9. Example scripts

The LAMMPS distribution includes an examples sub-directory with many sample problems. Many are 2d models that run quickly and are straightforward to visualize, requiring at most a couple of minutes to run on a desktop machine. Each problem has an input script (in.*) and produces a log file (log.*) when it runs. Some use a data file (data.*) of initial coordinates as additional input. A few sample log file run on different machines and different numbers of processors are included in the directories to compare your answers to. E.g. a log file like log.date.crack.foo.P means the “crack” example was run on P processors of machine “foo” on that date (i.e. with that version of LAMMPS).

Many of the input files have commented-out lines for creating dump files and image files.

If you uncomment the dump command in the input script, a text dump file will be produced, which can be animated by various visualization programs.

If you uncomment the dump image command in the input script, and assuming you have built LAMMPS with a JPG library, JPG snapshot images will be produced when the simulation runs. They can be quickly post-processed into a movie using commands described on the dump image doc page.

Animations of many of the examples can be viewed on the Movies section of the LAMMPS web site.

There are two kinds of sub-directories in the examples dir. Lowercase dirs contain one or a few simple, quick-to-run problems. Uppercase dirs contain up to several complex scripts that illustrate a particular kind of simulation method or model. Some of these run for longer times, e.g. to measure a particular quantity.

Lists of both kinds of directories are given below.


9.1. Lowercase directories

accelerate

run with various acceleration options (OpenMP, GPU, Phi)

airebo

polyethylene with AIREBO potential

atm

Axilrod-Teller-Muto potential example

balance

dynamic load balancing, 2d system

body

body particles, 2d system

cmap

CMAP 5-body contributions to CHARMM force field

colloid

big colloid particles in a small particle solvent, 2d system

comb

models using the COMB potential

controller

use of fix controller as a thermostat

coreshell

core/shell model using CORESHELL package

crack

crack propagation in a 2d solid

deposit

deposit atoms and molecules on a surface

dipole

point dipolar particles, 2d system

dreiding

methanol via Dreiding FF

eim

NaCl using the EIM potential

ellipse

ellipsoidal particles in spherical solvent, 2d system

flow

Couette and Poiseuille flow in a 2d channel

friction

frictional contact of spherical asperities between 2d surfaces

gcmc

Grand Canonical Monte Carlo (GCMC) via the fix gcmc command

granregion

use of fix wall/region/gran as boundary on granular particles

hugoniostat

Hugoniostat shock dynamics

hyper

global and local hyperdynamics of diffusion on Pt surface

indent

spherical indenter into a 2d solid

kim

use of potentials from the OpenKIM Repository

latte

examples for using fix latte for DFTB via the LATTE library

meam

MEAM test for SiC and shear (same as shear examples)

melt

rapid melt of 3d LJ system

message

demos for LAMMPS client/server coupling with the MESSAGE package

micelle

self-assembly of small lipid-like molecules into 2d bilayers

min

energy minimization of 2d LJ melt

mscg

parameterize a multi-scale coarse-graining (MSCG) model

msst

MSST shock dynamics

nb3b

use of non-bonded 3-body harmonic pair style

neb

nudged elastic band (NEB) calculation for barrier finding

nemd

non-equilibrium MD of 2d sheared system

obstacle

flow around two voids in a 2d channel

peptide

dynamics of a small solvated peptide chain (5-mer)

peri

Peridynamic model of cylinder impacted by indenter

pour

pouring of granular particles into a 3d box, then chute flow

prd

parallel replica dynamics of vacancy diffusion in bulk Si

python

using embedded Python in a LAMMPS input script

qeq

use of the QEQ package for charge equilibration

rdf-adf

computing radial and angle distribution functions for water

reax

RDX and TATB models using the ReaxFF

rigid

rigid bodies modeled as independent or coupled

shear

sideways shear applied to 2d solid, with and without a void

snap

NVE dynamics for BCC tantalum crystal using SNAP potential

srd

stochastic rotation dynamics (SRD) particles as solvent

streitz

use of Streitz/Mintmire potential with charge equilibration

tad

temperature-accelerated dynamics of vacancy diffusion in bulk Si

threebody

regression test input for a variety of manybody potentials

vashishta

use of the Vashishta potential

voronoi

Voronoi tesselation via compute voronoi/atom command

Here is how you can run and visualize one of the sample problems:

cd indent
cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
lmp_linux -in in.indent            # run the problem

Running the simulation produces the files dump.indent and log.lammps. You can visualize the dump file of snapshots with a variety of 3rd-party tools highlighted on the Visualization page of the LAMMPS web site.

If you uncomment the dump image line(s) in the input script a series of JPG images will be produced by the run (assuming you built LAMMPS with JPG support; see the Build_settings doc page for details). These can be viewed individually or turned into a movie or animated by tools like ImageMagick or QuickTime or various Windows-based tools. See the dump image doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser.

% convert -loop 1 *.jpg foo.gif

9.2. Uppercase directories

ASPHERE

various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc

COUPLE

examples of how to use LAMMPS as a library

DIFFUSE

compute diffusion coefficients via several methods

ELASTIC

compute elastic constants at zero temperature

ELASTIC_T

compute elastic constants at finite temperature

HEAT

compute thermal conductivity for LJ and water via fix ehex

KAPPA

compute thermal conductivity via several methods

MC

using LAMMPS in a Monte Carlo mode to relax the energy of a system

SPIN

examples for features of the SPIN package

UNITS

examples that run the same simulation in lj, real, metal units

USER

examples for USER packages and USER-contributed commands

VISCOSITY

compute viscosity via several methods

Nearly all of these directories have README files which give more details on how to understand and use their contents.

The USER directory has a large number of sub-directories which correspond by name to a USER package. They contain scripts that illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further instructions. See the Packages_details doc page for more info on specific USER packages.