7. Example problems
The LAMMPS distribution includes an examples sub-directory with many sample problems. Many are 2d models that run quickly are are straightforward to visualize, 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.*) when it runs. Some use a data file (data.*) of initial coordinates as additional input. A few sample log file run 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.date.crack.foo.P means the “crack” example was run on P processors of machine “foo” on that date (i.e. with that version of LAMMPS).
Many of the input files have commented-out lines for creating dump files and image files.
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.
Animations of many of the examples can be viewed on the Movies section of the LAMMPS web site.
There are two kinds of sub-directories in the examples dir. Lowercase dirs contain one or a few simple, quick-to-run problems. Uppercase dirs contain up to several complex scripts that illustrate a particular kind of simulation method or model. Some of these run for longer times, e.g. to measure a particular quantity.
Lists of both kinds of directories are given below.
7.1. Lowercase directories
|accelerate||run with various acceleration options (OpenMP, GPU, Phi)|
|airebo||polyethylene with AIREBO potential|
|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||core/shell model using CORESHELL package|
|controller||use of fix controller as a thermostat|
|crack||crack propagation in a 2d solid|
|deposit||deposit atoms and molecules on a surface|
|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||using embedded Python in a LAMMPS input script|
|qeq||use of the 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||NVE dynamics for BCC tantalum crystal using SNAP potential|
|srd||stochastic rotation dynamics (SRD) particles as solvent|
|streitz||use of Streitz/Mintmire potential with charge equilibration|
|tad||temperature-accelerated dynamics of vacancy diffusion in bulk Si|
|vashishta||use of the Vashishta potential|
|voronoi||Voronoi tesselation via compute voronoi/atom command|
Here is how you can run and visualize one of the sample problems:
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 of snapshots with a variety of 3rd-party tools highlighted on the Visualization page of the LAMMPS web site.
If you uncomment the dump image line(s) in the input script a series of JPG images will be produced by the run (assuming you built LAMMPS with JPG support; see Section 2.2 for details). 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
7.2. Uppercase directories
|ASPHERE||various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc|
|COUPLE||examples of how to use LAMMPS as a library|
|DIFFUSE||compute diffusion coefficients via several methods|
|ELASTIC||compute elastic constants at zero temperature|
|ELASTIC_T||compute elastic constants at finite temperature|
|KAPPA||compute thermal conductivity via several methods|
|MC||using LAMMPS in a Monte Carlo mode to relax the energy of a system|
|USER||examples for USER packages and USER-contributed commands|
|VISCOSITY||compute viscosity via several methods|
Nearly all of these directories have README files which give more details on how to understand and use their contents.
The USER directory has a large number of sub-directories which correspond by name to a USER package. They contain scripts that illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further instructions. See the Section 4 doc page for more info on specific USER packages.