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<div class="section" id="module-pymatgen.io.nwchem">
<span id="pymatgen-io-nwchem-module"></span><h1>pymatgen.io.nwchem module<a class="headerlink" href="#module-pymatgen.io.nwchem" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.io.nwchem.NwInput">
<em class="property">class </em><code class="descname">NwInput</code><span class="sig-paren">(</span><em>mol</em>, <em>tasks</em>, <em>directives=None</em>, <em>geometry_options=('units'</em>, <em>'angstroms')</em>, <em>symmetry_options=None</em>, <em>memory_options=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwInput"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwInput" 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>An object representing a Nwchem input file, which is essentially a list
of tasks on a particular molecule.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol</strong> – Input molecule. If molecule is a single string, it is used as a
direct input to the geometry section of the Gaussian input
file.</p></li>
<li><p><strong>tasks</strong> – List of NwTasks.</p></li>
<li><p><strong>directives</strong> – List of root level directives as tuple. E.g.,
[(“start”, “water”), (“print”, “high”)]</p></li>
<li><p><strong>geometry_options</strong> – Additional list of options to be supplied to the
geometry. E.g., [“units”, “angstroms”, “noautoz”]. Defaults to
(“units”, “angstroms”).</p></li>
<li><p><strong>symmetry_options</strong> – Addition list of option to be supplied to the
symmetry. E.g. [“c1”] to turn off the symmetry</p></li>
<li><p><strong>memory_options</strong> – Memory controlling options. str.
E.g “total 1000 mb stack 400 mb”</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.nwchem.NwInput.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwInput.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwInput.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.nwchem.NwInput.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/nwchem.html#NwInput.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwInput.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.nwchem.NwInput.from_file">
<em class="property">classmethod </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/nwchem.html#NwInput.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwInput.from_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Read an NwInput from a file. Currently tested to work with
files generated from this class itself.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>filename</strong> – Filename to parse.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>NwInput object</p>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.nwchem.NwInput.from_string">
<em class="property">classmethod </em><code class="descname">from_string</code><span class="sig-paren">(</span><em>string_input</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwInput.from_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwInput.from_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Read an NwInput from a string. Currently tested to work with
files generated from this class itself.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>string_input</strong> – string_input to parse.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>NwInput object</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.nwchem.NwInput.molecule">
<code class="descname">molecule</code><a class="headerlink" href="#pymatgen.io.nwchem.NwInput.molecule" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns molecule associated with this GaussianInput.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.nwchem.NwInput.write_file">
<code class="descname">write_file</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwInput.write_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwInput.write_file" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="exception">
<dt id="pymatgen.io.nwchem.NwInputError">
<em class="property">exception </em><code class="descname">NwInputError</code><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwInputError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwInputError" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Error class for NwInput.</p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.nwchem.NwOutput">
<em class="property">class </em><code class="descname">NwOutput</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwOutput"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwOutput" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A Nwchem output file parser. Very basic for now - supports only dft and
only parses energies and geometries. Please note that Nwchem typically
outputs energies in either au or kJ/mol. All energies are converted to
eV in the parser.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>filename</strong> – Filename to read.</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.nwchem.NwOutput.get_excitation_spectrum">
<code class="descname">get_excitation_spectrum</code><span class="sig-paren">(</span><em>width=0.1</em>, <em>npoints=2000</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwOutput.get_excitation_spectrum"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwOutput.get_excitation_spectrum" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate an excitation spectra from the singlet roots of TDDFT
calculations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>width</strong> (<em>float</em>) – Width for Gaussian smearing.</p></li>
<li><p><strong>npoints</strong> (<em>int</em>) – Number of energy points. More points => smoother
curve.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><dl class="simple">
<dt>(ExcitationSpectrum) which can be plotted using</dt><dd><p>pymatgen.vis.plotters.SpectrumPlotter.</p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.nwchem.NwOutput.parse_tddft">
<code class="descname">parse_tddft</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwOutput.parse_tddft"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwOutput.parse_tddft" title="Permalink to this definition">¶</a></dt>
<dd><p>Parses TDDFT roots. Adapted from nw_spectrum.py script.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p><dl>
<dt>{</dt><dd><dl>
<dt>“singlet”: [</dt><dd><dl class="simple">
<dt>{</dt><dd><p>“energy”: float,
“osc_strength: float</p>
</dd>
</dl>
<p>}</p>
</dd>
</dl>
<p>],
“triplet”: [</p>
<blockquote>
<div><dl class="simple">
<dt>{</dt><dd><p>“energy”: float</p>
</dd>
</dl>
<p>}</p>
</div></blockquote>
<p>]</p>
</dd>
</dl>
<p>}</p>
</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.nwchem.NwTask">
<em class="property">class </em><code class="descname">NwTask</code><span class="sig-paren">(</span><em>charge</em>, <em>spin_multiplicity</em>, <em>basis_set</em>, <em>basis_set_option='cartesian'</em>, <em>title=None</em>, <em>theory='dft'</em>, <em>operation='optimize'</em>, <em>theory_directives=None</em>, <em>alternate_directives=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwTask"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwTask" 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>Base task for Nwchem.</p>
<p>Very flexible arguments to support many types of potential setups.
Users should use more friendly static methods unless they need the
flexibility.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>charge</strong> – Charge of the molecule. If None, charge on molecule is
used. Defaults to None. This allows the input file to be set a
charge independently from the molecule itself.</p></li>
<li><p><strong>spin_multiplicity</strong> – Spin multiplicity of molecule. Defaults to None,
which means that the spin multiplicity is set to 1 if the
molecule has no unpaired electrons and to 2 if there are
unpaired electrons.</p></li>
<li><p><strong>basis_set</strong> – The basis set used for the task as a dict. E.g.,
{“C”: “6-311++G**”, “H”: “6-31++G**”}.</p></li>
<li><p><strong>basis_set_option</strong> – cartesian (default) | spherical,</p></li>
<li><p><strong>title</strong> – Title for the task. Defaults to None, which means a title
based on the theory and operation of the task is
autogenerated.</p></li>
<li><p><strong>theory</strong> – The theory used for the task. Defaults to “dft”.</p></li>
<li><p><strong>operation</strong> – The operation for the task. Defaults to “optimize”.</p></li>
<li><p><strong>theory_directives</strong> – A dict of theory directives. For example,
if you are running dft calculations, you may specify the
exchange correlation functional using {“xc”: “b3lyp”}.</p></li>
<li><p><strong>alternate_directives</strong> – A dict of alternate directives. For
example, to perform cosmo calculations and dielectric
constant of 78, you’d supply {‘cosmo’: {“dielectric”: 78}}.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.nwchem.NwTask.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwTask.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwTask.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.nwchem.NwTask.dft_task">
<em class="property">classmethod </em><code class="descname">dft_task</code><span class="sig-paren">(</span><em>mol</em>, <em>xc='b3lyp'</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwTask.dft_task"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwTask.dft_task" title="Permalink to this definition">¶</a></dt>
<dd><p>A class method for quickly creating DFT tasks with optional
cosmo parameter .</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol</strong> – Input molecule</p></li>
<li><p><strong>xc</strong> – Exchange correlation to use.</p></li>
<li><p><strong>**kwargs</strong> – Any of the other kwargs supported by NwTask. Note the
theory is always “dft” for a dft task.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.nwchem.NwTask.esp_task">
<em class="property">classmethod </em><code class="descname">esp_task</code><span class="sig-paren">(</span><em>mol</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwTask.esp_task"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwTask.esp_task" title="Permalink to this definition">¶</a></dt>
<dd><p>A class method for quickly creating ESP tasks with RESP
charge fitting.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol</strong> – Input molecule</p></li>
<li><p><strong>**kwargs</strong> – Any of the other kwargs supported by NwTask. Note the
theory is always “dft” for a dft task.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.nwchem.NwTask.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/nwchem.html#NwTask.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwTask.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.nwchem.NwTask.from_molecule">
<em class="property">classmethod </em><code class="descname">from_molecule</code><span class="sig-paren">(</span><em>mol</em>, <em>theory</em>, <em>charge=None</em>, <em>spin_multiplicity=None</em>, <em>basis_set='6-31g'</em>, <em>basis_set_option='cartesian'</em>, <em>title=None</em>, <em>operation='optimize'</em>, <em>theory_directives=None</em>, <em>alternate_directives=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/nwchem.html#NwTask.from_molecule"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.nwchem.NwTask.from_molecule" title="Permalink to this definition">¶</a></dt>
<dd><p>Very flexible arguments to support many types of potential setups.
Users should use more friendly static methods unless they need the
flexibility.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol</strong> – Input molecule</p></li>
<li><p><strong>charge</strong> – Charge of the molecule. If None, charge on molecule is
used. Defaults to None. This allows the input file to be set a
charge independently from the molecule itself.</p></li>
<li><p><strong>spin_multiplicity</strong> – Spin multiplicity of molecule. Defaults to None,
which means that the spin multiplicity is set to 1 if the
molecule has no unpaired electrons and to 2 if there are
unpaired electrons.</p></li>
<li><p><strong>basis_set</strong> – The basis set to be used as string or a dict. E.g.,
{“C”: “6-311++G**”, “H”: “6-31++G**”} or “6-31G”. If string,
same basis set is used for all elements.</p></li>
<li><p><strong>basis_set_option</strong> – cartesian (default) | spherical,</p></li>
<li><p><strong>title</strong> – Title for the task. Defaults to None, which means a title
based on the theory and operation of the task is
autogenerated.</p></li>
<li><p><strong>theory</strong> – The theory used for the task. Defaults to “dft”.</p></li>
<li><p><strong>operation</strong> – The operation for the task. Defaults to “optimize”.</p></li>
<li><p><strong>theory_directives</strong> – A dict of theory directives. For example,
if you are running dft calculations, you may specify the
exchange correlation functional using {“xc”: “b3lyp”}.</p></li>
<li><p><strong>alternate_directives</strong> – A dict of alternate directives. For
example, to perform cosmo calculations with DFT, you’d supply
{‘cosmo’: “cosmo”}.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.nwchem.NwTask.operations">
<code class="descname">operations</code><em class="property"> = {'': 'dummy', 'dynamics': 'Perform classical molecular dynamics.', 'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'gradient': 'Evaluate the derivative of the energy with respect to nuclear coordinates.', 'hessian': 'Compute second derivatives.', 'optimize': 'Minimize the energy by varying the molecular structure.', 'property': 'Calculate the properties for the wave function.', 'saddle': 'Conduct a search for a transition state (or saddle point).', 'thermodynamics': 'Perform multi-configuration thermodynamic integration using classical MD.', 'vscf': 'Compute anharmonic contributions to the vibrational modes.'}</em><a class="headerlink" href="#pymatgen.io.nwchem.NwTask.operations" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.nwchem.NwTask.theories">
<code class="descname">theories</code><em class="property"> = {'band': 'Pseudopotential plane-wave DFT for solids using NWPW', 'ccsd': 'Coupled-cluster single and double excitations', 'ccsd(t)': 'Coupled-cluster linearized triples approximation', 'ccsd+t(ccsd)': 'Fourth order triples contribution', 'dft': 'DFT', 'direct_mp2': 'MP2 using a full-direct algorithm', 'esp': 'ESP', 'g3gn': 'some description', 'mcscf': 'Multiconfiguration SCF', 'md': 'Classical molecular dynamics simulation', 'mp2': 'MP2 using a semi-direct algorithm', 'pspw': 'Pseudopotential plane-wave DFT for molecules and insulating solids using NWPW', 'rimp2': 'MP2 using the RI approximation', 'scf': 'Hartree-Fock', 'selci': 'Selected CI with perturbation correction', 'sodft': 'Spin-Orbit DFT', 'tce': 'Tensor Contraction Engine', 'tddft': 'Time Dependent DFT'}</em><a class="headerlink" href="#pymatgen.io.nwchem.NwTask.theories" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
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