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.*) or movie
(movie.mpg) 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.

Most of the example input scripts have commented-out lines that
produce dump snapshots of the running simulation in any of 3 formats.

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) such as VMD or
AtomEye.  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.

If you uncomment the dump movie command in the input script, and
assuming you have built LAMMPS with the FFMPEG library, an MPG movie
will be produced when the simulation runs.  The movie file can be
played using various viewers, such as mplayer or QuickTime.

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:

accelerate: use of all the various accelerator packages
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
coreshell: adiabatic core/shell model
comb:	  models using the COMB potential
controller: use of fix controller as a thermostat
crack:	  crack propagation in a 2d solid
deposit:  deposition of atoms and molecules onto a 3d substrate
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
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:   use of PYTHON package to invoke Python code from input script
qeq:      use of QEQ pacakge 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:     use of SNAP potential for Ta
srd:      stochastic rotation dynamics (SRD) particles as solvent
snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
streitz:  Streitz-Mintmire potential for Al2O3
tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
vashishta: models using the Vashishta potential
voronoi:  test of Voronoi tesselation in compute voronoi/atom

Here is a src/Make.py command which will perform a parallel build of a
LAMMPS executable "lmp_mpi" with all the packages needed by all the
examples, with the exception of the accelerate sub-directory.  See the
accelerate/README for Make.py commands suitable for its example
scripts.

cd src
Make.py -j 16 -p none std no-lib reax meam poems reaxc orig -a lib-all mpi

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

cd indent
cp ../../src/lmp_mpi .           # copy LAMMPS executable to this dir
lmp_mpi < 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 at zero temperature, using an Si example.  See the
ELASTIC/in.elastic file for more info.

The ELASTIC_T directory has an example script for computing elastic
constants at finite temperature, using an Si example.  See the
ELASTIC_T/in.elastic file for more info.

The HEAT directory has example scripts for heat exchange algorithms
(e.g. used for establishing a thermal gradient), using two different
methods.  See the HEAT/README file for more info.

The KAPPA directory has example scripts for computing the thermal
conductivity (kappa) of a LJ liquid using 5 different methods.  See
the KAPPA/README file for more info.

The MC directory has an example script for using LAMMPS as an
energy-evaluation engine in a iterative Monte Carlo energy-relaxation
loop.

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.

The VISCOSITY directory has example scripts for computing the
viscosity of a LJ liquid using 4 different methods.  See the
VISCOSITY/README file for more info.