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<li class="toctree-l2 current"><a class="current reference internal" href="#">2.4. The <code class="docutils literal notranslate"><span class="pre">lammps</span></code> Python module</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#the-lammps-class-api">2.4.1. The <code class="docutils literal notranslate"><span class="pre">lammps</span></code> class API</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#the-pylammps-class-api">2.4.2. The <code class="docutils literal notranslate"><span class="pre">PyLammps</span></code> class API</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#the-ipylammps-class-api">2.4.3. The <code class="docutils literal notranslate"><span class="pre">IPyLammps</span></code> class API</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#additional-components-of-the-lammps-module">2.4.4. Additional components of the <code class="docutils literal notranslate"><span class="pre">lammps</span></code> module</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="module-lammps">
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<span id="the-lammps-python-module"></span><h1><span class="section-number">2.4. </span>The <code class="docutils literal notranslate"><span class="pre">lammps</span></code> Python module<a class="headerlink" href="#module-lammps" title="Link to this heading"></a></h1>
|
||
<p>The LAMMPS Python interface is implemented as a module called <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a>
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which is defined in the <code class="docutils literal notranslate"><span class="pre">lammps</span></code> package in the <code class="docutils literal notranslate"><span class="pre">python</span></code> folder of the
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||
LAMMPS source code distribution. After compilation of LAMMPS, the module can
|
||
be installed into a Python system folder or a user folder with <code class="docutils literal notranslate"><span class="pre">make</span>
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||
<span class="pre">install-python</span></code>. Components of the module can then loaded into a Python
|
||
session with the <code class="docutils literal notranslate"><span class="pre">import</span></code> command.</p>
|
||
<p>There are multiple Python interface classes in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module:</p>
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||
<ul class="simple">
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||
<li><p>the <a class="reference internal" href="#lammps.lammps" title="lammps.lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> class. This is a wrapper around
|
||
the C-library interface and its member functions try to replicate the
|
||
<a class="reference internal" href="Library.html#lammps-c-api"><span class="std std-ref">C-library API</span></a> closely. This is the most
|
||
feature-complete Python API.</p></li>
|
||
<li><p>the <a class="reference internal" href="#lammps.PyLammps" title="lammps.PyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">PyLammps</span></code></a> class. This is a more high-level
|
||
and more Python style class implemented on top of the
|
||
<a class="reference internal" href="#lammps.lammps" title="lammps.lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> class.</p></li>
|
||
<li><p>the <a class="reference internal" href="#lammps.IPyLammps" title="lammps.IPyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">IPyLammps</span></code></a> class is derived from
|
||
<a class="reference internal" href="#lammps.PyLammps" title="lammps.PyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">PyLammps</span></code></a> and adds embedded graphics
|
||
features to conveniently include LAMMPS into <a class="reference external" href="https://jupyter.org/">Jupyter</a> notebooks.</p></li>
|
||
</ul>
|
||
<div class="note admonition">
|
||
<p class="admonition-title">Version check</p>
|
||
<p>The <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module stores the version number of the LAMMPS
|
||
version it is installed from. When initializing the
|
||
<a class="reference internal" href="#lammps.lammps" title="lammps.lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> class, this version is checked to
|
||
be the same as the result from <a class="reference internal" href="#lammps.lammps.version" title="lammps.lammps.version"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.version()</span></code></a>, the version
|
||
of the LAMMPS shared library that the module interfaces to. If the
|
||
they are not the same an AttributeError exception is raised since a
|
||
mismatch of versions (e.g. due to incorrect use of the
|
||
<code class="docutils literal notranslate"><span class="pre">LD_LIBRARY_PATH</span></code> or <code class="docutils literal notranslate"><span class="pre">PYTHONPATH</span></code> environment variables can lead
|
||
to crashes or data corruption and otherwise incorrect behavior.</p>
|
||
</div>
|
||
<p>LAMMPS module global members:</p>
|
||
<dl class="py data">
|
||
<dt class="sig sig-object py" id="lammps.__version__">
|
||
<span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">__version__</span></span><a class="headerlink" href="#lammps.__version__" title="Link to this definition"></a></dt>
|
||
<dd><p>Numerical representation of the LAMMPS version this
|
||
module was taken from. Has the same format as the
|
||
result of <a class="reference internal" href="#lammps.lammps.version" title="lammps.lammps.version"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.version()</span></code></a>.</p>
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</dd></dl>
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||
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||
<hr class="docutils" />
|
||
<section id="the-lammps-class-api">
|
||
<h2><span class="section-number">2.4.1. </span>The <code class="docutils literal notranslate"><span class="pre">lammps</span></code> class API<a class="headerlink" href="#the-lammps-class-api" title="Link to this heading"></a></h2>
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||
<p>The <a class="reference internal" href="#lammps.lammps" title="lammps.lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> class is the core of the LAMMPS
|
||
Python interfaces. It is a wrapper around the <a class="reference internal" href="Library.html#lammps-c-api"><span class="std std-ref">LAMMPS C library
|
||
API</span></a> using the <a class="reference external" href="https://docs.python.org/3/library/ctypes.html">Python ctypes module</a> and a shared library
|
||
compiled from the LAMMPS sources code. The individual methods in this
|
||
class try to closely follow the corresponding C functions. The handle
|
||
argument that needs to be passed to the C functions is stored internally
|
||
in the class and automatically added when calling the C library
|
||
functions. Below is a detailed documentation of the API.</p>
|
||
<dl class="py class">
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||
<dt class="sig sig-object py" id="lammps.lammps">
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||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">lammps</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmdargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps" title="Link to this definition"></a></dt>
|
||
<dd><p>Create an instance of the LAMMPS Python class.</p>
|
||
<p>This is a Python wrapper class that exposes the LAMMPS C-library
|
||
interface to Python. It either requires that LAMMPS has been compiled
|
||
as shared library which is then dynamically loaded via the ctypes
|
||
Python module or that this module called from a Python function that
|
||
is called from a Python interpreter embedded into a LAMMPS executable,
|
||
for example through the <a class="reference internal" href="python.html"><span class="doc">python invoke</span></a> command.
|
||
When the class is instantiated it calls the <a class="reference internal" href="Library_create.html#_CPPv411lammps_openiPPc8MPI_CommPPv" title="lammps_open"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_open()</span></code></a>
|
||
function of the LAMMPS C-library interface, which in
|
||
turn will create an instance of the <a class="reference internal" href="Classes_lammps.html#_CPPv4N9LAMMPS_NS6LAMMPSE" title="LAMMPS_NS::LAMMPS"><code class="xref cpp cpp-class docutils literal notranslate"><span class="pre">LAMMPS</span></code></a>
|
||
C++ class. The handle to this C++ class is stored internally
|
||
and automatically passed to the calls to the C library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – “machine” name of the shared LAMMPS library (“mpi” loads <code class="docutils literal notranslate"><span class="pre">liblammps_mpi.so</span></code>, “” loads <code class="docutils literal notranslate"><span class="pre">liblammps.so</span></code>)</p></li>
|
||
<li><p><strong>cmdargs</strong> (<em>list</em>) – list of command line arguments to be passed to the <a class="reference internal" href="Library_create.html#_CPPv411lammps_openiPPc8MPI_CommPPv" title="lammps_open"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_open()</span></code></a> function. The executable name is automatically added.</p></li>
|
||
<li><p><strong>ptr</strong> (<em>pointer</em>) – pointer to a LAMMPS C++ class instance when called from an embedded Python interpreter. None means load symbols from shared library.</p></li>
|
||
<li><p><strong>comm</strong> (<em>MPI_Comm</em>) – MPI communicator (as provided by <a class="reference external" href="https://mpi4py.readthedocs.io/">mpi4py</a>). <code class="docutils literal notranslate"><span class="pre">None</span></code> means use <code class="docutils literal notranslate"><span class="pre">MPI_COMM_WORLD</span></code> implicitly.</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.numpy">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">numpy</span></span><a class="headerlink" href="#lammps.lammps.numpy" title="Link to this definition"></a></dt>
|
||
<dd><p>Return object to access numpy versions of API</p>
|
||
<p>It provides alternative implementations of API functions that
|
||
return numpy arrays instead of ctypes pointers. If numpy is not installed,
|
||
accessing this property will lead to an ImportError.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>instance of numpy wrapper object</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p><a class="reference internal" href="#lammps.numpy_wrapper.numpy_wrapper" title="lammps.numpy_wrapper.numpy_wrapper">numpy_wrapper</a></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.close">
|
||
<span class="sig-name descname"><span class="pre">close</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.close" title="Link to this definition"></a></dt>
|
||
<dd><p>Explicitly delete a LAMMPS instance through the C-library interface.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_create.html#_CPPv412lammps_closePv" title="lammps_close"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_close()</span></code></a> function of the C-library interface.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.finalize">
|
||
<span class="sig-name descname"><span class="pre">finalize</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.finalize" title="Link to this definition"></a></dt>
|
||
<dd><p>Shut down the MPI communication and Kokkos environment (if active) through the
|
||
library interface by calling <a class="reference internal" href="Library_create.html#_CPPv419lammps_mpi_finalizev" title="lammps_mpi_finalize"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_mpi_finalize()</span></code></a> and
|
||
<a class="reference internal" href="Library_create.html#_CPPv422lammps_kokkos_finalizev" title="lammps_kokkos_finalize"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_kokkos_finalize()</span></code></a>.</p>
|
||
<p>You cannot create or use any LAMMPS instances after this function is called
|
||
unless LAMMPS was compiled without MPI and without Kokkos support.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.error">
|
||
<span class="sig-name descname"><span class="pre">error</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">error_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">error_text</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.error" title="Link to this definition"></a></dt>
|
||
<dd><p>Forward error to the LAMMPS Error class.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 3Nov2022.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_create.html#_CPPv412lammps_errorPviPKc" title="lammps_error"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_error()</span></code></a> function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>error_type</strong> (<em>int</em>)</p></li>
|
||
<li><p><strong>error_text</strong> (<em>string</em>)</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.version">
|
||
<span class="sig-name descname"><span class="pre">version</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.version" title="Link to this definition"></a></dt>
|
||
<dd><p>Return a numerical representation of the LAMMPS version in use.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv414lammps_versionPv" title="lammps_version"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_version()</span></code></a> function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>version number</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_os_info">
|
||
<span class="sig-name descname"><span class="pre">get_os_info</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_os_info" title="Link to this definition"></a></dt>
|
||
<dd><p>Return a string with information about the OS and compiler runtime</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv418lammps_get_os_infoPci" title="lammps_get_os_info"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_os_info()</span></code></a> function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>OS info string</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_mpi_comm">
|
||
<span class="sig-name descname"><span class="pre">get_mpi_comm</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_mpi_comm" title="Link to this definition"></a></dt>
|
||
<dd><p>Get the MPI communicator in use by the current LAMMPS instance</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv419lammps_get_mpi_commPv" title="lammps_get_mpi_comm"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_mpi_comm()</span></code></a> function
|
||
of the C-library interface. It will return <code class="docutils literal notranslate"><span class="pre">None</span></code> if either the
|
||
LAMMPS library was compiled without MPI support or the mpi4py
|
||
Python module is not available.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>MPI communicator</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>MPI_Comm</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.expand">
|
||
<span class="sig-name descname"><span class="pre">expand</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">line</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.expand" title="Link to this definition"></a></dt>
|
||
<dd><p>Expand a single LAMMPS string like an input line</p>
|
||
<p>This is a wrapper around the <code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_expand()</span></code>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>cmd</strong> (<em>string</em>) – a single lammps line</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>expanded string</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>string</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.file">
|
||
<span class="sig-name descname"><span class="pre">file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.file" title="Link to this definition"></a></dt>
|
||
<dd><p>Read LAMMPS commands from a file.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_execute.html#_CPPv411lammps_filePvPKc" title="lammps_file"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_file()</span></code></a> function of the C-library interface.
|
||
It will open the file with the name/path <cite>file</cite> and process the LAMMPS commands line by line until
|
||
the end. The function will return when the end of the file is reached.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>path</strong> (<em>string</em>) – Name of the file/path with LAMMPS commands</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.command">
|
||
<span class="sig-name descname"><span class="pre">command</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cmd</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.command" title="Link to this definition"></a></dt>
|
||
<dd><p>Process a single LAMMPS input command from a string.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_execute.html#_CPPv414lammps_commandPvPKc" title="lammps_command"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_command()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>cmd</strong> (<em>string</em>) – a single lammps command</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.commands_list">
|
||
<span class="sig-name descname"><span class="pre">commands_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cmdlist</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.commands_list" title="Link to this definition"></a></dt>
|
||
<dd><p>Process multiple LAMMPS input commands from a list of strings.</p>
|
||
<p>This is a wrapper around the
|
||
<a class="reference internal" href="Library_execute.html#_CPPv420lammps_commands_listPviPPKc" title="lammps_commands_list"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_commands_list()</span></code></a> function of
|
||
the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>cmdlist</strong> (<em>list</em><em> of </em><em>strings</em>) – a single lammps command</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.commands_string">
|
||
<span class="sig-name descname"><span class="pre">commands_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multicmd</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.commands_string" title="Link to this definition"></a></dt>
|
||
<dd><p>Process a block of LAMMPS input commands from a string.</p>
|
||
<p>This is a wrapper around the
|
||
<a class="reference internal" href="Library_execute.html#_CPPv422lammps_commands_stringPvPKc" title="lammps_commands_string"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_commands_string()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>multicmd</strong> (<em>string</em>) – text block of lammps commands</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_natoms">
|
||
<span class="sig-name descname"><span class="pre">get_natoms</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_natoms" title="Link to this definition"></a></dt>
|
||
<dd><p>Get the total number of atoms in the LAMMPS instance.</p>
|
||
<p>Will be precise up to 53-bit signed integer due to the
|
||
underlying <a class="reference internal" href="Library_properties.html#_CPPv417lammps_get_natomsPv" title="lammps_get_natoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_natoms()</span></code></a> function returning a double.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>number of atoms</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_box">
|
||
<span class="sig-name descname"><span class="pre">extract_box</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_box" title="Link to this definition"></a></dt>
|
||
<dd><p>Extract simulation box parameters</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv418lammps_extract_boxPvPdPdPdPdPdPiPi" title="lammps_extract_box"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_box()</span></code></a> function
|
||
of the C-library interface. Unlike in the C function, the result is
|
||
returned as a list.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>list of the extracted data: boxlo, boxhi, xy, yz, xz, periodicity, box_change</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>[ 3*double, 3*double, double, double, 3*int, int]</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.reset_box">
|
||
<span class="sig-name descname"><span class="pre">reset_box</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">boxlo</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boxhi</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">yz</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xz</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.reset_box" title="Link to this definition"></a></dt>
|
||
<dd><p>Reset simulation box parameters</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv416lammps_reset_boxPvPdPdddd" title="lammps_reset_box"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_reset_box()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>boxlo</strong> (<em>list</em><em> of </em><em>3 floating point numbers</em>) – new lower box boundaries</p></li>
|
||
<li><p><strong>boxhi</strong> (<em>list</em><em> of </em><em>3 floating point numbers</em>) – new upper box boundaries</p></li>
|
||
<li><p><strong>xy</strong> (<em>float</em>) – xy tilt factor</p></li>
|
||
<li><p><strong>yz</strong> (<em>float</em>) – yz tilt factor</p></li>
|
||
<li><p><strong>xz</strong> (<em>float</em>) – xz tilt factor</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_thermo">
|
||
<span class="sig-name descname"><span class="pre">get_thermo</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_thermo" title="Link to this definition"></a></dt>
|
||
<dd><p>Get current value of a thermo keyword</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv417lammps_get_thermoPvPKc" title="lammps_get_thermo"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_thermo()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>name</strong> (<em>string</em>) – name of thermo keyword</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>value of thermo keyword</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>double or None</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.last_thermo_step">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">last_thermo_step</span></span><a class="headerlink" href="#lammps.lammps.last_thermo_step" title="Link to this definition"></a></dt>
|
||
<dd><p>Get the last timestep where thermodynamic data was computed</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>the timestep or a negative number if there has not been any thermo output yet</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.last_thermo">
|
||
<span class="sig-name descname"><span class="pre">last_thermo</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.last_thermo" title="Link to this definition"></a></dt>
|
||
<dd><p>Get a dictionary of the last thermodynamic output</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv418lammps_last_thermoPvPKci" title="lammps_last_thermo"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_last_thermo()</span></code></a>
|
||
function of the C-library interface. It collects the cached thermo
|
||
data from the last timestep into a dictionary. The return value
|
||
is None, if there has not been any thermo output yet.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>a dictionary containing the last computed thermo output values</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>dict or None</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_setting">
|
||
<span class="sig-name descname"><span class="pre">extract_setting</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_setting" title="Link to this definition"></a></dt>
|
||
<dd><p>Query LAMMPS about global settings that can be expressed as an integer.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv422lammps_extract_settingPvPKc" title="lammps_extract_setting"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_setting()</span></code></a>
|
||
function of the C-library interface. Its documentation includes
|
||
a list of the supported keywords.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>name</strong> (<em>string</em>) – name of the setting</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>value of the setting</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_global_datatype">
|
||
<span class="sig-name descname"><span class="pre">extract_global_datatype</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_global_datatype" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global property datatype from LAMMPS</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv430lammps_extract_global_datatypePvPKc" title="lammps_extract_global_datatype"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_global_datatype()</span></code></a>
|
||
function of the C-library interface. Its documentation includes a
|
||
list of the supported keywords.
|
||
This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if the keyword is not
|
||
recognized. Otherwise it will return a positive integer value that
|
||
corresponds to one of the <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">data type</span></a>
|
||
constants defined in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>name</strong> (<em>string</em>) – name of the property</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>data type of global property, see <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">Data Types</span></a></p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_global">
|
||
<span class="sig-name descname"><span class="pre">extract_global</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_global" title="Link to this definition"></a></dt>
|
||
<dd><p>Query LAMMPS about global settings of different types.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv421lammps_extract_globalPvPKc" title="lammps_extract_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_global()</span></code></a> function
|
||
of the C-library interface. Since there are no pointers in Python, this
|
||
method will - unlike the C function - return the value or a list of
|
||
values. The <a class="reference internal" href="Library_properties.html#_CPPv421lammps_extract_globalPvPKc" title="lammps_extract_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_global()</span></code></a> documentation includes a
|
||
list of the supported keywords and their data types.
|
||
Since Python needs to know the data type to be able to interpret
|
||
the result, by default, this function will try to auto-detect the data type
|
||
by asking the library. You can also force a specific data type. For that
|
||
purpose the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module contains <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">data type</span></a>
|
||
constants. This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if either the keyword is not recognized,
|
||
or an invalid data type constant is used.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the property</p></li>
|
||
<li><p><strong>dtype</strong> (<em>int</em><em>, </em><em>optional</em>) – data type of the returned data (see <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">Data Types</span></a>)</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>value of the property or list of values or None</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int, float, list, or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_pair_dimension">
|
||
<span class="sig-name descname"><span class="pre">extract_pair_dimension</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_pair_dimension" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve pair style property dimensionality from LAMMPS</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 29Aug2024.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv429lammps_extract_pair_dimensionPvPKc" title="lammps_extract_pair_dimension"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_pair_dimension()</span></code></a>
|
||
function of the C-library interface. The list of supported keywords
|
||
depends on the pair style. This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if the keyword
|
||
is not recognized.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>name</strong> (<em>string</em>) – name of the property</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>dimensionality of the extractable data (typically 0, 1, or 2)</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_pair">
|
||
<span class="sig-name descname"><span class="pre">extract_pair</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_pair" title="Link to this definition"></a></dt>
|
||
<dd><p>Extract pair style data from LAMMPS.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 29Aug2024.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv419lammps_extract_pairPvPKc" title="lammps_extract_pair"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_pair()</span></code></a> function
|
||
of the C-library interface. Since there are no pointers in Python, this
|
||
method will - unlike the C function - return the value or a list of
|
||
values.
|
||
Since Python needs to know the dimensionality to be able to interpret
|
||
the result, this function will detect the dimensionality by asking the library.
|
||
This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if the keyword is not recognized.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>name</strong> (<em>string</em>) – name of the property</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>value of the property or list of values or None</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float, list of float, list of list of floats, or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.map_atom">
|
||
<span class="sig-name descname"><span class="pre">map_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">id</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.map_atom" title="Link to this definition"></a></dt>
|
||
<dd><p>Map a global atom ID (aka tag) to the local atom index</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_properties.html#_CPPv415lammps_map_atomPvPKv" title="lammps_map_atom"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_map_atom()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>id</strong> (<em>int</em>) – atom ID</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>local index</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_atom_datatype">
|
||
<span class="sig-name descname"><span class="pre">extract_atom_datatype</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_atom_datatype" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve per-atom property datatype from LAMMPS</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_atoms.html#_CPPv428lammps_extract_atom_datatypePvPKc" title="lammps_extract_atom_datatype"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_atom_datatype()</span></code></a>
|
||
function of the C-library interface. Its documentation includes a
|
||
list of the supported keywords.
|
||
This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if the keyword is not
|
||
recognized. Otherwise it will return an integer value that
|
||
corresponds to one of the <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">data type</span></a> constants
|
||
defined in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>name</strong> (<em>string</em>) – name of the property</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>data type of per-atom property (see <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">Data Types</span></a>)</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_atom_size">
|
||
<span class="sig-name descname"><span class="pre">extract_atom_size</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_atom_size" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve per-atom property dimensions from LAMMPS</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_atoms.html#_CPPv424lammps_extract_atom_sizePvPKci" title="lammps_extract_atom_size"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_atom_size()</span></code></a>
|
||
function of the C-library interface. Its documentation includes a
|
||
list of the supported keywords.
|
||
This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if the keyword is not
|
||
recognized. Otherwise it will return an integer value with the size
|
||
of the per-atom vector or array. If <em>name</em> corresponds to a per-atom
|
||
array, the <em>dtype</em> keyword must be either LMP_SIZE_ROWS or LMP_SIZE_COLS
|
||
from the <a class="reference internal" href="#py-type-constants"><span class="std std-ref">type</span></a> constants defined in the
|
||
<a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module. The return value is the requested size.
|
||
If <em>name</em> corresponds to a per-atom vector the <em>dtype</em> keyword is ignored.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the property</p></li>
|
||
<li><p><strong>type</strong> (<em>int</em>) – either LMP_SIZE_ROWS or LMP_SIZE_COLS for arrays, otherwise ignored</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>data type of per-atom property (see <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">Data Types</span></a>)</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_atom">
|
||
<span class="sig-name descname"><span class="pre">extract_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_atom" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve per-atom properties from LAMMPS</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_atoms.html#_CPPv419lammps_extract_atomPvPKc" title="lammps_extract_atom"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_atom()</span></code></a> function of the
|
||
C-library interface. Its documentation includes a list of the supported
|
||
keywords and their data types. Since Python needs to know the data type to
|
||
be able to interpret the result, by default, this function will try to
|
||
auto-detect the data type by asking the library. You can also force a
|
||
specific data type by setting <code class="docutils literal notranslate"><span class="pre">dtype</span></code> to one of the <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">data type</span></a> constants defined in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module.
|
||
This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if either the keyword is not recognized, or
|
||
an invalid data type constant is used.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>While the returned vectors or arrays of per-atom data are dimensioned for
|
||
the range [0:nmax] - as is the underlying storage - the data is usually
|
||
only valid for the range of [0:nlocal], unless the property of interest
|
||
is also updated for ghost atoms. In some cases, this depends on a LAMMPS
|
||
setting, see for example <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify vel yes</span></a>.
|
||
The actual size can be determined by calling
|
||
py:meth:<cite>extract_atom_size() <lammps.lammps.extract_atom_size></cite>.</p>
|
||
</div>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the property</p></li>
|
||
<li><p><strong>dtype</strong> (<em>int</em><em>, </em><em>optional</em>) – data type of the returned data (see <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">Data Types</span></a>)</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>requested data or <code class="docutils literal notranslate"><span class="pre">None</span></code></p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>ctypes.POINTER(ctypes.c_int32), ctypes.POINTER(ctypes.POINTER(ctypes.c_int32)),
|
||
ctypes.POINTER(ctypes.c_int64), ctypes.POINTER(ctypes.POINTER(ctypes.c_int64)),
|
||
ctypes.POINTER(ctypes.c_double), ctypes.POINTER(ctypes.POINTER(ctypes.c_double)),
|
||
or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_compute">
|
||
<span class="sig-name descname"><span class="pre">extract_compute</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cstyle</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ctype</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_compute" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve data from a LAMMPS compute</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_objects.html#_CPPv422lammps_extract_computePvPKcii" title="lammps_extract_compute"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_compute()</span></code></a>
|
||
function of the C-library interface.
|
||
This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if either the compute id is not
|
||
recognized, or an invalid combination of <a class="reference internal" href="#py-style-constants"><span class="std std-ref">cstyle</span></a>
|
||
and <a class="reference internal" href="#py-type-constants"><span class="std std-ref">ctype</span></a> constants is used. The
|
||
names and functionality of the constants are the same as for
|
||
the corresponding C-library function. For requests to return
|
||
a scalar or a size, the value is returned, otherwise a pointer.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>cid</strong> (<em>string</em>) – compute ID</p></li>
|
||
<li><p><strong>cstyle</strong> (<em>int</em>) – style of the data retrieve (global, atom, or local), see <a class="reference internal" href="#py-style-constants"><span class="std std-ref">Style Constants</span></a></p></li>
|
||
<li><p><strong>ctype</strong> (<em>int</em>) – type or size of the returned data (scalar, vector, or array), see <a class="reference internal" href="#py-type-constants"><span class="std std-ref">Type Constants</span></a></p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>requested data as scalar, pointer to 1d or 2d double array, or None</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_fix">
|
||
<span class="sig-name descname"><span class="pre">extract_fix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fstyle</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ftype</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nrow</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_fix" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve data from a LAMMPS fix</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_objects.html#_CPPv418lammps_extract_fixPvPKciiii" title="lammps_extract_fix"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_fix()</span></code></a> function
|
||
of the C-library interface. This function returns <code class="docutils literal notranslate"><span class="pre">None</span></code> if
|
||
either the fix id is not recognized, or an invalid combination of
|
||
<a class="reference internal" href="#py-style-constants"><span class="std std-ref">fstyle</span></a> and <a class="reference internal" href="#py-type-constants"><span class="std std-ref">ftype</span></a> constants is used. The names and functionality
|
||
of the constants are the same as for the corresponding C-library
|
||
function. For requests to return a scalar or a size, the value is
|
||
returned, also when accessing global vectors or arrays, otherwise a
|
||
pointer.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When requesting global data, the fix data can only be accessed
|
||
one item at a time without access to the whole vector or array.
|
||
Thus this function will always return a scalar. To access vector
|
||
or array elements the “nrow” and “ncol” arguments need to be set
|
||
accordingly (they default to 0).</p>
|
||
</div>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fid</strong> (<em>string</em>) – fix ID</p></li>
|
||
<li><p><strong>fstyle</strong> (<em>int</em>) – style of the data retrieve (global, atom, or local), see <a class="reference internal" href="#py-style-constants"><span class="std std-ref">Style Constants</span></a></p></li>
|
||
<li><p><strong>ftype</strong> (<em>int</em>) – type or size of the returned data (scalar, vector, or array), see <a class="reference internal" href="#py-type-constants"><span class="std std-ref">Type Constants</span></a></p></li>
|
||
<li><p><strong>nrow</strong> (<em>int</em>) – index of global vector element or row index of global array element</p></li>
|
||
<li><p><strong>ncol</strong> (<em>int</em>) – column index of global array element</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>requested data or None</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.extract_variable">
|
||
<span class="sig-name descname"><span class="pre">extract_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">group</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vartype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.extract_variable" title="Link to this definition"></a></dt>
|
||
<dd><p>Evaluate a LAMMPS variable and return its data</p>
|
||
<p>This function is a wrapper around the function
|
||
<a class="reference internal" href="Library_objects.html#_CPPv423lammps_extract_variablePvPKcPKc" title="lammps_extract_variable"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_variable()</span></code></a> of the C library interface,
|
||
evaluates variable name and returns a copy of the computed data.
|
||
The memory temporarily allocated by the C-interface is deleted
|
||
after the data is copied to a Python variable or list.
|
||
The variable must be either an equal-style (or equivalent)
|
||
variable or an atom-style variable. The variable type can be
|
||
provided as the <code class="docutils literal notranslate"><span class="pre">vartype</span></code> parameter, which may be one of several
|
||
constants: <code class="docutils literal notranslate"><span class="pre">LMP_VAR_EQUAL</span></code>, <code class="docutils literal notranslate"><span class="pre">LMP_VAR_ATOM</span></code>, <code class="docutils literal notranslate"><span class="pre">LMP_VAR_VECTOR</span></code>,
|
||
or <code class="docutils literal notranslate"><span class="pre">LMP_VAR_STRING</span></code>. If omitted or <code class="docutils literal notranslate"><span class="pre">None</span></code>, LAMMPS will determine its
|
||
value for you based on a call to
|
||
<a class="reference internal" href="Library_objects.html#_CPPv432lammps_extract_variable_datatypePvPKc" title="lammps_extract_variable_datatype"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_extract_variable_datatype()</span></code></a> from the C library interface.
|
||
The group parameter is only used for atom-style variables and defaults to
|
||
the group “all”.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the variable to execute</p></li>
|
||
<li><p><strong>group</strong> (<em>string</em><em>, </em><em>only for atom-style variables</em>) – name of group for atom-style variable</p></li>
|
||
<li><p><strong>vartype</strong> (<em>int</em>) – type of variable, see <a class="reference internal" href="#py-vartype-constants"><span class="std std-ref">Variable Type Constants</span></a></p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>the requested data</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>c_double, (c_double), or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.flush_buffers">
|
||
<span class="sig-name descname"><span class="pre">flush_buffers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.flush_buffers" title="Link to this definition"></a></dt>
|
||
<dd><p>Flush output buffers</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv420lammps_flush_buffersPv" title="lammps_flush_buffers"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_flush_buffers()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.set_variable">
|
||
<span class="sig-name descname"><span class="pre">set_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.set_variable" title="Link to this definition"></a></dt>
|
||
<dd><p>Set a new value for a LAMMPS string style variable</p>
|
||
<div class="deprecated">
|
||
<p><span class="versionmodified deprecated">Deprecated since version 7Feb2024.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_objects.html#_CPPv419lammps_set_variablePvPKcPKc" title="lammps_set_variable"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_set_variable()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the variable</p></li>
|
||
<li><p><strong>value</strong> (<em>any. will be converted to a string</em>) – new variable value</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>either 0 on success or -1 on failure</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.set_string_variable">
|
||
<span class="sig-name descname"><span class="pre">set_string_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.set_string_variable" title="Link to this definition"></a></dt>
|
||
<dd><p>Set a new value for a LAMMPS string style variable</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 7Feb2024.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_objects.html#_CPPv426lammps_set_string_variablePvPKcPKc" title="lammps_set_string_variable"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_set_string_variable()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the variable</p></li>
|
||
<li><p><strong>value</strong> (<em>any. will be converted to a string</em>) – new variable value</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>either 0 on success or -1 on failure</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.set_internal_variable">
|
||
<span class="sig-name descname"><span class="pre">set_internal_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.set_internal_variable" title="Link to this definition"></a></dt>
|
||
<dd><p>Set a new value for a LAMMPS internal style variable</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 7Feb2024.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_objects.html#_CPPv428lammps_set_internal_variablePvPKcd" title="lammps_set_internal_variable"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_set_internal_variable()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the variable</p></li>
|
||
<li><p><strong>value</strong> (<em>float</em><em> or </em><em>compatible. will be converted to float</em>) – new variable value</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>either 0 on success or -1 on failure</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.gather_bonds">
|
||
<span class="sig-name descname"><span class="pre">gather_bonds</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.gather_bonds" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of bonds</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_scatter.html#_CPPv419lammps_gather_bondsPvPv" title="lammps_gather_bonds"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_bonds()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<p>This function returns a tuple with the number of bonds and a
|
||
flat list of ctypes integer values with the bond type, bond atom1,
|
||
bond atom2 for each bond.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>a tuple with the number of bonds and a list of c_int or c_long</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>(int, 3*nbonds*c_tagint)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.gather_angles">
|
||
<span class="sig-name descname"><span class="pre">gather_angles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.gather_angles" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of angles</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_scatter.html#_CPPv420lammps_gather_anglesPvPv" title="lammps_gather_angles"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_angles()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<p>This function returns a tuple with the number of angles and a
|
||
flat list of ctypes integer values with the angle type, angle atom1,
|
||
angle atom2, angle atom3 for each angle.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>a tuple with the number of angles and a list of c_int or c_long</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>(int, 4*nangles*c_tagint)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.gather_dihedrals">
|
||
<span class="sig-name descname"><span class="pre">gather_dihedrals</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.gather_dihedrals" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of dihedrals</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_scatter.html#_CPPv423lammps_gather_dihedralsPvPv" title="lammps_gather_dihedrals"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_dihedrals()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<p>This function returns a tuple with the number of dihedrals and a
|
||
flat list of ctypes integer values with the dihedral type, dihedral atom1,
|
||
dihedral atom2, dihedral atom3, dihedral atom4 for each dihedral.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>a tuple with the number of dihedrals and a list of c_int or c_long</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>(int, 5*ndihedrals*c_tagint)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.gather_impropers">
|
||
<span class="sig-name descname"><span class="pre">gather_impropers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.gather_impropers" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of impropers</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_scatter.html#_CPPv423lammps_gather_impropersPvPv" title="lammps_gather_impropers"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_gather_impropers()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<p>This function returns a tuple with the number of impropers and a
|
||
flat list of ctypes integer values with the improper type, improper atom1,
|
||
improper atom2, improper atom3, improper atom4 for each improper.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>a tuple with the number of impropers and a list of c_int or c_long</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>(int, 5*nimpropers*c_tagint)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.encode_image_flags">
|
||
<span class="sig-name descname"><span class="pre">encode_image_flags</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">iy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">iz</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.encode_image_flags" title="Link to this definition"></a></dt>
|
||
<dd><p>convert 3 integers with image flags for x-, y-, and z-direction
|
||
into a single integer like it is used internally in LAMMPS</p>
|
||
<p>This method is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv425lammps_encode_image_flagsiii" title="lammps_encode_image_flags"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_encode_image_flags()</span></code></a>
|
||
function of library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>ix</strong> (<em>int</em>) – x-direction image flag</p></li>
|
||
<li><p><strong>iy</strong> (<em>int</em>) – y-direction image flag</p></li>
|
||
<li><p><strong>iz</strong> (<em>int</em>) – z-direction image flag</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>encoded image flags</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>lammps.c_imageint</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.decode_image_flags">
|
||
<span class="sig-name descname"><span class="pre">decode_image_flags</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">image</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.decode_image_flags" title="Link to this definition"></a></dt>
|
||
<dd><p>Convert encoded image flag integer into list of three regular integers.</p>
|
||
<p>This method is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv425lammps_decode_image_flagsiPi" title="lammps_decode_image_flags"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_decode_image_flags()</span></code></a>
|
||
function of library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>image</strong> (<em>lammps.c_imageint</em>) – encoded image flags</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list of three image flags in x-, y-, and z- direction</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>list of 3 int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.create_atoms">
|
||
<span class="sig-name descname"><span class="pre">create_atoms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">image</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shrinkexceed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.create_atoms" title="Link to this definition"></a></dt>
|
||
<dd><p>Create N atoms from list of coordinates and properties</p>
|
||
<p>This function is a wrapper around the <a class="reference internal" href="Library_scatter.html#_CPPv419lammps_create_atomsPviPKiPKiPKdPKdPKii" title="lammps_create_atoms"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_create_atoms()</span></code></a>
|
||
function of the C-library interface, and the behavior is similar except
|
||
that the <em>v</em>, <em>image</em>, and <em>shrinkexceed</em> arguments are optional and
|
||
default to <em>None</em>, <em>None</em>, and <em>False</em>, respectively. With <em>None</em> being
|
||
equivalent to a <code class="docutils literal notranslate"><span class="pre">NULL</span></code> pointer in C.</p>
|
||
<p>The lists of coordinates, types, atom IDs, velocities, image flags can
|
||
be provided in any format that may be converted into the required
|
||
internal data types. Also the list may contain more than <em>N</em> entries,
|
||
but not fewer. In the latter case, the function will return without
|
||
attempting to create atoms. You may use the <a class="reference internal" href="#lammps.lammps.encode_image_flags" title="lammps.lammps.encode_image_flags"><code class="xref py py-func docutils literal notranslate"><span class="pre">encode_image_flags</span></code></a> method to properly combine three integers
|
||
with image flags into a single integer.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>n</strong> (<em>int</em>) – number of atoms for which data is provided</p></li>
|
||
<li><p><strong>id</strong> (<em>list</em><em> of </em><em>lammps.tagint</em>) – list of atom IDs with at least n elements or None</p></li>
|
||
<li><p><strong>type</strong> (<em>list</em><em> of </em><em>int</em>) – list of atom types</p></li>
|
||
<li><p><strong>x</strong> (<em>list</em><em> of </em><em>float</em>) – list of coordinates for x-, y-, and z (flat list of 3n entries)</p></li>
|
||
<li><p><strong>v</strong> (<em>list</em><em> of </em><em>float</em>) – list of velocities for x-, y-, and z (flat list of 3n entries) or None (optional)</p></li>
|
||
<li><p><strong>image</strong> (<em>list</em><em> of </em><em>lammps.imageint</em>) – list of encoded image flags (optional)</p></li>
|
||
<li><p><strong>shrinkexceed</strong> (<em>bool</em>) – whether to expand shrink-wrap boundaries if atoms are outside the box (optional)</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>number of atoms created. 0 if insufficient or invalid data</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_mpi_support">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_mpi_support</span></span><a class="headerlink" href="#lammps.lammps.has_mpi_support" title="Link to this definition"></a></dt>
|
||
<dd><p>Report whether the LAMMPS shared library was compiled with a
|
||
real MPI library or in serial.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv429lammps_config_has_mpi_supportv" title="lammps_config_has_mpi_support"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_mpi_support()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>False when compiled with MPI STUBS, otherwise True</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.is_running">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_running</span></span><a class="headerlink" href="#lammps.lammps.is_running" title="Link to this definition"></a></dt>
|
||
<dd><p>Report whether being called from a function during a run or a minimization</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 9Oct2020.</span></p>
|
||
</div>
|
||
<p>Various LAMMPS commands must not be called during an ongoing
|
||
run or minimization. This property allows to check for that.
|
||
This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv417lammps_is_runningPv" title="lammps_is_running"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_is_running()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>True when called during a run otherwise false</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.force_timeout">
|
||
<span class="sig-name descname"><span class="pre">force_timeout</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.force_timeout" title="Link to this definition"></a></dt>
|
||
<dd><p>Trigger an immediate timeout, i.e. a “soft stop” of a run.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 9Oct2020.</span></p>
|
||
</div>
|
||
<p>This function allows to cleanly stop an ongoing run or minimization
|
||
at the next loop iteration.
|
||
This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv420lammps_force_timeoutPv" title="lammps_force_timeout"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_force_timeout()</span></code></a>
|
||
function of the library interface.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_exceptions">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_exceptions</span></span><a class="headerlink" href="#lammps.lammps.has_exceptions" title="Link to this definition"></a></dt>
|
||
<dd><p>Report whether the LAMMPS shared library was compiled with C++
|
||
exceptions handling enabled</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv428lammps_config_has_exceptionsv" title="lammps_config_has_exceptions"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_exceptions()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>state of C++ exception support</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_gzip_support">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_gzip_support</span></span><a class="headerlink" href="#lammps.lammps.has_gzip_support" title="Link to this definition"></a></dt>
|
||
<dd><p>Report whether the LAMMPS shared library was compiled with support
|
||
for reading and writing compressed files through <code class="docutils literal notranslate"><span class="pre">gzip</span></code>.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv430lammps_config_has_gzip_supportv" title="lammps_config_has_gzip_support"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_gzip_support()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>state of gzip support</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_png_support">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_png_support</span></span><a class="headerlink" href="#lammps.lammps.has_png_support" title="Link to this definition"></a></dt>
|
||
<dd><p>Report whether the LAMMPS shared library was compiled with support
|
||
for writing images in PNG format.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv429lammps_config_has_png_supportv" title="lammps_config_has_png_support"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_png_support()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>state of PNG support</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_jpeg_support">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_jpeg_support</span></span><a class="headerlink" href="#lammps.lammps.has_jpeg_support" title="Link to this definition"></a></dt>
|
||
<dd><p>Report whether the LAMMPS shared library was compiled with support
|
||
for writing images in JPEG format.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv430lammps_config_has_jpeg_supportv" title="lammps_config_has_jpeg_support"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_jpeg_support()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>state of JPEG support</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_ffmpeg_support">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_ffmpeg_support</span></span><a class="headerlink" href="#lammps.lammps.has_ffmpeg_support" title="Link to this definition"></a></dt>
|
||
<dd><p>State of support for writing movies with <code class="docutils literal notranslate"><span class="pre">ffmpeg</span></code> in the LAMMPS shared library</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv432lammps_config_has_ffmpeg_supportv" title="lammps_config_has_ffmpeg_support"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_ffmpeg_support()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>state of ffmpeg support</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_curl_support">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_curl_support</span></span><a class="headerlink" href="#lammps.lammps.has_curl_support" title="Link to this definition"></a></dt>
|
||
<dd><p>Report whether the LAMMPS shared library was compiled with support
|
||
for downloading files through libcurl.</p>
|
||
<p>This is a wrapper around the <code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_curl_support()</span></code>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>state of CURL support</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_package">
|
||
<span class="sig-name descname"><span class="pre">has_package</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.has_package" title="Link to this definition"></a></dt>
|
||
<dd><p>Report if the named package has been enabled in the LAMMPS shared library.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 3Nov2022.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv425lammps_config_has_packagePKc" title="lammps_config_has_package"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_has_package()</span></code></a>
|
||
function of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>name</strong> (<em>string</em>) – name of the package</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>state of package availability</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.accelerator_config">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">accelerator_config</span></span><a class="headerlink" href="#lammps.lammps.accelerator_config" title="Link to this definition"></a></dt>
|
||
<dd><p>Return table with available accelerator configuration settings.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv425lammps_config_acceleratorPKcPKcPKc" title="lammps_config_accelerator"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_accelerator()</span></code></a>
|
||
function of the library interface which loops over all known packages
|
||
and categories and returns enabled features as a nested dictionary
|
||
with all enabled settings as list of strings.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>nested dictionary with all known enabled settings as list of strings</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>dictionary</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_gpu_device">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">has_gpu_device</span></span><a class="headerlink" href="#lammps.lammps.has_gpu_device" title="Link to this definition"></a></dt>
|
||
<dd><p>Availability of GPU package compatible device</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv421lammps_has_gpu_devicev" title="lammps_has_gpu_device"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_has_gpu_device()</span></code></a>
|
||
function of the C library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>True if a GPU package compatible device is present, otherwise False</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_gpu_device_info">
|
||
<span class="sig-name descname"><span class="pre">get_gpu_device_info</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_gpu_device_info" title="Link to this definition"></a></dt>
|
||
<dd><p>Return a string with detailed information about any devices that are
|
||
usable by the GPU package.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_config.html#_CPPv426lammps_get_gpu_device_infoPci" title="lammps_get_gpu_device_info"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_get_gpu_device_info()</span></code></a>
|
||
function of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>GPU device info string</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.lammps.installed_packages">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">installed_packages</span></span><a class="headerlink" href="#lammps.lammps.installed_packages" title="Link to this definition"></a></dt>
|
||
<dd><p>List of the names of enabled packages in the LAMMPS shared library</p>
|
||
<p>This is a wrapper around the functions <a class="reference internal" href="Library_config.html#_CPPv427lammps_config_package_countv" title="lammps_config_package_count"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_package_count()</span></code></a>
|
||
and <a class="reference internal" href="Library_config.html#_CPPv426lammps_config_package_nameiPci" title="lammps_config_package_name"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_config_package_name()</span></code></a> of the library interface.</p>
|
||
<p>:return</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_style">
|
||
<span class="sig-name descname"><span class="pre">has_style</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">category</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.has_style" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns whether a given style name is available in a given category</p>
|
||
<p>This is a wrapper around the function <a class="reference internal" href="Library_config.html#_CPPv416lammps_has_stylePvPKcPKc" title="lammps_has_style"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_has_style()</span></code></a>
|
||
of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>category</strong> (<em>string</em>) – name of category</p></li>
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the style</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>true if style is available in given category</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.available_styles">
|
||
<span class="sig-name descname"><span class="pre">available_styles</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">category</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.available_styles" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns a list of styles available for a given category</p>
|
||
<p>This is a wrapper around the functions <a class="reference internal" href="Library_config.html#_CPPv418lammps_style_countPvPKc" title="lammps_style_count"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_style_count()</span></code></a>
|
||
and <a class="reference internal" href="Library_config.html#_CPPv417lammps_style_namePvPKciPci" title="lammps_style_name"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_style_name()</span></code></a> of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>category</strong> (<em>string</em>) – name of category</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list of style names in given category</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.has_id">
|
||
<span class="sig-name descname"><span class="pre">has_id</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">category</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.has_id" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns whether a given ID name is available in a given category</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 9Oct2020.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the function <a class="reference internal" href="Library_config.html#_CPPv413lammps_has_idPvPKcPKc" title="lammps_has_id"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_has_id()</span></code></a>
|
||
of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>category</strong> (<em>string</em>) – name of category</p></li>
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the ID</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>true if ID is available in given category</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.available_ids">
|
||
<span class="sig-name descname"><span class="pre">available_ids</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">category</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.available_ids" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns a list of IDs available for a given category</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 9Oct2020.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the functions <a class="reference internal" href="Library_config.html#_CPPv415lammps_id_countPvPKc" title="lammps_id_count"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_id_count()</span></code></a>
|
||
and <a class="reference internal" href="Library_config.html#_CPPv414lammps_id_namePvPKciPci" title="lammps_id_name"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_id_name()</span></code></a> of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>category</strong> (<em>string</em>) – name of category</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list of id names in given category</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.available_plugins">
|
||
<span class="sig-name descname"><span class="pre">available_plugins</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">category</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.available_plugins" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns a list of plugins available for a given category</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 10Mar2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the functions <code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_plugin_count()</span></code>
|
||
and <code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_plugin_name()</span></code> of the library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>list of style/name pairs of loaded plugins</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.set_fix_external_callback">
|
||
<span class="sig-name descname"><span class="pre">set_fix_external_callback</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">callback</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">caller</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.set_fix_external_callback" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the callback function for a fix external instance with a given fix ID.</p>
|
||
<p>Optionally also set a reference to the calling object.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv432lammps_set_fix_external_callbackPvPKc16FixExternalFnPtrPv" title="lammps_set_fix_external_callback"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_set_fix_external_callback()</span></code></a> function
|
||
of the C-library interface. However this is set up to call a Python function with
|
||
the following arguments.</p>
|
||
<ul class="simple">
|
||
<li><p>object is the value of the “caller” argument</p></li>
|
||
<li><p>ntimestep is the current timestep</p></li>
|
||
<li><p>nlocal is the number of local atoms on the current MPI process</p></li>
|
||
<li><p>tag is a 1d NumPy array of integers representing the atom IDs of the local atoms</p></li>
|
||
<li><p>x is a 2d NumPy array of doubles of the coordinates of the local atoms</p></li>
|
||
<li><p>f is a 2d NumPy array of doubles of the forces on the local atoms that will be added</p></li>
|
||
</ul>
|
||
<div class="versionchanged">
|
||
<p><span class="versionmodified changed">Changed in version 28Jul2021.</span></p>
|
||
</div>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>callback</strong> – Python function that will be called from fix external</p></li>
|
||
<li><p><strong>caller</strong> – reference to some object passed to the callback function</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>function</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>object, optional</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.fix_external_get_force">
|
||
<span class="sig-name descname"><span class="pre">fix_external_get_force</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.fix_external_get_force" title="Link to this definition"></a></dt>
|
||
<dd><p>Get access to the array with per-atom forces of a fix external instance with a given fix ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv429lammps_fix_external_get_forcePvPKc" title="lammps_fix_external_get_force"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_fix_external_get_force()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>requested data</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>ctypes.POINTER(ctypes.POINTER(ctypes.double))</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.fix_external_set_energy_global">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_energy_global</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eng</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.fix_external_set_energy_global" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the global energy contribution for a fix external instance with the given ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv437lammps_fix_external_set_energy_globalPvPKcd" title="lammps_fix_external_set_energy_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_fix_external_set_energy_global()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>eng</strong> – potential energy value to be added by fix external</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.fix_external_set_virial_global">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_virial_global</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">virial</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.fix_external_set_virial_global" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the global virial contribution for a fix external instance with the given ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv437lammps_fix_external_set_virial_globalPvPKcPd" title="lammps_fix_external_set_virial_global"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_fix_external_set_virial_global()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>eng</strong> – list of 6 floating point numbers with the virial to be added by fix external</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.fix_external_set_energy_peratom">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_energy_peratom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eatom</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.fix_external_set_energy_peratom" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the per-atom energy contribution for a fix external instance with the given ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv438lammps_fix_external_set_energy_peratomPvPKcPd" title="lammps_fix_external_set_energy_peratom"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_fix_external_set_energy_peratom()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>eatom</strong> – list of potential energy values for local atoms to be added by fix external</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.fix_external_set_virial_peratom">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_virial_peratom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vatom</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.fix_external_set_virial_peratom" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the per-atom virial contribution for a fix external instance with the given ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv438lammps_fix_external_set_virial_peratomPvPKcPPd" title="lammps_fix_external_set_virial_peratom"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_fix_external_set_virial_peratom()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>vatom</strong> – list of natoms lists with 6 floating point numbers to be added by fix external</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.fix_external_set_vector_length">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_vector_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">length</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.fix_external_set_vector_length" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the vector length for a global vector stored with fix external for analysis</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv437lammps_fix_external_set_vector_lengthPvPKci" title="lammps_fix_external_set_vector_length"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_fix_external_set_vector_length()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>length</strong> – length of the global vector</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.fix_external_set_vector">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_vector</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">val</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.fix_external_set_vector" title="Link to this definition"></a></dt>
|
||
<dd><p>Store a global vector value for a fix external instance with the given ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around the <a class="reference internal" href="Library_utility.html#_CPPv430lammps_fix_external_set_vectorPvPKcid" title="lammps_fix_external_set_vector"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_fix_external_set_vector()</span></code></a> function
|
||
of the C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>idx</strong> – 1-based index of the value in the global vector</p></li>
|
||
<li><p><strong>val</strong> – value to be stored in the global vector</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_neighlist">
|
||
<span class="sig-name descname"><span class="pre">get_neighlist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_neighlist" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns an instance of <a class="reference internal" href="#lammps.NeighList" title="lammps.NeighList"><code class="xref py py-class docutils literal notranslate"><span class="pre">NeighList</span></code></a> which wraps access to the neighbor list with the given index</p>
|
||
<p>See <a class="reference internal" href="#lammps.numpy_wrapper.numpy_wrapper.get_neighlist" title="lammps.numpy_wrapper.numpy_wrapper.get_neighlist"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.numpy.get_neighlist()</span></code></a> if you want to use
|
||
NumPy arrays instead of <code class="docutils literal notranslate"><span class="pre">c_int</span></code> pointers.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>idx</strong> (<em>int</em>) – index of neighbor list</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>an instance of <a class="reference internal" href="#lammps.NeighList" title="lammps.NeighList"><code class="xref py py-class docutils literal notranslate"><span class="pre">NeighList</span></code></a> wrapping access to neighbor list data</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><a class="reference internal" href="#lammps.NeighList" title="lammps.NeighList">NeighList</a></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_neighlist_size">
|
||
<span class="sig-name descname"><span class="pre">get_neighlist_size</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_neighlist_size" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the number of elements in neighbor list with the given index</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>idx</strong> (<em>int</em>) – neighbor list index</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>number of elements in neighbor list with index idx</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.get_neighlist_element_neighbors">
|
||
<span class="sig-name descname"><span class="pre">get_neighlist_element_neighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.get_neighlist_element_neighbors" title="Link to this definition"></a></dt>
|
||
<dd><p>Return data of neighbor list entry</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>element</strong> (<em>int</em>) – neighbor list index</p></li>
|
||
<li><p><strong>element</strong> – neighbor list element index</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>tuple with atom local index, number of neighbors and array of neighbor local atom indices</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>(int, int, POINTER(c_int))</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.find_pair_neighlist">
|
||
<span class="sig-name descname"><span class="pre">find_pair_neighlist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">style</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exact</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nsub</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reqid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.find_pair_neighlist" title="Link to this definition"></a></dt>
|
||
<dd><p>Find neighbor list index of pair style neighbor list</p>
|
||
<p>Search for a neighbor list requested by a pair style instance that
|
||
matches “style”. If exact is True, the pair style name must match
|
||
exactly. If exact is False, the pair style name is matched against
|
||
“style” as regular expression or sub-string. If the pair style is a
|
||
hybrid pair style, the style is instead matched against the hybrid
|
||
sub-styles. If the same pair style is used as sub-style multiple
|
||
types, you must set nsub to a value n > 0 which indicates the nth
|
||
instance of that sub-style to be used (same as for the pair_coeff
|
||
command). The default value of 0 will fail to match in that case.</p>
|
||
<p>Once the pair style instance has been identified, it may have
|
||
requested multiple neighbor lists. Those are uniquely identified by
|
||
a request ID > 0 as set by the pair style. Otherwise the request
|
||
ID is 0.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>style</strong> (<em>string</em>) – name of pair style that should be searched for</p></li>
|
||
<li><p><strong>exact</strong> (<em>bool</em><em>, </em><em>optional</em>) – controls whether style should match exactly or only must be contained in pair style name, defaults to True</p></li>
|
||
<li><p><strong>nsub</strong> (<em>int</em><em>, </em><em>optional</em>) – match nsub-th hybrid sub-style, defaults to 0</p></li>
|
||
<li><p><strong>reqid</strong> (<em>int</em><em>, </em><em>optional</em>) – list request id, > 0 in case there are more than one, defaults to 0</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>neighbor list index if found, otherwise -1</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.find_fix_neighlist">
|
||
<span class="sig-name descname"><span class="pre">find_fix_neighlist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fixid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reqid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.find_fix_neighlist" title="Link to this definition"></a></dt>
|
||
<dd><p>Find neighbor list index of fix neighbor list</p>
|
||
<p>The fix instance requesting the neighbor list is uniquely identified
|
||
by the fix ID. In case the fix has requested multiple neighbor
|
||
lists, those are uniquely identified by a request ID > 0 as set by
|
||
the fix. Otherwise the request ID is 0 (the default).</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fixid</strong> (<em>string</em>) – name of fix</p></li>
|
||
<li><p><strong>reqid</strong> (<em>int</em><em>, </em><em>optional</em>) – id of neighbor list request, in case there are more than one request, defaults to 0</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>neighbor list index if found, otherwise -1</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.lammps.find_compute_neighlist">
|
||
<span class="sig-name descname"><span class="pre">find_compute_neighlist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">computeid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reqid</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.lammps.find_compute_neighlist" title="Link to this definition"></a></dt>
|
||
<dd><p>Find neighbor list index of compute neighbor list</p>
|
||
<p>The compute instance requesting the neighbor list is uniquely
|
||
identified by the compute ID. In case the compute has requested
|
||
multiple neighbor lists, those are uniquely identified by a request
|
||
ID > 0 as set by the compute. Otherwise the request ID is 0 (the
|
||
default).</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>computeid</strong> (<em>string</em>) – name of compute</p></li>
|
||
<li><p><strong>reqid</strong> (<em>int</em><em>, </em><em>optional</em>) – index of neighbor list request, in case there are more than one request, defaults to 0</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>neighbor list index if found, otherwise -1</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.numpy_wrapper.</span></span><span class="sig-name descname"><span class="pre">numpy_wrapper</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lmp</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper" title="Link to this definition"></a></dt>
|
||
<dd><p>lammps API NumPy Wrapper</p>
|
||
<p>This is a wrapper class that provides additional methods on top of an
|
||
existing <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> instance. The methods transform raw ctypes
|
||
pointers into NumPy arrays, which give direct access to the
|
||
original data while protecting against out-of-bounds accesses.</p>
|
||
<p>There is no need to explicitly instantiate this class. Each instance
|
||
of <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> has a <code class="xref py py-attr docutils literal notranslate"><span class="pre">numpy</span></code> property
|
||
that returns an instance.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>lmp</strong> (<a class="reference internal" href="#lammps.lammps" title="lammps.lammps"><em>lammps</em></a>) – instance of the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> class</p>
|
||
</dd>
|
||
</dl>
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.extract_atom">
|
||
<span class="sig-name descname"><span class="pre">extract_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nelem</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.extract_atom" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve per-atom properties from LAMMPS as NumPy arrays</p>
|
||
<p>This is a wrapper around the <code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_atom()</span></code> method.
|
||
It behaves the same as the original method, but returns NumPy arrays
|
||
instead of <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointers.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>The returned vectors or arrays of per-atom data are dimensioned
|
||
according to the return value of <code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_atom_size()</span></code>.
|
||
Except for the “mass” property, the underlying storage will always be
|
||
dimensioned for the range [0:nmax]. The actual usable data may be
|
||
only in the range [0:nlocal] or [0:nlocal][0:dim]. Whether there is
|
||
valid data in the range [nlocal:nlocal+nghost] or [nlocal:local+nghost][0:dim]
|
||
depends on whether the property of interest is also updated for ghost atoms.
|
||
Also the value of <em>dim</em> depends on the value of <em>name</em>. By using the optional
|
||
<em>nelem</em> and <em>dim</em> parameters the dimensions of the returned NumPy array can
|
||
be overridden. There is no check whether the number of elements chosen is valid.</p>
|
||
</div>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the property</p></li>
|
||
<li><p><strong>dtype</strong> (<em>int</em><em>, </em><em>optional</em>) – type of the returned data (see <a class="reference internal" href="#py-datatype-constants"><span class="std std-ref">Data Types</span></a>)</p></li>
|
||
<li><p><strong>nelem</strong> (<em>int</em><em>, </em><em>optional</em>) – number of elements in array</p></li>
|
||
<li><p><strong>dim</strong> (<em>int</em><em>, </em><em>optional</em>) – dimension of each element</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>requested data as NumPy array with direct access to C data or None</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.extract_compute">
|
||
<span class="sig-name descname"><span class="pre">extract_compute</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cstyle</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ctype</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.extract_compute" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve data from a LAMMPS compute</p>
|
||
<p>This is a wrapper around the
|
||
<a class="reference internal" href="#lammps.lammps.extract_compute" title="lammps.lammps.extract_compute"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_compute()</span></code></a> method.
|
||
It behaves the same as the original method, but returns NumPy arrays
|
||
instead of <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointers.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>cid</strong> (<em>string</em>) – compute ID</p></li>
|
||
<li><p><strong>cstyle</strong> (<em>int</em>) – style of the data retrieve (global, atom, or local), see <a class="reference internal" href="#py-style-constants"><span class="std std-ref">Style Constants</span></a></p></li>
|
||
<li><p><strong>ctype</strong> (<em>int</em>) – type of the returned data (scalar, vector, or array), see <a class="reference internal" href="#py-type-constants"><span class="std std-ref">Type Constants</span></a></p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>requested data either as float, as NumPy array with direct access to C data, or None</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float, numpy.array, or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.extract_fix">
|
||
<span class="sig-name descname"><span class="pre">extract_fix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fstyle</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ftype</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nrow</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ncol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.extract_fix" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve data from a LAMMPS fix</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="#lammps.lammps.extract_fix" title="lammps.lammps.extract_fix"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_fix()</span></code></a> method.
|
||
It behaves the same as the original method, but returns NumPy arrays
|
||
instead of <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointers.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>When requesting global data, the fix data can only be accessed one
|
||
item at a time without access to the whole vector or array. Thus this
|
||
function will always return a scalar. To access vector or array elements
|
||
the “nrow” and “ncol” arguments need to be set accordingly (they default to 0).</p>
|
||
</div>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fid</strong> (<em>string</em>) – fix ID</p></li>
|
||
<li><p><strong>fstyle</strong> (<em>int</em>) – style of the data retrieve (global, atom, or local), see <a class="reference internal" href="#py-style-constants"><span class="std std-ref">Style Constants</span></a></p></li>
|
||
<li><p><strong>ftype</strong> (<em>int</em>) – type or size of the returned data (scalar, vector, or array), see <a class="reference internal" href="#py-type-constants"><span class="std std-ref">Type Constants</span></a></p></li>
|
||
<li><p><strong>nrow</strong> (<em>int</em>) – index of global vector element or row index of global array element</p></li>
|
||
<li><p><strong>ncol</strong> (<em>int</em>) – column index of global array element</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>requested data</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>integer or double value, pointer to 1d or 2d double array or None</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.extract_variable">
|
||
<span class="sig-name descname"><span class="pre">extract_variable</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">group</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vartype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.extract_variable" title="Link to this definition"></a></dt>
|
||
<dd><p>Evaluate a LAMMPS variable and return its data</p>
|
||
<p>This function is a wrapper around the function
|
||
<a class="reference internal" href="#lammps.lammps.extract_variable" title="lammps.lammps.extract_variable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.extract_variable()</span></code></a>
|
||
method. It behaves the same as the original method, but returns NumPy arrays
|
||
instead of <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointers.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – name of the variable to execute</p></li>
|
||
<li><p><strong>group</strong> (<em>string</em>) – name of group for atom-style variable (ignored for equal-style variables)</p></li>
|
||
<li><p><strong>vartype</strong> (<em>int</em>) – type of variable, see <a class="reference internal" href="#py-vartype-constants"><span class="std std-ref">Variable Type Constants</span></a></p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>the requested data or None</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>c_double, numpy.array, or NoneType</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.gather_bonds">
|
||
<span class="sig-name descname"><span class="pre">gather_bonds</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.gather_bonds" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of bonds as a NumPy array</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around <a class="reference internal" href="#lammps.lammps.gather_bonds" title="lammps.lammps.gather_bonds"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.gather_bonds()</span></code></a>.
|
||
It behaves the same as the original method, but returns a NumPy array instead
|
||
of a <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> list.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>the requested data as a 2d-integer numpy array</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>numpy.array(nbonds,3)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.gather_angles">
|
||
<span class="sig-name descname"><span class="pre">gather_angles</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.gather_angles" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of angles as a NumPy array</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around <a class="reference internal" href="#lammps.lammps.gather_angles" title="lammps.lammps.gather_angles"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.gather_angles()</span></code></a>.
|
||
It behaves the same as the original method, but returns a NumPy array instead
|
||
of a <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> list.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>the requested data as a 2d-integer numpy array</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>numpy.array(nangles,4)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.gather_dihedrals">
|
||
<span class="sig-name descname"><span class="pre">gather_dihedrals</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.gather_dihedrals" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of dihedrals as a NumPy array</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around <a class="reference internal" href="#lammps.lammps.gather_dihedrals" title="lammps.lammps.gather_dihedrals"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.gather_dihedrals()</span></code></a>.
|
||
It behaves the same as the original method, but returns a NumPy array instead
|
||
of a <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> list.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>the requested data as a 2d-integer numpy array</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>numpy.array(ndihedrals,5)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.gather_impropers">
|
||
<span class="sig-name descname"><span class="pre">gather_impropers</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.gather_impropers" title="Link to this definition"></a></dt>
|
||
<dd><p>Retrieve global list of impropers as a NumPy array</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 8Feb2023.</span></p>
|
||
</div>
|
||
<p>This is a wrapper around <a class="reference internal" href="#lammps.lammps.gather_impropers" title="lammps.lammps.gather_impropers"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.gather_impropers()</span></code></a>.
|
||
It behaves the same as the original method, but returns a NumPy array instead
|
||
of a <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> list.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>the requested data as a 2d-integer numpy array</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>numpy.array(nimpropers,5)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.fix_external_get_force">
|
||
<span class="sig-name descname"><span class="pre">fix_external_get_force</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.fix_external_get_force" title="Link to this definition"></a></dt>
|
||
<dd><p>Get access to the array with per-atom forces of a fix external instance with a given fix ID.</p>
|
||
<div class="versionchanged">
|
||
<p><span class="versionmodified changed">Changed in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This function is a wrapper around the
|
||
<a class="reference internal" href="#lammps.lammps.fix_external_get_force" title="lammps.lammps.fix_external_get_force"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.fix_external_get_force()</span></code></a>
|
||
method. It behaves the same as the original method, but returns a NumPy array instead
|
||
of a <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointer.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>requested data</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>numpy.array</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.fix_external_set_energy_peratom">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_energy_peratom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eatom</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.fix_external_set_energy_peratom" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the per-atom energy contribution for a fix external instance with the given ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This function is an alternative to
|
||
<a class="reference internal" href="#lammps.lammps.fix_external_set_energy_peratom" title="lammps.lammps.fix_external_set_energy_peratom"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.fix_external_set_energy_peratom()</span></code></a>
|
||
method. It behaves the same as the original method, but accepts a NumPy array
|
||
instead of a list as argument.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>eatom</strong> – per-atom potential energy</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.fix_external_set_virial_peratom">
|
||
<span class="sig-name descname"><span class="pre">fix_external_set_virial_peratom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fix_id</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vatom</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.fix_external_set_virial_peratom" title="Link to this definition"></a></dt>
|
||
<dd><p>Set the per-atom virial contribution for a fix external instance with the given ID.</p>
|
||
<div class="versionadded">
|
||
<p><span class="versionmodified added">Added in version 28Jul2021.</span></p>
|
||
</div>
|
||
<p>This function is an alternative to
|
||
<a class="reference internal" href="#lammps.lammps.fix_external_set_virial_peratom" title="lammps.lammps.fix_external_set_virial_peratom"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.fix_external_set_virial_peratom()</span></code></a>
|
||
method. It behaves the same as the original method, but accepts a NumPy array
|
||
instead of a list as argument.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>fix_id</strong> – Fix-ID of a fix external instance</p></li>
|
||
<li><p><strong>eatom</strong> – per-atom potential energy</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>string</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.get_neighlist">
|
||
<span class="sig-name descname"><span class="pre">get_neighlist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.get_neighlist" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns an instance of <a class="reference internal" href="#lammps.numpy_wrapper.NumPyNeighList" title="lammps.numpy_wrapper.NumPyNeighList"><code class="xref py py-class docutils literal notranslate"><span class="pre">NumPyNeighList</span></code></a> which wraps access to the neighbor list with the given index</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>idx</strong> (<em>int</em>) – index of neighbor list</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>an instance of <a class="reference internal" href="#lammps.numpy_wrapper.NumPyNeighList" title="lammps.numpy_wrapper.NumPyNeighList"><code class="xref py py-class docutils literal notranslate"><span class="pre">NumPyNeighList</span></code></a> wrapping access to neighbor list data</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><a class="reference internal" href="#lammps.numpy_wrapper.NumPyNeighList" title="lammps.numpy_wrapper.NumPyNeighList">NumPyNeighList</a></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors">
|
||
<span class="sig-name descname"><span class="pre">get_neighlist_element_neighbors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors" title="Link to this definition"></a></dt>
|
||
<dd><p>Return data of neighbor list entry</p>
|
||
<p>This function is a wrapper around the function
|
||
<a class="reference internal" href="#lammps.lammps.get_neighlist_element_neighbors" title="lammps.lammps.get_neighlist_element_neighbors"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.get_neighlist_element_neighbors()</span></code></a>
|
||
method. It behaves the same as the original method, but returns a NumPy array containing the neighbors
|
||
instead of a <code class="docutils literal notranslate"><span class="pre">ctypes</span></code> pointer.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>element</strong> (<em>int</em>) – neighbor list index</p></li>
|
||
<li><p><strong>element</strong> – neighbor list element index</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>tuple with atom local index and numpy array of neighbor local atom indices</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>(int, numpy.array)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="the-pylammps-class-api">
|
||
<h2><span class="section-number">2.4.2. </span>The <code class="docutils literal notranslate"><span class="pre">PyLammps</span></code> class API<a class="headerlink" href="#the-pylammps-class-api" title="Link to this heading"></a></h2>
|
||
<p>The <a class="reference internal" href="#lammps.PyLammps" title="lammps.PyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">PyLammps</span></code></a> class is a wrapper that creates a
|
||
simpler, more “Pythonic” interface to common LAMMPS functionality. LAMMPS
|
||
data structures are exposed through objects and properties. This makes Python
|
||
scripts shorter and more concise. See the <a class="reference internal" href="Howto_pylammps.html"><span class="doc">PyLammps Tutorial</span></a> for an introduction on how to use this interface.</p>
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">PyLammps</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmdargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps" title="Link to this definition"></a></dt>
|
||
<dd><p>This is a Python wrapper class around the lower-level
|
||
<a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> class, exposing a more Python-like,
|
||
object-oriented interface for prototyping systems inside of IPython and
|
||
Jupyter notebooks.</p>
|
||
<p>It either creates its own instance of <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> or can be
|
||
initialized with an existing instance. The arguments are the same of the
|
||
lower-level interface. The original interface can still be accessed via
|
||
<code class="xref py py-attr docutils literal notranslate"><span class="pre">PyLammps.lmp</span></code>.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – “machine” name of the shared LAMMPS library (“mpi” loads <code class="docutils literal notranslate"><span class="pre">liblammps_mpi.so</span></code>, “” loads <code class="docutils literal notranslate"><span class="pre">liblammps.so</span></code>)</p></li>
|
||
<li><p><strong>cmdargs</strong> (<em>list</em>) – list of command line arguments to be passed to the <a class="reference internal" href="Library_create.html#_CPPv411lammps_openiPPc8MPI_CommPPv" title="lammps_open"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_open()</span></code></a> function. The executable name is automatically added.</p></li>
|
||
<li><p><strong>ptr</strong> (<em>pointer</em>) – pointer to a LAMMPS C++ class instance when called from an embedded Python interpreter. None means load symbols from shared library.</p></li>
|
||
<li><p><strong>comm</strong> (<em>MPI_Comm</em>) – MPI communicator (as provided by <a class="reference external" href="https://mpi4py.readthedocs.io/">mpi4py</a>). <code class="docutils literal notranslate"><span class="pre">None</span></code> means use <code class="docutils literal notranslate"><span class="pre">MPI_COMM_WORLD</span></code> implicitly.</p></li>
|
||
<li><p><strong>verbose</strong> (<em>bool</em>) – print all LAMMPS output to stdout</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Variables<span class="colon">:</span></dt>
|
||
<dd class="field-even"><ul class="simple">
|
||
<li><p><strong>lmp</strong> (<a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a>) – instance of original LAMMPS Python interface</p></li>
|
||
<li><p><strong>runs</strong> – list of completed runs, each storing the thermo output</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.close">
|
||
<span class="sig-name descname"><span class="pre">close</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.close" title="Link to this definition"></a></dt>
|
||
<dd><p>Explicitly delete a LAMMPS instance</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="#lammps.lammps.close" title="lammps.lammps.close"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.close()</span></code></a> of the Python interface.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.version">
|
||
<span class="sig-name descname"><span class="pre">version</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.version" title="Link to this definition"></a></dt>
|
||
<dd><p>Return a numerical representation of the LAMMPS version in use.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="#lammps.lammps.version" title="lammps.lammps.version"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.version()</span></code></a> function of the Python interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>version number</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.file">
|
||
<span class="sig-name descname"><span class="pre">file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.file" title="Link to this definition"></a></dt>
|
||
<dd><p>Read LAMMPS commands from a file.</p>
|
||
<p>This is a wrapper around the <a class="reference internal" href="#lammps.lammps.file" title="lammps.lammps.file"><code class="xref py py-meth docutils literal notranslate"><span class="pre">lammps.file()</span></code></a> function of the Python interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>path</strong> (<em>string</em>) – Name of the file/path with LAMMPS commands</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.enable_cmd_history">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">enable_cmd_history</span></span><a class="headerlink" href="#lammps.PyLammps.enable_cmd_history" title="Link to this definition"></a></dt>
|
||
<dd><dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Return whether command history is saved</p>
|
||
</dd>
|
||
<dt class="field-even">Setter<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>Set if command history should be saved</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>bool</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.write_script">
|
||
<span class="sig-name descname"><span class="pre">write_script</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filepath</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.write_script" title="Link to this definition"></a></dt>
|
||
<dd><p>Write LAMMPS script file containing all commands executed up until now</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>filepath</strong> (<em>string</em>) – path to script file that should be written</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.clear_cmd_history">
|
||
<span class="sig-name descname"><span class="pre">clear_cmd_history</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.clear_cmd_history" title="Link to this definition"></a></dt>
|
||
<dd><p>Clear LAMMPS command history up to this point</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.append_cmd_history">
|
||
<span class="sig-name descname"><span class="pre">append_cmd_history</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cmd</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.append_cmd_history" title="Link to this definition"></a></dt>
|
||
<dd><p>Commands will be added to the command history but not executed.</p>
|
||
<p>Add <cite>commands</cite> only to the command history, but do not execute them, so that you can
|
||
conveniently create LAMMPS input files, using
|
||
<a class="reference internal" href="#lammps.PyLammps.write_script" title="lammps.PyLammps.write_script"><code class="xref py py-meth docutils literal notranslate"><span class="pre">PyLammps.write_script()</span></code></a>.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.command">
|
||
<span class="sig-name descname"><span class="pre">command</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cmd</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.command" title="Link to this definition"></a></dt>
|
||
<dd><p>Execute LAMMPS command</p>
|
||
<p>If <a class="reference internal" href="#lammps.PyLammps.enable_cmd_history" title="lammps.PyLammps.enable_cmd_history"><code class="xref py py-attr docutils literal notranslate"><span class="pre">PyLammps.enable_cmd_history</span></code></a> is set to <code class="docutils literal notranslate"><span class="pre">True</span></code>, commands executed
|
||
will be recorded. The entire command history can be written to a file using
|
||
<a class="reference internal" href="#lammps.PyLammps.write_script" title="lammps.PyLammps.write_script"><code class="xref py py-meth docutils literal notranslate"><span class="pre">PyLammps.write_script()</span></code></a>. To clear the command history, use
|
||
<a class="reference internal" href="#lammps.PyLammps.clear_cmd_history" title="lammps.PyLammps.clear_cmd_history"><code class="xref py py-meth docutils literal notranslate"><span class="pre">PyLammps.clear_cmd_history()</span></code></a>.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>cmd</strong> – command string that should be executed</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>cmd: string</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.run">
|
||
<span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.run" title="Link to this definition"></a></dt>
|
||
<dd><p>Execute LAMMPS run command with given arguments</p>
|
||
<p>Thermo data of the run is recorded and saved as new entry in
|
||
<code class="xref py py-attr docutils literal notranslate"><span class="pre">PyLammps.runs</span></code>. The latest run can be retrieved by
|
||
<a class="reference internal" href="#lammps.PyLammps.last_run" title="lammps.PyLammps.last_run"><code class="xref py py-attr docutils literal notranslate"><span class="pre">PyLammps.last_run</span></code></a>.</p>
|
||
<p>Note, for recording of all thermo steps during a run, the PYTHON package
|
||
needs to be enabled in LAMMPS. Otherwise, it will only capture the final
|
||
timestep.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.last_run">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">last_run</span></span><a class="headerlink" href="#lammps.PyLammps.last_run" title="Link to this definition"></a></dt>
|
||
<dd><p>Return data produced of last completed run command</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns an object containing information about the last run command</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>dict</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.atoms">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">atoms</span></span><a class="headerlink" href="#lammps.PyLammps.atoms" title="Link to this definition"></a></dt>
|
||
<dd><p>All atoms of this LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns a list of atoms currently in the system</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p><a class="reference internal" href="#lammps.AtomList" title="lammps.AtomList">AtomList</a></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.system">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">system</span></span><a class="headerlink" href="#lammps.PyLammps.system" title="Link to this definition"></a></dt>
|
||
<dd><p>The system state of this LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns an object with properties storing the current system state</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>namedtuple</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.communication">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">communication</span></span><a class="headerlink" href="#lammps.PyLammps.communication" title="Link to this definition"></a></dt>
|
||
<dd><p>The communication state of this LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns an object with properties storing the current communication state</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>namedtuple</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.computes">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">computes</span></span><a class="headerlink" href="#lammps.PyLammps.computes" title="Link to this definition"></a></dt>
|
||
<dd><p>The list of active computes of this LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns a list of computes that are currently active in this LAMMPS instance</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.dumps">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">dumps</span></span><a class="headerlink" href="#lammps.PyLammps.dumps" title="Link to this definition"></a></dt>
|
||
<dd><p>The list of active dumps of this LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns a list of dumps that are currently active in this LAMMPS instance</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.fixes">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">fixes</span></span><a class="headerlink" href="#lammps.PyLammps.fixes" title="Link to this definition"></a></dt>
|
||
<dd><p>The list of active fixes of this LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns a list of fixes that are currently active in this LAMMPS instance</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.groups">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">groups</span></span><a class="headerlink" href="#lammps.PyLammps.groups" title="Link to this definition"></a></dt>
|
||
<dd><p>The list of active atom groups of this LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns a list of atom groups that are currently active in this LAMMPS instance</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.variables">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">variables</span></span><a class="headerlink" href="#lammps.PyLammps.variables" title="Link to this definition"></a></dt>
|
||
<dd><p>Returns a dictionary of all variables defined in the current LAMMPS instance</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Returns a dictionary of all variables that are defined in this LAMMPS instance</p>
|
||
</dd>
|
||
<dt class="field-even">Type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>dict</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.eval">
|
||
<span class="sig-name descname"><span class="pre">eval</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">expr</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.eval" title="Link to this definition"></a></dt>
|
||
<dd><p>Evaluate LAMMPS input file expression.</p>
|
||
<p>This is equivalent to using immediate variable expressions in the format “$(…)”
|
||
in the LAMMPS input and will return the result of that expression.</p>
|
||
<div class="admonition warning">
|
||
<p class="admonition-title">Warning</p>
|
||
<p>This function is only supported on MPI rank 0. Calling it from a different
|
||
MPI rank will raise an exception.</p>
|
||
</div>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>expr</strong> (<em>string</em>) – the expression string that should be evaluated inside of LAMMPS</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>the value of the evaluated expression</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float if numeric, string otherwise</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.PyLammps.lmp_print">
|
||
<span class="sig-name descname"><span class="pre">lmp_print</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.PyLammps.lmp_print" title="Link to this definition"></a></dt>
|
||
<dd><p>needed for Python2 compatibility, since print is a reserved keyword</p>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.AtomList">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">AtomList</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pylammps_instance</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.AtomList" title="Link to this definition"></a></dt>
|
||
<dd><p>A dynamic list of atoms that returns either an <a class="reference internal" href="#lammps.Atom" title="lammps.Atom"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom</span></code></a> or
|
||
<a class="reference internal" href="#lammps.Atom2D" title="lammps.Atom2D"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom2D</span></code></a> instance for each atom. Instances are only allocated
|
||
when accessed.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Variables<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>natoms</strong> – total number of atoms</p></li>
|
||
<li><p><strong>dimensions</strong> – number of dimensions in system</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.Atom">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">Atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pylammps_instance</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.Atom" title="Link to this definition"></a></dt>
|
||
<dd><p>A wrapper class then represents a single atom inside of LAMMPS</p>
|
||
<p>It provides access to properties of the atom and allows you to change some of them.</p>
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.id">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">id</span></span><a class="headerlink" href="#lammps.Atom.id" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the atom ID</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.type">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">type</span></span><a class="headerlink" href="#lammps.Atom.type" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the atom type</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.mol">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mol</span></span><a class="headerlink" href="#lammps.Atom.mol" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the atom molecule index</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>int</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.mass">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mass</span></span><a class="headerlink" href="#lammps.Atom.mass" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the atom mass as a per-atom property.
|
||
This returns either the per-type mass or the per-atom
|
||
mass (AKA ‘rmass’) depending on what is available with
|
||
preference for the per-atom mass.</p>
|
||
<div class="versionchanged">
|
||
<p><span class="versionmodified changed">Changed in version 17Apr2024: </span>Support both per-type and per-atom masses. With
|
||
per-type return “mass[type[i]]” else return “rmass[i]”.
|
||
Per-atom mass is preferred if available.</p>
|
||
</div>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.radius">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">radius</span></span><a class="headerlink" href="#lammps.Atom.radius" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the particle radius</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.position">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">position</span></span><a class="headerlink" href="#lammps.Atom.position" title="Link to this definition"></a></dt>
|
||
<dd><dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Return position of atom</p>
|
||
</dd>
|
||
<dt class="field-even">Setter<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>Set position of atom</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.velocity">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">velocity</span></span><a class="headerlink" href="#lammps.Atom.velocity" title="Link to this definition"></a></dt>
|
||
<dd><dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Return velocity of atom</p>
|
||
</dd>
|
||
<dt class="field-even">Setter<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>Set velocity of atom</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.force">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">force</span></span><a class="headerlink" href="#lammps.Atom.force" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the total force acting on the atom</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.omega">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">omega</span></span><a class="headerlink" href="#lammps.Atom.omega" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the rotational velocity of the particle</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.torque">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">torque</span></span><a class="headerlink" href="#lammps.Atom.torque" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the total torque acting on the particle</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.angular_momentum">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">angular_momentum</span></span><a class="headerlink" href="#lammps.Atom.angular_momentum" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the angular momentum of the particle</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom.charge">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">charge</span></span><a class="headerlink" href="#lammps.Atom.charge" title="Link to this definition"></a></dt>
|
||
<dd><p>Return the atom charge</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>float</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.Atom2D">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">Atom2D</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pylammps_instance</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.Atom2D" title="Link to this definition"></a></dt>
|
||
<dd><p>A wrapper class then represents a single 2D atom inside of LAMMPS</p>
|
||
<p>Inherits all properties from the <a class="reference internal" href="#lammps.Atom" title="lammps.Atom"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atom</span></code></a> class, but returns 2D versions
|
||
of position, velocity, and force.</p>
|
||
<p>It provides access to properties of the atom and allows you to change some of them.</p>
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom2D.position">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">position</span></span><a class="headerlink" href="#lammps.Atom2D.position" title="Link to this definition"></a></dt>
|
||
<dd><p>Access to coordinates of an atom</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Return position of atom</p>
|
||
</dd>
|
||
<dt class="field-even">Setter<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>Set position of atom</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom2D.velocity">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">velocity</span></span><a class="headerlink" href="#lammps.Atom2D.velocity" title="Link to this definition"></a></dt>
|
||
<dd><p>Access to velocity of an atom</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Return velocity of atom</p>
|
||
</dd>
|
||
<dt class="field-even">Setter<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>Set velocity of atom</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.Atom2D.force">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">force</span></span><a class="headerlink" href="#lammps.Atom2D.force" title="Link to this definition"></a></dt>
|
||
<dd><p>Access to force of an atom</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Getter<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>Return force of atom</p>
|
||
</dd>
|
||
<dt class="field-even">Setter<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>Set force of atom</p>
|
||
</dd>
|
||
<dt class="field-odd">Type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy.array (float, float)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="the-ipylammps-class-api">
|
||
<h2><span class="section-number">2.4.3. </span>The <code class="docutils literal notranslate"><span class="pre">IPyLammps</span></code> class API<a class="headerlink" href="#the-ipylammps-class-api" title="Link to this heading"></a></h2>
|
||
<p>The <a class="reference internal" href="#lammps.PyLammps" title="lammps.PyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">IPyLammps</span></code></a> class is an extension of
|
||
<a class="reference internal" href="#lammps.PyLammps" title="lammps.PyLammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">PyLammps</span></code></a>, adding additional functions to
|
||
quickly display visualizations such as images and videos inside of IPython.
|
||
See the <a class="reference internal" href="Howto_pylammps.html"><span class="doc">PyLammps Tutorial</span></a> for examples.</p>
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.IPyLammps">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">IPyLammps</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmdargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ptr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.IPyLammps" title="Link to this definition"></a></dt>
|
||
<dd><p>IPython wrapper for LAMMPS which adds embedded graphics capabilities to PyLammps interface</p>
|
||
<p>It either creates its own instance of <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a> or can be
|
||
initialized with an existing instance. The arguments are the same of the
|
||
lower-level interface. The original interface can still be accessed via
|
||
<code class="xref py py-attr docutils literal notranslate"><span class="pre">PyLammps.lmp</span></code>.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>name</strong> (<em>string</em>) – “machine” name of the shared LAMMPS library (“mpi” loads <code class="docutils literal notranslate"><span class="pre">liblammps_mpi.so</span></code>, “” loads <code class="docutils literal notranslate"><span class="pre">liblammps.so</span></code>)</p></li>
|
||
<li><p><strong>cmdargs</strong> (<em>list</em>) – list of command line arguments to be passed to the <a class="reference internal" href="Library_create.html#_CPPv411lammps_openiPPc8MPI_CommPPv" title="lammps_open"><code class="xref cpp cpp-func docutils literal notranslate"><span class="pre">lammps_open()</span></code></a> function. The executable name is automatically added.</p></li>
|
||
<li><p><strong>ptr</strong> (<em>pointer</em>) – pointer to a LAMMPS C++ class instance when called from an embedded Python interpreter. None means load symbols from shared library.</p></li>
|
||
<li><p><strong>comm</strong> (<em>MPI_Comm</em>) – MPI communicator (as provided by <a class="reference external" href="https://mpi4py.readthedocs.io/">mpi4py</a>). <code class="docutils literal notranslate"><span class="pre">None</span></code> means use <code class="docutils literal notranslate"><span class="pre">MPI_COMM_WORLD</span></code> implicitly.</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.IPyLammps.image">
|
||
<span class="sig-name descname"><span class="pre">image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'snapshot.png'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">group</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'all'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'type'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diameter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'type'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">view</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">up</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zoom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">background_color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'white'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.IPyLammps.image" title="Link to this definition"></a></dt>
|
||
<dd><p>Generate image using write_dump command and display it</p>
|
||
<p>See <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> for more information.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>filename</strong> (<em>string</em>) – Name of the image file that should be generated. The extension determines whether it is PNG or JPEG</p></li>
|
||
<li><p><strong>group</strong> (<em>string</em>) – the group of atoms write_image should use</p></li>
|
||
<li><p><strong>color</strong> (<em>string</em>) – name of property used to determine color</p></li>
|
||
<li><p><strong>diameter</strong> (<em>string</em>) – name of property used to determine atom diameter</p></li>
|
||
<li><p><strong>size</strong> (<em>tuple</em><em> (</em><em>width</em><em>, </em><em>height</em><em>)</em>) – dimensions of image</p></li>
|
||
<li><p><strong>view</strong> (<em>tuple</em><em> (</em><em>theta</em><em>, </em><em>phi</em><em>)</em>) – view parameters</p></li>
|
||
<li><p><strong>center</strong> (<em>tuple</em><em> (</em><em>flag</em><em>, </em><em>center_x</em><em>, </em><em>center_y</em><em>, </em><em>center_z</em><em>)</em>) – center parameters</p></li>
|
||
<li><p><strong>up</strong> (<em>tuple</em><em> (</em><em>up_x</em><em>, </em><em>up_y</em><em>, </em><em>up_z</em><em>)</em>) – vector pointing to up direction</p></li>
|
||
<li><p><strong>zoom</strong> (<em>float</em>) – zoom factor</p></li>
|
||
<li><p><strong>background_color</strong> (<em>string</em>) – background color of scene</p></li>
|
||
</ul>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>Image instance used to display image in notebook</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">IPython.core.display.Image</span></code></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.IPyLammps.video">
|
||
<span class="sig-name descname"><span class="pre">video</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.IPyLammps.video" title="Link to this definition"></a></dt>
|
||
<dd><p>Load video from file</p>
|
||
<p>Can be used to visualize videos from <a class="reference internal" href="dump_image.html"><span class="doc">dump movie</span></a>.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>filename</strong> (<em>string</em>) – Path to video file</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>HTML Video Tag used by notebook to embed a video</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">IPython.display.HTML</span></code></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<hr class="docutils" />
|
||
<section id="additional-components-of-the-lammps-module">
|
||
<h2><span class="section-number">2.4.4. </span>Additional components of the <code class="docutils literal notranslate"><span class="pre">lammps</span></code> module<a class="headerlink" href="#additional-components-of-the-lammps-module" title="Link to this heading"></a></h2>
|
||
<p>The <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module additionally contains several constants
|
||
and the <a class="reference internal" href="#lammps.NeighList" title="lammps.NeighList"><code class="xref py py-class docutils literal notranslate"><span class="pre">NeighList</span></code></a> class:</p>
|
||
<section id="data-types">
|
||
<span id="py-datatype-constants"></span><h3>Data Types<a class="headerlink" href="#data-types" title="Link to this heading"></a></h3>
|
||
<dl class="py data">
|
||
<dt class="sig sig-object py">
|
||
<span class="sig-name descname"><span class="pre">LAMMPS_INT,</span> <span class="pre">LAMMPS_INT_2D,</span> <span class="pre">LAMMPS_DOUBLE,</span> <span class="pre">LAMMPS_DOUBLE_2D,</span> <span class="pre">LAMMPS_INT64,</span> <span class="pre">LAMMPS_INT64_2D,</span> <span class="pre">LAMMPS_STRING</span></span></dt>
|
||
<dd><p>Constants in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module to indicate how to
|
||
cast data when the C library function returns a void pointer.
|
||
Used in <a class="reference internal" href="#lammps.lammps.extract_global" title="lammps.lammps.extract_global"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.extract_global()</span></code></a> and <a class="reference internal" href="#lammps.lammps.extract_atom" title="lammps.lammps.extract_atom"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.extract_atom()</span></code></a>.
|
||
See <code class="xref cpp cpp-enum docutils literal notranslate"><span class="pre">_LMP_DATATYPE_CONST</span></code> for the equivalent constants in the
|
||
C library interface.</p>
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<section id="style-constants">
|
||
<span id="py-style-constants"></span><h3>Style Constants<a class="headerlink" href="#style-constants" title="Link to this heading"></a></h3>
|
||
<dl class="py data">
|
||
<dt class="sig sig-object py">
|
||
<span class="sig-name descname"><span class="pre">LMP_STYLE_GLOBAL,</span> <span class="pre">LMP_STYLE_ATOM,</span> <span class="pre">LMP_STYLE_LOCAL</span></span></dt>
|
||
<dd><p>Constants in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module to select what style of data
|
||
to request from computes or fixes. See <a class="reference internal" href="Library_objects.html#_CPPv416_LMP_STYLE_CONST" title="_LMP_STYLE_CONST"><code class="xref cpp cpp-enum docutils literal notranslate"><span class="pre">_LMP_STYLE_CONST</span></code></a>
|
||
for the equivalent constants in the C library interface. Used in
|
||
<a class="reference internal" href="#lammps.lammps.extract_compute" title="lammps.lammps.extract_compute"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.extract_compute()</span></code></a>, <a class="reference internal" href="#lammps.lammps.extract_fix" title="lammps.lammps.extract_fix"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.extract_fix()</span></code></a>, and their NumPy variants
|
||
<a class="reference internal" href="#lammps.numpy_wrapper.numpy_wrapper.extract_compute" title="lammps.numpy_wrapper.numpy_wrapper.extract_compute"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.numpy.extract_compute()</span></code></a> and
|
||
<a class="reference internal" href="#lammps.numpy_wrapper.numpy_wrapper.extract_fix" title="lammps.numpy_wrapper.numpy_wrapper.extract_fix"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.numpy.extract_fix()</span></code></a>.</p>
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<section id="type-constants">
|
||
<span id="py-type-constants"></span><h3>Type Constants<a class="headerlink" href="#type-constants" title="Link to this heading"></a></h3>
|
||
<dl class="py data">
|
||
<dt class="sig sig-object py">
|
||
<span class="sig-name descname"><span class="pre">LMP_TYPE_SCALAR,</span> <span class="pre">LMP_TYPE_VECTOR,</span> <span class="pre">LMP_TYPE_ARRAY,</span> <span class="pre">LMP_SIZE_VECTOR,</span> <span class="pre">LMP_SIZE_ROWS,</span> <span class="pre">LMP_SIZE_COLS</span></span></dt>
|
||
<dd><p>Constants in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module to select what type of data
|
||
to request from computes or fixes. See <a class="reference internal" href="Library_objects.html#_CPPv415_LMP_TYPE_CONST" title="_LMP_TYPE_CONST"><code class="xref cpp cpp-enum docutils literal notranslate"><span class="pre">_LMP_TYPE_CONST</span></code></a>
|
||
for the equivalent constants in the C library interface. Used in
|
||
<a class="reference internal" href="#lammps.lammps.extract_compute" title="lammps.lammps.extract_compute"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.extract_compute()</span></code></a>, <a class="reference internal" href="#lammps.lammps.extract_fix" title="lammps.lammps.extract_fix"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.extract_fix()</span></code></a>, and their NumPy variants
|
||
<a class="reference internal" href="#lammps.numpy_wrapper.numpy_wrapper.extract_compute" title="lammps.numpy_wrapper.numpy_wrapper.extract_compute"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.numpy.extract_compute()</span></code></a> and
|
||
<a class="reference internal" href="#lammps.numpy_wrapper.numpy_wrapper.extract_fix" title="lammps.numpy_wrapper.numpy_wrapper.extract_fix"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.numpy.extract_fix()</span></code></a>.</p>
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<section id="variable-type-constants">
|
||
<span id="py-vartype-constants"></span><h3>Variable Type Constants<a class="headerlink" href="#variable-type-constants" title="Link to this heading"></a></h3>
|
||
<dl class="py data">
|
||
<dt class="sig sig-object py">
|
||
<span class="sig-name descname"><span class="pre">LMP_VAR_EQUAL,</span> <span class="pre">LMP_VAR_ATOM</span></span></dt>
|
||
<dd><p>Constants in the <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-mod docutils literal notranslate"><span class="pre">lammps</span></code></a> module to select what type of
|
||
variable to query when calling <a class="reference internal" href="#lammps.lammps.extract_variable" title="lammps.lammps.extract_variable"><code class="xref py py-func docutils literal notranslate"><span class="pre">lammps.extract_variable()</span></code></a>. See also: <a class="reference internal" href="variable.html"><span class="doc">variable command</span></a>.</p>
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<section id="classes-representing-internal-objects">
|
||
<h3>Classes representing internal objects<a class="headerlink" href="#classes-representing-internal-objects" title="Link to this heading"></a></h3>
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.NeighList">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.</span></span><span class="sig-name descname"><span class="pre">NeighList</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lmp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">idx</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.NeighList" title="Link to this definition"></a></dt>
|
||
<dd><p>This is a wrapper class that exposes the contents of a neighbor list.</p>
|
||
<p>It can be used like a regular Python list. Each element is a tuple of:</p>
|
||
<ul class="simple">
|
||
<li><p>the atom local index</p></li>
|
||
<li><p>its number of neighbors</p></li>
|
||
<li><p>and a pointer to an c_int array containing local atom indices of its
|
||
neighbors</p></li>
|
||
</ul>
|
||
<p>Internally it uses the lower-level LAMMPS C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>lmp</strong> (<a class="reference internal" href="#lammps.lammps" title="lammps.lammps"><em>lammps</em></a>) – reference to instance of <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a></p></li>
|
||
<li><p><strong>idx</strong> (<em>int</em>) – neighbor list index</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="lammps.NeighList.size">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">size</span></span><a class="headerlink" href="#lammps.NeighList.size" title="Link to this definition"></a></dt>
|
||
<dd><dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>number of elements in neighbor list</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.NeighList.get">
|
||
<span class="sig-name descname"><span class="pre">get</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.NeighList.get" title="Link to this definition"></a></dt>
|
||
<dd><p>Access a specific neighbor list entry. “element” must be a number from 0 to the size-1 of the list</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>tuple with atom local index, number of neighbors and ctypes pointer to neighbor’s local atom indices</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>(int, int, ctypes.POINTER(c_int))</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.NeighList.find">
|
||
<span class="sig-name descname"><span class="pre">find</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iatom</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.NeighList.find" title="Link to this definition"></a></dt>
|
||
<dd><p>Find the neighbor list for a specific (local) atom iatom.
|
||
If there is no list for iatom, (-1, None) is returned.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>tuple with number of neighbors and ctypes pointer to neighbor’s local atom indices</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>(int, ctypes.POINTER(c_int))</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.NumPyNeighList">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">lammps.numpy_wrapper.</span></span><span class="sig-name descname"><span class="pre">NumPyNeighList</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lmp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">idx</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.NumPyNeighList" title="Link to this definition"></a></dt>
|
||
<dd><p>This is a wrapper class that exposes the contents of a neighbor list.</p>
|
||
<p>It can be used like a regular Python list. Each element is a tuple of:</p>
|
||
<ul class="simple">
|
||
<li><p>the atom local index</p></li>
|
||
<li><p>a NumPy array containing the local atom indices of its neighbors</p></li>
|
||
</ul>
|
||
<p>Internally it uses the lower-level LAMMPS C-library interface.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><ul class="simple">
|
||
<li><p><strong>lmp</strong> (<a class="reference internal" href="#lammps.lammps" title="lammps.lammps"><em>lammps</em></a>) – reference to instance of <a class="reference internal" href="#module-lammps" title="lammps"><code class="xref py py-class docutils literal notranslate"><span class="pre">lammps</span></code></a></p></li>
|
||
<li><p><strong>idx</strong> (<em>int</em>) – neighbor list index</p></li>
|
||
</ul>
|
||
</dd>
|
||
</dl>
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.NumPyNeighList.get">
|
||
<span class="sig-name descname"><span class="pre">get</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.NumPyNeighList.get" title="Link to this definition"></a></dt>
|
||
<dd><p>Access a specific neighbor list entry. “element” must be a number from 0 to the size-1 of the list</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>tuple with atom local index, numpy array of neighbor local atom indices</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>(int, numpy.array)</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="lammps.numpy_wrapper.NumPyNeighList.find">
|
||
<span class="sig-name descname"><span class="pre">find</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">iatom</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#lammps.numpy_wrapper.NumPyNeighList.find" title="Link to this definition"></a></dt>
|
||
<dd><p>Find the neighbor list for a specific (local) atom iatom.
|
||
If there is no list for iatom, None is returned.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p>numpy array of neighbor local atom indices</p>
|
||
</dd>
|
||
<dt class="field-even">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>numpy.array or None</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</dd></dl>
|
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|
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</section>
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