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- <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
+<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
@@ -146,252 +20,111 @@ input script (in.*) and produces a log file (log.*) and dump file
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>If you uncomment the <a class="reference internal" href="dump.html"><em>dump</em></a> command in the input script, a
+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 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
+<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 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>Here is how you might run and visualize one of the sample problems:</p>
-<div class="highlight-python"><div class="highlight"><pre>cd indent
+<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 WIDTH="0%" 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></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
+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 class="reference internal" href="dump_image.html"><em>dump image</em></a> doc page for more details. E.g. this
+<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>
-<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
+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
+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>
-
-
- </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>
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diff --git a/doc/Section_example.txt b/doc/Section_example.txt
index 51aaf511c55aa54dc6b5a4396270e5d7f65d320b..3cbd54a9671f067358eac6e666c5a0c8eca3c94f 100644
--- a/doc/Section_example.txt
+++ b/doc/Section_example.txt
@@ -109,8 +109,12 @@ a library, either by itself or in tandem with another code or library.
See the COUPLE/README file to get started.
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.
+computing elastic constants at zero temperature, using an Si example. See
+the ELASTIC/in.elastic file for more info.
+
+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.
There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in