LAMMPS example problems

There are 3 flavors of sub-directories in this file, each with sample
problems you can run with LAMMPS.

lower-case directories = simple test problems for LAMMPS and its packages
upper-case directories = more complex problems
USER directory with its own sub-directories = tests for USER packages

Each is discussed below.

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Lower-case directories

Each of these sub-directories contains a sample problem you can run
with LAMMPS.  Most are 2d models so that they run quickly, requiring a
few seconds to a few minutes to run on a desktop machine.  Each
problem has an input script (in.*) and produces a log file (log.*) and
(optionally) a dump file (dump.*) or image files (image.*) when it
runs.  Some use a data file (data.*) of initial coordinates as
additional input.  Some require that you install one or more optional
LAMMPS packages.

A few sample log file outputs 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.crack.date.foo.P means it ran on
P processors of machine "foo" with the dated version of LAMMPS.  Note
that these problems should get statistically similar answers when run
on different machines or different numbers of processors, but not
identical answers to those in the log of dump files included here.
See the Errors section of the LAMMPS documentation for more
discussion.

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 (see http://lammps.sandia.gov/viz.html).  It can also be
animated using the xmovie tool described in the Additional Tools
section of the LAMMPS documentation.

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 these examples can be viewed on the Movies
section of the LAMMPS WWW Site.

These are the sample problems and their output in the various
sub-directories:

body:     body particles, 2d system
colloid:  big colloid particles in a small particle solvent, 2d system
comb:	  models using the COMB potential
crack:	  crack propagation in a 2d solid
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
gpu:      use of the GPU package for GPU acceleration
hugoniostat: Hugoniostat shock dynamics
indent:	  spherical indenter into a 2d solid
kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
line:     line segment particles in 2d rigid bodies
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
msst:	  MSST shock dynamics
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
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
srd:      stochastic rotation dynamics (SRD) particles as solvent
tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
tri:      triangular particles in rigid bodies
voronoi:  test of Voronoi tesselation in compute voronoi/atom

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

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

Running the simulation produces the files {dump.indent} and
{log.lammps}.  You can visualize the dump file as follows:

../../tools/xmovie/xmovie -scale dump.indent

If you uncomment the dump image line(s) in the input script a series
of JPG images will be produced by the run.  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

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Upper-case directories

The ASPHERE directory has examples of how to model aspherical
particles with or without solvent, in 3 styles LAMMPS provides.
Namely point ellipsoids, rigid bodies, and generalized aspherical
bodies built from line/triangle surface facets in 2d/3d.  See the
ASPHERE/README file to get started.

The COUPLE directory has examples of how to use LAMMPS as a library,
either by itself or in tandem with another code or library.  See the
COUPLE/README file to get started.

The ELASTIC directory has an example script for computing elastic
constants, using a zero temperature Si example.  See the
ELASTIC/in.elastic file for more info.

The KAPPA directory has an example scripts for computing the thermal
conductivity (kappa) of a LJ liquid using 4 different methods.  See
the KAPPA/README file for more info.

The USER directory contains subdirectories of user-provided example
scripts for ser packages.  See the README files in those directories
for more info.  See the doc/Section_start.html file for more info
about installing and building user packages.

