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Steve Plimpton
2016-09-14 10:22:46 -06:00
parent 717e719b83
commit 2f298951cf
797 changed files with 123225 additions and 4062 deletions
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@ -73,7 +73,8 @@
<ul class="current">
<p class="caption"><span class="caption-text">User Documentation</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
@ -103,6 +104,18 @@
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
<p class="caption"><span class="caption-text">Index</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
</ul>
@ -182,9 +195,9 @@ drive a program through its library interface, or to hook multiple
pieces of software together, such as a simulation package plus a
visualization package, or to run a coupled multiscale or multiphysics
model.</p>
<p>See <a class="reference internal" href="Section_howto.html#howto-10"><span class="std std-ref">Section_howto 10</span></a> of the manual and
<p>See <a class="reference internal" href="Section_howto.html#howto-10"><span class="std std-ref">Section 6.10</span></a> of the manual and
the couple directory of the distribution for more ideas about coupling
LAMMPS to other codes. See <a class="reference internal" href="Section_howto.html#howto-19"><span class="std std-ref">Section_howto 19</span></a> for a description of the LAMMPS
LAMMPS to other codes. See <a class="reference internal" href="Section_howto.html#howto-19"><span class="std std-ref">Section 6.19</span></a> for a description of the LAMMPS
library interface provided in src/library.cpp and src/library.h, and
how to extend it for your needs. As described below, that interface
is what is exposed to Python either when calling LAMMPS from Python or
@ -302,7 +315,7 @@ file and the shared library.</p>
<div class="section" id="building-lammps-as-a-shared-library">
<span id="py-3"></span><h2>11.3. Building LAMMPS as a shared library</h2>
<p>Instructions on how to build LAMMPS as a shared library are given in
<a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a>. A shared library is one
<a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section 2.5</span></a>. A shared library is one
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in &#8221;.so&#8221;, not &#8221;.a&#8221;.</p>
<p>From the src directory, type</p>
@ -321,7 +334,7 @@ most recently built version.</p>
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
<a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a> for more details.</p>
<a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section 2.5</span></a> for more details.</p>
</div>
<hr class="docutils" />
</div>
@ -531,7 +544,7 @@ first importing from the lammps.py file:</p>
<span class="gp">&gt;&gt;&gt; </span><span class="n">CDLL</span><span class="p">(</span><span class="s2">&quot;liblammps.so&quot;</span><span class="p">)</span>
</pre></div>
</div>
<p>If an error occurs, carefully go thru the steps in <a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a> and above about building a shared
<p>If an error occurs, carefully go thru the steps in <a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section 2.5</span></a> and above about building a shared
library and about insuring Python can find the necessary two files
it needs.</p>
<div class="section" id="test-lammps-and-python-in-serial">
@ -762,7 +775,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> of the manual for a
See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section 6.15</span></a> of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
<a class="reference internal" href="compute.html"><span class="doc">computes</span></a> and <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a> for a description of what