These tables map general molecular dynamics (MD) and computational terminology to specific LAMMPS commands and sections of the LAMMPS documentation. Last updated for 13 March 2018 version.
| 1-2, 1-3, 1-4 pairwise interactions | special_bonds |
| 2d simulations | Howto 2d, fixenforce2d |
| 2d manifolds (surfaces) | MANIFOLD |
| 2d vs 3d | dimension |
| Ackland lattice structure | compute ackland/atom |
| AGNI potential | pair_style agni |
| AIREBO potential | pair_style airebo |
| AMBER force field | Howto bioFF, special_bonds amber |
| angle potentials | angle_style |
| angular dependent potential | pair_style adp |
| angular momentum | compute angmom/chunk, variable angmom |
| angular momentum zeroing | fix momentum, velocity |
| angular velocity | compute omega/chunk, variable omega |
| aspherical particles | ASPHERE package,Howto spherical, atom_style ellipsoid, body, lammps/examples/ASPHERE dir |
| AtomEye CFG file format | dump cfg |
| atom averaging | fix ave/atom |
| atom properties | atom_style, set |
| atom swapping | fix atom/swap |
| atom to continuum coupling | ATC package, fix atc |
| averaging | see atom averaging, spatial averaging, correlation, histogramming, timeaveraging, chunks |
| AWPMD = Antisymmetrized Wave Packet MD | AWPMD package, pair_style awpmd/cut |
| barostatting | Howto barostat |
| basal plane vector | compute basal/atom |
| bcc lattice | lattice |
| bead-spring model | see FENE bond-spring model |
| Beck potential | pair_style beck |
| benchmarking | Speed bench, lammps/bench dir |
| Berendsen barostat | fix press/berendsen |
| Berendsen thermostat | fix temp/berendsen |
| body particles with internal geometry/state | BODY package, atom_style body, body |
| Boltzmann distribution | velocity |
| bond breaking | fix bond/break, bond_style quartic |
| bond creation | fix bond/create |
| bond crossing prevention | pair_style srp |
| bond potentials | bond_style |
| bond swapping | fix bond/swap |
| bond-order potentials | MANYBODY package, pair_style tersoff, pair_style meam, pair_style reax |
| BOP = bond-order potential | pair_style bop |
| Born potential | pair_style born |
| boundary conditions | boundary |
| Brownian motion | fix langevin, pair_style brownian |
| box boundaries | boundary |
| box deformation | change_box, fix deform |
| box relaxation | fix box/relax |
| Buckingham potential | pair_style buck |
| canonical sampling thermostat | fix temp.csvr, fix temp/csld |
| CD-EAM = concentration dependent EAM | pair_styleeam/cd |
| CMAP crossterms for CHARMM | fix cmap |
| center-of-mass | compute com, compute com/chunk, variable xcm |
| center-of-mass force | variable fcm |
| center-of-mass velocity | compute vcm/chunk, variable vcm |
| centro-symmetry factor | compute centro/atom |
| CFG (AtomEye) file format | dump cfg |
| change atom properties | set |
| charge equilibration | QEQ package, fix qeq and variants, fix qeq/comb, fix qeq/reax |
| charged particles | atom_style charge |
| CHARMM force field | Howto bioFF, pair_style charmm, special_bonds charmm |
| chunks of atoms | Howto chunk, see groups |
| class2 force-field | CLASS2 package, pair_style lj/class2, bond_style class2 |
| cluster identification | >>computecluster/atom,aggregate/atom,fragment/atom |
| coarse-graining models | MSCG package, CG-DNApackage, CG-SPICApackage, DPD-MESOpackage, see oxDNA force field |
| Couette flow | lammps/example/flow, see walls |
| CNA = common neighbor analysis | compute cna/atom |
| CNP = common neighborhood parameter | compute cnp/atom |
| collective variables | COLVARS package, fix colvars, doc/PDF/colvars-refman-lammps.pdf |
| colloidal particles | COLLOID package, atom_style colloid |
| colloidal potentials | pair_style colloid |
| COLVARS package | see collective variables |
| COMB potential | pair_style comb, pair_style comb3 |
| communication between processors | comm_style, comm_modify |
| COMPASS force-field | CLASS2 package, pair_style lj/class2, bond_style class2 |
| compression of I/O files | COMPRESS package |
| constrained motion | fix move, fix lineforce, fix planeforce, fix restrain, fix spring and variants, fix drag |
| continuum coupling | ATC package, fix atc |
| conjugate gradient minimization | min_style cg |
| contact identification | compute contact/atom |
| cooling & heating | fix heat |
| coordintation number | compute coord/atom |
| core/shell model | CORESHELL package, Howto coreshell |
| correlation, time | fix ave/correlate, fix ave/correlate/long |
| Coulomb potential | pair_style coul, kspace_style |
| coupling to another code | Howto couple, fix external, lammps/example/COUPLE dir |
| CPU timings | timer |
| cross-linking | see bond creation |
| cubic lattice | lattice |
| CUDA for GPUs | see GPU |
| cutoff | pair_style |
| CVFF force-field | improper_style cvff, harmonic bond, angle, dihedral styles |
| damage (Peridynamic) | compute damage/atom |
| damped dynamics minimization | min_style fire, min_style quickmin |
| damped shifted force model | pair_style lj/cut/coul/dsf |
| data files | read_data, write_data |
| DCD file format | dump dcd |
| Debye screening | pair_style lj/cut/coul/debye |
| deformation | see box deformation |
| delete atoms | delete_atoms |
| delete bonds | delete_bonds |
| density functional tight binding | LATTE package |
| depositing atoms & molecules | fix deposit |
| DFTB = density functional tight binding | LATTE package |
| dielectric constant | dielectric, pair_style coul/diel |
| dispersion, long-range | kspace_style pppm/disp, kspace_style ewald/disp, Howto dipersion |
| diffraction patterns | compute saed, compute xrd, DIFFRACTION package, compute saed, compute xrd |
| diffusion coefficient | Howto diffusion, compute msd, compute vacf, lammps/examples/DIFFUSE dir |
| dihedral potentials | dihedral_style |
| dilatation (Peridynamic) | compute dilatation/atom |
| dipole moment | compute dipole/chunk |
| dipoles | see electric dipoles |
| diplacement vector | computediplace/atom |
| dissipative particle dynamics | see DPD |
| DLVO potential | pair_style colloid |
| DNA coarse-grained model | see oxDNA force field |
| DPD = dissipative particle dynamics | atom_styledpd, pair_style dpd,DPD-BASIC package,DPD-MESO package,DPD-REACT package |
| DPD thermostat | pair_style dpd/tstat |
| Dreiding force-field | Howto bioFF, pair_style dreiding |
| Drude model | DRUDE package, fix drude, Howto drude, Howto drude2 |
| DSMC = Direct Simulation Monte Carlo | pair_style dsmc |
| dump files | dump, write_dump, read_dump |
| dynamical matrix | see phonons |
| dynamics | see run dynamics |
| EAM = embedded atom method potentials | pair_style eam |
| EDIP potential | pair_style edip |
| EFF = electron force field | EFF package, pair_style eff/cut |
| EHEX = enhanced heat exchange | fix ehex |
| EIM = embedded ion method | pair_style eim |
| elastic constants | Howto elastic, lammps/examples/ELASTIC and lammps/examples/ELASTIC_T dirs |
| electric field | fix efield |
| electron dynamics | AWPMD package, EFF package |
| electric dipole pairwise interactions | pair_style lj/cut/dipole |
| electric dipole long-range interactions | kspace_style ewald/disp |
| electric dipoles | DIPOLE package, atom_style dipole |
| electrons | atom_style electron |
| ellipsoidal particles | atom_style ellipsoid, ASPHERE package, pair_style gayberne, pair_style resquared |
| embedding Python | see Python |
| energy minimization | see minimization |
| energy, kinetic | see kinetic energy |
| energy, potential | see potential energy |
| energy, rotational | see rotational energy |
| evaporation | fix evaporate |
| error and warning messages | Errors |
| Ewald summation | kspace_style ewald, kspace_style ewald/disp |
| excluded pair interactions | special_bonds |
| extended Tersoff potential | see Tersoff extended potential |
| extensional flow | UEF package |
| FLD = fast lubrication dynamics | FLD package, pair_style lubricateU |
| fcc lattice | lattice |
| FENE bead-spring model | bond_style fene |
| finite-size particles | see spherical or ellipsoidal particles |
| Finnis-Sinclaire EAM potential | pair_style eam/fs |
| FIRE damped dynamics minimization | min_style fire |
| force-bias Monte Carlo | fix tfmc |
| free energy | compute ti,fix colvars, fix adapt/fep,compute fep, FEP package,PLUMED |
| freezing atoms | fix freeze |
| frictional potentials | see granular models |
| g(r) | see radial distribution function |
| Gao Weber potential | pair_style gao/weber |
| GAP = Gaussian approximation potential | pair_stylequip, QUIP package |
| Gaussian dynamics (GD) method | fix flow/gauss |
| Gaussian potential | pair_style gauss, pair_style gauss/cut |
| GayBerne potential | pair_style gayberne, doc/PDF/pair_gayberne_extra.pdf |
| GCMC = grand-canonical Monte Carlo | fix gcmc |
| generalized Langevin dynamics | fix gld |
| generalized Langevin equation thermostat | fix gle |
| generalized replica exchange | fix grem, see tempering |
| geometric regions | region |
| Gibbs free energy | see free energy |
| grain boundary creation | lattice orient, create_atoms |
| grain boundary forces | fix orient/fcc, fix orient/bcc |
| granular models | GRANULAR package, Howto granular, pair_style granular, LIGGGHTS |
| granular particles | atom_style sphere |
| granular potentials | pair_style granular |
| gravity | fix gravity |
| GPU = graphical processing units | GPU package, KOKKOS package, Speed_packages |
| Gromacs force field | pair_style gromacs |
| Gromacs index file | group2ndx |
| groups of atoms | group, see chunks |
| Hamiltonian dynamics thermostat | see canonical sampling thermostat |
| harmonic angle potentials | angle_style harmonic |
| harmonic bond potentials | bond_style harmonic |
| harmonic dihedral potentials | dihedral_style harmonic |
| harmonic improper potentials | improper_style harmonic |
| hcp lattice | lattice |
| HDF5 file format | dump h5md, H5MD package |
| heat flux | compute heat/flux |
| heating & cooling | fix heat |
| hexatic order parameter | compute hexorder/atom |
| HFTN = Hessian-free truncated-Newton minimization | min_style hftn |
| hexagonal lattice | lattice |
| hierarchical time stepping | run-style respa |
| histogramming | fix ave/histo, fix ave/histo.weight |
| history-dependent potential | pair_style granular |
| Hugoniostat equations of motion | fix nphug, SHOCK package |
| hybrid models and potentials | pair_style hybrid |
| hydrogen-bonding potential | pair_style dreiding |
| implicit solvent | pair_style lj/cut/coul/debye, pair_style coul/diel |
| improper potentials | improper_style |
| indentation | fix indent |
| inertia tensor | compute inertia/chunk, variable inertia |
| input to simulation | Commands, read_data |
| Intel CPU optimization | INTEL package, OPT package, Speed packages |
| Intel Phi | see Xeon Phi |
| interactive MD & visualization | fix imd |
| i-PI Python | see PIMD |
| JPG files | dump image |
| kappa | see thermal conductivity |
| KIM = Knowledbase of Interatomic Models | KIM package, pair_style kim |
| kinetic energy | compute ke, compute ke/atom |
| KOKKOS = performance portability package | KOKKOSpackage |
| Kolmogorov-Crespi potential | pair_stylekolmogorov/crespi/z |
| K-space solvers | see long-range solvers |
| Langevin dynamics | fix langevin, fix gld |
| Langevin dynamics thermostat | see canonical sampling thermostat |
| Langevin thermostat | fix langevin |
| LATTE density functional tight binding code | LATTE package |
| lattice Bolztmann fluid | LATBOLTZ package, fix lb/fluid |
| lattices of atoms | lattice, create_atoms |
| LCBOP = long-range bond-order potential | pair_style lcbop |
| Lennard-Jones potential | pair_style lj |
| library interface and API | Howto library |
| LIGGGHTS = LAMMPS Improved for General Granular and Granular Heat Transfer Simulations | LIGGGHTS web site |
| line (2d) particles | atom_style line, fix rigid |
| line/line interactions | pair_style line/lj |
| linear momentum zeroing | fix momentum, velocity |
| load balancing | balance, fix balance |
| load, imposed | fix aveforce |
| long-range order biasing | fix_rhok |
| long-range solvers | KSPACE package, kspace_style, doc/PDF/kpace.pdf |
| long-range Coulombics | see long-range solvers |
| long-range dipoles | kspace_style ewald/disp |
| long-range dispersion | see long-range solvers |
| lubrication potential | pair_style lubricate |
| machine learned potentials | SNAPpackage, see GAP potential, see AGNI potential |
| manifolds = 2d surfaces | MANIFOLD |
| manybody potentials | MANYBODY package, pair_style |
| mass of atoms | mass |
| MEAM = modified EAM potential | MEAM and MEAM packages, pair_style meam, pair_style meam/spline |
| MEAM-SW = MEAM + Stillinger-Weber | pair_style meam/sw/spline |
| mean-squared displacement | compute msd, compute msd/chunk |
| mesoscale models | see coarse-graining |
| metal-organic many-body potential (MOMB) | see MOMB potential |
| MGPT potential | pair_style mgpt, MGPT package |
| Mie potential | pair_style mie |
| minimization | minimize, min_style |
| mixing of potential parameters | pair_modifymix |
| MOF-FF force field | MOFFF package |
| molecular force fields | MOLECULE package |
| molecule templates & topology | molecule, read_data |
| molecules | atom_style molecular, molecule |
| molfile plug-ins for VMD | dump molfile,MOLFILE package |
| mollified impulse method | fixfilter/corotate |
| MOMB = metal-organic many-body potential | pair_style momb |
| moments of inertia | see inertia tensor |
| momentum zeroing | see linear momentum zeroing and angular momentum zeroing |
| Monte Carlo methods | MC package, fix atom/swap, fix gcmc, fix tfmc, lammps/examples/MC dir |
| Morse bond potential | bond_style morse |
| Morse pair potential | pair_style morse |
| movies | dump movie |
| MPCD = multi-particle collision dynamics | see SRD |
| MPI-IO parallel I/O | MPIIO package, dump mpiio, write_resatrt, read_restart |
| MSCG = multi-scale coarse-graining model | MGCG package |
| MSM = multi-level summation Coulombics | kspace_style msm |
| MSST = multi-scale shock technique | fix msst, fix qmbsst |
| multilevel summation method (MSM) | kspace_style msm |
| multiple simulations | Howto multiple |
| multi-replica methods | REPLICA package, Howto replica, temper, prd, tad |
| multi-scale coarse-graining (MSCG) model | MGCG package |
| neighbor lists | neighbor, neigh_modify |
| neighbor skin distance | neighbor |
| NEB = nudged elastic band | neb |
| NEMD = non-equilibrium MD | Howto nemd, fixdeform |
| NetCDF file format | dump netcdf, NETCDF package |
| Newton's 3rd law | newton |
| NGP = non-Gaussian parameter | compute msd/nongauss |
| N-M potential for ionic liquids | pair_style nm |
| nonbond interactions | pair_style |
| nonbonded 3-body harmonic potential | pair_style nb3b/harmonic |
| non-Gaussian mean-squared displacement | compute msd/nongauss |
| non-orthogonal simulation box | see triclinic simulation box |
| non-periodic boundary conditions | boundary |
| normalization | thermo_modify norm |
| Nose/Hoover barostat | fix npt, fix nph |
| Nose/Hoover thermostat | fix nvt |
| NPH ensemble | fix nph and variants |
| NPT ensemble | fix npt and variants |
| nudged elastic band | see NEB |
| NUMA mapping | processors |
| NVE ensemble | fix nve and variants |
| NVK (isokinetic) ensemble | fix nvk |
| NVT ensemble | fix nvt and variants |
| one-way motion | fix oneway |
| OpenMP usage | OPENMP package, KOKKOS package, Speed packages |
| OPLS force field | dihedral_style opls |
| orientational order | compute orientorder/atom |
| orthogonal simulation box | create_box, change_box, Howto triclinic |
| out-of-plane potentials | improper_style |
| output from simulation | Howto output |
| overlapping atoms | delete_atoms |
| overlayed potentials | pair_stylehybrid/overlay |
| oxDNA force field | pair oxdna/* |
| pair potentials | pair_style |
| pairwise interactions | pair_style |
| parallel I/O via MPI-IO | dump mpiio, write_resatrt, read_restart |
| parallel replica dynamics | see PRD |
| parallel tempering | see tempering |
| particle mesh Ewald | see PME |
| performance monitoring | timer, Speed measure, lammps/bench dir |
| Peridynamics | atom_style peri, PERI package, doc/PDF/PDLampps_overview.pdf |
| periodic boundary conditions | boundary |
| Phi, Intel | see Xeon Phi |
| phonons | PHONON package,fix phonon |
| PID controller (proportional, integrative, derivative) | fixcontroller |
| PIMD = path-integral MD | fix ipi, fix pimd |
| piston | fix wall/piston |
| plasticity (Peridynamic) | compute plasticity/atom |
| plotting of output data | Tools, Tools python |
| PME = particle-mesh Ewald | kspace_style pppm |
| PNG files | dump image |
| POEMS = constrained rigid-body motion | POEMS package, fix poems |
| point dipoles | atom_style dipole, pair lj/cut/dipole |
| Poiseuille flow | lammps/examples/flow, fix addforce |
| polarizable models | Howto polarizable |
| polymer equilibration | see bond swapping |
| polymorphic potential | pair_style polymorphic |
| post-processing of output data | Tools |
| potential energy | compute pe, compute pe/atom |
| pouring of particles | fix pour |
| PPM files | dump image |
| PPPM = particle-particle particle-mesh | kspace_style pppm |
| PRD = parallel replica dynamics | prd |
| pre-processing of input data | Tools |
| pressure and stress | compute pressure, compute stress/atom, TALLY package |
| processor mapping | processors, see NUMA |
| PUT = profile unbiased thermostat | compute temp/profile |
| Python | Python, PYTHON package, python,, lammps/python dir |
| QBMSST = quantum-bath coupled multi-scale shock technique | see MSST |
| QEq | see charge equilibration |
| QMMM = quantum mechanics/molecular mechanics | fix qmmm |
| Quantum Espresso coupling | see QMMM |
| quantum coupling | see QMMM, see DFTB |
| quantum nuclear effects | fix qtb, QTB package |
| quantum thermal bath | fix qtb, QTB package |
| QuickMin damped dynamics minimization | min_style quickmin |
| QUIP potentials | pair_style quip, QUIP package |
| radial distribution function | compute rdf |
| radius of gyration | compute gyration, compute gyration/chunk |
| RATTLE constraints | fix rattle |
| RCB = recursive coordinate bisectioning | balance, fix balance |
| reactive dissipative particle dynamics | see DPD |
| reactive force field (ReaxFF) | see ReaxFF potential |
| ReaxFF potential | REAX and REAXFF package, pair_stylereax, pair_style reax/c |
| ReaxFF bonds | fix reax/bonds |
| REBO potential | pair_style rebo |
| regions, geometric | region |
| reflective wall | fix wall/reflect |
| replica methods | REPLICA package |
| replica exchange | see tempering |
| replicate a system | replicate |
| rerun a simulation | rerun |
| RE-squared anisotropic potential | pair_style resquared |
| restart files | restart, write_restart, read_restart |
| restarting a simulation | Howto restart |
| rigid bodies | RIGID package, fix rigid and variants, fix rigid/small and variants, POEMS package |
| rotational energy | compute erotate/sphere, compute erotate/asphere |
| rRESPA time stepping | run_style respa |
| run dynamics | run |
| running multiple simulations | Howto multiple |
| SPICA coarse-grained MD | CG-SPICA package, pair_style lj/spica |
| set atom properties | set |
| SHAKE constraints | fix shake |
| Shardlow splitting for DPD | fix shardlow |
| shell commands | shell |
| shift of potential | pair_modify shift |
| shock propagation | SHOCK package, fix msst, fix append/atoms |
| skin distance, neighbor | neighbor |
| simulation box | see orthogonal or triclinic simulation box |
| simulation input | Commands, read_data |
| simulation output | Howto output |
| SLLOD equationsxs of motion | fix nvt/sllod |
| SNAP = spectral neighbor analysis potential | pair_style snap, SNAP package |
| snapshots of atoms | see dump |
| soft potential | pair_style soft |
| spatial averaging | fix ave/chunk |
| smoothed Mach dynamics | atom_style smd,MACHDYN package, SPHpackage,doc/PDF/SMD_LAMMPS_userguide.pdf |
| smoothed particle hydrodynamics | see SPH |
| SMTBQ = second-moment tight-binding QEq potential | pair_style smtbq, SMTBQ package |
| SPC water | Howto spc |
| SPH = smoothed particle hydrodynamics | atom_style meso, SPH package, MACHDYN package, doc/PDF/SPH_LAMMPS_userguide.pdf |
| spherical particles | Howto spherical, atom_style sphere |
| spring force constraints | fix spring, fix spring/rg, fix spring/self |
| square lattice | lattice |
| SRD = stochastic rotation dynamics | SRD package, fix srd |
| steepest descent minimization | min_style sd |
| steered MD | fix smd |
| Stillinger-Weber potential | pair_style sw |
| Stockmayer model | pair_style lj/cut/dipole/long |
| Stokesian dynamics | FLD package, pair_style lubricateU |
| Streitz-Mintmire potential | pair_style coul/streitz |
| stress | see pressure and stress |
| stress/strain calculations | fix deform |
| tabulated potentials | pair_style table, bond_style table, angle_style table, diherdral_style table |
| TAD = temperature accelerated dynamics | tad |
| tail contribution of potential | pair_modify tail |
| taper functions for potentials | pair_style mdf |
| targeted MD | fix tmd |
| temperature | Howto temperature, compute temp and variants |
| temperature accelerated dynamics | see TAD |
| temperature rescaling | fix temp/rescale |
| tempering | temper, temper/npt, temper/grem, Howto replica |
| tethering potential | pair_style gauss, pair_style gauss/cut |
| Tersoff extended potential | pair_style extep |
| Tersoff potential | pair_style tersoff |
| Tersoff modified potential | pair_style tersoff/mod |
| Tersoff ZBL potential | pair_style tersoff/zbl |
| thermal conductivity | Howto kappa, lammps/examples/KAPPA andlammps/examples/HEAT dirs |
| thermodynamic integration | compute ti, fix adapt, fix ti/spring |
| thermodynamic output | thermo, thermo_style |
| thermostatting | Howto thermostat |
| threading | see OpenMP usage |
| time averaging | fix ave/time |
| time correlation | fix ave/correlate |
| time integration | run, run_style run |
| timestep | timestep, fix dt/reset, reset_timestep |
| timestep limiting | fix nve/limit |
| timings (CPU) | timer |
| TIP3P water | Howto tip3p |
| TIP4P water | Howto tip4p |
| torque | variable torque, fix addtorque, compute torque/chunk |
| torsional potentials | dihedral_style |
| triangular lattice | lattice |
| triqngular particles | atom_style tri, fix rigid |
| tri/tri interactions | pair_style tri/lj |
| triclinic simulation box | create_box, region prism, change_box, box, Howto triclinic |
| two-temperature electron model | fix ttm, fix ttm/mod |
| UFM Uhlenbech-Ford potential | pair_style ufm |
| umbrella sampling | fix spring |
| units | units |
| VACF = velocity auto-correlation function | compute vacf |
| variable timestep | fix dt/reset |
| Vashishita potential | pair_style vashishita |
| velocity, setting of | velocity |
| Verlet time stepping | run_style verlet |
| virial computation | compute pressure, compute stress/atom |
| viscosity | Howto viscosity, lammps/examples/VISCOSITY dir |
| viscous damping | fix viscous |
| visualization | Howto viz, dump image, dump movie |
| VMD molfile plug-ins | see molfile plug-ins for VMD |
| Voronoi tesselation | VORONOI package, compute voronoi/atom |
| VTK file format | dump vtk, VTK package |
| walls | Howto walls, fix wall and variants |
| warning and error messages | Errors |
| water models | Howto spc, Howto tip3p, Howto tip4p, |
| Wolf potential | pair_style coul/wolf |
| Xeon Phi (Intel) | INTEL package, KOKKOS package, Speed packages |
| XTC file format | dump xtc, XTC package |
| XYZ file format | dump xyz |
| Yukawa potential | pair_style yukawa |
| Yukawa colloid potential | pair_style yukawa/colloid |
| ZBL = Ziegler-Biersack-Littmark potential | pair_style zbl |