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7. Example problems :h3

The LAMMPS distribution includes an examples sub-directory with
several sample problems.  Each problem is in a sub-directory of its
own.  Most are 2d models so that they run quickly, 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.*) and dump file
(dump.*) when it runs.  Some use a data file (data.*) of initial
coordinates as additional input.  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.foo.P means it ran on P processors of machine "foo".

For examples that use input data files, many of them were produced by
"Pizza.py"_http://pizza.sandia.gov or setup tools described in the
"Additional Tools"_Section_tools.html section of the LAMMPS
documentation and provided with the LAMMPS distribution.

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.  It can
also be animated using the xmovie tool described in the "Additional
Tools"_Section_tools.html section of the LAMMPS documentation.

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

These are the sample problems in the examples 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 :tb(s=:)

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 :pre

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 :pre

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.  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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There is also a COUPLE directory with 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.

There is also an ELASTIC directory with an example script for
computing elastic constants, using a zero temperature Si example.  See
the in.elastic file for more info.

There is also a USER directory which contains subdirectories of
user-provided examples for user packages.  See the README files in
those directories for more info.  See the
"Section_start.html"_Section_start.html file for more info about user
packages.
