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<section id="module-pymatgen.io.core">
<span id="pymatgen-io-core-module"></span><h1>pymatgen.io.core module<a class="headerlink" href="#module-pymatgen.io.core" title="Permalink to this heading"></a></h1>
<p>This module defines the abstract interface for reading and writing calculation
inputs in pymatgen. The interface comprises a 3-tiered hierarchy of classes.</p>
<ol class="arabic simple">
<li><p>An InputFile object represents the contents of a single input file, e.g.
the INCAR. This class standardizes file read and write operations.</p></li>
<li><p>An InputSet is a dict-like container that maps filenames (keys) to file
contents (either strings or InputFile objects). This class provides a standard
write_input() method.</p></li>
<li><p>InputGenerator classes implement a get_input_set method that, when provided
with a structure, return an InputSet object with all parameters set correctly.
Calculation input files can be written to disk with the write_inputs method.</p></li>
</ol>
<p>If you want to implement a new InputGenerator, please take note of the following:</p>
<ol class="arabic simple">
<li><p>You must implement a get_input_set method that returns an InputSet</p></li>
<li><p>All customization of calculation parameters should be done in the __init__
method of the InputGenerator. The idea is that the generator contains
the “recipe”, but nothing that is specific to a particular system. get_input_set
takes system-specific information (such as structure) and applies the recipe.</p></li>
<li><p>All InputGenerator must save all supplied args and kwargs as instance variables.
E.g., self.my_arg = my_arg and self.kwargs = kwargs in the __init__. This
ensures the as_dict and from_dict work correctly.</p></li>
</ol>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.core.InputFile">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">InputFile</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L43-L102"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputFile" 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>Abstract base class to represent a single input file. Note that use
of this class is optional; it is possible create an InputSet that
does not rely on underlying Inputfile objects.</p>
<p>All InputFile classes must implement a get_string method, which
is called by write_file.</p>
<p>If InputFile classes implement an __init__ method, they must assign all
arguments to __init__ as attributes.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputFile.from_file">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L86-L99"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputFile.from_file" title="Permalink to this definition"></a></dt>
<dd><p>Creates an InputFile object from a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>path</strong> – Filename to read, including path.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>InputFile</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputFile.from_string">
<em class="property"><span class="pre">abstract</span><span class="w"> </span><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_string</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">contents</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L73-L84"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputFile.from_string" title="Permalink to this definition"></a></dt>
<dd><p>Create an InputFile object from a string</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>contents</strong> – The contents of the file as a single string</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>InputFile</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputFile.get_string">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_string</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">str</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L56-L60"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputFile.get_string" title="Permalink to this definition"></a></dt>
<dd><p>Return a string representation of an entire input file.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputFile.write_file">
<span class="sig-name descname"><span class="pre">write_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</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/../io/core.py#L62-L71"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputFile.write_file" title="Permalink to this definition"></a></dt>
<dd><p>Write the input file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> – The filename to output to, including path.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.core.InputGenerator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">InputGenerator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L247-L259"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputGenerator" 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>InputGenerator classes serve as generators for Input objects. They contain
settings or sets of instructions for how to create Input from a set of
coordinates or a previous calculation directory.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputGenerator.get_input_set">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_input_set</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"><a class="reference internal" href="#pymatgen.io.core.InputSet" title="pymatgen.io.core.InputSet"><span class="pre">InputSet</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L254-L259"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputGenerator.get_input_set" title="Permalink to this definition"></a></dt>
<dd><p>Generate an InputSet object. Typically the first argument to this method
will be a Structure or other form of atomic coordinates.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.io.core.InputSet">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">InputSet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">inputs</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="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">pathlib.Path</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#pymatgen.io.core.InputFile" title="pymatgen.io.core.InputFile"><span class="pre">pymatgen.io.core.InputFile</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L105-L244"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputSet" 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>, <code class="xref py py-class docutils literal notranslate"><span class="pre">MutableMapping</span></code></p>
<p>Abstract base class for all InputSet classes. InputSet are dict-like
containers for all calculation input data.</p>
<p>Since InputSet inherits dict, it can be instantiated in the same manner,
or a custom __init__ can be provided. Either way, <cite>self</cite> should be
populated with keys that are filenames to be written, and values that are
InputFile objects or strings representing the entire contents of the file.</p>
<p>All InputSet must implement from_directory. Implementing the validate method
is optional.</p>
<p>Instantiate an InputSet.</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>inputs</strong> – The core mapping of filename: file contents that defines the InputSet data.
This should be a dict where keys are filenames and values are InputFile objects
or strings representing the entire contents of the file. If a value is not an
InputFile object nor a str, but has a __str__ method, this str representation
of the object will be written to the corresponding file. This mapping will
become the .inputs attribute of the InputSet.</p></li>
<li><p><strong>**kwargs</strong> – Any kwargs passed will be set as class attributes e.g.
InputSet(inputs={}, foo=’bar’) will make InputSet.foo == ‘bar’.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputSet.from_directory">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_directory</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L227-L235"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputSet.from_directory" title="Permalink to this definition"></a></dt>
<dd><p>Construct an InputSet from a directory of one or more files.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>directory</strong> – Directory to read input files from</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputSet.validate">
<span class="sig-name descname"><span class="pre">validate</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">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L237-L244"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputSet.validate" title="Permalink to this definition"></a></dt>
<dd><p>A place to implement basic checks to verify the validity of an
input set. Can be as simple or as complex as desired.</p>
<p>Will raise a NotImplementedError unless overloaded by the inheriting class.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.io.core.InputSet.write_input">
<span class="sig-name descname"><span class="pre">write_input</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">directory</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">Path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">make_dir</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">overwrite</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">zip_inputs</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><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2023.5.10/pymatgen/core/../io/core.py#L179-L225"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.io.core.InputSet.write_input" title="Permalink to this definition"></a></dt>
<dd><p>Write Inputs to one or more files</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>directory</strong> – Directory to write input files to</p></li>
<li><p><strong>make_dir</strong> – Whether to create the directory if it does not already exist.</p></li>
<li><p><strong>overwrite</strong> – Whether to overwrite an input file if it already exists.</p></li>
<li><p><strong>generate_inputs</strong> (<em>Additional kwargs are passed to</em>) – </p></li>
<li><p><strong>zip_inputs</strong> – If True, inputs will be zipped into a file with the
same name as the InputSet (e.g., InputSet.zip)</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
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