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5. 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".

The dump files produced by the example runs can be animated using the xmovie tool described in the Tools section. MPEG versions of most of the xmovie animations are also viewable from the Examples page of the LAMMPS WWW Site.

These are the sample problems in the examples sub-directories:

crack crack propagation in a 2d solid
flow Couette and Poisseuille flow in a 2d channel
friction frictional contact of spherical asperities between 2d surfaces
indent spherical indenter into a 2d solid
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
obstacle flow around two voids in a 2d channel
peptide dynamics of a small solvated peptide chain (5-mer)
pour pouring of granular particles into a 3d box, then chute flow
rigid rigid bodies modeled as independent or coupled
shear sideways shear applied to 2d solid, with and without a void

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 

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.