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<section id="module-pymatgen.alchemy.materials">
<span id="pymatgen-alchemy-materials-module"></span><h1>pymatgen.alchemy.materials module<a class="headerlink" href="#module-pymatgen.alchemy.materials" title="Permalink to this heading"></a></h1>
<p>This module provides various representations of transformed structures. A
TransformedStructure is a structure that has been modified by undergoing a
series of transformations.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TransformedStructure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">transformations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><span class="pre">AbstractTransformation</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">history</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><span class="pre">AbstractTransformation</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">other_parameters</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L29-L392"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure" title="Permalink to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Container object for new structures that include history of
transformations.</p>
<p>Each transformed structure is made up of a sequence of structures with
associated transformation history.</p>
<p>Initializes a transformed structure from a structure.</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>structure</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure</p></li>
<li><p><strong>transformations</strong> (<em>list</em><em>[</em><em>Transformation</em><em>]</em>) – List of transformations to
apply.</p></li>
<li><p><strong>history</strong> (<em>list</em><em>[</em><em>Transformation</em><em>]</em>) – Previous history.</p></li>
<li><p><strong>other_parameters</strong> (<em>dict</em>) – Additional parameters to be added.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.append_filter">
<span class="sig-name descname"><span class="pre">append_filter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_filter</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.alchemy.filters.html#pymatgen.alchemy.filters.AbstractStructureFilter" title="pymatgen.alchemy.filters.AbstractStructureFilter"><span class="pre">AbstractStructureFilter</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L160-L170"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.append_filter" title="Permalink to this definition"></a></dt>
<dd><p>Adds a filter.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure_filter</strong> (<em>StructureFilter</em>) – A filter implementing the
AbstractStructureFilter API. Tells transmuter what structures to retain.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.append_transformation">
<span class="sig-name descname"><span class="pre">append_transformation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">transformation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_alternatives</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clear_redo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><span class="pre">pymatgen.alchemy.materials.TransformedStructure</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L102-L158"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.append_transformation" title="Permalink to this definition"></a></dt>
<dd><p>Appends a transformation to the TransformedStructure.</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>transformation</strong> – Transformation to append</p></li>
<li><p><strong>return_alternatives</strong> – Whether to return alternative
TransformedStructures for one-to-many transformations.
return_alternatives can be a number, which stipulates the
total number of structures to return.</p></li>
<li><p><strong>clear_redo</strong> – Boolean indicating 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>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L333-L343"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.as_dict" title="Permalink to this definition"></a></dt>
<dd><p>Dict representation of the TransformedStructure.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.extend_transformations">
<span class="sig-name descname"><span class="pre">extend_transformations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">transformations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><span class="pre">AbstractTransformation</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_alternatives</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L172-L186"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.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<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>transformations</strong> – Sequence of Transformations</p></li>
<li><p><strong>return_alternatives</strong> – Whether to return alternative
TransformedStructures for one-to-many transformations.
return_alternatives can be a number, which stipulates the
total number of structures to return.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.from_cif_string">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_cif_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cif_string</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transformations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><span class="pre">AbstractTransformation</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primitive</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">occupancy_tolerance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><span class="pre">TransformedStructure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L261-L305"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.from_cif_string" title="Permalink to this definition"></a></dt>
<dd><p>Generates TransformedStructure from a cif string.</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>cif_string</strong> (<em>str</em>) – Input cif string. Should contain only one
structure. For CIFs containing multiple structures, please use
CifTransmuter.</p></li>
<li><p><strong>transformations</strong> (<em>list</em><em>[</em><em>Transformation</em><em>]</em>) – Sequence of transformations
to be applied to the input structure.</p></li>
<li><p><strong>primitive</strong> (<em>bool</em>) – Option to set if the primitive cell should be
extracted. Defaults to True. However, there are certain
instances where you might want to use a non-primitive cell,
e.g., if you are trying to generate all possible orderings of
partial removals or order a disordered structure.</p></li>
<li><p><strong>occupancy_tolerance</strong> (<em>float</em>) – If total occupancy of a site is
between 1 and occupancy_tolerance, the occupancies will be
scaled down to 1.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>TransformedStructure</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">d</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><span class="pre">TransformedStructure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L345-L351"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.from_dict" title="Permalink to this definition"></a></dt>
<dd><p>Creates a TransformedStructure from a dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.from_poscar_string">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_poscar_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">poscar_string</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">transformations</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.transformations.transformation_abc.html#pymatgen.transformations.transformation_abc.AbstractTransformation" title="pymatgen.transformations.transformation_abc.AbstractTransformation"><span class="pre">AbstractTransformation</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><span class="pre">TransformedStructure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L307-L331"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.from_poscar_string" title="Permalink to this definition"></a></dt>
<dd><p>Generates TransformedStructure from a poscar string.</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>poscar_string</strong> (<em>str</em>) – Input POSCAR string.</p></li>
<li><p><strong>transformations</strong> (<em>list</em><em>[</em><em>Transformation</em><em>]</em>) – Sequence of transformations
to be applied to the input structure.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.from_snl">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_snl</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">snl</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.util.provenance.html#pymatgen.util.provenance.StructureNL" title="pymatgen.util.provenance.StructureNL"><span class="pre">StructureNL</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.alchemy.materials.TransformedStructure" title="pymatgen.alchemy.materials.TransformedStructure"><span class="pre">TransformedStructure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L376-L392"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.from_snl" title="Permalink to this definition"></a></dt>
<dd><p>Create TransformedStructure from SNL.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>snl</strong> (<a class="reference internal" href="pymatgen.util.provenance.html#pymatgen.util.provenance.StructureNL" title="pymatgen.util.provenance.StructureNL"><em>StructureNL</em></a>) – Starting snl</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>TransformedStructure</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.get_vasp_input">
<span class="sig-name descname"><span class="pre">get_vasp_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vasp_input_set:</span> <span class="pre">type[pymatgen.io.vasp.sets.VaspInputSet]</span> <span class="pre">=</span> <span class="pre"><class</span> <span class="pre">'pymatgen.io.vasp.sets.MPRelaxSet'></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">**kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L188-L199"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.get_vasp_input" title="Permalink to this definition"></a></dt>
<dd><p>Returns VASP input as a dict of VASP objects.</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>vasp_input_set</strong> (<a class="reference internal" href="pymatgen.io.vasp.sets.html#pymatgen.io.vasp.sets.VaspInputSet" title="pymatgen.io.vasp.sets.VaspInputSet"><em>pymatgen.io.vasp.sets.VaspInputSet</em></a>) – input set
to create VASP input files from structures</p></li>
<li><p><strong>**kwargs</strong> – All keyword args supported by the VASP input set.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.redo_next_change">
<span class="sig-name descname"><span class="pre">redo_next_change</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L82-L93"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.redo_next_change" title="Permalink to this definition"></a></dt>
<dd><p>Redo the last undone change in the TransformedStructure.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>IndexError</strong> – If already at the latest change.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.set_parameter">
<span class="sig-name descname"><span class="pre">set_parameter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L233-L240"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.set_parameter" title="Permalink to this definition"></a></dt>
<dd><p>Set a parameter</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>key</strong> – The string key</p></li>
<li><p><strong>value</strong> – The value.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.structures">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">pymatgen.core.structure.Structure</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/alchemy/materials.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.structures" title="Permalink to this definition"></a></dt>
<dd><p>Copy of all structures in the TransformedStructure. A
structure is stored after every single transformation.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.to_snl">
<span class="sig-name descname"><span class="pre">to_snl</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">authors</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> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.util.provenance.html#pymatgen.util.provenance.StructureNL" title="pymatgen.util.provenance.StructureNL"><span class="pre">StructureNL</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L353-L374"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.to_snl" title="Permalink to this definition"></a></dt>
<dd><p>Generate SNL from TransformedStructure.</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>authors</strong> – List of authors</p></li>
<li><p><strong>**kwargs</strong> – <p>All kwargs supported by StructureNL.</p>
</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>StructureNL</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.undo_last_change">
<span class="sig-name descname"><span class="pre">undo_last_change</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L64-L80"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.undo_last_change" title="Permalink to this definition"></a></dt>
<dd><p>Undo the last change in the TransformedStructure.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>IndexError</strong> – If already at the oldest change.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.was_modified">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">was_modified</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/alchemy/materials.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.was_modified" title="Permalink to this definition"></a></dt>
<dd><p>Boolean describing whether the last transformation on the structure
made any alterations to it one example of when this would return false
is in the case of performing a substitution transformation on the
structure when the specie to replace isn’t in the structure.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.alchemy.materials.TransformedStructure.write_vasp_input">
<span class="sig-name descname"><span class="pre">write_vasp_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vasp_input_set:</span> <span class="pre">type[pymatgen.io.vasp.sets.VaspInputSet]</span> <span class="pre">=</span> <span class="pre"><class</span> <span class="pre">'pymatgen.io.vasp.sets.MPRelaxSet'></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_dir:</span> <span class="pre">str</span> <span class="pre">=</span> <span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">create_directory:</span> <span class="pre">bool</span> <span class="pre">=</span> <span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">**kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../alchemy/materials.py#L201-L221"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.alchemy.materials.TransformedStructure.write_vasp_input" title="Permalink to this definition"></a></dt>
<dd><p>Writes VASP input to an output_dir.</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>vasp_input_set</strong> – pymatgen.io.vasp.sets.VaspInputSet like object that 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> – Create the directory if not present. Defaults to
True.</p></li>
<li><p><strong>**kwargs</strong> – All keyword args supported by the VASP input set.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
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