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  <div class="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 headline">¶</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 id="pymatgen.alchemy.materials. TransformedStructure">
<em class="property">class </em><code class="sig-name descname">TransformedStructure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">transformations</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">history</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">other_parameters</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L29-L375"><span class="viewcode-link">[source]</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">monty.json. 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</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>[</em><em>Transformations</em><em>]</em>) – List of transformations to
apply.</p></li>
<li><p><strong>history</strong> (<em>list</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 id="pymatgen.alchemy.materials. TransformedStructure.append_filter">
<code class="sig-name descname">append_filter</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure_filter</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L154-L165"><span class="viewcode-link">[source]</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</dt>
<dd class="field-odd"><p><strong>structure_filter</strong> (<em>StructureFilter</em>) – A filter implementating the
AbstractStructureFilter API.  Tells transmuter waht structures
to retain.</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt id="pymatgen.alchemy.materials. TransformedStructure.append_transformation">
<code class="sig-name descname">append_transformation</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">transformation</span></em>, <em class="sig-param"><span class="n">return_alternatives</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">clear_redo</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L98-L152"><span class="viewcode-link">[source]</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</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 id="pymatgen.alchemy.materials. TransformedStructure.as_dict">
<code class="sig-name descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L317-L327"><span class="viewcode-link">[source]</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 id="pymatgen.alchemy.materials. TransformedStructure.extend_transformations">
<code class="sig-name descname">extend_transformations</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">transformations</span></em>, <em class="sig-param"><span class="n">return_alternatives</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L167-L181"><span class="viewcode-link">[source]</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</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 id="pymatgen.alchemy.materials. TransformedStructure.from_cif_string">
<em class="property">static </em><code class="sig-name descname">from_cif_string</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">cif_string</span></em>, <em class="sig-param"><span class="n">transformations</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">primitive</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">occupancy_tolerance</span><span class="o">=</span><span class="default_value">1.0</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L256-L294"><span class="viewcode-link">[source]</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</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>[</em><em>Transformations</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</dt>
<dd class="field-even"><p>TransformedStructure</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt id="pymatgen.alchemy.materials. TransformedStructure.from_dict">
<em class="property">classmethod </em><code class="sig-name descname">from_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">d</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L329-L336"><span class="viewcode-link">[source]</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 id="pymatgen.alchemy.materials. TransformedStructure.from_poscar_string">
<em class="property">static </em><code class="sig-name descname">from_poscar_string</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">poscar_string</span></em>, <em class="sig-param"><span class="n">transformations</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L296-L315"><span class="viewcode-link">[source]</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</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>[</em><em>Transformations</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 id="pymatgen.alchemy.materials. TransformedStructure.from_snl">
<em class="property">classmethod </em><code class="sig-name descname">from_snl</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">snl</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L359-L375"><span class="viewcode-link">[source]</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</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</dt>
<dd class="field-even"><p>TransformedStructure</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt id="pymatgen.alchemy.materials. TransformedStructure.get_vasp_input">
<code class="sig-name descname">get_vasp_input</code><span class="sig-paren">(</span><em class="sig-param">vasp_input_set=&lt;class 'pymatgen.io.vasp.sets. MPRelaxSet'&gt;</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L183-L193"><span class="viewcode-link">[source]</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</dt>
<dd class="field-odd"><p><strong>vasp_input_set</strong> (<em>pymatgen.io.vaspio_set. VaspInputSet</em>) – input set
to create vasp input files from structures</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt id="pymatgen.alchemy.materials. TransformedStructure.redo_next_change">
<code class="sig-name descname">redo_next_change</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L78-L89"><span class="viewcode-link">[source]</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</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 id="pymatgen.alchemy.materials. TransformedStructure.set_parameter">
<code class="sig-name descname">set_parameter</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">key</span></em>, <em class="sig-param"><span class="n">value</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L227-L234"><span class="viewcode-link">[source]</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</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 method">
<dt id="pymatgen.alchemy.materials. TransformedStructure.structures">
<em class="property">property </em><code class="sig-name descname">structures</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py"><span class="viewcode-link">[source]</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 id="pymatgen.alchemy.materials. TransformedStructure.to_snl">
<code class="sig-name descname">to_snl</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">authors</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwargs</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L338-L357"><span class="viewcode-link">[source]</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</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</dt>
<dd class="field-even"><p>StructureNL</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt id="pymatgen.alchemy.materials. TransformedStructure.undo_last_change">
<code class="sig-name descname">undo_last_change</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L59-L76"><span class="viewcode-link">[source]</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</dt>
<dd class="field-odd"><p><strong>IndexError</strong> – If already at the oldest change.</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt id="pymatgen.alchemy.materials. TransformedStructure.was_modified">
<em class="property">property </em><code class="sig-name descname">was_modified</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py"><span class="viewcode-link">[source]</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 id="pymatgen.alchemy.materials. TransformedStructure.write_vasp_input">
<code class="sig-name descname">write_vasp_input</code><span class="sig-paren">(</span><em class="sig-param">vasp_input_set=&lt;class 'pymatgen.io.vasp.sets. MPRelaxSet'&gt;</em>, <em class="sig-param">output_dir='. '</em>, <em class="sig-param">create_directory=True</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2020.9.14/pymatgen/alchemy/materials.py#L195-L212"><span class="viewcode-link">[source]</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</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>vasp_input_set</strong> – pymatgen.io.vaspio_set. 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>

</div>


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