ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14349 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2015-12-10 17:23:56 +00:00
parent 8550cacf18
commit 28bf73fbf7
688 changed files with 6410 additions and 6513 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
doc/Manual.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>LAMMPS Documentation &mdash; LAMMPS 15 May 2015 version documentation</title> <title>LAMMPS Documentation &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="1. Introduction" href="Section_intro.html"/> <link rel="next" title="1. Introduction" href="Section_intro.html"/>
@ -401,7 +401,7 @@ it gives quick access to documentation for all LAMMPS commands.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -422,7 +422,7 @@ it gives quick access to documentation for all LAMMPS commands.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

36
doc/Section_accelerate.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5. Accelerating LAMMPS performance &mdash; LAMMPS 15 May 2015 version documentation</title> <title>5. Accelerating LAMMPS performance &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="6. How-to discussions" href="Section_howto.html"/> <link rel="next" title="6. How-to discussions" href="Section_howto.html"/>
<link rel="prev" title="4. Packages" href="Section_packages.html"/> <link rel="prev" title="4. Packages" href="Section_packages.html"/>
@ -257,12 +257,12 @@ different methods are shown in the figure below. For this system,
staggered PPPM (using ik differentiation) becomes useful when using a staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.</p> relative accuracy of slightly greater than 1e-5 and above.</p>
<img alt="_images/rhodo_staggered.jpg" class="align-center" src="_images/rhodo_staggered.jpg" /> <img alt="_images/rhodo_staggered.jpg" class="align-center" src="_images/rhodo_staggered.jpg" />
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Using staggered PPPM may not give the same increase in <p class="last">Using staggered PPPM may not give the same increase in accuracy
accuracy of energy and pressure as it does in forces, so some caution of energy and pressure as it does in forces, so some caution must be
must be used if energy and/or pressure are quantities of interest, used if energy and/or pressure are quantities of interest, such as
such as when using a barostat.</p> when using a barostat.</p>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -410,14 +410,14 @@ launched, without changing your input script, as illustrated in the
individual accelerator sections. Or you can add individual accelerator sections. Or you can add
<a class="reference internal" href="package.html"><em>package</em></a> and <a class="reference internal" href="suffix.html"><em>suffix</em></a> commands to your input <a class="reference internal" href="package.html"><em>package</em></a> and <a class="reference internal" href="suffix.html"><em>suffix</em></a> commands to your input
script.</p> script.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">With a few exceptions, you can build a single LAMMPS <p class="last">With a few exceptions, you can build a single LAMMPS executable
executable with all its accelerator packages installed. Note however with all its accelerator packages installed. Note however that the
that the USER-INTEL and KOKKOS packages require you to choose one of USER-INTEL and KOKKOS packages require you to choose one of their
their hardware options when building for a specific platform. hardware options when building for a specific platform. I.e. CPU or
I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP, Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
Cuda, or Phi option for the KOKKOS package.</p> option for the KOKKOS package.</p>
</div> </div>
<p>These are the exceptions. You cannot build a single executable with:</p> <p>These are the exceptions. You cannot build a single executable with:</p>
<ul class="simple"> <ul class="simple">
@ -587,7 +587,7 @@ to benchmark the performance of both packages on your system.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -608,7 +608,7 @@ to benchmark the performance of both packages on your system.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

20
doc/Section_accelerate.txt
View File

@ -134,10 +134,10 @@ relative accuracy of slightly greater than 1e-5 and above.
:c,image(JPG/rhodo_staggered.jpg) :c,image(JPG/rhodo_staggered.jpg)
IMPORTANT NOTE: Using staggered PPPM may not give the same increase in NOTE: Using staggered PPPM may not give the same increase in accuracy
accuracy of energy and pressure as it does in forces, so some caution of energy and pressure as it does in forces, so some caution must be
must be used if energy and/or pressure are quantities of interest, used if energy and/or pressure are quantities of interest, such as
such as when using a barostat. when using a barostat.
:line :line
@ -240,12 +240,12 @@ individual accelerator sections. Or you can add
"package"_package.html and "suffix"_suffix.html commands to your input "package"_package.html and "suffix"_suffix.html commands to your input
script. script.
IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS NOTE: With a few exceptions, you can build a single LAMMPS executable
executable with all its accelerator packages installed. Note however with all its accelerator packages installed. Note however that the
that the USER-INTEL and KOKKOS packages require you to choose one of USER-INTEL and KOKKOS packages require you to choose one of their
their hardware options when building for a specific platform. hardware options when building for a specific platform. I.e. CPU or
I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP, Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
Cuda, or Phi option for the KOKKOS package. option for the KOKKOS package.
These are the exceptions. You cannot build a single executable with: These are the exceptions. You cannot build a single executable with:

16
doc/Section_commands.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>3. Commands &mdash; LAMMPS 15 May 2015 version documentation</title> <title>3. Commands &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="4. Packages" href="Section_packages.html"/> <link rel="next" title="4. Packages" href="Section_packages.html"/>
<link rel="prev" title="2. Getting Started" href="Section_start.html"/> <link rel="prev" title="2. Getting Started" href="Section_start.html"/>
@ -302,10 +302,10 @@ the single argument they enclose is stored internally.</p>
<a class="reference internal" href="if.html"><em>if</em></a>, and <a class="reference internal" href="python.html"><em>python</em></a> commands for examples.</p> <a class="reference internal" href="if.html"><em>if</em></a>, and <a class="reference internal" href="python.html"><em>python</em></a> commands for examples.</p>
<p>A &#8220;#&#8221; or &#8220;$&#8221; character that is between quotes will not be treated as a <p>A &#8220;#&#8221; or &#8220;$&#8221; character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).</p> comment indicator in (2) or substituted for as a variable in (3).</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">If the argument is itself a command that requires a <p class="last">If the argument is itself a command that requires a quoted
quoted argument (e.g. using a <a class="reference internal" href="print.html"><em>print</em></a> command as part of an argument (e.g. using a <a class="reference internal" href="print.html"><em>print</em></a> command as part of an
<a class="reference internal" href="if.html"><em>if</em></a> or <a class="reference internal" href="run.html"><em>run every</em></a> command), then single, double, or <a class="reference internal" href="if.html"><em>if</em></a> or <a class="reference internal" href="run.html"><em>run every</em></a> command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is for those commands for examples. Only one of level of nesting is
@ -1481,7 +1481,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -1502,7 +1502,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

4
doc/Section_commands.txt
View File

@ -181,8 +181,8 @@ See the "dump modify format"_dump_modify.html, "print"_print.html,
A "#" or "$" character that is between quotes will not be treated as a A "#" or "$" character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3). comment indicator in (2) or substituted for as a variable in (3).
IMPORTANT NOTE: If the argument is itself a command that requires a NOTE: If the argument is itself a command that requires a quoted
quoted argument (e.g. using a "print"_print.html command as part of an argument (e.g. using a "print"_print.html command as part of an
"if"_if.html or "run every"_run.html command), then single, double, or "if"_if.html or "run every"_run.html command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is for those commands for examples. Only one of level of nesting is

8
doc/Section_errors.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>12. Errors &mdash; LAMMPS 15 May 2015 version documentation</title> <title>12. Errors &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="13. Future and history" href="Section_history.html"/> <link rel="next" title="13. Future and history" href="Section_history.html"/>
<link rel="prev" title="11. Python interface to LAMMPS" href="Section_python.html"/> <link rel="prev" title="11. Python interface to LAMMPS" href="Section_python.html"/>
@ -6323,7 +6323,7 @@ infinity.</dd>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -6344,7 +6344,7 @@ infinity.</dd>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/Section_example.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>7. Example problems &mdash; LAMMPS 15 May 2015 version documentation</title> <title>7. Example problems &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="8. Performance &amp; scalability" href="Section_perf.html"/> <link rel="next" title="8. Performance &amp; scalability" href="Section_perf.html"/>
<link rel="prev" title="6. How-to discussions" href="Section_howto.html"/> <link rel="prev" title="6. How-to discussions" href="Section_howto.html"/>
@ -346,7 +346,7 @@ packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -367,7 +367,7 @@ packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/Section_history.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>13. Future and history &mdash; LAMMPS 15 May 2015 version documentation</title> <title>13. Future and history &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="prev" title="12. Errors" href="Section_errors.html"/> <link rel="prev" title="12. Errors" href="Section_errors.html"/>
@ -258,7 +258,7 @@ internally. A brief listing of their features is given here.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -279,7 +279,7 @@ internally. A brief listing of their features is given here.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

69
doc/Section_howto.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>6. How-to discussions &mdash; LAMMPS 15 May 2015 version documentation</title> <title>6. How-to discussions &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="7. Example problems" href="Section_example.html"/> <link rel="next" title="7. Example problems" href="Section_example.html"/>
<link rel="prev" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/> <link rel="prev" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
@ -342,12 +342,12 @@ are zeroed out every timestep. The reason to make it the last fix is
so that any forces induced by other fixes will be zeroed out.</p> so that any forces induced by other fixes will be zeroed out.</p>
<p>Many of the example input scripts included in the LAMMPS distribution <p>Many of the example input scripts included in the LAMMPS distribution
are for 2d models.</p> are for 2d models.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Some models in LAMMPS treat particles as finite-size <p class="last">Some models in LAMMPS treat particles as finite-size spheres, as
spheres, as opposed to point particles. In 2d, the particles will opposed to point particles. In 2d, the particles will still be
still be spheres, not disks, meaning their moment of inertia will be spheres, not disks, meaning their moment of inertia will be the same
the same as in 3d.</p> as in 3d.</p>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -363,8 +363,8 @@ commands like <a class="reference internal" href="pair_coeff.html"><em>pair_coef
<a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a> <a class="reference internal" href="bond_coeff.html"><em>bond_coeff</em></a>. See <a class="reference internal" href="Section_tools.html"><em>Section_tools</em></a>
for additional tools that can use CHARMM or AMBER to assign force for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.</p> field coefficients and convert their output into LAMMPS input.</p>
<p>See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force <p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force
field. See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a> for a description of the AMBER force field. See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
field.</p> field.</p>
<p>These style choices compute force field formulas that are consistent <p>These style choices compute force field formulas that are consistent
with common options in CHARMM or AMBER. See each command&#8217;s with common options in CHARMM or AMBER. See each command&#8217;s
@ -389,7 +389,7 @@ atoms involved in the bond, angle, or torsion terms. DREIDING has an
<a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe <a class="reference internal" href="pair_hbond_dreiding.html"><em>explicit hydrogen bond term</em></a> to describe
interactions involving a hydrogen atom on very electronegative atoms interactions involving a hydrogen atom on very electronegative atoms
(N, O, F).</p> (N, O, F).</p>
<p>See <a class="reference internal" href="#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p> <p>See <a class="reference internal" href="special_bonds.html#mayo"><span>(Mayo)</span></a> for a description of the DREIDING force field</p>
<p>These style choices compute force field formulas that are consistent <p>These style choices compute force field formulas that are consistent
with the DREIDING force field. See each command&#8217;s with the DREIDING force field. See each command&#8217;s
documentation for the formula it computes.</p> documentation for the formula it computes.</p>
@ -587,7 +587,7 @@ computations between frozen atoms by using this command:</p>
<div class="section" id="tip3p-water-model"> <div class="section" id="tip3p-water-model">
<span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2> <span id="howto-7"></span><h2>6.7. TIP3P water model<a class="headerlink" href="#tip3p-water-model" title="Permalink to this headline"></a></h2>
<p>The TIP3P water model as implemented in CHARMM <p>The TIP3P water model as implemented in CHARMM
<a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms. charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold In LAMMPS the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -598,7 +598,7 @@ atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
cutoff. The K values can be used if a flexible TIP3P model (without cutoff. The K values can be used if a flexible TIP3P model (without
fix shake) is desired. If the LJ epsilon and sigma for HH and OH are fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
set to 0.0, it corresponds to the original 1983 TIP3P model set to 0.0, it corresponds to the original 1983 TIP3P model
<a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>.</p> <a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>.</p>
<div class="line-block"> <div class="line-block">
<div class="line">O mass = 15.9994</div> <div class="line">O mass = 15.9994</div>
<div class="line">H mass = 1.008</div> <div class="line">H mass = 1.008</div>
@ -617,7 +617,7 @@ set to 0.0, it corresponds to the original 1983 TIP3P model
<div class="line"><br /></div> <div class="line"><br /></div>
</div> </div>
<p>These are the parameters to use for TIP3P with a long-range Coulombic <p>These are the parameters to use for TIP3P with a long-range Coulombic
solver (e.g. Ewald or PPPM in LAMMPS), see <a class="reference internal" href="#price"><span>(Price)</span></a> for solver (e.g. Ewald or PPPM in LAMMPS), see <a class="reference internal" href="pair_dipole.html#price"><span>(Price)</span></a> for
details:</p> details:</p>
<div class="line-block"> <div class="line-block">
<div class="line">O mass = 15.9994</div> <div class="line">O mass = 15.9994</div>
@ -656,7 +656,7 @@ for a cutoff model:</p>
using the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command.</p> using the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command.</p>
<p>These are the additional parameters (in real units) to set for O and H <p>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff atoms and the water molecule to run a rigid TIP4P model with a cutoff
<a class="reference internal" href="#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in <a class="reference internal" href="pair_lj.html#jorgensen"><span>(Jorgensen)</span></a>. Note that the OM distance is specified in
the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, not as part of the pair the <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command, not as part of the pair
coefficients.</p> coefficients.</p>
<div class="line-block"> <div class="line-block">
@ -766,7 +766,7 @@ the partial charge assignemnts change:</p>
<div class="line">H charge = 0.4238</div> <div class="line">H charge = 0.4238</div>
<div class="line"><br /></div> <div class="line"><br /></div>
</div> </div>
<p>See the <a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a> reference for more details on both <p>See the <a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span>(Berendsen)</span></a> reference for more details on both
the SPC and SPC/E models.</p> the SPC and SPC/E models.</p>
<p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p> <p>Wikipedia also has a nice article on <a class="reference external" href="http://en.wikipedia.org/wiki/Water_model">water models</a>.</p>
<hr class="docutils" /> <hr class="docutils" />
@ -1764,14 +1764,13 @@ apply a thermostat to only the x and z components of velocity by using
it in conjunction with <a class="reference internal" href="compute_temp_partial.html"><em>compute temp/partial</em></a>. Of you could thermostat only it in conjunction with <a class="reference internal" href="compute_temp_partial.html"><em>compute temp/partial</em></a>. Of you could thermostat only
the thermal temperature of a streaming flow of particles without the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using <a class="reference internal" href="compute_temp_profile.html"><em>compute temp/profile</em></a>.</p> affecting the streaming velocity, by using <a class="reference internal" href="compute_temp_profile.html"><em>compute temp/profile</em></a>.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Only the nvt fixes perform time integration, meaning <p class="last">Only the nvt fixes perform time integration, meaning they update
they update the velocities and positions of particles due to forces the velocities and positions of particles due to forces and velocities
and velocities respectively. The other thermostat fixes only adjust respectively. The other thermostat fixes only adjust velocities; they
velocities; they do NOT perform time integration updates. Thus they do NOT perform time integration updates. Thus they should be used in
should be used in conjunction with a constant NVE integration fix such conjunction with a constant NVE integration fix such as these:</p>
as these:</p>
</div> </div>
<ul class="simple"> <ul class="simple">
<li><a class="reference internal" href="fix_nve.html"><em>fix nve</em></a></li> <li><a class="reference internal" href="fix_nve.html"><em>fix nve</em></a></li>
@ -1804,12 +1803,12 @@ computing the kinetic componenet which contributes to the current
pressure. See the doc pages for the individual fixes and for the pressure. See the doc pages for the individual fixes and for the
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command for instructions on how to assign <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command for instructions on how to assign
a temperature or pressure compute to a barostatting fix.</p> a temperature or pressure compute to a barostatting fix.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">As with the thermostats, the Nose/Hoover methods (<a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>) perform time <p class="last">As with the thermostats, the Nose/Hoover methods (<a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>) perform time integration.
integration. <a class="reference internal" href="fix_press_berendsen.html"><em>Fix press/berendsen</em></a> does NOT, <a class="reference internal" href="fix_press_berendsen.html"><em>Fix press/berendsen</em></a> does NOT, so it should
so it should be used with one of the constant NVE fixes or with one of be used with one of the constant NVE fixes or with one of the NVT
the NVT fixes.</p> fixes.</p>
</div> </div>
<p>Finally, thermodynamic output, which can be setup via the <p>Finally, thermodynamic output, which can be setup via the
<a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command, often includes temperature <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command, often includes temperature
@ -1918,7 +1917,7 @@ the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress fully equilibrate the deformed cell before sampling the stress
tensor. Another approach is to sample the triclinic cell fluctuations tensor. Another approach is to sample the triclinic cell fluctuations
that occur in an NPT simulation. This method can also be slow to that occur in an NPT simulation. This method can also be slow to
converge and requires careful post-processing <a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a></p> converge and requires careful post-processing <a class="reference internal" href="pair_sdk.html#shinoda"><span>(Shinoda)</span></a></p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
<div class="section" id="library-interface-to-lammps"> <div class="section" id="library-interface-to-lammps">
@ -2541,7 +2540,7 @@ well.</p>
</div> </div>
<div class="section" id="adiabatic-core-shell-model"> <div class="section" id="adiabatic-core-shell-model">
<span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline"></a></h2> <span id="howto-26"></span><h2>6.26. Adiabatic core/shell model<a class="headerlink" href="#adiabatic-core-shell-model" title="Permalink to this headline"></a></h2>
<p>The adiabatic core-shell model by <a class="reference internal" href="compute_temp_cs.html#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding <p>The adiabatic core-shell model by <a class="reference internal" href="pair_cs.html#mitchellfinchham"><span>Mitchell and Finchham</span></a> is a simple method for adding
polarizability to a system. In order to mimic the electron shell of polarizability to a system. In order to mimic the electron shell of
an ion, a satellite particle is attached to it. This way the ions are an ion, a satellite particle is attached to it. This way the ions are
split into a core and a shell where the latter is meant to react to split into a core and a shell where the latter is meant to react to
@ -2750,7 +2749,7 @@ fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
model, representes induced dipoles by a pair of charges (the core atom model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems model has a number of features aimed at its use in molecular systems
(<a class="reference internal" href="#lamoureux"><span>Lamoureux and Roux</span></a>):</p> (<a class="reference internal" href="tutorial_drude.html#lamoureux"><span>Lamoureux and Roux</span></a>):</p>
<ul class="simple"> <ul class="simple">
<li>Thermostating of the additional degrees of freedom associated with the <li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced induced dipoles at very low temperature, in terms of the reduced
@ -2836,7 +2835,7 @@ Phys, 79, 926 (1983).</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -2857,7 +2856,7 @@ Phys, 79, 926 (1983).</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

29
doc/Section_howto.txt
View File

@ -164,10 +164,10 @@ so that any forces induced by other fixes will be zeroed out.
Many of the example input scripts included in the LAMMPS distribution Many of the example input scripts included in the LAMMPS distribution
are for 2d models. are for 2d models.
IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
spheres, as opposed to point particles. In 2d, the particles will opposed to point particles. In 2d, the particles will still be
still be spheres, not disks, meaning their moment of inertia will be spheres, not disks, meaning their moment of inertia will be the same
the same as in 3d. as in 3d.
:line :line
@ -1658,12 +1658,11 @@ the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using "compute affecting the streaming velocity, by using "compute
temp/profile"_compute_temp_profile.html. temp/profile"_compute_temp_profile.html.
IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning NOTE: Only the nvt fixes perform time integration, meaning they update
they update the velocities and positions of particles due to forces the velocities and positions of particles due to forces and velocities
and velocities respectively. The other thermostat fixes only adjust respectively. The other thermostat fixes only adjust velocities; they
velocities; they do NOT perform time integration updates. Thus they do NOT perform time integration updates. Thus they should be used in
should be used in conjunction with a constant NVE integration fix such conjunction with a constant NVE integration fix such as these:
as these:
"fix nve"_fix_nve.html "fix nve"_fix_nve.html
"fix nve/sphere"_fix_nve_sphere.html "fix nve/sphere"_fix_nve_sphere.html
@ -1705,11 +1704,11 @@ pressure. See the doc pages for the individual fixes and for the
"fix_modify"_fix_modify.html command for instructions on how to assign "fix_modify"_fix_modify.html command for instructions on how to assign
a temperature or pressure compute to a barostatting fix. a temperature or pressure compute to a barostatting fix.
IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods ("fix NOTE: As with the thermostats, the Nose/Hoover methods ("fix
npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
integration. "Fix press/berendsen"_fix_press_berendsen.html does NOT, "Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
so it should be used with one of the constant NVE fixes or with one of be used with one of the constant NVE fixes or with one of the NVT
the NVT fixes. fixes.
Finally, thermodynamic output, which can be setup via the Finally, thermodynamic output, which can be setup via the
"thermo_style"_thermo_style.html command, often includes temperature "thermo_style"_thermo_style.html command, often includes temperature

8
doc/Section_intro.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>1. Introduction &mdash; LAMMPS 15 May 2015 version documentation</title> <title>1. Introduction &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="2. Getting Started" href="Section_start.html"/> <link rel="next" title="2. Getting Started" href="Section_start.html"/>
<link rel="prev" title="LAMMPS Documentation" href="Manual.html"/> <link rel="prev" title="LAMMPS Documentation" href="Manual.html"/>
@ -640,7 +640,7 @@ version of LAMMPS were the following:</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -661,7 +661,7 @@ version of LAMMPS were the following:</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

16
doc/Section_modify.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>10. Modifying &amp; extending LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title> <title>10. Modifying &amp; extending LAMMPS &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="11. Python interface to LAMMPS" href="Section_python.html"/> <link rel="next" title="11. Python interface to LAMMPS" href="Section_python.html"/>
<link rel="prev" title="9. Additional tools" href="Section_tools.html"/> <link rel="prev" title="9. Additional tools" href="Section_tools.html"/>
@ -379,10 +379,10 @@ that you must set when defining a new atom style, which are documented
in atom_vec.h. New atom arrays are defined in atom.cpp. Search for in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
the word &#8220;customize&#8221; and you will find locations you will need to the word &#8220;customize&#8221; and you will find locations you will need to
modify.</p> modify.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">It is possible to add some attributes, such as a <p class="last">It is possible to add some attributes, such as a molecule ID, to
molecule ID, to atom styles that do not have them via the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. This command also atom styles that do not have them via the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. This command also
allows new custom attributes consisting of extra integer or allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> doc page for examples of cases floating-point values to be added to atoms. See the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> doc page for examples of cases
where this is useful and details on how to initialize, access, and where this is useful and details on how to initialize, access, and
@ -1199,7 +1199,7 @@ feature.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -1220,7 +1220,7 @@ feature.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

4
doc/Section_modify.txt
View File

@ -187,8 +187,8 @@ in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
the word "customize" and you will find locations you will need to the word "customize" and you will find locations you will need to
modify. modify.
IMPORTANT NOTE: It is possible to add some attributes, such as a NOTE: It is possible to add some attributes, such as a molecule ID, to
molecule ID, to atom styles that do not have them via the "fix atom styles that do not have them via the "fix
property/atom"_fix_property_atom.html command. This command also property/atom"_fix_property_atom.html command. This command also
allows new custom attributes consisting of extra integer or allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the "fix floating-point values to be added to atoms. See the "fix

8
doc/Section_packages.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>4. Packages &mdash; LAMMPS 15 May 2015 version documentation</title> <title>4. Packages &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/> <link rel="next" title="5. Accelerating LAMMPS performance" href="Section_accelerate.html"/>
<link rel="prev" title="3. Commands" href="Section_commands.html"/> <link rel="prev" title="3. Commands" href="Section_commands.html"/>
@ -1536,7 +1536,7 @@ you have questions.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -1557,7 +1557,7 @@ you have questions.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/Section_perf.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>8. Performance &amp; scalability &mdash; LAMMPS 15 May 2015 version documentation</title> <title>8. Performance &amp; scalability &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="9. Additional tools" href="Section_tools.html"/> <link rel="next" title="9. Additional tools" href="Section_tools.html"/>
<link rel="prev" title="7. Example problems" href="Section_example.html"/> <link rel="prev" title="7. Example problems" href="Section_example.html"/>
@ -249,7 +249,7 @@ on 1500 processors that ran at 85% parallel efficiency.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -270,7 +270,7 @@ on 1500 processors that ran at 85% parallel efficiency.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

68
doc/Section_python.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>11. Python interface to LAMMPS &mdash; LAMMPS 15 May 2015 version documentation</title> <title>11. Python interface to LAMMPS &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="12. Errors" href="Section_errors.html"/> <link rel="next" title="12. Errors" href="Section_errors.html"/>
<link rel="prev" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/> <link rel="prev" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
@ -238,12 +238,12 @@ check which version of Python you have installed, by simply typing
</div> </div>
<div class="section" id="overview-of-using-python-from-a-lammps-script"> <div class="section" id="overview-of-using-python-from-a-lammps-script">
<span id="py-2"></span><h2>11.2. Overview of using Python from a LAMMPS script<a class="headerlink" href="#overview-of-using-python-from-a-lammps-script" title="Permalink to this headline"></a></h2> <span id="py-2"></span><h2>11.2. Overview of using Python from a LAMMPS script<a class="headerlink" href="#overview-of-using-python-from-a-lammps-script" title="Permalink to this headline"></a></h2>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">It is not currently possible to use the <p class="last">It is not currently possible to use the <a class="reference internal" href="python.html"><em>python</em></a>
<a class="reference internal" href="python.html"><em>python</em></a> command described in this section with Python 3, command described in this section with Python 3, only with Python 2.
only with Python 2. The C API changed from Python 2 to 3 and the The C API changed from Python 2 to 3 and the LAMMPS code is not
LAMMPS code is not compatible with both.</p> compatible with both.</p>
</div> </div>
<p>LAMMPS has a <a class="reference internal" href="python.html"><em>python</em></a> command which can be used in an <p>LAMMPS has a <a class="reference internal" href="python.html"><em>python</em></a> command which can be used in an
input script to define and execute a Python function that you write input script to define and execute a Python function that you write
@ -457,13 +457,13 @@ print &quot;Proc %d out of %d procs&quot; % (pypar.rank(),pypar.size())
</pre></div> </pre></div>
</div> </div>
<p>and see one line of output for each processor you run on.</p> <p>and see one line of output for each processor you run on.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">To use Pypar and LAMMPS in parallel from Python, you <p class="last">To use Pypar and LAMMPS in parallel from Python, you must insure
must insure both are using the same version of MPI. If you only have both are using the same version of MPI. If you only have one MPI
one MPI installed on your system, this is not an issue, but it can be installed on your system, this is not an issue, but it can be if you
if you have multiple MPIs. Your LAMMPS build is explicit about which have multiple MPIs. Your LAMMPS build is explicit about which MPI it
MPI it is using, since you specify the details in your lo-level is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Pypar uses the &#8220;mpicc&#8221; command to find src/MAKE/Makefile.foo file. Pypar uses the &#8220;mpicc&#8221; command to find
information about the MPI it uses to build against. And it tries to information about the MPI it uses to build against. And it tries to
load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find
@ -502,13 +502,13 @@ print &quot;Proc %d out of %d procs&quot; % (comm.Get_rank(),comm.Get_size())
</pre></div> </pre></div>
</div> </div>
<p>and see one line of output for each processor you run on.</p> <p>and see one line of output for each processor you run on.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">To use mpi4py and LAMMPS in parallel from Python, you <p class="last">To use mpi4py and LAMMPS in parallel from Python, you must
must insure both are using the same version of MPI. If you only have insure both are using the same version of MPI. If you only have one
one MPI installed on your system, this is not an issue, but it can be MPI installed on your system, this is not an issue, but it can be if
if you have multiple MPIs. Your LAMMPS build is explicit about which you have multiple MPIs. Your LAMMPS build is explicit about which MPI
MPI it is using, since you specify the details in your lo-level it is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Mpi4py uses the &#8220;mpicc&#8221; command to find src/MAKE/Makefile.foo file. Mpi4py uses the &#8220;mpicc&#8221; command to find
information about the MPI it uses to build against. And it tries to information about the MPI it uses to build against. And it tries to
load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find
@ -715,16 +715,16 @@ lmp = lammps(name=&quot;g++&quot;,cmdargs=list) # add LAMMPS command-line arg
</pre></div> </pre></div>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Currently, the creation of a LAMMPS object from within <p class="last">Currently, the creation of a LAMMPS object from within lammps.py
lammps.py does not take an MPI communicator as an argument. There does not take an MPI communicator as an argument. There should be a
should be a way to do this, so that the LAMMPS instance runs on a way to do this, so that the LAMMPS instance runs on a subset of
subset of processors if desired, but I don&#8217;t know how to do it from processors if desired, but I don&#8217;t know how to do it from Pypar. So
Pypar. So for now, it runs with MPI_COMM_WORLD, which is all the for now, it runs with MPI_COMM_WORLD, which is all the processors. If
processors. If someone figures out how to do this with one or more of someone figures out how to do this with one or more of the Python
the Python wrappers for MPI, like Pypar, please let us know and we wrappers for MPI, like Pypar, please let us know and we will amend
will amend these doc pages.</p> these doc pages.</p>
</div> </div>
<p>The lines</p> <p>The lines</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span> <div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">lammps</span> <span class="kn">import</span> <span class="n">lammps</span>
@ -995,7 +995,7 @@ different visualization package options. Click to see larger images:</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -1016,7 +1016,7 @@ different visualization package options. Click to see larger images:</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

44
doc/Section_python.txt
View File

@ -110,10 +110,10 @@ check which version of Python you have installed, by simply typing
11.2 Overview of using Python from a LAMMPS script :link(py_2),h4 11.2 Overview of using Python from a LAMMPS script :link(py_2),h4
IMPORTANT NOTE: It is not currently possible to use the NOTE: It is not currently possible to use the "python"_python.html
"python"_python.html command described in this section with Python 3, command described in this section with Python 3, only with Python 2.
only with Python 2. The C API changed from Python 2 to 3 and the The C API changed from Python 2 to 3 and the LAMMPS code is not
LAMMPS code is not compatible with both. compatible with both.
LAMMPS has a "python"_python.html command which can be used in an LAMMPS has a "python"_python.html command which can be used in an
input script to define and execute a Python function that you write input script to define and execute a Python function that you write
@ -354,11 +354,11 @@ print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre
and see one line of output for each processor you run on. and see one line of output for each processor you run on.
IMPORTANT NOTE: To use Pypar and LAMMPS in parallel from Python, you NOTE: To use Pypar and LAMMPS in parallel from Python, you must insure
must insure both are using the same version of MPI. If you only have both are using the same version of MPI. If you only have one MPI
one MPI installed on your system, this is not an issue, but it can be installed on your system, this is not an issue, but it can be if you
if you have multiple MPIs. Your LAMMPS build is explicit about which have multiple MPIs. Your LAMMPS build is explicit about which MPI it
MPI it is using, since you specify the details in your lo-level 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 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 load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find
@ -399,11 +399,11 @@ print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre
and see one line of output for each processor you run on. and see one line of output for each processor you run on.
IMPORTANT NOTE: To use mpi4py and LAMMPS in parallel from Python, you NOTE: To use mpi4py and LAMMPS in parallel from Python, you must
must insure both are using the same version of MPI. If you only have insure both are using the same version of MPI. If you only have one
one MPI installed on your system, this is not an issue, but it can be MPI installed on your system, this is not an issue, but it can be if
if you have multiple MPIs. Your LAMMPS build is explicit about which you have multiple MPIs. Your LAMMPS build is explicit about which MPI
MPI it is using, since you specify the details in your lo-level it is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find
information about the MPI it uses to build against. And it tries to 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 load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find
@ -610,14 +610,14 @@ lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms
:line :line
IMPORTANT NOTE: Currently, the creation of a LAMMPS object from within NOTE: Currently, the creation of a LAMMPS object from within lammps.py
lammps.py does not take an MPI communicator as an argument. There does not take an MPI communicator as an argument. There should be a
should be a way to do this, so that the LAMMPS instance runs on a way to do this, so that the LAMMPS instance runs on a subset of
subset of processors if desired, but I don't know how to do it from processors if desired, but I don't know how to do it from Pypar. So
Pypar. So for now, it runs with MPI_COMM_WORLD, which is all the for now, it runs with MPI_COMM_WORLD, which is all the processors. If
processors. If someone figures out how to do this with one or more of someone figures out how to do this with one or more of the Python
the Python wrappers for MPI, like Pypar, please let us know and we wrappers for MPI, like Pypar, please let us know and we will amend
will amend these doc pages. these doc pages.
The lines The lines

73
doc/Section_start.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>2. Getting Started &mdash; LAMMPS 15 May 2015 version documentation</title> <title>2. Getting Started &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="3. Commands" href="Section_commands.html"/> <link rel="next" title="3. Commands" href="Section_commands.html"/>
<link rel="prev" title="1. Introduction" href="Section_intro.html"/> <link rel="prev" title="1. Introduction" href="Section_intro.html"/>
@ -397,10 +397,10 @@ within the LAMMPS code. The options that are currently recogized are:</p>
compile with -DLAMMPS_GZIP. It requires that your machine supports compile with -DLAMMPS_GZIP. It requires that your machine supports
the &#8220;popen()&#8221; function in the standard runtime library and that a gzip the &#8220;popen()&#8221; function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.</p> executable can be found by LAMMPS during a run.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">on some clusters with high-speed networks, using the <p class="last">on some clusters with high-speed networks, using the fork()
fork() library calls (required by popen()) can interfere with the fast library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are I/O is also available using a compression library instead, which are
@ -420,10 +420,10 @@ will be available to support on-the-fly generation of rendered movies
the need to store intermediate image files. It requires that your the need to store intermediate image files. It requires that your
machines supports the &#8220;popen&#8221; function in the standard runtime library machines supports the &#8220;popen&#8221; function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run.</p> and that an FFmpeg executable can be found by LAMMPS during the run.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Similar to the note above, this option can conflict <p class="last">Similar to the note above, this option can conflict with
with high-speed networks, because it uses popen().</p> high-speed networks, because it uses popen().</p>
</div> </div>
<p>Using -DLAMMPS_MEMALIGN=&lt;bytes&gt; enables the use of the <p>Using -DLAMMPS_MEMALIGN=&lt;bytes&gt; enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory posix_memalign() call instead of malloc() when large chunks or memory
@ -588,17 +588,16 @@ gmake foo
<p>You should get the executable lmp_foo when the build is complete.</p> <p>You should get the executable lmp_foo when the build is complete.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-2-3"><strong>*Errors that can occur when making LAMMPS:*</strong></p> <p id="start-2-3"><strong>*Errors that can occur when making LAMMPS:*</strong></p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">If an error occurs when building LAMMPS, the compiler <p class="last">If an error occurs when building LAMMPS, the compiler or linker
or linker will state very explicitly what the problem is. The error will state very explicitly what the problem is. The error message
message should give you a hint as to which of the steps above has should give you a hint as to which of the steps above has failed, and
failed, and what you need to do in order to fix it. Building a code what you need to do in order to fix it. Building a code with a
with a Makefile is a very logical process. The compiler and linker Makefile is a very logical process. The compiler and linker need to
need to find the appropriate files and those files need to be find the appropriate files and those files need to be compatible with
compatible with LAMMPS source files. When a make fails, there is LAMMPS source files. When a make fails, there is usually a very
usually a very simple reason, which you or a local expert will need to simple reason, which you or a local expert will need to fix.</p>
fix.</p>
</div> </div>
<p>Here are two non-obvious errors that can occur:</p> <p>Here are two non-obvious errors that can occur:</p>
<p>(1) If the make command breaks immediately with errors that indicate <p>(1) If the make command breaks immediately with errors that indicate
@ -769,13 +768,13 @@ make g++
make g++ make g++
</pre></div> </pre></div>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">You should NOT include/exclude packages and build <p class="last">You should NOT include/exclude packages and build LAMMPS in a
LAMMPS in a single make command using multiple targets, e.g. make single make command using multiple targets, e.g. make yes-colloid g++.
yes-colloid g++. This is because the make procedure creates a list of This is because the make procedure creates a list of source files that
source files that will be out-of-date for the build if the package will be out-of-date for the build if the package configuration changes
configuration changes within the same command.</p> within the same command.</p>
</div> </div>
<p>Some packages have individual files that depend on other packages <p>Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing. being included. LAMMPS checks for this and does the right thing.
@ -799,13 +798,13 @@ no-standard&#8221;, &#8220;make yes-std&#8221;, &#8220;make no-std&#8221;, &#822
no-user&#8221;, &#8220;make yes-all&#8221; or &#8220;make no-all&#8221; to include/exclude various no-user&#8221;, &#8220;make yes-all&#8221; or &#8220;make no-all&#8221; to include/exclude various
sets of packages. Type &#8220;make package&#8221; to see the all of the sets of packages. Type &#8220;make package&#8221; to see the all of the
package-related make options.</p> package-related make options.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Inclusion/exclusion of a package works by simply <p class="last">Inclusion/exclusion of a package works by simply moving files
moving files back and forth between the main src directory and back and forth between the main src directory and sub-directories with
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
so that the files are seen or not seen when LAMMPS is built. After are seen or not seen when LAMMPS is built. After you have included or
you have included or excluded a package, you must re-build LAMMPS.</p> excluded a package, you must re-build LAMMPS.</p>
</div> </div>
<p>Additional package-related make options exist to help manage LAMMPS <p>Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package files that exist in both the src directory and in package
@ -1935,7 +1934,7 @@ close if you have setup the problem for both codes the same.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -1956,7 +1955,7 @@ close if you have setup the problem for both codes the same.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

45
doc/Section_start.txt
View File

@ -269,8 +269,8 @@ compile with -DLAMMPS_GZIP. It requires that your machine supports
the "popen()" function in the standard runtime library and that a gzip the "popen()" function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run. executable can be found by LAMMPS during a run.
IMPORTANT NOTE: on some clusters with high-speed networks, using the NOTE: on some clusters with high-speed networks, using the fork()
fork() library calls (required by popen()) can interfere with the fast library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are I/O is also available using a compression library instead, which are
@ -292,8 +292,8 @@ the need to store intermediate image files. It requires that your
machines supports the "popen" function in the standard runtime library machines supports the "popen" function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run. and that an FFmpeg executable can be found by LAMMPS during the run.
IMPORTANT NOTE: Similar to the note above, this option can conflict NOTE: Similar to the note above, this option can conflict with
with high-speed networks, because it uses popen(). high-speed networks, because it uses popen().
Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory posix_memalign() call instead of malloc() when large chunks or memory
@ -493,15 +493,14 @@ You should get the executable lmp_foo when the build is complete.
[{Errors that can occur when making LAMMPS:}] :link(start_2_3) [{Errors that can occur when making LAMMPS:}] :link(start_2_3)
IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler NOTE: If an error occurs when building LAMMPS, the compiler or linker
or linker will state very explicitly what the problem is. The error will state very explicitly what the problem is. The error message
message should give you a hint as to which of the steps above has should give you a hint as to which of the steps above has failed, and
failed, and what you need to do in order to fix it. Building a code what you need to do in order to fix it. Building a code with a
with a Makefile is a very logical process. The compiler and linker Makefile is a very logical process. The compiler and linker need to
need to find the appropriate files and those files need to be find the appropriate files and those files need to be compatible with
compatible with LAMMPS source files. When a make fails, there is LAMMPS source files. When a make fails, there is usually a very
usually a very simple reason, which you or a local expert will need to simple reason, which you or a local expert will need to fix.
fix.
Here are two non-obvious errors that can occur: Here are two non-obvious errors that can occur:
@ -712,11 +711,11 @@ or
make no-manybody make no-manybody
make g++ :pre make g++ :pre
IMPORTANT NOTE: You should NOT include/exclude packages and build NOTE: You should NOT include/exclude packages and build LAMMPS in a
LAMMPS in a single make command using multiple targets, e.g. make single make command using multiple targets, e.g. make yes-colloid g++.
yes-colloid g++. This is because the make procedure creates a list of This is because the make procedure creates a list of source files that
source files that will be out-of-date for the build if the package will be out-of-date for the build if the package configuration changes
configuration changes within the same command. within the same command.
Some packages have individual files that depend on other packages Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing. being included. LAMMPS checks for this and does the right thing.
@ -744,11 +743,11 @@ no-user", "make yes-all" or "make no-all" to include/exclude various
sets of packages. Type "make package" to see the all of the sets of packages. Type "make package" to see the all of the
package-related make options. package-related make options.
IMPORTANT NOTE: Inclusion/exclusion of a package works by simply NOTE: Inclusion/exclusion of a package works by simply moving files
moving files back and forth between the main src directory and back and forth between the main src directory and sub-directories with
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC), the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
so that the files are seen or not seen when LAMMPS is built. After are seen or not seen when LAMMPS is built. After you have included or
you have included or excluded a package, you must re-build LAMMPS. excluded a package, you must re-build LAMMPS.
Additional package-related make options exist to help manage LAMMPS Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package files that exist in both the src directory and in package

16
doc/Section_tools.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>9. Additional tools &mdash; LAMMPS 15 May 2015 version documentation</title> <title>9. Additional tools &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/> <link rel="next" title="10. Modifying &amp; extending LAMMPS" href="Section_modify.html"/>
<link rel="prev" title="8. Performance &amp; scalability" href="Section_perf.html"/> <link rel="prev" title="8. Performance &amp; scalability" href="Section_perf.html"/>
@ -548,10 +548,10 @@ the README.txt file for more info.</p>
</div> </div>
<div class="section" id="restart2data-tool"> <div class="section" id="restart2data-tool">
<span id="restart"></span><h2>9.28. restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline"></a></h2> <span id="restart"></span><h2>9.28. restart2data tool<a class="headerlink" href="#restart2data-tool" title="Permalink to this headline"></a></h2>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">This tool is now obsolete and is not included in the <p class="last">This tool is now obsolete and is not included in the current
current LAMMPS distribution. This is becaues there is now a LAMMPS distribution. This is becaues there is now a
<a class="reference internal" href="write_data.html"><em>write_data</em></a> command, which can create a data file <a class="reference internal" href="write_data.html"><em>write_data</em></a> command, which can create a data file
from within an input script. Running LAMMPS with the &#8220;-r&#8221; from within an input script. Running LAMMPS with the &#8220;-r&#8221;
<a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> as follows:</p> <a class="reference internal" href="Section_start.html#start-7"><span>command-line switch</span></a> as follows:</p>
@ -652,7 +652,7 @@ distributing his great tool!</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -673,7 +673,7 @@ distributing his great tool!</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

4
doc/Section_tools.txt
View File

@ -468,8 +468,8 @@ These tools were written by Aidan Thompson at Sandia.
restart2data tool :h4,link(restart) restart2data tool :h4,link(restart)
IMPORTANT NOTE: This tool is now obsolete and is not included in the NOTE: This tool is now obsolete and is not included in the current
current LAMMPS distribution. This is becaues there is now a LAMMPS distribution. This is becaues there is now a
"write_data"_write_data.html command, which can create a data file "write_data"_write_data.html command, which can create a data file
from within an input script. Running LAMMPS with the "-r" from within an input script. Running LAMMPS with the "-r"
"command-line switch"_Section_start.html#start_7 as follows: "command-line switch"_Section_start.html#start_7 as follows:

13
doc/_static/css/theme.css vendored
View File

@ -3508,7 +3508,7 @@ input[type="radio"][disabled], input[type="checkbox"][disabled] {
font-size: 90%; font-size: 90%;
margin: 0; margin: 0;
overflow: visible; overflow: visible;
padding: 8px 16px; padding: 4px;
} }
.wy-table td:first-child, .rst-content table.docutils td:first-child, .rst-content table.field-list td:first-child, .wy-table th:first-child, .rst-content table.docutils th:first-child, .rst-content table.field-list th:first-child { .wy-table td:first-child, .rst-content table.docutils td:first-child, .rst-content table.field-list td:first-child, .wy-table th:first-child, .rst-content table.docutils th:first-child, .rst-content table.field-list th:first-child {
border-left-width: 0; border-left-width: 0;
@ -3563,11 +3563,11 @@ input[type="radio"][disabled], input[type="checkbox"][disabled] {
/* BORDERED TABLES */ /* BORDERED TABLES */
.wy-table-bordered-all, .rst-content table.docutils { .wy-table-bordered-all, .rst-content table.docutils {
border: 1px solid #e1e4e5; border: 1px solid #black;
} }
.wy-table-bordered-all td, .rst-content table.docutils td { .wy-table-bordered-all td, .rst-content table.docutils td {
border-bottom: 1px solid #e1e4e5; border-bottom: 1px solid black;
border-left: 1px solid #e1e4e5; border-left: 1px solid black;
} }
.wy-table-bordered-all tbody > tr:last-child td, .rst-content table.docutils tbody > tr:last-child td { .wy-table-bordered-all tbody > tr:last-child td, .rst-content table.docutils tbody > tr:last-child td {
border-bottom-width: 0; border-bottom-width: 0;
@ -3741,9 +3741,8 @@ h6 {
hr { hr {
display: block; display: block;
height: 1px; border-top: 2px solid #8c8b8b;
border: 0; border-bottom: 2px solid #fff;
border-top: 2px solid #e1e4e5;
margin: 24px 0; margin: 24px 0;
padding: 0; padding: 0;
} }

8
doc/accelerate_cuda.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.USER-CUDA package &mdash; LAMMPS 15 May 2015 version documentation</title> <title>5.USER-CUDA package &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -317,7 +317,7 @@ occurs, the faster your simulation will run.</li>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -338,7 +338,7 @@ occurs, the faster your simulation will run.</li>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/accelerate_gpu.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.GPU package &mdash; LAMMPS 15 May 2015 version documentation</title> <title>5.GPU package &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -346,7 +346,7 @@ storage by a single MPI process.</li>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -367,7 +367,7 @@ storage by a single MPI process.</li>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

35
doc/accelerate_intel.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.USER-INTEL package &mdash; LAMMPS 15 May 2015 version documentation</title> <title>5.USER-INTEL package &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -313,19 +313,20 @@ single, mixed).</p>
<p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the <p>See the <a class="reference external" href="http://lammps.sandia.gov/bench.html">Benchmark page</a> of the
LAMMPS web site for performance of the USER-INTEL package on different LAMMPS web site for performance of the USER-INTEL package on different
hardware.</p> hardware.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Setting core affinity is often used to pin MPI tasks <p class="last">Setting core affinity is often used to pin MPI tasks and OpenMP
and OpenMP threads to a core or group of cores so that memory access threads to a core or group of cores so that memory access can be
can be uniform. Unless disabled at build time, affinity for MPI tasks uniform. Unless disabled at build time, affinity for MPI tasks and
and OpenMP threads on the host (CPU) will be set by default on the OpenMP threads on the host (CPU) will be set by default on the host
host when using offload to a coprocessor. In this case, it is when using offload to a coprocessor. In this case, it is unnecessary
unnecessary to use other methods to control affinity (e.g. taskset, to use other methods to control affinity (e.g. taskset, numactl,
numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script with
script with the <em>no_affinity</em> option to the <a class="reference internal" href="package.html"><em>package intel</em></a> command or by disabling the option at build time the <em>no_affinity</em> option to the <a class="reference internal" href="package.html"><em>package intel</em></a> command
(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your or by disabling the option at build time (by adding
Makefile). Disabling this option is not recommended, especially when -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
running on a machine with hyperthreading disabled.</p> Disabling this option is not recommended, especially when running on a
machine with hyperthreading disabled.</p>
</div> </div>
<p><strong>Guidelines for best performance on an Intel(R) Xeon Phi(TM) <p><strong>Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:</strong></p> coprocessor:</strong></p>
@ -406,7 +407,7 @@ supported.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -427,7 +428,7 @@ supported.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

24
doc/accelerate_intel.txt
View File

@ -234,18 +234,18 @@ See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
LAMMPS web site for performance of the USER-INTEL package on different LAMMPS web site for performance of the USER-INTEL package on different
hardware. hardware.
IMPORTANT NOTE: Setting core affinity is often used to pin MPI tasks NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP
and OpenMP threads to a core or group of cores so that memory access threads to a core or group of cores so that memory access can be
can be uniform. Unless disabled at build time, affinity for MPI tasks uniform. Unless disabled at build time, affinity for MPI tasks and
and OpenMP threads on the host (CPU) will be set by default on the OpenMP threads on the host (CPU) will be set by default on the host
host when using offload to a coprocessor. In this case, it is when using offload to a coprocessor. In this case, it is unnecessary
unnecessary to use other methods to control affinity (e.g. taskset, to use other methods to control affinity (e.g. taskset, numactl,
numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script with
script with the {no_affinity} option to the "package the {no_affinity} option to the "package intel"_package.html command
intel"_package.html command or by disabling the option at build time or by disabling the option at build time (by adding
(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
Makefile). Disabling this option is not recommended, especially when Disabling this option is not recommended, especially when running on a
running on a machine with hyperthreading disabled. machine with hyperthreading disabled.
[Guidelines for best performance on an Intel(R) Xeon Phi(TM) [Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:] coprocessor:]

80
doc/accelerate_kokkos.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.KOKKOS package &mdash; LAMMPS 15 May 2015 version documentation</title> <title>5.KOKKOS package &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -226,12 +226,12 @@ version 6.5 or later must be installed on your system. See the
discussion for the <a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA</em></a> and discussion for the <a class="reference internal" href="accelerate_cuda.html"><em>USER-CUDA</em></a> and
<a class="reference internal" href="accelerate_gpu.html"><em>GPU</em></a> packages for details of how to check and do <a class="reference internal" href="accelerate_gpu.html"><em>GPU</em></a> packages for details of how to check and do
this.</p> this.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">For good performance of the KOKKOS package on GPUs, <p class="last">For good performance of the KOKKOS package on GPUs, you must
you must have Kepler generation GPUs (or later). The Kokkos library have Kepler generation GPUs (or later). The Kokkos library exploits
exploits texture cache options not supported by Telsa generation GPUs texture cache options not supported by Telsa generation GPUs (or
(or older).</p> older).</p>
</div> </div>
<p>To build with Kokkos support for Intel Xeon Phi coprocessors, your <p>To build with Kokkos support for Intel Xeon Phi coprocessors, your
sysmte must be configured to use them in &#8220;native&#8221; mode, not &#8220;offload&#8221; sysmte must be configured to use them in &#8220;native&#8221; mode, not &#8220;offload&#8221;
@ -272,14 +272,13 @@ make cuda KOKKOS_DEVICES=Cuda
<p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the <p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try make command line which requires a GNU-compatible make command. Try
&#8220;gmake&#8221; if your system&#8217;s standard make complains.</p> &#8220;gmake&#8221; if your system&#8217;s standard make complains.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">If you build using make line variables and re-build <p class="last">If you build using make line variables and re-build LAMMPS twice
LAMMPS twice with different KOKKOS options and the <em>same</em> target, with different KOKKOS options and the <em>same</em> target, e.g. g++ in the
e.g. g++ in the first two examples above, then you <em>must</em> perform a first two examples above, then you <em>must</em> perform a &#8220;make clean-all&#8221;
&#8220;make clean-all&#8221; or &#8220;make clean-machine&#8221; before each build. This is or &#8220;make clean-machine&#8221; before each build. This is to force all the
to force all the KOKKOS-dependent files to be re-compiled with the new KOKKOS-dependent files to be re-compiled with the new options.</p>
options.</p>
</div> </div>
<p>You can also hardwire these make variables in the specified machine <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, makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
@ -291,23 +290,22 @@ with a line like:</p>
different KOKKOS options (defined in different machine makefiles), you different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a &#8220;clean&#8221; in between. This is do not have to worry about doing a &#8220;clean&#8221; in between. This is
because the targets will be different.</p> because the targets will be different.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">The 3rd example above for a GPU, uses a different <p class="last">The 3rd example above for a GPU, uses a different machine
machine makefile, in this case src/MAKE/Makefile.cuda, which is makefile, in this case src/MAKE/Makefile.cuda, which is included in
included in the LAMMPS distribution. To build the KOKKOS package for the LAMMPS distribution. To build the KOKKOS package for a GPU, this
a GPU, this makefile must use the NVIDA &#8220;nvcc&#8221; compiler. And it must makefile must use the NVIDA &#8220;nvcc&#8221; compiler. And it must have a
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and
hardware and installed software. Typical values for KOKKOS_ARCH are given installed software. Typical values for KOKKOS_ARCH are given below,
below, as well as well as other settings that must be included in the machine
as other settings that must be included in the machine makefile, if makefile, if you create your own.</p>
you create your own.</p>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Currently, there are no precision options with the <p class="last">Currently, there are no precision options with the KOKKOS
KOKKOS package. All compilation and computation is performed in package. All compilation and computation is performed in double
double precision.</p> precision.</p>
</div> </div>
<p>There are other allowed options when building with the KOKKOS package. <p>There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line As above, they can be set either as variables on the make command line
@ -508,13 +506,13 @@ threads/task to a smaller value. This is because using all the cores
on a dual-socket node will incur extra cost to copy memory from the on a dual-socket node will incur extra cost to copy memory from the
2nd socket to the GPU.</p> 2nd socket to the GPU.</p>
<p>Examples of mpirun commands that follow these rules are shown above.</p> <p>Examples of mpirun commands that follow these rules are shown above.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">When using a GPU, you will achieve the best <p class="last">When using a GPU, you will achieve the best performance if your
performance if your input script does not use any fix or compute input script does not use any fix or compute styles which are not yet
styles which are not yet Kokkos-enabled. This allows data to stay on Kokkos-enabled. This allows data to stay on the GPU for multiple
the GPU for multiple timesteps, without being copied back to the host timesteps, without being copied back to the host CPU. Invoking a
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for non-Kokkos fix or compute, or performing I/O for
<a class="reference internal" href="thermo_style.html"><em>thermo</em></a> or <a class="reference internal" href="dump.html"><em>dump</em></a> output will cause data <a class="reference internal" href="thermo_style.html"><em>thermo</em></a> or <a class="reference internal" href="dump.html"><em>dump</em></a> output will cause data
to be copied back to the CPU.</p> to be copied back to the CPU.</p>
</div> </div>
@ -567,7 +565,7 @@ change in the future.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -588,7 +586,7 @@ change in the future.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

52
doc/accelerate_kokkos.txt
View File

@ -126,10 +126,10 @@ discussion for the "USER-CUDA"_accelerate_cuda.html and
"GPU"_accelerate_gpu.html packages for details of how to check and do "GPU"_accelerate_gpu.html packages for details of how to check and do
this. this.
IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs, NOTE: For good performance of the KOKKOS package on GPUs, you must
you must have Kepler generation GPUs (or later). The Kokkos library have Kepler generation GPUs (or later). The Kokkos library exploits
exploits texture cache options not supported by Telsa generation GPUs texture cache options not supported by Telsa generation GPUs (or
(or older). older).
To build with Kokkos support for Intel Xeon Phi coprocessors, your To build with Kokkos support for Intel Xeon Phi coprocessors, your
sysmte must be configured to use them in "native" mode, not "offload" sysmte must be configured to use them in "native" mode, not "offload"
@ -179,12 +179,11 @@ These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try make command line which requires a GNU-compatible make command. Try
"gmake" if your system's standard make complains. "gmake" if your system's standard make complains.
IMPORTANT NOTE: If you build using make line variables and re-build NOTE: If you build using make line variables and re-build LAMMPS twice
LAMMPS twice with different KOKKOS options and the *same* target, with different KOKKOS options and the *same* target, e.g. g++ in the
e.g. g++ in the first two examples above, then you *must* perform a first two examples above, then you *must* perform a "make clean-all"
"make clean-all" or "make clean-machine" before each build. This is or "make clean-machine" before each build. This is to force all the
to force all the KOKKOS-dependent files to be re-compiled with the new KOKKOS-dependent files to be re-compiled with the new options.
options.
You can also hardwire these make variables in the specified machine You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above, makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
@ -197,19 +196,18 @@ different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a "clean" in between. This is do not have to worry about doing a "clean" in between. This is
because the targets will be different. because the targets will be different.
IMPORTANT NOTE: The 3rd example above for a GPU, uses a different NOTE: The 3rd example above for a GPU, uses a different machine
machine makefile, in this case src/MAKE/Makefile.cuda, which is makefile, in this case src/MAKE/Makefile.cuda, which is included in
included in the LAMMPS distribution. To build the KOKKOS package for the LAMMPS distribution. To build the KOKKOS package for a GPU, this
a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must makefile must use the NVIDA "nvcc" compiler. And it must have a
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and
hardware and installed software. Typical values for KOKKOS_ARCH are given installed software. Typical values for KOKKOS_ARCH are given below,
below, as well as well as other settings that must be included in the machine
as other settings that must be included in the machine makefile, if makefile, if you create your own.
you create your own.
IMPORTANT NOTE: Currently, there are no precision options with the NOTE: Currently, there are no precision options with the KOKKOS
KOKKOS package. All compilation and computation is performed in package. All compilation and computation is performed in double
double precision. precision.
There are other allowed options when building with the KOKKOS package. There are other allowed options when building with the KOKKOS package.
As above, they can be set either as variables on the make command line As above, they can be set either as variables on the make command line
@ -461,11 +459,11 @@ on a dual-socket node will incur extra cost to copy memory from the
Examples of mpirun commands that follow these rules are shown above. Examples of mpirun commands that follow these rules are shown above.
IMPORTANT NOTE: When using a GPU, you will achieve the best NOTE: When using a GPU, you will achieve the best performance if your
performance if your input script does not use any fix or compute input script does not use any fix or compute styles which are not yet
styles which are not yet Kokkos-enabled. This allows data to stay on Kokkos-enabled. This allows data to stay on the GPU for multiple
the GPU for multiple timesteps, without being copied back to the host timesteps, without being copied back to the host CPU. Invoking a
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for non-Kokkos fix or compute, or performing I/O for
"thermo"_thermo_style.html or "dump"_dump.html output will cause data "thermo"_thermo_style.html or "dump"_dump.html output will cause data
to be copied back to the CPU. to be copied back to the CPU.

19
doc/accelerate_omp.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.USER-OMP package &mdash; LAMMPS 15 May 2015 version documentation</title> <title>5.USER-OMP package &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -260,12 +260,11 @@ when there is at least one MPI task per physical CPU chip, i.e. socket
or die.</li> or die.</li>
<li>It is usually most efficient to restrict threading to a single <li>It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket.</li> socket, i.e. use one or more MPI task per socket.</li>
<li>IMPORTANT NOTE: By default, several current MPI implementations use a <li>NOTE: By default, several current MPI implementations use a processor
processor affinity setting that restricts each MPI task to a single affinity setting that restricts each MPI task to a single CPU core.
CPU core. Using multi-threading in this mode will force all threads Using multi-threading in this mode will force all threads to share the
to share the one core and thus is likely to be counterproductive. one core and thus is likely to be counterproductive. Instead, binding
Instead, binding MPI tasks to a (multi-core) socket, should solve this MPI tasks to a (multi-core) socket, should solve this issue.</li>
issue.</li>
</ul> </ul>
<div class="section" id="restrictions"> <div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2> <h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
@ -283,7 +282,7 @@ issue.</li>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -304,7 +303,7 @@ issue.</li>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

11
doc/accelerate_omp.txt
View File

@ -174,12 +174,11 @@ or die. :ulb,l
It is usually most efficient to restrict threading to a single It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket. :l socket, i.e. use one or more MPI task per socket. :l
IMPORTANT NOTE: By default, several current MPI implementations use a NOTE: By default, several current MPI implementations use a processor
processor affinity setting that restricts each MPI task to a single affinity setting that restricts each MPI task to a single CPU core.
CPU core. Using multi-threading in this mode will force all threads Using multi-threading in this mode will force all threads to share the
to share the one core and thus is likely to be counterproductive. one core and thus is likely to be counterproductive. Instead, binding
Instead, binding MPI tasks to a (multi-core) socket, should solve this MPI tasks to a (multi-core) socket, should solve this issue. :l,ule
issue. :l,ule
[Restrictions:] [Restrictions:]

8
doc/accelerate_opt.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>5.OPT package &mdash; LAMMPS 15 May 2015 version documentation</title> <title>5.OPT package &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -184,7 +184,7 @@ of a run. On most machines for reasonable problem sizes, it will be a
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -205,7 +205,7 @@ of a run. On most machines for reasonable problem sizes, it will be a
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_charmm.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style charmm command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style charmm command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -209,7 +209,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -230,7 +230,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_class2.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style class2 command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style class2 command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -236,7 +236,7 @@ for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -257,7 +257,7 @@ for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_coeff.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_coeff command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_coeff command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -224,7 +224,7 @@ set, either in the input script or in a data file.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -245,7 +245,7 @@ set, either in the input script or in a data file.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_cosine.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style cosine command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -194,7 +194,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -215,7 +215,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_cosine_delta.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/delta command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style cosine/delta command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -198,7 +198,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_cosine_periodic.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/periodic command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style cosine/periodic command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -208,7 +208,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -229,7 +229,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_cosine_shift.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/shift command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style cosine/shift command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -199,7 +199,7 @@ section for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -220,7 +220,7 @@ section for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_cosine_shift_exp.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/shift/exp command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style cosine/shift/exp command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -210,7 +210,7 @@ section for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -231,7 +231,7 @@ section for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_cosine_squared.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style cosine/squared command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style cosine/squared command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -198,7 +198,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

30
doc/angle_dipole.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style dipole command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style dipole command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -159,7 +159,7 @@ and the reference (bond) vector r_ij:</p>
angle.</p> angle.</p>
<p>The torque on the dipole can be obtained by differentiating the <p>The torque on the dipole can be obtained by differentiating the
potential using the &#8216;chain rule&#8217; as in appendix C.3 of potential using the &#8216;chain rule&#8217; as in appendix C.3 of
<a class="reference internal" href="#allen"><span>(Allen)</span></a>:</p> <a class="reference internal" href="pair_gayberne.html#allen"><span>(Allen)</span></a>:</p>
<img alt="_images/angle_dipole_torque.jpg" class="align-center" src="_images/angle_dipole_torque.jpg" /> <img alt="_images/angle_dipole_torque.jpg" class="align-center" src="_images/angle_dipole_torque.jpg" />
<p>Example: if gamma0 is set to 0 degrees, the torque generated by <p>Example: if gamma0 is set to 0 degrees, the torque generated by
the potential will tend to align the dipole along the reference the potential will tend to align the dipole along the reference
@ -200,16 +200,16 @@ more instructions on how to use the accelerated styles effectively.</p>
<p>This angle style can only be used if LAMMPS was built with the <p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span> USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
section for more info on packages.</p> section for more info on packages.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">In the &#8220;Angles&#8221; section of the data file, the atom ID <p class="last">In the &#8220;Angles&#8221; section of the data file, the atom ID &#8216;j&#8217;
&#8216;j&#8217; corresponding to the dipole to restrain must come before the atom corresponding to the dipole to restrain must come before the atom ID
ID of the reference atom &#8216;i&#8217;. A third atom ID &#8216;k&#8217; must also be of the reference atom &#8216;i&#8217;. A third atom ID &#8216;k&#8217; must also be provided,
provided, although &#8216;k&#8217; is just a &#8216;dummy&#8217; atom which can be any atom; although &#8216;k&#8217; is just a &#8216;dummy&#8217; atom which can be any atom; it may be
it may be useful to choose a convention (e.g., &#8216;k&#8217;=&#8217;i&#8217;) and adhere to useful to choose a convention (e.g., &#8216;k&#8217;=&#8217;i&#8217;) and adhere to it. For
it. For example, if ID=1 for the dipolar atom to restrain, and ID=2 example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
for the reference atom, the corresponding line in the &#8220;Angles&#8221; section reference atom, the corresponding line in the &#8220;Angles&#8221; section of the
of the data file would read: X X 1 2 2</p> data file would read: X X 1 2 2</p>
</div> </div>
<p>The &#8220;newton&#8221; command for intramolecular interactions must be &#8220;on&#8221; <p>The &#8220;newton&#8221; command for intramolecular interactions must be &#8220;on&#8221;
(which is the default).</p> (which is the default).</p>
@ -237,7 +237,7 @@ Clarendon Press, Oxford, 1987.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -258,7 +258,7 @@ Clarendon Press, Oxford, 1987.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

16
doc/angle_dipole.txt
View File

@ -95,14 +95,14 @@ This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3 USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info on packages. section for more info on packages.
IMPORTANT NOTE: In the "Angles" section of the data file, the atom ID NOTE: In the "Angles" section of the data file, the atom ID 'j'
'j' corresponding to the dipole to restrain must come before the atom corresponding to the dipole to restrain must come before the atom ID
ID of the reference atom 'i'. A third atom ID 'k' must also be of the reference atom 'i'. A third atom ID 'k' must also be provided,
provided, although 'k' is just a 'dummy' atom which can be any atom; although 'k' is just a 'dummy' atom which can be any atom; it may be
it may be useful to choose a convention (e.g., 'k'='i') and adhere to useful to choose a convention (e.g., 'k'='i') and adhere to it. For
it. For example, if ID=1 for the dipolar atom to restrain, and ID=2 example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
for the reference atom, the corresponding line in the "Angles" section reference atom, the corresponding line in the "Angles" section of the
of the data file would read: X X 1 2 2 data file would read: X X 1 2 2
The "newton" command for intramolecular interactions must be "on" The "newton" command for intramolecular interactions must be "on"
(which is the default). (which is the default).

8
doc/angle_fourier.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style fourier command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style fourier command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -195,7 +195,7 @@ section for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -216,7 +216,7 @@ section for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_fourier_simple.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style fourier/simple command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style fourier/simple command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -194,7 +194,7 @@ section for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -215,7 +215,7 @@ section for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_harmonic.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style harmonic command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style harmonic command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -203,7 +203,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -224,7 +224,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_hybrid.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style hybrid command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style hybrid command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -219,7 +219,7 @@ file, you need to re-specify angle_coeff commands.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -240,7 +240,7 @@ file, you need to re-specify angle_coeff commands.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_none.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style none command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style none command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -163,7 +163,7 @@ if triplets of angle atoms were listed in the data file read by the
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -184,7 +184,7 @@ if triplets of angle atoms were listed in the data file read by the
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_quartic.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style quartic command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style quartic command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -201,7 +201,7 @@ section for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -222,7 +222,7 @@ section for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/angle_sdk.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style sdk command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style sdk command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -187,7 +187,7 @@ USER-CG-CMM package. See the <a class="reference internal" href="Section_start.
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -208,7 +208,7 @@ USER-CG-CMM package. See the <a class="reference internal" href="Section_start.
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

12
doc/angle_style.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -161,8 +161,8 @@ restarts a simulation. See the <a class="reference internal" href="read_restart
command for details on how to do this. The one exception is that command for details on how to do this. The one exception is that
angle_style <em>hybrid</em> only stores the list of sub-styles in the restart angle_style <em>hybrid</em> only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified.</p> file; angle coefficients need to be re-specified.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">When both an angle and pair style is defined, the <p class="last">When both an angle and pair style is defined, the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command often needs to be used to <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise turn off (or weight) the pairwise interaction that would otherwise
@ -222,7 +222,7 @@ package.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -243,7 +243,7 @@ package.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

2
doc/angle_style.txt
View File

@ -43,7 +43,7 @@ command for details on how to do this. The one exception is that
angle_style {hybrid} only stores the list of sub-styles in the restart angle_style {hybrid} only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified. file; angle coefficients need to be re-specified.
IMPORTANT NOTE: When both an angle and pair style is defined, the NOTE: When both an angle and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to "special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise turn off (or weight) the pairwise interaction that would otherwise
exist between 3 bonded atoms. exist between 3 bonded atoms.

8
doc/angle_table.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>angle_style table command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>angle_style table command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -272,7 +272,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -293,7 +293,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

16
doc/atom_modify.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>atom_modify command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>atom_modify command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -244,10 +244,10 @@ pairwise intereractions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.</p> cache locality will be undermined.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Running a simulation with sorting on versus off should <p class="last">Running a simulation with sorting on versus off should not
not change the simulation results in a statistical sense. However, a change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations. to diverging trajectories over time when comparing two simluations.
Various commands, particularly those which use random numbers Various commands, particularly those which use random numbers
@ -288,7 +288,7 @@ cutoff will be used to set the bin size.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -309,7 +309,7 @@ cutoff will be used to set the bin size.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

4
doc/atom_modify.txt
View File

@ -135,8 +135,8 @@ bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined. cache locality will be undermined.
IMPORTANT NOTE: Running a simulation with sorting on versus off should NOTE: Running a simulation with sorting on versus off should not
not change the simulation results in a statistical sense. However, a change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations. to diverging trajectories over time when comparing two simluations.
Various commands, particularly those which use random numbers Various commands, particularly those which use random numbers

20
doc/atom_style.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>atom_style command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>atom_style command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -263,10 +263,10 @@ quantities.</p>
</tr> </tr>
</tbody> </tbody>
</table> </table>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">It is possible to add some attributes, such as a <p class="last">It is possible to add some attributes, such as a molecule ID, to
molecule ID, to atom styles that do not have them via the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. This command also atom styles that do not have them via the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. This command also
allows new custom attributes consisting of extra integer or allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> doc page for examples of cases floating-point values to be added to atoms. See the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> doc page for examples of cases
where this is useful and details on how to initialize, access, and where this is useful and details on how to initialize, access, and
@ -325,8 +325,8 @@ can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in <a class="reference internal" href="#grime"><span>(Grime)</span></a>, for examples of how this paper by Grime and Voth, in <a class="reference internal" href="#grime"><span>(Grime)</span></a>, for examples of how this
can be advantageous for large-scale coarse-grained systems.</p> can be advantageous for large-scale coarse-grained systems.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">When using the <em>template</em> style with a <a class="reference internal" href="molecule.html"><em>molecule template</em></a> that contains multiple molecules, you should <p class="last">When using the <em>template</em> style with a <a class="reference internal" href="molecule.html"><em>molecule template</em></a> that contains multiple molecules, you should
insure the atom types, bond types, angle_types, etc in all the insure the atom types, bond types, angle_types, etc in all the
molecules are consistent. E.g. if one molecule represents H2O and molecules are consistent. E.g. if one molecule represents H2O and
@ -427,7 +427,7 @@ only enabled if LAMMPS was built with that package. See the <a class="reference
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -448,7 +448,7 @@ only enabled if LAMMPS was built with that package. See the <a class="reference
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

6
doc/atom_style.txt
View File

@ -83,8 +83,8 @@ quantities.
{tri} | corner points, angular momentum | rigid bodies | {tri} | corner points, angular momentum | rigid bodies |
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|) {wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
IMPORTANT NOTE: It is possible to add some attributes, such as a NOTE: It is possible to add some attributes, such as a molecule ID, to
molecule ID, to atom styles that do not have them via the "fix atom styles that do not have them via the "fix
property/atom"_fix_property_atom.html command. This command also property/atom"_fix_property_atom.html command. This command also
allows new custom attributes consisting of extra integer or allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the "fix floating-point values to be added to atoms. See the "fix
@ -158,7 +158,7 @@ molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this
can be advantageous for large-scale coarse-grained systems. can be advantageous for large-scale coarse-grained systems.
IMPORTANT NOTE: When using the {template} style with a "molecule NOTE: When using the {template} style with a "molecule
template"_molecule.html that contains multiple molecules, you should template"_molecule.html that contains multiple molecules, you should
insure the atom types, bond types, angle_types, etc in all the insure the atom types, bond types, angle_types, etc in all the
molecules are consistent. E.g. if one molecule represents H2O and molecules are consistent. E.g. if one molecule represents H2O and

93
doc/balance.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>balance command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>balance command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -210,14 +210,15 @@ most heavily loaded processor has 1200 particles, then the factor is
1.2, meaning there is a 20% imbalance. Note that a re-balance can be 1.2, meaning there is a 20% imbalance. Note that a re-balance can be
forced even if the current balance is perfect (1.0) be specifying a forced even if the current balance is perfect (1.0) be specifying a
<em>thresh</em> &lt; 1.0.</p> <em>thresh</em> &lt; 1.0.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Balancing is performed even if the imbalance factor <p class="last">Balancing is performed even if the imbalance factor does not
does not exceed the <em>thresh</em> parameter if a &#8220;grid&#8221; style is specified exceed the <em>thresh</em> parameter if a &#8220;grid&#8221; style is specified when the
when the current partitioning is &#8220;tiled&#8221;. The meaning of &#8220;grid&#8221; vs current partitioning is &#8220;tiled&#8221;. The meaning of &#8220;grid&#8221; vs &#8220;tiled&#8221; is
&#8220;tiled&#8221; is explained below. This is to allow forcing of the explained below. This is to allow forcing of the partitioning to
partitioning to &#8220;grid&#8221; so that the <a class="reference internal" href="comm_style.html"><em>comm_style brick</em></a> &#8220;grid&#8221; so that the <a class="reference internal" href="comm_style.html"><em>comm_style brick</em></a> command can then
command can then be used to replace a current <a class="reference internal" href="comm_style.html"><em>comm_style tiled</em></a> setting.</p> be used to replace a current <a class="reference internal" href="comm_style.html"><em>comm_style tiled</em></a>
setting.</p>
</div> </div>
<p>When the balance command completes, it prints statistics about the <p>When the balance command completes, it prints statistics about the
result, including the change in the imbalance factor and the change in result, including the change in the imbalance factor and the change in
@ -225,32 +226,30 @@ the maximum number of particles on any processor. For &#8220;grid&#8221; method
(defined below) that create a logical 3d grid of processors, the (defined below) that create a logical 3d grid of processors, the
positions of all cutting planes in each of the 3 dimensions (as positions of all cutting planes in each of the 3 dimensions (as
fractions of the box length) are also printed.</p> fractions of the box length) are also printed.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">This command attempts to minimize the imbalance <p class="last">This command attempts to minimize the imbalance factor, as
factor, as defined above. But depending on the method a perfect defined above. But depending on the method a perfect balance (1.0)
balance (1.0) may not be achieved. For example, &#8220;grid&#8221; methods may not be achieved. For example, &#8220;grid&#8221; methods (defined below) that
(defined below) that create a logical 3d grid cannot achieve perfect create a logical 3d grid cannot achieve perfect balance for many
balance for many irregular distributions of particles. Likewise, if a irregular distributions of particles. Likewise, if a portion of the
portion of the system is a perfect lattice, e.g. the intiial system is system is a perfect lattice, e.g. the intiial system is generated by
generated by the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, then &#8220;grid&#8221; the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, then &#8220;grid&#8221; methods may
methods may be unable to achieve exact balance. This is because be unable to achieve exact balance. This is because entire lattice
entire lattice planes will be owned or not owned by a single planes will be owned or not owned by a single processor.</p>
processor.</p>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">The imbalance factor is also an estimate of the <p class="last">The imbalance factor is also an estimate of the maximum speed-up
maximum speed-up you can hope to achieve by running a perfectly you can hope to achieve by running a perfectly balanced simulation
balanced simulation versus an imbalanced one. In the example above, versus an imbalanced one. In the example above, the 10000 particle
the 10000 particle simulation could run up to 20% faster if it were simulation could run up to 20% faster if it were perfectly balanced,
perfectly balanced, versus when imbalanced. However, computational versus when imbalanced. However, computational cost is not strictly
cost is not strictly proportional to particle count, and changing the proportional to particle count, and changing the relative size and
relative size and shape of processor sub-domains may lead to shape of processor sub-domains may lead to additional computational
additional computational and communication overheads, e.g. in the PPPM and communication overheads, e.g. in the PPPM solver used via the
solver used via the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Thus <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Thus you should benchmark
you should benchmark the run times of a simulation before and after the run times of a simulation before and after balancing.</p>
balancing.</p>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
<p>The method used to perform a load balance is specified by one of the <p>The method used to perform a load balance is specified by one of the
@ -374,16 +373,16 @@ plane gets closer to the target value.</p>
<p>Once the rebalancing is complete and final processor sub-domains <p>Once the rebalancing is complete and final processor sub-domains
assigned, particles are migrated to their new owning processor, and assigned, particles are migrated to their new owning processor, and
the balance procedure ends.</p> the balance procedure ends.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">At each rebalance operation, the bisectioning for each <p class="last">At each rebalance operation, the bisectioning for each cutting
cutting plane (line in 2d) typcially starts with low and high bounds plane (line in 2d) typcially starts with low and high bounds separated
separated by the extent of a processor&#8217;s sub-domain in one dimension. by the extent of a processor&#8217;s sub-domain in one dimension. The size
The size of this bracketing region shrinks by 1/2 every iteration. of this bracketing region shrinks by 1/2 every iteration. Thus if
Thus if <em>Niter</em> is specified as 10, the cutting plane will typically <em>Niter</em> is specified as 10, the cutting plane will typically be
be positioned to 1 part in 1000 accuracy (relative to the perfect positioned to 1 part in 1000 accuracy (relative to the perfect target
target position). For <em>Niter</em> = 20, it will be accurate to 1 part in position). For <em>Niter</em> = 20, it will be accurate to 1 part in a
a million. Thus there is no need ot set <em>Niter</em> to a large value. million. Thus there is no need ot set <em>Niter</em> to a large value.
LAMMPS will check if the threshold accuracy is reached (in a LAMMPS will check if the threshold accuracy is reached (in a
dimension) is less iterations than <em>Niter</em> and exit early. However, dimension) is less iterations than <em>Niter</em> and exit early. However,
<em>Niter</em> should also not be set too small, since it will take roughly <em>Niter</em> should also not be set too small, since it will take roughly
@ -488,7 +487,7 @@ appear in <em>dimstr</em> for the <em>shift</em> style.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -509,7 +508,7 @@ appear in <em>dimstr</em> for the <em>shift</em> style.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

70
doc/balance.txt
View File

@ -88,13 +88,13 @@ most heavily loaded processor has 1200 particles, then the factor is
forced even if the current balance is perfect (1.0) be specifying a forced even if the current balance is perfect (1.0) be specifying a
{thresh} < 1.0. {thresh} < 1.0.
IMPORTANT NOTE: Balancing is performed even if the imbalance factor NOTE: Balancing is performed even if the imbalance factor does not
does not exceed the {thresh} parameter if a "grid" style is specified exceed the {thresh} parameter if a "grid" style is specified when the
when the current partitioning is "tiled". The meaning of "grid" vs current partitioning is "tiled". The meaning of "grid" vs "tiled" is
"tiled" is explained below. This is to allow forcing of the explained below. This is to allow forcing of the partitioning to
partitioning to "grid" so that the "comm_style brick"_comm_style.html "grid" so that the "comm_style brick"_comm_style.html command can then
command can then be used to replace a current "comm_style be used to replace a current "comm_style tiled"_comm_style.html
tiled"_comm_style.html setting. setting.
When the balance command completes, it prints statistics about the When the balance command completes, it prints statistics about the
result, including the change in the imbalance factor and the change in result, including the change in the imbalance factor and the change in
@ -103,28 +103,26 @@ the maximum number of particles on any processor. For "grid" methods
positions of all cutting planes in each of the 3 dimensions (as positions of all cutting planes in each of the 3 dimensions (as
fractions of the box length) are also printed. fractions of the box length) are also printed.
IMPORTANT NOTE: This command attempts to minimize the imbalance NOTE: This command attempts to minimize the imbalance factor, as
factor, as defined above. But depending on the method a perfect defined above. But depending on the method a perfect balance (1.0)
balance (1.0) may not be achieved. For example, "grid" methods may not be achieved. For example, "grid" methods (defined below) that
(defined below) that create a logical 3d grid cannot achieve perfect create a logical 3d grid cannot achieve perfect balance for many
balance for many irregular distributions of particles. Likewise, if a irregular distributions of particles. Likewise, if a portion of the
portion of the system is a perfect lattice, e.g. the intiial system is system is a perfect lattice, e.g. the intiial system is generated by
generated by the "create_atoms"_create_atoms.html command, then "grid" the "create_atoms"_create_atoms.html command, then "grid" methods may
methods may be unable to achieve exact balance. This is because be unable to achieve exact balance. This is because entire lattice
entire lattice planes will be owned or not owned by a single planes will be owned or not owned by a single processor.
processor.
IMPORTANT NOTE: The imbalance factor is also an estimate of the NOTE: The imbalance factor is also an estimate of the maximum speed-up
maximum speed-up you can hope to achieve by running a perfectly you can hope to achieve by running a perfectly balanced simulation
balanced simulation versus an imbalanced one. In the example above, versus an imbalanced one. In the example above, the 10000 particle
the 10000 particle simulation could run up to 20% faster if it were simulation could run up to 20% faster if it were perfectly balanced,
perfectly balanced, versus when imbalanced. However, computational versus when imbalanced. However, computational cost is not strictly
cost is not strictly proportional to particle count, and changing the proportional to particle count, and changing the relative size and
relative size and shape of processor sub-domains may lead to shape of processor sub-domains may lead to additional computational
additional computational and communication overheads, e.g. in the PPPM and communication overheads, e.g. in the PPPM solver used via the
solver used via the "kspace_style"_kspace_style.html command. Thus "kspace_style"_kspace_style.html command. Thus you should benchmark
you should benchmark the run times of a simulation before and after the run times of a simulation before and after balancing.
balancing.
:line :line
@ -238,14 +236,14 @@ Once the rebalancing is complete and final processor sub-domains
assigned, particles are migrated to their new owning processor, and assigned, particles are migrated to their new owning processor, and
the balance procedure ends. the balance procedure ends.
IMPORTANT NOTE: At each rebalance operation, the bisectioning for each NOTE: At each rebalance operation, the bisectioning for each cutting
cutting plane (line in 2d) typcially starts with low and high bounds plane (line in 2d) typcially starts with low and high bounds separated
separated by the extent of a processor's sub-domain in one dimension. by the extent of a processor's sub-domain in one dimension. The size
The size of this bracketing region shrinks by 1/2 every iteration. of this bracketing region shrinks by 1/2 every iteration. Thus if
Thus if {Niter} is specified as 10, the cutting plane will typically {Niter} is specified as 10, the cutting plane will typically be
be positioned to 1 part in 1000 accuracy (relative to the perfect positioned to 1 part in 1000 accuracy (relative to the perfect target
target position). For {Niter} = 20, it will be accurate to 1 part in position). For {Niter} = 20, it will be accurate to 1 part in a
a million. Thus there is no need ot set {Niter} to a large value. million. Thus there is no need ot set {Niter} to a large value.
LAMMPS will check if the threshold accuracy is reached (in a LAMMPS will check if the threshold accuracy is reached (in a
dimension) is less iterations than {Niter} and exit early. However, dimension) is less iterations than {Niter} and exit early. However,
{Niter} should also not be set too small, since it will take roughly {Niter} should also not be set too small, since it will take roughly

8
doc/body.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Body particles &mdash; LAMMPS 15 May 2015 version documentation</title> <title>Body particles &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -282,7 +282,7 @@ current COM and orientiation of the body particle.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -303,7 +303,7 @@ current COM and orientiation of the body particle.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_class2.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style class2 command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style class2 command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -201,7 +201,7 @@ for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -222,7 +222,7 @@ for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_coeff.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_coeff command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_coeff command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -221,7 +221,7 @@ either in the input script or in a data file.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -242,7 +242,7 @@ either in the input script or in a data file.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_fene.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style fene command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style fene command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -209,7 +209,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -230,7 +230,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_fene_expand.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style fene/expand command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style fene/expand command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -210,7 +210,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -231,7 +231,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_harmonic.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style harmonic command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style harmonic command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -199,7 +199,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -220,7 +220,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_harmonic_shift.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style harmonic/shift command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style harmonic/shift command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -201,7 +201,7 @@ section for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -222,7 +222,7 @@ section for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_harmonic_shift_cut.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style harmonic/shift/cut command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style harmonic/shift/cut command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -202,7 +202,7 @@ section for more info on packages.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -223,7 +223,7 @@ section for more info on packages.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_hybrid.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style hybrid command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style hybrid command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -202,7 +202,7 @@ file, you need to re-specify bond_coeff commands.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -223,7 +223,7 @@ file, you need to re-specify bond_coeff commands.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_morse.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style morse command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style morse command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -197,7 +197,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -218,7 +218,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_none.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style none command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style none command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -163,7 +163,7 @@ pairs of bonded atoms were listed in the data file read by the
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -184,7 +184,7 @@ pairs of bonded atoms were listed in the data file read by the
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_nonlinear.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style nonlinear command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style nonlinear command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -199,7 +199,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -220,7 +220,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/bond_quartic.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style quartic command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style quartic command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -231,7 +231,7 @@ dihedral, etc) cannot be used with <em>quartic</em> bonds.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -252,7 +252,7 @@ dihedral, etc) cannot be used with <em>quartic</em> bonds.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

12
doc/bond_style.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -171,8 +171,8 @@ simulation. See the <a class="reference internal" href="read_restart.html"><em>
details on how to do this. The one exception is that bond_style details on how to do this. The one exception is that bond_style
<em>hybrid</em> only stores the list of sub-styles in the restart file; bond <em>hybrid</em> only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.</p> coefficients need to be re-specified.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">When both a bond and pair style is defined, the <p class="last">When both a bond and pair style is defined, the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command often needs to be used to <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise turn off (or weight) the pairwise interaction that would otherwise
@ -230,7 +230,7 @@ package.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -251,7 +251,7 @@ package.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

2
doc/bond_style.txt
View File

@ -51,7 +51,7 @@ details on how to do this. The one exception is that bond_style
{hybrid} only stores the list of sub-styles in the restart file; bond {hybrid} only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified. coefficients need to be re-specified.
IMPORTANT NOTE: When both a bond and pair style is defined, the NOTE: When both a bond and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to "special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms. exist between 2 bonded atoms.

8
doc/bond_table.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>bond_style table command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>bond_style table command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -269,7 +269,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -290,7 +290,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/boundary.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>boundary command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>boundary command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -227,7 +227,7 @@ of lost atoms.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -248,7 +248,7 @@ of lost atoms.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/box.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>box command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>box command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -191,7 +191,7 @@ error.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -212,7 +212,7 @@ error.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

83
doc/change_box.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>change_box command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>change_box command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -214,13 +214,16 @@ current one.</p>
conditions are invoked (see the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command) conditions are invoked (see the <a class="reference internal" href="boundary.html"><em>boundary</em></a> command)
which may change simulation box boundaries, and atoms are migrated to which may change simulation box boundaries, and atoms are migrated to
new owning processors.</p> new owning processors.</p>
<p>IMPORTANT_NOTE: This means that you cannot use the change_box command <div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This means that you cannot use the change_box command
to enlarge a shrink-wrapped box, e.g. to make room to insert more to enlarge a shrink-wrapped box, e.g. to make room to insert more
atoms via the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, because the atoms via the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, because the
simulation box will be re-shrink-wrapped before the change_box command simulation box will be re-shrink-wrapped before the change_box command
completes. Instead you could do something like this, assuming the completes. Instead you could do something like this, assuming the
simulation box is non-periodic and atoms extend from 0 to 20 in all simulation box is non-periodic and atoms extend from 0 to 20 in all
dimensions:</p> dimensions:</p>
</div>
<div class="highlight-python"><div class="highlight"><pre>change_box all x final -10 20 <div class="highlight-python"><div class="highlight"><pre>change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom create_atoms 1 single -5 5 5 # this will fail to insert an atom
</pre></div> </pre></div>
@ -230,45 +233,45 @@ create_atoms 1 single -5 5 5
change_box boundary s s s # this will work change_box boundary s s s # this will work
</pre></div> </pre></div>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this <p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this command, atom
command, atom remapping is NOT performed by default. This command remapping is NOT performed by default. This command allows remapping
allows remapping to be done in a more general way, exactly when you to be done in a more general way, exactly when you specify it (zero or
specify it (zero or more times) in the sequence of transformations. more times) in the sequence of transformations. Thus if you do not
Thus if you do not use the <em>remap</em> keyword, atom coordinates will not use the <em>remap</em> keyword, atom coordinates will not be changed even if
be changed even if the box size/shape changes. If a uniformly the box size/shape changes. If a uniformly strained state is desired,
strained state is desired, the <em>remap</em> keyword should be specified.</p> the <em>remap</em> keyword should be specified.</p>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">It is possible to lose atoms with this command. <p class="last">It is possible to lose atoms with this command. E.g. by
E.g. by changing the box without remapping the atoms, and having atoms changing the box without remapping the atoms, and having atoms end up
end up outside of non-periodic boundaries. It is also possible to outside of non-periodic boundaries. It is also possible to alter
alter bonds between atoms straddling a boundary in bad ways. E.g. by bonds between atoms straddling a boundary in bad ways. E.g. by
converting a boundary from periodic to non-periodic. It is also converting a boundary from periodic to non-periodic. It is also
possible when remapping atoms to put them (nearly) on top of each possible when remapping atoms to put them (nearly) on top of each
other. E.g. by converting a boundary from non-periodic to periodic. other. E.g. by converting a boundary from non-periodic to periodic.
All of these will typically lead to bad dynamics and/or generate error All of these will typically lead to bad dynamics and/or generate error
messages.</p> messages.</p>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">The simulation box size/shape can be changed by <p class="last">The simulation box size/shape can be changed by arbitrarily
arbitrarily large amounts by this command. This is not a problem, large amounts by this command. This is not a problem, except that the
except that the mapping of processors to the simulation box is not mapping of processors to the simulation box is not changed from its
changed from its initial 3d configuration; see the initial 3d configuration; see the <a class="reference internal" href="processors.html"><em>processors</em></a>
<a class="reference internal" href="processors.html"><em>processors</em></a> command. Thus, if the box size/shape command. Thus, if the box size/shape changes dramatically, the
changes dramatically, the mapping of processors to the simulation box mapping of processors to the simulation box may not end up as optimal
may not end up as optimal as the initial mapping attempted to be.</p> as the initial mapping attempted to be.</p>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">Because the keywords used in this command are applied <p class="last">Because the keywords used in this command are applied one at a
one at a time to the simulation box and the atoms in it, care must be time to the simulation box and the atoms in it, care must be taken
taken with triclinic cells to avoid exceeding the limits on skew after with triclinic cells to avoid exceeding the limits on skew after each
each transformation in the sequence. If skew is exceeded before the transformation in the sequence. If skew is exceeded before the final
final transformation this can be avoided by changing the order of the transformation this can be avoided by changing the order of the
sequence, or breaking the transformation into two or more smaller sequence, or breaking the transformation into two or more smaller
transformations. For more information on the allowed limits for box transformations. For more information on the allowed limits for box
skew see the discussion on triclinic boxes on <a class="reference internal" href="Section_howto.html#howto-12"><span>this page</span></a>.</p> skew see the discussion on triclinic boxes on <a class="reference internal" href="Section_howto.html#howto-12"><span>this page</span></a>.</p>
@ -317,10 +320,10 @@ keep the volume constant:</p>
<div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 z volume y scale 1.1 z volume <div class="highlight-python"><div class="highlight"><pre>change_box all x scale 1.1 z volume y scale 1.1 z volume
</pre></div> </pre></div>
</div> </div>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">For solids or liquids, when one dimension of the box <p class="last">For solids or liquids, when one dimension of the box is
is expanded, it may be physically undesirable to hold the other 2 box expanded, it may be physically undesirable to hold the other 2 box
lengths constant since that implies a density change. For solids, lengths constant since that implies a density change. For solids,
adjusting the other dimensions via the <em>volume</em> style may make adjusting the other dimensions via the <em>volume</em> style may make
physical sense (just as for a liquid), but may not be correct for physical sense (just as for a liquid), but may not be correct for
@ -443,7 +446,7 @@ change_box command is issued, so long as an <a class="reference internal" href="
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -464,7 +467,7 @@ change_box command is issued, so long as an <a class="reference internal" href="
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

52
doc/change_box.txt
View File

@ -93,7 +93,7 @@ conditions are invoked (see the "boundary"_boundary.html command)
which may change simulation box boundaries, and atoms are migrated to which may change simulation box boundaries, and atoms are migrated to
new owning processors. new owning processors.
IMPORTANT_NOTE: This means that you cannot use the change_box command NOTE: This means that you cannot use the change_box command
to enlarge a shrink-wrapped box, e.g. to make room to insert more to enlarge a shrink-wrapped box, e.g. to make room to insert more
atoms via the "create_atoms"_create_atoms.html command, because the atoms via the "create_atoms"_create_atoms.html command, because the
simulation box will be re-shrink-wrapped before the change_box command simulation box will be re-shrink-wrapped before the change_box command
@ -108,37 +108,37 @@ change_box all x final -10 20 boundary f s s
create_atoms 1 single -5 5 5 create_atoms 1 single -5 5 5
change_box boundary s s s # this will work :pre change_box boundary s s s # this will work :pre
IMPORTANT NOTE: Unlike the earlier "displace_box" version of this NOTE: Unlike the earlier "displace_box" version of this command, atom
command, atom remapping is NOT performed by default. This command remapping is NOT performed by default. This command allows remapping
allows remapping to be done in a more general way, exactly when you to be done in a more general way, exactly when you specify it (zero or
specify it (zero or more times) in the sequence of transformations. more times) in the sequence of transformations. Thus if you do not
Thus if you do not use the {remap} keyword, atom coordinates will not use the {remap} keyword, atom coordinates will not be changed even if
be changed even if the box size/shape changes. If a uniformly the box size/shape changes. If a uniformly strained state is desired,
strained state is desired, the {remap} keyword should be specified. the {remap} keyword should be specified.
IMPORTANT NOTE: It is possible to lose atoms with this command. NOTE: It is possible to lose atoms with this command. E.g. by
E.g. by changing the box without remapping the atoms, and having atoms changing the box without remapping the atoms, and having atoms end up
end up outside of non-periodic boundaries. It is also possible to outside of non-periodic boundaries. It is also possible to alter
alter bonds between atoms straddling a boundary in bad ways. E.g. by bonds between atoms straddling a boundary in bad ways. E.g. by
converting a boundary from periodic to non-periodic. It is also converting a boundary from periodic to non-periodic. It is also
possible when remapping atoms to put them (nearly) on top of each possible when remapping atoms to put them (nearly) on top of each
other. E.g. by converting a boundary from non-periodic to periodic. other. E.g. by converting a boundary from non-periodic to periodic.
All of these will typically lead to bad dynamics and/or generate error All of these will typically lead to bad dynamics and/or generate error
messages. messages.
IMPORTANT NOTE: The simulation box size/shape can be changed by NOTE: The simulation box size/shape can be changed by arbitrarily
arbitrarily large amounts by this command. This is not a problem, large amounts by this command. This is not a problem, except that the
except that the mapping of processors to the simulation box is not mapping of processors to the simulation box is not changed from its
changed from its initial 3d configuration; see the initial 3d configuration; see the "processors"_processors.html
"processors"_processors.html command. Thus, if the box size/shape command. Thus, if the box size/shape changes dramatically, the
changes dramatically, the mapping of processors to the simulation box mapping of processors to the simulation box may not end up as optimal
may not end up as optimal as the initial mapping attempted to be. as the initial mapping attempted to be.
IMPORTANT NOTE: Because the keywords used in this command are applied NOTE: Because the keywords used in this command are applied one at a
one at a time to the simulation box and the atoms in it, care must be time to the simulation box and the atoms in it, care must be taken
taken with triclinic cells to avoid exceeding the limits on skew after with triclinic cells to avoid exceeding the limits on skew after each
each transformation in the sequence. If skew is exceeded before the transformation in the sequence. If skew is exceeded before the final
final transformation this can be avoided by changing the order of the transformation this can be avoided by changing the order of the
sequence, or breaking the transformation into two or more smaller sequence, or breaking the transformation into two or more smaller
transformations. For more information on the allowed limits for box transformations. For more information on the allowed limits for box
skew see the discussion on triclinic boxes on "this skew see the discussion on triclinic boxes on "this
@ -194,8 +194,8 @@ keep the volume constant:
change_box all x scale 1.1 z volume y scale 1.1 z volume :pre change_box all x scale 1.1 z volume y scale 1.1 z volume :pre
IMPORTANT NOTE: For solids or liquids, when one dimension of the box NOTE: For solids or liquids, when one dimension of the box is
is expanded, it may be physically undesirable to hold the other 2 box expanded, it may be physically undesirable to hold the other 2 box
lengths constant since that implies a density change. For solids, lengths constant since that implies a density change. For solids,
adjusting the other dimensions via the {volume} style may make adjusting the other dimensions via the {volume} style may make
physical sense (just as for a liquid), but may not be correct for physical sense (just as for a liquid), but may not be correct for

8
doc/clear.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>clear command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>clear command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -171,7 +171,7 @@ input script variables (<a class="reference internal" href="variable.html"><em>v
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -192,7 +192,7 @@ input script variables (<a class="reference internal" href="variable.html"><em>v
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

40
doc/comm_modify.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>comm_modify command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>comm_modify command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -162,14 +162,14 @@ comm_modify cutoff/multi * 0.0
communication of atom information that occurs each timestep as communication of atom information that occurs each timestep as
coordinates and other properties are exchanged between neighboring coordinates and other properties are exchanged between neighboring
processors and stored as properties of ghost atoms.</p> processors and stored as properties of ghost atoms.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">These options apply to the currently defined comm <p class="last">These options apply to the currently defined comm style. When
style. When you specify a <a class="reference internal" href="comm_style.html"><em>comm_style</em></a> command, all you specify a <a class="reference internal" href="comm_style.html"><em>comm_style</em></a> command, all communication
communication settings are restored to their default values, including settings are restored to their default values, including those
those previously reset by a comm_modify command. Thus if your input previously reset by a comm_modify command. Thus if your input script
script specifies a comm_style command, you should use the comm_modify specifies a comm_style command, you should use the comm_modify command
command after it.</p> after it.</p>
</div> </div>
<p>The <em>mode</em> keyword determines whether a single or multiple cutoff <p>The <em>mode</em> keyword determines whether a single or multiple cutoff
distances are used to determine which atoms to communicate.</p> distances are used to determine which atoms to communicate.</p>
@ -228,14 +228,14 @@ atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair performs (e.g. locate neighbors of ghost atoms in a multibody pair
potential). Setting the ghost cutoff appropriately can insure it will potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.</p> find the needed atoms.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">In these scenarios, if you do not set the ghost cutoff <p class="last">In these scenarios, if you do not set the ghost cutoff long
long enough, and if there is only one processor in a periodic enough, and if there is only one processor in a periodic dimension
dimension (e.g. you are running in serial), then LAMMPS may &#8220;find&#8221; the (e.g. you are running in serial), then LAMMPS may &#8220;find&#8221; the atom it
atom it is looking for (e.g. the partner atom in a bond), that is on is looking for (e.g. the partner atom in a bond), that is on the far
the far side of the simulation box, across a periodic boundary. This side of the simulation box, across a periodic boundary. This will
will typically lead to bad dynamics (i.e. the bond length is now the typically lead to bad dynamics (i.e. the bond length is now the
simulation box length). To detect if this is happening, see the simulation box length). To detect if this is happening, see the
<a class="reference internal" href="neigh_modify.html"><em>neigh_modify cluster</em></a> command.</p> <a class="reference internal" href="neigh_modify.html"><em>neigh_modify cluster</em></a> command.</p>
</div> </div>
@ -286,7 +286,7 @@ cutoff = pairwise force cutoff + neighbor skin.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -307,7 +307,7 @@ cutoff = pairwise force cutoff + neighbor skin.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

24
doc/comm_modify.txt
View File

@ -39,12 +39,12 @@ communication of atom information that occurs each timestep as
coordinates and other properties are exchanged between neighboring coordinates and other properties are exchanged between neighboring
processors and stored as properties of ghost atoms. processors and stored as properties of ghost atoms.
IMPORTANT NOTE: These options apply to the currently defined comm NOTE: These options apply to the currently defined comm style. When
style. When you specify a "comm_style"_comm_style.html command, all you specify a "comm_style"_comm_style.html command, all communication
communication settings are restored to their default values, including settings are restored to their default values, including those
those previously reset by a comm_modify command. Thus if your input previously reset by a comm_modify command. Thus if your input script
script specifies a comm_style command, you should use the comm_modify specifies a comm_style command, you should use the comm_modify command
command after it. after it.
The {mode} keyword determines whether a single or multiple cutoff The {mode} keyword determines whether a single or multiple cutoff
distances are used to determine which atoms to communicate. distances are used to determine which atoms to communicate.
@ -112,12 +112,12 @@ performs (e.g. locate neighbors of ghost atoms in a multibody pair
potential). Setting the ghost cutoff appropriately can insure it will potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms. find the needed atoms.
IMPORTANT NOTE: In these scenarios, if you do not set the ghost cutoff NOTE: In these scenarios, if you do not set the ghost cutoff long
long enough, and if there is only one processor in a periodic enough, and if there is only one processor in a periodic dimension
dimension (e.g. you are running in serial), then LAMMPS may "find" the (e.g. you are running in serial), then LAMMPS may "find" the atom it
atom it is looking for (e.g. the partner atom in a bond), that is on is looking for (e.g. the partner atom in a bond), that is on the far
the far side of the simulation box, across a periodic boundary. This side of the simulation box, across a periodic boundary. This will
will typically lead to bad dynamics (i.e. the bond length is now the typically lead to bad dynamics (i.e. the bond length is now the
simulation box length). To detect if this is happening, see the simulation box length). To detect if this is happening, see the
"neigh_modify cluster"_neigh_modify.html command. "neigh_modify cluster"_neigh_modify.html command.

8
doc/comm_style.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>comm_style command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>comm_style command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -196,7 +196,7 @@ commands. The decomposition can be changed via the
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -217,7 +217,7 @@ commands. The decomposition can be changed via the
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/compute.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -374,7 +374,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -395,7 +395,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/compute_ackland_atom.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute ackland/atom command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute ackland/atom command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -197,7 +197,7 @@ integers defined above.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -218,7 +218,7 @@ integers defined above.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/compute_angle_local.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute angle/local command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute angle/local command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -205,7 +205,7 @@ be in energy <a class="reference internal" href="units.html"><em>units</em></a>.
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -226,7 +226,7 @@ be in energy <a class="reference internal" href="units.html"><em>units</em></a>.
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

24
doc/compute_angmom_chunk.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute angmom/chunk command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute angmom/chunk command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -165,14 +165,14 @@ in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the thus also not contribute to this calculation. You can specify the
&#8220;all&#8221; group for this command if you simply want to include atoms with &#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p> non-zero chunk IDs.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s <p class="last">The coordinates of an atom contribute to the chunk&#8217;s angular
angular momentum in &#8220;unwrapped&#8221; form, by using the image flags momentum in &#8220;unwrapped&#8221; form, by using the image flags associated with
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of of &#8220;unwrapped&#8221; coordinates. See the Atoms section of the
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags and
and how they are set for each atom. You can reset the image flags how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p> (e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div> </div>
<p>The simplest way to output the results of the compute angmom/chunk <p>The simplest way to output the results of the compute angmom/chunk
@ -215,7 +215,7 @@ mass-velocity-distance <a class="reference internal" href="units.html"><em>units
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -236,7 +236,7 @@ mass-velocity-distance <a class="reference internal" href="units.html"><em>units
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

12
doc/compute_angmom_chunk.txt
View File

@ -49,12 +49,12 @@ thus also not contribute to this calculation. You can specify the
"all" group for this command if you simply want to include atoms with "all" group for this command if you simply want to include atoms with
non-zero chunk IDs. non-zero chunk IDs.
IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's NOTE: The coordinates of an atom contribute to the chunk's angular
angular momentum in "unwrapped" form, by using the image flags momentum in "unwrapped" form, by using the image flags associated with
associated with each atom. See the "dump custom"_dump.html command each atom. See the "dump custom"_dump.html command for a discussion
for a discussion of "unwrapped" coordinates. See the Atoms section of of "unwrapped" coordinates. See the Atoms section of the
the "read_data"_read_data.html command for a discussion of image flags "read_data"_read_data.html command for a discussion of image flags and
and how they are set for each atom. You can reset the image flags how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the "set (e.g. to 0) before invoking this compute by using the "set
image"_set.html command. image"_set.html command.

8
doc/compute_basal_atom.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute basal/atom command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute basal/atom command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -195,7 +195,7 @@ well-defined basal plane.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -216,7 +216,7 @@ well-defined basal plane.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/compute_body_local.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute body/local command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute body/local command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -217,7 +217,7 @@ options.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -238,7 +238,7 @@ options.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/compute_bond_local.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute bond/local command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute bond/local command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -213,7 +213,7 @@ output for <em>eng</em> will be in energy <a class="reference internal" href="un
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -234,7 +234,7 @@ output for <em>eng</em> will be in energy <a class="reference internal" href="un
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

8
doc/compute_centro_atom.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute centro/atom command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute centro/atom command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -242,7 +242,7 @@ of 12.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -263,7 +263,7 @@ of 12.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

49
doc/compute_chunk_atom.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute chunk/atom command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute chunk/atom command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -438,13 +438,14 @@ the first step of the time window will persist until the end of the
time window.</p> time window.</p>
<p>If the setting is <em>every</em>, which is the default, then chunk IDs are <p>If the setting is <em>every</em>, which is the default, then chunk IDs are
re-calculated on any timestep this compute is invoked.</p> re-calculated on any timestep this compute is invoked.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">If you want the persistent chunk-IDs calculated by <p class="last">If you want the persistent chunk-IDs calculated by this compute
this compute to be continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>, then you should use the same ID for this to be continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>,
compute, as in the original run. This is so that the fix this compute then you should use the same ID for this compute, as in the original
creates to store per-atom quantities will also have the same ID, and run. This is so that the fix this compute creates to store per-atom
thus be initialized correctly with chunk IDs from the restart file.</p> quantities will also have the same ID, and thus be initialized
correctly with chunk IDs from the restart file.</p>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
<p>The <em>compress</em> keyword applies to all chunk styles and affects how <p>The <em>compress</em> keyword applies to all chunk styles and affects how
@ -480,19 +481,19 @@ renumbered to (1,2,3,4,5). The original values (27,...,1000000) can
be output to a file by the <a class="reference internal" href="fix_ave_chunk.html"><em>fix ave/chunk</em></a> command, be output to a file by the <a class="reference internal" href="fix_ave_chunk.html"><em>fix ave/chunk</em></a> command,
or by using the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command in or by using the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command in
conjunction with the <a class="reference internal" href="compute_property_chunk.html"><em>compute property/chunk</em></a> command.</p> conjunction with the <a class="reference internal" href="compute_property_chunk.html"><em>compute property/chunk</em></a> command.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">The compression operation requires global <p class="last">The compression operation requires global communication across
communication across all processors to share their chunk ID values. all processors to share their chunk ID values. It can require large
It can require large memory on every processor to store them, even memory on every processor to store them, even after they are
after they are compressed, if there are are a large number of unique compressed, if there are are a large number of unique chunk IDs with
chunk IDs with atoms assigned to them. It uses a STL map to find atoms assigned to them. It uses a STL map to find unique chunk IDs
unique chunk IDs and store them in sorted order. Each time an atom is and store them in sorted order. Each time an atom is assigned a
assigned a compressed chunk ID, it must access the STL map. All of compressed chunk ID, it must access the STL map. All of this means
this means that compression can be expensive, both in memory and CPU that compression can be expensive, both in memory and CPU time. The
time. The use of the <em>limit</em> keyword in conjunction with the use of the <em>limit</em> keyword in conjunction with the <em>compress</em> keyword
<em>compress</em> keyword can affect these costs, depending on which keyword can affect these costs, depending on which keyword is used first. So
is used first. So use this option with care.</p> use this option with care.</p>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
<p>The <em>discard</em> keyword applies to all chunk styles. It affects what <p>The <em>discard</em> keyword applies to all chunk styles. It affects what
@ -613,7 +614,7 @@ the restarted simulation begins.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -634,7 +635,7 @@ the restarted simulation begins.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

34
doc/compute_chunk_atom.txt
View File

@ -377,12 +377,12 @@ time window.
If the setting is {every}, which is the default, then chunk IDs are If the setting is {every}, which is the default, then chunk IDs are
re-calculated on any timestep this compute is invoked. re-calculated on any timestep this compute is invoked.
IMPORTANT NOTE: If you want the persistent chunk-IDs calculated by NOTE: If you want the persistent chunk-IDs calculated by this compute
this compute to be continuous when running from a "restart to be continuous when running from a "restart file"_read_restart.html,
file"_read_restart.html, then you should use the same ID for this then you should use the same ID for this compute, as in the original
compute, as in the original run. This is so that the fix this compute run. This is so that the fix this compute creates to store per-atom
creates to store per-atom quantities will also have the same ID, and quantities will also have the same ID, and thus be initialized
thus be initialized correctly with chunk IDs from the restart file. correctly with chunk IDs from the restart file.
:line :line
@ -424,17 +424,17 @@ or by using the "fix ave/time"_fix_ave_time.html command in
conjunction with the "compute conjunction with the "compute
property/chunk"_compute_property_chunk.html command. property/chunk"_compute_property_chunk.html command.
IMPORTANT NOTE: The compression operation requires global NOTE: The compression operation requires global communication across
communication across all processors to share their chunk ID values. all processors to share their chunk ID values. It can require large
It can require large memory on every processor to store them, even memory on every processor to store them, even after they are
after they are compressed, if there are are a large number of unique compressed, if there are are a large number of unique chunk IDs with
chunk IDs with atoms assigned to them. It uses a STL map to find atoms assigned to them. It uses a STL map to find unique chunk IDs
unique chunk IDs and store them in sorted order. Each time an atom is and store them in sorted order. Each time an atom is assigned a
assigned a compressed chunk ID, it must access the STL map. All of compressed chunk ID, it must access the STL map. All of this means
this means that compression can be expensive, both in memory and CPU that compression can be expensive, both in memory and CPU time. The
time. The use of the {limit} keyword in conjunction with the use of the {limit} keyword in conjunction with the {compress} keyword
{compress} keyword can affect these costs, depending on which keyword can affect these costs, depending on which keyword is used first. So
is used first. So use this option with care. use this option with care.
:line :line

12
doc/compute_cluster_atom.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute cluster/atom command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute cluster/atom command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -158,8 +158,8 @@ time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a too frequently or to have multiple compute/dump commands, each of a
<em>clsuter/atom</em> style.</p> <em>clsuter/atom</em> style.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">If you have a bonded system, then the settings of <p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This interactions between atoms in the same bond, angle, or dihedral. This
@ -205,7 +205,7 @@ LAMMPS output options.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -226,7 +226,7 @@ LAMMPS output options.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

2
doc/compute_cluster_atom.txt
View File

@ -39,7 +39,7 @@ is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each of a too frequently or to have multiple compute/dump commands, each of a
{clsuter/atom} style. {clsuter/atom} style.
IMPORTANT NOTE: If you have a bonded system, then the settings of NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise "special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html is the default setting for the "special_bonds"_special_bonds.html

8
doc/compute_cna_atom.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute cna/atom command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute cna/atom command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -217,7 +217,7 @@ above.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -238,7 +238,7 @@ above.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

24
doc/compute_com.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute com command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute com command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -149,14 +149,14 @@ of atoms, including all effects due to atoms passing thru periodic
boundaries.</p> boundaries.</p>
<p>A vector of three quantites is calculated by this compute, which <p>A vector of three quantites is calculated by this compute, which
are the x,y,z coordinates of the center of mass.</p> are the x,y,z coordinates of the center of mass.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to the <p class="last">The coordinates of an atom contribute to the center-of-mass in
center-of-mass in &#8220;unwrapped&#8221; form, by using the image flags &#8220;unwrapped&#8221; form, by using the image flags associated with each atom.
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion of
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of &#8220;unwrapped&#8221; coordinates. See the Atoms section of the
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags and
and how they are set for each atom. You can reset the image flags how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p> (e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div> </div>
<p><strong>Output info:</strong></p> <p><strong>Output info:</strong></p>
@ -189,7 +189,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -210,7 +210,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

12
doc/compute_com.txt
View File

@ -28,12 +28,12 @@ boundaries.
A vector of three quantites is calculated by this compute, which A vector of three quantites is calculated by this compute, which
are the x,y,z coordinates of the center of mass. are the x,y,z coordinates of the center of mass.
IMPORTANT NOTE: The coordinates of an atom contribute to the NOTE: The coordinates of an atom contribute to the center-of-mass in
center-of-mass in "unwrapped" form, by using the image flags "unwrapped" form, by using the image flags associated with each atom.
associated with each atom. See the "dump custom"_dump.html command See the "dump custom"_dump.html command for a discussion of
for a discussion of "unwrapped" coordinates. See the Atoms section of "unwrapped" coordinates. See the Atoms section of the
the "read_data"_read_data.html command for a discussion of image flags "read_data"_read_data.html command for a discussion of image flags and
and how they are set for each atom. You can reset the image flags how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the "set (e.g. to 0) before invoking this compute by using the "set
image"_set.html command. image"_set.html command.

12
doc/compute_com_chunk.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute com/chunk command &mdash; LAMMPS 15 May 2015 version documentation</title> <title>compute com/chunk command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/> <link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script> <script src="_static/js/modernizr.min.js"></script>
@ -163,8 +163,8 @@ in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the thus also not contribute to this calculation. You can specify the
&#8220;all&#8221; group for this command if you simply want to include atoms with &#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p> non-zero chunk IDs.</p>
<div class="admonition warning"> <div class="admonition note">
<p class="first admonition-title">Warning</p> <p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s <p class="last">The coordinates of an atom contribute to the chunk&#8217;s
center-of-mass in &#8220;unwrapped&#8221; form, by using the image flags center-of-mass in &#8220;unwrapped&#8221; form, by using the image flags
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
@ -213,7 +213,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<div role="contentinfo"> <div role="contentinfo">
<p> <p>
&copy; Copyright . &copy; Copyright 2013 Sandia Corporation.
</p> </p>
</div> </div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -234,7 +234,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<script type="text/javascript"> <script type="text/javascript">
var DOCUMENTATION_OPTIONS = { var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./', URL_ROOT:'./',
VERSION:'15 May 2015 version', VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false, COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html', FILE_SUFFIX:'.html',
HAS_SOURCE: true HAS_SOURCE: true

2
doc/compute_com_chunk.txt
View File

@ -47,7 +47,7 @@ thus also not contribute to this calculation. You can specify the
"all" group for this command if you simply want to include atoms with "all" group for this command if you simply want to include atoms with
non-zero chunk IDs. non-zero chunk IDs.
IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's NOTE: The coordinates of an atom contribute to the chunk's
center-of-mass in "unwrapped" form, by using the image flags center-of-mass in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of for a discussion of "unwrapped" coordinates. See the Atoms section of

Some files were not shown because too many files have changed in this diff Show More