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<div class="section" id="module-pymatgen.io.abinit.pseudos">
<span id="pymatgen-io-abinit-pseudos-module"></span><h1>pymatgen.io.abinit.pseudos module<a class="headerlink" href="#module-pymatgen.io.abinit.pseudos" title="Permalink to this headline">¶</a></h1>
<p>This module provides objects describing the basic parameters of the
pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..</p>
<dl class="class">
<dt id="pymatgen.io.abinit.pseudos.Pseudo">
<em class="property">class </em><code class="descname">Pseudo</code><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo" 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>Abstract base class defining the methods that must be
implemented by the concrete pseudopotential sub-classes.</p>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.Z">
<code class="descname">Z</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.Z" title="Permalink to this definition">¶</a></dt>
<dd><p>The atomic number of the atom.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.Z_val">
<code class="descname">Z_val</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.Z_val" title="Permalink to this definition">¶</a></dt>
<dd><p>Valence charge.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>A JSON serializable dict representation of an object.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.as_pseudo">
<em class="property">classmethod </em><code class="descname">as_pseudo</code><span class="sig-paren">(</span><em>obj</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.as_pseudo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.as_pseudo" title="Permalink to this definition">¶</a></dt>
<dd><p>Convert obj into a pseudo. Accepts:</p>
<blockquote>
<div><ul class="simple">
<li><p>Pseudo object.</p></li>
<li><p>string defining a valid path.</p></li>
</ul>
</div></blockquote>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.as_tmpfile">
<code class="descname">as_tmpfile</code><span class="sig-paren">(</span><em>tmpdir=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.as_tmpfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.as_tmpfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Copy the pseudopotential to a temporary a file and returns a new pseudopotential object.
Useful for unit tests in which we have to change the content of the file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>tmpdir</strong> – If None, a new temporary directory is created and files are copied here
else tmpdir is used.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.basename">
<code class="descname">basename</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.basename" title="Permalink to this definition">¶</a></dt>
<dd><p>File basename.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.compute_md5">
<code class="descname">compute_md5</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.compute_md5"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.compute_md5" title="Permalink to this definition">¶</a></dt>
<dd><p>Compute and erturn MD5 hash value.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.djrepo_path">
<code class="descname">djrepo_path</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.djrepo_path" title="Permalink to this definition">¶</a></dt>
<dd><p>The path of the djrepo file. None if file does not exist.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.element">
<code class="descname">element</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.element" title="Permalink to this definition">¶</a></dt>
<dd><p>Pymatgen <code class="xref py py-class docutils literal notranslate"><span class="pre">Element</span></code>.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.filepath">
<code class="descname">filepath</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.filepath" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.from_file">
<em class="property">static </em><code class="descname">from_file</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.from_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Build an instance of a concrete Pseudo subclass from filename.
Note: the parser knows the concrete class that should be instantiated
Client code should rely on the abstract interface provided by Pseudo.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.has_dojo_report">
<code class="descname">has_dojo_report</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.has_dojo_report" title="Permalink to this definition">¶</a></dt>
<dd><p>True if the pseudo has an associated <cite>DOJO_REPORT</cite> section.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.has_hints">
<code class="descname">has_hints</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.has_hints" title="Permalink to this definition">¶</a></dt>
<dd><p>True if self provides hints on the cutoff energy.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.hint_for_accuracy">
<code class="descname">hint_for_accuracy</code><span class="sig-paren">(</span><em>accuracy='normal'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.hint_for_accuracy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.hint_for_accuracy" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a <code class="xref py py-class docutils literal notranslate"><span class="pre">Hint</span></code> object with the suggested value of ecut [Ha] and
pawecutdg [Ha] for the given accuracy.
ecut and pawecutdg are set to zero if no hint is available.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>accuracy</strong> – [“low”, “normal”, “high”]</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.isnc">
<code class="descname">isnc</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.isnc" title="Permalink to this definition">¶</a></dt>
<dd><p>True if norm-conserving pseudopotential.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.ispaw">
<code class="descname">ispaw</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.ispaw" title="Permalink to this definition">¶</a></dt>
<dd><p>True if PAW pseudopotential.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.l_local">
<code class="descname">l_local</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.l_local" title="Permalink to this definition">¶</a></dt>
<dd><p>Angular momentum used for the local part.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.l_max">
<code class="descname">l_max</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.l_max" title="Permalink to this definition">¶</a></dt>
<dd><p>Maximum angular momentum.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.md5">
<code class="descname">md5</code><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.md5"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.md5" title="Permalink to this definition">¶</a></dt>
<dd><p>MD5 hash value.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.open_pspsfile">
<code class="descname">open_pspsfile</code><span class="sig-paren">(</span><em>ecut=20</em>, <em>pawecutdg=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.open_pspsfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.open_pspsfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Calls Abinit to compute the internal tables for the application of the
pseudopotential part. Returns <code class="xref py py-class docutils literal notranslate"><span class="pre">PspsFile</span></code> object providing methods
to plot and analyze the data or None if file is not found or it’s not readable.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ecut</strong> – Cutoff energy in Hartree.</p></li>
<li><p><strong>pawecutdg</strong> – Cutoff energy for the PAW double grid.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.summary">
<code class="descname">summary</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.summary" title="Permalink to this definition">¶</a></dt>
<dd><p>String summarizing the most important properties.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.supports_soc">
<code class="descname">supports_soc</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.supports_soc" title="Permalink to this definition">¶</a></dt>
<dd><p>True if the pseudo can be used in a calculation with spin-orbit coupling.
Base classes should provide a concrete implementation that computes this value.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.symbol">
<code class="descname">symbol</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.symbol" title="Permalink to this definition">¶</a></dt>
<dd><p>Element symbol.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.to_string">
<code class="descname">to_string</code><span class="sig-paren">(</span><em>verbose=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#Pseudo.to_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.to_string" title="Permalink to this definition">¶</a></dt>
<dd><p>String representation.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.Pseudo.type">
<code class="descname">type</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.Pseudo.type" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable">
<em class="property">class </em><code class="descname">PseudoTable</code><span class="sig-paren">(</span><em>pseudos</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">collections.abc.Sequence</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>Define the pseudopotentials from the element table.
Individidual elements are accessed by name, symbol or atomic number.</p>
<p>For example, the following all retrieve iron:</p>
<p>print elements[26]
Fe
print elements.Fe
Fe
print elements.symbol(‘Fe’)
Fe
print elements.name(‘iron’)
Fe
print elements.isotope(‘Fe’)
Fe</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>pseudos</strong> – List of pseudopotentials or filepaths</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.all_combinations_for_elements">
<code class="descname">all_combinations_for_elements</code><span class="sig-paren">(</span><em>element_symbols</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.all_combinations_for_elements"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.all_combinations_for_elements" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a list with all the the possible combination of pseudos
for the given list of element_symbols.
Each item is a list of pseudopotential objects.</p>
<p>Example:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">table</span><span class="o">.</span><span class="n">all_combinations_for_elements</span><span class="p">([</span><span class="s2">"Li"</span><span class="p">,</span> <span class="s2">"F"</span><span class="p">])</span>
</pre></div>
</div>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.allnc">
<code class="descname">allnc</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.allnc" title="Permalink to this definition">¶</a></dt>
<dd><p>True if all pseudos are norm-conserving.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.allpaw">
<code class="descname">allpaw</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.allpaw" title="Permalink to this definition">¶</a></dt>
<dd><p>True if all pseudos are PAW.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>A JSON serializable dict representation of an object.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.as_table">
<em class="property">classmethod </em><code class="descname">as_table</code><span class="sig-paren">(</span><em>items</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.as_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.as_table" title="Permalink to this definition">¶</a></dt>
<dd><p>Return an instance of <a class="reference internal" href="#pymatgen.io.abinit.pseudos.PseudoTable" title="pymatgen.io.abinit.pseudos.PseudoTable"><code class="xref py py-class docutils literal notranslate"><span class="pre">PseudoTable</span></code></a> from the iterable items.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.from_dir">
<em class="property">classmethod </em><code class="descname">from_dir</code><span class="sig-paren">(</span><em>top</em>, <em>exts=None</em>, <em>exclude_dirs='_*'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.from_dir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.from_dir" title="Permalink to this definition">¶</a></dt>
<dd><p>Find all pseudos in the directory tree starting from top.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>top</strong> – Top of the directory tree</p></li>
<li><p><strong>exts</strong> – List of files extensions. if exts == “all_files”
we try to open all files in top</p></li>
<li><p><strong>exclude_dirs</strong> – Wildcard used to exclude directories.</p></li>
</ul>
</dd>
</dl>
<p>return: <a class="reference internal" href="#pymatgen.io.abinit.pseudos.PseudoTable" title="pymatgen.io.abinit.pseudos.PseudoTable"><code class="xref py py-class docutils literal notranslate"><span class="pre">PseudoTable</span></code></a> sorted by atomic number Z.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.get_pseudos_for_structure">
<code class="descname">get_pseudos_for_structure</code><span class="sig-paren">(</span><em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.get_pseudos_for_structure"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.get_pseudos_for_structure" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the list of <a class="reference internal" href="#pymatgen.io.abinit.pseudos.Pseudo" title="pymatgen.io.abinit.pseudos.Pseudo"><code class="xref py py-class docutils literal notranslate"><span class="pre">Pseudo</span></code></a> objects to be used for this <code class="xref py py-class docutils literal notranslate"><span class="pre">Structure</span></code>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>structure</strong> – pymatgen <code class="xref py py-class docutils literal notranslate"><span class="pre">Structure</span></code>.</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>ValueError</strong> – </p></li>
<li><p><strong>multiple occurences are present in the table.</strong> – </p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.is_complete">
<code class="descname">is_complete</code><span class="sig-paren">(</span><em>zmax=118</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.is_complete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.is_complete" title="Permalink to this definition">¶</a></dt>
<dd><p>True if table is complete i.e. all elements with Z < zmax have at least on pseudopotential</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.print_table">
<code class="descname">print_table</code><span class="sig-paren">(</span><em>stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'></em>, <em>filter_function=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.print_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.print_table" title="Permalink to this definition">¶</a></dt>
<dd><p>A pretty ASCII printer for the periodic table, based on some filter_function.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>stream</strong> – file-like object</p></li>
<li><p><strong>filter_function</strong> – A filtering function that take a Pseudo as input and returns a boolean.
For example, setting filter_function = lambda p: p.Z_val > 2 will print
a periodic table containing only pseudos with Z_val > 2.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.pseudo_with_symbol">
<code class="descname">pseudo_with_symbol</code><span class="sig-paren">(</span><em>symbol</em>, <em>allow_multi=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.pseudo_with_symbol"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.pseudo_with_symbol" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the pseudo with the given chemical symbol.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symbols</strong> – String with the chemical symbol of the element</p></li>
<li><p><strong>allow_multi</strong> – By default, the method raises ValueError
if multiple occurrences are found. Use allow_multi to prevent this.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><strong>ValueError if symbol is not found</strong><strong> or </strong><strong>multiple occurences are present and not allow_multi</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.pseudos_with_symbols">
<code class="descname">pseudos_with_symbols</code><span class="sig-paren">(</span><em>symbols</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.pseudos_with_symbols"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.pseudos_with_symbols" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the pseudos with the given chemical symbols.</p>
<dl class="field-list simple">
<dt class="field-odd">Raises</dt>
<dd class="field-odd"><p><strong>ValueError if one of the symbols is not found</strong><strong> or </strong><strong>multiple occurences are present.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.select">
<code class="descname">select</code><span class="sig-paren">(</span><em>condition</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.select"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.select" title="Permalink to this definition">¶</a></dt>
<dd><p>Select only those pseudopotentials for which condition is True.
Return new class:<cite>PseudoTable</cite> object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>condition</strong> – Function that accepts a <a class="reference internal" href="#pymatgen.io.abinit.pseudos.Pseudo" title="pymatgen.io.abinit.pseudos.Pseudo"><code class="xref py py-class docutils literal notranslate"><span class="pre">Pseudo</span></code></a> object and returns True or False.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.select_family">
<code class="descname">select_family</code><span class="sig-paren">(</span><em>family</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.select_family"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.select_family" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.select_rows">
<code class="descname">select_rows</code><span class="sig-paren">(</span><em>rows</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.select_rows"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.select_rows" title="Permalink to this definition">¶</a></dt>
<dd><p>Return new class:<cite>PseudoTable</cite> object with pseudos in the given rows of the periodic table.
rows can be either a int or a list of integers.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.select_symbols">
<code class="descname">select_symbols</code><span class="sig-paren">(</span><em>symbols</em>, <em>ret_list=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.select_symbols"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.select_symbols" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a <a class="reference internal" href="#pymatgen.io.abinit.pseudos.PseudoTable" title="pymatgen.io.abinit.pseudos.PseudoTable"><code class="xref py py-class docutils literal notranslate"><span class="pre">PseudoTable</span></code></a> with the pseudopotentials with the given list of chemical symbols.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symbols</strong> – str or list of symbols
Prepend the symbol string with “-“, to exclude pseudos.</p></li>
<li><p><strong>ret_list</strong> – if True a list of pseudos is returned instead of a <a class="reference internal" href="#pymatgen.io.abinit.pseudos.PseudoTable" title="pymatgen.io.abinit.pseudos.PseudoTable"><code class="xref py py-class docutils literal notranslate"><span class="pre">PseudoTable</span></code></a></p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.sort_by_z">
<code class="descname">sort_by_z</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.sort_by_z"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.sort_by_z" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a new <a class="reference internal" href="#pymatgen.io.abinit.pseudos.PseudoTable" title="pymatgen.io.abinit.pseudos.PseudoTable"><code class="xref py py-class docutils literal notranslate"><span class="pre">PseudoTable</span></code></a> with pseudos sorted by Z</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.sorted">
<code class="descname">sorted</code><span class="sig-paren">(</span><em>attrname</em>, <em>reverse=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.sorted"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.sorted" title="Permalink to this definition">¶</a></dt>
<dd><p>Sort the table according to the value of attribute attrname.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p><cite>PseudoTable</cite> object</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p>New class</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.to_table">
<code class="descname">to_table</code><span class="sig-paren">(</span><em>filter_function=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.to_table"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.to_table" title="Permalink to this definition">¶</a></dt>
<dd><p>Return string with data in tabular form.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.with_dojo_report">
<code class="descname">with_dojo_report</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/abinit/pseudos.html#PseudoTable.with_dojo_report"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.with_dojo_report" title="Permalink to this definition">¶</a></dt>
<dd><p>Select pseudos containing the DOJO_REPORT section. Return new class:<cite>PseudoTable</cite> object.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.abinit.pseudos.PseudoTable.zlist">
<code class="descname">zlist</code><a class="headerlink" href="#pymatgen.io.abinit.pseudos.PseudoTable.zlist" title="Permalink to this definition">¶</a></dt>
<dd><p>Ordered list with the atomic numbers available in the table.</p>
</dd></dl>
</dd></dl>
</div>
</div>
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