7. Example problems

The LAMMPS distribution includes an examples sub-directory with many sample problems. Many are 2d models that run quickly are 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.

7.1. Lowercase directories

accelerate run with various acceleration options (OpenMP, GPU, Phi)
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
coreshell core/shell model using CORESHELL package
controller use of fix controller as a thermostat
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
indent spherical indenter into a 2d solid
kim use of potentials in Knowledge Base for Interatomic Models (KIM)
meam MEAM test for SiC and shear (same as shear examples)
melt rapid melt of 3d LJ system
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 nonbonded 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
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
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 Section 2.2 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

7.2. 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
KAPPA compute thermal conductivity via several methods
MC using LAMMPS in a Monte Carlo mode to relax the energy of a system
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 Section 4 doc page for more info on specific USER packages.