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<div class="section" id="module-pymatgen.alchemy.transmuters">
<span id="pymatgen-alchemy-transmuters-module"></span><h1>pymatgen.alchemy.transmuters module<a class="headerlink" href="#module-pymatgen.alchemy.transmuters" title="Permalink to this headline">¶</a></h1>
<p>This module implements various transmuter classes.
Transmuters are essentially classes that generate TransformedStructures from
various data sources. They enable the high-throughput generation of new
structures and input files.</p>
<p>It also includes the helper function, batch_write_vasp_input to generate an
entire directory of vasp input files for running.</p>
<dl class="class">
<dt id="pymatgen.alchemy.transmuters.CifTransmuter">
<em class="property">class </em><code class="descname">CifTransmuter</code><span class="sig-paren">(</span><em>cif_string</em>, <em>transformations=None</em>, <em>primitive=True</em>, <em>extend_collection=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#CifTransmuter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.CifTransmuter" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.alchemy.transmuters.StandardTransmuter" title="pymatgen.alchemy.transmuters.StandardTransmuter"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.alchemy.transmuters.StandardTransmuter</span></code></a></p>
<p>Generates a Transmuter from a cif string, possibly containing multiple
structures.</p>
<p>Generates a Transmuter from a cif string, possibly
containing multiple structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>cif_string</strong> – A string containing a cif or a series of cifs</p></li>
<li><p><strong>transformations</strong> – New transformations to be applied to all
structures</p></li>
<li><p><strong>primitive</strong> – Whether to generate the primitive cell from the cif.</p></li>
<li><p><strong>extend_collection</strong> – Whether to use more than one output structure
from one-to-many transformations. extend_collection can be a
number, which determines the maximum branching for each
transformation.</p></li>
</ul>
</dd>
</dl>
<dl class="staticmethod">
<dt id="pymatgen.alchemy.transmuters.CifTransmuter.from_filenames">
<em class="property">static </em><code class="descname">from_filenames</code><span class="sig-paren">(</span><em>filenames</em>, <em>transformations=None</em>, <em>primitive=True</em>, <em>extend_collection=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#CifTransmuter.from_filenames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.CifTransmuter.from_filenames" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates a TransformedStructureCollection from a cif, possibly
containing multiple structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filenames</strong> – List of strings of the cif files</p></li>
<li><p><strong>transformations</strong> – New transformations to be applied to all
structures</p></li>
<li><p><strong>primitive</strong> – Same meaning as in __init__.</p></li>
<li><p><strong>extend_collection</strong> – Same meaning as in __init__.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.alchemy.transmuters.PoscarTransmuter">
<em class="property">class </em><code class="descname">PoscarTransmuter</code><span class="sig-paren">(</span><em>poscar_string</em>, <em>transformations=None</em>, <em>extend_collection=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#PoscarTransmuter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.PoscarTransmuter" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.alchemy.transmuters.StandardTransmuter" title="pymatgen.alchemy.transmuters.StandardTransmuter"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.alchemy.transmuters.StandardTransmuter</span></code></a></p>
<p>Generates a transmuter from a sequence of POSCARs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>poscar_string</strong> – List of POSCAR strings</p></li>
<li><p><strong>transformations</strong> – New transformations to be applied to all
structures.</p></li>
<li><p><strong>extend_collection</strong> – Whether to use more than one output structure
from one-to-many transformations.</p></li>
</ul>
</dd>
</dl>
<dl class="staticmethod">
<dt id="pymatgen.alchemy.transmuters.PoscarTransmuter.from_filenames">
<em class="property">static </em><code class="descname">from_filenames</code><span class="sig-paren">(</span><em>poscar_filenames</em>, <em>transformations=None</em>, <em>extend_collection=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#PoscarTransmuter.from_filenames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.PoscarTransmuter.from_filenames" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenient constructor to generates a POSCAR transmuter from a list of
POSCAR filenames.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>poscar_filenames</strong> – List of POSCAR filenames</p></li>
<li><p><strong>transformations</strong> – New transformations to be applied to all
structures.</p></li>
<li><p><strong>extend_collection</strong> – Same meaning as in __init__.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter">
<em class="property">class </em><code class="descname">StandardTransmuter</code><span class="sig-paren">(</span><em>transformed_structures</em>, <em>transformations=None</em>, <em>extend_collection=0</em>, <em>ncores=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>An example of a Transmuter object, which performs a sequence of
transformations on many structures to generate TransformedStructures.</p>
<p>Initializes a transmuter from an initial list of
<a class="reference internal" href="pymatgen.alchemy.materials.html#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.alchemy.materials.TransformedStructure</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>transformed_structures</strong> (<em>[</em><a class="reference internal" href="pymatgen.alchemy.materials.html#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><em>TransformedStructure</em></a><em>]</em>) – Input transformed
structures</p></li>
<li><p><strong>transformations</strong> (<em>[</em><em>Transformations</em><em>]</em>) – New transformations to be
applied to all structures.</p></li>
<li><p><strong>extend_collection</strong> (<em>int</em>) – Whether to use more than one output
structure from one-to-many transformations. extend_collection
can be an int, which determines the maximum branching for each
transformation.</p></li>
<li><p><strong>ncores</strong> (<em>int</em>) – Number of cores to use for applying transformations.
Uses multiprocessing.Pool. Default is None, which implies
serial.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.add_tags">
<code class="descname">add_tags</code><span class="sig-paren">(</span><em>tags</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.add_tags"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.add_tags" title="Permalink to this definition">¶</a></dt>
<dd><p>Add tags for the structures generated by the transmuter.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>tags</strong> – A sequence of tags. Note that this should be a sequence of
strings, e.g., [“My awesome structures”, “Project X”].</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.append_transformation">
<code class="descname">append_transformation</code><span class="sig-paren">(</span><em>transformation</em>, <em>extend_collection=False</em>, <em>clear_redo=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.append_transformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.append_transformation" title="Permalink to this definition">¶</a></dt>
<dd><p>Appends a transformation to all TransformedStructures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>transformation</strong> – Transformation to append</p></li>
<li><p><strong>extend_collection</strong> – Whether to use more than one output structure
from one-to-many transformations. extend_collection can be a
number, which determines the maximum branching for each
transformation.</p></li>
<li><p><strong>clear_redo</strong> (<em>bool</em>) – Whether to clear the redo list. By default,
this is True, meaning any appends clears the history of
undoing. However, when using append_transformation to do a
redo, the redo list should not be cleared to allow multiple
redos.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>List of booleans corresponding to initial transformed structures
each boolean describes whether the transformation altered the
structure</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.append_transformed_structures">
<code class="descname">append_transformed_structures</code><span class="sig-paren">(</span><em>tstructs_or_transmuter</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.append_transformed_structures"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.append_transformed_structures" title="Permalink to this definition">¶</a></dt>
<dd><p>Method is overloaded to accept either a list of transformed structures
or transmuter, it which case it appends the second transmuter”s
structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>tstructs_or_transmuter</strong> – A list of transformed structures or a
transmuter.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.apply_filter">
<code class="descname">apply_filter</code><span class="sig-paren">(</span><em>structure_filter</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.apply_filter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.apply_filter" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies a structure_filter to the list of TransformedStructures
in the transmuter.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>structure_filter</strong> – StructureFilter to apply.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.extend_transformations">
<code class="descname">extend_transformations</code><span class="sig-paren">(</span><em>transformations</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.extend_transformations"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.extend_transformations" title="Permalink to this definition">¶</a></dt>
<dd><p>Extends a sequence of transformations to the TransformedStructure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>transformations</strong> – Sequence of Transformations</p>
</dd>
</dl>
</dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.from_structures">
<em class="property">static </em><code class="descname">from_structures</code><span class="sig-paren">(</span><em>structures</em>, <em>transformations=None</em>, <em>extend_collection=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.from_structures"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.from_structures" title="Permalink to this definition">¶</a></dt>
<dd><p>Alternative constructor from structures rather than
TransformedStructures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structures</strong> – Sequence of structures</p></li>
<li><p><strong>transformations</strong> – New transformations to be applied to all
structures</p></li>
<li><p><strong>extend_collection</strong> – Whether to use more than one output structure
from one-to-many transformations. extend_collection can be a
number, which determines the maximum branching for each
transformation.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>StandardTransmuter</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.redo_next_change">
<code class="descname">redo_next_change</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.redo_next_change"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.redo_next_change" title="Permalink to this definition">¶</a></dt>
<dd><p>Redo the last undone transformation in the TransformedStructure.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>IndexError if already at the latest change.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.set_parameter">
<code class="descname">set_parameter</code><span class="sig-paren">(</span><em>key</em>, <em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.set_parameter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.set_parameter" title="Permalink to this definition">¶</a></dt>
<dd><p>Add parameters to the transmuter. Additional parameters are stored in
the as_dict() output.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>key</strong> – The key for the parameter.</p></li>
<li><p><strong>value</strong> – The value for the parameter.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.undo_last_change">
<code class="descname">undo_last_change</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.undo_last_change"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.undo_last_change" title="Permalink to this definition">¶</a></dt>
<dd><p>Undo the last transformation in the TransformedStructure.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>IndexError if already at the oldest change.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.alchemy.transmuters.StandardTransmuter.write_vasp_input">
<code class="descname">write_vasp_input</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#StandardTransmuter.write_vasp_input"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.StandardTransmuter.write_vasp_input" title="Permalink to this definition">¶</a></dt>
<dd><p>Batch write vasp input for a sequence of transformed structures to
output_dir, following the format output_dir/{formula}_{number}.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>**kwargs</strong> – All kwargs supported by batch_write_vasp_input.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.alchemy.transmuters.batch_write_vasp_input">
<code class="descname">batch_write_vasp_input</code><span class="sig-paren">(</span><em>transformed_structures</em>, <em>vasp_input_set=<class 'pymatgen.io.vasp.sets.MPRelaxSet'></em>, <em>output_dir='.'</em>, <em>create_directory=True</em>, <em>subfolder=None</em>, <em>include_cif=False</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/alchemy/transmuters.html#batch_write_vasp_input"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.alchemy.transmuters.batch_write_vasp_input" title="Permalink to this definition">¶</a></dt>
<dd><p>Batch write vasp input for a sequence of transformed structures to
output_dir, following the format output_dir/{group}/{formula}_{number}.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>transformed_structures</strong> – Sequence of TransformedStructures.</p></li>
<li><p><strong>vasp_input_set</strong> – pymatgen.io.vaspio_set.VaspInputSet to creates
vasp input files from structures.</p></li>
<li><p><strong>output_dir</strong> – Directory to output files</p></li>
<li><p><strong>create_directory</strong> (<em>bool</em>) – Create the directory if not present.
Defaults to True.</p></li>
<li><p><strong>subfolder</strong> – Function to create subdirectory name from
transformed_structure.
e.g., lambda x: x.other_parameters[“tags”][0] to use the first
tag.</p></li>
<li><p><strong>include_cif</strong> (<em>bool</em>) – Boolean indication whether to output a CIF as
well. CIF files are generally better supported in visualization
programs.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
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