visualizing LAMMPS snapshots......................................................................................75
6.12 Triclinic (non-orthogonal) simulation boxes....................................................................75
6.13 NEMD simulations...........................................................................................................79
6.14 Finite-size spherical and aspherical particles....................................................................80
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables).............................83
6.16 Thermostatting, barostatting, and computing temperature...............................................88
6.17 Walls.................................................................................................................................90
6.18 Elastic constants................................................................................................................91
6.19 Library interface to LAMMPS.........................................................................................91
6.20 Calculating thermal conductivity......................................................................................93
6.21 Calculating viscosity.........................................................................................................94
6.22 Calculating a diffusion coefficient....................................................................................95
7. Example problems.......................................................................................................................97
8. Performance & scalability...........................................................................................................99
9. Additional tools.........................................................................................................................101
amber2lmp tool.......................................................................................................................102
binary2txt tool.........................................................................................................................102
ch2lmp tool.............................................................................................................................102
chain tool.................................................................................................................................102
LAMMPS-ICMS Users Manual
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Table of Contents
colvars tools............................................................................................................................103
createatoms tool......................................................................................................................103
data2xmovie tool.....................................................................................................................103
eam database tool....................................................................................................................103
eam generate tool....................................................................................................................103
eff tool.....................................................................................................................................104
emacs tool...............................................................................................................................104
ipp tool....................................................................................................................................104
kate tool...................................................................................................................................104
lmp2arc tool............................................................................................................................104
lmp2cfg tool............................................................................................................................104
lmp2vmd tool..........................................................................................................................105
matlab tool..............................................................................................................................105
micelle2d tool.........................................................................................................................105
moltemplate tool.....................................................................................................................105
msi2lmp tool...........................................................................................................................105
phonon tool.............................................................................................................................106
polymer bonding tool..............................................................................................................106
pymol_asphere tool.................................................................................................................106
python tool..............................................................................................................................106
reax tool..................................................................................................................................106
restart2data tool.......................................................................................................................107
vim tool...................................................................................................................................107
xmgrace tool...........................................................................................................................107
xmovie tool.............................................................................................................................108
10. Modifying & extending LAMMPS.........................................................................................109
10.1 Atom styles.....................................................................................................................110
10.2 Bond, angle, dihedral, improper potentials.....................................................................112
10.3 Compute styles................................................................................................................112
10.4 Dump styles....................................................................................................................113
10.5 Dump custom output options..........................................................................................113
10.6 Fix styles.........................................................................................................................114
10.7 Input script commands....................................................................................................116
10.8 Kspace computations......................................................................................................116
10.9 Minimization styles.........................................................................................................116
10.10 Pairwise potentials........................................................................................................116
10.11 Region styles.................................................................................................................117
10.11 Body styles....................................................................................................................117
10.13 Thermodynamic output options....................................................................................118
10.14 Variable options............................................................................................................118
10.15 Submitting new features for inclusion in LAMMPS....................................................119
11. Python interface to LAMMPS.................................................................................................121
11.1 Building LAMMPS as a shared library..........................................................................122
11.2 Installing the Python wrapper into Python.....................................................................122
11.3 Extending Python with MPI to run in parallel................................................................123
11.4 Testing the Python-LAMMPS interface.........................................................................124
11.5 Using LAMMPS from Python........................................................................................126
11.6 Example Python scripts that use LAMMPS...................................................................129
LAMMPS-ICMS Users Manual
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Table of Contents
12. Errors.......................................................................................................................................131
12.1 Common problems..........................................................................................................131
12.2 Reporting bugs................................................................................................................132
12.3 Error & warning messages..............................................................................................132
Errors:.....................................................................................................................................133
Warnings:................................................................................................................................219
13. Future and history....................................................................................................................227
13.1 Coming attractions..........................................................................................................227
13.2 Past versions...................................................................................................................227
balance command..........................................................................................................................229
box command................................................................................................................................233
boundary command.......................................................................................................................234
change_box command...................................................................................................................236
clear command..............................................................................................................................241
communicate command.................................................................................................................242
create_atoms command.................................................................................................................244
create_box command.....................................................................................................................248
delete_atoms command.................................................................................................................250
delete_bonds command.................................................................................................................252
dielectric command.......................................................................................................................254
dimension command......................................................................................................................255
displace_atoms command..............................................................................................................256
echo command...............................................................................................................................258
group command.............................................................................................................................259
group2ndx command.....................................................................................................................263
if command....................................................................................................................................264
include command..........................................................................................................................267
jump command..............................................................................................................................268
label command..............................................................................................................................270
lattice command............................................................................................................................271
log command.................................................................................................................................275
mass command..............................................................................................................................276
minimize command.......................................................................................................................278
min_style command......................................................................................................................282
min_modify command..................................................................................................................284
neb command................................................................................................................................286
neighbor command........................................................................................................................292
neigh_modify command................................................................................................................294
newton command..........................................................................................................................297
next command...............................................................................................................................298
package command.........................................................................................................................301
partition command.........................................................................................................................305
prd command.................................................................................................................................307
print command...............................................................................................................................312
processors command.....................................................................................................................314
quit command................................................................................................................................319
region command............................................................................................................................320
replicate command........................................................................................................................325
LAMMPS-ICMS Users Manual
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