Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/_sources/Section_example.txt
caf9483a0a7clammm-master-deprecated

Last Change
Raw File

Section_example.txt
View Options

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 <dump>` command in the input script, a
text dump file will be produced, which can be animated by various
`visualization programs <http://lammps.sandia.gov/viz.html>`_. It can
also be animated using the xmovie tool described in the :doc:`Additional Tools <Section_tools>` section of the LAMMPS documentation.
If you uncomment the :doc:`dump image <dump>` 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 <dump_image>` doc page.
Animations of many of the examples can be viewed on the Movies section
of the `LAMMPS web site <lws_>`_.
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 <http://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
web site.
If you uncomment the :doc:`dump image <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 <Section_start>` 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 <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 <Section_packages>` doc
page for more info on specific USER packages.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help