LAMMPS手册 分子动力学模拟

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

1. Introduction................................................................................................................................................3

1.1 What is LAMMPS.............................................................................................................................3

1.2 LAMMPS features.............................................................................................................................4

Diagnostics..............................................................................................................................................6

Output......................................................................................................................................................6

Multi−replica models...............................................................................................................................6

Pre− and post−processing........................................................................................................................6

Specialized features.................................................................................................................................6

1.3 LAMMPS non−features....................................................................................................................6

1.4 Open source distribution....................................................................................................................8

1.5 Acknowledgments and citations........................................................................................................9

2. Getting Started.........................................................................................................................................13

2.1 What's in the LAMMPS distribution...............................................................................................13

2.8 Running on GPUs............................................................................................................................26

GPU configuration.................................................................................................................................26

GPU input script....................................................................................................................................27

GPU asynchronous pair computation....................................................................................................27

GPU timing............................................................................................................................................27

GPU single vs double precision............................................................................................................27

2.9 Tips for users of previous LAMMPS versions................................................................................27

3. Commands...............................................................................................................................................29

3.1 LAMMPS input script.....................................................................................................................29

3.2 Parsing rules....................................................................................................................................30

Bond_style potentials............................................................................................................................34

Angle_style potentials...........................................................................................................................35

Dihedral_style potentials.......................................................................................................................35

Improper_style potentials......................................................................................................................35

Kspace solvers.......................................................................................................................................35

4. How−to discussions.................................................................................................................................36

LAMMPS Users Manual

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4.1 Restarting a simulation....................................................................................................................36

4.2 2d simulations..................................................................................................................................37

4.3 CHARMM, AMBER, and DREIDING force fields.......................................................................38

4.4 Running multiple simulations from one input script.......................................................................39

4.11 Visualizing LAMMPS snapshots..................................................................................................46

4.12 Triclinic (non−orthogonal) simulation boxes................................................................................46

4.13 NEMD simulations........................................................................................................................48

4.14 Extended spherical and aspherical particles..................................................................................49

4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)..........................................51

4.16 Thermostatting, barostatting, and computing temperature............................................................55

4.17 Walls..............................................................................................................................................57

4.18 Elastic constants............................................................................................................................58

4.19 Library interface to LAMMPS......................................................................................................58

4.20 Calculating thermal conductivity..................................................................................................60

ch2lmp tool............................................................................................................................................67

chain tool...............................................................................................................................................67

createatoms tool.....................................................................................................................................67

data2xmovie tool...................................................................................................................................68

eam database tool..................................................................................................................................68

eam generate tool...................................................................................................................................68

eff tool...................................................................................................................................................68

emacs tool..............................................................................................................................................68

ipp tool...................................................................................................................................................68

lmp2arc tool...........................................................................................................................................69

pymol_asphere tool...............................................................................................................................70

python tool.............................................................................................................................................70

reax tool.................................................................................................................................................70

restart2data tool.....................................................................................................................................70

thermo_extract tool................................................................................................................................71

vim tool..................................................................................................................................................71

LAMMPS Users Manual

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xmovie tool............................................................................................................................................71

8. Modifying &extending LAMMPS...........................................................................................................72

Atom styles............................................................................................................................................73

Bond, angle, dihedral, improper potentials...........................................................................................74

Minimization solvers.............................................................................................................................78

Pairwise potentials.................................................................................................................................78

Region styles.........................................................................................................................................78

Thermodynamic output options.............................................................................................................79

Variable options.....................................................................................................................................79

Submitting new features to the developers to include in LAMMPS.....................................................80

10. Errors......................................................................................................................................................82

10.1 Common problems........................................................................................................................82

10.2 Reporting bugs...............................................................................................................................83

10.3 Error &warning messages.............................................................................................................83

angle_style class2 command......................................................................................................................144

angle_style cg/cmm command...................................................................................................................146

angle_coeff command................................................................................................................................147

angle_style cosine command.....................................................................................................................149

angle_style cosine/delta command.............................................................................................................150

angle_style cosine/periodic command.......................................................................................................151

angle_style cosine/squared command........................................................................................................152

angle_style harmonic command.................................................................................................................153

angle_style hybrid command.....................................................................................................................154

angle_style none command........................................................................................................................155

bond_style fene command.........................................................................................................................167

bond_style fene/expand command.............................................................................................................168

bond_style harmonic command.................................................................................................................170

bond_style hybrid command......................................................................................................................171

bond_style morse command.......................................................................................................................172

bond_style none command.........................................................................................................................173

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bond_style nonlinear command.................................................................................................................174

bond_style quartic command.....................................................................................................................175

bond_style command.................................................................................................................................177

bond_style table command.........................................................................................................................179

compute angle/local command...................................................................................................................192

compute atom/molecule command............................................................................................................194

compute bond/local command...................................................................................................................196

compute centro/atom command.................................................................................................................198

compute cna/atom command.....................................................................................................................200

compute com command.............................................................................................................................202

compute com/molecule command.............................................................................................................203

compute coord/atom command..................................................................................................................205

compute damage/atom command...............................................................................................................206

compute dihedral/local command..............................................................................................................207

compute gyration/molecule command.......................................................................................................215

compute heat/flux command......................................................................................................................217

compute improper/local command.............................................................................................................220

compute ke command................................................................................................................................221

compute ke/atom command.......................................................................................................................222

compute ke/atom/eff command..................................................................................................................223

compute ke/eff command...........................................................................................................................225

compute_modify command........................................................................................................................227

compute msd command.............................................................................................................................228

compute msd/molecule command..............................................................................................................230

compute property/local command..............................................................................................................244

compute property/molecule command.......................................................................................................246

compute rdf command...............................................................................................................................247

compute reduce command.........................................................................................................................249

compute reduce/region command..............................................................................................................249

compute stress/atom command..................................................................................................................252

LAMMPS Users Manual