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@ -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,
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