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7. Example problems :h3

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"_dump.html command in the input script, a
text dump file will be produced, which can be animated by various
"visualization programs"_http://lammps.sandia.gov/viz.html.

If you uncomment the "dump image"_dump.html 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"_dump_image.html doc page.

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

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.

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Lowercase directories :h4

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 :tb(s=:)

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 :pre

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"_http://lammps.sandia.gov/viz.html page of the LAMMPS
web site.

If you uncomment the "dump image"_dump_image.html 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"_Section_start.html#start_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"_dump_image.html 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 :pre

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Uppercase directories :h4

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 :tb(s=:)

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"_Section_packages.html doc
page for more info on specific USER packages.
