forked from lijiext/lammps
Merge pull request #23 from akohlmey/doc-corrections-and-updates
Doc corrections and updates
This commit is contained in:
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GitHub
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5d0da95a0b
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@ -141,7 +141,9 @@
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<h2>Version info:</h2>
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<p>The LAMMPS “version” is the date when it was released, such as 1 May
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2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
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feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Each dated copy of LAMMPS contains all the
|
||||
feature, we release it immediately, and post a notice on <a class="reference external" href="http://lammps.sandia.gov/bug.html">this page of the WWW site</a>. Every 2-4 months one of the incremental releases
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is subjected to more thorough testing and labeled as a <em>stable</em> version.</p>
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<p>Each dated copy of LAMMPS contains all the
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features and bug-fixes up to and including that version date. The
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version date is printed to the screen and logfile every time you run
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LAMMPS. It is also in the file src/version.h and in the LAMMPS
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@ -166,11 +168,20 @@ run efficiently on parallel computers. It was developed at Sandia
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National Laboratories, a US Department of Energy facility, with
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funding from the DOE. It is an open-source code, distributed freely
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under the terms of the GNU Public License (GPL).</p>
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<p>The primary developers of LAMMPS are <a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, Aidan
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Thompson, and Paul Crozier who can be contacted at
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sjplimp,athomps,pscrozi at sandia.gov. The <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW Site</a> at
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<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information about the code and its
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uses.</p>
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<p>The current core group of LAMMPS developers is at Sandia National
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Labs and Temple University:</p>
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<ul class="simple">
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<li><a class="reference external" href="http://www.sandia.gov/~sjplimp">Steve Plimpton</a>, sjplimp at sandia.gov</li>
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<li>Aidan Thompson, athomps at sandia.gov</li>
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<li>Stan Moore, stamoore at sandia.gov</li>
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<li><a class="reference external" href="http://goo.gl/1wk0">Axel Kohlmeyer</a>, akohlmey at gmail.com</li>
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</ul>
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<p>Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
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all at Sandia. The <strong>LAMMPS home page</strong> at
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<a class="reference external" href="http://lammps.sandia.gov">http://lammps.sandia.gov</a> has more information
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about the code and its uses. Interaction with external LAMMPS developers,
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bug reports and feature requests are mainly coordinated through the
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<a class="reference external" href="https://github.com/lammps/lammps">LAMMPS project on GitHub.</a></p>
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<hr class="docutils" />
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<p>The LAMMPS documentation is organized into the following sections. If
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you find errors or omissions in this manual or have suggestions for
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|
|
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@ -346,8 +346,8 @@ package and are explained in the individual accelerator doc pages,
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listed above:</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="26%" />
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<col width="74%" />
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<col width="64%" />
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<col width="36%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>build the accelerator library</td>
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@ -356,40 +356,24 @@ listed above:</p>
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<tr class="row-even"><td>install the accelerator package</td>
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<td>make yes-opt, make yes-user-intel, etc</td>
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</tr>
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</tbody>
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</table>
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<div class="line-block">
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<div class="line">install the accelerator package | make yes-opt, make yes-user-intel, etc |</div>
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</div>
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<blockquote>
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<div>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |</div></blockquote>
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<table border="1" class="docutils">
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<colgroup>
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<col width="26%" />
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<col width="74%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>re-build LAMMPS</td>
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<tr class="row-odd"><td>add compile/link flags to Makefile.machine in src/MAKE</td>
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<td>only for USER-INTEL, KOKKOS, USER-OMP, OPT packages</td>
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</tr>
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<tr class="row-even"><td>re-build LAMMPS</td>
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<td>make machine</td>
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</tr>
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</tbody>
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</table>
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<div class="line-block">
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<div class="line">re-build LAMMPS | make machine |</div>
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</div>
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<blockquote>
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<div>mpirun -np 32 lmp_machine -in in.script |</div></blockquote>
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<blockquote>
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<div>only for KOKKOS package |</div></blockquote>
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<blockquote>
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<div><a class="reference internal" href="package.html"><span class="doc">package</span></a> command, <br>
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only if defaults need to be changed |</div></blockquote>
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<blockquote>
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<div><a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command |</div></blockquote>
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<table border="1" class="docutils">
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<colgroup>
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>prepare and test a regular LAMMPS simulation</td>
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<td>lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script</td>
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</tr>
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<tr class="row-even"><td>enable specific accelerator support via ‘-k on’ <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>,</td>
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<td>only needed for KOKKOS package</td>
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</tr>
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<tr class="row-odd"><td>set any needed options for the package via “-pk” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="package.html"><span class="doc">package</span></a> command,</td>
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<td>only if defaults need to be changed</td>
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</tr>
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<tr class="row-even"><td>use accelerated styles in your input via “-sf” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command</td>
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<td>lmp_machine -in in.script -sf gpu</td>
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</tr>
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</tbody>
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</table>
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<p>Note that the first 4 steps can be done as a single command, using the
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@ -528,7 +512,7 @@ full 16 lanes to each of the PCIe 2.0 16x slots.</li>
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<li>The GPU package accelerates only pair force, neighbor list, and PPPM
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calculations.</li>
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<li>The GPU package requires neighbor lists to be built on the CPU when using
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exclusion lists or a triclinic simulation box.</li>
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exclusion lists, hybrid pair styles, or a triclinic simulation box.</li>
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</ul>
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</div>
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</div>
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|
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@ -247,15 +247,15 @@ inside the parenthesis is treated as an “immediate” variable and
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evaluated as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>. This is a way
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to use numeric formulas in an input script without having to assign
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them to variable names. For example, these 3 input script lines:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span>variable X equal (xlo+xhi)/2+sqrt(v_area)
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<pre class="literal-block">
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variable X equal (xlo+xhi)/2+sqrt(v_area)
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region 1 block $X 2 INF INF EDGE EDGE
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variable X delete
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</pre></div>
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</div>
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</pre>
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<p>can be replaced by</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
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</pre></div>
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</div>
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<pre class="literal-block">
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region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
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</pre>
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<p>so that you do not have to define (or discard) a temporary variable X.</p>
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<p>Note that neither the curly-bracket or immediate form of variables can
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contain nested $ characters for other variables to substitute for.
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|
|
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@ -486,8 +486,7 @@ be computed.</dd>
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<dt><em>Bad TIP4P bond type for PPPMDisp/TIP4P</em></dt>
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<dd>Specified bond type is not valid.</dd>
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<dt><em>Bad fix ID in fix append/atoms command</em></dt>
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<dd>The value of the fix_id for keyword spatial must start with the suffix
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<a href="#id6"><span class="problematic" id="id7">f_</span></a>.</dd>
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<dd>The value of the fix_id for keyword spatial must start with ‘f_’.</dd>
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<dt><em>Bad grid of processors</em></dt>
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<dd>The 3d grid of processors defined by the processors command does not
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match the number of processors LAMMPS is being run on.</dd>
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@ -6359,13 +6358,13 @@ have an infinite periodic crystal with bonds then it is impossible to
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have fully consistent image flags, since some bonds will cross
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periodic boundaries and connect two atoms with the same image
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flag.</dd>
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<dt><em>KIM Model does not provide `energy’; Potential energy will be zero</em></dt>
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<dt><em>KIM Model does not provide ‘energy’; Potential energy will be zero</em></dt>
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<dd>Self-explanatory.</dd>
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<dt><em>KIM Model does not provide `forces’; Forces will be zero</em></dt>
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<dt><em>KIM Model does not provide ‘forces’; Forces will be zero</em></dt>
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<dd>Self-explanatory.</dd>
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<dt><em>KIM Model does not provide `particleEnergy’; energy per atom will be zero</em></dt>
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<dt><em>KIM Model does not provide ‘particleEnergy’; energy per atom will be zero</em></dt>
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<dd>Self-explanatory.</dd>
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<dt><em>KIM Model does not provide `particleVirial’; virial per atom will be zero</em></dt>
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<dt><em>KIM Model does not provide ‘particleVirial’; virial per atom will be zero</em></dt>
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<dd>Self-explanatory.</dd>
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<dt><em>Kspace_modify slab param < 2.0 may cause unphysical behavior</em></dt>
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<dd>The kspace_modify slab parameter should be larger to insure periodic
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|
|
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@ -303,11 +303,11 @@ longer times, e.g. to measure a particular quantity.</p>
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</tbody>
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||||
</table>
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<p>Here is how you can run and visualize one of the sample problems:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">indent</span>
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<span class="n">cp</span> <span class="o">../../</span><span class="n">src</span><span class="o">/</span><span class="n">lmp_linux</span> <span class="o">.</span> <span class="c1"># copy LAMMPS executable to this dir</span>
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<span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">indent</span> <span class="c1"># run the problem</span>
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</pre></div>
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</div>
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||||
<pre class="literal-block">
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||||
cd indent
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cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
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lmp_linux -in in.indent # run the problem
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||||
</pre>
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||||
<p>Running the simulation produces the files <em>dump.indent</em> and
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||||
<em>log.lammps</em>. You can visualize the dump file of snapshots with a
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variety of 3rd-party tools highlighted on the
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||||
|
|
@ -321,17 +321,17 @@ ImageMagick or QuickTime or various Windows-based tools. See the
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|||
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for more details. E.g. this
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||||
Imagemagick command would create a GIF file suitable for viewing in a
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||||
browser.</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
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||||
</pre></div>
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||||
</div>
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||||
<pre class="literal-block">
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||||
% convert -loop 1 *.jpg foo.gif
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</pre>
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||||
</div>
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||||
<hr class="docutils" />
|
||||
<div class="section" id="uppercase-directories">
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||||
<h2>7.2. Uppercase directories</h2>
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||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="10%" />
|
||||
<col width="90%" />
|
||||
<col width="11%" />
|
||||
<col width="89%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
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<tr class="row-odd"><td>ASPHERE</td>
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|
|
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@ -252,13 +252,13 @@ scripts are based on. If that script had the line</p>
|
|||
and tmp.restart.100) as it ran.</p>
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||||
<p>This script could be used to read the 1st restart file and re-run the
|
||||
last 50 timesteps:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_restart</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="mi">50</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="mf">0.4</span> <span class="nb">bin</span>
|
||||
<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
read_restart tmp.restart.50
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
neighbor 0.4 bin
|
||||
neigh_modify every 1 delay 1
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
|
||||
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span>
|
||||
</pre></div>
|
||||
|
|
@ -281,25 +281,25 @@ notice that the thermodynamic data match at step 50 (if you also put a
|
|||
uses random numbers in a way that does not allow for perfect restarts.</p>
|
||||
<p>As an alternate approach, the restart file could be converted to a data
|
||||
file as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">r</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="mi">50</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">data</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_g++ -r tmp.restart.50 tmp.restart.data
|
||||
</pre>
|
||||
<p>Then, this script could be used to re-run the last 50 steps:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span>
|
||||
<span class="n">atom_style</span> <span class="n">bond</span>
|
||||
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.12</span>
|
||||
<span class="n">pair_modify</span> <span class="n">shift</span> <span class="n">yes</span>
|
||||
<span class="n">bond_style</span> <span class="n">fene</span>
|
||||
<span class="n">special_bonds</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_data</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">data</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="mf">0.4</span> <span class="nb">bin</span>
|
||||
<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
units lj
|
||||
atom_style bond
|
||||
pair_style lj/cut 1.12
|
||||
pair_modify shift yes
|
||||
bond_style fene
|
||||
special_bonds 0.0 1.0 1.0
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
read_data tmp.restart.data
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
neighbor 0.4 bin
|
||||
neigh_modify every 1 delay 1
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
|
||||
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span>
|
||||
</pre></div>
|
||||
|
|
@ -307,10 +307,10 @@ file as follows:</p>
|
|||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span> <span class="mf">0.012</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">reset_timestep</span> <span class="mi">50</span>
|
||||
<span class="n">run</span> <span class="mi">50</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
reset_timestep 50
|
||||
run 50
|
||||
</pre>
|
||||
<p>Note that nearly all the settings specified in the original <em>in.chain</em>
|
||||
script must be repeated, except the <em>pair_coeff</em> and <em>bond_coeff</em>
|
||||
commands since the new data file lists the force field coefficients.
|
||||
|
|
@ -420,39 +420,40 @@ individual commands for more details on how these examples work.</p>
|
|||
<p>If “multiple simulations” means continue a previous simulation for
|
||||
more timesteps, then you simply use the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command
|
||||
multiple times. For example, this script</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span>
|
||||
<span class="n">atom_style</span> <span class="n">atomic</span>
|
||||
<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span>
|
||||
<span class="n">run</span> <span class="mi">10000</span>
|
||||
<span class="n">run</span> <span class="mi">10000</span>
|
||||
<span class="n">run</span> <span class="mi">10000</span>
|
||||
<span class="n">run</span> <span class="mi">10000</span>
|
||||
<span class="n">run</span> <span class="mi">10000</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
units lj
|
||||
atom_style atomic
|
||||
read_data data.lj
|
||||
run 10000
|
||||
run 10000
|
||||
run 10000
|
||||
run 10000
|
||||
run 10000
|
||||
</pre>
|
||||
<p>would run 5 successive simulations of the same system for a total of
|
||||
50,000 timesteps.</p>
|
||||
<p>If you wish to run totally different simulations, one after the other,
|
||||
the <a class="reference internal" href="clear.html"><span class="doc">clear</span></a> command can be used in between them to
|
||||
re-initialize LAMMPS. For example, this script</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span>
|
||||
<span class="n">atom_style</span> <span class="n">atomic</span>
|
||||
<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span>
|
||||
<span class="n">run</span> <span class="mi">10000</span>
|
||||
<span class="n">clear</span>
|
||||
<span class="n">units</span> <span class="n">lj</span>
|
||||
<span class="n">atom_style</span> <span class="n">atomic</span>
|
||||
<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span><span class="o">.</span><span class="n">new</span>
|
||||
<span class="n">run</span> <span class="mi">10000</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
units lj
|
||||
atom_style atomic
|
||||
read_data data.lj
|
||||
run 10000
|
||||
clear
|
||||
units lj
|
||||
atom_style atomic
|
||||
read_data data.lj.new
|
||||
run 10000
|
||||
</pre>
|
||||
<p>would run 2 independent simulations, one after the other.</p>
|
||||
<p>For large numbers of independent simulations, you can use
|
||||
<a class="reference internal" href="variable.html"><span class="doc">variables</span></a> and the <a class="reference internal" href="next.html"><span class="doc">next</span></a> and
|
||||
<a class="reference internal" href="jump.html"><span class="doc">jump</span></a> commands to loop over the same input script
|
||||
multiple times with different settings. For example, this
|
||||
script, named in.polymer</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>variable d index run1 run2 run3 run4 run5 run6 run7 run8
|
||||
<pre class="literal-block">
|
||||
variable d index run1 run2 run3 run4 run5 run6 run7 run8
|
||||
shell cd $d
|
||||
read_data data.polymer
|
||||
run 10000
|
||||
|
|
@ -460,8 +461,7 @@ shell cd ..
|
|||
clear
|
||||
next d
|
||||
jump in.polymer
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<p>would run 8 simulations in different directories, using a data.polymer
|
||||
file in each directory. The same concept could be used to run the
|
||||
same system at 8 different temperatures, using a temperature variable
|
||||
|
|
@ -528,10 +528,10 @@ replica. The processors assigned to each replica are determined at
|
|||
run-time by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-partition command-line switch</span></a> to launch LAMMPS on multiple
|
||||
partitions, which in this context are the same as replicas. E.g.
|
||||
these commands:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">8</span><span class="n">x2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">temper</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">8</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">8</span><span class="n">x1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">neb</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
|
||||
mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
|
||||
</pre>
|
||||
<p>would each run 8 replicas, on either 16 or 8 processors. Note the use
|
||||
of the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-in command-line switch</span></a> to specify
|
||||
the input script which is required when running in multi-replica mode.</p>
|
||||
|
|
@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on
|
|||
<strong>A</strong> x <strong>B</strong> . <strong>C</strong> > 0. The equivalent LAMMPS <strong>a</strong>,<strong>b</strong>,<strong>c</strong> are a linear
|
||||
rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p>
|
||||
<img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" />
|
||||
<p>where A = <a href="#id3"><span class="problematic" id="id4">|</span></a><strong>A</strong>| indicates the scalar length of <strong>A</strong>. The ^ hat symbol
|
||||
<p>where A = | <strong>A</strong> | indicates the scalar length of <strong>A</strong>. The hat symbol (^)
|
||||
indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles
|
||||
between the vectors described below. Note that by construction,
|
||||
<strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively.
|
||||
|
|
@ -1037,23 +1037,23 @@ BOUNDS for a snapshot is written to a dump file for a triclinic box,
|
|||
an orthogonal bounding box which encloses the triclinic simulation box
|
||||
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
|
||||
box, formatted as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span> <span class="n">xy</span> <span class="n">xz</span> <span class="n">yz</span>
|
||||
<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span>
|
||||
<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span>
|
||||
<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
ITEM: BOX BOUNDS xy xz yz
|
||||
xlo_bound xhi_bound xy
|
||||
ylo_bound yhi_bound xz
|
||||
zlo_bound zhi_bound yz
|
||||
</pre>
|
||||
<p>This bounding box is convenient for many visualization programs and is
|
||||
calculated from the 9 triclinic box parameters
|
||||
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xlo_bound</span> <span class="o">=</span> <span class="n">xlo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span>
|
||||
<span class="n">xhi_bound</span> <span class="o">=</span> <span class="n">xhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span>
|
||||
<span class="n">ylo_bound</span> <span class="o">=</span> <span class="n">ylo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span>
|
||||
<span class="n">yhi_bound</span> <span class="o">=</span> <span class="n">yhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span>
|
||||
<span class="n">zlo_bound</span> <span class="o">=</span> <span class="n">zlo</span>
|
||||
<span class="n">zhi_bound</span> <span class="o">=</span> <span class="n">zhi</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
|
||||
xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
|
||||
ylo_bound = ylo + MIN(0.0,yz)
|
||||
yhi_bound = yhi + MAX(0.0,yz)
|
||||
zlo_bound = zlo
|
||||
zhi_bound = zhi
|
||||
</pre>
|
||||
<p>These formulas can be inverted if you need to convert the bounding box
|
||||
back into the triclinic box parameters, e.g. xlo = xlo_bound -
|
||||
MIN(0.0,xy,xz,xy+xz).</p>
|
||||
|
|
@ -1136,9 +1136,9 @@ of individual particles, after then are created.</p>
|
|||
<p>The dipole style does not actually define finite-size particles, but
|
||||
is often used in conjunction with spherical particles, via a command
|
||||
like</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">sphere</span> <span class="n">dipole</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
atom_style hybrid sphere dipole
|
||||
</pre>
|
||||
<p>This is because when dipoles interact with each other, they induce
|
||||
torques, and a particle must be finite-size (i.e. have a moment of
|
||||
inertia) in order to respond and rotate. See the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a> command for details. The “set” command can be
|
||||
|
|
@ -1372,11 +1372,11 @@ per-atom vector.</p>
|
|||
<p>When a quantity is accessed, as in many of the output commands
|
||||
discussed below, it can be referenced via the following bracket
|
||||
notation, where ID in this case is the ID of a compute. The leading
|
||||
“<a href="#id74"><span class="problematic" id="id75">c_</span></a>” would be replaced by “<a href="#id76"><span class="problematic" id="id77">f_</span></a>” for a fix, or “<a href="#id78"><span class="problematic" id="id79">v_</span></a>” for a variable:</p>
|
||||
“c_” would be replaced by “f_” for a fix, or “v_” for a variable:</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="21%" />
|
||||
<col width="79%" />
|
||||
<col width="23%" />
|
||||
<col width="77%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>c_ID</td>
|
||||
|
|
@ -1911,13 +1911,13 @@ internal LAMMPS operations. Note that LAMMPS classes are defined
|
|||
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
|
||||
application.</p>
|
||||
<p>Library.cpp contains these 5 basic functions:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="n">lammps_open</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">char</span> <span class="o">**</span><span class="p">,</span> <span class="n">MPI_Comm</span><span class="p">,</span> <span class="n">void</span> <span class="o">**</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="n">lammps_close</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="nb">int</span> <span class="n">lammps_version</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="n">lammps_file</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="n">char</span> <span class="o">*</span><span class="n">lammps_command</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
void lammps_open(int, char **, MPI_Comm, void **)
|
||||
void lammps_close(void *)
|
||||
int lammps_version(void *)
|
||||
void lammps_file(void *, char *)
|
||||
char *lammps_command(void *, char *)
|
||||
</pre>
|
||||
<p>The lammps_open() function is used to initialize LAMMPS, passing in a
|
||||
list of strings as if they were <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line arguments</span></a> when LAMMPS is run in
|
||||
stand-alone mode from the command line, and a MPI communicator for
|
||||
|
|
@ -1951,17 +1951,17 @@ interleaving the lammps_command() calls with other calls to extract
|
|||
information from LAMMPS, perform its own operations, or call another
|
||||
code’s library.</p>
|
||||
<p>Other useful functions are also included in library.cpp. For example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_atom</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_compute</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_fix</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_variable</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="nb">int</span> <span class="n">lammps_set_variable</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="nb">int</span> <span class="n">lammps_get_natoms</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="n">lammps_get_coords</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">double</span> <span class="o">*</span><span class="p">)</span>
|
||||
<span class="n">void</span> <span class="n">lammps_put_coords</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">double</span> <span class="o">*</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
void *lammps_extract_global(void *, char *)
|
||||
void *lammps_extract_atom(void *, char *)
|
||||
void *lammps_extract_compute(void *, char *, int, int)
|
||||
void *lammps_extract_fix(void *, char *, int, int, int, int)
|
||||
void *lammps_extract_variable(void *, char *, char *)
|
||||
int lammps_set_variable(void *, char *, char *)
|
||||
int lammps_get_natoms(void *)
|
||||
void lammps_get_coords(void *, double *)
|
||||
void lammps_put_coords(void *, double *)
|
||||
</pre>
|
||||
<p>These can extract various global or per-atom quantities from LAMMPS as
|
||||
well as values calculated by a compute, fix, or variable. The
|
||||
“set_variable” function can set an existing string-style variable to a
|
||||
|
|
@ -2087,29 +2087,30 @@ liquid Ar via the GK formalism:</p>
|
|||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for viscosity of liquid Ar</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>units real
|
||||
<pre class="literal-block">
|
||||
units real
|
||||
variable T equal 86.4956
|
||||
variable V equal vol
|
||||
variable dt equal 4.0
|
||||
variable p equal 400 # correlation length
|
||||
variable s equal 5 # sample interval
|
||||
variable d equal $p*$s # dump interval
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>variable kB equal 1.3806504e-23 # [J/K/** Boltzmann
|
||||
<pre class="literal-block">
|
||||
variable kB equal 1.3806504e-23 # [J/K/** Boltzmann
|
||||
variable atm2Pa equal 101325.0
|
||||
variable A2m equal 1.0e-10
|
||||
variable fs2s equal 1.0e-15
|
||||
variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>dimension 3
|
||||
<pre class="literal-block">
|
||||
dimension 3
|
||||
boundary p p p
|
||||
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||
region box block 0 4 0 4 0 4
|
||||
|
|
@ -2120,8 +2121,7 @@ pair_style lj/cut 13.0
|
|||
pair_coeff * * 0.2381 3.405
|
||||
timestep ${dt}
|
||||
thermo $d
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
|
|
@ -2137,7 +2137,8 @@ run 8000
|
|||
<span class="c1">#fix NVE all nve</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0
|
||||
<pre class="literal-block">
|
||||
reset_timestep 0
|
||||
variable pxy equal pxy
|
||||
variable pxz equal pxz
|
||||
variable pyz equal pyz
|
||||
|
|
@ -2151,9 +2152,8 @@ thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
|
|||
run 100000
|
||||
variable v equal (v_v11+v_v22+v_v33)/3.0
|
||||
variable ndens equal count(all)/vol
|
||||
print "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3"
|
||||
</pre></div>
|
||||
</div>
|
||||
print "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3"
|
||||
</pre>
|
||||
<p>The fifth method is related to the above Green-Kubo method,
|
||||
but uses the Einstein formulation, analogous to the Einstein
|
||||
mean-square-displacement formulation for self-diffusivity. The
|
||||
|
|
@ -2274,7 +2274,7 @@ fix produces a global array as output with one row of values per
|
|||
chunk.</p>
|
||||
</div>
|
||||
<div class="section" id="compute-chunk-commands">
|
||||
<h3>6.23.3. Compute <a href="#id71"><span class="problematic" id="id72">*</span></a>/chunk commands:</h3>
|
||||
<h3>6.23.3. Compute */chunk commands:</h3>
|
||||
<p>Currently the following computes operate on chunks of atoms to produce
|
||||
per-chunk values.</p>
|
||||
<ul class="simple">
|
||||
|
|
@ -2331,31 +2331,31 @@ velocity:</p>
|
|||
<ol class="arabic simple" start="3">
|
||||
<li>Center of mass of each molecule:</li>
|
||||
</ol>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute cc1 all chunk/atom molecule
|
||||
compute myChunk all com/chunk cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
|
||||
</pre>
|
||||
<ol class="arabic simple" start="4">
|
||||
<li>Total force on each molecule and ave/max across all molecules:</li>
|
||||
</ol>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">1000</span> <span class="mi">1</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span>
|
||||
<span class="n">variable</span> <span class="n">xave</span> <span class="n">equal</span> <span class="n">ave</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
|
||||
<span class="n">variable</span> <span class="n">xmax</span> <span class="n">equal</span> <span class="nb">max</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
|
||||
<span class="n">thermo</span> <span class="mi">1000</span>
|
||||
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">v_xave</span> <span class="n">v_xmax</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute cc1 all chunk/atom molecule
|
||||
fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
|
||||
variable xave equal ave(f_1[2])
|
||||
variable xmax equal max(f_1[2])
|
||||
thermo 1000
|
||||
thermo_style custom step temp v_xave v_xmax
|
||||
</pre>
|
||||
<ol class="arabic simple" start="5">
|
||||
<li>Histogram of cluster sizes:</li>
|
||||
</ol>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cluster</span> <span class="nb">all</span> <span class="n">cluster</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.0</span>
|
||||
<span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">c_cluster</span> <span class="n">compress</span> <span class="n">yes</span>
|
||||
<span class="n">compute</span> <span class="n">size</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">count</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">0</span> <span class="mi">20</span> <span class="mi">20</span> <span class="n">c_size</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">beyond</span> <span class="n">ignore</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">histo</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute cluster all cluster/atom 1.0
|
||||
compute cc1 all chunk/atom c_cluster compress yes
|
||||
compute size all property/chunk cc1 count
|
||||
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
</div>
|
||||
|
|
@ -2607,18 +2607,18 @@ by the <a class="reference internal" href="kspace_style.html"><span class="doc">
|
|||
Ewald solvers can be used.</p>
|
||||
<p>For the NaCL example problem, these pair style and bond style settings
|
||||
are used:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">20.0</span> <span class="mf">20.0</span>
|
||||
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.0</span> <span class="mf">1.000</span> <span class="mf">0.00</span> <span class="mf">0.00</span> <span class="mf">0.00</span>
|
||||
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mf">487.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span> <span class="mf">1.05</span> <span class="mf">0.50</span> <span class="c1">#Na-Na</span>
|
||||
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">145134.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span> <span class="mf">6.99</span> <span class="mf">8.70</span> <span class="c1">#Na-Cl</span>
|
||||
<span class="n">pair_coeff</span> <span class="mi">4</span> <span class="mi">4</span> <span class="mf">405774.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span> <span class="mf">72.40</span> <span class="mf">145.40</span> <span class="c1">#Cl-Cl</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">63.014</span> <span class="mf">0.0</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">25.724</span> <span class="mf">0.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
pair_style born/coul/long/cs 20.0 20.0
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
</pre>
|
||||
<p>When running dynamics with the adiabatic core/shell model, the
|
||||
following issues should be considered. Since the relative motion of
|
||||
the core and shell particles corresponds to the polarization, typical
|
||||
|
|
@ -2645,15 +2645,15 @@ used to assign the compute to the thermostat fix. Likewise the
|
|||
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify temp</span></a> command can be used to make
|
||||
this temperature be output for the overall system.</p>
|
||||
<p>For the NaCl example, this can be done as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">group</span> <span class="n">cores</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
<span class="n">group</span> <span class="n">shells</span> <span class="nb">type</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
<span class="n">compute</span> <span class="n">CSequ</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">cores</span> <span class="n">shells</span>
|
||||
<span class="n">fix</span> <span class="n">thermoberendsen</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">berendsen</span> <span class="mi">1427</span> <span class="mi">1427</span> <span class="mf">0.4</span> <span class="c1"># thermostat for the true physical system</span>
|
||||
<span class="n">fix</span> <span class="n">thermostatequ</span> <span class="nb">all</span> <span class="n">nve</span> <span class="c1"># integrator as needed for the berendsen thermostat</span>
|
||||
<span class="n">fix_modify</span> <span class="n">thermoberendsen</span> <span class="n">temp</span> <span class="n">CSequ</span>
|
||||
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">CSequ</span> <span class="c1"># output of center-of-mass derived temperature</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
group cores type 1 2
|
||||
group shells type 3 4
|
||||
compute CSequ all temp/cs cores shells
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
|
||||
fix thermostatequ all nve # integrator as needed for the berendsen thermostat
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
thermo_modify temp CSequ # output of center-of-mass derived temperature
|
||||
</pre>
|
||||
<p>If <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a> is used, the decoupled
|
||||
relative motion of the core and the shell should in theory be
|
||||
stable. However numerical fluctuation can introduce a small
|
||||
|
|
@ -2702,14 +2702,14 @@ accessed by the <a class="reference internal" href="compute_property_atom.html">
|
|||
command, to use as input to the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command to define the core/shell
|
||||
pairs as chunks.</p>
|
||||
<p>For example,</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">csinfo</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">i_CSID</span> <span class="c1"># property/atom command</span>
|
||||
<span class="n">read_data</span> <span class="n">NaCl_CS_x0</span><span class="o">.</span><span class="mi">1</span><span class="n">_prop</span><span class="o">.</span><span class="n">data</span> <span class="n">fix</span> <span class="n">csinfo</span> <span class="n">NULL</span> <span class="n">CS</span><span class="o">-</span><span class="n">Info</span> <span class="c1"># atom property added in the data-file</span>
|
||||
<span class="n">compute</span> <span class="n">prop</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">i_CSID</span>
|
||||
<span class="n">compute</span> <span class="n">cs_chunk</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">c_prop</span>
|
||||
<span class="n">compute</span> <span class="n">cstherm</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cs_chunk</span> <span class="n">temp</span> <span class="n">internal</span> <span class="n">com</span> <span class="n">yes</span> <span class="n">cdof</span> <span class="mf">3.0</span> <span class="c1"># note the chosen degrees of freedom for the core/shell pairs</span>
|
||||
<span class="n">fix</span> <span class="n">ave_chunk</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">10</span> <span class="mi">1</span> <span class="mi">10</span> <span class="n">c_cstherm</span> <span class="n">file</span> <span class="n">chunk</span><span class="o">.</span><span class="n">dump</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix csinfo all property/atom i_CSID # property/atom command
|
||||
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
|
||||
compute prop all property/atom i_CSID
|
||||
compute cs_chunk all chunk/atom c_prop
|
||||
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
|
||||
fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
|
||||
</pre>
|
||||
<p>The additional section in the date file would be formatted like this:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CS</span><span class="o">-</span><span class="n">Info</span> <span class="c1"># header of additional section</span>
|
||||
</pre></div>
|
||||
|
|
|
|||
|
|
@ -193,8 +193,8 @@ C-style data structures (vectors and arrays).</p>
|
|||
<p>Most of the new features described in this section require you to
|
||||
write a new C++ derived class (except for exceptions described below,
|
||||
where you can make small edits to existing files). Creating a new
|
||||
class requires 2 files, a source code file (<em>.cpp) and a header file
|
||||
(</em>.h). The derived class must provide certain methods to work as a
|
||||
class requires 2 files, a source code file (*.cpp) and a header file
|
||||
(*.h). The derived class must provide certain methods to work as a
|
||||
new option. Depending on how different your new feature is compared
|
||||
to existing features, you can either derive from the base class
|
||||
itself, or from a derived class that already exists. Enabling LAMMPS
|
||||
|
|
@ -209,19 +209,19 @@ and pair_foo.h that define a new class PairFoo that computes pairwise
|
|||
potentials described in the classic 1997 <a class="reference internal" href="#foo"><span class="std std-ref">paper</span></a> by Foo, et al.
|
||||
If you wish to invoke those potentials in a LAMMPS input script with a
|
||||
command like</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">foo</span> <span class="mf">0.1</span> <span class="mf">3.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
pair_style foo 0.1 3.5
|
||||
</pre>
|
||||
<p>then your pair_foo.h file should be structured as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1">#ifdef PAIR_CLASS</span>
|
||||
<span class="n">PairStyle</span><span class="p">(</span><span class="n">foo</span><span class="p">,</span><span class="n">PairFoo</span><span class="p">)</span>
|
||||
<span class="c1">#else</span>
|
||||
<span class="o">...</span>
|
||||
<span class="p">(</span><span class="k">class</span> <span class="nc">definition</span> <span class="k">for</span> <span class="n">PairFoo</span><span class="p">)</span>
|
||||
<span class="o">...</span>
|
||||
<span class="c1">#endif</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
#ifdef PAIR_CLASS
|
||||
PairStyle(foo,PairFoo)
|
||||
#else
|
||||
...
|
||||
(class definition for PairFoo)
|
||||
...
|
||||
#endif
|
||||
</pre>
|
||||
<p>where “foo” is the style keyword in the pair_style command, and
|
||||
PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
|
||||
files.</p>
|
||||
|
|
@ -275,8 +275,8 @@ atoms.</p>
|
|||
class. See atom_vec.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="22%" />
|
||||
<col width="78%" />
|
||||
<col width="24%" />
|
||||
<col width="76%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>init</td>
|
||||
|
|
@ -393,18 +393,18 @@ output the custom values.</p>
|
|||
The code for these classes can use the per-atom properties defined by
|
||||
fix property/atom. The Atom class has a find_custom() method that is
|
||||
useful in this context:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="n">index</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-></span><span class="n">find_custom</span><span class="p">(</span><span class="n">char</span> <span class="o">*</span><span class="n">name</span><span class="p">,</span> <span class="nb">int</span> <span class="o">&</span><span class="n">flag</span><span class="p">);</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
int index = atom->find_custom(char *name, int &flag);
|
||||
</pre>
|
||||
<p>The “name” of a custom attribute, as specified in the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command, is checked to verify
|
||||
that it exists and its index is returned. The method also sets flag =
|
||||
0/1 depending on whether it is an integer or floating-point attribute.
|
||||
The vector of values associated with the attribute can then be
|
||||
accessed using the returned index as</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="o">*</span><span class="n">ivector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-></span><span class="n">ivector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span>
|
||||
<span class="n">double</span> <span class="o">*</span><span class="n">dvector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-></span><span class="n">dvector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
int *ivector = atom->ivector[index];
|
||||
double *dvector = atom->dvector[index];
|
||||
</pre>
|
||||
<p>Ivector or dvector are vectors of length Nlocal = # of owned atoms,
|
||||
which store the attributes of individual atoms.</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -474,8 +474,8 @@ per-atom kinetic energy.</p>
|
|||
class. See compute.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="24%" />
|
||||
<col width="76%" />
|
||||
<col width="26%" />
|
||||
<col width="74%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>init</td>
|
||||
|
|
@ -551,8 +551,8 @@ DumpCustom class contained in the dump_custom.cpp file.</p>
|
|||
class. See dump.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="22%" />
|
||||
<col width="78%" />
|
||||
<col width="23%" />
|
||||
<col width="77%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>write_header</td>
|
||||
|
|
@ -597,8 +597,8 @@ implement.</p>
|
|||
derived class. See fix.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="22%" />
|
||||
<col width="78%" />
|
||||
<col width="23%" />
|
||||
<col width="77%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>setmask</td>
|
||||
|
|
@ -823,8 +823,8 @@ styles can be created to add new K-space options to LAMMPS.</p>
|
|||
class. See kspace.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="23%" />
|
||||
<col width="77%" />
|
||||
<col width="25%" />
|
||||
<col width="75%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>init</td>
|
||||
|
|
@ -853,8 +853,8 @@ LAMMPS.</p>
|
|||
class. See min.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="25%" />
|
||||
<col width="75%" />
|
||||
<col width="26%" />
|
||||
<col width="74%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>init</td>
|
||||
|
|
@ -882,8 +882,8 @@ includes some optional methods to enable its use with rRESPA.</p>
|
|||
<p>Here is a brief description of the class methods in pair.h:</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="32%" />
|
||||
<col width="68%" />
|
||||
<col width="33%" />
|
||||
<col width="67%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>compute</td>
|
||||
|
|
@ -929,8 +929,8 @@ styles can be created to add new region shapes to LAMMPS.</p>
|
|||
class. See region.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="21%" />
|
||||
<col width="79%" />
|
||||
<col width="22%" />
|
||||
<col width="78%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>inside</td>
|
||||
|
|
@ -965,8 +965,8 @@ a rigid body containing N sub-particles.</p>
|
|||
class. See body.h for details.</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="25%" />
|
||||
<col width="75%" />
|
||||
<col width="27%" />
|
||||
<col width="73%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>data_body</td>
|
||||
|
|
@ -1030,17 +1030,17 @@ via the <a class="reference internal" href="print.html"><span class="doc">print<
|
|||
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> commands. Variables of style
|
||||
“equal” can compute complex equations that involve the following types
|
||||
of arguments:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo</span> <span class="n">keywords</span> <span class="o">=</span> <span class="n">ke</span><span class="p">,</span> <span class="n">vol</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="o">...</span>
|
||||
<span class="n">other</span> <span class="n">variables</span> <span class="o">=</span> <span class="n">v_a</span><span class="p">,</span> <span class="n">v_myvar</span><span class="p">,</span> <span class="o">...</span>
|
||||
<span class="n">math</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">div</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="n">mult</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="n">add</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="o">...</span>
|
||||
<span class="n">group</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">mass</span><span class="p">(</span><span class="n">group</span><span class="p">),</span> <span class="n">xcm</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">x</span><span class="p">),</span> <span class="o">...</span>
|
||||
<span class="n">atom</span> <span class="n">values</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">123</span><span class="p">],</span> <span class="n">y</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">vx</span><span class="p">[</span><span class="mi">34</span><span class="p">],</span> <span class="o">...</span>
|
||||
<span class="n">compute</span> <span class="n">values</span> <span class="o">=</span> <span class="n">c_mytemp</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
thermo keywords = ke, vol, atoms, ...
|
||||
other variables = v_a, v_myvar, ...
|
||||
math functions = div(x,y), mult(x,y), add(x,y), ...
|
||||
group functions = mass(group), xcm(group,x), ...
|
||||
atom values = x[123], y[3], vx[34], ...
|
||||
compute values = c_mytemp[0], c_thermo_press[3], ...
|
||||
</pre>
|
||||
<p>Adding keywords for the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command
|
||||
(which can then be accessed by variables) was discussed
|
||||
<a class="reference internal" href="Section_howto.html#thermo"><span class="std std-ref">here</span></a> on this page.</p>
|
||||
<a class="reference internal" href="#mod-13"><span class="std std-ref">here</span></a> on this page.</p>
|
||||
<p>Adding a new math function of one or two arguments can be done by
|
||||
editing one section of the Variable::evaulate() method. Search for
|
||||
the word “customize” to find the appropriate location.</p>
|
||||
|
|
@ -1053,7 +1053,7 @@ of the Variable::evaulate() method. Search for the word “customize”
|
|||
to find the appropriate location.</p>
|
||||
<p>Adding new <a class="reference internal" href="compute.html"><span class="doc">compute styles</span></a> (whose calculated values can
|
||||
then be accessed by variables) was discussed
|
||||
<a class="reference internal" href="Section_howto.html#compute"><span class="std std-ref">here</span></a> on this page.</p>
|
||||
<a class="reference internal" href="#mod-3"><span class="std std-ref">here</span></a> on this page.</p>
|
||||
</div>
|
||||
<div class="section" id="submitting-new-features-for-inclusion-in-lammps">
|
||||
<span id="mod-15"></span><h2>10.15. Submitting new features for inclusion in LAMMPS</h2>
|
||||
|
|
@ -1157,7 +1157,7 @@ structures, performs its operations, and is formatted similar to other
|
|||
LAMMPS source files, including the use of the error class for error
|
||||
and warning messages.</li>
|
||||
<li>If you want your contribution to be added as a user-contributed
|
||||
feature, and it’s a single file (actually a <a href="#id8"><span class="problematic" id="id9">*</span></a>.cpp and <a href="#id10"><span class="problematic" id="id11">*</span></a>.h file) it can
|
||||
feature, and it’s a single file (actually a *.cpp and *.h file) it can
|
||||
rapidly be added to the USER-MISC directory. Send us the one-line
|
||||
entry to add to the USER-MISC/README file in that dir, along with the
|
||||
2 source files. You can do this multiple times if you wish to
|
||||
|
|
@ -1192,12 +1192,12 @@ to HTML and PDF. The tools for this conversion are included in the
|
|||
source distribution, and the translation can be as simple as doing
|
||||
“make html pdf” in the doc folder.
|
||||
Thus the documentation source files must be in the same format and
|
||||
style as other <em>.txt files in the lammps/doc/src directory for similar
|
||||
style as other *.txt files in the lammps/doc/src directory for similar
|
||||
commands and styles; use one or more of them as a starting point.
|
||||
A description of the markup can also be found in
|
||||
lammps/doc/utils/txt2html/README.html
|
||||
As appropriate, the text files can include links to equations
|
||||
(see doc/Eqs/</em>.tex for examples, we auto-create the associated JPG
|
||||
(see doc/Eqs/*.tex for examples, we auto-create the associated JPG
|
||||
files), or figures (see doc/JPG for examples), or even additional PDF
|
||||
files with further details (see doc/PDF for examples). The doc page
|
||||
should also include literature citations as appropriate; see the
|
||||
|
|
@ -1220,7 +1220,7 @@ These example inputs are also required for validating memory accesses
|
|||
and testing for memory leaks with valgrind</li>
|
||||
<li>If there is a paper of yours describing your feature (either the
|
||||
algorithm/science behind the feature itself, or its initial usage, or
|
||||
its implementation in LAMMPS), you can add the citation to the <a href="#id12"><span class="problematic" id="id13">*</span></a>.cpp
|
||||
its implementation in LAMMPS), you can add the citation to the *.cpp
|
||||
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
|
||||
A LaTeX citation is stored in a variable at the top of the file and a
|
||||
single line of code that references the variable is added to the
|
||||
|
|
|
|||
|
|
@ -630,9 +630,9 @@ for aspherical particle models: ellipsoids, 2d lines, 3d triangles.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">asphere</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^asphere -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section howto 6.14</span></a>,
|
||||
<a class="reference internal" href="pair_gayberne.html"><span class="doc">pair_style gayberne</span></a>, <a class="reference internal" href="pair_resquared.html"><span class="doc">pair_style resquared</span></a>,
|
||||
<a class="reference external" href="PDF/pair_gayberne_extra.pdf">doc/PDF/pair_gayberne_extra.pdf</a>,
|
||||
|
|
@ -658,9 +658,9 @@ themselves. See the <a class="reference internal" href="body.html"><span class=
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">body</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^body -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>, <a class="reference internal" href="body.html"><span class="doc">body</span></a>,
|
||||
<a class="reference internal" href="pair_body.html"><span class="doc">pair_style body</span></a>, examples/body</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -682,9 +682,9 @@ COMPASS CLASS2 molecular force field.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">class2</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^class2 -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a>, <a class="reference internal" href="angle_class2.html"><span class="doc">angle_style class2</span></a>, <a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style class2</span></a>, <a class="reference internal" href="improper_class2.html"><span class="doc">improper_style class2</span></a>, <a class="reference internal" href="pair_class2.html"><span class="doc">pair_style lj/class2</span></a></p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -708,9 +708,9 @@ approximation to Stokesian dynamics.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">colloid</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^colloid -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="fix_wall.html"><span class="doc">fix wall/colloid</span></a>, <a class="reference internal" href="pair_colloid.html"><span class="doc">pair_style colloid</span></a>, <a class="reference internal" href="pair_yukawa_colloid.html"><span class="doc">pair_style yukawa/colloid</span></a>, <a class="reference internal" href="pair_brownian.html"><span class="doc">pair_style brownian</span></a>, <a class="reference internal" href="pair_lubricate.html"><span class="doc">pair_style lubricate</span></a>, <a class="reference internal" href="pair_lubricateU.html"><span class="doc">pair_style lubricateU</span></a>, examples/colloid, examples/srd</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -737,9 +737,9 @@ zlib info it specifies.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">compress</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^compress -a machine
|
||||
</pre>
|
||||
<p>Supporting info: src/COMPRESS/README, lib/compress/README, <a class="reference internal" href="dump.html"><span class="doc">dump atom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump cfg/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump custom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump xyz/gz</span></a></p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -764,9 +764,9 @@ package.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">coreshell</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^coreshell -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-26"><span class="std std-ref">Section howto 6.26</span></a>, <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a>,
|
||||
<a class="reference internal" href="pair_cs.html"><span class="doc">pair_style born/coul/long/cs</span></a>, <a class="reference internal" href="pair_cs.html"><span class="doc">pair_style buck/coul/long/cs</span></a>, pair_style
|
||||
lj/cut/coul/long/cs”_pair_lj.html, examples/coreshell</p>
|
||||
|
|
@ -789,9 +789,9 @@ dipole models with short-range or long-range interactions.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">dipole</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^dipole -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/cut</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/long</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/long/dipole/long</span></a>, examples/dipole</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -841,9 +841,9 @@ one step, with Type “python src/Make.py -h -gpu” to see the details.
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">gpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^gpu -a machine
|
||||
</pre>
|
||||
<p>Supporting info: src/GPU/README, lib/gpu/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_gpu.html"><span class="doc">Section accelerate gpu</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed with a (g),
|
||||
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>, <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a>,
|
||||
examples/accelerate, bench/FERMI, bench/KEPLER</p>
|
||||
|
|
@ -867,9 +867,9 @@ frictional and dissipative potentials.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">granular</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^granular -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-6"><span class="std std-ref">Section howto 6.6</span></a>, <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, <a class="reference internal" href="fix_wall_gran.html"><span class="doc">fix wall/gran</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hooke</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hertz/history</span></a>, examples/pour, bench/in.chute</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -896,9 +896,9 @@ process. You should not need to edit this file.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kim</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^kim -a machine
|
||||
</pre>
|
||||
<p>Supporting info: src/KIM/README, lib/kim/README, <a class="reference internal" href="pair_kim.html"><span class="doc">pair_style kim</span></a>, examples/kim</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -928,12 +928,12 @@ choose which hardware to build for. Type “python src/Make.py -h
|
|||
system, you will need to read the <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a> doc page for details of what
|
||||
Makefile.machine settings are needed.</p>
|
||||
<p>To install via make or Make.py for each of 3 hardware options:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">kokkos_omp</span> <span class="c1"># for CPUs with OpenMP</span>
|
||||
<span class="n">make</span> <span class="n">kokkos_cuda</span> <span class="c1"># for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda</span>
|
||||
<span class="n">make</span> <span class="n">kokkos_phi</span> <span class="c1"># for Xeon Phis</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
make yes-kokkos
|
||||
make kokkos_omp # for CPUs with OpenMP
|
||||
make kokkos_cuda # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
|
||||
make kokkos_phi # for Xeon Phis
|
||||
</pre>
|
||||
<p>Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP
|
||||
Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch
|
||||
Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis</p>
|
||||
|
|
@ -942,9 +942,9 @@ Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kokkos</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^kokkos -a machine
|
||||
</pre>
|
||||
<p>Supporting info: src/KOKKOS/README, lib/kokkos/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed
|
||||
with a (k), <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a>,
|
||||
examples/accelerate, bench/FERMI, bench/KEPLER</p>
|
||||
|
|
@ -977,9 +977,9 @@ see the details.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kspace</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^kspace -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>,
|
||||
<a class="reference external" href="PDF/kspace.pdf">doc/PDF/kspace.pdf</a>, <a class="reference internal" href="Section_howto.html#howto-7"><span class="std std-ref">Section howto 6.7</span></a>, <a class="reference internal" href="Section_howto.html#howto-8"><span class="std std-ref">Section howto 6.8</span></a>, <a class="reference internal" href="Section_howto.html#howto-9"><span class="std std-ref">Section howto 6.9</span></a>, <a class="reference internal" href="pair_coul.html"><span class="doc">pair_style coul</span></a>,
|
||||
other pair style command doc pages which have “long” or “msm” in their
|
||||
|
|
@ -1005,9 +1005,9 @@ the full list.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">manybody</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^manybody -a machine
|
||||
</pre>
|
||||
<p>Supporting info:</p>
|
||||
<p>Examples: Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a>, examples/comb, examples/eim,
|
||||
examples/nb3d, examples/vashishta</p>
|
||||
|
|
@ -1032,9 +1032,9 @@ in conjuction with dynamics.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">mc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^mc -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="fix_atom_swap.html"><span class="doc">fix atom/swap</span></a>, <a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a>, <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a>, <a class="reference internal" href="fix_bond_swap.html"><span class="doc">fix bond/swap</span></a>,
|
||||
<a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a>, <a class="reference internal" href="pair_dsmc.html"><span class="doc">pair_style dsmc</span></a></p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1079,9 +1079,9 @@ Intel Fortran compiler, rather than the GNU Fortran compiler.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">meam</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^meam -a machine
|
||||
</pre>
|
||||
<p>Supporting info: lib/meam/README, <a class="reference internal" href="pair_meam.html"><span class="doc">pair_style meam</span></a>,
|
||||
examples/meam</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1104,9 +1104,9 @@ listing, “ls src/MISC”, to see the list of commands.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">misc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^misc -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="compute_ti.html"><span class="doc">compute ti</span></a>, <a class="reference internal" href="fix_evaporate.html"><span class="doc">fix evaporate</span></a>, <a class="reference internal" href="fix_ttm.html"><span class="doc">fix tmm</span></a>, <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a>, examples/misc</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -1129,9 +1129,9 @@ covalent bonds. The pair styles include terms for the Dreiding
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">molecule</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^molecule -a machine
|
||||
</pre>
|
||||
<p>Supporting info:<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>,
|
||||
<a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>, <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>,
|
||||
<a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>,
|
||||
|
|
@ -1159,9 +1159,9 @@ are also written and read in parallel.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">mpiio</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^mpiio -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a>,
|
||||
<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a></p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1192,9 +1192,9 @@ creates and uses.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">opt</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^opt -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_opt.html"><span class="doc">Section accelerate opt</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed
|
||||
with an (o), examples/accelerate, bench/KEPLER</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1218,9 +1218,9 @@ styles which implement different materials models.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">peri</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^peri -a machine
|
||||
</pre>
|
||||
<p>Supporting info:
|
||||
<a class="reference external" href="PDF/PDLammps_overview.pdf">doc/PDF/PDLammps_overview.pdf</a>,
|
||||
<a class="reference external" href="PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</a>,
|
||||
|
|
@ -1261,9 +1261,9 @@ one step. Type “python src/Make.py -h -poems” to see the details.</
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">meam</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^meam -a machine
|
||||
</pre>
|
||||
<p>Supporting info: src/POEMS/README, lib/poems/README,
|
||||
<a class="reference internal" href="fix_poems.html"><span class="doc">fix poems</span></a>, examples/rigid</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1296,9 +1296,9 @@ in one step. Type “python src/Make.py -h -python” to see the detail
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">python</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^python -a machine
|
||||
</pre>
|
||||
<p>Supporting info: examples/python</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -1320,9 +1320,9 @@ that use QEq as part of their formulation.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">qeq</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^qeq -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="fix_qeq.html"><span class="doc">fix qeq/*</span></a>, examples/qeq</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -1362,9 +1362,9 @@ one step. Type “python src/Make.py -h -reax” to see the details.</p
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">reax</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^reax -a machine
|
||||
</pre>
|
||||
<p>Supporting info: lib/reax/README, <a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a>,
|
||||
<a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>, examples/reax</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1394,9 +1394,9 @@ field calcalation on another set.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">replica</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^replica -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">Section howto 6.5</span></a>,
|
||||
<a class="reference internal" href="neb.html"><span class="doc">neb</span></a>, <a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="tad.html"><span class="doc">tad</span></a>, <a class="reference internal" href="temper.html"><span class="doc">temper</span></a>,
|
||||
<a class="reference internal" href="run_style.html"><span class="doc">run_style verlet/split</span></a>, examples/neb, examples/prd,
|
||||
|
|
@ -1422,9 +1422,9 @@ few large bodies or many small bodies.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">rigid</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^rigid -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="compute_erotate_rigid.html"><span class="doc">compute erotate/rigid</span></a>,
|
||||
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>, <a class="reference internal" href="fix_shake.html"><span class="doc">fix rattle</span></a>, <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*</span></a>, examples/ASPHERE, examples/rigid</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1446,9 +1446,9 @@ simulations where a shock-wave passes through a material.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">shock</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^shock -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="fix_append_atoms.html"><span class="doc">fix append/atoms</span></a>, <a class="reference internal" href="fix_msst.html"><span class="doc">fix msst</span></a>, <a class="reference internal" href="fix_nphug.html"><span class="doc">fix nphug</span></a>, <a class="reference internal" href="fix_wall_piston.html"><span class="doc">fix wall/piston</span></a>, examples/hugoniostat, examples/msst</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -1471,9 +1471,9 @@ properties of the potential are also included.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">snap</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^snap -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="pair_snap.html"><span class="doc">pair snap</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snad/atom</span></a>,
|
||||
<a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snav/atom</span></a>, examples/snap</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -1496,9 +1496,9 @@ colloidal-scale particles.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">srd</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^srd -a machine
|
||||
</pre>
|
||||
<p>Supporting info: <a class="reference internal" href="fix_srd.html"><span class="doc">fix srd</span></a>, <a class="reference internal" href="fix_wall_srd.html"><span class="doc">fix wall/srd</span></a>, examples/srd, examples/ASPHERE</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -1541,9 +1541,9 @@ src/Make.py -h -voronoi” to see the details.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">voronoi</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^voronoi -a machine
|
||||
</pre>
|
||||
<p>Supporting info: src/VORONOI/README, lib/voronoi/README, <a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">compute voronoi/atom</span></a>, examples/voronoi</p>
|
||||
<hr class="docutils" />
|
||||
</div>
|
||||
|
|
@ -1860,7 +1860,7 @@ src/Make.py -h -voronoi” to see the details.</p>
|
|||
<tr class="row-even"><td><a class="reference internal" href="#user-smd"><span class="std std-ref">USER-SMD</span></a></td>
|
||||
<td>smoothed Mach dynamics</td>
|
||||
<td>Georg Ganzenmuller (EMI)</td>
|
||||
<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</a></td>
|
||||
<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">SMD User Guide</a></td>
|
||||
<td>USER/smd</td>
|
||||
<td><ul class="first last simple">
|
||||
<li></li>
|
||||
|
|
@ -1888,7 +1888,7 @@ src/Make.py -h -voronoi” to see the details.</p>
|
|||
<tr class="row-even"><td><a class="reference internal" href="#user-sph"><span class="std std-ref">USER-SPH</span></a></td>
|
||||
<td>smoothed particle hydrodynamics</td>
|
||||
<td>Georg Ganzenmuller (EMI)</td>
|
||||
<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td>
|
||||
<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">SPH User Guide</a></td>
|
||||
<td>USER/sph</td>
|
||||
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td>
|
||||
<td><ul class="first last simple">
|
||||
|
|
@ -1986,9 +1986,9 @@ more details.</p>
|
|||
<span class="n">make</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">atc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -p ^atc -a machine
|
||||
</pre>
|
||||
<p>Supporting <a class="reference external" href="info:src/USER-ATC/README">info:src/USER-ATC/README</a>, <a class="reference internal" href="fix_atc.html"><span class="doc">fix atc</span></a>,
|
||||
examples/USER/atc</p>
|
||||
<p>Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
|
||||
|
|
@ -2064,10 +2064,9 @@ equations of motion are integrated efficiently through the Shardlow
|
|||
splitting algorithm. See src/USER-DPD/README for more details.</p>
|
||||
<p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a>
|
||||
<a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>
|
||||
<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a></p>
|
||||
<blockquote>
|
||||
<div><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a></div></blockquote>
|
||||
<p><a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> <a class="reference internal" href="pair_table_rx.html"><span class="doc">pair table/rx</span></a>
|
||||
<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a>
|
||||
<a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>
|
||||
<a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> <a class="reference internal" href="pair_table_rx.html"><span class="doc">pair table/rx</span></a>
|
||||
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt</span></a> <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a>
|
||||
<a class="reference internal" href="pair_exp6_rx.html"><span class="doc">pair exp6/rx</span></a> <a class="reference internal" href="pair_multi_lucy.html"><span class="doc">pair multi/lucy</span></a>
|
||||
<a class="reference internal" href="pair_multi_lucy_rx.html"><span class="doc">pair multi/lucy/rx</span></a>, examples/USER/dpd</p>
|
||||
|
|
@ -2213,7 +2212,7 @@ Contact them directly if you have any questions.</p>
|
|||
<p>Supporting info:</p>
|
||||
<p>The files in this package are a potpourri of (mostly) unrelated
|
||||
features contributed to LAMMPS by users. Each feature is a single
|
||||
pair of files (<a href="#id2"><span class="problematic" id="id3">*</span></a>.cpp and <a href="#id4"><span class="problematic" id="id5">*</span></a>.h).</p>
|
||||
pair of files (*.cpp and *.h).</p>
|
||||
<p>More information about each feature can be found by reading its doc
|
||||
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
|
||||
input script commands is as follows:</p>
|
||||
|
|
@ -2382,18 +2381,18 @@ questions.</p>
|
|||
<p>Supporting info:</p>
|
||||
<p>This package implements smoothed Mach dynamics (SMD) in
|
||||
LAMMPS. Currently, the package has the following features:</p>
|
||||
<ul class="simple">
|
||||
<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li>
|
||||
<li>Also solves solids mechanics problems via a state of the art
|
||||
stabilized meshless method with hourglass control.</li>
|
||||
<li>Can specify hydrostatic interactions independently from material
|
||||
strength models, i.e. pressure and deviatoric stresses are separated.</li>
|
||||
<li>Many material models available (Johnson-Cook, plasticity with
|
||||
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
|
||||
material models.</li>
|
||||
<li>Rigid boundary conditions (walls) can be loaded as surface geometries
|
||||
from <a href="#id8"><span class="problematic" id="id9">*</span></a>.STL files.</li>
|
||||
</ul>
|
||||
<p>* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</p>
|
||||
<dl class="docutils">
|
||||
<dt>* Also solves solids mechanics problems via a state of the art</dt>
|
||||
<dd>stabilized meshless method with hourglass control.</dd>
|
||||
<dt>* Can specify hydrostatic interactions independently from material</dt>
|
||||
<dd>strength models, i.e. pressure and deviatoric stresses are separated.</dd>
|
||||
<dt>* Many material models available (Johnson-Cook, plasticity with</dt>
|
||||
<dd>hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
|
||||
material models.</dd>
|
||||
<dt>* Rigid boundary conditions (walls) can be loaded as surface geometries</dt>
|
||||
<dd>from *.STL files.</dd>
|
||||
</dl>
|
||||
<p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
|
||||
<p>There are example scripts for using this package in examples/USER/smd.</p>
|
||||
<p>The person who created this package is Georg Ganzenmuller at the
|
||||
|
|
@ -2424,16 +2423,18 @@ them directly if you have any questions.</p>
|
|||
<p>Supporting info:</p>
|
||||
<p>This package implements smoothed particle hydrodynamics (SPH) in
|
||||
LAMMPS. Currently, the package has the following features:</p>
|
||||
<ul class="simple">
|
||||
<li>Tait, ideal gas, Lennard-Jones equation of states, full support for
|
||||
complete (i.e. internal-energy dependent) equations of state</li>
|
||||
<li>Plain or Monaghans XSPH integration of the equations of motion</li>
|
||||
<li>Density continuity or density summation to propagate the density field</li>
|
||||
<li>Commands to set internal energy and density of particles from the
|
||||
input script</li>
|
||||
<li>Output commands to access internal energy and density for dumping and
|
||||
thermo output</li>
|
||||
</ul>
|
||||
<dl class="docutils">
|
||||
<dt>* Tait, ideal gas, Lennard-Jones equation of states, full support for</dt>
|
||||
<dd>complete (i.e. internal-energy dependent) equations of state</dd>
|
||||
</dl>
|
||||
<p>* Plain or Monaghans XSPH integration of the equations of motion</p>
|
||||
<p>* Density continuity or density summation to propagate the density field</p>
|
||||
<dl class="docutils">
|
||||
<dt>* Commands to set internal energy and density of particles from the</dt>
|
||||
<dd>input script</dd>
|
||||
<dt>* Output commands to access internal energy and density for dumping and</dt>
|
||||
<dd>thermo output</dd>
|
||||
</dl>
|
||||
<p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
|
||||
<p>There are example scripts for using this package in examples/USER/sph.</p>
|
||||
<p>The person who created this package is Georg Ganzenmuller at the
|
||||
|
|
|
|||
|
|
@ -343,10 +343,10 @@ described above.</p>
|
|||
<p>If you set the paths to these files as environment variables, you only
|
||||
have to do it once. For the csh or tcsh shells, add something like
|
||||
this to your ~/.cshrc file, one line for each of the two files:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
|
||||
<pre class="literal-block">
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<p>If you use the python/install.py script, you need to invoke it every
|
||||
time you rebuild LAMMPS (as a shared library) or make changes to the
|
||||
python/lammps.py file.</p>
|
||||
|
|
@ -393,39 +393,21 @@ environment variable as described above.</p>
|
|||
your Python with an interface to MPI. This also allows you to
|
||||
make MPI calls directly from Python in your script, if you desire.</p>
|
||||
<p>There are several Python packages available that purport to wrap MPI
|
||||
as a library and allow MPI functions to be called from Python.</p>
|
||||
<p>These include</p>
|
||||
as a library and allow MPI functions to be called from Python. However,
|
||||
development on most of them seems to be halted except on:</p>
|
||||
<ul class="simple">
|
||||
<li><a class="reference external" href="http://pympi.sourceforge.net/">pyMPI</a></li>
|
||||
<li><a class="reference external" href="http://code.google.com/p/maroonmpi/">maroonmpi</a></li>
|
||||
<li><a class="reference external" href="http://code.google.com/p/mpi4py/">mpi4py</a></li>
|
||||
<li><a class="reference external" href="http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16">myMPI</a></li>
|
||||
<li><a class="reference external" href="http://code.google.com/p/pypar">Pypar</a></li>
|
||||
<li><a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a></li>
|
||||
<li><a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a></li>
|
||||
</ul>
|
||||
<p>All of these except pyMPI work by wrapping the MPI library and
|
||||
exposing (some portion of) its interface to your Python script. This
|
||||
means Python cannot be used interactively in parallel, since they do
|
||||
not address the issue of interactive input to multiple instances of
|
||||
Python running on different processors. The one exception is pyMPI,
|
||||
which alters the Python interpreter to address this issue, and (I
|
||||
believe) creates a new alternate executable (in place of “python”
|
||||
itself) as a result.</p>
|
||||
<p>In principle any of these Python/MPI packages should work to invoke
|
||||
LAMMPS in parallel and to make MPI calls themselves from a Python
|
||||
script which is itself running in parallel. However, when I
|
||||
downloaded and looked at a few of them, their documentation was
|
||||
incomplete and I had trouble with their installation. It’s not clear
|
||||
if some of the packages are still being actively developed and
|
||||
supported.</p>
|
||||
<p>The packages Pypar and mpi4py have both been successfully tested with
|
||||
LAMMPS. Pypar is simpler and easy to set up and use, but supports
|
||||
<p>Both packages, PyPar and mpi4py have been successfully tested with
|
||||
LAMMPS. PyPar is simpler and easy to set up and use, but supports
|
||||
only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
|
||||
bit more complex to use. As of version 2.0.0, mpi4py is the only
|
||||
python MPI wrapper that allows passing a custom MPI communicator to
|
||||
the LAMMPS constructor, which means one can easily run one or more
|
||||
LAMMPS instances on subsets of the total MPI ranks.</p>
|
||||
<hr class="docutils" />
|
||||
<p>Pypar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
|
||||
<p>PyPar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
|
||||
be installed in your Python. After launching Python, type</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span>
|
||||
</pre></div>
|
||||
|
|
@ -439,15 +421,15 @@ top-level directory, type</p>
|
|||
</div>
|
||||
<p>The “sudo” is only needed if required to copy Numpy files into your
|
||||
Python distribution’s site-packages directory.</p>
|
||||
<p>To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
|
||||
<p>To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it
|
||||
and from its “source” directory, type</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span>
|
||||
<span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Again, the “sudo” is only needed if required to copy Pypar files into
|
||||
<p>Again, the “sudo” is only needed if required to copy PyPar files into
|
||||
your Python distribution’s site-packages directory.</p>
|
||||
<p>If you have successully installed Pypar, you should be able to run
|
||||
<p>If you have successully installed PyPar, you should be able to run
|
||||
Python and type</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
|
||||
</pre></div>
|
||||
|
|
@ -465,17 +447,17 @@ on a simple test script</p>
|
|||
<p>and see one line of output for each processor you run on.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">To use Pypar and LAMMPS in parallel from Python, you must insure
|
||||
<p class="last">To use PyPar and LAMMPS in parallel from Python, you must insure
|
||||
both are using the same version of MPI. If you only have one MPI
|
||||
installed on your system, this is not an issue, but it can be if you
|
||||
have multiple MPIs. Your LAMMPS build is explicit about which MPI it
|
||||
is using, since you specify the details in your lo-level
|
||||
src/MAKE/Makefile.foo file. Pypar uses the “mpicc” command to find
|
||||
src/MAKE/Makefile.foo file. PyPar uses the “mpicc” command to find
|
||||
information about the MPI it uses to build against. And it tries to
|
||||
load “libmpi.so” from the LD_LIBRARY_PATH. This may or may not find
|
||||
the MPI library that LAMMPS is using. If you have problems running
|
||||
both Pypar and LAMMPS together, this is an issue you may need to
|
||||
address, e.g. by moving other MPI installations so that Pypar finds
|
||||
both PyPar and LAMMPS together, this is an issue you may need to
|
||||
address, e.g. by moving other MPI installations so that PyPar finds
|
||||
the right one.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -502,11 +484,11 @@ on a simple test script</p>
|
|||
</pre></div>
|
||||
</div>
|
||||
<p>where test.py contains the lines</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span>
|
||||
<span class="n">comm</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span>
|
||||
<span class="nb">print</span> <span class="s2">"Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs"</span> <span class="o">%</span> <span class="p">(</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">(),</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_size</span><span class="p">())</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
from mpi4py import MPI
|
||||
comm = MPI.COMM_WORLD
|
||||
print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())
|
||||
</pre>
|
||||
<p>and see one line of output for each processor you run on.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
|
|
@ -568,15 +550,15 @@ interactively from the bench directory:</p>
|
|||
<p>Either way, you should see the results of running the in.lj benchmark
|
||||
on a single processor appear on the screen, the same as if you had
|
||||
typed something like:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_g++ -in in.lj
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="test-lammps-and-python-in-parallel">
|
||||
<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></h3>
|
||||
<p>To run LAMMPS in parallel, assuming you have installed the
|
||||
<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file
|
||||
containing these lines:</p>
|
||||
<a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a> package as discussed
|
||||
above, create a test.py file containing these lines:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
|
||||
<span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
|
||||
|
|
@ -586,36 +568,36 @@ containing these lines:</p>
|
|||
</pre></div>
|
||||
</div>
|
||||
<p>To run LAMMPS in parallel, assuming you have installed the
|
||||
<a class="reference external" href="mpi4py">mpi4py</a> package as discussed above, create a test.py file
|
||||
containing these lines:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span>
|
||||
<span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">"in.lj"</span><span class="p">)</span>
|
||||
<span class="n">me</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">()</span>
|
||||
<span class="n">nprocs</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_size</span><span class="p">()</span>
|
||||
<span class="nb">print</span> <span class="s2">"Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs has"</span> <span class="o">%</span> <span class="p">(</span><span class="n">me</span><span class="p">,</span><span class="n">nprocs</span><span class="p">),</span><span class="n">lmp</span>
|
||||
<span class="n">MPI</span><span class="o">.</span><span class="n">Finalize</span><span class="p">()</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a> package as discussed
|
||||
above, create a test.py file containing these lines:</p>
|
||||
<pre class="literal-block">
|
||||
from mpi4py import MPI
|
||||
from lammps import lammps
|
||||
lmp = lammps()
|
||||
lmp.file("in.lj")
|
||||
me = MPI.COMM_WORLD.Get_rank()
|
||||
nprocs = MPI.COMM_WORLD.Get_size()
|
||||
print "Proc %d out of %d procs has" % (me,nprocs),lmp
|
||||
MPI.Finalize()
|
||||
</pre>
|
||||
<p>You can either script in parallel as:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">python</span> <span class="n">test</span><span class="o">.</span><span class="n">py</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>and you should see the same output as if you had typed</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Note that if you leave out the 3 lines from test.py that specify Pypar
|
||||
<pre class="literal-block">
|
||||
% mpirun -np 4 lmp_g++ -in in.lj
|
||||
</pre>
|
||||
<p>Note that if you leave out the 3 lines from test.py that specify PyPar
|
||||
commands you will instantiate and run LAMMPS independently on each of
|
||||
the P processors specified in the mpirun command. In this case you
|
||||
should get 4 sets of output, each showing that a LAMMPS run was made
|
||||
on a single processor, instead of one set of output showing that
|
||||
LAMMPS ran on 4 processors. If the 1-processor outputs occur, it
|
||||
means that Pypar is not working correctly.</p>
|
||||
<p>Also note that once you import the PyPar module, Pypar initializes MPI
|
||||
means that PyPar is not working correctly.</p>
|
||||
<p>Also note that once you import the PyPar module, PyPar initializes MPI
|
||||
for you, and you can use MPI calls directly in your Python script, as
|
||||
described in the Pypar documentation. The last line of your Python
|
||||
described in the PyPar documentation. The last line of your Python
|
||||
script should be pypar.finalize(), to insure MPI is shut down
|
||||
correctly.</p>
|
||||
</div>
|
||||
|
|
@ -661,14 +643,14 @@ Python script, as follows:</p>
|
|||
the files src/library.cpp and src/library.h you will see that they
|
||||
correspond one-to-one with calls you can make to the LAMMPS library
|
||||
from a C++ or C or Fortran program.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span> <span class="c1"># create a LAMMPS object using the default liblammps.so library</span>
|
||||
<span class="mi">4</span> <span class="n">optional</span> <span class="n">args</span> <span class="n">are</span> <span class="n">allowed</span><span class="p">:</span> <span class="n">name</span><span class="p">,</span> <span class="n">cmdargs</span><span class="p">,</span> <span class="n">ptr</span><span class="p">,</span> <span class="n">comm</span>
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span> <span class="c1"># use lmpptr as previously created LAMMPS object</span>
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">comm</span><span class="o">=</span><span class="n">split</span><span class="p">)</span> <span class="c1"># create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later</span>
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"g++"</span><span class="p">)</span> <span class="c1"># create a LAMMPS object using the liblammps_g++.so library</span>
|
||||
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"g++"</span><span class="p">,</span><span class="n">cmdargs</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span> <span class="c1"># add LAMMPS command-line args, e.g. list = ["-echo","screen"]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
|
||||
4 optional args are allowed: name, cmdargs, ptr, comm
|
||||
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
|
||||
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
|
||||
lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
|
||||
lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = ["-echo","screen"]
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c1"># destroy a LAMMPS object</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
|
|
@ -677,49 +659,49 @@ from a C++ or C or Fortran program.</p>
|
|||
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span> <span class="c1"># invoke a single LAMMPS command, cmd = "run 100"</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xlo</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_global</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract a global quantity</span>
|
||||
<span class="c1"># name = "boxxlo", "nlocal", etc</span>
|
||||
<span class="c1"># type = 0 = int</span>
|
||||
<span class="c1"># 1 = double</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">coords</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_atom</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract a per-atom quantity</span>
|
||||
<span class="c1"># name = "x", "type", etc</span>
|
||||
<span class="c1"># type = 0 = vector of ints</span>
|
||||
<span class="c1"># 1 = array of ints</span>
|
||||
<span class="c1"># 2 = vector of doubles</span>
|
||||
<span class="c1"># 3 = array of doubles</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">eng</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract value(s) from a compute</span>
|
||||
<span class="n">v3</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_fix</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">)</span> <span class="c1"># extract value(s) from a fix</span>
|
||||
<span class="c1"># id = ID of compute or fix</span>
|
||||
<span class="c1"># style = 0 = global data</span>
|
||||
<span class="c1"># 1 = per-atom data</span>
|
||||
<span class="c1"># 2 = local data</span>
|
||||
<span class="c1"># type = 0 = scalar</span>
|
||||
<span class="c1"># 1 = vector</span>
|
||||
<span class="c1"># 2 = array</span>
|
||||
<span class="c1"># i,j = indices of value in global vector or array</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">var</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">group</span><span class="p">,</span><span class="n">flag</span><span class="p">)</span> <span class="c1"># extract value(s) from a variable</span>
|
||||
<span class="c1"># name = name of variable</span>
|
||||
<span class="c1"># group = group ID (ignored for equal-style variables)</span>
|
||||
<span class="c1"># flag = 0 = equal-style variable</span>
|
||||
<span class="c1"># 1 = atom-style variable</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">flag</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">value</span><span class="p">)</span> <span class="c1"># set existing named string-style variable to value, flag = 0 if successful</span>
|
||||
<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span> <span class="c1"># total # of atoms as int</span>
|
||||
<span class="n">data</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">gather_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">)</span> <span class="c1"># return atom attribute of all atoms gathered into data, ordered by atom ID</span>
|
||||
<span class="c1"># name = "x", "charge", "type", etc</span>
|
||||
<span class="c1"># count = # of per-atom values, 1 or 3, etc</span>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> <span class="c1"># scatter atom attribute of all atoms from data, ordered by atom ID</span>
|
||||
<span class="c1"># name = "x", "charge", "type", etc</span>
|
||||
<span class="c1"># count = # of per-atom values, 1 or 3, etc</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
xlo = lmp.extract_global(name,type) # extract a global quantity
|
||||
# name = "boxxlo", "nlocal", etc
|
||||
# type = 0 = int
|
||||
# 1 = double
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
|
||||
# name = "x", "type", etc
|
||||
# type = 0 = vector of ints
|
||||
# 1 = array of ints
|
||||
# 2 = vector of doubles
|
||||
# 3 = array of doubles
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
|
||||
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
|
||||
# id = ID of compute or fix
|
||||
# style = 0 = global data
|
||||
# 1 = per-atom data
|
||||
# 2 = local data
|
||||
# type = 0 = scalar
|
||||
# 1 = vector
|
||||
# 2 = array
|
||||
# i,j = indices of value in global vector or array
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
|
||||
# name = name of variable
|
||||
# group = group ID (ignored for equal-style variables)
|
||||
# flag = 0 = equal-style variable
|
||||
# 1 = atom-style variable
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
|
||||
natoms = lmp.get_natoms() # total # of atoms as int
|
||||
data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
|
||||
# name = "x", "charge", "type", etc
|
||||
# count = # of per-atom values, 1 or 3, etc
|
||||
lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID
|
||||
# name = "x", "charge", "type", etc
|
||||
# count = # of per-atom values, 1 or 3, etc
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The lines</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
|
||||
|
|
@ -767,8 +749,8 @@ argument.</p>
|
|||
returned, which you can use via normal Python subscripting. See the
|
||||
extract() method in the src/atom.cpp file for a list of valid names.
|
||||
Again, new names could easily be added. A pointer to a vector of
|
||||
doubles or integers, or a pointer to an array of doubles (double <a href="#id3"><span class="problematic" id="id4">**</span></a>)
|
||||
or integers (int <a href="#id5"><span class="problematic" id="id6">**</span></a>) is returned. You need to specify the appropriate
|
||||
doubles or integers, or a pointer to an array of doubles (double **)
|
||||
or integers (int **) is returned. You need to specify the appropriate
|
||||
data type via the type argument.</p>
|
||||
<p>For extract_compute() and extract_fix(), the global, per-atom, or
|
||||
local data calulated by the compute or fix can be accessed. What is
|
||||
|
|
@ -824,19 +806,19 @@ consecutively ordered, no coordinates are reset.</p>
|
|||
<p>The array of coordinates passed to scatter_atoms() must be a ctypes
|
||||
vector of ints or doubles, allocated and initialized something like
|
||||
this:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ctypes</span> <span class="k">import</span> <span class="o">*</span>
|
||||
<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>
|
||||
<span class="n">n3</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="n">natoms</span>
|
||||
<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">n3</span><span class="o">*</span><span class="n">c_double</span><span class="p">)()</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">2</span>
|
||||
<span class="o">...</span>
|
||||
<span class="n">x</span><span class="p">[</span><span class="n">n3</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="n">natoms</span>
|
||||
<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_coords</span><span class="p">(</span><span class="s2">"x"</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="n">x</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
from ctypes import *
|
||||
natoms = lmp.get_natoms()
|
||||
n3 = 3*natoms
|
||||
x = (n3*c_double)()
|
||||
x[0] = x coord of atom with ID 1
|
||||
x[1] = y coord of atom with ID 1
|
||||
x[2] = z coord of atom with ID 1
|
||||
x[3] = x coord of atom with ID 2
|
||||
...
|
||||
x[n3-1] = z coord of atom with ID natoms
|
||||
lmp.scatter_coords("x",1,3,x)
|
||||
</pre>
|
||||
<p>Alternatively, you can just change values in the vector returned by
|
||||
gather_atoms(“x”,1,3), since it is a ctypes vector of doubles.</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -915,10 +897,10 @@ capability needed by these Python scripts.</p>
|
|||
open-source version of PyMol in your Python, so that you can import it
|
||||
from a Python script. See the PyMol WWW pages <a class="reference external" href="http://www.pymol.org">here</a> or
|
||||
<a class="reference external" href="http://sourceforge.net/scm/?type=svn&group_id=4546">here</a> for more details:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>http://www.pymol.org
|
||||
http://sourceforge.net/scm/?type=svn&group_id=4546
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
<a class="reference external" href="http://www.pymol.org">http://www.pymol.org</a>
|
||||
<a class="reference external" href="http://sourceforge.net/scm/?type=svn&group_id=4546">http://sourceforge.net/scm/?type=svn&group_id=4546</a>
|
||||
</pre>
|
||||
<p>The latter link is to the open-source version.</p>
|
||||
<p>Note that for VMD, you need a fairly current version (1.8.7 works for
|
||||
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
|
||||
|
|
|
|||
|
|
@ -173,10 +173,10 @@ experienced users.</p>
|
|||
<p>When you download a LAMMPS tarball you will need to unzip and untar
|
||||
the downloaded file with the following commands, after placing the
|
||||
tarball in an appropriate directory.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">gunzip</span> <span class="n">lammps</span><span class="o">*.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span>
|
||||
<span class="n">tar</span> <span class="n">xvf</span> <span class="n">lammps</span><span class="o">*.</span><span class="n">tar</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
gunzip lammps*.tar.gz
|
||||
tar xvf lammps*.tar
|
||||
</pre>
|
||||
<p>This will create a LAMMPS directory containing two files and several
|
||||
sub-directories:</p>
|
||||
<table border="1" class="docutils">
|
||||
|
|
@ -315,13 +315,13 @@ it will be never be touched by any LAMMPS updates.</p>
|
|||
a list of available choices from src/MAKE and all of its
|
||||
sub-directories. If one of those has the options you want or is the
|
||||
machine you want, you can type a command like:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">mpi</span>
|
||||
<span class="ow">or</span>
|
||||
<span class="n">make</span> <span class="n">serial_icc</span>
|
||||
<span class="ow">or</span>
|
||||
<span class="n">gmake</span> <span class="n">mac</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
make mpi
|
||||
or
|
||||
make serial_icc
|
||||
or
|
||||
gmake mac
|
||||
</pre>
|
||||
<p>Note that the corresponding Makefile.machine can exist in src/MAKE or
|
||||
any of its sub-directories. If a file with the same name appears in
|
||||
multiple places (not a good idea), the order they are used is as
|
||||
|
|
@ -362,13 +362,13 @@ then you should list them as part of the LIB variable. You should
|
|||
not need to do this if you use mpicxx.</p>
|
||||
<p>The DEPFLAGS setting is what triggers the C++ compiler to create a
|
||||
dependency list for a source file. This speeds re-compilation when
|
||||
source (<em>.cpp) or header (</em>.h) files are edited. Some compilers do
|
||||
source (*.cpp) or header (*.h) files are edited. Some compilers do
|
||||
not support dependency file creation, or may use a different switch
|
||||
than -D. GNU g++ and Intel icc works with -D. If your compiler can’t
|
||||
create dependency files, then you’ll need to create a Makefile.foo
|
||||
patterned after Makefile.storm, which uses different rules that do not
|
||||
involve dependency files. Note that when you build LAMMPS for the
|
||||
first time on a new platform, a long list of <a href="#id5"><span class="problematic" id="id6">*</span></a>.d files will be printed
|
||||
first time on a new platform, a long list of *.d files will be printed
|
||||
out rapidly. This is not an error; it is the Makefile doing its
|
||||
normal creation of dependencies.</p>
|
||||
<p><strong>Step 4</strong></p>
|
||||
|
|
@ -598,7 +598,7 @@ faster, depending on how many cores your compilation machine has. N
|
|||
is the number of cores the build runs on.</p>
|
||||
<p>You should get the executable lmp_foo when the build is complete.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-2-3"><a href="#id7"><span class="problematic" id="id8">**</span></a><em>Errors that can occur when making LAMMPS:</em>**</p>
|
||||
<p id="start-2-3"><a href="#id5"><span class="problematic" id="id6">**</span></a><em>Errors that can occur when making LAMMPS:</em>**</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">If an error occurs when building LAMMPS, the compiler or linker
|
||||
|
|
@ -632,17 +632,17 @@ is undefined’, then your machine does not support “long long”
|
|||
integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
|
||||
above in Step 4.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-2-4"><a href="#id9"><span class="problematic" id="id10">**</span></a><em>Additional build tips:</em>**</p>
|
||||
<p id="start-2-4"><a href="#id7"><span class="problematic" id="id8">**</span></a><em>Additional build tips:</em>**</p>
|
||||
<ol class="arabic simple">
|
||||
<li>Building LAMMPS for multiple platforms.</li>
|
||||
</ol>
|
||||
<p>You can make LAMMPS for multiple platforms from the same src
|
||||
directory. Each target creates its own object sub-directory called
|
||||
Obj_target where it stores the system-specific <a href="#id11"><span class="problematic" id="id12">*</span></a>.o files.</p>
|
||||
Obj_target where it stores the system-specific *.o files.</p>
|
||||
<ol class="arabic simple" start="2">
|
||||
<li>Cleaning up.</li>
|
||||
</ol>
|
||||
<p>Typing “make clean-all” or “make clean-machine” will delete <a href="#id13"><span class="problematic" id="id14">*</span></a>.o object
|
||||
<p>Typing “make clean-all” or “make clean-machine” will delete *.o object
|
||||
files created when LAMMPS is built, for either all builds or for a
|
||||
particular machine.</p>
|
||||
<p>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
|
||||
|
|
@ -686,11 +686,11 @@ basis is limited by 4-byte integer storage to 2^31 atoms per processor
|
|||
a problem would have a huge per-processor memory footprint due to
|
||||
neighbor lists and would run very slowly in terms of CPU secs/timestep.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-2-5"><a href="#id15"><span class="problematic" id="id16">**</span></a><em>Building for a Mac:</em>**</p>
|
||||
<p id="start-2-5"><a href="#id9"><span class="problematic" id="id10">**</span></a><em>Building for a Mac:</em>**</p>
|
||||
<p>OS X is BSD Unix, so it should just work. See the
|
||||
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-2-6"><a href="#id17"><span class="problematic" id="id18">**</span></a><em>Building for Windows:</em>**</p>
|
||||
<p id="start-2-6"><a href="#id11"><span class="problematic" id="id12">**</span></a><em>Building for Windows:</em>**</p>
|
||||
<p>The LAMMPS download page has an option to download both a serial and
|
||||
parallel pre-built Windows executable. See the <a class="reference internal" href="#start-6"><span class="std std-ref">Running LAMMPS</span></a> section for instructions on running these executables
|
||||
on a Windows box.</p>
|
||||
|
|
@ -725,7 +725,7 @@ tool which can be used to install/un-install packages and build the
|
|||
auxiliary libraries which some of them use. It can also auto-edit a
|
||||
Makefile.machine to add settings needed by some packages.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-3-1"><a href="#id19"><span class="problematic" id="id20">**</span></a><em>Package basics:</em>**</p>
|
||||
<p id="start-3-1"><a href="#id13"><span class="problematic" id="id14">**</span></a><em>Package basics:</em>**</p>
|
||||
<p>The source code for LAMMPS is structured as a set of core files which
|
||||
are always included, plus optional packages. Packages are groups of
|
||||
files that enable a specific set of features. For example, force
|
||||
|
|
@ -742,9 +742,9 @@ package, you must have built LAMMPS with that package, else you will
|
|||
get an error that the style is invalid or the command is unknown.
|
||||
Every command’s doc page specfies if it is part of a package. You can
|
||||
also type</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">h</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_machine -h
|
||||
</pre>
|
||||
<p>to run your executable with the optional <a class="reference internal" href="#start-7"><span class="std std-ref">-h command-line switch</span></a> for “help”, which will simply list the styles and
|
||||
commands known to your executable, and immediately exit.</p>
|
||||
<p>There are two kinds of packages in LAMMPS, standard and user packages.
|
||||
|
|
@ -768,7 +768,7 @@ Information on how to submit additions you make to LAMMPS as single
|
|||
files or either a standard or user-contributed package are given in
|
||||
<a class="reference internal" href="Section_modify.html#mod-15"><span class="std std-ref">this section</span></a> of the documentation.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-3-2"><a href="#id21"><span class="problematic" id="id22">**</span></a><em>Including/excluding packages:</em>**</p>
|
||||
<p id="start-3-2"><a href="#id15"><span class="problematic" id="id16">**</span></a><em>Including/excluding packages:</em>**</p>
|
||||
<p>To use (or not use) a package you must include it (or exclude it)
|
||||
before building LAMMPS. From the src directory, this is typically as
|
||||
simple as:</p>
|
||||
|
|
@ -837,7 +837,7 @@ sub-directory. Typing “make package-diff” lists all differences
|
|||
between these files. Again, type “make package” to see all of the
|
||||
package-related make options.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-3-3"><a href="#id23"><span class="problematic" id="id24">**</span></a><em>Packages that require extra libraries:</em>**</p>
|
||||
<p id="start-3-3"><a href="#id17"><span class="problematic" id="id18">**</span></a><em>Packages that require extra libraries:</em>**</p>
|
||||
<p>A few of the standard and user packages require additional auxiliary
|
||||
libraries. Many of them are provided with LAMMPS, in which case they
|
||||
must be compiled first, before LAMMPS is built, if you wish to include
|
||||
|
|
@ -908,7 +908,7 @@ needed soft links. Type “python install.py” for further instruction
|
|||
or settings in the lib/package/Makefile.lammps files are not correct,
|
||||
the LAMMPS build will typically fail.</p>
|
||||
<hr class="docutils" />
|
||||
<p id="start-3-4"><a href="#id25"><span class="problematic" id="id26">**</span></a><em>Packages that require Makefile.machine settings</em>**</p>
|
||||
<p id="start-3-4"><a href="#id19"><span class="problematic" id="id20">**</span></a><em>Packages that require Makefile.machine settings</em>**</p>
|
||||
<p>A few packages require specific settings in Makefile.machine, to
|
||||
either build or use the package effectively. These are the
|
||||
USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
|
||||
|
|
@ -1081,7 +1081,7 @@ LAMMPS to other codes. See <a class="reference internal" href="Section_python.h
|
|||
more info on wrapping and running LAMMPS from Python.</p>
|
||||
<div class="section" id="static-library">
|
||||
<h3>2.5.1. <strong>Static library:</strong></h3>
|
||||
<p>To build LAMMPS as a static library (<a href="#id27"><span class="problematic" id="id28">*</span></a>.a file on Linux), type</p>
|
||||
<p>To build LAMMPS as a static library (*.a file on Linux), type</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">lib</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
|
|
@ -1095,7 +1095,7 @@ point to the most recently built static library.</p>
|
|||
</div>
|
||||
<div class="section" id="shared-library">
|
||||
<h3>2.5.2. <strong>Shared library:</strong></h3>
|
||||
<p>To build LAMMPS as a shared library (<a href="#id29"><span class="problematic" id="id30">*</span></a>.so file on Linux), which can be
|
||||
<p>To build LAMMPS as a shared library (*.so file on Linux), which can be
|
||||
dynamically loaded, e.g. from Python, type</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">shlib</span>
|
||||
</pre></div>
|
||||
|
|
@ -1122,18 +1122,18 @@ of the auxiliary library. The build instructions for the library
|
|||
should tell you how to do this.</p>
|
||||
<p>Here is an example of such errors when the system FFTW or provided
|
||||
lib/colvars library have not been built as shared libraries:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
|
||||
R_X86_64_32 against `.rodata' can not be used when making a shared
|
||||
<pre class="literal-block">
|
||||
/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
|
||||
R_X86_64_32 against '.rodata' can not be used when making a shared
|
||||
object; recompile with -fPIC
|
||||
/usr/local/lib/libfftw3.a: could not read symbols: Bad value
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
|
||||
relocation R_X86_64_32 against `__pthread_key_create' can not be used
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
|
||||
relocation R_X86_64_32 against '__pthread_key_create' can not be used
|
||||
when making a shared object; recompile with -fPIC
|
||||
../../lib/colvars/libcolvars.a: error adding symbols: Bad value
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<p>As an example, here is how to build and install the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPICH library</a>, a popular open-source version of MPI, distributed by
|
||||
Argonne National Labs, as a shared library in the default
|
||||
/usr/local/lib location:</p>
|
||||
|
|
@ -1157,9 +1157,9 @@ current version of the shared library is always available to programs
|
|||
that use it.</p>
|
||||
<p>For the csh or tcsh shells, you would add something like this to your
|
||||
~/.cshrc file:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="calling-the-lammps-library">
|
||||
<h3>2.5.4. <strong>Calling the LAMMPS library:</strong></h3>
|
||||
|
|
@ -1188,20 +1188,20 @@ interface and how to extend it for your needs.</p>
|
|||
<span id="start-6"></span><h2>2.6. Running LAMMPS</h2>
|
||||
<p>By default, LAMMPS runs by reading commands from standard input. Thus
|
||||
if you run the LAMMPS executable by itself, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_linux
|
||||
</pre>
|
||||
<p>it will simply wait, expecting commands from the keyboard. Typically
|
||||
you should put commands in an input script and use I/O redirection,
|
||||
e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span> <span class="o"><</span> <span class="ow">in</span><span class="o">.</span><span class="n">file</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_linux < in.file
|
||||
</pre>
|
||||
<p>For parallel environments this should also work. If it does not, use
|
||||
the ‘-in’ command-line switch, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">file</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_linux -in in.file
|
||||
</pre>
|
||||
<p><a class="reference internal" href="Section_commands.html"><span class="doc">This section</span></a> describes how input scripts are
|
||||
structured and what commands they contain.</p>
|
||||
<p>You can test LAMMPS on any of the sample inputs provided in the
|
||||
|
|
@ -1210,13 +1210,13 @@ outputs are named log.*.name.P where name is a machine and P is the
|
|||
number of processors it was run on.</p>
|
||||
<p>Here is how you might run a standard Lennard-Jones benchmark on a
|
||||
Linux box, using mpirun to launch a parallel job:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">linux</span>
|
||||
<span class="n">cp</span> <span class="n">lmp_linux</span> <span class="o">../</span><span class="n">bench</span>
|
||||
<span class="n">cd</span> <span class="o">../</span><span class="n">bench</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
cd src
|
||||
make linux
|
||||
cp lmp_linux ../bench
|
||||
cd ../bench
|
||||
mpirun -np 4 lmp_linux -in in.lj
|
||||
</pre>
|
||||
<p>See <a class="reference external" href="http://lammps.sandia.gov/bench.html">this page</a> for timings for this and the other benchmarks on
|
||||
various platforms. Note that some of the example scripts require
|
||||
LAMMPS to be built with one or more of its optional packages.</p>
|
||||
|
|
@ -1256,7 +1256,7 @@ in.lj”, replacing in.lj with the name of your LAMMPS input script.</li>
|
|||
matter what you type).</li>
|
||||
<li>In this mode, output may not immediately show up on the screen, so if
|
||||
your input script takes a long time to execute, you may need to be
|
||||
patient before the output shows up. :l Alternatively, you can still
|
||||
patient before the output shows up. Alternatively, you can still
|
||||
use this executable to run on a single processor by typing something
|
||||
like: “lmp_win_mpi -in in.lj”.</li>
|
||||
</ul>
|
||||
|
|
@ -1309,10 +1309,10 @@ letter abbreviation can be used:</p>
|
|||
<li>-v or -var</li>
|
||||
</ul>
|
||||
<p>For example, lmp_ibm might be launched as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">v</span> <span class="n">f</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="o">-</span><span class="n">l</span> <span class="n">my</span><span class="o">.</span><span class="n">log</span> <span class="o">-</span><span class="n">sc</span> <span class="n">none</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">alloy</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">var</span> <span class="n">f</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="o">-</span><span class="n">log</span> <span class="n">my</span><span class="o">.</span><span class="n">log</span> <span class="o">-</span><span class="n">screen</span> <span class="n">none</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">alloy</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
|
||||
mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
|
||||
</pre>
|
||||
<p>Here are the details on the options:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">echo</span> <span class="n">style</span>
|
||||
</pre></div>
|
||||
|
|
@ -1395,11 +1395,11 @@ are intended for computational work like running LAMMPS. By default
|
|||
Ng = 1 and Ns is not set.</p>
|
||||
<p>Depending on which flavor of MPI you are running, LAMMPS will look for
|
||||
one of these 3 environment variables</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">SLURM_LOCALID</span> <span class="p">(</span><span class="n">various</span> <span class="n">MPI</span> <span class="n">variants</span> <span class="n">compiled</span> <span class="k">with</span> <span class="n">SLURM</span> <span class="n">support</span><span class="p">)</span>
|
||||
<span class="n">MV2_COMM_WORLD_LOCAL_RANK</span> <span class="p">(</span><span class="n">Mvapich</span><span class="p">)</span>
|
||||
<span class="n">OMPI_COMM_WORLD_LOCAL_RANK</span> <span class="p">(</span><span class="n">OpenMPI</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
SLURM_LOCALID (various MPI variants compiled with SLURM support)
|
||||
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
|
||||
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
|
||||
</pre>
|
||||
<p>which are initialized by the “srun”, “mpirun” or “mpiexec” commands.
|
||||
The environment variable setting for each MPI rank is used to assign a
|
||||
unique GPU ID to the MPI task.</p>
|
||||
|
|
|
|||
|
|
@ -218,7 +218,7 @@ own sub-directories with their own Makefiles.</p>
|
|||
<li><a class="reference internal" href="#polybond"><span class="std std-ref">polymer bonding</span></a></li>
|
||||
<li><span class="xref std std-ref">pymol_asphere</span></li>
|
||||
<li><a class="reference internal" href="#pythontools"><span class="std std-ref">python</span></a></li>
|
||||
<li><a class="reference internal" href="#reax"><span class="std std-ref">reax</span></a></li>
|
||||
<li><a class="reference internal" href="#reax-tool"><span class="std std-ref">reax</span></a></li>
|
||||
<li><a class="reference internal" href="#restart"><span class="std std-ref">restart2data</span></a></li>
|
||||
<li><a class="reference internal" href="#vim"><span class="std std-ref">vim</span></a></li>
|
||||
<li><a class="reference internal" href="#xmgrace"><span class="std std-ref">xmgrace</span></a></li>
|
||||
|
|
@ -289,9 +289,9 @@ at: <a class="reference external" href="https://github.com/colvars/colvars/issue
|
|||
<p>abf_integrate:</p>
|
||||
<p>MC-based integration of multidimensional free energy gradient
|
||||
Version 20110511</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Syntax</span><span class="p">:</span> <span class="o">./</span><span class="n">abf_integrate</span> <span class="o"><</span> <span class="n">filename</span> <span class="o">></span> <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="o"><</span> <span class="n">nsteps</span> <span class="o">></span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">t</span> <span class="o"><</span> <span class="n">temp</span> <span class="o">></span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">m</span> <span class="p">[</span><span class="mi">0</span><span class="o">|</span><span class="mi">1</span><span class="p">]</span> <span class="p">(</span><span class="n">metadynamics</span><span class="p">)]</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span> <span class="o"><</span> <span class="n">hill_height</span> <span class="o">></span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span> <span class="o"><</span> <span class="n">variable_hill_factor</span> <span class="o">></span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
|
||||
</pre>
|
||||
<p>The LAMMPS interface to the colvars collective variable library, as
|
||||
well as these tools, were created by Axel Kohlmeyer (akohlmey at
|
||||
gmail.com) at ICTP, Italy.</p>
|
||||
|
|
@ -419,7 +419,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
|
|||
<div class="section" id="lmp2cfg-tool">
|
||||
<span id="cfg"></span><h2>9.17. lmp2cfg tool</h2>
|
||||
<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
|
||||
files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the
|
||||
files into a series of *.cfg files which can be read into the
|
||||
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See
|
||||
the README file for more information.</p>
|
||||
<p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p>
|
||||
|
|
@ -538,7 +538,7 @@ README for more info on Pizza.py and how to use these scripts.</p>
|
|||
<hr class="docutils" />
|
||||
</div>
|
||||
<div class="section" id="reax-tool">
|
||||
<span id="reax"></span><h2>9.27. reax tool</h2>
|
||||
<span id="id4"></span><h2>9.27. reax tool</h2>
|
||||
<p>The reax sub-directory contains stand-alond codes that can
|
||||
post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>
|
||||
command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><span class="doc">ReaxFF</span></a>. See
|
||||
|
|
|
|||
|
|
@ -202,11 +202,11 @@ attention to 3 settings in this makefile.</p>
|
|||
<p>See lib/gpu/Makefile.linux.double for examples of the ARCH settings
|
||||
for different GPU choices, e.g. Fermi vs Kepler. It also lists the
|
||||
possible precision settings:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_SINGLE</span> <span class="c1"># single precision for all calculations</span>
|
||||
<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_DOUBLE_DOUBLE</span> <span class="c1"># double precision for all calculations</span>
|
||||
<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_DOUBLE</span> <span class="c1"># accumulation of forces, etc, in double</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
CUDA_PREC = -D_SINGLE_SINGLE # single precision for all calculations
|
||||
CUDA_PREC = -D_DOUBLE_DOUBLE # double precision for all calculations
|
||||
CUDA_PREC = -D_SINGLE_DOUBLE # accumulation of forces, etc, in double
|
||||
</pre>
|
||||
<p>The last setting is the mixed mode referred to above. Note that your
|
||||
GPU must support double precision to use either the 2nd or 3rd of
|
||||
these settings.</p>
|
||||
|
|
@ -253,11 +253,11 @@ shared by 4 MPI tasks.</p>
|
|||
which will automatically append “gpu” to styles that support it. Use
|
||||
the “-pk gpu Ng” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to
|
||||
set Ng = # of GPUs/node to use.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task uses 1 GPU</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">48</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># ditto on 4 16-core nodes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
|
||||
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
|
||||
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
|
||||
</pre>
|
||||
<p>Note that if the “-sf gpu” switch is used, it also issues a default
|
||||
<a class="reference internal" href="package.html"><span class="doc">package gpu 1</span></a> command, which sets the number of
|
||||
GPUs/node to 1.</p>
|
||||
|
|
@ -276,9 +276,9 @@ GPU package pair styles.</p>
|
|||
and use of multiple MPI tasks/GPU is the same.</p>
|
||||
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix gpu</span></a> command, or you can explicitly add an
|
||||
“gpu” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">gpu</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
pair_style lj/cut/gpu 2.5
|
||||
</pre>
|
||||
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a> command to enable the
|
||||
GPU package, unless the “-sf gpu” or “-pk gpu” <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> were used. It specifies the
|
||||
number of GPUs/node to use, as well as other options.</p>
|
||||
|
|
|
|||
|
|
@ -268,30 +268,30 @@ this information can normally be obtained with:</p>
|
|||
</div>
|
||||
<p>Several example Makefiles for building with the Intel compiler are
|
||||
included with LAMMPS in the src/MAKE/OPTIONS/ directory:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_intelmpi</span> <span class="c1"># Intel Compiler, Intel MPI, No Offload</span>
|
||||
<span class="n">Makefile</span><span class="o">.</span><span class="n">knl</span> <span class="c1"># Intel Compiler, Intel MPI, No Offload</span>
|
||||
<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_mpich</span> <span class="c1"># Intel Compiler, MPICH, No Offload</span>
|
||||
<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_openpmi</span> <span class="c1"># Intel Compiler, OpenMPI, No Offload</span>
|
||||
<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_coprocessor</span> <span class="c1"># Intel Compiler, Intel MPI, Offload</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
|
||||
Makefile.knl # Intel Compiler, Intel MPI, No Offload
|
||||
Makefile.intel_cpu_mpich # Intel Compiler, MPICH, No Offload
|
||||
Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload
|
||||
Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload
|
||||
</pre>
|
||||
<p>Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
|
||||
it explicitly specifies that vectorization should be for Intel
|
||||
Xeon Phi x200 processors making it easier to cross-compile. For
|
||||
users with recent installations of Intel Parallel Studio, the
|
||||
process can be as simple as:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">user</span><span class="o">-</span><span class="n">intel</span>
|
||||
<span class="n">source</span> <span class="o">/</span><span class="n">opt</span><span class="o">/</span><span class="n">intel</span><span class="o">/</span><span class="n">parallel_studio_xe_2016</span><span class="o">.</span><span class="mf">3.067</span><span class="o">/</span><span class="n">psxevars</span><span class="o">.</span><span class="n">sh</span>
|
||||
<span class="c1"># or psxevars.csh for C-shell</span>
|
||||
<span class="n">make</span> <span class="n">intel_cpu_intelmpi</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
make yes-user-intel
|
||||
source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
|
||||
# or psxevars.csh for C-shell
|
||||
make intel_cpu_intelmpi
|
||||
</pre>
|
||||
<p>Alternatively, the build can be accomplished with the src/Make.py
|
||||
script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the
|
||||
manual. Type “Make.py -h” for help. For an example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">intel</span> <span class="n">cpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">intel_cpu_intelmpi</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi
|
||||
</pre>
|
||||
<p>Note that if you build with support for a Phi coprocessor, the same
|
||||
binary can be used on nodes with or without coprocessors installed.
|
||||
However, if you do not have coprocessors on your system, building
|
||||
|
|
@ -385,10 +385,10 @@ set the number of OpenMP threads via the OMP_NUM_THREADS environment
|
|||
variable if desired.</p>
|
||||
<p>Examples (see documentation for your MPI/Machine for differences in
|
||||
launching MPI applications):</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">72</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">36</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">72</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">36</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">0</span> <span class="n">omp</span> <span class="mi">2</span> <span class="n">mode</span> <span class="n">double</span> <span class="c1"># Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
|
||||
mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision
|
||||
</pre>
|
||||
<p><strong>Or run with the USER-INTEL package by editing an input script:</strong></p>
|
||||
<p>As an alternative to adding command-line arguments, the input script
|
||||
can be edited to enable the USER-INTEL package. This requires adding
|
||||
|
|
@ -399,9 +399,9 @@ script. For the second example above, this would be:</p>
|
|||
</div>
|
||||
<p>To enable the USER-INTEL package only for individual styles, you can
|
||||
add an “intel” suffix to the individual style, e.g.:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">intel</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
pair_style lj/cut/intel 2.5
|
||||
</pre>
|
||||
<p>Alternatively, the <a class="reference internal" href="suffix.html"><span class="doc">suffix intel</span></a> command can be added to
|
||||
the input script to enable USER-INTEL styles for the commands that
|
||||
follow in the input script.</p>
|
||||
|
|
|
|||
|
|
@ -166,19 +166,19 @@ produce an executable compatible with specific hardware.</p>
|
|||
<p>Here is a quick overview of how to use the KOKKOS package
|
||||
for CPU acceleration, assuming one or more 16-core nodes.
|
||||
More details follow.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">mpi</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> <span class="c1"># build with the KOKKOS package</span>
|
||||
<span class="n">make</span> <span class="n">kokkos_omp</span> <span class="c1"># or Makefile.kokkos_omp already has variable set</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 node, 16 MPI tasks/node, no threads</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">16</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 2 nodes, 1 MPI task/node, 16 threads/task</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 node, 2 MPI tasks/node, 8 threads/task</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">4</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
use a C++11 compatible compiler
|
||||
make yes-kokkos
|
||||
make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package
|
||||
make kokkos_omp # or Makefile.kokkos_omp already has variable set
|
||||
Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads
|
||||
mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
|
||||
mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
|
||||
mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support</li>
|
||||
<li>include the KOKKOS package and build LAMMPS</li>
|
||||
|
|
@ -188,39 +188,39 @@ More details follow.</p>
|
|||
assuming one or more nodes, each with 16 cores and a GPU. More
|
||||
details follow.</p>
|
||||
<p>discuss use of NVCC, which Makefiles to examine</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
|
||||
<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">Cuda</span><span class="p">,</span> <span class="n">OpenMP</span>
|
||||
<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">Kepler35</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">machine</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">cuda</span> <span class="n">arch</span><span class="o">=</span><span class="mi">31</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_cuda</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">kokkos_cuda</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># one MPI task, 6 threads on CPU</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 4 nodes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># two MPI tasks, 8 threads per CPU</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 16 nodes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
use a C++11 compatible compiler
|
||||
KOKKOS_DEVICES = Cuda, OpenMP
|
||||
KOKKOS_ARCH = Kepler35
|
||||
make yes-kokkos
|
||||
make machine
|
||||
Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
|
||||
mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
|
||||
mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
|
||||
</pre>
|
||||
<p>Here is a quick overview of how to use the KOKKOS package
|
||||
for the Intel Phi:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span>
|
||||
<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">OpenMP</span>
|
||||
<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">machine</span>
|
||||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">phi</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_phi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">host</span><span class="o">=</span><span class="n">MIC</span><span class="p">,</span> <span class="n">Intel</span> <span class="n">Phi</span> <span class="k">with</span> <span class="mi">61</span> <span class="n">cores</span> <span class="p">(</span><span class="mi">240</span> <span class="n">threads</span><span class="o">/</span><span class="n">phi</span> <span class="n">via</span> <span class="mi">4</span><span class="n">x</span> <span class="n">hardware</span> <span class="n">threading</span><span class="p">):</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">240</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 MPI task on 1 Phi, 1*240 = 240</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">30</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 30 MPI tasks on 1 Phi, 30*8 = 240</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 12 MPI tasks on 1 Phi, 12*20 = 240</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">96</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 8 Phis</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
use a C++11 compatible compiler
|
||||
KOKKOS_DEVICES = OpenMP
|
||||
KOKKOS_ARCH = KNC
|
||||
make yes-kokkos
|
||||
make machine
|
||||
Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
|
||||
mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
|
||||
mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
|
||||
mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
|
||||
mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
|
||||
</pre>
|
||||
<p><strong>Required hardware/software:</strong></p>
|
||||
<p>Kokkos support within LAMMPS must be built with a C++11 compatible
|
||||
compiler. If using gcc, version 4.8.1 or later is required.</p>
|
||||
|
|
@ -257,40 +257,40 @@ respectively. Or the effect of the “-pk” or “-sf” switc
|
|||
duplicated by adding the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> commands respectively to your input script.</p>
|
||||
<p>Or you can follow these steps:</p>
|
||||
<p>CPU-only (run all-MPI or with OpenMP threading):</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
cd lammps/src
|
||||
make yes-kokkos
|
||||
make g++ KOKKOS_DEVICES=OpenMP
|
||||
</pre>
|
||||
<p>Intel Xeon Phi:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> <span class="n">KOKKOS_ARCH</span><span class="o">=</span><span class="n">KNC</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
cd lammps/src
|
||||
make yes-kokkos
|
||||
make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
|
||||
</pre>
|
||||
<p>CPUs and GPUs:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span>
|
||||
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span>
|
||||
<span class="n">make</span> <span class="n">cuda</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">Cuda</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
cd lammps/src
|
||||
make yes-kokkos
|
||||
make cuda KOKKOS_DEVICES=Cuda
|
||||
</pre>
|
||||
<p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
|
||||
make command line which requires a GNU-compatible make command. Try
|
||||
“gmake” if your system’s standard make complains.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">If you build using make line variables and re-build LAMMPS twice
|
||||
with different KOKKOS options and the <em>same</em> target, e.g. g++ in the
|
||||
first two examples above, then you <em>must</em> perform a “make clean-all”
|
||||
with different KOKKOS options and the *same* target, e.g. g++ in the
|
||||
first two examples above, then you *must* perform a “make clean-all”
|
||||
or “make clean-machine” before each build. This is to force all the
|
||||
KOKKOS-dependent files to be re-compiled with the new options.</p>
|
||||
</div>
|
||||
<p>You can also hardwire these make variables in the specified machine
|
||||
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
|
||||
with a line like:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
KOKKOS_ARCH = KNC
|
||||
</pre>
|
||||
<p>Note that if you build LAMMPS multiple times in this manner, using
|
||||
different KOKKOS options (defined in different machine makefiles), you
|
||||
do not have to worry about doing a “clean” in between. This is
|
||||
|
|
@ -342,7 +342,7 @@ with compute capability 3.x. For the LINK setting, “nvcc” should no
|
|||
be used; instead use g++ or another compiler suitable for linking C++
|
||||
applications. Often you will want to use your MPI compiler wrapper
|
||||
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
|
||||
also have a “Compilation rule” for creating <a href="#id1"><span class="problematic" id="id2">*</span></a>.o files from <a href="#id3"><span class="problematic" id="id4">*</span></a>.cu files.
|
||||
also have a “Compilation rule” for creating *.o files from *.cu files.
|
||||
See src/Makefile.cuda for an example of a lo-level Makefile with all
|
||||
of these settings.</p>
|
||||
<p>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
|
||||
|
|
@ -430,9 +430,9 @@ specify its additional arguments for hardware options appopriate to
|
|||
your system, as documented above.</p>
|
||||
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> command, or you can explicitly add a
|
||||
“kk” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">kk</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
pair_style lj/cut/kk 2.5
|
||||
</pre>
|
||||
<p>You only need to use the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> command if you
|
||||
wish to change any of its option defaults, as set by the “-k on”
|
||||
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p>
|
||||
|
|
@ -483,10 +483,10 @@ performance to bind both MPI tasks to physical cores, and threads to
|
|||
physical cores, so they do not migrate during a simulation.</p>
|
||||
<p>If you are not certain MPI tasks are being bound (check the defaults
|
||||
for your MPI installation), binding can be forced with these flags:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">OpenMPI</span> <span class="mf">1.8</span><span class="p">:</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_openmpi</span> <span class="o">...</span>
|
||||
<span class="n">Mvapich2</span> <span class="mf">2.0</span><span class="p">:</span> <span class="n">mpiexec</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_mvapich</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
|
||||
Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
|
||||
</pre>
|
||||
<p>For binding threads with the KOKKOS OMP option, use thread affinity
|
||||
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
|
||||
later, intel 12 or later) setting the environment variable
|
||||
|
|
|
|||
|
|
@ -141,11 +141,11 @@ one or more 16-core nodes. More details follow.</p>
|
|||
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">16</span> <span class="o"><</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task, 16 threads</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 4 MPI tasks, 4 threads/task</span>
|
||||
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads
|
||||
mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
|
||||
mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task
|
||||
</pre>
|
||||
<p><strong>Required hardware/software:</strong></p>
|
||||
<p>Your compiler must support the OpenMP interface. You should have one
|
||||
or more multi-core CPUs so that multiple threads can be launched by
|
||||
|
|
@ -184,9 +184,9 @@ threads via the OMP_NUM_THREADS environment variable.</p>
|
|||
and threads/MPI task is the same.</p>
|
||||
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix omp</span></a> command, or you can explicitly add an
|
||||
“omp” suffix to individual styles in your input script, e.g.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">omp</span> <span class="mf">2.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
pair_style lj/cut/omp 2.5
|
||||
</pre>
|
||||
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command to enable the
|
||||
USER-OMP package. When you do this you also specify how many threads
|
||||
per MPI task to use. The command doc page explains other options and
|
||||
|
|
|
|||
|
|
@ -137,16 +137,16 @@
|
|||
<h1>angle_style charmm/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style charmm
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span> <span class="mf">50.0</span> <span class="mf">3.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style charmm
|
||||
angle_coeff 1 300.0 107.0 50.0 3.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,18 +131,18 @@
|
|||
<h1>angle_style class2/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style class2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="n">bb</span> <span class="mf">10.5872</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="n">ba</span> <span class="mf">3.6551</span> <span class="mf">24.895</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style class2
|
||||
angle_coeff * 75.0
|
||||
angle_coeff 1 bb 10.5872 1.0119 1.5228
|
||||
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style cosine/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine
|
||||
angle_coeff * 75.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style cosine/delta/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/delta
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/delta
|
||||
angle_coeff 2*4 75.0 100.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style cosine/periodic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/periodic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span> <span class="mi">1</span> <span class="mi">6</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/periodic
|
||||
angle_coeff * 75.0 1 6
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style cosine/shift/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/shift
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/shift
|
||||
angle_coeff * 10.0 45.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style cosine/shift/exp/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/shift/exp
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
|
||||
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/shift/exp
|
||||
angle_coeff * 10.0 45.0 2.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style cosine/squared/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/squared
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style cosine/squared
|
||||
angle_coeff 2*4 75.0 100.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style dipole/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style dipole
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">6</span> <span class="mf">2.1</span> <span class="mf">180.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style dipole
|
||||
angle_coeff 6 2.1 180.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,9 +131,9 @@
|
|||
<h1>angle_style fourier/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style fourier
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
|
|
|
|||
|
|
@ -131,9 +131,9 @@
|
|||
<h1>angle_style fourier/simple/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span><span class="o">/</span><span class="n">simple</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style fourier/simple
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
|
|
|
|||
|
|
@ -137,16 +137,16 @@
|
|||
<h1>angle_style harmonic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style harmonic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style harmonic
|
||||
angle_coeff 1 300.0 107.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>angle_style quartic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style quartic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">129.1948</span> <span class="mf">56.8726</span> <span class="o">-</span><span class="mf">25.9442</span> <span class="o">-</span><span class="mf">14.2221</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style quartic
|
||||
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -128,19 +128,19 @@
|
|||
<span id="index-0"></span><h1>angle_style sdk command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span><span class="o">/</span><span class="n">omp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style sdk
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
angle_style sdk/omp
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
|
||||
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
angle_style sdk
|
||||
angle_coeff 1 300.0 107.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>atom_modify command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
atom_modify keyword values ...
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>one or more keyword/value pairs may be appended</li>
|
||||
<li>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></li>
|
||||
|
|
@ -146,11 +146,11 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="nb">map</span> <span class="nb">hash</span>
|
||||
<span class="n">atom_modify</span> <span class="nb">map</span> <span class="n">array</span> <span class="n">sort</span> <span class="mi">10000</span> <span class="mf">2.0</span>
|
||||
<span class="n">atom_modify</span> <span class="n">first</span> <span class="n">colloid</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
atom_modify map hash
|
||||
atom_modify map array sort 10000 2.0
|
||||
atom_modify first colloid
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>atom_style command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">style</span> <span class="n">args</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
atom_style style args
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>dpd</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
|
||||
</ul>
|
||||
|
|
@ -150,15 +150,15 @@ args = none for any style except the following
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">atomic</span>
|
||||
<span class="n">atom_style</span> <span class="n">bond</span>
|
||||
<span class="n">atom_style</span> <span class="n">full</span>
|
||||
<span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">10</span>
|
||||
<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">bond</span>
|
||||
<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">5</span>
|
||||
<span class="n">atom_style</span> <span class="n">template</span> <span class="n">myMols</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
atom_style atomic
|
||||
atom_style bond
|
||||
atom_style full
|
||||
atom_style body nparticle 2 10
|
||||
atom_style hybrid charge bond
|
||||
atom_style hybrid charge body nparticle 2 5
|
||||
atom_style template myMols
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -247,11 +247,11 @@ mentioned above, the <a class="reference internal" href="fix_rigid.html"><span c
|
|||
duplicates its functionality.</p>
|
||||
<p>The atom_style body command for this body style takes two additional
|
||||
arguments:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
|
||||
<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of sub-particles in any body in the system</span>
|
||||
<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of sub-particles in any body in the system</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
atom_style body nparticle Nmin Nmax
|
||||
Nmin = minimum # of sub-particles in any body in the system
|
||||
Nmax = maximum # of sub-particles in any body in the system
|
||||
</pre>
|
||||
<p>The Nmin and Nmax arguments are used to bound the size of data
|
||||
structures used internally by each particle.</p>
|
||||
<p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
|
||||
|
|
@ -313,11 +313,11 @@ used for 2d models. One example use of this body style is for 2d
|
|||
discrete element models, as described in <a class="reference internal" href="#fraige"><span class="std std-ref">Fraige</span></a>. Similar to
|
||||
body style <em>nparticle</em>, the atom_style body command for this body
|
||||
style takes two additional arguments:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">rounded</span><span class="o">/</span><span class="n">polygon</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
|
||||
<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of vertices in any body in the system</span>
|
||||
<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of vertices in any body in the system</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
atom_style body rounded/polygon Nmin Nmax
|
||||
Nmin = minimum # of vertices in any body in the system
|
||||
Nmax = maximum # of vertices in any body in the system
|
||||
</pre>
|
||||
<p>The Nmin and Nmax arguments are used to bound the size of data
|
||||
structures used internally by each particle.</p>
|
||||
<p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>bond_style class2/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style class2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">100.0</span> <span class="mf">80.0</span> <span class="mf">80.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style class2
|
||||
bond_coeff 1 1.0 100.0 80.0 80.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -137,16 +137,16 @@
|
|||
<h1>bond_style fene/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style fene
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>bond_style fene/expand/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style fene/expand
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style fene/expand
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -137,16 +137,16 @@
|
|||
<h1>bond_style harmonic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style harmonic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style harmonic
|
||||
bond_coeff 5 80.0 1.2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>bond_style harmonic/shift/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style harmonic/shift
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style harmonic/shift
|
||||
bond_coeff 5 10.0 0.5 1.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>bond_style harmonic/shift/cut/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style harmonic/shift/cut
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style harmonic/shift/cut
|
||||
bond_coeff 5 10.0 0.5 1.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>bond_style morse/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style morse
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">1.0</span> <span class="mf">2.0</span> <span class="mf">1.2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style morse
|
||||
bond_coeff 5 1.0 2.0 1.2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>bond_style nonlinear/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style nonlinear
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">100.0</span> <span class="mf">1.1</span> <span class="mf">1.4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style nonlinear
|
||||
bond_coeff 2 100.0 1.1 1.4
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>bond_style quartic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style quartic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
|
||||
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mi">1200</span> <span class="o">-</span><span class="mf">0.55</span> <span class="mf">0.25</span> <span class="mf">1.3</span> <span class="mf">34.6878</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
bond_style quartic
|
||||
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -184,10 +184,10 @@ to 1,1,1, as indicated as a restriction below.</p>
|
|||
<p>Note that when bonds are dumped to a file via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command, bonds with type 0 are not included. The
|
||||
<a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command can also be used to query the
|
||||
status of broken bonds or permanently delete them, e.g.:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
|
||||
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span> <span class="n">remove</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
delete_bonds all stats
|
||||
delete_bonds all bond 0 remove
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>change_box command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">parameter</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
change_box group-ID parameter args ... keyword args ...
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>group-ID = ID of group of atoms to (optionally) displace</li>
|
||||
<li>one or more parameter/arg pairs may be appended</li>
|
||||
|
|
@ -175,10 +175,10 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em>
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">xy</span> <span class="n">final</span> <span class="o">-</span><span class="mf">2.0</span> <span class="n">z</span> <span class="n">final</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">f</span> <span class="n">remap</span> <span class="n">units</span> <span class="n">box</span>
|
||||
<span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">remap</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
|
||||
change_box all x scale 1.1 y volume z volume remap
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -223,15 +223,15 @@ will be re-shrink-wrapped before the change_box command completes.
|
|||
Instead you could do something like this, assuming the simulation box
|
||||
is non-periodic and atoms extend from 0 to 20 in all dimensions:</p>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="c1"># this will fail to insert an atom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span> <span class="n">boundary</span> <span class="n">f</span> <span class="n">s</span> <span class="n">s</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>
|
||||
<span class="n">change_box</span> <span class="n">boundary</span> <span class="n">s</span> <span class="n">s</span> <span class="n">s</span> <span class="c1"># this will work</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
change_box all x final -10 20
|
||||
create_atoms 1 single -5 5 5 # this will fail to insert an atom
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
change_box all x final -10 20 boundary f s s
|
||||
create_atoms 1 single -5 5 5
|
||||
change_box boundary s s s # this will work
|
||||
</pre>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">Unlike the earlier “displace_box” version of this command, atom
|
||||
|
|
@ -295,30 +295,30 @@ used following a keyword that changed the volume, which is any of the
|
|||
<em>x</em>, <em>y</em>, <em>z</em> keywords. If the preceding keyword “key” had a <em>volume</em>
|
||||
style, then both it and the current keyword apply to the keyword
|
||||
preceding “key”. I.e. this sequence of keywords is allowed:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
change_box all x scale 1.1 y volume z volume
|
||||
</pre>
|
||||
<p>The <em>volume</em> style changes the associated dimension so that the
|
||||
overall box volume is unchanged relative to its value before the
|
||||
preceding keyword was invoked.</p>
|
||||
<p>If the following command is used, then the z box length will shrink by
|
||||
the same 1.1 factor the x box length was increased by:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
change_box all x scale 1.1 z volume
|
||||
</pre>
|
||||
<p>If the following command is used, then the y,z box lengths will each
|
||||
shrink by sqrt(1.1) to keep the volume constant. In this case, the
|
||||
y,z box lengths shrink so as to keep their relative aspect ratio
|
||||
constant:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span><span class="s2">"x scale 1.1 y volume z volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
change_box all"x scale 1.1 y volume z volume
|
||||
</pre>
|
||||
<p>If the following command is used, then the final box will be a factor
|
||||
of 10% larger in x and y, and a factor of 21% smaller in z, so as to
|
||||
keep the volume constant:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">y</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
change_box all x scale 1.1 z volume y scale 1.1 z volume
|
||||
</pre>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">For solids or liquids, when one dimension of the box is
|
||||
|
|
|
|||
|
|
@ -186,8 +186,8 @@ discussed below, it can be referenced via the following bracket
|
|||
notation, where ID is the ID of the compute:</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="21%" />
|
||||
<col width="79%" />
|
||||
<col width="23%" />
|
||||
<col width="77%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>c_ID</td>
|
||||
|
|
@ -245,11 +245,11 @@ computes for further info.</p>
|
|||
Three computes are always created, named “thermo_temp”,
|
||||
“thermo_press”, and “thermo_pe”, as if these commands had been invoked
|
||||
in the input script:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_temp</span> <span class="nb">all</span> <span class="n">temp</span>
|
||||
<span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
|
||||
<span class="n">compute</span> <span class="n">thermo_pe</span> <span class="nb">all</span> <span class="n">pe</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute thermo_temp all temp
|
||||
compute thermo_press all pressure thermo_temp
|
||||
compute thermo_pe all pe
|
||||
</pre>
|
||||
<p>Additional computes for other quantities are created if the thermo
|
||||
style requires it. See the documentation for the
|
||||
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p>
|
||||
|
|
|
|||
|
|
@ -177,11 +177,11 @@ For example, bond output from the <a class="reference internal" href="compute_pr
|
|||
with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
|
||||
command in a consistent way.</p>
|
||||
<p>Here is an example of how to do this:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">btype</span> <span class="n">batom1</span> <span class="n">batom2</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all property/local btype batom1 batom2
|
||||
compute 2 all bond/local dist eng
|
||||
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
|
||||
</pre>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a local vector or local array depending on the
|
||||
number of keywords. The length of the vector or number of rows in the
|
||||
|
|
|
|||
|
|
@ -234,7 +234,7 @@ simulation into gold (FCC). These were provided by Jon Zimmerman
|
|||
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>These values are <em>not</em> normalized by the square of the lattice
|
||||
<p>These values are *not* normalized by the square of the lattice
|
||||
parameter. If they were, normalized values would be:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
|
||||
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span>
|
||||
|
|
|
|||
|
|
@ -181,11 +181,11 @@ and how they are set for each atom. You can reset the image flags
|
|||
<p>The simplest way to output the results of the compute com/chunk
|
||||
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute cc1 all chunk/atom molecule
|
||||
compute myChunk all dipole/chunk cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
|
||||
</pre>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global array where the number of rows = the
|
||||
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of columns =
|
||||
|
|
|
|||
|
|
@ -164,10 +164,10 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">298</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">sigma</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">volume</span> <span class="n">yes</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">300</span> <span class="n">atom</span> <span class="n">charge</span> <span class="mi">2</span> <span class="n">v_delta</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
|
||||
compute 1 all fep 300 atom charge 2 v_delta
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -307,7 +307,7 @@ each, as in the 1st example above. I <= J is required. LAMMPS sets
|
|||
the coefficients for the symmetric J,I interaction to the same
|
||||
values. A wild-card asterisk can be used in place of or in conjunction
|
||||
with the I,J arguments to set the coefficients for multiple pairs of
|
||||
atom types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N =
|
||||
atom types. This takes the form “*” or “*n” or “n*” or “m*n”. If N =
|
||||
the number of atom types, then an asterisk with no numeric values
|
||||
means all types from 1 to N. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from n to N
|
||||
|
|
|
|||
|
|
@ -193,11 +193,11 @@ using the <a class="reference internal" href="set.html"><span class="doc">set im
|
|||
<p>The simplest way to output the results of the compute gyration/chunk
|
||||
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute cc1 all chunk/atom molecule
|
||||
compute myChunk all gyration/chunk cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
|
||||
</pre>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global vector if the <em>tensor</em> keyword is not
|
||||
specified and a global array if it is. The length of the vector or
|
||||
|
|
|
|||
|
|
@ -237,29 +237,30 @@ energy/area/time <a class="reference internal" href="units.html"><span class="do
|
|||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for thermal conductivity of solid Ar</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>units real
|
||||
<pre class="literal-block">
|
||||
units real
|
||||
variable T equal 70
|
||||
variable V equal vol
|
||||
variable dt equal 4.0
|
||||
variable p equal 200 # correlation length
|
||||
variable s equal 10 # sample interval
|
||||
variable d equal $p*$s # dump interval
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>variable kB equal 1.3806504e-23 # [J/K] Boltzmann
|
||||
<pre class="literal-block">
|
||||
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
|
||||
variable kCal2J equal 4186.0/6.02214e23
|
||||
variable A2m equal 1.0e-10
|
||||
variable fs2s equal 1.0e-15
|
||||
variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>dimension 3
|
||||
<pre class="literal-block">
|
||||
dimension 3
|
||||
boundary p p p
|
||||
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
|
||||
region box block 0 4 0 4 0 4
|
||||
|
|
@ -270,8 +271,7 @@ pair_style lj/cut 13.0
|
|||
pair_coeff * * 0.2381 3.405
|
||||
timestep ${dt}
|
||||
thermo $d
|
||||
</pre></div>
|
||||
</div>
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
|
|
@ -287,7 +287,8 @@ run 8000
|
|||
<span class="c1">#fix NVE all nve</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0
|
||||
<pre class="literal-block">
|
||||
reset_timestep 0
|
||||
compute myKE all ke/atom
|
||||
compute myPE all pe/atom
|
||||
compute myStress all stress/atom NULL virial
|
||||
|
|
@ -305,9 +306,8 @@ thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
|
|||
run 100000
|
||||
variable k equal (v_k11+v_k22+v_k33)/3.0
|
||||
variable ndens equal count(all)/vol
|
||||
print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
|
||||
</pre></div>
|
||||
</div>
|
||||
print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -177,11 +177,11 @@ how they are set for each atom. You can reset the image flags
|
|||
<p>The simplest way to output the results of the compute inertia/chunk
|
||||
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">inertia</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute cc1 all chunk/atom molecule
|
||||
compute myChunk all inertia/chunk cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
|
||||
</pre>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global array where the number of rows = the
|
||||
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of columns =
|
||||
|
|
|
|||
|
|
@ -168,11 +168,11 @@ eFF.</p>
|
|||
thermodynamic output by using the <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>
|
||||
command, as shown in the following example:</p>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
|
||||
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
|
||||
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute effTemp all temp/eff
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
</pre>
|
||||
<p>The value of the kinetic energy will be 0.0 for atoms (nuclei or
|
||||
electrons) not in the specified compute group.</p>
|
||||
<p><strong>Output info:</strong></p>
|
||||
|
|
|
|||
|
|
@ -169,11 +169,11 @@ the <a class="reference internal" href="compute_temp_eff.html"><span class="doc"
|
|||
printed with thermodynamic output by using the
|
||||
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
|
||||
example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
|
||||
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
|
||||
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute effTemp all temp/eff
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
</pre>
|
||||
<p>See <a class="reference internal" href="compute_temp_eff.html"><span class="doc">compute temp/eff</span></a>.</p>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global scalar (the KE). This value can be
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>compute_modify command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute_modify compute-ID keyword value ...
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>compute-ID = ID of the compute to modify</li>
|
||||
<li>one or more keyword/value pairs may be listed</li>
|
||||
|
|
@ -145,10 +145,10 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">myTemp</span> <span class="n">extra</span> <span class="mi">0</span>
|
||||
<span class="n">compute_modify</span> <span class="n">newtemp</span> <span class="n">dynamic</span> <span class="n">yes</span> <span class="n">extra</span> <span class="mi">600</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute_modify myTemp extra 0
|
||||
compute_modify newtemp dynamic yes extra 600
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -185,11 +185,11 @@ command.</p>
|
|||
<p>As an example of per-atom potential energy compared to total potential
|
||||
energy, these lines in an input script should yield the same result
|
||||
in the last 2 columns of thermo output:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">peratom</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
|
||||
<span class="n">compute</span> <span class="n">pe</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span>
|
||||
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">pe</span> <span class="n">c_pe</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute peratom all pe/atom
|
||||
compute pe all reduce sum c_peratom
|
||||
thermo_style custom step temp etotal press pe c_pe
|
||||
</pre>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">The per-atom energy does not any Lennard-Jones tail corrections
|
||||
|
|
|
|||
|
|
@ -141,10 +141,10 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">NULL</span> <span class="n">pair</span> <span class="n">bond</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all pressure thermo_temp
|
||||
compute 1 all pressure NULL pair bond
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -196,9 +196,9 @@ degrees-of-freedom divided by d = dimensionality, where the DOF value
|
|||
is calcluated by the temperature compute. See the various <a class="reference internal" href="compute.html"><span class="doc">compute temperature</span></a> styles for details.</p>
|
||||
<p>A compute of this style with the ID of “thermo_press” is created when
|
||||
LAMMPS starts up, as if this command were in the input script:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute thermo_press all pressure thermo_temp
|
||||
</pre>
|
||||
<p>where “thermo_temp” is the ID of a similarly defined compute of style
|
||||
“temp”. See the “thermo_style” command for more details.</p>
|
||||
<hr class="docutils" />
|
||||
|
|
|
|||
|
|
@ -136,25 +136,25 @@
|
|||
<li>property/atom = style name of this compute command</li>
|
||||
<li>input = one or more atom attributes</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">proc</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
|
||||
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
|
||||
<span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
|
||||
<span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
|
||||
<span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
|
||||
<span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span>
|
||||
<span class="n">shapex</span><span class="p">,</span><span class="n">shapey</span><span class="p">,</span> <span class="n">shapez</span><span class="p">,</span>
|
||||
<span class="n">quatw</span><span class="p">,</span> <span class="n">quati</span><span class="p">,</span> <span class="n">quatj</span><span class="p">,</span> <span class="n">quatk</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
|
||||
<span class="n">end1x</span><span class="p">,</span> <span class="n">end1y</span><span class="p">,</span> <span class="n">end1z</span><span class="p">,</span> <span class="n">end2x</span><span class="p">,</span> <span class="n">end2y</span><span class="p">,</span> <span class="n">end2z</span><span class="p">,</span>
|
||||
<span class="n">corner1x</span><span class="p">,</span> <span class="n">corner1y</span><span class="p">,</span> <span class="n">corner1z</span><span class="p">,</span>
|
||||
<span class="n">corner2x</span><span class="p">,</span> <span class="n">corner2y</span><span class="p">,</span> <span class="n">corner2z</span><span class="p">,</span>
|
||||
<span class="n">corner3x</span><span class="p">,</span> <span class="n">corner3y</span><span class="p">,</span> <span class="n">corner3z</span><span class="p">,</span>
|
||||
<span class="n">nbonds</span><span class="p">,</span>
|
||||
<span class="n">vfrac</span><span class="p">,</span> <span class="n">s0</span><span class="p">,</span>
|
||||
<span class="n">spin</span><span class="p">,</span> <span class="n">eradius</span><span class="p">,</span> <span class="n">ervel</span><span class="p">,</span> <span class="n">erforce</span><span class="p">,</span>
|
||||
<span class="n">rho</span><span class="p">,</span> <span class="n">drho</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">de</span><span class="p">,</span> <span class="n">cv</span><span class="p">,</span>
|
||||
<span class="n">i_name</span><span class="p">,</span> <span class="n">d_name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
possible attributes = id, mol, proc, type, mass,
|
||||
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
|
||||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, diameter, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
shapex,shapey, shapez,
|
||||
quatw, quati, quatj, quatk, tqx, tqy, tqz,
|
||||
end1x, end1y, end1z, end2x, end2y, end2z,
|
||||
corner1x, corner1y, corner1z,
|
||||
corner2x, corner2y, corner2z,
|
||||
corner3x, corner3y, corner3z,
|
||||
nbonds,
|
||||
vfrac, s0,
|
||||
spin, eradius, ervel, erforce,
|
||||
rho, drho, e, de, cv,
|
||||
i_name, d_name
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
|
||||
<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
|
||||
<span class="n">proc</span> <span class="o">=</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">processor</span> <span class="n">that</span> <span class="n">owns</span> <span class="n">atom</span>
|
||||
|
|
|
|||
|
|
@ -192,12 +192,12 @@ will be in unitless reduced units (0-1).</p>
|
|||
<p>The simplest way to output the results of the compute property/chunk
|
||||
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">count</span>
|
||||
<span class="n">compute</span> <span class="n">myChunk2</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk1</span> <span class="n">c_myChunk2</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute cc1 all chunk/atom molecule
|
||||
compute myChunk1 all property/chunk cc1 count
|
||||
compute myChunk2 all com/chunk cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
|
||||
</pre>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global vector or global array depending on
|
||||
the number of input values. The length of the vector or number of
|
||||
|
|
|
|||
|
|
@ -148,14 +148,14 @@
|
|||
<li>one or more inputs can be listed</li>
|
||||
<li>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
|
||||
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
|
||||
c_ID = per-atom or local vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
|
||||
f_ID = per-atom or local vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/args pairs may be appended</li>
|
||||
<li>keyword = <em>replace</em></li>
|
||||
|
|
@ -168,13 +168,13 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_force</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span><span class="o">/</span><span class="n">region</span> <span class="n">subbox</span> <span class="nb">sum</span> <span class="n">c_force</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
|
||||
<span class="n">compute</span> <span class="mi">3</span> <span class="n">fluid</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_dist</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all reduce sum c_force
|
||||
compute 1 all reduce/region subbox sum c_force
|
||||
compute 2 all reduce min c_press[2] f_ave v_myKE
|
||||
compute 2 all reduce min c_press[*] f_ave v_myKE
|
||||
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -211,7 +211,7 @@ component) or can be the result of a <a class="reference internal" href="compute
|
|||
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.</p>
|
||||
<p>Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
|
||||
specify multiple values. This takes the form “*” or “*n” or “n*” or
|
||||
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
|
||||
number of columns in the array (for <em>mode</em> = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to N. A leading
|
||||
|
|
@ -222,18 +222,18 @@ means all indices from m to n (inclusive).</p>
|
|||
had been listed one by one. E.g. these 2 compute reduce commands are
|
||||
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
|
||||
command creates a per-atom array with 6 columns:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
|
||||
<span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute myPress all stress/atom NULL
|
||||
compute 2 all reduce min myPress[*]
|
||||
compute 2 all reduce min myPress[1] myPress[2] myPress[3] &
|
||||
myPress[4] myPress[5] myPress[6]
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
|
||||
self-explanatory. Note that other atom attributes can be used as
|
||||
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
|
||||
an input value from that compute.</p>
|
||||
<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
||||
<p>If a value begins with “c_”, a compute ID must follow which has been
|
||||
previously defined in the input script. Computes can generate
|
||||
per-atom or local quantities. See the individual
|
||||
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page for details. If no bracketed integer
|
||||
|
|
@ -243,7 +243,7 @@ by the compute is used. Users can also write code for their own
|
|||
compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the
|
||||
discussion above for how I can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.</p>
|
||||
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
||||
<p>If a value begins with “f_”, a fix ID must follow which has been
|
||||
previously defined in the input script. Fixes can generate per-atom
|
||||
or local quantities. See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
|
||||
details. Note that some fixes only produce their values on certain
|
||||
|
|
@ -254,7 +254,7 @@ integer is appended, the Ith column of the array calculated by the fix
|
|||
is used. Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how
|
||||
I can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
||||
<p>If a value begins with “v_”, a variable name must follow which has
|
||||
been previously defined in the input script. It must be an
|
||||
<a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>. Atom-style variables can
|
||||
reference thermodynamic keywords and various per-atom attributes, or
|
||||
|
|
@ -271,12 +271,12 @@ Then, instead of performing a min/max on the <em>vec1</em> input vector, the
|
|||
stored index is used to select the Nth element of the <em>vec1</em> vector.</p>
|
||||
<p>Thus, for example, if you wish to use this compute to find the bond
|
||||
with maximum stretch, you can do it as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span>
|
||||
<span class="n">compute</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_2</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all property/local batom1 batom2
|
||||
compute 2 all bond/local dist
|
||||
compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
|
||||
thermo_style custom step temp c_3[1] c_3[2] c_3[3]
|
||||
</pre>
|
||||
<p>The first two input values in the compute reduce command are vectors
|
||||
with the IDs of the 2 atoms in each bond, using the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command. The last input
|
||||
value is bond distance, using the <a class="reference internal" href="compute_bond_local.html"><span class="doc">compute bond/local</span></a> command. Instead of taking the
|
||||
|
|
|
|||
|
|
@ -202,10 +202,10 @@ there will be no consistent ordering of the entries within the local
|
|||
vector or array from one timestep to the next.</p>
|
||||
<p>Here is an example of how to use this compute to dump rigid body info
|
||||
to a file:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rigid</span><span class="o">/</span><span class="n">local</span> <span class="n">myRigid</span> <span class="n">mol</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all rigid/local myRigid mol x y z fx fy fz
|
||||
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>This section explains the rigid body attributes that can be specified.</p>
|
||||
<p>The <em>id</em> attribute is the atomID of the atom which owns the rigid body, which is
|
||||
|
|
|
|||
|
|
@ -157,14 +157,14 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="n">dR_Ewald</span> <span class="mf">0.01</span> <span class="n">c</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">0.5</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Ni</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">manual</span> <span class="n">echo</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_1</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
|
||||
<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_2</span> <span class="n">file</span> <span class="n">Ni_000</span><span class="o">.</span><span class="n">saed</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
|
||||
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
|
||||
fix saed/vtk 1 1 1 c_2 file Ni_000.saed
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -193,7 +193,7 @@ shown in the 2D diagram below.</p>
|
|||
height="auto"
|
||||
alt=""/>
|
||||
</a><p>For a mesh defined by the simulation domain, a rectilinear grid is
|
||||
constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice
|
||||
constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
|
||||
axis. Where A are the vectors corresponding to the edges of the
|
||||
simulation cell. If one or two directions has non-periodic boundary
|
||||
conditions, then the spacing in these directions is defined from the
|
||||
|
|
|
|||
|
|
@ -134,11 +134,11 @@
|
|||
<h1>compute snav/atom command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snad</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snav</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
||||
<li>sna/atom = style name of this compute command</li>
|
||||
|
|
@ -276,22 +276,22 @@ corresponding to a particular bispectrum component. The total number
|
|||
of columns and the identities of the bispectrum component contained in
|
||||
each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as
|
||||
described by the following piece of python code:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">j1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">twojmax</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
|
||||
<span class="k">if</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">2</span><span class="p">):</span>
|
||||
<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span>
|
||||
<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">1</span><span class="p">):</span>
|
||||
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="mi">2</span><span class="o">*</span><span class="n">j1</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
|
||||
<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
|
||||
<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">0</span><span class="p">):</span>
|
||||
<span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
|
||||
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
|
||||
<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
|
||||
<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">3</span><span class="p">):</span>
|
||||
<span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
|
||||
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
|
||||
<span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">>=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
for j1 in range(0,twojmax+1):
|
||||
if(diagonal==2):
|
||||
print j1/2.,j1/2.,j1/2.
|
||||
elif(diagonal==1):
|
||||
for j in range(0,min(twojmax,2*j1)+1,2):
|
||||
print j1/2.,j1/2.,j/2.
|
||||
elif(diagonal==0):
|
||||
for j2 in range(0,j1+1):
|
||||
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
|
||||
print j1/2.,j2/2.,j/2.
|
||||
elif(diagonal==3):
|
||||
for j2 in range(0,j1+1):
|
||||
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
|
||||
if (j>=j1): print j1/2.,j2/2.,j/2.
|
||||
</pre>
|
||||
<p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are
|
||||
arranged into <em>ntypes</em> blocks, listed in order of atom type <em>I</em>. Each
|
||||
block contains three sub-blocks corresponding to the <em>x</em>, <em>y</em>, and <em>z</em>
|
||||
|
|
|
|||
|
|
@ -234,12 +234,12 @@ d = dimension and V is the volume of the system, the result should be
|
|||
-P, where P is the total pressure of the system.</p>
|
||||
<p>These lines in an input script for a 3d system should yield that
|
||||
result. I.e. the last 2 columns of thermo output will be the same:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">peratom</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
|
||||
<span class="n">compute</span> <span class="n">p</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
|
||||
<span class="n">variable</span> <span class="n">press</span> <span class="n">equal</span> <span class="o">-</span><span class="p">(</span><span class="n">c_p</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span><span class="o">/</span><span class="p">(</span><span class="mi">3</span><span class="o">*</span><span class="n">vol</span><span class="p">)</span>
|
||||
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">v_press</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
thermo_style custom step temp etotal press v_press
|
||||
</pre>
|
||||
<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a per-atom array with 6 columns, which can be
|
||||
accessed by indices 1-6 by any command that uses per-atom values from
|
||||
|
|
|
|||
|
|
@ -140,10 +140,10 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">oxygen_c</span><span class="o">-</span><span class="n">s</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">O_core</span> <span class="n">O_shell</span>
|
||||
<span class="n">compute</span> <span class="n">core_shells</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">cores</span> <span class="n">shells</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute oxygen_c-s all temp/cs O_core O_shell
|
||||
compute core_shells all temp/cs cores shells
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -170,11 +170,11 @@ reported by LAMMPS in the thermodynamic quantities reported via the
|
|||
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
|
||||
example:</p>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
|
||||
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
|
||||
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute effTemp all temp/eff
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
</pre>
|
||||
<p>A 6-component kinetic energy tensor is also calculated by this compute
|
||||
for use in the computation of a pressure tensor. The formula for the
|
||||
components of the tensor is the same as the above formula, except that
|
||||
|
|
|
|||
|
|
@ -154,10 +154,10 @@ pair style args = atype v_name1 v_name2
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mi">2</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="mi">1</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
|
||||
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="o">*</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="o">*</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
|
||||
compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -192,7 +192,7 @@ with respect to <em>lambda</em>.</p>
|
|||
numeric values can be used, as in the 1st example above. Or a
|
||||
wildcard asterisk can be used in place of or in conjunction with the
|
||||
<em>atype</em> argument to select multiple atom types. This takes the form
|
||||
“*” or “<em>n” or “n</em>” or “m*n”. If N = the number of atom types, then
|
||||
“*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then
|
||||
an asterisk with no numeric values means all types from 1 to N. A
|
||||
leading asterisk means all types from 1 to n (inclusive). A trailing
|
||||
asterisk means all types from n to N (inclusive). A middle asterisk
|
||||
|
|
|
|||
|
|
@ -158,14 +158,14 @@ or <em>face_threshold</em> or <em>neighbors</em> or <em>peratom</em></li>
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">surface</span> <span class="n">matrix</span>
|
||||
<span class="n">compute</span> <span class="mi">3</span><span class="n">b</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span> <span class="n">v_r</span>
|
||||
<span class="n">compute</span> <span class="mi">4</span> <span class="n">solute</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">only_group</span>
|
||||
<span class="n">compute</span> <span class="mi">5</span> <span class="n">defects</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">occupation</span>
|
||||
<span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all voronoi/atom
|
||||
compute 2 precipitate voronoi/atom surface matrix
|
||||
compute 3b precipitate voronoi/atom radius v_r
|
||||
compute 4 solute voronoi/atom only_group
|
||||
compute 5 defects voronoi/atom occupation
|
||||
compute 6 all voronoi/atom neighbors yes
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -199,11 +199,11 @@ can be obtained by running a “reduce sum” compute on c_2[3]</p>
|
|||
<p>If the <em>radius</em> keyword is specified with an atom style variable as
|
||||
the argument, a poly-disperse Voronoi tessellation is
|
||||
performed. Examples for radius variables are</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">r1</span> <span class="n">atom</span> <span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mf">0.1</span><span class="o">+</span><span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">2</span><span class="p">)</span><span class="o">*</span><span class="mf">0.4</span>
|
||||
<span class="n">compute</span> <span class="n">radius</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span>
|
||||
<span class="n">variable</span> <span class="n">r2</span> <span class="n">atom</span> <span class="n">c_radius</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
variable r1 atom (type==1)*0.1+(type==2)*0.4
|
||||
compute radius all property/atom radius
|
||||
variable r2 atom c_radius
|
||||
</pre>
|
||||
<p>Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms
|
||||
and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
|
||||
present in atom_style sphere for granular models.</p>
|
||||
|
|
@ -247,10 +247,10 @@ uses local values from a compute as input. See <a class="reference internal" hr
|
|||
options. More specifically, the array can be accessed by a
|
||||
<a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command to write a file containing
|
||||
all the Voronoi neighbors in a system:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
|
||||
<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1</span> <span class="n">dump</span><span class="o">.</span><span class="n">neighbors</span> <span class="n">index</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 6 all voronoi/atom neighbors yes
|
||||
dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
|
||||
</pre>
|
||||
<p>If the <em>face_threshold</em> keyword is used, then only faces
|
||||
with areas greater than the threshold are stored.</p>
|
||||
<hr class="docutils" />
|
||||
|
|
|
|||
|
|
@ -159,10 +159,10 @@
|
|||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">xrd</span> <span class="mf">1.541838</span> <span class="n">Al</span> <span class="n">O</span> <span class="mi">2</span><span class="n">Theta</span> <span class="mi">10</span> <span class="mi">100</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">LP</span> <span class="mi">1</span> <span class="n">manual</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.087</span> <span class="mf">0.87</span> <span class="mi">250</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Rad2Theta</span><span class="o">.</span><span class="n">xrd</span>
|
||||
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">250</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Deg2Theta</span><span class="o">.</span><span class="n">xrd</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
|
||||
fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -196,7 +196,7 @@ shown in the 2D diagram below.</p>
|
|||
height="auto"
|
||||
alt=""/>
|
||||
</a><p>For a mesh defined by the simulation domain, a rectilinear grid is
|
||||
constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice
|
||||
constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
|
||||
axis. Where A are the vectors corresponding to the edges of the
|
||||
simulation cell. If one or two directions has non-periodic boundary
|
||||
conditions, then the spacing in these directions is defined from the
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>create_atoms command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="nb">type</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
create_atoms type style args keyword values ...
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
|
||||
<li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
|
||||
|
|
@ -172,12 +172,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">region</span> <span class="n">regsphere</span> <span class="n">basis</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">single</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xpos</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">ypos</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
create_atoms 1 box
|
||||
create_atoms 3 region regsphere basis 2 3
|
||||
create_atoms 3 single 0 0 5
|
||||
create_atoms 1 box var v set x xpos set y ypos
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -328,19 +328,19 @@ the sinusoid would appear to be “smoother”. Also note the use of th
|
|||
“xlat” and “ylat” <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> keywords which
|
||||
converts lattice spacings to distance. Click on the image for a
|
||||
larger version.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>variable x equal 100
|
||||
<pre class="literal-block">
|
||||
variable x equal 100
|
||||
variable y equal 25
|
||||
lattice hex 0.8442
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
create_box 1 box
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">xx</span> <span class="n">equal</span> <span class="mf">0.0</span>
|
||||
<span class="n">variable</span> <span class="n">yy</span> <span class="n">equal</span> <span class="mf">0.0</span>
|
||||
<span class="n">variable</span> <span class="n">v</span> <span class="n">equal</span> <span class="s2">"(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"</span>
|
||||
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xx</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">yy</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
create_box 1 box
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
variable xx equal 0.0
|
||||
variable yy equal 0.0
|
||||
variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
|
||||
create_atoms 1 box var v set x xx set y yy
|
||||
</pre>
|
||||
<a class=""
|
||||
data-lightbox="group-default"
|
||||
href="_images/sinusoid.jpg"
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>delete_bonds command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">arg</span> <span class="n">keyword</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
delete_bonds group-ID style arg keyword ...
|
||||
</pre>
|
||||
<ul>
|
||||
<li><p class="first">group-ID = group ID</p>
|
||||
</li>
|
||||
|
|
@ -157,12 +157,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">frozen</span> <span class="n">multi</span> <span class="n">remove</span>
|
||||
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">4</span> <span class="n">special</span>
|
||||
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span><span class="o">*</span><span class="mi">3</span> <span class="n">special</span>
|
||||
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
delete_bonds frozen multi remove
|
||||
delete_bonds all atom 4 special
|
||||
delete_bonds all bond 0*3 special
|
||||
delete_bonds all stats
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -183,7 +183,7 @@ be an integer from 0 to N, where N is the number of relevant types
|
|||
(atom types, bond types, etc). A value of 0 is only relevant for
|
||||
style <em>bond</em>; see details below. In all cases, a wildcard asterisk
|
||||
can be used in place of or in conjunction with the <em>type</em> argument to
|
||||
specify a range of types. This takes the form “*” or “<em>n” or “n</em>” or
|
||||
specify a range of types. This takes the form “*” or “*n” or “n*” or
|
||||
“m*n”. If N = the number of types, then an asterisk with no numeric
|
||||
values means all types from 0 to N. A leading asterisk means all
|
||||
types from 0 to n (inclusive). A trailing asterisk means all types
|
||||
|
|
|
|||
|
|
@ -137,18 +137,18 @@
|
|||
<h1>dihedral_style charmm/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style charmm
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">0.2</span> <span class="mi">1</span> <span class="mi">180</span> <span class="mf">1.0</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="mf">1.8</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">1.0</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">3.1</span> <span class="mi">2</span> <span class="mi">180</span> <span class="mf">0.5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style charmm
|
||||
dihedral_coeff 1 0.2 1 180 1.0
|
||||
dihedral_coeff 2 1.8 1 0 1.0
|
||||
dihedral_coeff 1 3.1 2 180 0.5
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,21 +131,21 @@
|
|||
<h1>dihedral_style class2/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style class2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">75</span> <span class="mi">100</span> <span class="mi">70</span> <span class="mi">80</span> <span class="mi">60</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">mbt</span> <span class="mf">3.5945</span> <span class="mf">0.1704</span> <span class="o">-</span><span class="mf">0.5490</span> <span class="mf">1.5228</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">ebt</span> <span class="mf">0.3417</span> <span class="mf">0.3264</span> <span class="o">-</span><span class="mf">0.9036</span> <span class="mf">0.1368</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.8080</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">at</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.1850</span> <span class="o">-</span><span class="mf">0.7963</span> <span class="o">-</span><span class="mf">2.0220</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.3991</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">aat</span> <span class="o">-</span><span class="mf">13.5271</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">bb13</span> <span class="mf">0.0</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style class2
|
||||
dihedral_coeff 1 100 75 100 70 80 60
|
||||
dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
|
||||
dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
|
||||
dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
|
||||
dihedral_coeff * aat -13.5271 110.2453 105.1270
|
||||
dihedral_coeff * bb13 0.0 1.0119 1.1010
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>dihedral_style cosine/shift/exp/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style cosine/shift/exp
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style cosine/shift/exp
|
||||
dihedral_coeff 1 10.0 45.0 2.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>dihedral_style fourier/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style fourier
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="o">-</span><span class="mf">0.846200</span> <span class="mi">3</span> <span class="mf">0.0</span> <span class="mf">7.578800</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">0.138000</span> <span class="mi">2</span> <span class="o">-</span><span class="mf">180.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style fourier
|
||||
dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -134,16 +134,16 @@
|
|||
<h1>dihedral_style harmonic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style harmonic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style harmonic
|
||||
dihedral_coeff 1 80.0 1 2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>dihedral_style helix/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style helix
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mf">100.0</span> <span class="mf">40.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style helix
|
||||
dihedral_coeff 1 80.0 100.0 40.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>dihedral_style multi/harmonic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style multi/harmonic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style multi/harmonic
|
||||
dihedral_coeff 1 20 20 20 20 20
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>dihedral_style nharmonic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style nharmonic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">10.0</span> <span class="mf">20.0</span> <span class="mf">30.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style nharmonic
|
||||
dihedral_coeff 3 10.0 20.0 30.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -137,18 +137,18 @@
|
|||
<h1>dihedral_style opls/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style opls
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">1.740</span> <span class="o">-</span><span class="mf">0.157</span> <span class="mf">0.279</span> <span class="mf">0.00</span> <span class="c1"># CT-CT-CT-CT</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.366</span> <span class="mf">0.000</span> <span class="c1"># CT-CT-CT-HC</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.318</span> <span class="mf">0.000</span> <span class="c1"># HC-CT-CT-HC</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style opls
|
||||
dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
|
||||
dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC
|
||||
dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,16 +131,16 @@
|
|||
<h1>dihedral_style quadratic/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style quadratic
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mf">100.0</span> <span class="mf">80.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style quadratic
|
||||
dihedral_coeff 100.0 80.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -128,18 +128,18 @@
|
|||
<span id="index-0"></span><h1>dihedral_style spherical command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">spherical</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style spherical
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">286.1</span> <span class="mi">1</span> <span class="mi">124</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mf">286.1</span> <span class="mi">1</span> <span class="mi">114</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">90</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span> <span class="o">&</span>
|
||||
<span class="mf">17.3</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">158</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="o">&</span>
|
||||
<span class="mf">15.1</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">167.3</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
|
||||
dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 &
|
||||
17.3 0 0.0 0 1 158 1 0 0.0 0 &
|
||||
15.1 0 0.0 0 0 0.0 0 1 167.3 1
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -128,20 +128,20 @@
|
|||
<span id="index-0"></span><h1>dihedral_style command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">style</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style style
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>harmonic</em> or <em>helix</em> or <em>multi/harmonic</em> or <em>opls</em></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span>
|
||||
<span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
|
||||
<span class="n">dihedral_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">charmm</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style harmonic
|
||||
dihedral_style multi/harmonic
|
||||
dihedral_style hybrid harmonic charmm
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
|
|||
|
|
@ -131,9 +131,9 @@
|
|||
<h1>dihedral_style table/omp command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">Ntable</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style table style Ntable
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
|
||||
<li>Ntable = size of the internal lookup table</li>
|
||||
|
|
@ -141,12 +141,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">spline</span> <span class="mi">400</span>
|
||||
<span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE1</span>
|
||||
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dihedral_style table spline 400
|
||||
dihedral_style table linear 1000
|
||||
dihedral_coeff 1 file.table DIH_TABLE1
|
||||
dihedral_coeff 2 file.table DIH_TABLE2
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -185,23 +185,23 @@ or blank lines.</p>
|
|||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Table of the potential and its negative derivative</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE1</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
|
||||
<span class="n">N</span> <span class="mi">30</span> <span class="n">DEGREES</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">NOF</span><span class="p">,</span> <span class="n">DEGREES</span><span class="p">,</span> <span class="n">RADIANS</span><span class="p">,</span> <span class="n">CHECKU</span><span class="o">/</span><span class="n">F</span><span class="p">)</span>
|
||||
<span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span>
|
||||
<span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span> <span class="mf">0.0423346818422</span>
|
||||
<span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span> <span class="mf">0.00811786522531</span>
|
||||
<span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span> <span class="o">-</span><span class="mf">0.0184129719987</span>
|
||||
<span class="o">...</span>
|
||||
<span class="mi">30</span> <span class="mf">180.0</span> <span class="o">-</span><span class="mf">0.707106781187</span> <span class="mf">0.0719306095245</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
DIH_TABLE1 (keyword is the first text on line)
|
||||
N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
|
||||
(blank line)
|
||||
1 -168.0 -1.40351172223 0.0423346818422
|
||||
2 -156.0 -1.70447981034 0.00811786522531
|
||||
3 -144.0 -1.62956100432 -0.0184129719987
|
||||
...
|
||||
30 180.0 -0.707106781187 0.0719306095245
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example 2: table of the potential. Forces omitted</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE2</span>
|
||||
<span class="n">N</span> <span class="mi">30</span> <span class="n">NOF</span> <span class="n">CHECKU</span> <span class="n">testU</span><span class="o">.</span><span class="n">dat</span> <span class="n">CHECKF</span> <span class="n">testF</span><span class="o">.</span><span class="n">dat</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
DIH_TABLE2
|
||||
N 30 NOF CHECKU testU.dat CHECKF testF.dat
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span>
|
||||
<span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span>
|
||||
<span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span>
|
||||
|
|
|
|||
|
|
@ -239,19 +239,19 @@ i_name = per-atom integer vector with name, managed by fix property/atom
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span>
|
||||
<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">mpiio</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">mpiio</span>
|
||||
<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">gz</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">gz</span>
|
||||
<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">bin</span>
|
||||
<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">mpiio</span><span class="o">.</span><span class="n">bin</span>
|
||||
<span class="n">dump</span> <span class="mi">4</span><span class="n">a</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">myforce</span><span class="o">.*</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">fx</span>
|
||||
<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
|
||||
<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">v_ke</span>
|
||||
<span class="n">dump</span> <span class="mi">2</span> <span class="n">inner</span> <span class="n">cfg</span> <span class="mi">10</span> <span class="n">dump</span><span class="o">.</span><span class="n">snap</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
|
||||
<span class="n">dump</span> <span class="n">snap</span> <span class="nb">all</span> <span class="n">cfg</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">config</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_Stress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">xtc</span> <span class="mi">1000</span> <span class="n">file</span><span class="o">.</span><span class="n">xtc</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dump myDump all atom 100 dump.atom
|
||||
dump myDump all atom/mpiio 100 dump.atom.mpiio
|
||||
dump myDump all atom/gz 100 dump.atom.gz
|
||||
dump 2 subgroup atom 50 dump.run.bin
|
||||
dump 2 subgroup atom 50 dump.run.mpiio.bin
|
||||
dump 4a all custom 100 dump.myforce.* id type x y vx fx
|
||||
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
|
||||
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
|
||||
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
|
||||
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
|
||||
dump 1 all xtc 1000 file.xtc
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -347,12 +347,12 @@ or m = shrink wrapped with a minimum value. See the
|
|||
bounding box which encloses the triclinic simulation box is output,
|
||||
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
|
||||
formatted as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span> <span class="n">xy</span> <span class="n">xz</span> <span class="n">yz</span> <span class="n">xx</span> <span class="n">yy</span> <span class="n">zz</span>
|
||||
<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span>
|
||||
<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span>
|
||||
<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
ITEM: BOX BOUNDS xy xz yz xx yy zz
|
||||
xlo_bound xhi_bound xy
|
||||
ylo_bound yhi_bound xz
|
||||
zlo_bound zhi_bound yz
|
||||
</pre>
|
||||
<p>The presence of the text “xy xz yz” in the ITEM line indicates that
|
||||
the 3 tilt factors will be included on each of the 3 following lines.
|
||||
This bounding box is convenient for many visualization programs. The
|
||||
|
|
@ -541,7 +541,7 @@ styles.</p>
|
|||
reference values from a compute or fix, like the <em>custom</em>, <em>cfg</em>, or
|
||||
<em>local</em> styles, the bracketed index I can be specified using a
|
||||
wildcard asterisk with the index to effectively specify multiple
|
||||
values. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
|
||||
values. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
|
||||
size of the vector (for <em>mode</em> = scalar) or the number of columns in
|
||||
the array (for <em>mode</em> = vector), then an asterisk with no numeric
|
||||
values means all indices from 1 to N. A leading asterisk means all
|
||||
|
|
@ -552,12 +552,12 @@ from m to n (inclusive).</p>
|
|||
had been listed one by one. E.g. these 2 dump commands are
|
||||
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
|
||||
command creates a per-atom array with 6 columns:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
|
||||
<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
|
||||
<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
|
||||
<span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute myPress all stress/atom NULL
|
||||
dump 2 all custom 100 tmp.dump id myPress[*]
|
||||
dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
|
||||
myPress[4] myPress[5] myPress[6]
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>This section explains the local attributes that can be specified as
|
||||
part of the <em>local</em> style.</p>
|
||||
|
|
@ -598,11 +598,11 @@ be specified with a wildcard asterisk to effectively specify multiple
|
|||
values.</p>
|
||||
<p>Here is an example of how to dump bond info for a system, including
|
||||
the distance and energy of each bond:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span> <span class="n">btype</span>
|
||||
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all property/local batom1 batom2 btype
|
||||
compute 2 all bond/local dist eng
|
||||
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>This section explains the atom attributes that can be specified as
|
||||
part of the <em>custom</em> and <em>cfg</em> styles.</p>
|
||||
|
|
|
|||
|
|
@ -182,15 +182,15 @@ v_name = per-atom vector calculated by an atom-style variable with name
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">dmpvtk</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">myforce</span><span class="o">.</span><span class="n">vtk</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">vx</span> <span class="n">fx</span>
|
||||
<span class="n">dump</span> <span class="n">dmpvtp</span> <span class="n">flow</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.%.</span><span class="n">displace</span><span class="o">.</span><span class="n">vtp</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
|
||||
<span class="n">dump</span> <span class="n">e_data</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">vtu</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">spin</span> <span class="n">eradius</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">eforce</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
|
||||
dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
|
||||
dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
|
||||
</pre>
|
||||
<p>The style <em>custom/vtk</em> is similar to the <a class="reference internal" href="dump.html"><span class="doc">custom</span></a> style but
|
||||
uses the VTK library to write data to VTK simple legacy or XML format
|
||||
depending on the filename extension specified. This can be either
|
||||
<a href="#id1"><span class="problematic" id="id2">**</span></a>.vtk* for the legacy format or <a href="#id3"><span class="problematic" id="id4">**</span></a>.vtp* and <a href="#id5"><span class="problematic" id="id6">**</span></a>.vtu*, respectively,
|
||||
<em>*.vtk</em> for the legacy format or <em>*.vtp</em> and <em>*.vtu</em>, respectively,
|
||||
for the XML format; see the <a class="reference external" href="http://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
|
||||
description of these formats. Since this naming convention conflicts
|
||||
with the way binary output is usually specified (see below),
|
||||
|
|
|
|||
|
|
@ -206,14 +206,14 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">d0</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.*.</span><span class="n">jpg</span> <span class="nb">type</span> <span class="nb">type</span>
|
||||
<span class="n">dump</span> <span class="n">d1</span> <span class="n">mobile</span> <span class="n">image</span> <span class="mi">500</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">png</span> <span class="n">element</span> <span class="n">element</span> <span class="n">ssao</span> <span class="n">yes</span> <span class="mi">4539</span> <span class="mf">0.6</span>
|
||||
<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">200</span> <span class="n">img</span><span class="o">-*.</span><span class="n">ppm</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">2.5</span> <span class="n">adiam</span> <span class="mf">1.5</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span>
|
||||
<span class="n">dump</span> <span class="n">m0</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">mpg</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span>
|
||||
<span class="n">dump</span> <span class="n">m1</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span>
|
||||
<span class="n">dump</span> <span class="n">m2</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">100</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">1.8</span> <span class="n">adiam</span> <span class="n">v_value</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dump d0 all image 100 dump.*.jpg type type
|
||||
dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
|
||||
dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
|
||||
dump m0 all movie 1000 movie.mpg type type size 640 480
|
||||
dump m1 all movie 1000 movie.avi type type size 640 480
|
||||
dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -310,7 +310,7 @@ atoms rendered in the image. They can be any atom attribute defined
|
|||
for the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, including <em>type</em> and
|
||||
<em>element</em>. This includes per-atom quantities calculated by a
|
||||
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>,
|
||||
which are prefixed by “<a href="#id9"><span class="problematic" id="id10">c_</span></a>”, “<a href="#id11"><span class="problematic" id="id12">f_</span></a>”, or “<a href="#id13"><span class="problematic" id="id14">v_</span></a>” respectively. Note that the
|
||||
which are prefixed by “c_”, “f_”, or “v_” respectively. Note that the
|
||||
<em>diameter</em> setting can be overridden with a numeric value applied to
|
||||
all atoms by the optional <em>adiam</em> keyword.</p>
|
||||
<p>If <em>type</em> is specified for the <em>color</em> setting, then the color of each
|
||||
|
|
@ -545,9 +545,9 @@ plane perpendicular to the view vector implied by the <em>theta</em> and
|
|||
<em>pni</em> values, and which is also in the plane defined by the view
|
||||
vector and user-specified up vector. Thus this internal vector is
|
||||
computed from the user-specified <em>up</em> vector as</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">up_internal</span> <span class="o">=</span> <span class="n">view</span> <span class="n">cross</span> <span class="p">(</span><span class="n">up</span> <span class="n">cross</span> <span class="n">view</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
up_internal = view cross (up cross view)
|
||||
</pre>
|
||||
<p>This means the only restriction on the specified <em>up</em> vector is that
|
||||
it cannot be parallel to the <em>view</em> vector, implied by the <em>theta</em> and
|
||||
<em>phi</em> values.</p>
|
||||
|
|
@ -619,10 +619,10 @@ MPEG or other movie file you can use:</p>
|
|||
</ol>
|
||||
</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
|
||||
<span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">ppm</span> <span class="n">foo</span><span class="o">.</span><span class="n">mpg</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
% convert *.jpg foo.gif
|
||||
% convert -loop 1 *.ppm foo.mpg
|
||||
</pre>
|
||||
<p>Animated GIF files from ImageMagick are unoptimized. You can use a
|
||||
program like gifsicle to optimize and massively shrink them.
|
||||
MPEG files created by ImageMagick are in MPEG-1 format with rather
|
||||
|
|
@ -635,7 +635,7 @@ inefficient compression and low quality.</p>
|
|||
</ul>
|
||||
<p>Select “Open Image Sequence” under the File menu Load the images into
|
||||
QuickTime to animate them Select “Export” under the File menu Save the
|
||||
movie as a QuickTime movie (<a href="#id7"><span class="problematic" id="id8">*</span></a>.mov) or in another format. QuickTime
|
||||
movie as a QuickTime movie (*.mov) or in another format. QuickTime
|
||||
can generate very high quality and efficiently compressed movie
|
||||
files. Some of the supported formats require to buy a license and some
|
||||
are not readable on all platforms until specific runtime libraries are
|
||||
|
|
@ -648,10 +648,10 @@ installed.</p>
|
|||
</ul>
|
||||
<p>FFmpeg is a command line tool that is available on many platforms and
|
||||
allows extremely flexible encoding and decoding of movies.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">jpg</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">mjpeg</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2000</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span>
|
||||
<span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">ppm</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">ppm</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2400</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
|
||||
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
|
||||
</pre>
|
||||
<p>Frontends for FFmpeg exist for multiple platforms. For more
|
||||
information see the <a class="reference external" href="http://www.ffmpeg.org/">FFmpeg homepage</a></p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -678,9 +678,9 @@ variety of file formats and decoders.</li>
|
|||
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</a>,
|
||||
which works directly on a series of image files.</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">a</span> <span class="o">=</span> <span class="n">animate</span><span class="p">(</span><span class="s2">"foo*.jpg"</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
a = animate("foo*.jpg")
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>d) QuickTime and other Windows- or MacOS-based media players can
|
||||
obviously play movie files directly. Similarly for corresponding tools
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>dump_modify command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="n">dump</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dump_modify dump-ID keyword values ...
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>dump-ID = ID of dump to modify</li>
|
||||
<li>one or more keyword/value pairs may be appended</li>
|
||||
|
|
@ -228,16 +228,16 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="n">line</span> <span class="s2">"</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%20.15g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2">"</span> <span class="n">scale</span> <span class="n">yes</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="nb">float</span> <span class="o">%</span><span class="mf">20.15</span><span class="n">g</span> <span class="n">scale</span> <span class="n">yes</span>
|
||||
<span class="n">dump_modify</span> <span class="n">myDump</span> <span class="n">image</span> <span class="n">yes</span> <span class="n">scale</span> <span class="n">no</span> <span class="n">flush</span> <span class="n">yes</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">region</span> <span class="n">mySphere</span> <span class="n">thresh</span> <span class="n">x</span> <span class="o"><</span> <span class="mf">0.0</span> <span class="n">thresh</span> <span class="n">epair</span> <span class="o">>=</span> <span class="mf">3.2</span>
|
||||
<span class="n">dump_modify</span> <span class="n">xtcdump</span> <span class="n">precision</span> <span class="mi">10000</span> <span class="n">sfactor</span> <span class="mf">0.1</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="mi">1000</span> <span class="n">nfile</span> <span class="mi">20</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_myVar</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">amap</span> <span class="nb">min</span> <span class="nb">max</span> <span class="n">cf</span> <span class="mf">0.0</span> <span class="mi">3</span> <span class="nb">min</span> <span class="n">green</span> <span class="mf">0.5</span> <span class="n">yellow</span> <span class="nb">max</span> <span class="n">blue</span> <span class="n">boxcolor</span> <span class="n">red</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
|
||||
dump_modify 1 format float %20.15g scale yes
|
||||
dump_modify myDump image yes scale no flush yes
|
||||
dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
|
||||
dump_modify xtcdump precision 10000 sfactor 0.1
|
||||
dump_modify 1 every 1000 nfile 20
|
||||
dump_modify 1 every v_myVar
|
||||
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -318,19 +318,19 @@ to the dump file. The <em>every</em> keyword cannot be used with the dump
|
|||
<em>dcd</em> style.</p>
|
||||
<p>For example, the following commands will
|
||||
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="n">logfreq</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span> <span class="n">first</span> <span class="n">yes</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
variable s equal logfreq(10,3,10)
|
||||
dump 1 all atom 100 tmp.dump
|
||||
dump_modify 1 every v_s first yes
|
||||
</pre>
|
||||
<p>The following commands would write snapshots at the timesteps listed
|
||||
in file tmp.times:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">f</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">times</span>
|
||||
<span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="nb">next</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
variable f file tmp.times
|
||||
variable s equal next(f)
|
||||
dump 1 all atom 100 tmp.dump
|
||||
dump_modify 1 every v_s
|
||||
</pre>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">When using a file-style variable with the <em>every</em> keyword, the
|
||||
|
|
@ -406,11 +406,11 @@ an integer and you wish it to appear in the text dump file as a
|
|||
(large) integer, then you need to use an appropriate format. For
|
||||
example, these commands:</p>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
|
||||
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">bonds</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
||||
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="s2">"</span><span class="si">%d</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2">"</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute 1 all property/local batom1 batom2
|
||||
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
|
||||
dump_modify 1 format "%d %0.0f %0.0f"
|
||||
</pre>
|
||||
<p>will output the two atom IDs for atoms in each bond as integers. If
|
||||
the dump_modify command were omitted, they would appear as
|
||||
floating-point values, assuming they were large integers (more than 6
|
||||
|
|
@ -566,7 +566,7 @@ atoms of each type will be drawn in the image.</p>
|
|||
<p>The specified <em>type</em> should be an integer from 1 to Ntypes = the
|
||||
number of atom types. A wildcard asterisk can be used in place of or
|
||||
in conjunction with the <em>type</em> argument to specify a range of atom
|
||||
types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
|
||||
types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
|
||||
number of atom types, then an asterisk with no numeric values means
|
||||
all types from 1 to N. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from n to N
|
||||
|
|
@ -689,15 +689,15 @@ color map without having to specify where all the bin boundaries are.</p>
|
|||
atoms in individual molecules with a different color. See the
|
||||
examples/pour/in.pour.2d.molecule input script for an example of how
|
||||
this is used.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span>variable colors string &
|
||||
<pre class="literal-block">
|
||||
variable colors string &
|
||||
"red green blue yellow white &
|
||||
purple pink orange lime gray"
|
||||
variable mol atom mol%10
|
||||
dump 1 all image 250 image.*.jpg v_mol type &
|
||||
zoom 1.6 adiam 1.5
|
||||
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
</pre></div>
|
||||
</div>
|
||||
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
</pre>
|
||||
<p>In this case, 10 colors are defined, and molecule IDs are
|
||||
mapped to one of the colors, even if there are 1000s of molecules.</p>
|
||||
<hr class="docutils" />
|
||||
|
|
@ -711,7 +711,7 @@ set the color that bonds of each type will be drawn in the image.</p>
|
|||
<p>The specified <em>type</em> should be an integer from 1 to Nbondtypes = the
|
||||
number of bond types. A wildcard asterisk can be used in place of or
|
||||
in conjunction with the <em>type</em> argument to specify a range of bond
|
||||
types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
|
||||
types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
|
||||
number of bond types, then an asterisk with no numeric values means
|
||||
all types from 1 to N. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from n to N
|
||||
|
|
|
|||
|
|
@ -210,8 +210,8 @@ discussed below, it can be referenced via the following bracket
|
|||
notation, where ID is the ID of the fix:</p>
|
||||
<table border="1" class="docutils">
|
||||
<colgroup>
|
||||
<col width="21%" />
|
||||
<col width="79%" />
|
||||
<col width="23%" />
|
||||
<col width="77%" />
|
||||
</colgroup>
|
||||
<tbody valign="top">
|
||||
<tr class="row-odd"><td>f_ID</td>
|
||||
|
|
|
|||
|
|
@ -170,12 +170,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">v_prefactor</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">2</span><span class="o">*</span> <span class="mi">3</span> <span class="n">v_prefactor</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_scale1</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="n">scale</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">v_scale2</span> <span class="n">scale</span> <span class="n">yes</span> <span class="n">reset</span> <span class="n">yes</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="mi">1</span> <span class="n">v_size</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
|
||||
fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
|
||||
fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
|
||||
fix 1 all adapt/fep 10 atom diameter 1 v_size
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -307,7 +307,7 @@ each, as in the 1st example above. I <= J is required. LAMMPS sets
|
|||
the coefficients for the symmetric J,I interaction to the same values.</p>
|
||||
<p>A wild-card asterisk can be used in place of or in conjunction with
|
||||
the I,J arguments to set the coefficients for multiple pairs of atom
|
||||
types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
|
||||
types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
|
||||
number of atom types, then an asterisk with no numeric values means
|
||||
all types from 1 to N. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from n to N
|
||||
|
|
@ -333,10 +333,10 @@ details.</p>
|
|||
<p>For example, these commands would change the prefactor coefficient of
|
||||
the <a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a> potential from 10.0 to 30.0 in a
|
||||
linear fashion over the course of a simulation:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">prefactor</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">30</span><span class="p">)</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_prefactor</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
variable prefactor equal ramp(10,30)
|
||||
fix 1 all adapt 1 pair soft a * * v_prefactor
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>kspace</em> keyword used the specified variable as a scale factor on
|
||||
the energy, forces, virial calculated by whatever K-Space solver is
|
||||
|
|
@ -369,16 +369,14 @@ constant).</p>
|
|||
<p>For example, these commands would shrink the diameter of all granular
|
||||
particles in the “center” group from 1.0 to 0.1 in a linear fashion
|
||||
over the course of a 1000-step simulation:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">size</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">0.1</span><span class="p">)</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="n">center</span> <span class="n">adapt</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="o">*</span> <span class="n">v_size</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
variable size equal ramp(1.0,0.1)
|
||||
fix 1 center adapt 10 atom diameter * v_size
|
||||
</pre>
|
||||
<p>For <a class="reference internal" href="run_style.html"><span class="doc">rRESPA time integration</span></a>, this fix changes
|
||||
parameters on the outermost rRESPA level.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
|
||||
|
|
|
|||
|
|
@ -140,10 +140,10 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">kick</span> <span class="n">bead</span> <span class="n">addtorque</span> <span class="mf">2.0</span> <span class="mf">3.0</span> <span class="mf">5.0</span>
|
||||
<span class="n">fix</span> <span class="n">kick</span> <span class="n">bead</span> <span class="n">addtorque</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">v_oscillate</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix kick bead addtorque 2.0 3.0 5.0
|
||||
fix kick bead addtorque 0.0 0.0 v_oscillate
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -166,10 +166,8 @@ torque component.</p>
|
|||
functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
|
||||
keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify a time-dependent torque.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
|
||||
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
|
||||
fix to add the potential “energy” inferred by the added forces to the
|
||||
|
|
|
|||
|
|
@ -128,9 +128,9 @@
|
|||
<span id="index-0"></span><h1>fix atc command</h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="o"><</span><span class="n">fixID</span><span class="o">></span> <span class="o"><</span><span class="n">group</span><span class="o">></span> <span class="n">atc</span> <span class="o"><</span><span class="nb">type</span><span class="o">></span> <span class="o"><</span><span class="n">parameter_file</span><span class="o">></span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix <fixID> <group> atc <type> <parameter_file>
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>fixID = name of fix</li>
|
||||
<li>group = name of group fix is to be applied</li>
|
||||
|
|
@ -148,12 +148,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">dat</span>
|
||||
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">two_temperature</span> <span class="n">Ar_ttm</span><span class="o">.</span><span class="n">mat</span>
|
||||
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
|
||||
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">field</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix AtC internal atc thermal Ar_thermal.dat
|
||||
fix AtC internal atc two_temperature Ar_ttm.mat
|
||||
fix AtC internal atc hardy
|
||||
fix AtC internal atc field
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -163,31 +163,31 @@
|
|||
<span class="c1"># ... commands to create and initialize the MD system</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># initial fix to designate coupling type and group to apply it to</span>
|
||||
<span class="c1"># tag group physics material_file</span>
|
||||
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">mat</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 12 x 2 x 2 mesh that covers region contain the group</span>
|
||||
<span class="c1"># nx ny nz region periodicity</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">12</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">mdRegion</span> <span class="n">f</span> <span class="n">p</span> <span class="n">p</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the control method for the type of coupling</span>
|
||||
<span class="c1"># physics control_type</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">thermal</span> <span class="n">control</span> <span class="n">flux</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the initial values for the empirical field "temperature"</span>
|
||||
<span class="c1"># field node_group value</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">initial</span> <span class="n">temperature</span> <span class="nb">all</span> <span class="mi">30</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span>
|
||||
<span class="c1"># filename output_frequency</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">atc_fe_output</span> <span class="mi">100</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
# initial fix to designate coupling type and group to apply it to
|
||||
# tag group physics material_file
|
||||
fix AtC internal atc thermal Ar_thermal.mat
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# create a uniform 12 x 2 x 2 mesh that covers region contain the group
|
||||
# nx ny nz region periodicity
|
||||
fix_modify AtC mesh create 12 2 2 mdRegion f p p
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# specify the control method for the type of coupling
|
||||
# physics control_type
|
||||
fix_modify AtC thermal control flux
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# specify the initial values for the empirical field "temperature"
|
||||
# field node_group value
|
||||
fix_modify AtC initial temperature all 30
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output atc_fe_output 100
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
|
|
@ -200,30 +200,30 @@
|
|||
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># for hardy fix, specific kernel function (function type and range) to # be used as a localization function</span>
|
||||
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">kernel</span> <span class="n">quartic_sphere</span> <span class="mf">10.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 1 x 1 x 1 mesh that covers region contain the group</span>
|
||||
<span class="c1"># with periodicity this effectively creats a system average</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">p</span> <span class="n">p</span> <span class="n">p</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># change from default lagrangian map to eulerian</span>
|
||||
<span class="c1"># refreshed every 100 steps</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">atom_element_map</span> <span class="n">eulerian</span> <span class="mi">100</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># start with no field defined</span>
|
||||
<span class="c1"># add mass density, potential energy density, stress and temperature</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">fields</span> <span class="n">add</span> <span class="n">density</span> <span class="n">energy</span> <span class="n">stress</span> <span class="n">temperature</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span>
|
||||
<span class="c1"># filename output_frequency</span>
|
||||
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">nvtFE</span> <span class="mi">100</span> <span class="n">text</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
|
||||
fix AtC kernel quartic_sphere 10.0
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# create a uniform 1 x 1 x 1 mesh that covers region contain the group
|
||||
# with periodicity this effectively creats a system average
|
||||
fix_modify AtC mesh create 1 1 1 box p p p
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# change from default lagrangian map to eulerian
|
||||
# refreshed every 100 steps
|
||||
fix_modify AtC atom_element_map eulerian 100
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# start with no field defined
|
||||
# add mass density, potential energy density, stress and temperature
|
||||
fix_modify AtC fields add density energy stress temperature
|
||||
</pre>
|
||||
<pre class="literal-block">
|
||||
# create an output stream for nodal fields
|
||||
# filename output_frequency
|
||||
fix_modify AtC output nvtFE 100 text
|
||||
</pre>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
|
|
@ -235,10 +235,8 @@
|
|||
<p>fix_modify AtC mesh create 1 1 1 box p p p</p>
|
||||
<p>...</p>
|
||||
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
|
|
|
|||
|
|
@ -156,11 +156,11 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">29494</span> <span class="mf">300.0</span> <span class="n">ke</span> <span class="n">no</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
<span class="n">fix</span> <span class="n">myFix</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">12345</span> <span class="mf">298.0</span> <span class="n">region</span> <span class="n">my_swap_region</span> <span class="n">types</span> <span class="mi">5</span> <span class="mi">6</span>
|
||||
<span class="n">fix</span> <span class="n">SGMC</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">345</span> <span class="mf">1.0</span> <span class="n">semi</span><span class="o">-</span><span class="n">grand</span> <span class="n">yes</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="n">mu</span> <span class="mf">0.0</span> <span class="mf">4.3</span> <span class="o">-</span><span class="mf">5.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
|
||||
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
|
||||
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -250,9 +250,7 @@ system (the quantity used when performing GCMC moves),
|
|||
you MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for
|
||||
that fix. The doc pages for individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands
|
||||
specify if this should be done.</p>
|
||||
</div>
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about the random
|
||||
number generator seed, the next timestep for MC exchanges, etc. See
|
||||
the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to
|
||||
|
|
|
|||
|
|
@ -140,22 +140,22 @@
|
|||
one or more input values can be listed</li>
|
||||
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
|
||||
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">100</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all ave/atom 1 100 100 vx vy vz
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress[1]
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress[*]
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -181,7 +181,7 @@ are the only ones that can be used with this fix since they produce
|
|||
per-atom vectors.</p>
|
||||
<p>Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
|
||||
specify multiple values. This takes the form “*” or “*n” or “n*” or
|
||||
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
|
||||
number of columns in the array (for <em>mode</em> = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to N. A leading
|
||||
|
|
@ -192,13 +192,13 @@ means all indices from m to n (inclusive).</p>
|
|||
had been listed one by one. E.g. these 2 fix ave/atom commands are
|
||||
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
|
||||
command creates a per-atom array with 6 columns:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">my_stress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&</span>
|
||||
<span class="n">c_my_stress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="o">&</span>
|
||||
<span class="n">c_my_stress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute my_stress all stress/atom NULL
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress[*]
|
||||
fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
|
||||
c_my_stress[3] c_my_stress[4] &
|
||||
c_my_stress[5] c_my_stress[6]
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
||||
timesteps the input values will be used in order to contribute to the
|
||||
|
|
@ -228,7 +228,7 @@ this is not what you want, consider averaging unwrapped coordinates,
|
|||
which can be provided by the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command via its xu,yu,zu
|
||||
attributes.</p>
|
||||
</div>
|
||||
<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
||||
<p>If a value begins with “c_”, a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed term containing an index I is appended, the Ith column of
|
||||
|
|
@ -236,7 +236,7 @@ the per-atom array calculated by the compute is used. Users can also
|
|||
write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how I can
|
||||
be specified with a wildcard asterisk to effectively specify multiple
|
||||
values.</p>
|
||||
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
||||
<p>If a value begins with “f_”, a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed term containing an index I is appended, the Ith column of
|
||||
|
|
@ -246,15 +246,13 @@ compatible with <em>Nevery</em>, else an error will result. Users can also
|
|||
write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how I can
|
||||
be specified with a wildcard asterisk to effectively specify multiple
|
||||
values.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
||||
<p>If a value begins with “v_”, a variable name must follow which has
|
||||
been previously defined in the input script as an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a> Variables of style <em>atom</em> can reference
|
||||
thermodynamic keywords, or invoke other computes, fixes, or variables
|
||||
when they are evaluated, so this is a very general means of generating
|
||||
per-atom quantities to time average.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix. No global scalar or vector quantities are
|
||||
stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>
|
||||
|
|
|
|||
|
|
@ -141,16 +141,16 @@
|
|||
<li>one or more input values can be listed</li>
|
||||
<li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
|
||||
<span class="n">density</span><span class="o">/</span><span class="n">number</span><span class="p">,</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="o">=</span> <span class="n">number</span> <span class="ow">or</span> <span class="n">mass</span> <span class="n">density</span>
|
||||
<span class="n">temp</span> <span class="o">=</span> <span class="n">temperature</span>
|
||||
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
||||
density/number, density/mass = number or mass density
|
||||
temp = temperature
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
|
||||
v_name = per-atom vector calculated by an atom-style variable with name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/arg pairs may be appended</li>
|
||||
<li>keyword = <em>norm</em> or <em>ave</em> or <em>bias</em> or <em>adof</em> or <em>cdof</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
|
||||
|
|
@ -185,12 +185,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10000</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="n">binchunk</span> <span class="n">c_myCentro</span> <span class="n">title1</span> <span class="s2">"My output values"</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">molchunk</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
|
||||
fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
|
||||
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
|
||||
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
|
||||
</pre>
|
||||
<p><strong>NOTE:</strong></p>
|
||||
<p>If you are trying to replace a deprectated fix ave/spatial command
|
||||
with the newer, more flexible fix ave/chunk and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands, you simply need to split
|
||||
|
|
@ -242,7 +242,7 @@ ones that can be used with this fix since all other styles of variable
|
|||
produce global quantities.</p>
|
||||
<p>Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
|
||||
specify multiple values. This takes the form “*” or “*n” or “n*” or
|
||||
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
|
||||
number of columns in the array (for <em>mode</em> = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to N. A leading
|
||||
|
|
@ -253,11 +253,11 @@ means all indices from m to n (inclusive).</p>
|
|||
had been listed one by one. E.g. these 2 fix ave/chunk commands are
|
||||
equivalent, since the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command creates, in this
|
||||
case, a per-atom array with 3 columns:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myAng</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">angmomx</span> <span class="n">angmomy</span> <span class="n">angmomz</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
|
||||
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute myAng all property/atom angmomx angmomy angmomz
|
||||
fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
|
||||
fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
|
||||
</pre>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">This fix works by creating an array of size <em>Nchunk</em> by Nvalues
|
||||
|
|
@ -349,7 +349,7 @@ in the chunk on different timesteps were collected together as one set
|
|||
of atoms to calculate their temperature. The compute allows the
|
||||
center-of-mass velocity of each chunk to be subtracted before
|
||||
calculating the temperature; this fix does not.</p>
|
||||
<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
||||
<p>If a value begins with “c_”, a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
|
|
@ -357,7 +357,7 @@ calculated by the compute is used. Users can also write code for
|
|||
their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.
|
||||
See the discussion above for how I can be specified with a wildcard
|
||||
asterisk to effectively specify multiple values.</p>
|
||||
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
||||
<p>If a value begins with “f_”, a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
|
|
@ -367,7 +367,7 @@ their values on certain timesteps, which must be compatible with
|
|||
own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the
|
||||
discussion above for how I can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
||||
<p>If a value begins with “v_”, a variable name must follow which has
|
||||
been previously defined in the input script. Variables of style
|
||||
<em>atom</em> can reference thermodynamic keywords and various per-atom
|
||||
attributes, or invoke other computes, fixes, or variables when they
|
||||
|
|
@ -502,10 +502,8 @@ value of the <em>units</em> keyword is <em>reduced</em>, the coordinate values w
|
|||
be in unitless reduced units (0-1). This is not true for the Coord1 value
|
||||
of style <em>bin/sphere</em> or <em>bin/cylinder</em> which both represent radial
|
||||
dimensions. Those values are always in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix.</p>
|
||||
<p>This fix computes a global array of values which can be accessed by
|
||||
|
|
|
|||
|
|
@ -140,14 +140,14 @@
|
|||
<li>one or more input values can be listed</li>
|
||||
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">v_name</span> <span class="o">=</span> <span class="k">global</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
c_ID = global scalar calculated by a compute with ID
|
||||
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
|
||||
f_ID = global scalar calculated by a fix with ID
|
||||
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
|
||||
v_name = global value calculated by an equal-style variable with name
|
||||
v_name[I] = Ith component of a vector-style variable with name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/arg pairs may be appended</li>
|
||||
<li>keyword = <em>type</em> or <em>ave</em> or <em>start</em> or <em>prefactor</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
|
||||
|
|
@ -180,12 +180,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">5</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">correlate</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="o">&</span>
|
||||
<span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
|
||||
<span class="nb">type</span> <span class="n">upper</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">title1</span> <span class="s2">"My correlation data"</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
|
||||
fix 1 all ave/correlate 1 50 10000 &
|
||||
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
|
||||
type upper ave running title1 "My correlation data"
|
||||
</pre>
|
||||
<p>fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]</p>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
|
|
@ -221,7 +221,7 @@ ones that can be used with this fix. Variables of style <em>atom</em> cannot
|
|||
be used, since they produce per-atom values.</p>
|
||||
<p>Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
|
||||
specify multiple values. This takes the form “*” or “*n” or “n*” or
|
||||
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
|
||||
number of columns in the array (for <em>mode</em> = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to N. A leading
|
||||
|
|
@ -232,13 +232,13 @@ means all indices from m to n (inclusive).</p>
|
|||
vector had been listed one by one. E.g. these 2 fix ave/correlate
|
||||
commands are equivalent, since the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> command creates a global vector with 6
|
||||
values.</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">NULL</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="n">c_myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span> <span class="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="o">&</span>
|
||||
<span class="n">c_myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
|
||||
<span class="n">c_myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute myPress all pressure NULL
|
||||
fix 1 all ave/correlate 1 50 10000 c_myPress[*]
|
||||
fix 1 all ave/correlate 1 50 10000 &
|
||||
c_myPress[1] c_myPress[2] c_myPress[3] &
|
||||
c_myPress[4] c_myPress[5] c_myPress[6]
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
||||
timesteps the input values will be used to calculate correlation data.
|
||||
|
|
@ -249,9 +249,9 @@ initial time up to an output timestep. The initial time could be the
|
|||
beginning of the simulation or the last output time; see the <em>ave</em>
|
||||
keyword for options. For the set of samples, the correlation value
|
||||
Cij is calculated as:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Cij</span><span class="p">(</span><span class="n">delta</span><span class="p">)</span> <span class="o">=</span> <span class="n">ave</span><span class="p">(</span><span class="n">Vi</span><span class="p">(</span><span class="n">t</span><span class="p">)</span><span class="o">*</span><span class="n">Vj</span><span class="p">(</span><span class="n">t</span><span class="o">+</span><span class="n">delta</span><span class="p">))</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Cij(delta) = ave(Vi(t)*Vj(t+delta))
|
||||
</pre>
|
||||
<p>which is the correlation value between input values Vi and Vj,
|
||||
separated by time delta. Note that the second value Vj in the pair is
|
||||
always the one sampled at the later time. The ave() represents an
|
||||
|
|
@ -259,9 +259,9 @@ average over every pair of samples in the set that are separated by
|
|||
time delta. The maximum delta used is of size (<em>Nrepeat</em>-1)*<em>Nevery</em>.
|
||||
Thus the correlation between a pair of input values yields <em>Nrepeat</em>
|
||||
correlation datums:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Cij</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="n">Nevery</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Nevery</span><span class="p">),</span> <span class="o">...</span><span class="p">,</span> <span class="n">Cij</span><span class="p">((</span><span class="n">Nrepeat</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">Nevery</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
|
||||
</pre>
|
||||
<p>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 0,5,10,15,...,100 will be used to compute the final averages
|
||||
on timestep 100. Six averages will be computed: Cij(0), Cij(5),
|
||||
|
|
@ -272,7 +272,7 @@ Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).</p>
|
|||
non-zero. Also, if the <em>ave</em> keyword is set to <em>one</em> which is the
|
||||
default, then <em>Nfreq</em> >= (<em>Nrepeat</em>-1)*<em>Nevery</em> is required.</p>
|
||||
<hr class="docutils" />
|
||||
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">c_</span></a>”, a compute ID must follow which has been
|
||||
<p>If a value begins with “c_”, a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the global scalar calculated by the compute is used. If a
|
||||
bracketed term is appended, the Ith element of the global vector
|
||||
|
|
@ -286,7 +286,7 @@ defined not in your input script, but by <a class="reference internal" href="the
|
|||
or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See the doc pages for
|
||||
these commands which give the IDs of these computes. Users can also
|
||||
write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">f_</span></a>”, a fix ID must follow which has been
|
||||
<p>If a value begins with “f_”, a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the global scalar calculated by the fix is used. If a
|
||||
bracketed term is appended, the Ith element of the global vector
|
||||
|
|
@ -296,7 +296,7 @@ values.</p>
|
|||
<p>Note that some fixes only produce their values on certain timesteps,
|
||||
which must be compatible with <em>Nevery</em>, else an error will result.
|
||||
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If a value begins with “<a href="#id7"><span class="problematic" id="id8">v_</span></a>”, a variable name must follow which has
|
||||
<p>If a value begins with “v_”, a variable name must follow which has
|
||||
been previously defined in the input script. Only equal-style or
|
||||
vector-style variables can be referenced; the latter requires a
|
||||
bracketed term to specify the Ith element of the vector calculated by
|
||||
|
|
@ -366,11 +366,11 @@ the strings that will be printed as the first 3 lines of the output
|
|||
file, assuming the <em>file</em> keyword was used. LAMMPS uses default
|
||||
values for each of these, so they do not need to be specified.</p>
|
||||
<p>By default, these header lines are as follows:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Time-correlated data for fix ID</span>
|
||||
<span class="c1"># TimeStep Number-of-time-windows</span>
|
||||
<span class="c1"># Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
# Time-correlated data for fix ID
|
||||
# TimeStep Number-of-time-windows
|
||||
# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
|
||||
</pre>
|
||||
<p>In the first line, ID is replaced with the fix-ID. The second line
|
||||
describes the two values that are printed at the first of each section
|
||||
of output. In the third line the value pairs are replaced with the
|
||||
|
|
@ -378,9 +378,9 @@ appropriate fields from the fix ave/correlate command.</p>
|
|||
<hr class="docutils" />
|
||||
<p>Let Sij = a set of time correlation data for input values I and J,
|
||||
namely the <em>Nrepeat</em> values:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Sij</span> <span class="o">=</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="n">Nevery</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Nevery</span><span class="p">),</span> <span class="o">...</span><span class="p">,</span> <span class="n">Cij</span><span class="p">(</span><span class="o">*</span><span class="n">Nrepeat</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">Nevery</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
|
||||
</pre>
|
||||
<p>As explained below, these datums are output as one column of a global
|
||||
array, which is effectively the correlation matrix.</p>
|
||||
<p>The <em>trap</em> function defined for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>
|
||||
|
|
@ -389,10 +389,8 @@ using a trapezoidal rule. This is useful for calculating various
|
|||
quantities which can be derived from time correlation data. If a
|
||||
normalization factor is needed for the time integration, it can be
|
||||
included in the variable formula or via the <em>prefactor</em> keyword.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix.</p>
|
||||
<p>This fix computes a global array of values which can be accessed by
|
||||
|
|
|
|||
|
|
@ -139,13 +139,13 @@
|
|||
<li>one or more input values can be listed</li>
|
||||
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">v_name</span> <span class="o">=</span> <span class="k">global</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
c_ID = global scalar calculated by a compute with ID
|
||||
c_ID[I] = Ith component of global vector calculated by a compute with ID
|
||||
f_ID = global scalar calculated by a fix with ID
|
||||
f_ID[I] = Ith component of global vector calculated by a fix with ID
|
||||
v_name = global value calculated by an equal-style variable with name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/arg pairs may be appended</li>
|
||||
<li>keyword = <em>type</em> or <em>start</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>ncorr</em> or <em>p</em> or <em>m</em></li>
|
||||
|
|
@ -177,12 +177,12 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">correlate</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="o">&</span>
|
||||
<span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
|
||||
<span class="nb">type</span> <span class="n">upper</span> <span class="n">title1</span> <span class="s2">"My correlation data"</span> <span class="n">nlen</span> <span class="mi">15</span> <span class="n">ncount</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
|
||||
fix 1 all ave/correlate/long 1 10000 &
|
||||
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
|
||||
type upper title1 "My correlation data" nlen 15 ncount 3
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -221,9 +221,7 @@ steps can be calculated.</p>
|
|||
4*ncorr*nlen*8 bytes. With the default values of the parameters, this
|
||||
corresponds to about 10 KB.</p>
|
||||
<p>For the meaning of the additional optional keywords, see the <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a> doc page.</p>
|
||||
</div>
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>Since this fix in intended for the calculation of time correlation
|
||||
functions over very long MD simulations, the information about this
|
||||
fix is written automatically to binary restart files, so that the time
|
||||
|
|
|
|||
|
|
@ -145,15 +145,15 @@
|
|||
<li>one or more input values can be listed</li>
|
||||
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
|
||||
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
|
||||
c_ID = scalar or vector calculated by a compute with ID
|
||||
c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
|
||||
f_ID = scalar or vector calculated by a fix with ID
|
||||
f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
|
||||
v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
|
||||
v_name[I] = value calculated by a vector-style variable with name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/arg pairs may be appended</li>
|
||||
<li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>beyond</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
|
||||
|
|
@ -185,13 +185,13 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="mf">0.5</span> <span class="mf">1.5</span> <span class="mi">50</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">histo</span> <span class="n">ave</span> <span class="n">running</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">title1</span> <span class="s2">"My output values"</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="o">-</span><span class="mf">2.0</span> <span class="mf">2.0</span> <span class="mi">18</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">beyond</span> <span class="n">extra</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">2000</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
|
||||
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
|
||||
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
|
||||
fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
|
||||
fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -232,7 +232,7 @@ with a bracketed term appended, indicating the Ith column of the array
|
|||
is used.</p>
|
||||
<p>Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
|
||||
specify multiple values. This takes the form “*” or “*n” or “n*” or
|
||||
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
|
||||
number of columns in the array (for <em>mode</em> = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to N. A leading
|
||||
|
|
@ -243,11 +243,11 @@ means all indices from m to n (inclusive).</p>
|
|||
vector or columns of the array had been listed one by one. E.g. these
|
||||
2 fix ave/histo commands are equivalent, since the <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> command creates a global array with
|
||||
3 columns:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myCOM</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute myCOM all com/chunk
|
||||
fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
|
||||
fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
|
||||
</pre>
|
||||
<p>If the fix ave/histo/weight command is used, exactly two values must
|
||||
be specified. If the values are vectors, they must be the same
|
||||
length. The first value (a scalar or vector) is what is histogrammed
|
||||
|
|
@ -278,7 +278,7 @@ simply generated on timesteps 100,200,etc.</p>
|
|||
self-explanatory. Note that other atom attributes can be used as
|
||||
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
|
||||
an input value from that compute.</p>
|
||||
<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
||||
<p>If a value begins with “c_”, a compute ID must follow which has been
|
||||
previously defined in the input script. If <em>mode</em> = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the
|
||||
compute is used. If a bracketed term is appended, the Ith element of
|
||||
|
|
@ -295,7 +295,7 @@ can thus be accessed by fix ave/histo. Or it can be a compute defined
|
|||
not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See
|
||||
the doc pages for these commands which give the IDs of these computes.
|
||||
Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
||||
<p>If a value begins with “f_”, a fix ID must follow which has been
|
||||
previously defined in the input script. If <em>mode</em> = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the fix
|
||||
is used. If a bracketed term is appended, the Ith element of the
|
||||
|
|
@ -309,7 +309,7 @@ values.</p>
|
|||
<p>Note that some fixes only produce their values on certain timesteps,
|
||||
which must be compatible with <em>Nevery</em>, else an error will result.
|
||||
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
||||
<p>If a value begins with “v_”, a variable name must follow which has
|
||||
been previously defined in the input script. If <em>mode</em> = scalar, then
|
||||
only equal-style or vector-style variables can be used, which both
|
||||
produce global values. In this mode, a vector-style variable requires
|
||||
|
|
@ -399,10 +399,8 @@ values for each of these, so they do not need to be specified.</p>
|
|||
describes the six values that are printed at the first of each section
|
||||
of output. The third describes the 4 values printed for each bin in
|
||||
the histogram.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix.</p>
|
||||
<p>This fix produces a global vector and global array which can be
|
||||
|
|
|
|||
|
|
@ -140,14 +140,14 @@
|
|||
<li>one or more input values can be listed</li>
|
||||
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
|
||||
</ul>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
|
||||
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
|
||||
<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
c_ID = global scalar or vector calculated by a compute with ID
|
||||
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
|
||||
f_ID = global scalar or vector calculated by a fix with ID
|
||||
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
|
||||
v_name = value(s) calculated by an equal-style or vector-style variable with name
|
||||
v_name[I] = value calculated by a vector-style variable with name
|
||||
</pre>
|
||||
<ul class="simple">
|
||||
<li>zero or more keyword/arg pairs may be appended</li>
|
||||
<li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>off</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
|
||||
|
|
@ -179,13 +179,13 @@
|
|||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples</h2>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">c_thermo_temp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">profile</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">ave</span> <span class="n">window</span> <span class="mi">20</span> <span class="o">&</span>
|
||||
<span class="n">title1</span> <span class="s2">"My output values"</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">f_indent</span> <span class="n">f_indent</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">indent</span> <span class="n">off</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
|
||||
fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
|
||||
title1 "My output values"
|
||||
fix 1 all ave/time 100 5 1000 c_thermo_press[*]
|
||||
fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description</h2>
|
||||
|
|
@ -228,7 +228,7 @@ is used. All vectors must be the same length, which is the length of
|
|||
the vector or number of rows in the array.</p>
|
||||
<p>Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
|
||||
specify multiple values. This takes the form “*” or “*n” or “n*” or
|
||||
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
|
||||
number of columns in the array (for <em>mode</em> = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to N. A leading
|
||||
|
|
@ -239,11 +239,11 @@ means all indices from m to n (inclusive).</p>
|
|||
vector or columns of the array had been listed one by one. E.g. these
|
||||
2 fix ave/time commands are equivalent, since the <a class="reference internal" href="compute_rdf.html"><span class="doc">compute rdf</span></a> command creates, in this case, a global array
|
||||
with 3 columns, each of length 50:</p>
|
||||
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myRDF</span> <span class="nb">all</span> <span class="n">rdf</span> <span class="mi">50</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<pre class="literal-block">
|
||||
compute myRDF all rdf 50 1 2
|
||||
fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
|
||||
fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
|
||||
</pre>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
||||
timesteps the input values will be used in order to contribute to the
|
||||
|
|
@ -261,7 +261,7 @@ timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
|
|||
averaging is done; values are simply generated on timesteps
|
||||
100,200,etc.</p>
|
||||
<hr class="docutils" />
|
||||
<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
||||
<p>If a value begins with “c_”, a compute ID must follow which has been
|
||||
previously defined in the input script. If <em>mode</em> = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the
|
||||
compute is used. If a bracketed term is appended, the Ith element of
|
||||
|
|
@ -277,7 +277,7 @@ can thus be accessed by fix ave/time. Or it can be a compute defined
|
|||
not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See
|
||||
the doc pages for these commands which give the IDs of these computes.
|
||||
Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
||||
<p>If a value begins with “f_”, a fix ID must follow which has been
|
||||
previously defined in the input script. If <em>mode</em> = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the fix
|
||||
is used. If a bracketed term is appended, the Ith element of the
|
||||
|
|
@ -290,7 +290,7 @@ specify multiple values.</p>
|
|||
<p>Note that some fixes only produce their values on certain timesteps,
|
||||
which must be compatible with <em>Nevery</em>, else an error will result.
|
||||
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
||||
<p>If a value begins with “v_”, a variable name must follow which has
|
||||
been previously defined in the input script. If <em>mode</em> = scalar, then
|
||||
only equal-style or vector-style variables can be used, which both
|
||||
produce global values. In this mode, a vector-style variable requires
|
||||
|
|
@ -383,10 +383,8 @@ so the <em>title3</em> setting is ignored when <em>mode</em> = scalar.</p>
|
|||
describes the two values that are printed at the first of each section
|
||||
of output. In the third line the values are replaced with the
|
||||
appropriate fields from the fix ave/time command.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix.</p>
|
||||
<p>This fix produces a global scalar or global vector or global array
|
||||
|
|
|
|||
|
|
@ -432,10 +432,8 @@ will be duplicate nodes in the list.</p>
|
|||
rectangle for each processor (1 to 4).</p>
|
||||
<p>For a 3d problem, the syntax is similar with 8 vertices listed for
|
||||
each processor, instead of 4, and “SQUARES” replaced by “CUBES”.</p>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix.</p>
|
||||
<p>This fix computes a global scalar which is the imbalance factor
|
||||
|
|
|
|||
|
|
@ -224,10 +224,8 @@ dramatically released when the bond is broken. More generally, you
|
|||
may need to thermostat your system to compensate for energy changes
|
||||
resulting from broken bonds (and angles, dihedrals, impropers).</p>
|
||||
</div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix.</p>
|
||||
<p>This fix computes two statistics which it stores in a global vector of
|
||||
|
|
|
|||
|
|
@ -265,7 +265,7 @@ percolation simulation.</p>
|
|||
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
|
||||
the system) for use in weighting pairwise interactions for bonded
|
||||
atoms. Note that adding a single bond always adds a new 1st neighbor
|
||||
but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the
|
||||
but may also induce *many* new 2nd and 3rd neighbors, depending on the
|
||||
molecular topology of your system. The “extra special per atom”
|
||||
parameter must typically be set to allow for the new maximum total
|
||||
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
|
||||
|
|
@ -320,10 +320,8 @@ dramatically when the bond is formed. More generally, you may need to
|
|||
thermostat your system to compensate for energy changes resulting from
|
||||
created bonds (and angles, dihedrals, impropers).</p>
|
||||
</div>
|
||||
</div>
|
||||
<hr class="docutils" />
|
||||
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
||||
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
||||
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
|
||||
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
||||
are relevant to this fix.</p>
|
||||
<p>This fix computes two statistics which it stores in a global vector of
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
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Reference in New Issue