lammps users manual - sandia national laboratories

LAMMPS Users Manual5 Feb 2018 version

http://lammps.sandia.gov - Sandia National LaboratoriesCopyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.

Table of ContentsLAMMPS Documentation......................................................................................1

5 Feb 2018 version...........................................................................................1Version info:................................................................................................1

1. Introduction.................................................................................................51.1 What is LAMMPS..................................................................................51.2 LAMMPS features.................................................................................61.3 LAMMPS non-features..........................................................................91.4 Open source distribution....................................................................111.5 Acknowledgments and citations.........................................................12

2. Getting Started..........................................................................................142.1 What's in the LAMMPS distribution...................................................142.2 Making LAMMPS................................................................................152.3 Making LAMMPS with optional packages..........................................252.4 Building LAMMPS as a library............................................................292.5 Running LAMMPS...............................................................................312.6 Command-line options........................................................................332.7 LAMMPS screen output......................................................................402.8 Tips for users of previous LAMMPS versions.....................................43

3. Commands.................................................................................................453.1 LAMMPS input script..........................................................................453.2 Parsing rules.......................................................................................463.3 Input script structure..........................................................................483.4 Commands listed by category.............................................................493.5 Individual commands..........................................................................50Fix styles...................................................................................................51Compute styles..........................................................................................52Pair_style potentials..................................................................................52Bond_style potentials................................................................................54Angle_style potentials...............................................................................54Dihedral_style potentials..........................................................................55Improper_style potentials.........................................................................55Kspace solvers..........................................................................................55

4. Packages....................................................................................................57ASPHERE package....................................................................................60BODY package..........................................................................................61CLASS2 package.......................................................................................61COLLOID package....................................................................................62COMPRESS package.................................................................................63CORESHELL package...............................................................................63DIPOLE package.......................................................................................64GPU package.............................................................................................64GRANULAR package.................................................................................66KIM package.............................................................................................66KOKKOS package.....................................................................................68KSPACE package......................................................................................69LATTE package.........................................................................................70MANYBODY package................................................................................71MC package..............................................................................................72

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Table of ContentsMEAM package.........................................................................................72MISC package...........................................................................................73MOLECULE package................................................................................74MPIIO package.........................................................................................74MSCG package..........................................................................................75OPT package.............................................................................................76PERI package............................................................................................77POEMS package.......................................................................................77PYTHON package.....................................................................................78QEQ package............................................................................................79REAX package...........................................................................................79REPLICA package.....................................................................................80RIGID package..........................................................................................81SHOCK package........................................................................................82SNAP package...........................................................................................82SRD package.............................................................................................83VORONOI package...................................................................................83USER-ATC package...................................................................................84USER-AWPMD package............................................................................85USER-CGDNA package.............................................................................86USER-CGSDK package.............................................................................87USER-COLVARS package.........................................................................87USER-DIFFRACTION package.................................................................88USER-DPD package..................................................................................89USER-DRUDE package.............................................................................90USER-EFF package...................................................................................90USER-FEP package...................................................................................91USER-H5MD package...............................................................................92USER-INTEL package...............................................................................93USER-LB package.....................................................................................94USER-MGPT package...............................................................................94USER-MISC package................................................................................95USER-MANIFOLD package......................................................................96USER-MEAMC package............................................................................96USER-MESO package...............................................................................97USER-MOFFF package.............................................................................97USER-MOLFILE package..........................................................................98USER-NETCDF package...........................................................................99USER-OMP package...............................................................................100USER-PHONON package........................................................................101USER-QMMM package...........................................................................101USER-QTB package................................................................................102USER-QUIP package...............................................................................103USER-REAXC package............................................................................104USER-SMD package...............................................................................104USER-SMTBQ package...........................................................................105USER-SPH package................................................................................106USER-TALLY package.............................................................................106

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Table of ContentsUSER-UEF package................................................................................107USER-VTK package.................................................................................107

5. Accelerating LAMMPS performance........................................................1095.1 Measuring performance....................................................................1095.2 General strategies.............................................................................1105.3 Packages with optimized styles........................................................1115.4 Comparison of various accelerator packages...................................114

6. How-to discussions...................................................................................1456.1 Restarting a simulation.....................................................................1456.2 2d simulations...................................................................................1476.3 CHARMM, AMBER, and DREIDING force fields..............................1476.4 Running multiple simulations from one input script........................1496.5 Multi-replica simulations..................................................................1506.6 Granular models...............................................................................1516.7 TIP3P water model............................................................................1526.8 TIP4P water model............................................................................1536.9 SPC water model...............................................................................1556.10 Coupling LAMMPS to other codes..................................................1566.11 Visualizing LAMMPS snapshots......................................................1576.12 Triclinic (non-orthogonal) simulation boxes...................................1576.13 NEMD simulations..........................................................................1636.14 Finite-size spherical and aspherical particles.................................1636.15 Output from LAMMPS (thermo, dumps, computes, fixes,

variables).....................................................................................1676.16 Thermostatting, barostatting, and computing temperature...........1726.17 Walls...............................................................................................1756.18 Elastic constants.............................................................................1766.19 Library interface to LAMMPS.........................................................1776.20 Calculating thermal conductivity....................................................1806.21 Calculating viscosity.......................................................................1816.22 Calculating a diffusion coefficient..................................................1836.23 Using chunks to calculate system properties.................................1836.24 Setting parameters for the kspace_style pppm/disp command......1866.25 Polarizable models..........................................................................1886.26 Adiabatic core/shell model..............................................................1896.27 Drude induced dipoles....................................................................192

7. Example problems....................................................................................195Lowercase directories.............................................................................195Uppercase directories.............................................................................197

8. Performance & scalability........................................................................1989. Additional tools........................................................................................200

amber2lmp tool.......................................................................................200binary2txt tool.........................................................................................200ch2lmp tool.............................................................................................201chain tool................................................................................................201colvars tools............................................................................................201createatoms tool.....................................................................................202doxygen tool............................................................................................202

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Table of Contentsdrude tool................................................................................................202eam database tool...................................................................................202eam generate tool...................................................................................203eff tool.....................................................................................................203emacs tool...............................................................................................203fep tool....................................................................................................203i-pi tool....................................................................................................203ipp tool....................................................................................................204kate tool..................................................................................................204lmp2arc tool............................................................................................204lmp2cfg tool............................................................................................204matlab tool..............................................................................................204micelle2d tool..........................................................................................205moltemplate tool.....................................................................................205msi2lmp tool...........................................................................................205phonon tool.............................................................................................205polybond tool..........................................................................................206pymol_asphere tool.................................................................................206python tool..............................................................................................206reax tool..................................................................................................206smd tool..................................................................................................207vim tool...................................................................................................207xmgrace tool...........................................................................................207

10. Modifying & extending LAMMPS..........................................................20810.1 Atom styles......................................................................................21010.2 Bond, angle, dihedral, improper potentials....................................21110.3 Compute styles................................................................................21210.4 Dump styles....................................................................................21310.5 Dump custom output options..........................................................21310.6 Fix styles.........................................................................................21310.7 Input script commands...................................................................21610.8 Kspace computations......................................................................21610.9 Minimization styles.........................................................................21610.10 Pairwise potentials........................................................................21710.11 Region styles.................................................................................21710.12 Body styles....................................................................................21810.13 Thermodynamic output options....................................................21810.14 Variable options............................................................................21910.15 Submitting new features for inclusion in LAMMPS......................219

11. Python interface to LAMMPS.................................................................22411.1 Overview of running LAMMPS from Python...................................22511.2 Overview of using Python from a LAMMPS script..........................22611.3 Building LAMMPS as a shared library............................................22711.4 Installing the Python wrapper into Python.....................................22711.5 Extending Python with MPI to run in parallel................................22811.6 Testing the Python-LAMMPS interface...........................................23111.7 Using LAMMPS from Python..........................................................23311.8 Example Python scripts that use LAMMPS....................................237

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Table of Contents11.9 PyLammps interface.......................................................................238

12. Errors.....................................................................................................23912.1 Common problems..........................................................................23912.2 Reporting bugs................................................................................24112.3 Error & warning messages.............................................................241Errors:.....................................................................................................241Warnings:................................................................................................353

13. Future and history.................................................................................36513.1 Coming attractions.........................................................................36513.2 Past versions...................................................................................365

Using LAMMPS with Bash on Windows.......................................................368Installing Bash on Windows....................................................................368Compiling LAMMPS in Bash on Windows..............................................375

Tutorial for Thermalized Drude oscillators in LAMMPS..............................378LAMMPS GitHub tutorial.............................................................................386

PyLammps Tutorial.........................................................................................403Overview...........................................................................................................403

Comparison of lammps and PyLammps interfaces......................................403lammps.lammps......................................................................................403lammps.PyLammps.................................................................................403

Quick Start........................................................................................................403System-wide Installation..............................................................................403

Step 1: Building LAMMPS as a shared library.......................................403Step 2: Installing the LAMMPS Python package....................................404

Installation inside of a virtualenv.................................................................404Benefits of using a virtualenv.................................................................404Creating a virtualenv with lammps installed..........................................404

Creating a new instance of PyLammps.............................................................404Commands.........................................................................................................405System state......................................................................................................405Working with LAMMPS variables.....................................................................406Retrieving the value of an arbitrary LAMMPS expressions..............................406Accessing atom data.........................................................................................407Evaluating thermo data.....................................................................................407Error handling with PyLammps........................................................................408Using PyLammps in IPython notebooks and Jupyter........................................408IPyLammps Examples.......................................................................................408

Validating a dihedral potential.....................................................................408Running a Monte Carlo relaxation...............................................................410

Using PyLammps and mpi4py (Experimental)..................................................413Feedback and Contributing...............................................................................413

Body particles..............................................................................................414Manifolds (surfaces).....................................................................................419angle_coeff command...................................................................................421angle_style command...................................................................................423atom_modify command................................................................................425atom_style command....................................................................................428

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Table of ContentsPyLammps Tutorial

balance command........................................................................................434bond_coeff command...................................................................................443bond_style command....................................................................................445bond_write command...................................................................................447boundary command......................................................................................448box command...............................................................................................450change_box command..................................................................................451clear command.............................................................................................457comm_modify command...............................................................................458comm_style command..................................................................................461compute command.......................................................................................462compute_modify command...........................................................................467create_atoms command...............................................................................469create_bonds command................................................................................475create_box command...................................................................................479delete_atoms command................................................................................482delete_bonds command................................................................................485dielectric command......................................................................................488dihedral_coeff command..............................................................................489dihedral_style command..............................................................................491dimension command....................................................................................494displace_atoms command............................................................................495dump command............................................................................................498dump vtk command......................................................................................498dump h5md command..................................................................................498dump molfile command................................................................................498dump netcdf command.................................................................................498dump image command.................................................................................498dump movie command.................................................................................498dump h5md command..................................................................................509dump image command.................................................................................511dump movie command.................................................................................511dump_modify command...............................................................................523dump molfile command................................................................................538dump netcdf command.................................................................................540dump netcdf/mpiio command.......................................................................540dump vtk command......................................................................................542dump cfg/uef command................................................................................545echo command.............................................................................................546fix command.................................................................................................547fix_modify command....................................................................................553group command...........................................................................................555group2ndx command...................................................................................560ndx2group command...................................................................................560if command...................................................................................................562improper_coeff command.............................................................................566improper_style command.............................................................................568

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include command.........................................................................................570info command...............................................................................................571jump command.............................................................................................574kspace_modify command.............................................................................577kspace_style command.................................................................................583label command.............................................................................................590lattice command...........................................................................................591log command................................................................................................596mass command.............................................................................................597min_modify command..................................................................................599min_style command......................................................................................601minimize command......................................................................................603molecule command......................................................................................608neb command...............................................................................................616neigh_modify command...............................................................................623neighbor command......................................................................................627newton command.........................................................................................629next command..............................................................................................630package command.......................................................................................633pair_coeff command.....................................................................................643pair_modify command..................................................................................646pair_style command.....................................................................................651pair_write command....................................................................................656partition command.......................................................................................658prd command...............................................................................................660print command.............................................................................................666processors command...................................................................................668python command..........................................................................................674quit command..............................................................................................682read_data command.....................................................................................683read_dump command...................................................................................703read_restart command.................................................................................709region command..........................................................................................714replicate command.......................................................................................721rerun command............................................................................................723reset_timestep command.............................................................................727restart command..........................................................................................728run command...............................................................................................731run_style command......................................................................................735set command................................................................................................740shell command.............................................................................................748special_bonds command..............................................................................750suffix command............................................................................................754tad command................................................................................................756temper command.........................................................................................761temper/grem command................................................................................764temper/npt command...................................................................................766

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thermo command.........................................................................................768thermo_modify command.............................................................................769thermo_style command................................................................................772timer command............................................................................................779timestep command.......................................................................................782uncompute command...................................................................................783undump command........................................................................................784unfix command.............................................................................................785units command.............................................................................................786variable command........................................................................................791

Numbers, constants, and thermo keywords...........................................799Math Operators.......................................................................................799Math Functions.......................................................................................800Group and Region Functions..................................................................802Special Functions....................................................................................803Feature Functions...................................................................................804Atom Values and Vectors........................................................................805Compute References...............................................................................806Fix References........................................................................................807Variable References................................................................................808

velocity command........................................................................................813write_coeff command...................................................................................818write_data command....................................................................................819write_dump command..................................................................................821write_restart command................................................................................823fix adapt command.......................................................................................825fix adapt/fep command.................................................................................830fix addforce command..................................................................................835fix addtorque command...............................................................................838fix append/atoms command.........................................................................840fix atc command...........................................................................................842fix atom/swap command...............................................................................848fix ave/atom command.................................................................................851fix ave/chunk command...............................................................................854fix ave/correlate command...........................................................................862fix ave/correlate/long command...................................................................868fix ave/histo command.................................................................................871fix ave/histo/weight command......................................................................871fix ave/time command..................................................................................877fix aveforce command..................................................................................883fix balance command...................................................................................885fix bond/break command..............................................................................892fix bond/create command.............................................................................895fix bond/swap command...............................................................................899fix box/relax command.................................................................................903fix cmap command.......................................................................................909fix colvars command....................................................................................912

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fix controller command................................................................................915fix deform command....................................................................................919fix deform/kk command................................................................................919fix deposit command....................................................................................929fix dpd/energy command..............................................................................934fix dpd/energy/kk command.........................................................................934fix edpd/source command............................................................................936fix tdpd/source command.............................................................................936fix drag command........................................................................................938fix drude command......................................................................................939fix drude/transform/direct command...........................................................940fix drude/transform/inverse command.........................................................940fix dt/reset command...................................................................................943fix efield command.......................................................................................945fix ehex command........................................................................................948fix enforce2d command................................................................................951fix eos/cv command......................................................................................953fix eos/table command.................................................................................954fix eos/table/rx command.............................................................................956fix eos/table/rx/kk command........................................................................956fix evaporate command................................................................................960fix external command...................................................................................962fix filter/corotate command..........................................................................965fix flow/gauss command...............................................................................967fix freeze command......................................................................................970fix gcmc command.......................................................................................972fix gld command...........................................................................................980fix gle command...........................................................................................983fix gravity command.....................................................................................986fix gravity/omp command.............................................................................986fix grem command.......................................................................................989fix halt command..........................................................................................991fix heat command.........................................................................................994fix imd command..........................................................................................997fix indent command....................................................................................1000fix ipi command..........................................................................................1004fix langevin command................................................................................1006fix langevin/kk command...........................................................................1006fix langevin/drude command......................................................................1012fix langevin/eff command...........................................................................1016fix latte command.......................................................................................1018fix lb/fluid command...................................................................................1022fix lb/momentum command........................................................................1029fix lb/pc command......................................................................................1031fix lb/rigid/pc/sphere command.................................................................1032fix lb/viscous command..............................................................................1035fix lineforce command................................................................................1037

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fix manifoldforce command........................................................................1038fix meso command.....................................................................................1039fix meso/stationary command....................................................................1040fix momentum command............................................................................1041fix momentum/kk command.......................................................................1041fix move command.....................................................................................1043fix mscg command.....................................................................................1047 fix msst command.....................................................................................1050fix mvv/dpd command................................................................................1054fix mvv/edpd command..............................................................................1054fix mvv/tdpd command...............................................................................1054fix neb command........................................................................................1056fix nvt command.........................................................................................1060fix nvt/intel command.................................................................................1060fix nvt/kk command....................................................................................1060fix nvt/omp command.................................................................................1060fix npt command.........................................................................................1060fix npt/intel command................................................................................1060fix npt/kk command....................................................................................1060fix npt/omp command.................................................................................1060fix nph command........................................................................................1060fix nph/kk command...................................................................................1060fix nph/omp command................................................................................1060fix nvt/eff command...................................................................................1071fix npt/eff command...................................................................................1071fix nph/eff command...................................................................................1071fix nph/asphere command..........................................................................1074fix nph/asphere/omp command..................................................................1074fix nph/body command...............................................................................1077fix nph/sphere command............................................................................1080fix nph/sphere/omp command....................................................................1080fix nphug command....................................................................................1083fix nphug/omp command............................................................................1083fix npt/asphere command...........................................................................1087fix npt/asphere/omp command...................................................................1087fix npt/body command................................................................................1090fix npt/sphere command.............................................................................1093fix npt/sphere/omp command.....................................................................1093fix nve command........................................................................................1096fix nve/intel command................................................................................1096fix nve/kk command...................................................................................1096fix nve/omp command................................................................................1096fix nve/asphere command..........................................................................1098fix nve/asphere/intel command..................................................................1098fix nve/asphere/noforce command.............................................................1100fix nve/body command...............................................................................1101fix nve/dot command..................................................................................1102

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fix nve/dotc/langevin command..................................................................1103fix nve/eff command...................................................................................1106fix nve/limit command................................................................................1107fix nve/line command.................................................................................1109fix nve/manifold/rattle command...............................................................1110fix nve/noforce command...........................................................................1112fix nve/sphere command............................................................................1113fix nve/sphere/omp command....................................................................1113fix nve/tri command...................................................................................1115fix nvk command........................................................................................1116fix nvt/asphere command...........................................................................1118fix nvt/asphere/omp command...................................................................1118fix nvt/body command................................................................................1121fix nvt/manifold/rattle command................................................................1124fix nvt/sllod command................................................................................1126fix nvt/sllod/intel command........................................................................1126fix nvt/sllod/omp command........................................................................1126fix nvt/sllod/eff command...........................................................................1129fix nvt/sphere command.............................................................................1131fix nvt/sphere/omp command.....................................................................1131fix nvt/uef command...................................................................................1134fix npt/uef command..................................................................................1134fix oneway command..................................................................................1138fix orient/fcc command...............................................................................1139fix orient/bcc command..............................................................................1139fix phonon command..................................................................................1143fix pimd command......................................................................................1147fix planeforce command.............................................................................1151fix poems....................................................................................................1152fix pour command......................................................................................1155fix press/berendsen command...................................................................1160fix print command......................................................................................1164fix property/atom command.......................................................................1166fix python/invoke command.......................................................................1171fix python/move command.........................................................................1173fix qbmsst command..................................................................................1175fix qeq/point command...............................................................................1180fix qeq/shielded command.........................................................................1180fix qeq/slater command..............................................................................1180fix qeq/dynamic command.........................................................................1180fix qeq/fire command.................................................................................1180fix qeq/comb command..............................................................................1184fix qeq/comb/omp command......................................................................1184fix qeq/reax command................................................................................1187fix qeq/reax/kk command...........................................................................1187fix qeq/reax/omp command........................................................................1187fix qmmm command...................................................................................1190

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fix qtb command.........................................................................................1192fix reax/bonds command............................................................................1195fix reax/c/bonds command.........................................................................1195fix reax/c/bonds/kk command....................................................................1195fix reax/c/species command.......................................................................1197fix reax/c/species/kk command..................................................................1197fix recenter command................................................................................1200fix restrain command.................................................................................1202fix rigid command......................................................................................1206fix rigid/omp command..............................................................................1206fix rigid/nve command................................................................................1206fix rigid/nve/omp command........................................................................1206fix rigid/nvt command................................................................................1206fix rigid/nvt/omp command........................................................................1206fix rigid/npt command................................................................................1206fix rigid/npt/omp command........................................................................1206fix rigid/nph command...............................................................................1206fix rigid/nph/omp command.......................................................................1206fix rigid/small command.............................................................................1206fix rigid/small/omp command.....................................................................1206fix rigid/nve/small command......................................................................1206fix rigid/nvt/small command.......................................................................1206fix rigid/npt/small command......................................................................1206fix rigid/nph/small command......................................................................1206fix rhok command......................................................................................1220fix rx command...........................................................................................1222fix rx/kk command......................................................................................1222fix saed/vtk command................................................................................1227fix setforce command.................................................................................1230fix setforce/kk command............................................................................1230fix shake command.....................................................................................1233fix rattle command.....................................................................................1233fix shardlow command...............................................................................1237fix shardlow/kk command..........................................................................1237fix smd command.......................................................................................1239fix smd/adjust_dt command........................................................................1242fix smd/integrate_tlsph command..............................................................1243fix smd/integrate_ulsph command.............................................................1244fix smd/move_tri_surf command................................................................1245fix smd/setvel command.............................................................................1247fix smd/wall_surface command..................................................................1249fix spring command....................................................................................1251fix spring/chunk command.........................................................................1254fix spring/rg command...............................................................................1256fix spring/self command.............................................................................1258fix srd command.........................................................................................1260fix store/force command............................................................................1267

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fix store/state command.............................................................................1269fix temp/berendsen command....................................................................1271fix temp/csvr command..............................................................................1274fix temp/csld command..............................................................................1274fix temp/rescale command.........................................................................1277fix temp/rescale/eff command....................................................................1280fix tfmc command.......................................................................................1282fix thermal/conductivity command.............................................................1285fix ti/spring command................................................................................1288fix tmd command........................................................................................1291fix ttm command........................................................................................1294fix ttm/mod command................................................................................1294fix tune/kspace command...........................................................................1300fix vector command....................................................................................1302fix viscosity command................................................................................1305fix viscous command..................................................................................1308fix wall/lj93 command................................................................................1310fix wall/lj93/kk command...........................................................................1310fix wall/lj126 command..............................................................................1310fix wall/lj1043 command............................................................................1310fix wall/colloid command............................................................................1310fix wall/harmonic command.......................................................................1310fix wall/ees command.................................................................................1316fix wall/region/ees command.....................................................................1316fix wall/gran command...............................................................................1319fix wall/gran/region command...................................................................1322fix wall/piston command............................................................................1326fix wall/reflect command............................................................................1328fix wall/reflect/kk command.......................................................................1328fix wall/region command............................................................................1331fix wall/srd command.................................................................................1335compute ackland/atom command..............................................................1338compute angle command...........................................................................1340compute angle/local command...................................................................1341compute angmom/chunk command...........................................................1343compute basal/atom command...................................................................1345compute body/local command....................................................................1347compute bond command............................................................................1349compute bond/local command...................................................................1350compute centro/atom command.................................................................1353compute chunk/atom command.................................................................1356compute cluster/atom command................................................................1367compute fragment/atom command............................................................1367compute aggregate/atom command...........................................................1367compute cna/atom command.....................................................................1369compute cnp/atom command.....................................................................1372compute com command.............................................................................1375

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compute com/chunk command...................................................................1376compute contact/atom command...............................................................1378compute coord/atom command..................................................................1379compute damage/atom command..............................................................1382compute dihedral command.......................................................................1383compute dihedral/local command..............................................................1384compute dilatation/atom command............................................................1386compute dipole/chunk command...............................................................1388compute displace/atom command..............................................................1390compute dpd command..............................................................................1392compute dpd/atom command.....................................................................1394compute edpd/temp/atom command..........................................................1396compute erotate/asphere command...........................................................1397compute erotate/rigid command................................................................1399compute erotate/sphere command............................................................1400compute erotate/sphere/atom command...................................................1401compute event/displace command.............................................................1402compute fep command...............................................................................1404compute global/atom command.................................................................1409compute group/group command................................................................1413compute gyration command.......................................................................1416compute gyration/chunk command............................................................1418compute heat/flux command......................................................................1420compute hexorder/atom command............................................................1424compute improper command.....................................................................1426compute improper/local command.............................................................1427compute inertia/chunk command...............................................................1429compute ke command................................................................................1431compute ke/atom command.......................................................................1432compute ke/atom/eff command..................................................................1433compute ke/eff command...........................................................................1435compute ke/rigid command........................................................................1437compute meso/e/atom command................................................................1438compute meso/rho/atom command............................................................1439compute meso/t/atom command................................................................1440compute msd command.............................................................................1441compute msd/chunk command...................................................................1443compute msd/nongauss command.............................................................1445compute omega/chunk command...............................................................1447compute orientorder/atom command.........................................................1449compute pair command..............................................................................1452compute pair/local command.....................................................................1454compute pe command................................................................................1457compute pe/atom command.......................................................................1459compute plasticity/atom command............................................................1461compute pressure command......................................................................1463compute pressure/uef command................................................................1466

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compute property/atom command.............................................................1467compute property/chunk command...........................................................1470compute property/local command..............................................................1472compute rdf command...............................................................................1475compute reduce command.........................................................................1479compute reduce/region command..............................................................1479compute rigid/local command....................................................................1483compute saed command.............................................................................1487compute slice command.............................................................................1491compute smd/contact/radius command.....................................................1493compute smd/damage command................................................................1494compute smd/hourglass/error command...................................................1495compute smd/internal/energy command....................................................1496compute smd/plastic/strain command.......................................................1497compute smd/plastic/strain/rate command................................................1498compute smd/rho command.......................................................................1499compute smd/tlsph/defgrad command.......................................................1500compute smd/tlsph/dt command................................................................1501compute smd/tlsph/num/neighs command.................................................1502compute smd/tlsph/shape command..........................................................1503compute smd/tlsph/strain command..........................................................1504compute smd/tlsph/strain/rate command..................................................1505compute smd/tlsph/stress command..........................................................1506compute smd/triangle/mesh/vertices.........................................................1507compute smd/ulsph/num/neighs command................................................1508compute smd/ulsph/strain command.........................................................1509compute smd/ulsph/strain/rate command..................................................1510compute smd/ulsph/stress command.........................................................1511compute smd/vol command........................................................................1512compute sna/atom command.....................................................................1513compute snad/atom command...................................................................1513compute snav/atom command....................................................................1513compute stress/atom command.................................................................1519compute force/tally command....................................................................1522compute heat/flux/tally command..............................................................1522compute pe/tally command........................................................................1522compute pe/mol/tally command.................................................................1522compute stress/tally command...................................................................1522compute tdpd/cc/atom command...............................................................1524compute temp command............................................................................1525compute temp/kk command.......................................................................1525compute temp/asphere command..............................................................1527compute temp/body command...................................................................1530compute temp/chunk command.................................................................1533compute temp/com command....................................................................1537compute temp/cs command.......................................................................1539compute temp/deform command...............................................................1541

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compute temp/deform/eff command..........................................................1544compute temp/drude command.................................................................1546compute temp/eff command.......................................................................1548compute temp/partial command................................................................1550compute temp/profile command................................................................1552compute temp/ramp command..................................................................1555compute temp/region command................................................................1557compute temp/region/eff command...........................................................1559compute temp/rotate command.................................................................1560compute temp/sphere command................................................................1562compute temp/uef command......................................................................1565compute ti command..................................................................................1566compute torque/chunk command...............................................................1569compute vacf command.............................................................................1571compute vcm/chunk command...................................................................1573compute voronoi/atom command...............................................................1575compute xrd command...............................................................................1579pair_style adp command............................................................................1584pair_style adp/omp command....................................................................1584pair_style agni command...........................................................................1588pair_style agni/omp command...................................................................1588pair_style airebo command........................................................................1591pair_style airebo/intel command................................................................1591pair_style airebo/omp command................................................................1591pair_style airebo/morse command.............................................................1591pair_style airebo/morse/intel command.....................................................1591pair_style airebo/morse/omp command.....................................................1591pair_style rebo command...........................................................................1591pair_style rebo/intel command...................................................................1591pair_style rebo/omp command...................................................................1591pair_style awpmd/cut command.................................................................1596pair_style beck command...........................................................................1598pair_style beck/gpu command....................................................................1598pair_style beck/omp command...................................................................1598pair_style body command...........................................................................1600pair_style bop command............................................................................1602pair_style born command...........................................................................1610pair_style born/omp command...................................................................1610pair_style born/gpu command....................................................................1610pair_style born/coul/long command...........................................................1610pair_style born/coul/long/cs command.......................................................1610pair_style born/coul/long/gpu command....................................................1610pair_style born/coul/long/omp command...................................................1610pair_style born/coul/msm command..........................................................1610pair_style born/coul/msm/omp command...................................................1610pair_style born/coul/wolf command...........................................................1610pair_style born/coul/wolf/cs command.......................................................1610

LAMMPS Users Manual

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pair_style born/coul/wolf/gpu command....................................................1610pair_style born/coul/wolf/omp command...................................................1610pair_style born/coul/dsf command.............................................................1610pair_style born/coul/dsf/cs command.........................................................1610pair_style brownian command...................................................................1614pair_style brownian/omp command...........................................................1614pair_style brownian/poly command...........................................................1614pair_style brownian/poly/omp command....................................................1614pair_style buck command...........................................................................1617pair_style buck/gpu command...................................................................1617pair_style buck/intel command..................................................................1617pair_style buck/kk command......................................................................1617pair_style buck/omp command...................................................................1617pair_style buck/coul/cut command.............................................................1617pair_style buck/coul/cut/gpu command......................................................1617pair_style buck/coul/cut/intel command....................................................1617pair_style buck/coul/cut/kk command........................................................1617pair_style buck/coul/cut/omp command.....................................................1617pair_style buck/coul/long command...........................................................1617pair_style buck/coul/long/cs command......................................................1617pair_style buck/coul/long/gpu command....................................................1617pair_style buck/coul/long/intel command...................................................1617pair_style buck/coul/long/kk command......................................................1617pair_style buck/coul/long/omp command...................................................1617pair_style buck/coul/msm command..........................................................1617pair_style buck/coul/msm/omp command..................................................1617pair_style buck/long/coul/long command...................................................1621pair_style buck/long/coul/long/omp command...........................................1621pair_style lj/charmm/coul/charmm command............................................1624pair_style lj/charmm/coul/charmm/intel command....................................1624pair_style lj/charmm/coul/charmm/omp command....................................1624pair_style lj/charmm/coul/charmm/implicit command...............................1624pair_style lj/charmm/coul/charmm/implicit/omp command.......................1624pair_style lj/charmm/coul/long command..................................................1624pair_style lj/charmm/coul/long/gpu command...........................................1624pair_style lj/charmm/coul/long/intel command..........................................1624pair_style lj/charmm/coul/long/opt command............................................1624pair_style lj/charmm/coul/long/omp command..........................................1624pair_style lj/charmm/coul/msm command..................................................1624pair_style lj/charmm/coul/msm/omp command..........................................1624pair_style lj/charmmfsw/coul/charmmfsh command..................................1624pair_style lj/charmmfsw/coul/long command.............................................1624pair_style lj/class2 command.....................................................................1630pair_style lj/class2/gpu command..............................................................1630pair_style lj/class2/kk command................................................................1630pair_style lj/class2/omp command.............................................................1630pair_style lj/class2/coul/cut command........................................................1630

LAMMPS Users Manual

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pair_style lj/class2/coul/cut/kk command...................................................1630pair_style lj/class2/coul/cut/omp command................................................1630pair_style lj/class2/coul/long command......................................................1630pair_style lj/class2/coul/long/gpu command...............................................1630pair_style lj/class2/coul/long/kk command.................................................1630pair_style lj/class2/coul/long/omp command..............................................1630pair_style colloid command........................................................................1634pair_style colloid/gpu command.................................................................1634pair_style colloid/omp command................................................................1634pair_style comb command..........................................................................1639pair_style comb/omp command..................................................................1639pair_style comb3 command........................................................................1639pair_style coul/cut command.....................................................................1643pair_style coul/cut/gpu command..............................................................1643pair_style coul/cut/kk command.................................................................1643pair_style coul/cut/omp command..............................................................1643pair_style coul/debye command.................................................................1643pair_style coul/debye/gpu command..........................................................1643pair_style coul/debye/kk command............................................................1643pair_style coul/debye/omp command.........................................................1643pair_style coul/dsf command......................................................................1643pair_style coul/dsf/gpu command...............................................................1643pair_style coul/dsf/kk command.................................................................1643pair_style coul/dsf/omp command..............................................................1643pair_style coul/long command....................................................................1643pair_style coul/long/cs command...............................................................1643pair_style coul/long/omp command............................................................1643pair_style coul/long/gpu command............................................................1643pair_style coul/long/kk command...............................................................1643pair_style coul/msm command...................................................................1643pair_style coul/msm/omp command...........................................................1643pair_style coul/streitz command................................................................1643pair_style coul/wolf command....................................................................1643pair_style coul/wolf/kk command...............................................................1644pair_style coul/wolf/omp command............................................................1644pair_style coul/wolf/cs command...............................................................1644pair_style tip4p/cut command....................................................................1644pair_style tip4p/long command..................................................................1644pair_style tip4p/cut/omp command............................................................1644pair_style tip4p/long/omp command..........................................................1644pair_style coul/diel command.....................................................................1650pair_style coul/diel/omp command.............................................................1650pair_style born/coul/long/cs command.......................................................1652pair_style buck/coul/long/cs command......................................................1652pair_style born/coul/dsf/cs command.........................................................1652pair_style born/coul/wolf/cs command.......................................................1652pair_style lj/cut/dipole/cut command.........................................................1655

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pair_style lj/cut/dipole/cut/gpu command..................................................1655pair_style lj/cut/dipole/cut/omp command.................................................1655pair_style lj/sf/dipole/sf command..............................................................1655pair_style lj/sf/dipole/sf/gpu command.......................................................1655pair_style lj/sf/dipole/sf/omp command......................................................1655pair_style lj/cut/dipole/long command.......................................................1655pair_style lj/long/dipole/long command.....................................................1655pair_style dpd command............................................................................1664pair_style dpd/gpu command.....................................................................1664pair_style dpd/intel command....................................................................1664pair_style dpd/omp command....................................................................1664pair_style dpd/tstat command....................................................................1664pair_style dpd/tstat/gpu command.............................................................1664pair_style dpd/tstat/omp command............................................................1664pair_style dpd/fdt command.......................................................................1668pair_style dpd/fdt/energy command...........................................................1668pair_style dpd/fdt/energy/kk command......................................................1668pair_style dsmc command..........................................................................1672pair_style eam command............................................................................1675pair_style eam/gpu command....................................................................1675pair_style eam/intel command...................................................................1675pair_style eam/kk command.......................................................................1675pair_style eam/omp command....................................................................1675pair_style eam/opt command.....................................................................1675pair_style eam/alloy command...................................................................1675pair_style eam/alloy/gpu command............................................................1675pair_style eam/alloy/intel command...........................................................1675pair_style eam/alloy/kk c

lammps users manual - sandia national laboratories

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