Example problems ================ The LAMMPS distribution includes an examples sub-directory with several sample problems. Each problem is in a sub-directory of its own. Most are 2d models so that they run quickly, 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.*) and dump file (dump.*) when it runs. Some use a data file (data.*) of initial coordinates as additional input. 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.foo.P means it ran on P processors of machine "foo". For examples that use input data files, many of them were produced by `Pizza.py `_ or setup tools described in the :doc:`Additional Tools ` section of the LAMMPS documentation and provided with the LAMMPS distribution. 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 these examples can be viewed on the Movies section of the `LAMMPS WWW Site `_. These are the sample problems in the examples sub-directories: +-------------+----------------------------------------------------------------------------+ | 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 | +-------------+----------------------------------------------------------------------------+ | crack | crack propagation in a 2d solid | +-------------+----------------------------------------------------------------------------+ | cuda | use of the USER-CUDA package for GPU acceleration | +-------------+----------------------------------------------------------------------------+ | 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 | +-------------+----------------------------------------------------------------------------+ | gpu | use of the GPU package for GPU acceleration | +-------------+----------------------------------------------------------------------------+ | hugoniostat | Hugoniostat shock dynamics | +-------------+----------------------------------------------------------------------------+ | indent | spherical indenter into a 2d solid | +-------------+----------------------------------------------------------------------------+ | intel | use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor | +-------------+----------------------------------------------------------------------------+ | kim | use of potentials in Knowledge Base for Interatomic Models (KIM) | +-------------+----------------------------------------------------------------------------+ | line | line segment particles in 2d rigid bodies | +-------------+----------------------------------------------------------------------------+ | 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 | +-------------+----------------------------------------------------------------------------+ | qeq | use of the QEQ pacakge 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 | +-------------+----------------------------------------------------------------------------+ | tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si | +-------------+----------------------------------------------------------------------------+ | tri | triangular particles in rigid bodies | +-------------+----------------------------------------------------------------------------+ vashishta: models using the Vashishta potential Here is how you might 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 as follows: .. parsed-literal:: ../../tools/xmovie/xmovie -scale dump.indent If you uncomment the :doc:`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 :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 ---------- There is also a COUPLE directory with 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. There is also an ELASTIC directory with an example script for computing elastic constants at zero temperature, using an Si example. See the ELASTIC/in.elastic file for more info. There is also an ELASTIC_T directory with an example script for computing elastic constants at finite temperature, using an Si example. See the ELASTIC_T/in.elastic file for more info. There is also a USER directory which contains subdirectories of user-provided examples for user packages. See the README files in those directories for more info. See the :doc:`Section_start.html ` file for more info about user packages. .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm