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# 9. Example scripts¶

The LAMMPS distribution includes an examples subdirectory with many sample problems. Many are 2d models that run quickly and 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 command in the input script, a text dump file will be produced, which can be animated by various visualization programs.

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 website.

There are two kinds of subdirectories in the examples folder. Lower case named directories contain one or a few simple, quick-to-run problems. Upper case named directories 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.

## 9.1. Lowercase directories¶

 accelerate run with various acceleration options (OpenMP, GPU, Phi) airebo polyethylene with AIREBO potential atm Axilrod-Teller-Muto potential example balance dynamic load balancing, 2d system body body particles, 2d system bpm BPM simulations of pouring elastic grains and plate impact 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 controller use of fix controller as a thermostat coreshell core/shell model using CORESHELL package 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 mc Monte Carlo features via fix gcmc, widom and other commands granregion use of fix wall/region/gran as boundary on granular particles hugoniostat Hugoniostat shock dynamics hyper global and local hyperdynamics of diffusion on Pt surface indent spherical indenter into a 2d solid kim use of potentials from the OpenKIM Repository latte examples for using fix latte for DFTB via the LATTE library mdi use of the MDI package and MolSSI MDI code coupling library 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 multi multi neighboring for systems with large interaction disparities nb3b use of non-bonded 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 rdf-adf computing radial and angle distribution functions for water reax RDX and TATB models using the ReaxFF rerun use of rerun and read_dump commands 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 threebody regression test input for a variety of manybody potentials tracker track interactions in LJ melt 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 third-party tools highlighted on the Visualization page of the LAMMPS website.

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 the Build_settings page 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 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


## 9.2. 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 HEAT compute thermal conductivity for LJ and water via fix ehex KAPPA compute thermal conductivity via several methods MC-LOOP using LAMMPS in a Monte Carlo mode to relax the energy of a system in a input script loop PACKAGES examples for specific packages and contributed commands SPIN examples for features of the SPIN package UNITS examples that run the same simulation in lj, real, metal units 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 PACKAGES directory has a large number of subdirectories which correspond by name to specific packages. They contain scripts that illustrate how to use the command(s) provided in those packages. Many of the subdirectories have their own README files which give further instructions. See the Packages_details doc page for more info on specific packages.