2006-09-22 00:22:34 +08:00
|
|
|
<HTML>
|
|
|
|
|
<CENTER><A HREF = "Section_howto.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_perf.html">Next Section</A>
|
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
2011-08-26 00:17:31 +08:00
|
|
|
<H3>7. Example problems
|
2006-09-22 00:22:34 +08:00
|
|
|
</H3>
|
|
|
|
|
<P>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".
|
|
|
|
|
</P>
|
2013-02-01 04:12:57 +08:00
|
|
|
<P>For examples that use input data files, many of them were produced by
|
|
|
|
|
<A HREF = "http://pizza.sandia.gov">Pizza.py</A> or setup tools described in the
|
|
|
|
|
<A HREF = "Section_tools.html">Additional Tools</A> section of the LAMMPS
|
|
|
|
|
documentation and provided with the LAMMPS distribution.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If you uncomment the <A HREF = "dump.html">dump</A> command in the input script, a
|
|
|
|
|
text dump file will be produced, which can be animated by various
|
|
|
|
|
<A HREF = "http://lammps.sandia.gov/viz.html">visualization programs</A>. It can
|
|
|
|
|
also be animated using the xmovie tool described in the <A HREF = "Section_tools.html">Additional
|
|
|
|
|
Tools</A> section of the LAMMPS documentation.
|
|
|
|
|
</P>
|
|
|
|
|
<P>If you uncomment the <A HREF = "dump.html">dump image</A> 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
|
|
|
|
|
<A HREF = "dump_image.html">dump image</A> doc page.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Animations of many of these examples can be viewed on the Movies
|
|
|
|
|
section of the <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A>.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>These are the sample problems in the examples sub-directories:
|
|
|
|
|
</P>
|
2010-05-14 23:10:38 +08:00
|
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
2014-08-09 06:01:22 +08:00
|
|
|
<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
|
2013-02-01 03:46:51 +08:00
|
|
|
<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
|
2010-09-07 00:56:31 +08:00
|
|
|
<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
|
|
|
|
|
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
|
2013-02-01 03:46:51 +08:00
|
|
|
<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
|
2010-09-07 00:56:31 +08:00
|
|
|
<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
|
2008-03-01 09:13:20 +08:00
|
|
|
<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
|
2013-02-01 03:46:51 +08:00
|
|
|
<TR><TD >gpu</TD><TD > use of the GPU package for GPU acceleration</TD></TR>
|
|
|
|
|
<TR><TD >hugoniostat</TD><TD > Hugoniostat shock dynamics</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
|
2013-02-01 03:46:51 +08:00
|
|
|
<TR><TD >kim</TD><TD > use of potentials in Knowledge Base for Interatomic Models (KIM)</TD></TR>
|
|
|
|
|
<TR><TD >line</TD><TD > line segment particles in 2d rigid bodies</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
|
|
|
|
|
<TR><TD >melt</TD><TD > rapid melt of 3d LJ system</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
|
2010-09-07 00:56:31 +08:00
|
|
|
<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
|
2010-10-02 00:18:09 +08:00
|
|
|
<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
|
2007-06-23 07:41:35 +08:00
|
|
|
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
|
|
|
|
|
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
|
2010-09-07 00:56:31 +08:00
|
|
|
<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
|
2013-02-01 03:46:51 +08:00
|
|
|
<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
|
2010-09-07 00:56:31 +08:00
|
|
|
<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
|
2006-09-22 00:22:34 +08:00
|
|
|
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
|
2010-10-02 00:18:09 +08:00
|
|
|
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
|
2013-02-01 03:46:51 +08:00
|
|
|
<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent</TD></TR>
|
|
|
|
|
<TR><TD >tad</TD><TD > temperature-accelerated dynamics of vacancy diffusion in bulk Si</TD></TR>
|
|
|
|
|
<TR><TD >tri</TD><TD > triangular particles in rigid bodies
|
2006-09-22 00:22:34 +08:00
|
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
|
|
|
|
|
|
<P>Here is how you might run and visualize one of the sample problems:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>cd indent
|
|
|
|
|
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
|
|
|
|
|
lmp_linux < in.indent # run the problem
|
|
|
|
|
</PRE>
|
|
|
|
|
<P>Running the simulation produces the files <I>dump.indent</I> and
|
|
|
|
|
<I>log.lammps</I>. You can visualize the dump file as follows:
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>../../tools/xmovie/xmovie -scale dump.indent
|
|
|
|
|
</PRE>
|
2013-02-01 04:12:57 +08:00
|
|
|
<P>If you uncomment the <A HREF = "dump_image.html">dump image</A> 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
|
|
|
|
|
<A HREF = "dump_image.html">dump image</A> doc page for more details. E.g. this
|
|
|
|
|
Imagemagick command would create a GIF file suitable for viewing in a
|
|
|
|
|
browser.
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>% convert -loop 1 *.jpg foo.gif
|
|
|
|
|
</PRE>
|
2010-09-07 01:21:53 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2013-02-01 04:12:57 +08:00
|
|
|
<P>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.
|
|
|
|
|
</P>
|
2010-09-07 01:21:53 +08:00
|
|
|
<P>There is also an ELASTIC directory with an example script for
|
|
|
|
|
computing elastic constants, using a zero temperature Si example. See
|
|
|
|
|
the in.elastic file for more info.
|
|
|
|
|
</P>
|
2010-09-07 00:56:31 +08:00
|
|
|
<P>There is also a USER directory which contains subdirectories of
|
|
|
|
|
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
|
|
|
|
|
<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
|
|
|
|
|
packages.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
</HTML>
|
