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 comb: models using the COMB potential coreshell: adiabatic core/shell model 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 gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command 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 package 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: Voronoi tesselation via compute voronoi/atom command

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.