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<div class="section" id="module-pymatgen.io.gaussian">
<span id="pymatgen-io-gaussian-module"></span><h1>pymatgen.io.gaussian module<a class="headerlink" href="#module-pymatgen.io.gaussian" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.io.gaussian.GaussianInput">
<em class="property">class </em><code class="descname">GaussianInput</code><span class="sig-paren">(</span><em>mol</em>, <em>charge=None</em>, <em>spin_multiplicity=None</em>, <em>title=None</em>, <em>functional='HF'</em>, <em>basis_set='6-31G(d)'</em>, <em>route_parameters=None</em>, <em>input_parameters=None</em>, <em>link0_parameters=None</em>, <em>dieze_tag='#P'</em>, <em>gen_basis=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianInput"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput" 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>An object representing a Gaussian input file.</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>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>title</strong> – Title for run. Defaults to formula of molecule if None.</p></li>
<li><p><strong>functional</strong> – Functional for run.</p></li>
<li><p><strong>basis_set</strong> – Basis set for run.</p></li>
<li><p><strong>route_parameters</strong> – Additional route parameters as a dict. For example,
{‘SP’:”“, “SCF”:”Tight”}</p></li>
<li><p><strong>input_parameters</strong> – Additional input parameters for run as a dict. Used
for example, in PCM calculations. E.g., {“EPS”:12}</p></li>
<li><p><strong>link0_parameters</strong> – Link0 parameters as a dict. E.g., {“%mem”: “1000MW”}</p></li>
<li><p><strong>dieze_tag</strong> – # preceding the route line. E.g. “#p”</p></li>
<li><p><strong>gen_basis</strong> – allows a user-specified basis set to be used in a Gaussian
calculation. If this is not None, the attribute <code class="docutils literal notranslate"><span class="pre">basis_set</span></code> will
be set to “Gen”.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianInput.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/gaussian.html#GaussianInput.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.as_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.gaussian.GaussianInput.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/gaussian.html#GaussianInput.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.io.gaussian.GaussianInput.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/gaussian.html#GaussianInput.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.from_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates GaussianInput from a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>filename</strong> – Gaussian input filename</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>GaussianInput object</p>
</dd>
</dl>
</dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.io.gaussian.GaussianInput.from_string">
<em class="property">static </em><code class="descname">from_string</code><span class="sig-paren">(</span><em>contents</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianInput.from_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.from_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates GaussianInput from a string.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>contents</strong> – String representing an Gaussian input file.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>GaussianInput object</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianInput.get_cart_coords">
<code class="descname">get_cart_coords</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianInput.get_cart_coords"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.get_cart_coords" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the cartesian coordinates of the molecule</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianInput.get_zmatrix">
<code class="descname">get_zmatrix</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianInput.get_zmatrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.get_zmatrix" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a z-matrix representation of the molecule.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianInput.molecule">
<code class="descname">molecule</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.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.gaussian.GaussianInput.to_string">
<code class="descname">to_string</code><span class="sig-paren">(</span><em>cart_coords=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianInput.to_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.to_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Return GaussianInput string</p>
<dl class="simple">
<dt>Option: whe cart_coords sets to True return the cartesian coordinates</dt><dd><p>instead of the z-matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianInput.write_file">
<code class="descname">write_file</code><span class="sig-paren">(</span><em>filename</em>, <em>cart_coords=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianInput.write_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianInput.write_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Write the input string into a file</p>
<p>Option: see __str__ method</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.gaussian.GaussianOutput">
<em class="property">class </em><code class="descname">GaussianOutput</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput" 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>Parser for Gaussian output files.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>filename</strong> – Filename of Gaussian output file.</p>
</dd>
</dl>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Still in early beta.</p>
</div>
<p>Attributes:</p>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.structures">
<code class="descname">structures</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.structures" title="Permalink to this definition">¶</a></dt>
<dd><p>All structures from the calculation in the standard orientation. If the
symmetry is not considered, the standard orientation is not printed out
and the input orientation is used instead. Check the <cite>standard_orientation</cite>
attribute.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.structures_input_orientation">
<code class="descname">structures_input_orientation</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.structures_input_orientation" title="Permalink to this definition">¶</a></dt>
<dd><p>All structures from the calculation in the input orientation.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.energies">
<code class="descname">energies</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.energies" title="Permalink to this definition">¶</a></dt>
<dd><p>All energies from the calculation.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.eigenvalues">
<code class="descname">eigenvalues</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.eigenvalues" title="Permalink to this definition">¶</a></dt>
<dd><p>List of eigenvalues for the last geometry</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.MO_coefficients">
<code class="descname">MO_coefficients</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.MO_coefficients" title="Permalink to this definition">¶</a></dt>
<dd><p>Matrix of MO coefficients for the last geometry</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.cart_forces">
<code class="descname">cart_forces</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.cart_forces" title="Permalink to this definition">¶</a></dt>
<dd><p>All cartesian forces from the calculation.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.frequencies">
<code class="descname">frequencies</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.frequencies" title="Permalink to this definition">¶</a></dt>
<dd><p>A list for each freq calculation and for each mode of a dict with
{</p>
<blockquote>
<div><blockquote>
<div><p>“frequency”: freq in cm-1,
“symmetry”: symmetry tag
“r_mass”: Reduce mass,
“f_constant”: force constant,
“IR_intensity”: IR Intensity,
“mode”: normal mode</p>
</div></blockquote>
<p>}</p>
</div></blockquote>
<p>The normal mode is a 1D vector of dx, dy dz of each atom.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.hessian">
<code class="descname">hessian</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.hessian" title="Permalink to this definition">¶</a></dt>
<dd><p>Matrix of second derivatives of the energy with respect to cartesian
coordinates in the <strong>input orientation</strong> frame. Need #P in the
route section in order to be in the output.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.properly_terminated">
<code class="descname">properly_terminated</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.properly_terminated" title="Permalink to this definition">¶</a></dt>
<dd><p>True if run has properly terminated</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.is_pcm">
<code class="descname">is_pcm</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.is_pcm" title="Permalink to this definition">¶</a></dt>
<dd><p>True if run is a PCM run.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.is_spin">
<code class="descname">is_spin</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.is_spin" title="Permalink to this definition">¶</a></dt>
<dd><p>True if it is an unrestricted run</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.stationary_type">
<code class="descname">stationary_type</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.stationary_type" title="Permalink to this definition">¶</a></dt>
<dd><p>If it is a relaxation run, indicates whether it is a minimum (Minimum)
or a saddle point (“Saddle”).</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.corrections">
<code class="descname">corrections</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.corrections" title="Permalink to this definition">¶</a></dt>
<dd><p>Thermochemical corrections if this run is a Freq run as a dict. Keys
are “Zero-point”, “Thermal”, “Enthalpy” and “Gibbs Free Energy”</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.functional">
<code class="descname">functional</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.functional" title="Permalink to this definition">¶</a></dt>
<dd><p>Functional used in the run.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.basis_set">
<code class="descname">basis_set</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.basis_set" title="Permalink to this definition">¶</a></dt>
<dd><p>Basis set used in the run</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.route">
<code class="descname">route</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.route" title="Permalink to this definition">¶</a></dt>
<dd><dl class="simple">
<dt>Additional route parameters as a dict. For example,</dt><dd><p>{‘SP’:”“, “SCF”:”Tight”}</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.dieze_tag">
<code class="descname">dieze_tag</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.dieze_tag" title="Permalink to this definition">¶</a></dt>
<dd><p># preceding the route line, e.g. “#P”</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.link0">
<code class="descname">link0</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.link0" title="Permalink to this definition">¶</a></dt>
<dd><p>Link0 parameters as a dict. E.g., {“%mem”: “1000MW”}</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.charge">
<code class="descname">charge</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.charge" title="Permalink to this definition">¶</a></dt>
<dd><p>Charge for structure</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.spin_multiplicity">
<code class="descname">spin_multiplicity</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.spin_multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Spin multiplicity for structure</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.num_basis_func">
<code class="descname">num_basis_func</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.num_basis_func" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of basis functions in the run.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.electrons">
<code class="descname">electrons</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.electrons" title="Permalink to this definition">¶</a></dt>
<dd><p>number of alpha and beta electrons as (N alpha, N beta)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.pcm">
<code class="descname">pcm</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.pcm" title="Permalink to this definition">¶</a></dt>
<dd><p>PCM parameters and output if available.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.errors">
<code class="descname">errors</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.errors" title="Permalink to this definition">¶</a></dt>
<dd><p>error if not properly terminated (list to be completed in error_defs)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.Mulliken_charges">
<code class="descname">Mulliken_charges</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.Mulliken_charges" title="Permalink to this definition">¶</a></dt>
<dd><p>Mulliken atomic charges</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.eigenvectors">
<code class="descname">eigenvectors</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.eigenvectors" title="Permalink to this definition">¶</a></dt>
<dd><p>Matrix of shape (num_basis_func, num_basis_func). Each column is an
eigenvectors and contains AO coefficients of an MO.</p>
<p>eigenvectors[Spin] = mat(num_basis_func, num_basis_func)</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.molecular_orbital">
<code class="descname">molecular_orbital</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.molecular_orbital" title="Permalink to this definition">¶</a></dt>
<dd><p>MO development coefficients on AO in a more convenient array dict
for each atom and basis set label.</p>
<p>mo[Spin][OM j][atom i] = {AO_k: coeff, AO_k: coeff … }</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.atom_basis_labels">
<code class="descname">atom_basis_labels</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.atom_basis_labels" title="Permalink to this definition">¶</a></dt>
<dd><p>Labels of AO for each atoms. These labels are those used in the output
of molecular orbital coefficients (POP=Full) and in the
molecular_orbital array dict.</p>
<p>atom_basis_labels[iatom] = [AO_k, AO_k, …]</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.resumes">
<code class="descname">resumes</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.resumes" title="Permalink to this definition">¶</a></dt>
<dd><p>List of gaussian data resume given at the end of the output file before
the quotation. The resumes are given as string.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.title">
<code class="descname">title</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.title" title="Permalink to this definition">¶</a></dt>
<dd><p>Title of the gaussian run.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.standard_orientation">
<code class="descname">standard_orientation</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.standard_orientation" title="Permalink to this definition">¶</a></dt>
<dd><p>If True, the geometries stored in the structures are in the standard
orientation. Else, the geometries are in the input orientation.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.bond_orders">
<code class="descname">bond_orders</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.bond_orders" title="Permalink to this definition">¶</a></dt>
<dd><p>Dict of bond order values read in the output file such as:
{(0, 1): 0.8709, (1, 6): 1.234, …}</p>
<p>The keys are the atom indexes and the values are the Wiberg bond indexes
that are printed using <cite>pop=NBOREAD</cite> and <cite>$nbo bndidx $end</cite>.</p>
</dd></dl>
<p>Methods:</p>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.to_input">
<code class="descname">to_input</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.to_input"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.to_input" title="Permalink to this definition">¶</a></dt>
<dd><p>Return a GaussianInput object using the last geometry and the same
calculation parameters.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.read_scan">
<code class="descname">read_scan</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.read_scan"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.read_scan" title="Permalink to this definition">¶</a></dt>
<dd><p>Read a potential energy surface from a gaussian scan calculation.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.get_scan_plot">
<code class="descname">get_scan_plot</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.get_scan_plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.get_scan_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Get a matplotlib plot of the potential energy surface</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.save_scan_plot">
<code class="descname">save_scan_plot</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.save_scan_plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.save_scan_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Save a matplotlib plot of the potential energy surface to a file</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.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/gaussian.html#GaussianOutput.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Json-serializable dict representation.</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.final_energy">
<code class="descname">final_energy</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.final_energy" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.gaussian.GaussianOutput.final_structure">
<code class="descname">final_structure</code><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.final_structure" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt>
<code class="descname">get_scan_plot</code><span class="sig-paren">(</span><em>coords=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.get_scan_plot"><span class="viewcode-link">[source]</span></a></dt>
<dd><p>Get a matplotlib plot of the potential energy surface.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>coords</strong> – internal coordinate name to use as abcissa.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.get_spectre_plot">
<code class="descname">get_spectre_plot</code><span class="sig-paren">(</span><em>sigma=0.05</em>, <em>step=0.01</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.get_spectre_plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.get_spectre_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Get a matplotlib plot of the UV-visible xas. Transition are plotted
as vertical lines and as a sum of normal functions with sigma with. The
broadening is applied in energy and the xas is plotted as a function
of the wavelength.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sigma</strong> – Full width at half maximum in eV for normal functions.</p></li>
<li><p><strong>step</strong> – bin interval in eV</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><dl class="simple">
<dt>{“energies”: values, “lambda”: values, “xas”: values}</dt><dd><p>where values are lists of abscissa (energies, lamba) and
the sum of gaussian functions (xas).</p>
</dd>
</dl>
<p>A matplotlib plot.</p>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>A dict</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.read_excitation_energies">
<code class="descname">read_excitation_energies</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.read_excitation_energies"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.read_excitation_energies" title="Permalink to this definition">¶</a></dt>
<dd><p>Read a excitation energies after a TD-DFT calculation.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p><dl class="simple">
<dt>A list of tuple for each transition such as</dt><dd><p>[(energie (eV), lambda (nm), oscillatory strength), … ]</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p>A list</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt>
<code class="descname">read_scan</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.read_scan"><span class="viewcode-link">[source]</span></a></dt>
<dd><p>Read a potential energy surface from a gaussian scan calculation.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p><dl class="simple">
<dt>{“energies”: [ values ],</dt><dd><p>”coords”: {“d1”: [ values ], “A2”, [ values ], … }}</p>
</dd>
</dl>
<p>”energies” are the energies of all points of the potential energy
surface. “coords” are the internal coordinates used to compute the
potential energy surface and the internal coordinates optimized,
labelled by their name as defined in the calculation.</p>
</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p>A dict</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt>
<code class="descname">save_scan_plot</code><span class="sig-paren">(</span><em>filename='scan.pdf'</em>, <em>img_format='pdf'</em>, <em>coords=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.save_scan_plot"><span class="viewcode-link">[source]</span></a></dt>
<dd><p>Save matplotlib plot of the potential energy surface to a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> – Filename to write to.</p></li>
<li><p><strong>img_format</strong> – Image format to use. Defaults to EPS.</p></li>
<li><p><strong>coords</strong> – internal coordinate name to use as abcissa.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.gaussian.GaussianOutput.save_spectre_plot">
<code class="descname">save_spectre_plot</code><span class="sig-paren">(</span><em>filename='spectre.pdf'</em>, <em>img_format='pdf'</em>, <em>sigma=0.05</em>, <em>step=0.01</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.save_spectre_plot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.GaussianOutput.save_spectre_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Save matplotlib plot of the spectre to a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> – Filename to write to.</p></li>
<li><p><strong>img_format</strong> – Image format to use. Defaults to EPS.</p></li>
<li><p><strong>sigma</strong> – Full width at half maximum in eV for normal functions.</p></li>
<li><p><strong>step</strong> – bin interval in eV</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt>
<code class="descname">to_input</code><span class="sig-paren">(</span><em>mol=None</em>, <em>charge=None</em>, <em>spin_multiplicity=None</em>, <em>title=None</em>, <em>functional=None</em>, <em>basis_set=None</em>, <em>route_parameters=None</em>, <em>input_parameters=None</em>, <em>link0_parameters=None</em>, <em>dieze_tag=None</em>, <em>cart_coords=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#GaussianOutput.to_input"><span class="viewcode-link">[source]</span></a></dt>
<dd><p>Create a new input object using by default the last geometry read in
the output file and with the same calculation parameters. Arguments
are the same as GaussianInput class.</p>
<dl class="simple">
<dt>Returns</dt><dd><p>gaunip (GaussianInput) : the gaussian input object</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.io.gaussian.read_route_line">
<code class="descname">read_route_line</code><span class="sig-paren">(</span><em>route</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/gaussian.html#read_route_line"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.gaussian.read_route_line" title="Permalink to this definition">¶</a></dt>
<dd><p>read route line in gaussian input/output and return functional basis_set
and a dictionary of other route parameters</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>route</strong> (<em>str</em>) – the route line</p>
</dd>
</dl>
<dl class="simple">
<dt>return</dt><dd><p>functional (str) : the method (HF, PBE …)
basis_set (str) : the basis set
route (dict) : dictionary of parameters</p>
</dd>
</dl>
</dd></dl>
</div>
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