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5. 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".

The dump files produced by the example runs can be animated using the
xmovie tool described in the "Additional Tools"_Section_tools.html
section of the LAMMPS documentation.  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:

colloid:  big colloid particles in a small particle solvent, 2d system
crack:	  crack propagation in a 2d solid
dipole:   point dipolar particles, 2d system
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
indent:	  spherical indenter into a 2d solid
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
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:     Peridynamics example of cylinder hit by projectile
pour:     pouring of granular particles into a 3d box, then chute flow
prd:	  parallel replica dynamics of a vacancy diffusion in bulk Si
reax:     simple example for ReaxFF force field
rigid:    rigid bodies modeled as independent or coupled
shear:    sideways shear applied to 2d solid, with and without a void :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

There is also a directory "couple" in the examples sub-directory,
which contains a stand-alone code umbrella.cpp that links LAMMPS as a
library.  The README describes how to build the code.  The code itself
runs LAMMPS on a subset of processors, sets up a LAMMPS problem
by invoking LAMMPS input script commands one at a time, does
a run, grabs atom coordinates, changes one atom position, puts
them back into LAMMPS, and does another run.

This illustrates how an umbrella code could include new models and
physics while using LAMMPS to perform MD, or how the umbrella code
could call both LAMMPS and some other code to perform a coupled
calculation.
