226 lines
15 KiB
ReStructuredText
226 lines
15 KiB
ReStructuredText
Example scripts
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===============
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The LAMMPS distribution includes an examples sub-directory with many
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sample problems. Many are 2d models that run quickly and are
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straightforward to visualize, requiring at most a couple of minutes to
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run on a desktop machine. Each problem has an input script (in.\*) and
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produces a log file (log.\*) when it runs. Some use a data file
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(data.\*) of initial coordinates as additional input. A few sample log
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file run on different machines and different numbers of processors are
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included in the directories to compare your answers to. E.g. a log
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file like log.date.crack.foo.P means the "crack" example was run on P
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processors of machine "foo" on that date (i.e. with that version of
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LAMMPS).
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Many of the input files have commented-out lines for creating dump
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files and image files.
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If you uncomment the :doc:`dump <dump>` command in the input script, a
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text dump file will be produced, which can be animated by various
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`visualization programs <https://lammps.sandia.gov/viz.html>`_.
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If you uncomment the :doc:`dump image <dump>` command in the input
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script, and assuming you have built LAMMPS with a JPG library, JPG
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snapshot images will be produced when the simulation runs. They can
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be quickly post-processed into a movie using commands described on the
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:doc:`dump image <dump_image>` doc page.
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Animations of many of the examples can be viewed on the Movies section
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of the `LAMMPS web site <https://lammps.sandia.gov/movies.html>`_.
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There are two kinds of sub-directories in the examples folder. Lower
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case named directories contain one or a few simple, quick-to-run
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problems. Upper case named directories contain up to several complex
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scripts that illustrate a particular kind of simulation method or
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model. Some of these run for longer times, e.g. to measure a
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particular quantity.
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Lists of both kinds of directories are given below.
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----------
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Lowercase directories
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---------------------
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+-------------+------------------------------------------------------------------+
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| accelerate | run with various acceleration options (OpenMP, GPU, Phi) |
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+-------------+------------------------------------------------------------------+
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| airebo | polyethylene with AIREBO potential |
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+-------------+------------------------------------------------------------------+
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| atm | Axilrod-Teller-Muto potential example |
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+-------------+------------------------------------------------------------------+
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| balance | dynamic load balancing, 2d system |
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+-------------+------------------------------------------------------------------+
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| body | body particles, 2d system |
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+-------------+------------------------------------------------------------------+
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| cmap | CMAP 5-body contributions to CHARMM force field |
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+-------------+------------------------------------------------------------------+
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| colloid | big colloid particles in a small particle solvent, 2d system |
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+-------------+------------------------------------------------------------------+
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| comb | models using the COMB potential |
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+-------------+------------------------------------------------------------------+
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| controller | use of fix controller as a thermostat |
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+-------------+------------------------------------------------------------------+
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| coreshell | core/shell model using CORESHELL package |
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+-------------+------------------------------------------------------------------+
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| crack | crack propagation in a 2d solid |
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+-------------+------------------------------------------------------------------+
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| deposit | deposit atoms and molecules on a surface |
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+-------------+------------------------------------------------------------------+
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| dipole | point dipolar particles, 2d system |
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+-------------+------------------------------------------------------------------+
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| dreiding | methanol via Dreiding FF |
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+-------------+------------------------------------------------------------------+
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| eim | NaCl using the EIM potential |
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+-------------+------------------------------------------------------------------+
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| ellipse | ellipsoidal particles in spherical solvent, 2d system |
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+-------------+------------------------------------------------------------------+
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| flow | Couette and Poiseuille flow in a 2d channel |
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+-------------+------------------------------------------------------------------+
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| friction | frictional contact of spherical asperities between 2d surfaces |
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+-------------+------------------------------------------------------------------+
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| gcmc | Grand Canonical Monte Carlo (GCMC) via the fix gcmc command |
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+-------------+------------------------------------------------------------------+
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| granregion | use of fix wall/region/gran as boundary on granular particles |
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+-------------+------------------------------------------------------------------+
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| hugoniostat | Hugoniostat shock dynamics |
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+-------------+------------------------------------------------------------------+
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| hyper | global and local hyperdynamics of diffusion on Pt surface |
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+-------------+------------------------------------------------------------------+
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| indent | spherical indenter into a 2d solid |
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+-------------+------------------------------------------------------------------+
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| kim | use of potentials from the `OpenKIM Repository <openkim_>`_ |
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+-------------+------------------------------------------------------------------+
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| latte | examples for using fix latte for DFTB via the LATTE library |
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+-------------+------------------------------------------------------------------+
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| meam | MEAM test for SiC and shear (same as shear examples) |
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+-------------+------------------------------------------------------------------+
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| melt | rapid melt of 3d LJ system |
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+-------------+------------------------------------------------------------------+
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| message | demos for LAMMPS client/server coupling with the MESSAGE package |
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+-------------+------------------------------------------------------------------+
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| micelle | self-assembly of small lipid-like molecules into 2d bilayers |
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+-------------+------------------------------------------------------------------+
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| min | energy minimization of 2d LJ melt |
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+-------------+------------------------------------------------------------------+
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| mscg | parameterize a multi-scale coarse-graining (MSCG) model |
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+-------------+------------------------------------------------------------------+
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| msst | MSST shock dynamics |
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+-------------+------------------------------------------------------------------+
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| nb3b | use of non-bonded 3-body harmonic pair style |
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+-------------+------------------------------------------------------------------+
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| neb | nudged elastic band (NEB) calculation for barrier finding |
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+-------------+------------------------------------------------------------------+
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| nemd | non-equilibrium MD of 2d sheared system |
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+-------------+------------------------------------------------------------------+
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| obstacle | flow around two voids in a 2d channel |
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+-------------+------------------------------------------------------------------+
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| peptide | dynamics of a small solvated peptide chain (5-mer) |
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+-------------+------------------------------------------------------------------+
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| peri | Peridynamic model of cylinder impacted by indenter |
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+-------------+------------------------------------------------------------------+
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| pour | pouring of granular particles into a 3d box, then chute flow |
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+-------------+------------------------------------------------------------------+
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| prd | parallel replica dynamics of vacancy diffusion in bulk Si |
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+-------------+------------------------------------------------------------------+
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| python | using embedded Python in a LAMMPS input script |
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+-------------+------------------------------------------------------------------+
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| qeq | use of the QEQ package for charge equilibration |
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+-------------+------------------------------------------------------------------+
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| rdf-adf | computing radial and angle distribution functions for water |
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+-------------+------------------------------------------------------------------+
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| reax | RDX and TATB models using the ReaxFF |
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+-------------+------------------------------------------------------------------+
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| rerun | use of rerun and read_dump commands |
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+-------------+------------------------------------------------------------------+
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| rigid | rigid bodies modeled as independent or coupled |
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+-------------+------------------------------------------------------------------+
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| shear | sideways shear applied to 2d solid, with and without a void |
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+-------------+------------------------------------------------------------------+
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| snap | NVE dynamics for BCC tantalum crystal using SNAP potential |
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+-------------+------------------------------------------------------------------+
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| srd | stochastic rotation dynamics (SRD) particles as solvent |
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+-------------+------------------------------------------------------------------+
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| streitz | use of Streitz/Mintmire potential with charge equilibration |
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+-------------+------------------------------------------------------------------+
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| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
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+-------------+------------------------------------------------------------------+
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| threebody | regression test input for a variety of manybody potentials |
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+-------------+------------------------------------------------------------------+
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| vashishta | use of the Vashishta potential |
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+-------------+------------------------------------------------------------------+
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| voronoi | Voronoi tesselation via compute voronoi/atom command |
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+-------------+------------------------------------------------------------------+
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Here is how you can run and visualize one of the sample problems:
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.. code-block:: bash
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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 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 of snapshots with a
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variety of third-party tools highlighted on the
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`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
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web site.
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If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
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script a series of JPG images will be produced by the run (assuming
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you built LAMMPS with JPG support; see the
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:doc:`Build_settings <Build_settings>` doc page for details). These can
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be viewed individually or turned into a movie or animated by tools
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like ImageMagick or QuickTime or various Windows-based tools. See the
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:doc:`dump image <dump_image>` doc page for more details. E.g. this
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Imagemagick command would create a GIF file suitable for viewing in a
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browser.
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.. code-block:: bash
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% convert -loop 1 *.jpg foo.gif
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----------
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Uppercase directories
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---------------------
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+------------+--------------------------------------------------------------------------------------------------+
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| ASPHERE | various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc |
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+------------+--------------------------------------------------------------------------------------------------+
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| COUPLE | examples of how to use LAMMPS as a library |
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+------------+--------------------------------------------------------------------------------------------------+
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| DIFFUSE | compute diffusion coefficients via several methods |
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+------------+--------------------------------------------------------------------------------------------------+
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| ELASTIC | compute elastic constants at zero temperature |
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+------------+--------------------------------------------------------------------------------------------------+
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| ELASTIC_T | compute elastic constants at finite temperature |
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+------------+--------------------------------------------------------------------------------------------------+
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| HEAT | compute thermal conductivity for LJ and water via fix ehex |
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+------------+--------------------------------------------------------------------------------------------------+
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| KAPPA | compute thermal conductivity via several methods |
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+------------+--------------------------------------------------------------------------------------------------+
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| MC | using LAMMPS in a Monte Carlo mode to relax the energy of a system |
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+------------+--------------------------------------------------------------------------------------------------+
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| SPIN | examples for features of the SPIN package |
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+------------+--------------------------------------------------------------------------------------------------+
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| UNITS | examples that run the same simulation in lj, real, metal units |
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+------------+--------------------------------------------------------------------------------------------------+
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| USER | examples for USER packages and USER-contributed commands |
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+------------+--------------------------------------------------------------------------------------------------+
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| VISCOSITY | compute viscosity via several methods |
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+------------+--------------------------------------------------------------------------------------------------+
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Nearly all of these directories have README files which give more
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details on how to understand and use their contents.
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The USER directory has a large number of sub-directories which
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correspond by name to a USER package. They contain scripts that
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illustrate how to use the command(s) provided in that package. Many
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of the sub-directories have their own README files which give further
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instructions. See the :doc:`Packages_details <Packages_details>` doc
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page for more info on specific USER packages.
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.. _openkim: https://openkim.org
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