git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14724 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -80,7 +80,11 @@
|
||||
<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 current"><a class="current reference internal" href="">7. Example problems</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#lowercase-directories">7.1. Lowercase directories</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#uppercase-directories">7.2. Uppercase directories</a></li>
|
||||
</ul>
|
||||
</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>
|
||||
@ -137,20 +141,19 @@
|
||||
|
||||
<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
|
||||
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 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>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).</p>
|
||||
<p>Many of the input files have commented-out lines for creating dump
|
||||
files and image files.</p>
|
||||
<p>If you uncomment the <a class="reference internal" href="dump.html"><em>dump</em></a> command in the input script, a
|
||||
text dump file will be produced, which can be animated by various
|
||||
<a class="reference external" href="http://lammps.sandia.gov/viz.html">visualization programs</a>. It can
|
||||
@ -160,69 +163,77 @@ 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 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>
|
||||
<p>Animations of many of the examples can be viewed on the Movies section
|
||||
of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS web site</a>.</p>
|
||||
<p>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.</p>
|
||||
<p>Lists of both kinds of directories are given below.</p>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="lowercase-directories">
|
||||
<h2>7.1. Lowercase directories<a class="headerlink" href="#lowercase-directories" title="Permalink to this headline">¶</a></h2>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="15%" />
|
||||
<col width="85%" />
|
||||
<col width="16%" />
|
||||
<col width="84%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>balance</td>
|
||||
<tr class="row-odd"><td>accelerate</td>
|
||||
<td>run with various acceleration options (OpenMP, GPU, Phi)</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>balance</td>
|
||||
<td>dynamic load balancing, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>body</td>
|
||||
<tr class="row-odd"><td>body</td>
|
||||
<td>body particles, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>colloid</td>
|
||||
<tr class="row-even"><td>colloid</td>
|
||||
<td>big colloid particles in a small particle solvent, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>comb</td>
|
||||
<tr class="row-odd"><td>comb</td>
|
||||
<td>models using the COMB potential</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>coreshell</td>
|
||||
<td>core/shell model using CORESHELL package</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>
|
||||
<tr class="row-odd"><td>deposit</td>
|
||||
<td>deposit atoms and molecules on a surface</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>dipole</td>
|
||||
<td>point dipolar particles, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>dreiding</td>
|
||||
<tr class="row-odd"><td>dreiding</td>
|
||||
<td>methanol via Dreiding FF</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>eim</td>
|
||||
<tr class="row-even"><td>eim</td>
|
||||
<td>NaCl using the EIM potential</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>ellipse</td>
|
||||
<tr class="row-odd"><td>ellipse</td>
|
||||
<td>ellipsoidal particles in spherical solvent, 2d system</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>flow</td>
|
||||
<tr class="row-even"><td>flow</td>
|
||||
<td>Couette and Poiseuille flow in a 2d channel</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>friction</td>
|
||||
<tr class="row-odd"><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>
|
||||
<tr class="row-even"><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>
|
||||
@ -262,69 +273,108 @@ section of the <a class="reference external" href="http://lammps.sandia.gov">LAM
|
||||
<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>
|
||||
<tr class="row-even"><td>python</td>
|
||||
<td>using embedded Python in a LAMMPS input script</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>qeq</td>
|
||||
<td>use of the QEQ package for charge equilibration</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>reax</td>
|
||||
<tr class="row-even"><td>reax</td>
|
||||
<td>RDX and TATB models using the ReaxFF</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>rigid</td>
|
||||
<tr class="row-odd"><td>rigid</td>
|
||||
<td>rigid bodies modeled as independent or coupled</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>shear</td>
|
||||
<tr class="row-even"><td>shear</td>
|
||||
<td>sideways shear applied to 2d solid, with and without a void</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>snap</td>
|
||||
<tr class="row-odd"><td>snap</td>
|
||||
<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>srd</td>
|
||||
<tr class="row-even"><td>srd</td>
|
||||
<td>stochastic rotation dynamics (SRD) particles as solvent</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>streitz</td>
|
||||
<td>use of Streitz/Mintmire potential with charge equilibration</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 class="row-odd"><td>vashishta</td>
|
||||
<td>use of the Vashishta potential</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>
|
||||
<p>Here is how you can run and visualize one of the sample problems:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>cd indent
|
||||
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
|
||||
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>
|
||||
<em>log.lammps</em>. You can visualize the dump file of snapshots with a
|
||||
variety of 3rd-party tools highlighted on the
|
||||
<a class="reference external" href="http://lammps.sandia.gov/viz.html">Visualization</a> page of the LAMMPS
|
||||
web site.</p>
|
||||
<p>If you uncomment the <a class="reference internal" href="dump_image.html"><em>dump image</em></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
|
||||
script a series of JPG images will be produced by the run (assuming
|
||||
you built LAMMPS with JPG support; see <a class="reference internal" href="Section_start.html"><em>Section start 2.2</em></a> 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
|
||||
<a class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page for more details. E.g. this
|
||||
Imagemagick command would create a GIF file suitable for viewing in a
|
||||
browser.</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>% convert -loop 1 *.jpg foo.gif
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<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 at zero temperature, using an Si example. See
|
||||
the ELASTIC/in.elastic file for more info.</p>
|
||||
<p>There is also an ELASTIC_T directory with an example script for
|
||||
computing elastic constants at finite temperature, using an Si example. See
|
||||
the ELASTIC_T/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 class="reference internal" href="Section_start.html"><em>Section_start.html</em></a> file for more info about user
|
||||
packages.</p>
|
||||
<div class="section" id="uppercase-directories">
|
||||
<h2>7.2. Uppercase directories<a class="headerlink" href="#uppercase-directories" title="Permalink to this headline">¶</a></h2>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="10%" />
|
||||
<col width="90%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>ASPHERE</td>
|
||||
<td>various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>COUPLE</td>
|
||||
<td>examples of how to use LAMMPS as a library</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>DIFFUSE</td>
|
||||
<td>compute diffusion coefficients via several methods</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>ELASTIC</td>
|
||||
<td>compute elastic constants at zero temperature</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>ELASTIC_T</td>
|
||||
<td>compute elastic constants at finite temperature</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>KAPPA</td>
|
||||
<td>compute thermal conductivity via several methods</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>MC</td>
|
||||
<td>using LAMMPS in a Monte Carlo mode to relax the energy of a system</td>
|
||||
</tr>
|
||||
<tr class="row-even"><td>USER</td>
|
||||
<td>examples for USER packages and USER-contributed commands</td>
|
||||
</tr>
|
||||
<tr class="row-odd"><td>VISCOSITY</td>
|
||||
<td>compute viscosity via several methods</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Nearly all of these directories have README files which give more
|
||||
details on how to understand and use their contents.</p>
|
||||
<p>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 <a class="reference internal" href="Section_packages.html"><em>Section packages</em></a> doc
|
||||
page for more info on specific USER packages.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user