Glossary of Molecular Dynamics terms mapped to LAMMPS commands

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


1-2, 1-3, 1-4 pairwise interactions special_bonds
2d simulations Section 6.2, fix enforce2d
2d vs 3d dimension


Ackland lattice structure compute ackland/atom
AIREBO potential pair_style airebo
AMBER force field Section 6.3, special_bonds amber
angle potentials angle_style
angular dependent potential pair_style adp
angular momentum variable angmom
angular momentum zeroing fix momentum, velocity
angular velocity variable omega
aspherical particles ASPHERE package, Section 6.14, atom_style ellipsoid, body
atom properties atom_style, set
atom to continuum coupling USER-ATC package, fix atc
AWPMD = Antisymmetrized Wave Packet MD USER-AWPMD package, pair_style awpmd/cut


basal plane "c" vector compute basal/atom
barostatting Section 6.16
bcc lattice lattice
bead-spring model bond_style fene
Beck potential pair_style beck
Berendsen barostat fix press/berendsen
Berendsen thermostat fix temp/berendsen
bond breaking fix bond/break, bond_style quartic
bond creation fix bond/create
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


CD-EAM = concentration dependent EAM pair_style eam/cd
center-of-mass compute com, variable xcm
center-of-mass force variable fcm
center-of-mass velocity variable vcm
centro-symmetry factor compute centro/atom
CFG file output dump cfg
change atom properties set
charge equilibration fix qeq/comb, fix qeq/reax
CHARMM force field Section 6.3, pair_style charmm, special_bonds charmm
class2 force-field CLASS2 package, pair_style lj/class2, bond_style class2
CNA = common neighbor analysis compute cna/atom
collective variables USER-COLVARS package, fix colvars
colloidal particles COLLOID package, atom_style colloid
COMB potential pair_style comb, pair_style comb3
COMPASS force-field CLASS2 package, pair_style lj/class2, bond_style class2
constrained motion fix move, fix lineforce, fix planeforce, fix restrain, fix spring
continuum coupling USER-ATC package, fix atc
conjugate gradient minimization min_style cg
cooling & heating fix heat
coordintation number compute coord/atom
correlation, time fix ave/correlate
Coulomb potential pair_style coul
coupling to another code Section 6.10, fix external
cubic lattice lattice
cutoff pair_style
CUDA for GPUs GPU package, USER-CUDA package
CVFF force-field improper_style cvff


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 output dump dcd
Debye screening pair_style lj/cut/coul/debye
deformation fix deform
delete atoms delete_atoms
delete bonds delete_bonds
depositing atoms & molecules fix deposit
dielectric constant dielectric, pair_style coul/diel
dispersion, long-range kspace_style pppm/disp, kspace_style ewald/disp
diffusion coefficient compute msd, compute vacf
dihedral potentials dihedral_style
dipolar particles DIPOLE package, atom_style dipole, pair_style lj/cut/dipole
dipole pairwise interactions pair_style lj/cut/dipole
dipole long-range interactions kspace_style ewald/disp
DLVO potential pair_style colloid
DPD = dissipative particle dynamics pair_style dpd
DPD thermostat pair_style dpd/tstat
Dreiding force-field pair_style dreiding
DSMC = Direct Simulation Monte Carlo pair_style dsmc
dump files dump, write_dump, read_dump
dynamical matrix USER-PHONON package, fix phonon


EAM = embedded atom method pair_style eam
EDIP potential pair_style edip
EFF = electron force field USER-EFF package, pair_style eff/cut
EIM = embedded ion method pair_style eim
elastic constants Section 6.18
electric field fix efield
electron dynamics USER-AWPMD package, USER-EFF package
energy minimization minimize, min_style
evaporation fix evaporate
error and warning messages Section_errors
Ewald summation kspace_style ewald, kspace_style ewald/disp
excluded pair interactions special_bonds


FLD = fast lubrication dynamics FLD package, pair_style lubricateU
fcc lattice lattice
FENE bead-spring model bond_style fene
Finnis-Sinclaire EAM potential pair_style eam/fs
FIRE minimization min_style fire
free energy compute ti, fix colvars, fix adapt/fep, PLUMED
freezing atoms fix freeze
frictional potentials pair_style granular


g(r) compute rdf
Gaussian potential pair_style gauss, pair_style gauss/cut
GayBerne potential pair_style gayberne
GCMC = grand-canonical Monte Carlo fix gcmc
generalized Langevin dynamics fix gld
geometric regions region
Gibbs free energy see free energy
GPU = graphical processing units GPU package, USER-CUDA package, Section_accelerate
grain boundary creation lattice orient, create_atoms
grain boundary forces fix orient/fcc
granular modeling GRANULAR package, Section 6.6, pair_style granular, LIGGGHTS
granular particles atom_style granular
granular potentials pair_style granular
gravity fix gravity
GROMACS force field pair_style gromacs
groups of atoms group


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
heat flux compute heat/flux
heating & cooling fix heat
heirarchical time stepping run-style respa
HFTN = Hessian-free truncated-Newton minimization min_style hftn
hexagonal lattice lattice
histogramming fix ave/histo
history-dependent potential pair_style granular
Hugoniostat eqs of motion fix nphug
hybrid potentials pair_style hybrid
hydrogen-bonding pair_style dreiding


implicit solvent pair_style lj/cut/coul/debye, pair_style coul/diel
improper potentials improper_style
indentation fix indent
inertia, moments of variable inertia, compute inertia/molecule
input to simulation Section_commands, read_data
interactive MD & visualization fix imd



KIM = Knowledbase of Interatomic Models KIM package, pair_style kim
kinetic energy compute ke, compute ke/atom
K-space long-range solvers KSPACE package, kspace_style


Langevin dynamics fix langevin, fix gld
Langevin thermostat fix langevin
lattice Bolztmann fluid USER-LB package, fix lb/fluid
lattices of atoms lattice
LCBOP = long-range bond-order potential pair_style lcbop
Lennard-Jones potential pair_style lj
library interface and API Section 2.4, Section 6.19
line particles atom_style line
line/line interactions pair_style line/lj
linear momentum zeroing fix momentum, velocity
load balancing balance, fix balance
long-range Coulombics kspace_style
long-range dipoles kspace_style ewald/disp
long-range dispersion kspace_style pppm/disp, kspace_style ewald/disp
lubrication forces pair_style lubricate


many-body potentials MANYBODY package, pair_style
mass of atoms mass
MEAM = modified EAM potential pair_style meam
MEAM-SW = MEAM + Stillinger-Weber pair_style meam/sw/spline
mean-squared displacement compute msd
Mie potential pair_style mie
minimization minimize, min_style
mixing of potential pair_modify mix
molecule templates & topology molecule, read_data
moments of inertia variable inertia, compute inertia/molecule
momentum zeroing fix momentum, velocity
Monte Carlo options MC package, fix gcmc
Morse bond potential bond_style morse
Morse pair potential pair_style morse
MPCD = multi-particle collision dynamics SRD package, fix srd
MPI-IO parallel I/O dump mpiio, write_resatrt, read_restart
MSM = multi-level summation Coulombics kspace_style msm
MSST = multi-scale shock technique fix msst
multilevel summation method (MSM) kspace_style msm
multiple simulations Section 6.4
multi-replica methods REPLICA package, Section 6.5, temper, prd, tad


neighbor lists neighbor, neigh_modify
neighbor skin distance neighbor
NEB = nudged elastic band neb
NEMD = non-equilibrium MD Section 6.13, fix deform
Newton's 3rd law newton
NGP = non-Gaussian parameter compute msd/nonguass
N-M potential pair_style nm
nonbonded 3-body harmonic potential pair_style nb3b/harmonic
non-orthogonal simulation boxes Section 6.12
normalization thermo_modify norm
Nose/Hoover barostat fix npt, fix nph
Nose/Hoover thermostat fix nvt
NPH ensemble fix nph
NPT ensemble fix npt
nudged elastic band neb, fix neb
NVE ensemble fix nve
NVT ensemble fix nvt


OpenMP threading USER-OMP package, package
OPLS force field dihedral_style opls
out-of-plane potentials improper_style
output from simulation Section 6.15
overlayed potentials pair_style hybrid/overlay


pairwise interactions pair_style
parallel I/O via MPI-IO dump mpiio, write_resatrt, read_restart
parallel tempering temper
Peridynamics PERI package, pair_style peri
Peridynamic damage compute damage/atom
Peridynamic dilatation compute dilatation/atom
Peridynamic plasticity compute plasticity/atom
periodic boundary conditions boundary
phonons USER-PHONON package, fix phonon
piston fix wall/piston
plotting of output data Section_tools, tools/python
PME = particle-mesh Ewald kspace_style pppm
point dipoles atom_style dipole, pair lj/cut/dipole
POEMS = constrained rigid-body motion POEMS package, fix poems
post-processing of output data Section_tools
potential energy compute pe, compute pe/atom
pouring of particles fix pour
PPPM = particle-particle particle-mesh kspace_style pppm
PRD = parallel replica dynamics prd
pre-processing of input data Section_tools
pressure compute pressure, compute stress/atom
Python scripting Section_python


QeQ = charge equilibration fix qeq/comb, fix qeq/reax
QuickMin minimization min_style quickmin


radial distribution function compute rdf
radius of gyration compute gyration
ReaxFF potential REAX and USER-REAXC packages, pair_style reax, pair_style reax/c
REBO potential pair_style rebo
regions, geometric region
reflective wall fix wall/reflect
replica methods REPLICA package
replica exchange temper
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 Section 6.1
rigid bodies RIGID package, POEMS package, fix rigid, fix rigid/small
rRESPA time stepping run_style respa
run dynamics run
running multiple simulations Section 6.4


SDK coarse-grained MD USER-CG-CMM package, pair_style lj/sdk
set atom properties set
SHAKE constraints fix shake
shell commands shell
shift of potential pair_modify shift
shock-wave propagation SHOCK package, fix msst
skin distance, neighbor neighbor
simulation input Section_commands, read_data
simulation output Section 6.15
SLLOD eqs of motion fix nvt/sllod
snapshot files dump, write_dump, read_dump
soft potential pair_style soft
spatial averaging fix ave/spatial
SPC water Section 6.9
SPH = smoothed particle hydrodynamics USER-SPH package, pair_style sph/lj
spherical particles Section 6.14
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
stress compute pressure, compute stress/atom
stress/strain calculations fix deform


tabulated potentials pair_style table, bond_style table, angle_style table
TAD = temperature accelerated dynamics tad
tail contribution of potential pair_modify tail
targeted MD fix tmd
temperature Section 6.16, compute temp and variants
temperature rescaling fix temp/rescale
tempering temper
tethering potential pair_style gauss, pair_style gauss/cut
Tersoff potential pair_style tersoff
Tersoff modified potential pair_style tersoff/mod
Tersoff ZBL potential pair_style tersoff/zbl
thermal conductivity Section 6.20, examples/KAPPA
thermodynamic integration compute ti, fix adapt, fix ti/rs, fix ti/spring
thermodynamic output thermo, thermo_style
thermostatting Section 6.16
time averaging fix ave/time
time correlation fix ave/correlate
time integration run, run_style run
timestep timestep, fix dt/reset
TIP3P water Section 6.7
TIP4P water Section 6.8
torque variable torque, fix addtorque
torsional potentials dihedral_style
triangular lattice lattice
triangular particle atom_style tri
tri/tri interactions pair_style tri/lj
triclinic simulation boxes Section 6.12
two-temperature electron model fix ttm


umbrella sampling fix spring
units units


VACF = velocity auto-correlation function compute vacf
variable timestep fix dt/reset
velocity, setting of velocity
Verlet time stepping run_style verlet
virial computation compute presure, compute stress/atom
viscosity Section 6.21, examples/VISCOSITY
viscous damping fix viscous
visualization Section 6.11, dump image, dump movie
VMD molfile plug-in USER-MOLFILE package, dump molfile
Voronoi tesselation VORONOI package, compute voronoi/atom


walls Section 6.17
warning and error messages Section_errors
Wolf potential pair_style coul/wolf


XTC file output dump xtc
XYZ file output dump xyz


Yukawa potential pair_style yukawa
Yukawa colloid potential pair_style yukawa/colloid


ZBL = Ziegler-Biersack-Littmark potential pair_style zbl