2006-09-22 00:22:34 +08:00
2015-10-22 02:53:15 +08:00
<!DOCTYPE html>
<!-- [if IE 8]><html class="no - js lt - ie9" lang="en" > <![endif] -->
<!-- [if gt IE 8]><! --> < html class = "no-js" lang = "en" > <!-- <![endif] -->
< head >
< meta charset = "utf-8" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
2015-12-21 23:20:41 +08:00
< title > 7. Example problems — LAMMPS documentation< / title >
2015-10-22 02:53:15 +08:00
2006-09-22 00:22:34 +08:00
2015-10-22 02:53:15 +08:00
2006-09-22 00:22:34 +08:00
2015-10-22 02:53:15 +08:00
2006-09-22 00:22:34 +08:00
2015-10-22 02:53:15 +08:00
2006-09-22 00:22:34 +08:00
2015-10-22 02:53:15 +08:00
2006-09-22 00:22:34 +08:00
2015-10-22 02:53:15 +08:00
< link rel = "stylesheet" href = "_static/css/theme.css" type = "text/css" / >
< link rel = "stylesheet" href = "_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type = "text/css" / >
2015-12-21 23:20:41 +08:00
< link rel = "top" title = "LAMMPS documentation" href = "index.html" / >
2015-10-22 02:53:15 +08:00
< link rel = "next" title = "8. Performance & scalability" href = "Section_perf.html" / >
< link rel = "prev" title = "6. How-to discussions" href = "Section_howto.html" / >
< script src = "_static/js/modernizr.min.js" > < / script >
< / head >
< body class = "wy-body-for-nav" role = "document" >
< div class = "wy-grid-for-nav" >
< nav data-toggle = "wy-nav-shift" class = "wy-nav-side" >
< div class = "wy-side-nav-search" >
< a href = "Manual.html" class = "icon icon-home" > LAMMPS
< / a >
< div role = "search" >
< form id = "rtd-search-form" class = "wy-form" action = "search.html" method = "get" >
< input type = "text" name = "q" placeholder = "Search docs" / >
< input type = "hidden" name = "check_keywords" value = "yes" / >
< input type = "hidden" name = "area" value = "default" / >
< / form >
< / div >
< / div >
< div class = "wy-menu wy-menu-vertical" data-spy = "affix" role = "navigation" aria-label = "main navigation" >
< ul class = "current" >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_commands.html" > 3. Commands< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_packages.html" > 4. Packages< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_howto.html" > 6. How-to discussions< / a > < / li >
< li class = "toctree-l1 current" > < a class = "current reference internal" href = "" > 7. Example problems< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_perf.html" > 8. Performance & scalability< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_tools.html" > 9. Additional tools< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_errors.html" > 12. Errors< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_history.html" > 13. Future and history< / a > < / li >
< / ul >
< / div >
< / nav >
< section data-toggle = "wy-nav-shift" class = "wy-nav-content-wrap" >
< nav class = "wy-nav-top" role = "navigation" aria-label = "top navigation" >
< i data-toggle = "wy-nav-top" class = "fa fa-bars" > < / i >
< a href = "Manual.html" > LAMMPS< / a >
< / nav >
< div class = "wy-nav-content" >
< div class = "rst-content" >
< div role = "navigation" aria-label = "breadcrumbs navigation" >
< ul class = "wy-breadcrumbs" >
< li > < a href = "Manual.html" > Docs< / a > » < / li >
< li > 7. Example problems< / li >
< li class = "wy-breadcrumbs-aside" >
< a href = "http://lammps.sandia.gov" > Website< / a >
< a href = "Section_commands.html#comm" > Commands< / a >
< / li >
< / ul >
< hr / >
< div class = "rst-footer-buttons" style = "margin-bottom: 1em" role = "navigation" aria-label = "footer navigation" >
< a href = "Section_perf.html" class = "btn btn-neutral float-right" title = "8. Performance & scalability" accesskey = "n" > Next < span class = "fa fa-arrow-circle-right" > < / span > < / a >
< a href = "Section_howto.html" class = "btn btn-neutral" title = "6. How-to discussions" accesskey = "p" > < span class = "fa fa-arrow-circle-left" > < / span > Previous< / a >
< / div >
< / div >
< div role = "main" class = "document" itemscope = "itemscope" itemtype = "http://schema.org/Article" >
< div itemprop = "articleBody" >
< div class = "section" id = "example-problems" >
< h1 > 7. Example problems< a class = "headerlink" href = "#example-problems" title = "Permalink to this headline" > ¶< / a > < / h1 >
< p > The LAMMPS distribution includes an examples sub-directory with
2006-09-22 00:22:34 +08:00
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
2015-10-22 02:53:15 +08:00
log.crack.foo.P means it ran on P processors of machine “ foo” .< / p >
< p > For examples that use input data files, many of them were produced by
< a class = "reference external" href = "http://pizza.sandia.gov" > Pizza.py< / a > or setup tools described in the
< a class = "reference internal" href = "Section_tools.html" > < em > Additional Tools< / em > < / a > section of the LAMMPS
documentation and provided with the LAMMPS distribution.< / p >
< p > If you uncomment the < a class = "reference internal" href = "dump.html" > < em > dump< / em > < / a > command in the input script, a
2013-02-01 04:12:57 +08:00
text dump file will be produced, which can be animated by various
2015-10-22 02:53:15 +08:00
< a class = "reference external" href = "http://lammps.sandia.gov/viz.html" > visualization programs< / a > . It can
also be animated using the xmovie tool described in the < a class = "reference internal" href = "Section_tools.html" > < em > Additional Tools< / em > < / a > section of the LAMMPS documentation.< / p >
< p > If you uncomment the < a class = "reference internal" href = "dump.html" > < em > dump image< / em > < / a > command in the input
2013-02-01 04:12:57 +08:00
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
2015-10-22 02:53:15 +08:00
< a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > doc page.< / p >
< p > Animations of many of these examples can be viewed on the Movies
section of the < a class = "reference external" href = "http://lammps.sandia.gov" > LAMMPS WWW Site< / a > .< / p >
< p > These are the sample problems in the examples sub-directories:< / p >
< table border = "1" class = "docutils" >
< colgroup >
< col width = "15%" / >
< col width = "85%" / >
< / colgroup >
< tbody valign = "top" >
< tr class = "row-odd" > < td > balance< / td >
< td > dynamic load balancing, 2d system< / td >
< / tr >
< tr class = "row-even" > < td > body< / td >
< td > body particles, 2d system< / td >
< / tr >
< tr class = "row-odd" > < td > colloid< / td >
< td > big colloid particles in a small particle solvent, 2d system< / td >
< / tr >
< tr class = "row-even" > < td > comb< / td >
< td > models using the COMB potential< / td >
< / tr >
< tr class = "row-odd" > < td > crack< / td >
< td > crack propagation in a 2d solid< / td >
< / tr >
< tr class = "row-even" > < td > cuda< / td >
< td > use of the USER-CUDA package for GPU acceleration< / td >
< / tr >
< tr class = "row-odd" > < td > dipole< / td >
< td > point dipolar particles, 2d system< / td >
< / tr >
< tr class = "row-even" > < td > dreiding< / td >
< td > methanol via Dreiding FF< / td >
< / tr >
< tr class = "row-odd" > < td > eim< / td >
< td > NaCl using the EIM potential< / td >
< / tr >
< tr class = "row-even" > < td > ellipse< / td >
< td > ellipsoidal particles in spherical solvent, 2d system< / td >
< / tr >
< tr class = "row-odd" > < td > flow< / td >
< td > Couette and Poiseuille flow in a 2d channel< / td >
< / tr >
< tr class = "row-even" > < td > friction< / td >
< td > frictional contact of spherical asperities between 2d surfaces< / td >
< / tr >
< tr class = "row-odd" > < td > gpu< / td >
< td > use of the GPU package for GPU acceleration< / td >
< / tr >
< tr class = "row-even" > < td > hugoniostat< / td >
< td > Hugoniostat shock dynamics< / td >
< / tr >
< tr class = "row-odd" > < td > indent< / td >
< td > spherical indenter into a 2d solid< / td >
< / tr >
< tr class = "row-even" > < td > intel< / td >
< td > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor< / td >
< / tr >
< tr class = "row-odd" > < td > kim< / td >
< td > use of potentials in Knowledge Base for Interatomic Models (KIM)< / td >
< / tr >
< tr class = "row-even" > < td > line< / td >
< td > line segment particles in 2d rigid bodies< / td >
< / tr >
< tr class = "row-odd" > < td > meam< / td >
< td > MEAM test for SiC and shear (same as shear examples)< / td >
< / tr >
< tr class = "row-even" > < td > melt< / td >
< td > rapid melt of 3d LJ system< / td >
< / tr >
< tr class = "row-odd" > < td > micelle< / td >
< td > self-assembly of small lipid-like molecules into 2d bilayers< / td >
< / tr >
< tr class = "row-even" > < td > min< / td >
< td > energy minimization of 2d LJ melt< / td >
< / tr >
< tr class = "row-odd" > < td > msst< / td >
< td > MSST shock dynamics< / td >
< / tr >
< tr class = "row-even" > < td > nb3b< / td >
< td > use of nonbonded 3-body harmonic pair style< / td >
< / tr >
< tr class = "row-odd" > < td > neb< / td >
< td > nudged elastic band (NEB) calculation for barrier finding< / td >
< / tr >
< tr class = "row-even" > < td > nemd< / td >
< td > non-equilibrium MD of 2d sheared system< / td >
< / tr >
< tr class = "row-odd" > < td > obstacle< / td >
< td > flow around two voids in a 2d channel< / td >
< / tr >
< tr class = "row-even" > < td > peptide< / td >
< td > dynamics of a small solvated peptide chain (5-mer)< / td >
< / tr >
< tr class = "row-odd" > < td > peri< / td >
< td > Peridynamic model of cylinder impacted by indenter< / td >
< / tr >
< tr class = "row-even" > < td > pour< / td >
< td > pouring of granular particles into a 3d box, then chute flow< / td >
< / tr >
< tr class = "row-odd" > < td > prd< / td >
< td > parallel replica dynamics of vacancy diffusion in bulk Si< / td >
< / tr >
< tr class = "row-even" > < td > qeq< / td >
< td > use of the QEQ pacakge for charge equilibration< / td >
< / tr >
< tr class = "row-odd" > < td > reax< / td >
< td > RDX and TATB models using the ReaxFF< / td >
< / tr >
< tr class = "row-even" > < td > rigid< / td >
< td > rigid bodies modeled as independent or coupled< / td >
< / tr >
< tr class = "row-odd" > < td > shear< / td >
< td > sideways shear applied to 2d solid, with and without a void< / td >
< / tr >
< tr class = "row-even" > < td > snap< / td >
< td > NVE dynamics for BCC tantalum crystal using SNAP potential< / td >
< / tr >
< tr class = "row-odd" > < td > srd< / td >
< td > stochastic rotation dynamics (SRD) particles as solvent< / td >
< / tr >
< tr class = "row-even" > < td > tad< / td >
< td > temperature-accelerated dynamics of vacancy diffusion in bulk Si< / td >
< / tr >
< tr class = "row-odd" > < td > tri< / td >
< td > triangular particles in rigid bodies< / td >
< / tr >
< / tbody >
< / table >
< p > vashishta: models using the Vashishta potential< / p >
< p > Here is how you might run and visualize one of the sample problems:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > cd indent
2006-09-22 00:22:34 +08:00
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
2015-10-22 02:53:15 +08:00
lmp_linux -in in.indent # run the problem
< / pre > < / div >
< / div >
< p > Running the simulation produces the files < em > dump.indent< / em > and
< em > log.lammps< / em > . You can visualize the dump file as follows:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > ../../tools/xmovie/xmovie -scale dump.indent
< / pre > < / div >
< / div >
< p > If you uncomment the < a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > line(s) in the input
2013-02-01 04:12:57 +08:00
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
2015-10-22 02:53:15 +08:00
< a class = "reference internal" href = "dump_image.html" > < em > dump image< / em > < / a > doc page for more details. E.g. this
2013-02-01 04:12:57 +08:00
Imagemagick command would create a GIF file suitable for viewing in a
2015-10-22 02:53:15 +08:00
browser.< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > % convert -loop 1 *.jpg foo.gif
< / pre > < / div >
< / div >
< hr class = "docutils" / >
< p > There is also a COUPLE directory with examples of how to use LAMMPS as
2013-02-01 04:12:57 +08:00
a library, either by itself or in tandem with another code or library.
2015-10-22 02:53:15 +08:00
See the COUPLE/README file to get started.< / p >
< p > There is also an ELASTIC directory with an example script for
2015-10-06 02:25:21 +08:00
computing elastic constants at zero temperature, using an Si example. See
2015-10-22 02:53:15 +08:00
the ELASTIC/in.elastic file for more info.< / p >
< p > There is also an ELASTIC_T directory with an example script for
2015-10-06 02:25:21 +08:00
computing elastic constants at finite temperature, using an Si example. See
2015-10-22 02:53:15 +08:00
the ELASTIC_T/in.elastic file for more info.< / p >
< p > There is also a USER directory which contains subdirectories of
2010-09-07 00:56:31 +08:00
user-provided examples for user packages. See the README files in
2013-03-11 22:51:34 +08:00
those directories for more info. See the
2015-10-22 02:53:15 +08:00
< a class = "reference internal" href = "Section_start.html" > < em > Section_start.html< / em > < / a > file for more info about user
packages.< / p >
< / div >
< / div >
< / div >
< footer >
< div class = "rst-footer-buttons" role = "navigation" aria-label = "footer navigation" >
< a href = "Section_perf.html" class = "btn btn-neutral float-right" title = "8. Performance & scalability" accesskey = "n" > Next < span class = "fa fa-arrow-circle-right" > < / span > < / a >
< a href = "Section_howto.html" class = "btn btn-neutral" title = "6. How-to discussions" accesskey = "p" > < span class = "fa fa-arrow-circle-left" > < / span > Previous< / a >
< / div >
< hr / >
< div role = "contentinfo" >
< p >
2015-12-11 01:23:56 +08:00
© Copyright 2013 Sandia Corporation.
2015-10-22 02:53:15 +08:00
< / p >
< / div >
Built with < a href = "http://sphinx-doc.org/" > Sphinx< / a > using a < a href = "https://github.com/snide/sphinx_rtd_theme" > theme< / a > provided by < a href = "https://readthedocs.org" > Read the Docs< / a > .
< / footer >
< / div >
< / div >
< / section >
< / div >
< script type = "text/javascript" >
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
2015-12-21 23:20:41 +08:00
VERSION:'',
2015-10-22 02:53:15 +08:00
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
< / script >
< script type = "text/javascript" src = "_static/jquery.js" > < / script >
< script type = "text/javascript" src = "_static/underscore.js" > < / script >
< script type = "text/javascript" src = "_static/doctools.js" > < / script >
< script type = "text/javascript" src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js" > < / script >
< script type = "text/javascript" src = "_static/js/theme.js" > < / script >
< script type = "text/javascript" >
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
< / script >
< / body >
< / html >
