git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15492 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>11. Python interface to LAMMPS — LAMMPS documentation</title>
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<title>Python interface to LAMMPS — LAMMPS documentation</title>
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<link rel="top" title="LAMMPS documentation" href="index.html"/>
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<link rel="next" title="12. Errors" href="Section_errors.html"/>
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<link rel="prev" title="10. Modifying & extending LAMMPS" href="Section_modify.html"/>
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<link rel="top" title="LAMMPS documentation" href="index.html"/>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">11. Python interface to LAMMPS</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#overview-of-running-lammps-from-python">11.1. Overview of running LAMMPS from Python</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#overview-of-using-python-from-a-lammps-script">11.2. Overview of using Python from a LAMMPS script</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#building-lammps-as-a-shared-library">11.3. Building LAMMPS as a shared library</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#installing-the-python-wrapper-into-python">11.4. Installing the Python wrapper into Python</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#extending-python-with-mpi-to-run-in-parallel">11.5. Extending Python with MPI to run in parallel</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#testing-the-python-lammps-interface">11.6. Testing the Python-LAMMPS interface</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-serial">11.6.1. <strong>Test LAMMPS and Python in serial:</strong></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#test-lammps-and-python-in-parallel">11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#running-python-scripts">11.6.3. <strong>Running Python scripts:</strong></a></li>
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<!-- Local TOC -->
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<div class="local-toc"><ul>
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<li><a class="reference internal" href="#">Python interface to LAMMPS</a><ul>
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<li><a class="reference internal" href="#overview-of-running-lammps-from-python">Overview of running LAMMPS from Python</a></li>
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<li><a class="reference internal" href="#overview-of-using-python-from-a-lammps-script">Overview of using Python from a LAMMPS script</a></li>
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<li><a class="reference internal" href="#building-lammps-as-a-shared-library">Building LAMMPS as a shared library</a></li>
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<li><a class="reference internal" href="#installing-the-python-wrapper-into-python">Installing the Python wrapper into Python</a></li>
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<li><a class="reference internal" href="#extending-python-with-mpi-to-run-in-parallel">Extending Python with MPI to run in parallel</a></li>
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<li><a class="reference internal" href="#testing-the-python-lammps-interface">Testing the Python-LAMMPS interface</a><ul>
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<li><a class="reference internal" href="#test-lammps-and-python-in-serial"><strong>Test LAMMPS and Python in serial:</strong></a></li>
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<li><a class="reference internal" href="#test-lammps-and-python-in-parallel"><strong>Test LAMMPS and Python in parallel:</strong></a></li>
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<li><a class="reference internal" href="#running-python-scripts"><strong>Running Python scripts:</strong></a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="#using-lammps-from-python">11.7. Using LAMMPS from Python</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#example-python-scripts-that-use-lammps">11.8. Example Python scripts that use LAMMPS</a></li>
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<li><a class="reference internal" href="#using-lammps-from-python">Using LAMMPS from Python</a></li>
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<li><a class="reference internal" href="#example-python-scripts-that-use-lammps">Example Python scripts that use LAMMPS</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</ul>
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</div>
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</div>
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html">Docs</a> »</li>
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<li>11. Python interface to LAMMPS</li>
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<li>Python interface to LAMMPS</li>
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<li class="wy-breadcrumbs-aside">
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</ul>
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<hr/>
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<div class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
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<a href="Section_errors.html" class="btn btn-neutral float-right" title="12. Errors" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="Section_modify.html" class="btn btn-neutral" title="10. Modifying & extending LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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</div>
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</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div itemprop="articleBody">
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<div class="section" id="python-interface-to-lammps">
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<h1>11. Python interface to LAMMPS</h1>
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<h1>Python interface to LAMMPS</h1>
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<p>LAMMPS can work together with Python in two ways. First, Python can
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wrap LAMMPS through the <a class="reference internal" href="Section_howto.html#howto-19"><span class="std std-ref">LAMMPS library interface</span></a>, so that a Python script can
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create one or more instances of LAMMPS and launch one or more
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@ -197,7 +175,7 @@ interesting Python functions that can be called from a LAMMPS input
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script, that you think would be useful to other users, please <a class="reference external" href="http://lammps.sandia.gov/authors.html">email them to the developers</a>. We can
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include them in the LAMMPS distribution.</p>
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<div class="section" id="overview-of-running-lammps-from-python">
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<span id="py-1"></span><h2>11.1. Overview of running LAMMPS from Python</h2>
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<span id="py-1"></span><h2>Overview of running LAMMPS from Python</h2>
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<p>The LAMMPS distribution includes a python directory with all you need
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to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS
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library interface, with one wrapper function per LAMMPS library
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@ -237,7 +215,7 @@ check which version of Python you have installed, by simply typing
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<hr class="docutils" />
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</div>
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<div class="section" id="overview-of-using-python-from-a-lammps-script">
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<span id="py-2"></span><h2>11.2. Overview of using Python from a LAMMPS script</h2>
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<span id="py-2"></span><h2>Overview of using Python from a LAMMPS script</h2>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">It is not currently possible to use the <a class="reference internal" href="python.html"><span class="doc">python</span></a>
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@ -300,9 +278,9 @@ file and the shared library.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="building-lammps-as-a-shared-library">
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<span id="py-3"></span><h2>11.3. Building LAMMPS as a shared library</h2>
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<span id="py-3"></span><h2>Building LAMMPS as a shared library</h2>
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<p>Instructions on how to build LAMMPS as a shared library are given in
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<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
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<span class="xref std std-ref">Section_start 5</span>. A shared library is one
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that is dynamically loadable, which is what Python requires to wrap
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LAMMPS. On Linux this is a library file that ends in ”.so”, not ”.a”.</p>
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<p>From the src directory, type</p>
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@ -321,12 +299,12 @@ most recently built version.</p>
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auxiliary libraries (used by various packages), then all of these
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extra libraries must also be shared libraries. If the LAMMPS
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shared-library build fails with an error complaining about this, see
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<a class="reference internal" href="Section_start.html#start-5"><span class="std std-ref">Section_start 5</span></a> for more details.</p>
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<span class="xref std std-ref">Section_start 5</span> for more details.</p>
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</div>
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<hr class="docutils" />
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</div>
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<div class="section" id="installing-the-python-wrapper-into-python">
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<span id="py-4"></span><h2>11.4. Installing the Python wrapper into Python</h2>
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<span id="py-4"></span><h2>Installing the Python wrapper into Python</h2>
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<p>For Python to invoke LAMMPS, there are 2 files it needs to know about:</p>
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<ul class="simple">
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<li>python/lammps.py</li>
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@ -388,7 +366,7 @@ environment variable as described above.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="extending-python-with-mpi-to-run-in-parallel">
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<span id="py-5"></span><h2>11.5. Extending Python with MPI to run in parallel</h2>
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<span id="py-5"></span><h2>Extending Python with MPI to run in parallel</h2>
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<p>If you wish to run LAMMPS in parallel from Python, you need to extend
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your Python with an interface to MPI. This also allows you to
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make MPI calls directly from Python in your script, if you desire.</p>
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@ -526,7 +504,7 @@ the right one.</p>
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<hr class="docutils" />
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</div>
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<div class="section" id="testing-the-python-lammps-interface">
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<span id="py-6"></span><h2>11.6. Testing the Python-LAMMPS interface</h2>
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<span id="py-6"></span><h2>Testing the Python-LAMMPS interface</h2>
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<p>To test if LAMMPS is callable from Python, launch Python interactively
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and type:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
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<span class="gp">>>> </span><span class="n">CDLL</span><span class="p">(</span><span class="s2">"liblammps.so"</span><span class="p">)</span>
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</pre></div>
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</div>
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<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
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<p>If an error occurs, carefully go thru the steps in <span class="xref std std-ref">Section_start 5</span> and above about building a shared
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library and about insuring Python can find the necessary two files
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it needs.</p>
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<div class="section" id="test-lammps-and-python-in-serial">
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<h3>11.6.1. <strong>Test LAMMPS and Python in serial:</strong></h3>
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<h3><strong>Test LAMMPS and Python in serial:</strong></h3>
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<p>To run a LAMMPS test in serial, type these lines into Python
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interactively from the bench directory:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
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</div>
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</div>
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<div class="section" id="test-lammps-and-python-in-parallel">
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<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></h3>
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<h3><strong>Test LAMMPS and Python in parallel:</strong></h3>
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<p>To run LAMMPS in parallel, assuming you have installed the
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<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file
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containing these lines:</p>
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correctly.</p>
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</div>
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<div class="section" id="running-python-scripts">
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<h3>11.6.3. <strong>Running Python scripts:</strong></h3>
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<h3><strong>Running Python scripts:</strong></h3>
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<p>Note that any Python script (not just for LAMMPS) can be invoked in
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one of several ways:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">python</span> <span class="n">foo</span><span class="o">.</span><span class="n">script</span>
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</div>
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</div>
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<div class="section" id="using-lammps-from-python">
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<span id="py-7"></span><h2>11.7. Using LAMMPS from Python</h2>
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<span id="py-7"></span><h2>Using LAMMPS from Python</h2>
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<p>As described above, the Python interface to LAMMPS consists of a
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Python “lammps” module, the source code for which is in
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python/lammps.py, which creates a “lammps” object, with a set of
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</ul>
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</div>
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<div class="section" id="example-python-scripts-that-use-lammps">
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<span id="py-8"></span><h2>11.8. Example Python scripts that use LAMMPS</h2>
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<span id="py-8"></span><h2>Example Python scripts that use LAMMPS</h2>
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<p>These are the Python scripts included as demos in the python/examples
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directory of the LAMMPS distribution, to illustrate the kinds of
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things that are possible when Python wraps LAMMPS. If you create your
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@ -976,15 +954,6 @@ different visualization package options. Click to see larger images:</p>
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</div>
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<footer>
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<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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<a href="Section_errors.html" class="btn btn-neutral float-right" title="12. Errors" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<a href="Section_modify.html" class="btn btn-neutral" title="10. Modifying & extending LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
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