171 lines
11 KiB
Plaintext
171 lines
11 KiB
Plaintext
Example problems
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================
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The LAMMPS distribution includes an examples sub-directory with
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several sample problems. Each problem is in a sub-directory of its
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own. Most are 2d models so that they run quickly, requiring at most a
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couple of minutes to run on a desktop machine. Each problem has an
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input script (in.*) and produces a log file (log.*) and dump file
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(dump.*) when it runs. Some use a data file (data.*) of initial
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coordinates as additional input. A few sample log file outputs on
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different machines and different numbers of processors are included in
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the directories to compare your answers to. E.g. a log file like
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log.crack.foo.P means it ran on P processors of machine "foo".
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For examples that use input data files, many of them were produced by
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`Pizza.py <http://pizza.sandia.gov>`_ or setup tools described in the
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:doc:`Additional Tools <Section_tools>` section of the LAMMPS
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documentation and provided with the LAMMPS distribution.
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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 <http://lammps.sandia.gov/viz.html>`_. It can
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also be animated using the xmovie tool described in the :doc:`Additional Tools <Section_tools>` section of the LAMMPS documentation.
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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 these examples can be viewed on the Movies
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section of the `LAMMPS WWW Site <lws_>`_.
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These are the sample problems in the examples sub-directories:
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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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| 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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| crack | crack propagation in a 2d solid |
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+-------------+----------------------------------------------------------------------------+
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| cuda | use of the USER-CUDA package for GPU acceleration |
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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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| gpu | use of the GPU package for GPU acceleration |
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+-------------+----------------------------------------------------------------------------+
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| hugoniostat | Hugoniostat shock dynamics |
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+-------------+----------------------------------------------------------------------------+
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| indent | spherical indenter into a 2d solid |
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+-------------+----------------------------------------------------------------------------+
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| intel | use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor |
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+-------------+----------------------------------------------------------------------------+
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| kim | use of potentials in Knowledge Base for Interatomic Models (KIM) |
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+-------------+----------------------------------------------------------------------------+
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| line | line segment particles in 2d rigid bodies |
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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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| 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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| msst | MSST shock dynamics |
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+-------------+----------------------------------------------------------------------------+
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| nb3b | use of nonbonded 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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| qeq | use of the QEQ pacakge for charge equilibration |
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+-------------+----------------------------------------------------------------------------+
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| reax | RDX and TATB models using the ReaxFF |
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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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| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
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+-------------+----------------------------------------------------------------------------+
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| tri | triangular particles in rigid bodies |
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+-------------+----------------------------------------------------------------------------+
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vashishta: models using the Vashishta potential
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Here is how you might run and visualize one of the sample problems:
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.. parsed-literal::
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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 as follows:
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.. parsed-literal::
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../../tools/xmovie/xmovie -scale dump.indent
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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. 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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.. parsed-literal::
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% convert -loop 1 *.jpg foo.gif
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----------
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There is also a COUPLE directory with examples of how to use LAMMPS as
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a library, either by itself or in tandem with another code or library.
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See the COUPLE/README file to get started.
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There is also an ELASTIC directory with an example script for
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computing elastic constants at zero temperature, using an Si example. See
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the ELASTIC/in.elastic file for more info.
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There is also an ELASTIC_T directory with an example script for
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computing elastic constants at finite temperature, using an Si example. See
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the ELASTIC_T/in.elastic file for more info.
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There is also a USER directory which contains subdirectories of
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user-provided examples for user packages. See the README files in
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those directories for more info. See the
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:doc:`Section_start.html <Section_start>` file for more info about user
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packages.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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