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 :doc:`dump ` command in the input script, a text dump file will be produced, which can be animated by various `visualization programs `_. It can also be animated using the xmovie tool described in the :doc:`Additional Tools ` section of the LAMMPS documentation. If you uncomment the :doc:`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 :doc:`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. ---------- Lowercase directories --------------------- +-------------+------------------------------------------------------------------+ | accelerate | run with various acceleration options (OpenMP, GPU, Phi) | +-------------+------------------------------------------------------------------+ | balance | dynamic load balancing, 2d system | +-------------+------------------------------------------------------------------+ | body | body particles, 2d system | +-------------+------------------------------------------------------------------+ | colloid | big colloid particles in a small particle solvent, 2d system | +-------------+------------------------------------------------------------------+ | comb | models using the COMB potential | +-------------+------------------------------------------------------------------+ | 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 | +-------------+------------------------------------------------------------------+ | 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 | +-------------+------------------------------------------------------------------+ | 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 | +-------------+------------------------------------------------------------------+ Here is how you can run and visualize one of the sample problems: .. parsed-literal:: 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 :doc:`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 :doc:`Section start 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 :doc:`dump image ` doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser. .. parsed-literal:: % convert -loop 1 *.jpg foo.gif ---------- 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 :doc:`Section packages ` doc page for more info on specific USER packages. .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm