Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/doc2/Section_example.html
787cc145e8e0efficient_neuronet

Last Change
Raw File

Section_example.html
View Options

<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>
<H3>7. Example problems
</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>
<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>.
</P>
<P>These are the sample problems in the examples sub-directories:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >balance</TD><TD > dynamic load balancing, 2d system</TD></TR>
<TR><TD >body</TD><TD > body particles, 2d system</TD></TR>
<TR><TD >colloid</TD><TD > big colloid particles in a small particle solvent, 2d system</TD></TR>
<TR><TD >comb</TD><TD > models using the COMB potential</TD></TR>
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >cuda</TD><TD > use of the USER-CUDA package for GPU acceleration</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
<TR><TD >dreiding</TD><TD > methanol via Dreiding FF</TD></TR>
<TR><TD >eim</TD><TD > NaCl using the EIM potential</TD></TR>
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
<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>
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
<TR><TD >intel</TD><TD > use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor</TD></TR>
<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>
<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>
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
<TR><TD >nb3b</TD><TD > use of nonbonded 3-body harmonic pair style</TD></TR>
<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
<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>
<TR><TD >peri</TD><TD > Peridynamic model of cylinder impacted by indenter</TD></TR>
<TR><TD >pour</TD><TD > pouring of granular particles into a 3d box, then chute flow</TD></TR>
<TR><TD >prd</TD><TD > parallel replica dynamics of vacancy diffusion in bulk Si</TD></TR>
<TR><TD >qeq</TD><TD > use of the QEQ pacakge for charge equilibration</TD></TR>
<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
<TR><TD >snap</TD><TD > NVE dynamics for BCC tantalum crystal using SNAP potential</TD></TR>
<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
</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 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>
<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>
<HR>
<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>
<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>
<P>There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in
those directories for more info. See the
<A HREF = "Section_start.html">Section_start.html</A> file for more info about user
packages.
</P>
</HTML>
c4science · Help