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Example problems
================
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
:doc:`Additional Tools <Section_tools>` section of the LAMMPS
documentation and provided with the LAMMPS distribution.
If you uncomment the :doc:`dump <dump>` 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 :doc:`Additional Tools <Section_tools>` section of the LAMMPS documentation.
If you uncomment the :doc:`dump image <dump>` 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
:doc:`dump image <dump_image>` 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:
+-------------+----------------------------------------------------------------------------+
| balance | dynamic load balancing, 2d system |
+-------------+----------------------------------------------------------------------------+
| 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 |
+-------------+----------------------------------------------------------------------------+
| cuda | use of the USER-CUDA package for GPU acceleration |
+-------------+----------------------------------------------------------------------------+
| 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 |
+-------------+----------------------------------------------------------------------------+
| intel | use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor |
+-------------+----------------------------------------------------------------------------+
| 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 |
+-------------+----------------------------------------------------------------------------+
| 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 |
+-------------+----------------------------------------------------------------------------+
| qeq | use of the 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 | NVE dynamics for BCC tantalum crystal using SNAP potential |
+-------------+----------------------------------------------------------------------------+
| srd | stochastic rotation dynamics (SRD) particles as solvent |
+-------------+----------------------------------------------------------------------------+
| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
+-------------+----------------------------------------------------------------------------+
| tri | triangular particles in rigid bodies |
+-------------+----------------------------------------------------------------------------+
vashishta: models using the Vashishta potential
Here is how you might run and visualize one of the sample problems:
.. parsed-literal::
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux -in in.indent # run the problem
Running the simulation produces the files *dump.indent* and
*log.lammps*. You can visualize the dump file as follows:
.. parsed-literal::
../../tools/xmovie/xmovie -scale dump.indent
If you uncomment the :doc:`dump image <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
:doc:`dump image <dump_image>` doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
.. parsed-literal::
% convert -loop 1 *.jpg foo.gif
----------
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 at zero temperature, using an Si example. See
the ELASTIC/in.elastic file for more info.
There is also an ELASTIC_T directory with an example script for
computing elastic constants at finite temperature, using an Si example. See
the ELASTIC_T/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
:doc:`Section_start.html <Section_start>` file for more info about user
packages.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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