forked from lijiext/lammps
151 lines
6.6 KiB
Plaintext
151 lines
6.6 KiB
Plaintext
LAMMPS example problems
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There are 3 flavors of sub-directories in this file, each with sample
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problems you can run with LAMMPS.
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lower-case directories = simple test problems for LAMMPS and its packages
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upper-case directories = more complex problems
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USER directory with its own sub-directories = tests for USER packages
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Each is discussed below.
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------------------------------------------
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Lower-case directories
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Each of these sub-directories contains a sample problem you can run
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with LAMMPS. Most are 2d models so that they run quickly, requiring a
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few seconds to a few minutes to run on a desktop machine. Each
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problem has an input script (in.*) and produces a log file (log.*) and
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(optionally) a dump file (dump.*) or image files (image.*) or movie
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(movie.mpg) when it runs. Some use a data file (data.*) of initial
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coordinates as additional input. Some require that you install one or
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more optional LAMMPS packages.
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A few sample log file outputs on different machines and different
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numbers of processors are included in the directories to compare your
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answers to. E.g. a log file like log.crack.date.foo.P means it ran on
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P processors of machine "foo" with the dated version of LAMMPS. Note
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that these problems should get statistically similar answers when run
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on different machines or different numbers of processors, but not
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identical answers to those in the log of dump files included here.
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See the Errors section of the LAMMPS documentation for more
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discussion.
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Most of the example input scripts have commented-out lines that
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produce dump snapshots of the running simulation in any of 3 formats.
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If you uncomment the dump command in the input script, a text dump
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file will be produced, which can be animated by various visualization
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programs (see http://lammps.sandia.gov/viz.html) such as VMD or
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AtomEye. It can also be animated using the xmovie tool described in
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the Additional Tools section of the LAMMPS documentation.
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If you uncomment the dump image command in the input script, and
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assuming you have built LAMMPS with a JPG library, JPG snapshot images
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will be produced when the simulation runs. They can be quickly
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post-processed into a movie using commands described on the dump image
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doc page.
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If you uncomment the dump movie command in the input script, and
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assuming you have built LAMMPS with the FFMPEG library, an MPG movie
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will be produced when the simulation runs. The movie file can be
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played using various viewers, such as mplayer or QuickTime.
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Animations of many of these examples can be viewed on the Movies
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section of the LAMMPS WWW Site.
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These are the sample problems and their output in the various
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sub-directories:
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body: body particles, 2d system
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colloid: big colloid particles in a small particle solvent, 2d system
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comb: models using the COMB potential
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crack: crack propagation in a 2d solid
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deposit: deposition of atoms and molecules onto a 3d substrate
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dipole: point dipolar particles, 2d system
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dreiding: methanol via Dreiding FF
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eim: NaCl using the EIM potential
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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gpu: use of the GPU package for GPU acceleration
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hugoniostat: Hugoniostat shock dynamics
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indent: spherical indenter into a 2d solid
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kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
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kokkos: use of the KOKKOS package for multi-threading and GPU acceleration
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meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
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min: energy minimization of 2d LJ melt
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msst: MSST shock dynamics
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nb3b: use of NB3B pair style
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neb: nudged elastic band (NEB) calculation for barrier finding
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nemd: non-equilibrium MD of 2d sheared system
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obstacle: flow around two voids in a 2d channel
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peptide: dynamics of a small solvated peptide chain (5-mer)
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peri: Peridynamic model of cylinder impacted by indenter
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pour: pouring of granular particles into a 3d box, then chute flow
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prd: parallel replica dynamics of vacancy diffusion in bulk Si
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reax: RDX and TATB models using the ReaxFF
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void
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srd: stochastic rotation dynamics (SRD) particles as solvent
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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voronoi: test of Voronoi tesselation in compute voronoi/atom
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Here is how you might run and visualize one of the sample problems:
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cd indent
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cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
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lmp_linux < in.indent # run the problem
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Running the simulation produces the files {dump.indent} and
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{log.lammps}. You can visualize the dump file as follows:
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../../tools/xmovie/xmovie -scale dump.indent
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If you uncomment the dump image line(s) in the input script a series
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of JPG images will be produced by the run. These can be viewed
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individually or turned into a movie or animated by tools like
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ImageMagick or QuickTime or various Windows-based tools. See the dump
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image doc page for more details. E.g. this Imagemagick command would
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create a GIF file suitable for viewing in a browser.
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% convert -loop 1 *.jpg foo.gif
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------------------------------------------
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Upper-case directories
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The ASPHERE directory has examples of how to model aspherical
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particles with or without solvent, in 3 styles LAMMPS provides.
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Namely point ellipsoids, rigid bodies, and generalized aspherical
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bodies built from line/triangle surface facets in 2d/3d. See the
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ASPHERE/README file to get started.
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The COUPLE directory has examples of how to use LAMMPS as a library,
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either by itself or in tandem with another code or library. See the
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COUPLE/README file to get started.
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The ELASTIC directory has an example script for computing elastic
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constants, using a zero temperature Si example. See the
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ELASTIC/in.elastic file for more info.
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The KAPPA directory has example scripts for computing the thermal
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conductivity (kappa) of a LJ liquid using 4 different methods. See
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the KAPPA/README file for more info.
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The MC directory has an example script for using LAMMPS as an
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energy-evaluation engine in a iterative Monte Carlo energy-relaxation
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loop.
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The USER directory contains subdirectories of user-provided example
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scripts for ser packages. See the README files in those directories
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for more info. See the doc/Section_start.html file for more info
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about installing and building user packages.
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The VISCOSITY directory has example scripts for computing the
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viscosity of a LJ liquid using 4 different methods. See the
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VISCOSITY/README file for more info.
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