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8
doc/Manual.html
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@ -8,7 +8,7 @@
<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"/>
@ -401,7 +401,7 @@ it gives quick access to documentation for all LAMMPS commands.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -422,7 +422,7 @@ it gives quick access to documentation for all LAMMPS commands.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

36
doc/Section_accelerate.html
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@ -8,7 +8,7 @@
<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="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
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" />
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Using staggered PPPM may not give the same increase in
accuracy of energy and pressure as it does in forces, so some caution
must be used if energy and/or pressure are quantities of interest,
such as when using a barostat.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Using staggered PPPM may not give the same increase in accuracy
of energy and pressure as it does in forces, so some caution must be
used if energy and/or pressure are quantities of interest, such as
when using a barostat.</p>
</div>
<hr class="docutils" />
</div>
@ -410,14 +410,14 @@ launched, without changing your input script, as illustrated in the
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
script.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">With a few exceptions, you can build a single LAMMPS
executable with all its accelerator packages installed. Note however
that the USER-INTEL and KOKKOS packages require you to choose one of
their hardware options when building for a specific platform.
I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP,
Cuda, or Phi option for the KOKKOS package.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">With a few exceptions, you can build a single LAMMPS executable
with all its accelerator packages installed. Note however that the
USER-INTEL and KOKKOS packages require you to choose one of their
hardware options when building for a specific platform. I.e. CPU or
Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
option for the KOKKOS package.</p>
</div>
<p>These are the exceptions. You cannot build a single executable with:</p>
<ul class="simple">
@ -587,7 +587,7 @@ to benchmark the performance of both packages on your system.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -608,7 +608,7 @@ to benchmark the performance of both packages on your system.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

20
doc/Section_accelerate.txt
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@ -134,10 +134,10 @@ relative accuracy of slightly greater than 1e-5 and above.
:c,image(JPG/rhodo_staggered.jpg)
IMPORTANT NOTE: Using staggered PPPM may not give the same increase in
accuracy of energy and pressure as it does in forces, so some caution
must be used if energy and/or pressure are quantities of interest,
such as when using a barostat.
NOTE: Using staggered PPPM may not give the same increase in accuracy
of energy and pressure as it does in forces, so some caution must be
used if energy and/or pressure are quantities of interest, such as
when using a barostat.
:line
@ -240,12 +240,12 @@ individual accelerator sections. Or you can add
"package"_package.html and "suffix"_suffix.html commands to your input
script.
IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
executable with all its accelerator packages installed. Note however
that the USER-INTEL and KOKKOS packages require you to choose one of
their hardware options when building for a specific platform.
I.e. CPU or Phi option for the USER-INTEL package. Or the OpenMP,
Cuda, or Phi option for the KOKKOS package.
NOTE: With a few exceptions, you can build a single LAMMPS executable
with all its accelerator packages installed. Note however that the
USER-INTEL and KOKKOS packages require you to choose one of their
hardware options when building for a specific platform. I.e. CPU or
Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
option for the KOKKOS package.
These are the exceptions. You cannot build a single executable with:

16
doc/Section_commands.html
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@ -8,7 +8,7 @@
<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="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>
<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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If the argument is itself a command that requires a
quoted argument (e.g. using a <a class="reference internal" href="print.html"><em>print</em></a> command as part of an
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If the argument is itself a command that requires a quoted
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
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
@ -1481,7 +1481,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -1502,7 +1502,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

4
doc/Section_commands.txt
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@ -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
comment indicator in (2) or substituted for as a variable in (3).
IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a "print"_print.html command as part of an
NOTE: If the argument is itself a command that requires a quoted
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
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

8
doc/Section_errors.html
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@ -8,7 +8,7 @@
<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="prev" title="11. Python interface to LAMMPS" href="Section_python.html"/>
@ -6323,7 +6323,7 @@ infinity.</dd>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -6344,7 +6344,7 @@ infinity.</dd>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/Section_example.html
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@ -8,7 +8,7 @@
<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="prev" title="6. How-to discussions" href="Section_howto.html"/>
@ -346,7 +346,7 @@ packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -367,7 +367,7 @@ packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/Section_history.html
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@ -8,7 +8,7 @@
<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"/>
@ -258,7 +258,7 @@ internally. A brief listing of their features is given here.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -279,7 +279,7 @@ internally. A brief listing of their features is given here.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

69
doc/Section_howto.html
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@ -8,7 +8,7 @@
<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="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>
<p>Many of the example input scripts included in the LAMMPS distribution
are for 2d models.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Some models in LAMMPS treat particles as finite-size
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Some models in LAMMPS treat particles as finite-size spheres, as
opposed to point particles. In 2d, the particles will still be
spheres, not disks, meaning their moment of inertia will be the same
as in 3d.</p>
</div>
<hr class="docutils" />
</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>
for additional tools that can use CHARMM or AMBER to assign force
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
field. See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a> for a description of the AMBER 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="special_bonds.html#cornell"><span>(Cornell)</span></a> for a description of the AMBER force
field.</p>
<p>These style choices compute force field formulas that are consistent
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
interactions involving a hydrogen atom on very electronegative atoms
(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
with the DREIDING force field. See each command&#8217;s
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">
<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
<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.
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
@ -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
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
<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">O mass = 15.9994</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>
<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>
<div class="line-block">
<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>
<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
<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
coefficients.</p>
<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"><br /></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>
<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" />
@ -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
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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
velocities; they do NOT perform time integration updates. Thus they
should be used in conjunction with a constant NVE integration fix such
as these:</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Only the nvt fixes perform time integration, meaning they update
the velocities and positions of particles due to forces and velocities
respectively. The other thermostat fixes only adjust velocities; they
do NOT perform time integration updates. Thus they should be used in
conjunction with a constant NVE integration fix such as these:</p>
</div>
<ul class="simple">
<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
<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>
<div class="admonition warning">
<p class="first admonition-title">Warning</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
integration. <a class="reference internal" href="fix_press_berendsen.html"><em>Fix press/berendsen</em></a> does NOT,
so it should be used with one of the constant NVE fixes or with one of
the NVT fixes.</p>
<div class="admonition note">
<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 integration.
<a class="reference internal" href="fix_press_berendsen.html"><em>Fix press/berendsen</em></a> does NOT, so it should
be used with one of the constant NVE fixes or with one of the NVT
fixes.</p>
</div>
<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
@ -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
tensor. Another approach is to sample the triclinic cell fluctuations
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" />
</div>
<div class="section" id="library-interface-to-lammps">
@ -2541,7 +2540,7 @@ well.</p>
</div>
<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>
<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
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
@ -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
and the Drude particle) connected by a harmonic spring. The Drude
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">
<li>Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
@ -2836,7 +2835,7 @@ Phys, 79, 926 (1983).</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -2857,7 +2856,7 @@ Phys, 79, 926 (1983).</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
are for 2d models.
IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
spheres, as opposed to point particles. In 2d, the particles will
still be spheres, not disks, meaning their moment of inertia will be
the same as in 3d.
NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
opposed to point particles. In 2d, the particles will still be
spheres, not disks, meaning their moment of inertia will be the same
as in 3d.
:line
@ -1658,12 +1658,11 @@ the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using "compute
temp/profile"_compute_temp_profile.html.
IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
velocities; they do NOT perform time integration updates. Thus they
should be used in conjunction with a constant NVE integration fix such
as these:
NOTE: Only the nvt fixes perform time integration, meaning they update
the velocities and positions of particles due to forces and velocities
respectively. The other thermostat fixes only adjust velocities; they
do NOT perform time integration updates. Thus they should be used in
conjunction with a constant NVE integration fix such as these:
"fix nve"_fix_nve.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
a temperature or pressure compute to a barostatting fix.
IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods ("fix
npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time
integration. "Fix press/berendsen"_fix_press_berendsen.html does NOT,
so it should be used with one of the constant NVE fixes or with one of
the NVT fixes.
NOTE: As with the thermostats, the Nose/Hoover methods ("fix
npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration.
"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should
be used with one of the constant NVE fixes or with one of the NVT
fixes.
Finally, thermodynamic output, which can be setup via the
"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">
<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="prev" title="LAMMPS Documentation" href="Manual.html"/>
@ -640,7 +640,7 @@ version of LAMMPS were the following:</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -661,7 +661,7 @@ version of LAMMPS were the following:</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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="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
the word &#8220;customize&#8221; and you will find locations you will need to
modify.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is possible to add some attributes, such as a
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
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It is possible to add some attributes, such as a 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
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
where this is useful and details on how to initialize, access, and
@ -1199,7 +1199,7 @@ feature.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -1220,7 +1220,7 @@ feature.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
modify.
IMPORTANT NOTE: It is possible to add some attributes, such as a
molecule ID, to atom styles that do not have them via the "fix
NOTE: It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the "fix
property/atom"_fix_property_atom.html command. This command also
allows new custom attributes consisting of extra integer or
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">
<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="prev" title="3. Commands" href="Section_commands.html"/>
@ -1536,7 +1536,7 @@ you have questions.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -1557,7 +1557,7 @@ you have questions.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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="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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -270,7 +270,7 @@ on 1500 processors that ran at 85% parallel efficiency.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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="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 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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is not currently possible to use the
<a class="reference internal" href="python.html"><em>python</em></a> command described in this section with Python 3,
only with Python 2. The C API changed from Python 2 to 3 and the
LAMMPS code is not compatible with both.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It is not currently possible to use the <a class="reference internal" href="python.html"><em>python</em></a>
command described in this section with Python 3, only with Python 2.
The C API changed from Python 2 to 3 and the LAMMPS code is not
compatible with both.</p>
</div>
<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
@ -457,13 +457,13 @@ print &quot;Proc %d out of %d procs&quot; % (pypar.rank(),pypar.size())
</pre></div>
</div>
<p>and see one line of output for each processor you run on.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">To use Pypar and LAMMPS in parallel from Python, you
must insure both are using the same version of MPI. If you only have
one MPI installed on your system, this is not an issue, but it can be
if you have multiple MPIs. Your LAMMPS build is explicit about which
MPI it is using, since you specify the details in your lo-level
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">To use Pypar and LAMMPS in parallel from Python, you must insure
both are using the same version of MPI. If you only have one MPI
installed on your system, this is not an issue, but it can be if you
have multiple MPIs. Your LAMMPS build is explicit about which MPI it
is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Pypar uses the &#8220;mpicc&#8221; command to find
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
@ -502,13 +502,13 @@ print &quot;Proc %d out of %d procs&quot; % (comm.Get_rank(),comm.Get_size())
</pre></div>
</div>
<p>and see one line of output for each processor you run on.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">To use mpi4py and LAMMPS in parallel from Python, you
must insure both are using the same version of MPI. If you only have
one MPI installed on your system, this is not an issue, but it can be
if you have multiple MPIs. Your LAMMPS build is explicit about which
MPI it is using, since you specify the details in your lo-level
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">To use mpi4py and LAMMPS in parallel from Python, you must
insure both are using the same version of MPI. If you only have one
MPI installed on your system, this is not an issue, but it can be if
you have multiple MPIs. Your LAMMPS build is explicit about which MPI
it is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Mpi4py uses the &#8220;mpicc&#8221; command to find
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
@ -715,16 +715,16 @@ lmp = lammps(name=&quot;g++&quot;,cmdargs=list) # add LAMMPS command-line arg
</pre></div>
</div>
<hr class="docutils" />
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Currently, the creation of a LAMMPS object from within
lammps.py does not take an MPI communicator as an argument. There
should be a way to do this, so that the LAMMPS instance runs on a
subset of processors if desired, but I don&#8217;t know how to do it from
Pypar. So for now, it runs with MPI_COMM_WORLD, which is all the
processors. If someone figures out how to do this with one or more of
the Python wrappers for MPI, like Pypar, please let us know and we
will amend these doc pages.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently, the creation of a LAMMPS object from within lammps.py
does not take an MPI communicator as an argument. There should be a
way to do this, so that the LAMMPS instance runs on a subset of
processors if desired, but I don&#8217;t know how to do it from Pypar. So
for now, it runs with MPI_COMM_WORLD, which is all the processors. If
someone figures out how to do this with one or more of the Python
wrappers for MPI, like Pypar, please let us know and we will amend
these doc pages.</p>
</div>
<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>
@ -995,7 +995,7 @@ different visualization package options. Click to see larger images:</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -1016,7 +1016,7 @@ different visualization package options. Click to see larger images:</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
IMPORTANT NOTE: It is not currently possible to use the
"python"_python.html command described in this section with Python 3,
only with Python 2. The C API changed from Python 2 to 3 and the
LAMMPS code is not compatible with both.
NOTE: It is not currently possible to use the "python"_python.html
command described in this section with Python 3, only with Python 2.
The C API changed from Python 2 to 3 and the LAMMPS code is not
compatible with both.
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
@ -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.
IMPORTANT NOTE: To use Pypar and LAMMPS in parallel from Python, you
must insure both are using the same version of MPI. If you only have
one MPI installed on your system, this is not an issue, but it can be
if you have multiple MPIs. Your LAMMPS build is explicit about which
MPI it is using, since you specify the details in your lo-level
NOTE: To use Pypar and LAMMPS in parallel from Python, you must insure
both are using the same version of MPI. If you only have one MPI
installed on your system, this is not an issue, but it can be if you
have multiple MPIs. Your LAMMPS build is explicit about which MPI it
is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Pypar uses the "mpicc" command to find
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
@ -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.
IMPORTANT NOTE: To use mpi4py and LAMMPS in parallel from Python, you
must insure both are using the same version of MPI. If you only have
one MPI installed on your system, this is not an issue, but it can be
if you have multiple MPIs. Your LAMMPS build is explicit about which
MPI it is using, since you specify the details in your lo-level
NOTE: To use mpi4py and LAMMPS in parallel from Python, you must
insure both are using the same version of MPI. If you only have one
MPI installed on your system, this is not an issue, but it can be if
you have multiple MPIs. Your LAMMPS build is explicit about which MPI
it is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find
information about the MPI it uses to build against. And it tries to
load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find
@ -610,14 +610,14 @@ lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms
:line
IMPORTANT NOTE: Currently, the creation of a LAMMPS object from within
lammps.py does not take an MPI communicator as an argument. There
should be a way to do this, so that the LAMMPS instance runs on a
subset of processors if desired, but I don't know how to do it from
Pypar. So for now, it runs with MPI_COMM_WORLD, which is all the
processors. If someone figures out how to do this with one or more of
the Python wrappers for MPI, like Pypar, please let us know and we
will amend these doc pages.
NOTE: Currently, the creation of a LAMMPS object from within lammps.py
does not take an MPI communicator as an argument. There should be a
way to do this, so that the LAMMPS instance runs on a subset of
processors if desired, but I don't know how to do it from Pypar. So
for now, it runs with MPI_COMM_WORLD, which is all the processors. If
someone figures out how to do this with one or more of the Python
wrappers for MPI, like Pypar, please let us know and we will amend
these doc pages.
The lines

73
doc/Section_start.html
View File

@ -8,7 +8,7 @@
<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="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
the &#8220;popen()&#8221; function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">on some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
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
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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Similar to the note above, this option can conflict with
high-speed networks, because it uses popen().</p>
</div>
<p>Using -DLAMMPS_MEMALIGN=&lt;bytes&gt; enables the use of the
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>
<hr class="docutils" />
<p id="start-2-3"><strong>*Errors that can occur when making LAMMPS:*</strong></p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If an error occurs when building LAMMPS, the compiler or linker
will state very explicitly what the problem is. The error message
should give you a hint as to which of the steps above has failed, and
what you need to do in order to fix it. Building a code with a
Makefile is a very logical process. The compiler and linker need to
find the appropriate files and those files need to be compatible with
LAMMPS source files. When a make fails, there is usually a very
simple reason, which you or a local expert will need to fix.</p>
</div>
<p>Here are two non-obvious errors that can occur:</p>
<p>(1) If the make command breaks immediately with errors that indicate
@ -769,13 +768,13 @@ make g++
make g++
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">You should NOT include/exclude packages and build
LAMMPS in a single make command using multiple targets, e.g. make
yes-colloid g++. This is because the make procedure creates a list of
source files that will be out-of-date for the build if the package
configuration changes within the same command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">You should NOT include/exclude packages and build LAMMPS in a
single make command using multiple targets, e.g. make yes-colloid g++.
This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes
within the same command.</p>
</div>
<p>Some packages have individual files that depend on other packages
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
sets of packages. Type &#8220;make package&#8221; to see the all of the
package-related make options.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Inclusion/exclusion of a package works by simply moving files
back and forth between the main src directory and sub-directories with
the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
are seen or not seen when LAMMPS is built. After you have included or
excluded a package, you must re-build LAMMPS.</p>
</div>
<p>Additional package-related make options exist to help manage LAMMPS
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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -1956,7 +1955,7 @@ close if you have setup the problem for both codes the same.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
executable can be found by LAMMPS during a run.
IMPORTANT NOTE: on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
NOTE: on some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
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
and that an FFmpeg executable can be found by LAMMPS during the run.
IMPORTANT NOTE: Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().
NOTE: Similar to the note above, this option can conflict with
high-speed networks, because it uses popen().
Using -DLAMMPS_MEMALIGN=<bytes> enables the use of the
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)
IMPORTANT NOTE: If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.
NOTE: If an error occurs when building LAMMPS, the compiler or linker
will state very explicitly what the problem is. The error message
should give you a hint as to which of the steps above has failed, and
what you need to do in order to fix it. Building a code with a
Makefile is a very logical process. The compiler and linker need to
find the appropriate files and those files need to be compatible with
LAMMPS source files. When a make fails, there is usually a very
simple reason, which you or a local expert will need to fix.
Here are two non-obvious errors that can occur:
@ -712,11 +711,11 @@ or
make no-manybody
make g++ :pre
IMPORTANT NOTE: You should NOT include/exclude packages and build
LAMMPS in a single make command using multiple targets, e.g. make
yes-colloid g++. This is because the make procedure creates a list of
source files that will be out-of-date for the build if the package
configuration changes within the same command.
NOTE: You should NOT include/exclude packages and build LAMMPS in a
single make command using multiple targets, e.g. make yes-colloid g++.
This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes
within the same command.
Some packages have individual files that depend on other packages
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
package-related make options.
IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.
NOTE: Inclusion/exclusion of a package works by simply moving files
back and forth between the main src directory and sub-directories with
the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
are seen or not seen when LAMMPS is built. After you have included or
excluded a package, you must re-build LAMMPS.
Additional package-related make options exist to help manage LAMMPS
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">
<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="prev" title="8. Performance &amp; scalability" href="Section_perf.html"/>
@ -548,10 +548,10 @@ the README.txt file for more info.</p>
</div>
<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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">This tool is now obsolete and is not included in the
current LAMMPS distribution. This is becaues there is now a
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This tool is now obsolete and is not included in the current
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
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>
@ -652,7 +652,7 @@ distributing his great tool!</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -673,7 +673,7 @@ distributing his great tool!</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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)
IMPORTANT NOTE: This tool is now obsolete and is not included in the
current LAMMPS distribution. This is becaues there is now a
NOTE: This tool is now obsolete and is not included in the current
LAMMPS distribution. This is becaues there is now a
"write_data"_write_data.html command, which can create a data file
from within an input script. Running LAMMPS with the "-r"
"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%;
margin: 0;
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 {
border-left-width: 0;
@ -3563,11 +3563,11 @@ input[type="radio"][disabled], input[type="checkbox"][disabled] {
/* BORDERED TABLES */
.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 {
border-bottom: 1px solid #e1e4e5;
border-left: 1px solid #e1e4e5;
border-bottom: 1px solid black;
border-left: 1px solid black;
}
.wy-table-bordered-all tbody > tr:last-child td, .rst-content table.docutils tbody > tr:last-child td {
border-bottom-width: 0;
@ -3741,9 +3741,8 @@ h6 {
hr {
display: block;
height: 1px;
border: 0;
border-top: 2px solid #e1e4e5;
border-top: 2px solid #8c8b8b;
border-bottom: 2px solid #fff;
margin: 24px 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">
<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>
@ -317,7 +317,7 @@ occurs, the faster your simulation will run.</li>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -338,7 +338,7 @@ occurs, the faster your simulation will run.</li>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -346,7 +346,7 @@ storage by a single MPI process.</li>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -367,7 +367,7 @@ storage by a single MPI process.</li>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -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
LAMMPS web site for performance of the USER-INTEL package on different
hardware.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Setting core affinity is often used to pin MPI tasks
and OpenMP threads to a core or group of cores so that memory access
can be uniform. Unless disabled at build time, affinity for MPI tasks
and OpenMP threads on the host (CPU) will be set by default on the
host when using offload to a coprocessor. In this case, it is
unnecessary to use other methods to control affinity (e.g. taskset,
numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input
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
(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your
Makefile). Disabling this option is not recommended, especially when
running on a machine with hyperthreading disabled.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Setting core affinity is often used to pin MPI tasks and OpenMP
threads to a core or group of cores so that memory access can be
uniform. Unless disabled at build time, affinity for MPI tasks and
OpenMP threads on the host (CPU) will be set by default on the host
when using offload to a coprocessor. In this case, it is unnecessary
to use other methods to control affinity (e.g. taskset, numactl,
I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input 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 (by adding
-DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
Disabling this option is not recommended, especially when running on a
machine with hyperthreading disabled.</p>
</div>
<p><strong>Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:</strong></p>
@ -406,7 +407,7 @@ supported.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -427,7 +428,7 @@ supported.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
hardware.
IMPORTANT NOTE: Setting core affinity is often used to pin MPI tasks
and OpenMP threads to a core or group of cores so that memory access
can be uniform. Unless disabled at build time, affinity for MPI tasks
and OpenMP threads on the host (CPU) will be set by default on the
host when using offload to a coprocessor. In this case, it is
unnecessary to use other methods to control affinity (e.g. taskset,
numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input
script with the {no_affinity} option to the "package
intel"_package.html command or by disabling the option at build time
(by adding -DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your
Makefile). Disabling this option is not recommended, especially when
running on a machine with hyperthreading disabled.
NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP
threads to a core or group of cores so that memory access can be
uniform. Unless disabled at build time, affinity for MPI tasks and
OpenMP threads on the host (CPU) will be set by default on the host
when using offload to a coprocessor. In this case, it is unnecessary
to use other methods to control affinity (e.g. taskset, numactl,
I_MPI_PIN_DOMAIN, etc.). This can be disabled in an input script with
the {no_affinity} option to the "package intel"_package.html command
or by disabling the option at build time (by adding
-DINTEL_OFFLOAD_NOAFFINITY to the CCFLAGS line of your Makefile).
Disabling this option is not recommended, especially when running on a
machine with hyperthreading disabled.
[Guidelines for best performance on an Intel(R) Xeon Phi(TM)
coprocessor:]

80
doc/accelerate_kokkos.html
View File

@ -8,7 +8,7 @@
<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>
@ -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
<a class="reference internal" href="accelerate_gpu.html"><em>GPU</em></a> packages for details of how to check and do
this.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For good performance of the KOKKOS package on GPUs,
you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For good performance of the KOKKOS package on GPUs, you must
have Kepler generation GPUs (or later). The Kokkos library exploits
texture cache options not supported by Telsa generation GPUs (or
older).</p>
</div>
<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;
@ -272,14 +272,13 @@ make cuda KOKKOS_DEVICES=Cuda
<p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try
&#8220;gmake&#8221; if your system&#8217;s standard make complains.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the <em>same</em> target,
e.g. g++ in the first two examples above, then you <em>must</em> perform a
&#8220;make clean-all&#8221; or &#8220;make clean-machine&#8221; before each build. This is
to force all the KOKKOS-dependent files to be re-compiled with the new
options.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you build using make line variables and re-build LAMMPS twice
with different KOKKOS options and the <em>same</em> target, e.g. g++ in the
first two examples above, then you <em>must</em> perform a &#8220;make clean-all&#8221;
or &#8220;make clean-machine&#8221; before each build. This is to force all the
KOKKOS-dependent files to be re-compiled with the new options.</p>
</div>
<p>You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
@ -291,23 +290,22 @@ with a line like:</p>
different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a &#8220;clean&#8221; in between. This is
because the targets will be different.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The 3rd example above for a GPU, uses a different
machine makefile, in this case src/MAKE/Makefile.cuda, which is
included in the LAMMPS distribution. To build the KOKKOS package for
a GPU, this makefile must use the NVIDA &#8220;nvcc&#8221; compiler. And it must
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA
hardware and installed software. Typical values for KOKKOS_ARCH are given
below, as well
as other settings that must be included in the machine makefile, if
you create your own.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The 3rd example above for a GPU, uses a different machine
makefile, in this case src/MAKE/Makefile.cuda, which is included in
the LAMMPS distribution. To build the KOKKOS package for a GPU, this
makefile must use the NVIDA &#8220;nvcc&#8221; compiler. And it must have a
KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and
installed software. Typical values for KOKKOS_ARCH are given below,
as well as other settings that must be included in the machine
makefile, if you create your own.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Currently, there are no precision options with the
KOKKOS package. All compilation and computation is performed in
double precision.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently, there are no precision options with the KOKKOS
package. All compilation and computation is performed in double
precision.</p>
</div>
<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
@ -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
2nd socket to the GPU.</p>
<p>Examples of mpirun commands that follow these rules are shown above.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">When using a GPU, you will achieve the best
performance if your input script does not use any fix or compute
styles which are not yet Kokkos-enabled. This allows data to stay on
the GPU for multiple timesteps, without being copied back to the host
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using a GPU, you will achieve the best performance if your
input script does not use any fix or compute styles which are not yet
Kokkos-enabled. This allows data to stay on the GPU for multiple
timesteps, without being copied back to the host CPU. Invoking a
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
to be copied back to the CPU.</p>
</div>
@ -567,7 +565,7 @@ change in the future.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -588,7 +586,7 @@ change in the future.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

52
doc/accelerate_kokkos.txt
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@ -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
this.
IMPORTANT NOTE: For good performance of the KOKKOS package on GPUs,
you must have Kepler generation GPUs (or later). The Kokkos library
exploits texture cache options not supported by Telsa generation GPUs
(or older).
NOTE: For good performance of the KOKKOS package on GPUs, you must
have Kepler generation GPUs (or later). The Kokkos library exploits
texture cache options not supported by Telsa generation GPUs (or
older).
To build with Kokkos support for Intel Xeon Phi coprocessors, your
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
"gmake" if your system's standard make complains.
IMPORTANT NOTE: If you build using make line variables and re-build
LAMMPS twice with different KOKKOS options and the *same* target,
e.g. g++ in the first two examples above, then you *must* perform a
"make clean-all" or "make clean-machine" before each build. This is
to force all the KOKKOS-dependent files to be re-compiled with the new
options.
NOTE: If you build using make line variables and re-build LAMMPS twice
with different KOKKOS options and the *same* target, e.g. g++ in the
first two examples above, then you *must* perform a "make clean-all"
or "make clean-machine" before each build. This is to force all the
KOKKOS-dependent files to be re-compiled with the new options.
You can also hardwire these make variables in the specified machine
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
because the targets will be different.
IMPORTANT NOTE: The 3rd example above for a GPU, uses a different
machine makefile, in this case src/MAKE/Makefile.cuda, which is
included in the LAMMPS distribution. To build the KOKKOS package for
a GPU, this makefile must use the NVIDA "nvcc" compiler. And it must
have a KOKKOS_ARCH setting that is appropriate for your NVIDIA
hardware and installed software. Typical values for KOKKOS_ARCH are given
below, as well
as other settings that must be included in the machine makefile, if
you create your own.
NOTE: The 3rd example above for a GPU, uses a different machine
makefile, in this case src/MAKE/Makefile.cuda, which is included in
the LAMMPS distribution. To build the KOKKOS package for a GPU, this
makefile must use the NVIDA "nvcc" compiler. And it must have a
KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and
installed software. Typical values for KOKKOS_ARCH are given below,
as well as other settings that must be included in the machine
makefile, if you create your own.
IMPORTANT NOTE: Currently, there are no precision options with the
KOKKOS package. All compilation and computation is performed in
double precision.
NOTE: Currently, there are no precision options with the KOKKOS
package. All compilation and computation is performed in double
precision.
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
@ -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.
IMPORTANT NOTE: When using a GPU, you will achieve the best
performance if your input script does not use any fix or compute
styles which are not yet Kokkos-enabled. This allows data to stay on
the GPU for multiple timesteps, without being copied back to the host
CPU. Invoking a non-Kokkos fix or compute, or performing I/O for
NOTE: When using a GPU, you will achieve the best performance if your
input script does not use any fix or compute styles which are not yet
Kokkos-enabled. This allows data to stay on the GPU for multiple
timesteps, without being copied back to the host CPU. Invoking a
non-Kokkos fix or compute, or performing I/O for
"thermo"_thermo_style.html or "dump"_dump.html output will cause data
to be copied back to the CPU.

19
doc/accelerate_omp.html
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@ -8,7 +8,7 @@
<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>
@ -260,12 +260,11 @@ when there is at least one MPI task per physical CPU chip, i.e. socket
or die.</li>
<li>It is usually most efficient to restrict threading to a single
socket, i.e. use one or more MPI task per socket.</li>
<li>IMPORTANT NOTE: By default, several current MPI implementations use a
processor affinity setting that restricts each MPI task to a single
CPU core. Using multi-threading in this mode will force all threads
to share the one core and thus is likely to be counterproductive.
Instead, binding MPI tasks to a (multi-core) socket, should solve this
issue.</li>
<li>NOTE: By default, several current MPI implementations use a processor
affinity setting that restricts each MPI task to a single CPU core.
Using multi-threading in this mode will force all threads to share the
one core and thus is likely to be counterproductive. Instead, binding
MPI tasks to a (multi-core) socket, should solve this issue.</li>
</ul>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
@ -283,7 +282,7 @@ issue.</li>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -304,7 +303,7 @@ issue.</li>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
socket, i.e. use one or more MPI task per socket. :l
IMPORTANT NOTE: By default, several current MPI implementations use a
processor affinity setting that restricts each MPI task to a single
CPU core. Using multi-threading in this mode will force all threads
to share the one core and thus is likely to be counterproductive.
Instead, binding MPI tasks to a (multi-core) socket, should solve this
issue. :l,ule
NOTE: By default, several current MPI implementations use a processor
affinity setting that restricts each MPI task to a single CPU core.
Using multi-threading in this mode will force all threads to share the
one core and thus is likely to be counterproductive. Instead, binding
MPI tasks to a (multi-core) socket, should solve this issue. :l,ule
[Restrictions:]

8
doc/accelerate_opt.html
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@ -8,7 +8,7 @@
<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>
@ -184,7 +184,7 @@ of a run. On most machines for reasonable problem sizes, it will be a
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -205,7 +205,7 @@ of a run. On most machines for reasonable problem sizes, it will be a
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_charmm.html
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@ -8,7 +8,7 @@
<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>
@ -209,7 +209,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -230,7 +230,7 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -236,7 +236,7 @@ for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -257,7 +257,7 @@ for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_coeff.html
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@ -8,7 +8,7 @@
<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>
@ -224,7 +224,7 @@ set, either in the input script or in a data file.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -245,7 +245,7 @@ set, either in the input script or in a data file.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_cosine.html
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@ -8,7 +8,7 @@
<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>
@ -194,7 +194,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -215,7 +215,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_cosine_delta.html
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@ -8,7 +8,7 @@
<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>
@ -198,7 +198,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_cosine_periodic.html
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@ -8,7 +8,7 @@
<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>
@ -208,7 +208,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -229,7 +229,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_cosine_shift.html
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@ -8,7 +8,7 @@
<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>
@ -199,7 +199,7 @@ section for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -220,7 +220,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_cosine_shift_exp.html
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@ -8,7 +8,7 @@
<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>
@ -210,7 +210,7 @@ section for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -231,7 +231,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_cosine_squared.html
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@ -8,7 +8,7 @@
<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>
@ -198,7 +198,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -219,7 +219,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

30
doc/angle_dipole.html
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@ -8,7 +8,7 @@
<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>
@ -159,7 +159,7 @@ and the reference (bond) vector r_ij:</p>
angle.</p>
<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
<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" />
<p>Example: if gamma0 is set to 0 degrees, the torque generated by
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
USER-MISC package. See the <span class="xref std std-ref">Making LAMMPS</span>
section for more info on packages.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">In the &#8220;Angles&#8221; section of the data file, the atom ID
&#8216;j&#8217; corresponding to the dipole to restrain must come before the atom
ID of the reference atom &#8216;i&#8217;. A third atom ID &#8216;k&#8217; must also be
provided, although &#8216;k&#8217; is just a &#8216;dummy&#8217; atom which can be any atom;
it may be useful to choose a convention (e.g., &#8216;k&#8217;=&#8217;i&#8217;) and adhere to
it. For example, if ID=1 for the dipolar atom to restrain, and ID=2
for the reference atom, the corresponding line in the &#8220;Angles&#8221; section
of the data file would read: X X 1 2 2</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">In the &#8220;Angles&#8221; section of the data file, the atom ID &#8216;j&#8217;
corresponding to the dipole to restrain must come before the atom ID
of the reference atom &#8216;i&#8217;. A third atom ID &#8216;k&#8217; must also be provided,
although &#8216;k&#8217; is just a &#8216;dummy&#8217; atom which can be any atom; it may be
useful to choose a convention (e.g., &#8216;k&#8217;=&#8217;i&#8217;) and adhere to it. For
example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
reference atom, the corresponding line in the &#8220;Angles&#8221; section of the
data file would read: X X 1 2 2</p>
</div>
<p>The &#8220;newton&#8221; command for intramolecular interactions must be &#8220;on&#8221;
(which is the default).</p>
@ -237,7 +237,7 @@ Clarendon Press, Oxford, 1987.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
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@ -258,7 +258,7 @@ Clarendon Press, Oxford, 1987.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

16
doc/angle_dipole.txt
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@ -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
section for more info on packages.
IMPORTANT NOTE: In the "Angles" section of the data file, the atom ID
'j' corresponding to the dipole to restrain must come before the atom
ID of the reference atom 'i'. A third atom ID 'k' must also be
provided, although 'k' is just a 'dummy' atom which can be any atom;
it may be useful to choose a convention (e.g., 'k'='i') and adhere to
it. For example, if ID=1 for the dipolar atom to restrain, and ID=2
for the reference atom, the corresponding line in the "Angles" section
of the data file would read: X X 1 2 2
NOTE: In the "Angles" section of the data file, the atom ID 'j'
corresponding to the dipole to restrain must come before the atom ID
of the reference atom 'i'. A third atom ID 'k' must also be provided,
although 'k' is just a 'dummy' atom which can be any atom; it may be
useful to choose a convention (e.g., 'k'='i') and adhere to it. For
example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
reference atom, the corresponding line in the "Angles" section of the
data file would read: X X 1 2 2
The "newton" command for intramolecular interactions must be "on"
(which is the default).

8
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@ -8,7 +8,7 @@
<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>
@ -195,7 +195,7 @@ section for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -216,7 +216,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_fourier_simple.html
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@ -8,7 +8,7 @@
<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>
@ -194,7 +194,7 @@ section for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -215,7 +215,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_harmonic.html
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@ -8,7 +8,7 @@
<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>
@ -203,7 +203,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -224,7 +224,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_hybrid.html
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@ -8,7 +8,7 @@
<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>
@ -219,7 +219,7 @@ file, you need to re-specify angle_coeff commands.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -240,7 +240,7 @@ file, you need to re-specify angle_coeff commands.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_none.html
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@ -8,7 +8,7 @@
<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>
@ -163,7 +163,7 @@ if triplets of angle atoms were listed in the data file read by the
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -184,7 +184,7 @@ if triplets of angle atoms were listed in the data file read by the
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_quartic.html
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@ -8,7 +8,7 @@
<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>
@ -201,7 +201,7 @@ section for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -222,7 +222,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/angle_sdk.html
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@ -8,7 +8,7 @@
<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>
@ -187,7 +187,7 @@ USER-CG-CMM package. See the <a class="reference internal" href="Section_start.
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -208,7 +208,7 @@ USER-CG-CMM package. See the <a class="reference internal" href="Section_start.
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

12
doc/angle_style.html
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@ -8,7 +8,7 @@
<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>
@ -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
angle_style <em>hybrid</em> only stores the list of sub-styles in the restart
file; angle coefficients need to be re-specified.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<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
turn off (or weight) the pairwise interaction that would otherwise
@ -222,7 +222,7 @@ package.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -243,7 +243,7 @@ package.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
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
turn off (or weight) the pairwise interaction that would otherwise
exist between 3 bonded atoms.

8
doc/angle_table.html
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@ -8,7 +8,7 @@
<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>
@ -272,7 +272,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -293,7 +293,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

16
doc/atom_modify.html
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@ -8,7 +8,7 @@
<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>
@ -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
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Running a simulation with sorting on versus off should
not change the simulation results in a statistical sense. However, a
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations.
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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -309,7 +309,7 @@ cutoff will be used to set the bin size.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
cache locality will be undermined.
IMPORTANT NOTE: Running a simulation with sorting on versus off should
not change the simulation results in a statistical sense. However, a
NOTE: Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations.
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">
<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>
@ -263,10 +263,10 @@ quantities.</p>
</tr>
</tbody>
</table>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is possible to add some attributes, such as a
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
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It is possible to add some attributes, such as a 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
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
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
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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<div class="admonition note">
<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
insure the atom types, bond types, angle_types, etc in all the
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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -448,7 +448,7 @@ only enabled if LAMMPS was built with that package. See the <a class="reference
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

6
doc/atom_style.txt
View File

@ -83,8 +83,8 @@ quantities.
{tri} | corner points, angular momentum | rigid bodies |
{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
molecule ID, to atom styles that do not have them via the "fix
NOTE: It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the "fix
property/atom"_fix_property_atom.html command. This command also
allows new custom attributes consisting of extra integer or
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
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
insure the atom types, bond types, angle_types, etc in all the
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">
<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>
@ -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
forced even if the current balance is perfect (1.0) be specifying a
<em>thresh</em> &lt; 1.0.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Balancing is performed even if the imbalance factor
does not exceed the <em>thresh</em> parameter if a &#8220;grid&#8221; style is specified
when the current partitioning is &#8220;tiled&#8221;. The meaning of &#8220;grid&#8221; vs
&#8220;tiled&#8221; is explained below. This is to allow forcing of the
partitioning to &#8220;grid&#8221; so that the <a class="reference internal" href="comm_style.html"><em>comm_style brick</em></a>
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>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Balancing is performed even if the imbalance factor does not
exceed the <em>thresh</em> parameter if a &#8220;grid&#8221; style is specified when the
current partitioning is &#8220;tiled&#8221;. The meaning of &#8220;grid&#8221; vs &#8220;tiled&#8221; is
explained below. This is to allow forcing of the partitioning to
&#8220;grid&#8221; so that the <a class="reference internal" href="comm_style.html"><em>comm_style brick</em></a> 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>
</div>
<p>When the balance command completes, it prints statistics about the
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
positions of all cutting planes in each of the 3 dimensions (as
fractions of the box length) are also printed.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">This command attempts to minimize the imbalance
factor, as defined above. But depending on the method a perfect
balance (1.0) may not be achieved. For example, &#8220;grid&#8221; methods
(defined below) that create a logical 3d grid cannot achieve perfect
balance for many irregular distributions of particles. Likewise, if a
portion of the system is a perfect lattice, e.g. the intiial system is
generated by the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, then &#8220;grid&#8221;
methods may be unable to achieve exact balance. This is because
entire lattice planes will be owned or not owned by a single
processor.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This command attempts to minimize the imbalance factor, as
defined above. But depending on the method a perfect balance (1.0)
may not be achieved. For example, &#8220;grid&#8221; methods (defined below) that
create a logical 3d grid cannot achieve perfect balance for many
irregular distributions of particles. Likewise, if a portion of the
system is a perfect lattice, e.g. the intiial system is generated by
the <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a> command, then &#8220;grid&#8221; methods may
be unable to achieve exact balance. This is because entire lattice
planes will be owned or not owned by a single processor.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The imbalance factor is also an estimate of the
maximum speed-up you can hope to achieve by running a perfectly
balanced simulation versus an imbalanced one. In the example above,
the 10000 particle simulation could run up to 20% faster if it were
perfectly balanced, versus when imbalanced. However, computational
cost is not strictly proportional to particle count, and changing the
relative size and shape of processor sub-domains may lead to
additional computational and communication overheads, e.g. in the PPPM
solver used via the <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Thus
you should benchmark the run times of a simulation before and after
balancing.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The imbalance factor is also an estimate of the maximum speed-up
you can hope to achieve by running a perfectly balanced simulation
versus an imbalanced one. In the example above, the 10000 particle
simulation could run up to 20% faster if it were perfectly balanced,
versus when imbalanced. However, computational cost is not strictly
proportional to particle count, and changing the relative size and
shape of processor sub-domains may lead to additional computational
and communication overheads, e.g. in the PPPM solver used via the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> command. Thus you should benchmark
the run times of a simulation before and after balancing.</p>
</div>
<hr class="docutils" />
<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
assigned, particles are migrated to their new owning processor, and
the balance procedure ends.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">At each rebalance operation, the bisectioning for each
cutting plane (line in 2d) typcially starts with low and high bounds
separated by the extent of a processor&#8217;s sub-domain in one dimension.
The size of this bracketing region shrinks by 1/2 every iteration.
Thus if <em>Niter</em> is specified as 10, the cutting plane will typically
be positioned to 1 part in 1000 accuracy (relative to the perfect
target position). For <em>Niter</em> = 20, it will be accurate to 1 part in
a million. Thus there is no need ot set <em>Niter</em> to a large value.
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">At each rebalance operation, the bisectioning for each cutting
plane (line in 2d) typcially starts with low and high bounds separated
by the extent of a processor&#8217;s sub-domain in one dimension. The size
of this bracketing region shrinks by 1/2 every iteration. Thus if
<em>Niter</em> is specified as 10, the cutting plane will typically be
positioned to 1 part in 1000 accuracy (relative to the perfect target
position). For <em>Niter</em> = 20, it will be accurate to 1 part in a
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
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
@ -488,7 +487,7 @@ appear in <em>dimstr</em> for the <em>shift</em> style.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -509,7 +508,7 @@ appear in <em>dimstr</em> for the <em>shift</em> style.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
{thresh} < 1.0.
IMPORTANT NOTE: Balancing is performed even if the imbalance factor
does not exceed the {thresh} parameter if a "grid" style is specified
when the current partitioning is "tiled". The meaning of "grid" vs
"tiled" is explained below. This is to allow forcing of the
partitioning to "grid" so that the "comm_style brick"_comm_style.html
command can then be used to replace a current "comm_style
tiled"_comm_style.html setting.
NOTE: Balancing is performed even if the imbalance factor does not
exceed the {thresh} parameter if a "grid" style is specified when the
current partitioning is "tiled". The meaning of "grid" vs "tiled" is
explained below. This is to allow forcing of the partitioning to
"grid" so that the "comm_style brick"_comm_style.html command can then
be used to replace a current "comm_style tiled"_comm_style.html
setting.
When the balance command completes, it prints statistics about the
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
fractions of the box length) are also printed.
IMPORTANT NOTE: This command attempts to minimize the imbalance
factor, as defined above. But depending on the method a perfect
balance (1.0) may not be achieved. For example, "grid" methods
(defined below) that create a logical 3d grid cannot achieve perfect
balance for many irregular distributions of particles. Likewise, if a
portion of the system is a perfect lattice, e.g. the intiial system is
generated by the "create_atoms"_create_atoms.html command, then "grid"
methods may be unable to achieve exact balance. This is because
entire lattice planes will be owned or not owned by a single
processor.
NOTE: This command attempts to minimize the imbalance factor, as
defined above. But depending on the method a perfect balance (1.0)
may not be achieved. For example, "grid" methods (defined below) that
create a logical 3d grid cannot achieve perfect balance for many
irregular distributions of particles. Likewise, if a portion of the
system is a perfect lattice, e.g. the intiial system is generated by
the "create_atoms"_create_atoms.html command, then "grid" methods may
be unable to achieve exact balance. This is because entire lattice
planes will be owned or not owned by a single processor.
IMPORTANT NOTE: The imbalance factor is also an estimate of the
maximum speed-up you can hope to achieve by running a perfectly
balanced simulation versus an imbalanced one. In the example above,
the 10000 particle simulation could run up to 20% faster if it were
perfectly balanced, versus when imbalanced. However, computational
cost is not strictly proportional to particle count, and changing the
relative size and shape of processor sub-domains may lead to
additional computational and communication overheads, e.g. in the PPPM
solver used via the "kspace_style"_kspace_style.html command. Thus
you should benchmark the run times of a simulation before and after
balancing.
NOTE: The imbalance factor is also an estimate of the maximum speed-up
you can hope to achieve by running a perfectly balanced simulation
versus an imbalanced one. In the example above, the 10000 particle
simulation could run up to 20% faster if it were perfectly balanced,
versus when imbalanced. However, computational cost is not strictly
proportional to particle count, and changing the relative size and
shape of processor sub-domains may lead to additional computational
and communication overheads, e.g. in the PPPM solver used via the
"kspace_style"_kspace_style.html command. Thus you should benchmark
the run times of a simulation before and after balancing.
: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
the balance procedure ends.
IMPORTANT NOTE: At each rebalance operation, the bisectioning for each
cutting plane (line in 2d) typcially starts with low and high bounds
separated by the extent of a processor's sub-domain in one dimension.
The size of this bracketing region shrinks by 1/2 every iteration.
Thus if {Niter} is specified as 10, the cutting plane will typically
be positioned to 1 part in 1000 accuracy (relative to the perfect
target position). For {Niter} = 20, it will be accurate to 1 part in
a million. Thus there is no need ot set {Niter} to a large value.
NOTE: At each rebalance operation, the bisectioning for each cutting
plane (line in 2d) typcially starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks by 1/2 every iteration. Thus if
{Niter} is specified as 10, the cutting plane will typically be
positioned to 1 part in 1000 accuracy (relative to the perfect target
position). For {Niter} = 20, it will be accurate to 1 part in a
million. Thus there is no need ot set {Niter} to a large value.
LAMMPS will check if the threshold accuracy is reached (in a
dimension) is less iterations than {Niter} and exit early. However,
{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">
<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>
@ -282,7 +282,7 @@ current COM and orientiation of the body particle.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -303,7 +303,7 @@ current COM and orientiation of the body particle.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -201,7 +201,7 @@ for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -222,7 +222,7 @@ for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -221,7 +221,7 @@ either in the input script or in a data file.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -242,7 +242,7 @@ either in the input script or in a data file.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -209,7 +209,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -230,7 +230,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -210,7 +210,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -231,7 +231,7 @@ style. LAMMPS will issue a warning it that&#8217;s not the case.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -199,7 +199,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -220,7 +220,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -201,7 +201,7 @@ section for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -222,7 +222,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -202,7 +202,7 @@ section for more info on packages.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -223,7 +223,7 @@ section for more info on packages.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -202,7 +202,7 @@ file, you need to re-specify bond_coeff commands.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -223,7 +223,7 @@ file, you need to re-specify bond_coeff commands.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -197,7 +197,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -218,7 +218,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -163,7 +163,7 @@ pairs of bonded atoms were listed in the data file read by the
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -184,7 +184,7 @@ pairs of bonded atoms were listed in the data file read by the
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -199,7 +199,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -220,7 +220,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -231,7 +231,7 @@ dihedral, etc) cannot be used with <em>quartic</em> bonds.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -252,7 +252,7 @@ dihedral, etc) cannot be used with <em>quartic</em> bonds.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -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
<em>hybrid</em> only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<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
turn off (or weight) the pairwise interaction that would otherwise
@ -230,7 +230,7 @@ package.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -251,7 +251,7 @@ package.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
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
turn off (or weight) the pairwise interaction that would otherwise
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">
<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>
@ -269,7 +269,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -290,7 +290,7 @@ MOLECULE package (which it is by default). See the <a class="reference internal
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/boundary.html
View File

@ -8,7 +8,7 @@
<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>
@ -227,7 +227,7 @@ of lost atoms.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -248,7 +248,7 @@ of lost atoms.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/box.html
View File

@ -8,7 +8,7 @@
<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>
@ -191,7 +191,7 @@ error.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -212,7 +212,7 @@ error.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -214,13 +214,16 @@ current one.</p>
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
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
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
completes. Instead you could do something like this, assuming the
simulation box is non-periodic and atoms extend from 0 to 20 in all
dimensions:</p>
</div>
<div class="highlight-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
</pre></div>
@ -230,45 +233,45 @@ create_atoms 1 single -5 5 5
change_box boundary s s s # this will work
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this
command, atom remapping is NOT performed by default. This command
allows remapping to be done in a more general way, exactly when you
specify it (zero or more times) in the sequence of transformations.
Thus if you do not use the <em>remap</em> keyword, atom coordinates will not
be changed even if the box size/shape changes. If a uniformly
strained state is desired, the <em>remap</em> keyword should be specified.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this command, atom
remapping is NOT performed by default. This command allows remapping
to be done in a more general way, exactly when you specify it (zero or
more times) in the sequence of transformations. Thus if you do not
use the <em>remap</em> keyword, atom coordinates will not be changed even if
the box size/shape changes. If a uniformly strained state is desired,
the <em>remap</em> keyword should be specified.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is possible to lose atoms with this command.
E.g. by changing the box without remapping the atoms, and having atoms
end up outside of non-periodic boundaries. It is also possible to
alter bonds between atoms straddling a boundary in bad ways. E.g. by
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It is possible to lose atoms with this command. E.g. by
changing the box without remapping the atoms, and having atoms end up
outside of non-periodic boundaries. It is also possible to alter
bonds between atoms straddling a boundary in bad ways. E.g. by
converting a boundary from periodic to non-periodic. It is also
possible when remapping atoms to put them (nearly) on top of each
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
messages.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The simulation box size/shape can be changed by
arbitrarily large amounts by this command. This is not a problem,
except that the mapping of processors to the simulation box is not
changed from its initial 3d configuration; see the
<a class="reference internal" href="processors.html"><em>processors</em></a> command. Thus, if the box size/shape
changes dramatically, the mapping of processors to the simulation box
may not end up as optimal as the initial mapping attempted to be.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The simulation box size/shape can be changed by arbitrarily
large amounts by this command. This is not a problem, except that the
mapping of processors to the simulation box is not changed from its
initial 3d configuration; see the <a class="reference internal" href="processors.html"><em>processors</em></a>
command. Thus, if the box size/shape changes dramatically, the
mapping of processors to the simulation box may not end up as optimal
as the initial mapping attempted to be.</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Because the keywords used in this command are applied
one at a time to the simulation box and the atoms in it, care must be
taken with triclinic cells to avoid exceeding the limits on skew after
each transformation in the sequence. If skew is exceeded before the
final transformation this can be avoided by changing the order of the
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Because the keywords used in this command are applied one at a
time to the simulation box and the atoms in it, care must be taken
with triclinic cells to avoid exceeding the limits on skew after each
transformation in the sequence. If skew is exceeded before the final
transformation this can be avoided by changing the order of the
sequence, or breaking the transformation into two or more smaller
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>
@ -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
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">For solids or liquids, when one dimension of the box
is expanded, it may be physically undesirable to hold the other 2 box
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For solids or liquids, when one dimension of the box is
expanded, it may be physically undesirable to hold the other 2 box
lengths constant since that implies a density change. For solids,
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
@ -443,7 +446,7 @@ change_box command is issued, so long as an <a class="reference internal" href="
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -464,7 +467,7 @@ change_box command is issued, so long as an <a class="reference internal" href="
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
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
atoms via the "create_atoms"_create_atoms.html command, because the
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
change_box boundary s s s # this will work :pre
IMPORTANT NOTE: Unlike the earlier "displace_box" version of this
command, atom remapping is NOT performed by default. This command
allows remapping to be done in a more general way, exactly when you
specify it (zero or more times) in the sequence of transformations.
Thus if you do not use the {remap} keyword, atom coordinates will not
be changed even if the box size/shape changes. If a uniformly
strained state is desired, the {remap} keyword should be specified.
NOTE: Unlike the earlier "displace_box" version of this command, atom
remapping is NOT performed by default. This command allows remapping
to be done in a more general way, exactly when you specify it (zero or
more times) in the sequence of transformations. Thus if you do not
use the {remap} keyword, atom coordinates will not be changed even if
the box size/shape changes. If a uniformly strained state is desired,
the {remap} keyword should be specified.
IMPORTANT NOTE: It is possible to lose atoms with this command.
E.g. by changing the box without remapping the atoms, and having atoms
end up outside of non-periodic boundaries. It is also possible to
alter bonds between atoms straddling a boundary in bad ways. E.g. by
NOTE: It is possible to lose atoms with this command. E.g. by
changing the box without remapping the atoms, and having atoms end up
outside of non-periodic boundaries. It is also possible to alter
bonds between atoms straddling a boundary in bad ways. E.g. by
converting a boundary from periodic to non-periodic. It is also
possible when remapping atoms to put them (nearly) on top of each
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
messages.
IMPORTANT NOTE: The simulation box size/shape can be changed by
arbitrarily large amounts by this command. This is not a problem,
except that the mapping of processors to the simulation box is not
changed from its initial 3d configuration; see the
"processors"_processors.html command. Thus, if the box size/shape
changes dramatically, the mapping of processors to the simulation box
may not end up as optimal as the initial mapping attempted to be.
NOTE: The simulation box size/shape can be changed by arbitrarily
large amounts by this command. This is not a problem, except that the
mapping of processors to the simulation box is not changed from its
initial 3d configuration; see the "processors"_processors.html
command. Thus, if the box size/shape changes dramatically, the
mapping of processors to the simulation box may not end up as optimal
as the initial mapping attempted to be.
IMPORTANT NOTE: Because the keywords used in this command are applied
one at a time to the simulation box and the atoms in it, care must be
taken with triclinic cells to avoid exceeding the limits on skew after
each transformation in the sequence. If skew is exceeded before the
final transformation this can be avoided by changing the order of the
NOTE: Because the keywords used in this command are applied one at a
time to the simulation box and the atoms in it, care must be taken
with triclinic cells to avoid exceeding the limits on skew after each
transformation in the sequence. If skew is exceeded before the final
transformation this can be avoided by changing the order of the
sequence, or breaking the transformation into two or more smaller
transformations. For more information on the allowed limits for box
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
IMPORTANT NOTE: For solids or liquids, when one dimension of the box
is expanded, it may be physically undesirable to hold the other 2 box
NOTE: For solids or liquids, when one dimension of the box is
expanded, it may be physically undesirable to hold the other 2 box
lengths constant since that implies a density change. For solids,
adjusting the other dimensions via the {volume} style may make
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">
<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>
@ -171,7 +171,7 @@ input script variables (<a class="reference internal" href="variable.html"><em>v
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -192,7 +192,7 @@ input script variables (<a class="reference internal" href="variable.html"><em>v
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -162,14 +162,14 @@ comm_modify cutoff/multi * 0.0
communication of atom information that occurs each timestep as
coordinates and other properties are exchanged between neighboring
processors and stored as properties of ghost atoms.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">These options apply to the currently defined comm
style. When you specify a <a class="reference internal" href="comm_style.html"><em>comm_style</em></a> command, all
communication settings are restored to their default values, including
those previously reset by a comm_modify command. Thus if your input
script specifies a comm_style command, you should use the comm_modify
command after it.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">These options apply to the currently defined comm style. When
you specify a <a class="reference internal" href="comm_style.html"><em>comm_style</em></a> command, all communication
settings are restored to their default values, including those
previously reset by a comm_modify command. Thus if your input script
specifies a comm_style command, you should use the comm_modify command
after it.</p>
</div>
<p>The <em>mode</em> keyword determines whether a single or multiple cutoff
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
potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">In these scenarios, if you do not set the ghost cutoff
long enough, and if there is only one processor in a periodic
dimension (e.g. you are running in serial), then LAMMPS may &#8220;find&#8221; the
atom it is looking for (e.g. the partner atom in a bond), that is on
the far side of the simulation box, across a periodic boundary. This
will typically lead to bad dynamics (i.e. the bond length is now the
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">In these scenarios, if you do not set the ghost cutoff long
enough, and if there is only one processor in a periodic dimension
(e.g. you are running in serial), then LAMMPS may &#8220;find&#8221; the atom it
is looking for (e.g. the partner atom in a bond), that is on the far
side of the simulation box, across a periodic boundary. This will
typically lead to bad dynamics (i.e. the bond length is now 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>
</div>
@ -286,7 +286,7 @@ cutoff = pairwise force cutoff + neighbor skin.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -307,7 +307,7 @@ cutoff = pairwise force cutoff + neighbor skin.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
processors and stored as properties of ghost atoms.
IMPORTANT NOTE: These options apply to the currently defined comm
style. When you specify a "comm_style"_comm_style.html command, all
communication settings are restored to their default values, including
those previously reset by a comm_modify command. Thus if your input
script specifies a comm_style command, you should use the comm_modify
command after it.
NOTE: These options apply to the currently defined comm style. When
you specify a "comm_style"_comm_style.html command, all communication
settings are restored to their default values, including those
previously reset by a comm_modify command. Thus if your input script
specifies a comm_style command, you should use the comm_modify command
after it.
The {mode} keyword determines whether a single or multiple cutoff
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
find the needed atoms.
IMPORTANT NOTE: In these scenarios, if you do not set the ghost cutoff
long enough, and if there is only one processor in a periodic
dimension (e.g. you are running in serial), then LAMMPS may "find" the
atom it is looking for (e.g. the partner atom in a bond), that is on
the far side of the simulation box, across a periodic boundary. This
will typically lead to bad dynamics (i.e. the bond length is now the
NOTE: In these scenarios, if you do not set the ghost cutoff long
enough, and if there is only one processor in a periodic dimension
(e.g. you are running in serial), then LAMMPS may "find" the atom it
is looking for (e.g. the partner atom in a bond), that is on the far
side of the simulation box, across a periodic boundary. This will
typically lead to bad dynamics (i.e. the bond length is now the
simulation box length). To detect if this is happening, see the
"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">
<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>
@ -196,7 +196,7 @@ commands. The decomposition can be changed via the
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -217,7 +217,7 @@ commands. The decomposition can be changed via the
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/compute.html
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@ -8,7 +8,7 @@
<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>
@ -374,7 +374,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -395,7 +395,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/compute_ackland_atom.html
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@ -8,7 +8,7 @@
<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>
@ -197,7 +197,7 @@ integers defined above.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -218,7 +218,7 @@ integers defined above.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

8
doc/compute_angle_local.html
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@ -8,7 +8,7 @@
<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>
@ -205,7 +205,7 @@ be in energy <a class="reference internal" href="units.html"><em>units</em></a>.
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -226,7 +226,7 @@ be in energy <a class="reference internal" href="units.html"><em>units</em></a>.
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

24
doc/compute_angmom_chunk.html
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@ -8,7 +8,7 @@
<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>
@ -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
&#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s
angular momentum 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
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s angular
momentum 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 for a discussion
of &#8220;unwrapped&#8221; coordinates. See the Atoms section of the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags and
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>
</div>
<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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -236,7 +236,7 @@ mass-velocity-distance <a class="reference internal" href="units.html"><em>units
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
non-zero chunk IDs.
IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's
angular momentum in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the "read_data"_read_data.html command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
NOTE: The coordinates of an atom contribute to the chunk's angular
momentum in "unwrapped" form, by using the image flags associated with
each atom. See the "dump custom"_dump.html command for a discussion
of "unwrapped" coordinates. See the Atoms section of the
"read_data"_read_data.html command for a discussion of image flags and
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
image"_set.html command.

8
doc/compute_basal_atom.html
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@ -8,7 +8,7 @@
<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>
@ -195,7 +195,7 @@ well-defined basal plane.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -216,7 +216,7 @@ well-defined basal plane.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -217,7 +217,7 @@ options.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -238,7 +238,7 @@ options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -213,7 +213,7 @@ output for <em>eng</em> will be in energy <a class="reference internal" href="un
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -234,7 +234,7 @@ output for <em>eng</em> will be in energy <a class="reference internal" href="un
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -242,7 +242,7 @@ of 12.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -263,7 +263,7 @@ of 12.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true

49
doc/compute_chunk_atom.html
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@ -8,7 +8,7 @@
<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>
@ -438,13 +438,14 @@ the first step of the time window will persist until the end of the
time window.</p>
<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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you want the persistent chunk-IDs calculated by
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
compute, as in the original run. This is so that the fix this compute
creates to store per-atom quantities will also have the same ID, and
thus be initialized correctly with chunk IDs from the restart file.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you want the persistent chunk-IDs calculated by 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 compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with chunk IDs from the restart file.</p>
</div>
<hr class="docutils" />
<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,
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>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The compression operation requires global
communication across all processors to share their chunk ID values.
It can require large memory on every processor to store them, even
after they are compressed, if there are are a large number of unique
chunk IDs with atoms assigned to them. It uses a STL map to find
unique chunk IDs and store them in sorted order. Each time an atom is
assigned a compressed chunk ID, it must access the STL map. All of
this means that compression can be expensive, both in memory and CPU
time. The use of the <em>limit</em> keyword in conjunction with the
<em>compress</em> keyword can affect these costs, depending on which keyword
is used first. So use this option with care.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The compression operation requires global communication across
all processors to share their chunk ID values. It can require large
memory on every processor to store them, even after they are
compressed, if there are are a large number of unique chunk IDs with
atoms assigned to them. It uses a STL map to find unique chunk IDs
and store them in sorted order. Each time an atom is assigned a
compressed chunk ID, it must access the STL map. All of this means
that compression can be expensive, both in memory and CPU time. The
use of the <em>limit</em> keyword in conjunction with the <em>compress</em> keyword
can affect these costs, depending on which keyword is used first. So
use this option with care.</p>
</div>
<hr class="docutils" />
<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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -634,7 +635,7 @@ the restarted simulation begins.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
re-calculated on any timestep this compute is invoked.
IMPORTANT NOTE: If you want the persistent chunk-IDs calculated by
this compute to be continuous when running from a "restart
file"_read_restart.html, then you should use the same ID for this
compute, as in the original run. This is so that the fix this compute
creates to store per-atom quantities will also have the same ID, and
thus be initialized correctly with chunk IDs from the restart file.
NOTE: If you want the persistent chunk-IDs calculated by this compute
to be continuous when running from a "restart file"_read_restart.html,
then you should use the same ID for this compute, as in the original
run. This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with chunk IDs from the restart file.
:line
@ -424,17 +424,17 @@ or by using the "fix ave/time"_fix_ave_time.html command in
conjunction with the "compute
property/chunk"_compute_property_chunk.html command.
IMPORTANT NOTE: The compression operation requires global
communication across all processors to share their chunk ID values.
It can require large memory on every processor to store them, even
after they are compressed, if there are are a large number of unique
chunk IDs with atoms assigned to them. It uses a STL map to find
unique chunk IDs and store them in sorted order. Each time an atom is
assigned a compressed chunk ID, it must access the STL map. All of
this means that compression can be expensive, both in memory and CPU
time. The use of the {limit} keyword in conjunction with the
{compress} keyword can affect these costs, depending on which keyword
is used first. So use this option with care.
NOTE: The compression operation requires global communication across
all processors to share their chunk ID values. It can require large
memory on every processor to store them, even after they are
compressed, if there are are a large number of unique chunk IDs with
atoms assigned to them. It uses a STL map to find unique chunk IDs
and store them in sorted order. Each time an atom is assigned a
compressed chunk ID, it must access the STL map. All of this means
that compression can be expensive, both in memory and CPU time. The
use of the {limit} keyword in conjunction with the {compress} keyword
can affect these costs, depending on which keyword is used first. So
use this option with care.
:line

12
doc/compute_cluster_atom.html
View File

@ -8,7 +8,7 @@
<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>
@ -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
too frequently or to have multiple compute/dump commands, each of a
<em>clsuter/atom</em> style.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<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
interactions between atoms in the same bond, angle, or dihedral. This
@ -205,7 +205,7 @@ LAMMPS output options.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -226,7 +226,7 @@ LAMMPS output options.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
{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
interactions between atoms in the same bond, angle, or dihedral. This
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">
<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>
@ -217,7 +217,7 @@ above.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -238,7 +238,7 @@ above.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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">
<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>
@ -149,14 +149,14 @@ of atoms, including all effects due to atoms passing thru periodic
boundaries.</p>
<p>A vector of three quantites is calculated by this compute, which
are the x,y,z coordinates of the center of mass.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to the
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
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The coordinates of an atom contribute to the 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 for a discussion of
&#8220;unwrapped&#8221; coordinates. See the Atoms section of the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags and
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>
</div>
<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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -210,7 +210,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
are the x,y,z coordinates of the center of mass.
IMPORTANT NOTE: The coordinates of an atom contribute to the
center-of-mass in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the "read_data"_read_data.html command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
NOTE: The coordinates of an atom contribute to the center-of-mass in
"unwrapped" form, by using the image flags associated with each atom.
See the "dump custom"_dump.html command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
"read_data"_read_data.html command for a discussion of image flags and
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
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">
<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>
@ -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
&#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<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
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">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</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>.
@ -234,7 +234,7 @@ distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
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
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
associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of

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