lammps manual from sandia.gov

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LAMMPS Users Manual7 Dec 2015 version

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


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

7 Dec 2015 version...................................... ............................................................................................1Version info:.......................................... ...........................................................................................1

1. Introduction..................................................... ....................................................................................4

1.1 What is LAMMPS.................................... ..................................................................................41.2 LAMMPS features......................................................................................................................51.3 LAMMPS non-features...............................................................................................................81.4 Open sourcedistribution.............................................................................................................91.5 Acknowledgments and citations...............................................................................................10

2. Getting Started................................................................................ ...................................................122.1 What's in theLAMMPS distribution........................................................................................122.2 Making LAMMPS............................................... .....................................................................132.3 Making LAMMPS with optional packages..............................................................................212.4 Building LAMMPS via the Make.py tool.................................................................................252.5 Building LAMMPS as a library................................................................................................27

2.6 Running LAMMPS..................................................................... ..............................................292.7 Command-line options..............................................................................................................302.8 LAMMPS screen output...........................................................................................................362.9 Tips for users of previous LAMMPS versions.........................................................................38

3. Commands................................................... ......................................................................................403.1 LAMMPS input script...............................................................................................................403.2 Parsing rules......................................... .....................................................................................413.3 Input script structure.................................................................................................................423.4 Commands listed by category...................................................................................................433.5 Individual commands................................................................................................................44Fix styles.............................................. ...........................................................................................45Compute styles...................................... ..........................................................................................46

Pair_style potentials........................................................................................................................46Bond_style potentials......................................................................................................................48Angle_style potentials............... ......................................................................................................48Dihedral_style potentials................................................................................................................48Improper_style potentials...................... ..........................................................................................49Kspace solvers......................................................................... .......................................................49

4. Packages........................................................................ ....................................................................504.1 Standard packages.....................................................................................................................50Build instructions for COMPRESS package..................................................................................52Build instructions for GPU package...............................................................................................52Build instructions for KIM package...............................................................................................52Build instructions for KOKKOS package.......................................................................................52Build instructions for KSPACE package........................................................................................52Build instructions for MEAM package...........................................................................................52Build instructions for POEMS package..........................................................................................52Build instructions for PYTHON package.......................................................................................52Build instructions for REAX package............................................................................................52Build instructions for VORONOI package.....................................................................................52Build instructions for XTC package...............................................................................................524.2 User packages...........................................................................................................................53USER-ATC package.......................................................................................................................55

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Table of ContentsUSER-AWPMDpackage................................................................................................................55USER-CG-CMM package..............................................................................................................55USER-COLVARS package............................................................................................................56USER-CUDA package....................................................................................................................56

USER-DIFFRACTION package....................................................................................................57USER-DRUDE package.................................................................................................................57USER-EFF package........................................................................................................................57USER-FEP package........................................................................................................................58USER-H5MD package....................................................................................................................58USER-INTEL package...................................................................................................................58USER-LB package..........................................................................................................................59USER-MGPT package....................................................................................................................59USER-MISC package.....................................................................................................................59USER-MOLFILE package..............................................................................................................60USER-OMP package......................................................................................................................60

USER-PHONON package..............................................................................................................60USER-QMMM package.................................................................................................................60USER-QTB package.......................................................................................................................61USER-REAXC package.................................................................................................................61USER-SMDpackage......................................................................................................................62USER-SMTBQ package.................................................................................................................62USER-SPH package........................................................................................................................62

5. Accelerating LAMMPS performance................................................................................................645.1 Measuring performance........................................................... .................................................645.2 General strategies......................................................................................................................655.3 Packages with optimized styles................................................................................................665.4 Comparison of various accelerator packages............................................................................68

6. How-to discussions............................................................................................................................716.1 Restarting a simulation....................................................................... ......................................716.2 2d simulations...........................................................................................................................736.3 CHARMM, AMBER, and DREIDING force fields.................................................................736.4 Running multiple simulations from one input script................................................................746.5 Multi-replica simulations..........................................................................................................766.6 Granular models........................................................................................................................766.7 TIP3P water model...................................................................................................................776.8 TIP4P water model...................................................................................................................786.9 SPC water model.......................................................................................................................806.10 Coupling LAMMPS to other codes........................................................................................806.11 VisualizingLAMMPS snapshots............................................................................................816.12 Triclinic (non-orthogonal) simulation boxes..........................................................................826.13 NEMD simulations....................................................................................... ..........................866.14 Finite-size spherical and aspherical particles..........................................................................866.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)....................................906.16 Thermostatting, barostatting, and computing temperature.....................................................946.17 Walls...................................................................... .................................................................966.18 Elastic constants......................................................................................................................976.19 Library interface to LAMMPS................................................................................................986.20 Calculating thermal conductivity............................................................................................99

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Table of Contents6.21 Calculatingviscosity.............................................................................................................1006.22 Calculatinga diffusion coefficient........................................................................................1016.23 Using chunks to calculate system properties........................................................................1026.24 Setting parameters for the kspace_stylepppm/disp command.............................................104

6.25 Polarizable models................................................................................................................1066.26 Adiabatic core/shell model...................................................................................................1066.27 Drude induced dipoles..........................................................................................................109

7. Example problems...........................................................................................................................1128. Performance & scalability...............................................................................................................1159. Additional tools...............................................................................................................................116

amber2lmp tool.............................................................................................................................117binary2txt tool...............................................................................................................................117ch2lmp tool.................................. .................................................................................................117chain tool....................................... ................................................................................................117colvars tools................................... ...............................................................................................117

createatoms tool............................. ...............................................................................................118data2xmovie tool...........................................................................................................................118eam database tool..........................................................................................................................118eam generate tool..........................................................................................................................118eff tool...........................................................................................................................................119emacs tool.....................................................................................................................................119fep tool..........................................................................................................................................119i-pi tool..........................................................................................................................................119ipp tool..........................................................................................................................................119kate tool.................................... .....................................................................................................119lmp2arc tool..................................................................................................................................120lmp2cfg tool............................. .....................................................................................................120

lmp2vmd tool............................... .................................................................................................120matlab tool....................................................................................................................................120micelle2d tool................................................................................................................................120moltemplate tool...........................................................................................................................120msi2lmp tool..................................... ............................................................................................121phonon tool...................................................................................................................................121polymer bonding tool....................................................................................................................121pymol_asphere tool.......................................................................................................................121python tool....................................................................................................................................121reax tool........................................................................................................................................122restart2data tool.............................................................................................................................122vim tool..................................................................... ....................................................................122xmgrace tool................................. .................................................................................................123xmovie tool................................................................................... ................................................123

10. Modifying & extending LAMMPS...............................................................................................12410.1 Atom styles...........................................................................................................................12510.2 Bond, angle, dihedral, improper potentials...........................................................................12710.3 Compute styles......................................................................................................................12710.4 Dump styles..........................................................................................................................12810.5 Dump custom output options................................................................................................12810.6 Fix styles...............................................................................................................................128

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Table of Contents10.7 Input scriptcommands..........................................................................................................13010.8 Kspace computations............................................................................................................13110.9 Minimization styles...............................................................................................................13110.10 Pairwise potentials..............................................................................................................131

10.11 Region styles.......................................................................................................................13210.11 Body styles........................................................................................... ...............................13210.13 Thermodynamic output options..........................................................................................13210.14 Variable options....................................................................... ...........................................13310.15 Submitting new features for inclusion in LAMMPS..........................................................133

11. Python interfaceto LAMMPS.......................................................................................................13611.1 Overview of running LAMMPS from Python......................................................................13611.2 Overview of using Python from a LAMMPS script.............................................................13711.3 Building LAMMPS as a shared library................................................................................13811.4 Installing the Python wrapper into Python............................................................................13811.5 Extending Python with MPI to run in parallel......................................................................139

11.6 Testingthe Python-LAMMPS interface...............................................................................14111.7 Using LAMMPS from Python..............................................................................................14211.8 Example Python scripts that use LAMMPS.........................................................................146

12. Errors.................................................................... .........................................................................14812.1 Common problems................................................................................................................14812.2 Reporting bugs......................................................................................................................14912.3 Error &warning messages....................................................................................................149Errors:...................................................... .....................................................................................150Warnings:....................................... ...............................................................................................245

13. Future and history..........................................................................................................................25413.1 Coming attractions................................................................................................................25413.2 Past versions..........................................................................................................................254

5.3.1 USER-CUDA package.........................................................................................................2565.3.2 GPU package....................................... ................................................................................2605.3.3 USER-INTEL package........................................................................................................2645.3.4 KOKKOS package...............................................................................................................2695.3.5 USER-OMP package...........................................................................................................2775.3.6 OPT package........................................................................................................................280

angle_style charmm command............................................................................................................282angle_style charmm/kk command.......................................................................................................282angle_style charmm/omp command....................................................................................................282angle_style class2 command...............................................................................................................284angle_style class2/omp command.......................................................................................................284angle_coeff command.............................................. ...........................................................................286angle_style cosine command...............................................................................................................288angle_style cosine/omp command.......................................................................................................288angle_style cosine/delta command......................................................................................................290angle_style cosine/delta/omp command..............................................................................................290angle_style cosine/periodic command.................................................................................................292angle_style cosine/periodic/omp command........................................................................................292angle_style cosine/shift command.......................................................................................................294angle_style cosine/shift/omp command..............................................................................................294angle_style cosine/shift/exp command................................................................................................296

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Table of Contentsangle_style cosine/shift/exp/omp command........................................................................................296angle_style cosine/squared command.................................................................................................298angle_style cosine/squared/omp command.........................................................................................298angle_style dipole command...............................................................................................................300

angle_style dipole/omp command.......................................................................................................300angle_style fourier command..............................................................................................................302angle_style fourier/omp command......................................................................................................302angle_style fourier/simple command..................................................................................................304angle_style fourier/simple/omp command..........................................................................................304angle_style harmonic command..........................................................................................................306angle_style harmonic/kk command.....................................................................................................306angle_style harmonic/omp command..................................................................................................306angle_style hybrid command...............................................................................................................308angle_style nonecommand.................................................................................................................310angle_style quartic command..............................................................................................................311

angle_style quartic/omp command......................................................................................................311angle_style sdk command....................................................................................................................313angle_style command..........................................................................................................................314angle_style tablecommand.................................................................................................................316angle_style table/omp command.........................................................................................................316atom_modify command.......................................................................................................................319atom_style command...........................................................................................................................322balance command................................................................................................................................326Body particles....................................... ...............................................................................................331bond_style class2 command................................................................................................................334bond_style class2/omp command........................................................................................................334bond_coeff command..........................................................................................................................336

bond_style fene command...................................................................................................................338bond_style fene/kk command..............................................................................................................338bond_style fene/omp command...........................................................................................................338bond_style fene/expand command......................................................................................................340bond_style fene/expand/omp command..............................................................................................340bond_style harmonic command...........................................................................................................342bond_style harmonic/kk command......................................................................................................342bond_style harmonic/omp command..................................................................................................342bond_style harmonic/shift command..................................................................................................344bond_style harmonic/shift/omp command..........................................................................................344bond_style harmonic/shift/cut command............................................................................................346bond_style harmonic/shift/cut/omp command....................................................................................346bond_style hybrid command...............................................................................................................348bond_style morse command................................................................................................................350bond_style morse/omp command........................................................................................................350bond_style nonecommand..................................................................................................................352bond_style nonlinear command...........................................................................................................353bond_style nonlinear/omp command..................................................................................................353bond_style quartic command...............................................................................................................355bond_style quartic/omp command......................................................................................................355bond_style command...........................................................................................................................357

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Table of Contentsbond_style tablecommand..................................................................................................................359bond_style table/omp command..........................................................................................................359boundary command.............................................................................................................................362box command............................................ ..........................................................................................364

change_box command.........................................................................................................................365clear command................................. ....................................................................................................370comm_modify command.....................................................................................................................371comm_style command.........................................................................................................................374compute command...............................................................................................................................375compute ackland/atom command........................................................................................................379compute angle/local command............................................................................................................381compute angmom/chunk command.....................................................................................................383compute basal/atom command............................................................................................................385compute body/local command.............................................................................................................387compute bond/local command.............................................................................................................389

compute centro/atom command..........................................................................................................391compute chunk/atom command...........................................................................................................393compute cluster/atom command..........................................................................................................401compute cna/atom command...............................................................................................................403compute com command.......................................................................................................................405compute com/chunk command............................................................................................................406compute contact/atom command.........................................................................................................408compute coord/atom command...........................................................................................................409compute damage/atom command........................................................................................................411compute dihedral/local command........................................................................................................412compute dilatation/atom command.....................................................................................................413compute displace/atom command.......................................................................................................414

compute erotate/asphere command.....................................................................................................415compute erotate/rigid command..........................................................................................................416compute erotate/sphere command.......................................................................................................417compute erotate/sphere/atom command..............................................................................................418compute event/displace command.......................................................................................................419compute fep command.............................................. ..........................................................................420compute group/group command..........................................................................................................424compute gyration command................................................................................................................426compute gyration/chunk command.....................................................................................................428compute heat/flux command...............................................................................................................430compute hexorder/atom command......................................................................................................434compute improper/local command......................................................................................................436compute inertia/chunk command........................................................................................................437compute ke command..........................................................................................................................439compute ke/atomcommand.................................................................................................................440compute ke/atom/eff command...........................................................................................................441compute ke/eff command....................................................................................................................443compute ke/rigid command.................................................................................................................445compute meso_e/atom command........................................................................................................446compute meso_rho/atom command.....................................................................................................447compute meso_t/atom command.........................................................................................................448

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Table of Contentscompute_modify command.................................................................................................................449compute msd command.......................................................................................................................450compute msd/chunk command............................................................................................................452compute msd/nongauss command.......................................................................................................454

compute omega/chunk command........................................................................................................456compute orientorder/atom command...................................................................................................458compute pair command.......................................................................................................................460compute pair/local command..............................................................................................................462compute pe command..........................................................................................................................464compute pe/cuda command.................................................................................................................464compute pe/atomcommand.................................................................................................................466compute plasticity/atom command......................................................................................................468compute pressure command................................................................................................................469compute pressure/cuda command........................................................................................................469compute property/atom command.......................................................................................................472

compute property/chunk command.....................................................................................................475compute property/local command.......................................................................................................477compute rdf command.........................................................................................................................479compute reduce command...................................................................................................................482compute reduce/region command........................................................................................................482compute saed command........................................ ..............................................................................485compute slice command.................................................... ..................................................................489compute smd/contact_radius command..............................................................................................491compute smd/damage command.........................................................................................................492compute smd/hourglass_error command.............................................................................................493compute smd/internal_energy command.............................................................................................494compute smd/plastic_strain command................................................................................................495

compute smd/plastic_strain_rate command........................................................................................496compute smd/rho command................................................................................................................497compute smd/tlsph_defgrad command................................................................................................498compute smd/tlsph_dt command.........................................................................................................499compute smd/tlsph_num_neighs command........................................................................................500compute smd/tlsph_shape command...................................................................................................501compute smd/tlsph_strain command...................................................................................................502compute smd/tlsph_strain_rate command...........................................................................................503compute smd/tlsph_stress command...................................................................................................504compute smd/triangle_mesh_vertices.................................................................................................505compute smd/ulsph_num_neighs command........................................................................................506compute smd/ulsph_strain command..................................................................................................507compute smd/ulsph_strain_rate command..........................................................................................508compute smd/ulsph_stress command..................................................................................................509compute smd/vol command.................................................................................................................510compute sna/atom command...............................................................................................................511compute snad/atom command.............................................................................................................511compute snav/atom command.............................................................................................................511compute stress/atom command............................................................................................................516compute force/tally command.............................................................................................................519compute heat/flux/tally command.......................................................................................................519

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Table of Contentscompute pe/tallycommand..................................................................................................................519compute stress/tally command............................................................................................................519compute temp command......................................................................................................................521compute temp/cuda command.............................................................................................................521

compute temp/kk command................................................................................................................521compute temp/asphere command........................................................................................................523compute temp/chunk command...........................................................................................................526compute temp/com command..............................................................................................................530compute temp/cs command.................................................................................................................532compute temp/deform command.........................................................................................................534compute temp/deform/eff command...................................................................................................536compute temp/drude command...........................................................................................................537compute temp/eff command................................................................................................................539compute temp/partial command..........................................................................................................541compute temp/partial/cuda command..................................................................................................541

compute temp/profile command..........................................................................................................543compute temp/ramp command............................................................................................................546compute temp/region command..........................................................................................................548compute temp/region/eff command.....................................................................................................550compute temp/rotate command...........................................................................................................551compute temp/sphere command..........................................................................................................553compute ti command.......................................... .................................................................................555compute torque/chunk command........................................................................................................557compute vacf command.......................................................................................................................559compute vcm/chunk command............................................................................................................561compute voronoi/atom command........................................................................................................563compute xrd command........................................................................................................................566

create_atoms command.......................................................................................................................570create_bonds command.......................................................................................................................575create_box command...........................................................................................................................577delete_atoms command.......................................................................................................................579delete_bonds command.......................................................................................................................582dielectric command........................................................ .....................................................................585dihedral_style charmm command........................................................................................................586dihedral_style charmm/kk command..................................................................................................586dihedral_style charmm/omp command...............................................................................................586dihedral_style class2 command...........................................................................................................588dihedral_style class2/omp command...................................................................................................588dihedral_coeff command.....................................................................................................................592dihedral_style cosine/shift/exp command...........................................................................................594dihedral_style cosine/shift/exp/omp command...................................................................................594dihedral_style fourier command..........................................................................................................596dihedral_style fourier/omp command..................................................................................................596dihedral_style harmonic command......................................................................................................598dihedral_style harmonic/omp command.............................................................................................598dihedral_style helix command.............................................................................................................600dihedral_style helix/omp command....................................................................................................600dihedral_style hybrid command..........................................................................................................602

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Table of Contentsdihedral_style multi/harmonic command............................................................................................604dihedral_style multi/harmonic/omp command....................................................................................604dihedral_style nharmonic command....................................................................................................606dihedral_style nharmonic/omp command...........................................................................................606

dihedral_style none command.............................................................................................................608dihedral_style opls command..............................................................................................................609dihedral_style opls/kk command.........................................................................................................609dihedral_style opls/omp command......................................................................................................609dihedral_style quadratic command......................................................................................................611dihedral_style quadratic/omp command..............................................................................................611dihedral_style command......................................................................................................................613dihedral_style table command.............................................................................................................615dihedral_style table/omp command.....................................................................................................615dimension command............................................................................................................................618displace_atoms command....................................................................................................................619

dump command...................................... .............................................................................................621dump h5md command.........................................................................................................................621dump image command........................................................................................................................621dump movie command........................................................................................................................621dump molfile command.......................................................................................................................621dump h5md command.........................................................................................................................630dump image command........................................................................................................................632dump movie command........................................................................................................................632dump_modify command......................................................................................................................640dump molfile command................... ....................................................................................................651echo command........................................ .............................................................................................653fix command.......................................... ..............................................................................................654

fix adapt command..............................................................................................................................659fix adapt/fep command........................................................................................................................663fix addforce command.........................................................................................................................667fix addforce/cuda command................................................................................................................667fix addtorque command.......................................................................................................................670fix append/atoms command.................................................................................................................672fix atc command...................................... ............................................................................................674fix atom/swap command......................................................................................................................679fix ave/atom command........................................................................................................................682fix ave/chunk command......................................................................................................................684fix ave/correlatecommand..................................................................................................................690fix ave/correlate/long command..........................................................................................................695fix ave/histo command........................................ ................................................................................698fix ave/histo/weight command............................................................................................................698fix ave/spatial command......................................................................................................................703fix ave/spatial/sphere command..........................................................................................................709fix ave/time command.........................................................................................................................714fix aveforce command.........................................................................................................................719fix aveforce/cuda command................................................................................................................719fix balance command...........................................................................................................................721fix bond/break command.....................................................................................................................726

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Table of Contentsfix bond/create command....................................................................................................................729fix bond/swap command..................... .................................................................................................733fix box/relax command........................................................................................................................736fix colvars command...........................................................................................................................741

fix deform command...........................................................................................................................743fix deform/kk command......................................................................................................................743fix deposit command................................................... ........................................................................751fix drag command................................................................................................................................755fix drude command..............................................................................................................................756fix drude/transform/direct command...................................................................................................757fix drude/transform/inverse command................................................................................................757fix dt/reset command...........................................................................................................................760fix efield command..............................................................................................................................762fix enforce2d command.......................................................................................................................765fix enforce2d/cuda command..............................................................................................................765

fix evaporate command.......................................................................................................................766fix external command..........................................................................................................................768fix freeze command.............................................................................................................................771fix freeze/cuda command....................................................................................................................771fix gcmc command..............................................................................................................................773fix gld command..................................................................................................................................778fix gle command......................................... .........................................................................................781fix gravity command....................... .....................................................................................................784fix gravity/cuda command............. ......................................................................................................784fix gravity/omp command...................................................................................................................784fix heat command................................................................................................................................787fix imd command.................................................................................................................................789

fix indent command.............................................................................................................................792fix ipi command............................................... ....................................................................................795fix langevin command.........................................................................................................................797fix langevin/kk command....................................................................................................................797fix langevin/drude command...............................................................................................................802fix langevin/eff command................ ....................................................................................................806fix lb/fluid command...........................................................................................................................808fix lb/momentum command................................................................................................................814fix lb/pc command...............................................................................................................................816fix lb/rigid/pc/sphere command...........................................................................................................817fix lb/viscous command.......................................................................................................................819fix lineforce command.........................................................................................................................821fix meso command.................................... ..........................................................................................822fix meso/stationary command..............................................................................................................823fix_modify command..........................................................................................................................824fix momentum command.....................................................................................................................825fix move command..............................................................................................................................827fix msst command...............................................................................................................................831fix neb command.................................................................................................................................834fix nvt command..................................................................................................................................836fix nvt/cuda command.........................................................................................................................836

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Table of Contentsfix nvt/kk command.............................................................................................................................836fix nvt/omp command..........................................................................................................................836fix npt command..................................................................................................................................836fix npt/cuda command.........................................................................................................................836

fix npt/kk command.............................................................................................................................836fix npt/omp command..........................................................................................................................836fix nph command.................................................................................................................................836fix nph/kk command............................................................................................................................836fix nph/omp command.........................................................................................................................836fix nvt/eff command............................................................................................................................845fix npt/eff command............................................................................................................................845fix nph/eff command...........................................................................................................................845fix nph/asphere command....................................................................................................................848fix nph/asphere/omp command...........................................................................................................848fix nph/sphere command.....................................................................................................................851

fix nph/sphere/omp command.............................................................................................................851fix nphug command.............................................................................................................................854fix nphug/omp command.....................................................................................................................854fix npt/asphere command................................. ...................................................................................858fix npt/asphere/omp command............................................................................................................858fix npt/sphere command......................................................................................................................861fix npt/sphere/omp command..............................................................................................................861fix nve command.................................................................................................................................864fix nve/cuda command............................... .........................................................................................864fix nve/kk command............................................................................................................................864fix nve/omp command.........................................................................................................................864fix nve/asphere command....................................................................................................................866

fix nve/asphere/noforce command......................................................................................................867fix nve/body command........................................................................................................................868fix nve/eff command............................................................................................................................869fix nve/limit command........................................................................................................................870fix nve/line command..........................................................................................................................872fix nve/noforce command....................................................................................................................873fix nve/sphere command......................................................................................................................874fix nve/sphere/omp command.............................................................................................................874fix nve/tri command............................................................................................................................876fix nvt/asphere command.............................. ......................................................................................877fix nvt/asphere/omp command............................................................................................................877fix nvt/sllod command.........................................................................................................................880fix nvt/sllod/omp command.................................................................................................................880fix nvt/sllod/eff command...................................................................................................................883fix nvt/sphere command......................................................................................................................885fix nvt/sphere/omp command..............................................................................................................885fix oneway command..........................................................................................................................888fix orient/fcc command........................................................................................................................889fix phonon command...........................................................................................................................893fix pimd command...............................................................................................................................896fix planeforce command......................................................................................................................900

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Table of Contentsfix poems........................................ .....................................................................................................901fix pour command................................................................................................................................903fix press/berendsen command.............................................................................................................907fix print command...............................................................................................................................910

fix property/atom command................................................................................................................912fix qbmsst command............................................................................................................................915fix qeq/point command........................................................................................................................919fix qeq/shielded command...................................................................................................................919fix qeq/slater command.......................................................................................................................919fix qeq/dynamiccommand..................................................................................................................919fix qeq/comb command.......................................................................................................................922fix qeq/comb/omp command...............................................................................................................922fix qeq/reax command.........................................................................................................................924fix qmmm command............................................................................................................................926fix qtb command..................................................................................................................................927

fix reax/bonds command.....................................................................................................................930fix reax/c/bondscommand..................................................................................................................930fix reax/c/species command................................................................................................................931fix recenter command..........................................................................................................................934fix restrain command...........................................................................................................................936fix rigid command...............................................................................................................................939fix rigid/nve command........................................................................................................................939fix rigid/nvt command.........................................................................................................................939fix rigid/npt command.........................................................................................................................939fix rigid/nph command........................................................................................................................939fix rigid/small command......................................................................................................................939fix rigid/nve/small command...............................................................................................................939

fix rigid/nvt/small command...............................................................................................................939fix rigid/npt/small command...............................................................................................................939fix rigid/nph/small command..............................................................................................................939fix saed/vtk command..........................................................................................................................950fix setforce command..........................................................................................................................953fix setforce/cudacommand..................................................................................................................953fix shake command..............................................................................................................................955fix shake/cuda command.....................................................................................................................955fix rattle command...............................................................................................................................955fix smd command.................................................... ............................................................................959fix smd/adjust_dt command................................................................................................................962fix smd/integrate_tlsph command.......................................................................................................963fix smd/integrate_ulsph command......................................................................................................964fix smd/move_tri_surf command........................................................................................................965fix smd/setvel command......................................................................................................................967fix smd/wall_surface command...........................................................................................................970fix spring command.............................................................................................................................971fix spring/rg command........................................................................................................................973fix spring/self command......................................................................................................................975fix srd command..................................................................................................................................977fix store/force command......................................................................................................................983

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Table of Contentsfix store/state command.......................................................................................................................984fix temp/berendsen command..............................................................................................................986fix temp/berendsen/cuda command.....................................................................................................986fix temp/csvr command.......................................................................................................................989

fix temp/csld command................................................. ......................................................................989fix temp/rescale command...................................................................................................................992fix temp/rescale/cuda command..........................................................................................................992fix temp/rescale/limit/cuda command.................................................................................................992fix temp/rescale/eff command.............................................................................................................995fix tfmc command................................................................................................................................997fix thermal/conductivity command....................................................................................................1000fix ti/rs command...............................................................................................................................1003fix ti/spring command........................................................................................................................1006fix tmd command...............................................................................................................................1009fix ttm command................................................................................................................................1011

fix ttm/mod command.......................................................................................................................1011fix tune/kspace command..................................................................................................................1016fix vector command...........................................................................................................................1018fix viscosity command.......................................................................................................................1021fix viscous command.........................................................................................................................1024fix viscous/cudacommand................................................................................................................1024fix wall/lj93 command.......................................................................................................................1026fix wall/lj126 command.....................................................................................................................1026fix wall/lj1043 command...................................................................................................................1026fix wall/colloid command..................................................................................................................1026fix wall/harmonic command..............................................................................................................1026fix wall/gran command......................................................................................................................1031

fix wall/piston command...................................................................................................................1034fix wall/reflect command...................................................................................................................1036fix wall/reflect/kk command..............................................................................................................1036fix wall/region command...................................................................................................................1039fix wall/srd command........................................................................................................................1043group command..................................................... ............................................................................1046group2ndx command.........................................................................................................................1050if command................................................. .......................................................................................1051improper_style class2 command.......................................................................................................1054improper_style class2/omp command...............................................................................................1054improper_coeff command................................. ................................................................................1057improper_style cossq command........................................................................................................1059improper_style cossq/omp command................................................................................................1059improper_style cvff command...........................................................................................................1061improper_style cvff/omp command..................................................................................................1061improper_style fourier command......................................................................................................1063improper_style fourier/omp command..............................................................................................1063improper_style harmonic command..................................................................................................1065improper_style harmonic/kk command.............................................................................................1065improper_style harmonic/omp command..........................................................................................1065improper_style hybrid command.......................................................................................................1067

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Table of Contentsimproper_style none command.........................................................................................................1068improper_style ring command...........................................................................................................1069improper_style ring/omp command..................................................................................................1069improper_style command..................................................................................................................1071

improper_style umbrella command...................................................................................................1073improper_style umbrella/omp command...........................................................................................1073include command....................................................................................................

lammps manual from sandia.gov

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