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LAMMPS Users Manual
Large-scale Atomic/Molecular Massively Parallel Simulator
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
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........................................................................................................................................5
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...................................................................................................................24
2.7 Command-line options..............................................................................................................25
2.8 LAMMPS screen output...........................................................................................................29
2.9 Tips for users of previous LAMMPS versions.........................................................................30
3. Commands.........................................................................................................................................32
3.1 LAMMPS input script...............................................................................................................32
3.2 Parsing rules..............................................................................................................................33
3.3 Input script structure.................................................................................................................33
3.4 Commands listed by category...................................................................................................35
3.5 Individual commands................................................................................................................35
Fix styles.........................................................................................................................................36
Compute styles................................................................................................................................37
Pair_style potentials........................................................................................................................37
Bond_style potentials......................................................................................................................39
Angle_style potentials.....................................................................................................................39
Dihedral_style potentials................................................................................................................39
Improper_style potentials................................................................................................................40
Kspace solvers................................................................................................................................40
4. Packages............................................................................................................................................41
4.1 Standard packages.....................................................................................................................41
4.2 User packages...........................................................................................................................42
USER-MISC package.....................................................................................................................43
USER-ATC package.......................................................................................................................43
LAMMPS Users Manual
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Table of Contents
USER-AWPMD package................................................................................................................44
USER-COLVARS package............................................................................................................44
USER-CG-CMM package..............................................................................................................45
USER-CUDA package....................................................................................................................45
USER-EFF package........................................................................................................................45
USER-EWALDN package..............................................................................................................46
USER-OMP package......................................................................................................................46
USER-REAXC package.................................................................................................................47
USER-SPH package........................................................................................................................47
5. Accelerating LAMMPS performance................................................................................................48
5.1 Measuring performance............................................................................................................48
5.2 General strategies......................................................................................................................49
5.3 Packages with optimized styles................................................................................................49
5.4 OPT package.............................................................................................................................50
5.5 USER-OMP package................................................................................................................50
5.6 GPU package............................................................................................................................52
5.7 USER-CUDA package..............................................................................................................54
5.8 Comparison of GPU and USER-CUDA packages...................................................................56
6. How-to discussions............................................................................................................................58
6.1 Restarting a simulation.............................................................................................................58
6.2 2d simulations...........................................................................................................................60
6.3 CHARMM, AMBER, and DREIDING force fields.................................................................60
6.4 Running multiple simulations from one input script................................................................61
6.5 Multi-replica simulations..........................................................................................................63
6.6 Granular models........................................................................................................................63
6.7 TIP3P water model...................................................................................................................64
6.8 TIP4P water model...................................................................................................................65
6.9 SPC water model.......................................................................................................................66
6.10 Coupling LAMMPS to other codes........................................................................................67
6.11 Visualizing LAMMPS snapshots............................................................................................68
6.12 Triclinic (non-orthogonal) simulation boxes..........................................................................69
6.13 NEMD simulations.................................................................................................................73
6.14 Extended spherical and aspherical particles...........................................................................73
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)....................................76
6.16 Thermostatting, barostatting, and computing temperature.....................................................80
6.17 Walls.......................................................................................................................................82
6.18 Elastic constants......................................................................................................................83
6.19 Library interface to LAMMPS................................................................................................84
6.20 Calculating thermal conductivity............................................................................................85
6.21 Calculating viscosity...............................................................................................................86
7. Example problems.............................................................................................................................89
8. Performance & scalability.................................................................................................................91
9. Additional tools.................................................................................................................................92
amber2lmp tool...............................................................................................................................92
binary2txt tool.................................................................................................................................93
ch2lmp tool.....................................................................................................................................93
chain tool.........................................................................................................................................93
createatoms tool..............................................................................................................................93
LAMMPS Users Manual
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Table of Contents
data2xmovie tool.............................................................................................................................94
eam database tool............................................................................................................................94
eam generate tool............................................................................................................................94
eff tool.............................................................................................................................................94
emacs tool.......................................................................................................................................94
ipp tool............................................................................................................................................94
lmp2arc tool....................................................................................................................................95
lmp2cfg tool....................................................................................................................................95
lmp2vmd tool..................................................................................................................................95
matlab tool......................................................................................................................................95
micelle2d tool..................................................................................................................................95
msi2lmp tool...................................................................................................................................95
pymol_asphere tool.........................................................................................................................96
python tool......................................................................................................................................96
reax tool..........................................................................................................................................96
restart2data tool...............................................................................................................................96
thermo_extract tool.........................................................................................................................97
vim tool...........................................................................................................................................97
xmovie tool.....................................................................................................................................97
10. Modifying & extending LAMMPS.................................................................................................98
10.1 Atom styles.............................................................................................................................99
10.2 Bond, angle, dihedral, improper potentials...........................................................................100
10.3 Compute styles......................................................................................................................101
10.4 Dump styles..........................................................................................................................101
10.5 Dump custom output options................................................................................................102
10.6 Fix styles...............................................................................................................................102
10.7 Input script commands..........................................................................................................104
10.8 Kspace computations............................................................................................................104
10.9 Minimization styles...............................................................................................................104
10.10 Pairwise potentials..............................................................................................................105
10.11 Region styles.......................................................................................................................105
10.12 Thermodynamic output options..........................................................................................106
10.13 Variable options..................................................................................................................106
10.14 Submitting new features for inclusion in LAMMPS..........................................................107
11. Python interface to LAMMPS.......................................................................................................109
11.1 Building LAMMPS as a shared library................................................................................110
11.2 Installing the Python wrapper into Python............................................................................110
11.3 Extending Python with MPI to run in parallel......................................................................111
11.4 Testing the Python-LAMMPS interface...............................................................................112
11.5 Using LAMMPS from Python..............................................................................................114
11.6 Example Python scripts that use LAMMPS.........................................................................117
12. Errors.............................................................................................................................................119
12.1 Common problems................................................................................................................119
12.2 Reporting bugs......................................................................................................................120
12.3 Error & warning messages....................................................................................................120
Errors:...........................................................................................................................................121
Warnings:......................................................................................................................................187
13. Future and history..........................................................................................................................193
LAMMPS Users Manual
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Table of Contents
13.1 Coming attractions................................................................................................................193
13.2 Past versions..........................................................................................................................193
angle_style charmm command............................................................................................................195
angle_style charmm/omp command....................................................................................................195
angle_style class2 command...............................................................................................................197
angle_style class2/omp command.......................................................................................................197
angle_coeff command.........................................................................................................................199
angle_style cosine command...............................................................................................................201
angle_style cosine/omp command.......................................................................................................201
angle_style cosine/delta command......................................................................................................203
angle_style cosine/delta/omp command..............................................................................................203
angle_style cosine/periodic command.................................................................................................205
angle_style cosine/periodic/omp command........................................................................................205
angle_style cosine/shift command.......................................................................................................207
angle_style cosine/shift/omp command..............................................................................................207
angle_style cosine/shift/exp command................................................................................................209
angle_style cosine/shift/exp/omp command........................................................................................209
angle_style cosine/squared command.................................................................................................211
angle_style cosine/squared/omp command.........................................................................................211
angle_style dipole command...............................................................................................................213
angle_style dipole/omp command.......................................................................................................213
angle_style harmonic command..........................................................................................................215
angle_style harmonic/omp command..................................................................................................215
angle_style hybrid command...............................................................................................................217
angle_style none command.................................................................................................................219
angle_style sdk command....................................................................................................................220
angle_style command..........................................................................................................................221
angle_style table command.................................................................................................................223
angle_style table/omp command.........................................................................................................223
atom_modify command.......................................................................................................................226
atom_style command...........................................................................................................................228
balance command................................................................................................................................231
bond_style class2 command................................................................................................................235
bond_style class2/omp command........................................................................................................235
bond_coeff command..........................................................................................................................237
bond_style fene command...................................................................................................................239
bond_style fene/omp command...........................................................................................................239
bond_style fene/expand command......................................................................................................241
bond_style fene/expand/omp command..............................................................................................241
bond_style harmonic command...........................................................................................................243
bond_style harmonic/omp command..................................................................................................243
bond_style harmonic/shift command..................................................................................................245
bond_style harmonic/shift/omp command..........................................................................................245
bond_style harmonic/shift/cut command............................................................................................247
bond_style harmonic/shift/cut/omp command....................................................................................247
bond_style hybrid command...............................................................................................................249
bond_style morse command................................................................................................................251
bond_style morse/omp command........................................................................................................251
LAMMPS Users Manual
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