LAMMPS website

Glossary

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 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z


0,1,2,3,4,5,6,7,8,9

1-2, 1-3, 1-4 pairwise interactions special_bonds
2d simulations Howto 2d, fixenforce2d
2d manifolds (surfaces) USER-MANIFOLD
2d vs 3d dimension

A

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 USER-ATC package, fix atc
averaging see atom averaging, spatial averaging, correlation, histogramming, timeaveraging, chunks
AWPMD = Antisymmetrized Wave Packet MD USER-AWPMD package, pair_style awpmd/cut

B

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

C

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, USER-CGDNApackage, USER-CGSDKpackage, USER-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 USER-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 USER-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

D

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, USER-DIFFRACTION package, compute saed, compute xrd
diffusion coefficient Howto diffusion, compute msd, compute vacf, lammps/examples/DIFFUSE dir
dihedral potentials dihedral_style
dilitation (Peridynamic) compute dilitation/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,USER-DPD package,USER-MESO package
DPD thermostat pair_style dpd/tstat
Dreiding force-field Howto bioFF, pair_style dreiding
Drude model USER-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

E

EAM = embedded atom method potentials pair_style eam
EDIP potential pair_style edip
EFF = electron force field USER-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 USER-AWPMD package, USER-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 USER-UEF package

F

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, USER-FEP package, PLUMED
freezing atoms fix freeze
frictional potentials see granular models

G

g(r) see radial distribution function
Gao Weber potential pair_style gao/weber
GAP = Gaussian approximation potential pair_stylequip, USER-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

H

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, USER-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

I

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 USER-INTEL package, OPT package, Speed packages
Intel Phi see Xeon Phi
interactive MD & visualization fix imd
i-PI Python see PIMD

J

JPG files dump image

K

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

L

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 USER-LB 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

M

machine learned potentials SNAPpackage, see GAP potential, see AGNI potential
manifolds = 2d surfaces USER-MANIFOLD
manybody potentials MANYBODY package, pair_style
mass of atoms mass
MEAM = modified EAM potential MEAM and MEAMC 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, USER-MGPT package
Mie potential pair_style mie
minimization minimize, min_style
mixing of potential parameters pair_modifymix
MOF-FF force field USER-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,USER-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

N

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, USER-NETCDF package
Newton's 3rd law newton
NGP = non-Gaussian parameter compute msd/nonguass
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

O

one-way motion fix oneway
OpenMP usage USER-OMP package, KOKKOS package, Speed packages
OPLS force field dihedral_style opls
orientational order compute orientorder/atom
orthogonal simulation box create_box, change_box, 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/*

P

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 USER-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, USER-TALLY package
processor mapping processors, see NUMA
PUT = profile unbiased thermostat compute temp/profile
Python Python, PYTHON package, python,, lammps/python dir

Q

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, USER-QTB package
quantum thermal bath fix qtb, USER-QTB package
QuickMin damped dynamics minimization min_style quickmin
QUIP potentials pair_style quip, USER-QUIP package

R

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 USER-REAXC packages, 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

S

SDK coarse-grained MD USER-CG-CMM package, pair_style lj/sdk
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
SMD = smoothed Mach dynamics atom_style smd,USER-SMD package, USER-SPHpackage,doc/PDF/SMD_LAMMPS_userguide.pdf
smoothed Mach dynamics see SMD
smoothed particle hydrodynamics see SPH
SMTBQ = second-moment tight-binding QEq potential pair_style smtbq, USER-SMTBQ package
SPC water Howto spc
SPH = smoothed particle hydrodynamics atom_style meso, USER-SPH package, USER-SMD 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

T

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

U

UFM Uhlenbech-Ford potential pair_style ufm
umbrella sampling fix spring
units units

V

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, USER-VTK package

W

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

X

Xeon Phi (Intel) USER-INTEL package, KOKKOS package, Speed packages
XTC file format dump xtc, XTC package
XYZ file format dump xyz

Y

Yukawa potential pair_style yukawa
Yukawa colloid potential pair_style yukawa/colloid

Z

ZBL = Ziegler-Biersack-Littmark potential pair_style zbl