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Glossary of Molecular Dynamics terms mapped to LAMMPS commands

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MD term should be a generic molecular dynamics simulation term.
List one or more LAMMPS commands, separated by commas. So the doc page can be linked to, specify the command name as you would in an input script, e.g. pair_style lj/cut. You can also list a section of the manual, e.g. Section_intro or Section_howto intro_7. See examples below.
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Glossary entries:

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	fix enforce2d, Section_howto howto_2

A

AI-REBO potential	pair_style airebo
AMBER force field	special_bonds
angle potentials	angle_style
aspherical particles	Section_howto howto_14
atom properties	atom_style
atom to continuum coupling	fix atc

B

barostatting	Section_howto howto_16
bcc lattice	lattice
bead-spring model	bond_style fene
bond breaking	fix bond/break
bond creation	fix bond/create
bond potentials	bond_style
bond swapping	fix bond_swap
bond-order potentials	pair_style tersoff, pair_style meam, pair_style reax
box deformation	fix deform, Section_howto howto_12
Buckingham potential	pair_style buck

C

center-of-mass	compute com
centro-symmetry factor	compute centro/atom
CFG file output	dump cfg
CHARMM force field	pair_style charmm, special_bonds
class 2 potentials	pair_style class2, bond_style class2
CNA = common neighbor analysis	compute cna/atom
colloidal particles	atom_style colloid
COMPASS potentials	pair_style class2, bond_style class2
conjugate gradient minimization	min_style cg
continuum coupling	fix atc
coordintation number	compute coord/atom
cubic lattice	lattice

D

DCD file output	dump dcd
Debye screening	pair_style lj
delete bonds	delete_bonds
depositing atoms	fix deposit
diffusion coefficient	compute msd
dihedral potentials	dihedral_style
dipole moments	dipole, pair_style dipole/cut, atom_style dipole
DPD = dissipative particle dynamics	pair_style dpd
DSMC = Direct Simulation Monte Carlo	pair_style dsmc
dump file output	dump

E

EAM = embedded atom method	pair_style eam
electric field application	fix efield
energy minimization	minimize
evaporating atoms	fix evaporate
Ewald sums	kspace_style
excluded pair interactions	special_bonds

F

fcc lattice	lattice
FENE bead-spring model	bond_style fene

G

g(r)	compute rdf
GayBerne potential	pair_style gayberne
geometric regions	region
grain boundary creation	lattice, create_atoms
grain boundary forces	fix orient/fcc
granular particles	atom_style granular
gravity	fix gravity
GROMACS force field	pair_style gromacs
groups of atoms	group

H

heat flux calculation	compute heat/flux
heirarchical time stepping	run-style respa
hexagonal lattice	lattice
hybrid potentials	pair_style hybrid, bond_style hybrid

I

improper potentials	improper_style
integrate	run
interactive visualization	fix imd

J

K

kinetic energy	compute ke, compute ke/atom

L

Langevin thermostat	fix langevin
lattices of atoms	lattice
long-range Coulombics	kspace_style
lubrication potential	pair_style lubricate

M

MEAM = modified EAM potential	pair_style meam
mean-squared displacement	compute msd
Morse potential	pair_style morse

N

neighbor lists	neighbor, neigh_modify
NEB = nudged elastic band	neb
NEMD = non-equilibrium MD	Section_howto howto_13
Newtons law	newton
non-orthogonal simulation boxes	Section_howto howto_12
Nose/Hoover barostat	fix npt
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

O

out-of-plane potentials	improper_style

P

parallel tempering	temper
Peridynamics	pair_style peri/pmb
periodic boundary conditions	boundary
PME = particle-mesh Ewald	kspace_style
point dipoles	dipole, pair_style dipole/cut, atomstyle dipole
potential energy	compute pe, compute pe/atom
PPPM = particle-particle particle-mesh	kspace_style
PRD = parallel replica dynamics	prd
pressure	compute pressure, compute stress/atom

Q

R

radial distribution function	compute rdf
radius of gyration	compute gyration
ReaxFF potential	pair_style reax
REBO potential	pair_style airebo
replica exchange	temper
replicate a system	replicate
REsquared colloidal potential	pair_style resquared
rigid bodies	fix rigid, fix poems
rigid ion potential	atom_style charge, pair_style buck/coul/long, set charge
rRESPA time stepping	run_style respa

S

SHAKE constraints	fix shake
SLLOD	fix nvt/sllod
snapshot file output	dump
spatial averaging	fix ave/spatial
SPC water	Section_howto howto_9
spherical particles	Section_howto howto_14
spring force constraints	fix spring, fix spring/rg, fix spring/self
square lattice	lattice
steepest descent minimization	min_style sd
steered MD	fix smd
Stillinger-Weber potential	pair_style sw
stochastic rotation dynamics (SRD)	fix srd
stress/strain calculations	fix deform

T

tabulated potentials	pair_style table, bond_style table, angle_style table
TAD = temperature accelerated dynamics	tad
targeted MD	fix tmd
temperature	compute temp, compute temp/com, compute temp/sphere, compute temp/partial
tempering	temper
Tersoff potential	pair_style tersoff
thermal conductivity calculation	fix thermal/conductivity
thermodynamic output	thermo, thermo_style
thermostatting	Section_howto howto_16
time averaging	fix ave/time
time integration	run_style, run
timestep	timestep, fix dt/reset
TIP3P water	Section_howto howto_7
TIP4P water	Section_howto howto_8
torsional potentials	dihedral_style
triangular lattice	lattice
triclinic simulation boxes	Section_howto howto_12
two-temperature electron model	fix ttm

U

umbrella sampling	fix spring

V

velocity setting	velocity
Verlet time integration	run_style verlet
virial computation	compute presure, compute stress/atom
viscosity calculation	fix viscosity, fix deform, fix nvt/sllod
viscous drag	fix viscous
visualization	Section_howto howto_11

W

walls	Section_howto howto_17

X

XTC file output	dump xtc
XYZ file output	dump xyz

Y

Yukawa potential	pair_style yukawa

Z