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<div class="section" id="module-pymatgen.io.qchem_deprecated">
<span id="pymatgen-io-qchem-deprecated-module"></span><h1>pymatgen.io.qchem_deprecated module<a class="headerlink" href="#module-pymatgen.io.qchem_deprecated" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.io.qchem_deprecated.QcInput">
<em class="property">class </em><code class="descname">QcInput</code><span class="sig-paren">(</span><em>jobs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcInput"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcInput" 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 multiple step QChem input file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>jobs</strong> – The QChem jobs (List of QcInput object)</p>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcInput.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/qchem_deprecated.html#QcInput.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcInput.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.qchem_deprecated.QcInput.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/qchem_deprecated.html#QcInput.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcInput.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.qchem_deprecated.QcInput.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/qchem_deprecated.html#QcInput.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcInput.from_file" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.qchem_deprecated.QcInput.from_string">
<em class="property">classmethod </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/qchem_deprecated.html#QcInput.from_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcInput.from_string" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcInput.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/qchem_deprecated.html#QcInput.write_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcInput.write_file" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.qchem_deprecated.QcNucVeloc">
<em class="property">class </em><code class="descname">QcNucVeloc</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcNucVeloc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcNucVeloc" 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>class to QChem AMID NucVeloc file.</p>
<blockquote>
<div><dl class="simple">
<dt>Args:</dt><dd><p>filename (str): Filename to parse</p>
</dd>
</dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcNucVeloc.time_steps">
<code class="descname">time_steps</code><span class="sig-paren">(</span><em>fs</em><span class="sig-paren">)</span><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcNucVeloc.time_steps" title="Permalink to this definition">¶</a></dt>
<dt>
<code class="descname">The AIMD time stamp for each frame</code></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcNucVeloc.velocities">
<code class="descname">velocities</code><span class="sig-paren">(</span><em>a.u.</em><span class="sig-paren">)</span><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcNucVeloc.velocities" title="Permalink to this definition">¶</a></dt>
<dt>
<code class="descname">The atom velocities for each frame. Format:</code></dt>
<dt>
<code class="descname">[[[x, y, z]</code></dt>
<dt>
<code class="descname">[x, y, z]</code></dt>
<dt>
<code class="descname">... ] ## frame 1</code></dt>
<dt>
<code class="descname">...</code></dt>
<dt>
<code class="descname">[[x, y, z]</code></dt>
<dt>
<code class="descname">[x, y, z]</code></dt>
<dt>
<code class="descname">... ] ## frame N</code></dt>
<dt>
<code class="descname">]</code></dt>
<dd></dd></dl>
</div></blockquote>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.qchem_deprecated.QcOutput">
<em class="property">class </em><code class="descname">QcOutput</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcOutput"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcOutput" 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>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcOutput.final_energy">
<code class="descname">final_energy</code><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcOutput.final_energy" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcOutput.final_structure">
<code class="descname">final_structure</code><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcOutput.final_structure" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcOutput.kcal_per_mol_2_eV">
<code class="descname">kcal_per_mol_2_eV</code><em class="property"> = 0.043363</em><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcOutput.kcal_per_mol_2_eV" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.io.qchem_deprecated.QcTask">
<em class="property">class </em><code class="descname">QcTask</code><span class="sig-paren">(</span><em>molecule=None</em>, <em>charge=None</em>, <em>spin_multiplicity=None</em>, <em>jobtype='SP'</em>, <em>title=None</em>, <em>exchange='HF'</em>, <em>correlation=None</em>, <em>basis_set='6-31+G*'</em>, <em>aux_basis_set=None</em>, <em>ecp=None</em>, <em>rem_params=None</em>, <em>optional_params=None</em>, <em>ghost_atoms=None</em>, <em>method=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask" 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 QChem input file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – The input molecule. If it is None of string “read”,
QChem will read geometry from checkpoint file. If it is a
Molecule object, QcInput will convert it into Cartesian
coordinates. Valid values: pymatgen Molecule object, “read”, None
Defaults to None.</p></li>
<li><p><strong>charge</strong> (<em>int</em>) – Charge of the molecule. If None, charge on molecule is
used. Defaults to None.</p></li>
<li><p><strong>spin_multiplicity</strong> (<em>int</em>) – 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>jobtype</strong> (<em>str</em>) – The type the QChem job. “SP” for Single Point Energy,
“opt” for geometry optimization, “freq” for
vibrational frequency.</p></li>
<li><p><strong>title</strong> (<em>str</em>) – Comments for the job. Defaults to None. Which means the
$comment section will be discarded.</p></li>
<li><p><strong>exchange</strong> (<em>str</em>) – The exchange methods of the theory. Examples including:
“B” (in pure BLYP), “PW91”, “PBE”, “TPSS”.
Defaults to “HF”.
This parameter can also be common names of hybrid
functionals, such as B3LYP, TPSSh, XYGJOS. In such cases,
the correlation parameter should be left as None.</p></li>
<li><p><strong>correlation</strong> (<em>str</em>) – The correlation level of the theory. Example
including: “MP2”, “RI-MP2”, “CCSD(T)”, “LYP”, “PBE”, “TPSS”
Defaults to None.</p></li>
<li><p><strong>basis_set</strong> (<em>str/dict</em>) – The basis set.
If it is a dict, each element can use different basis set.</p></li>
<li><p><strong>aux_basis_set</strong> (<em>str/dict</em>) – Auxiliary basis set. For methods,
like RI-MP2, XYG3, OXYJ-OS, auxiliary basis set is required.
If it is a dict, each element can use different auxiliary
basis set.</p></li>
<li><p><strong>ecp</strong> – Effective core potential (ECP) to be used.
If it is a dict, each element can use different ECP.</p></li>
<li><p><strong>rem_params</strong> (<em>dict</em>) – The parameters supposed to write in the $rem
section. Dict of key/value pairs.
Example: {“scf_algorithm”: “diis_gdm”, “scf_max_cycles”: 100}</p></li>
<li><p><strong>optional_params</strong> (<em>dict</em>) – The parameter for keywords other than $rem
section. Dict of key/value pairs.
Example: {“basis”: {“Li”: “cc-PVTZ”, “B”: “aug-cc-PVTZ”,
“F”: “aug-cc-PVTZ”} “ecp”: {“Cd”: “srsc”, “Br”: “srlc”}}</p></li>
<li><p><strong>ghost_atom</strong> (<em>list</em>) – List of ghost atoms indices. Indices start from 0.
The ghost atom will be represented in of the form of @element_symmbol</p></li>
</ul>
</dd>
</dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcTask.alternative_keys">
<code class="descname">alternative_keys</code><em class="property"> = {'job_type': 'jobtype', 'scf_max_cycles': 'max_scf_cycles', 'symmetry_ignore': 'sym_ignore'}</em><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.alternative_keys" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcTask.alternative_values">
<code class="descname">alternative_values</code><em class="property"> = {'frequency': 'freq', 'optimization': 'opt'}</em><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.alternative_values" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.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/qchem_deprecated.html#QcTask.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>A JSON serializable dict representation of an object.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.disable_symmetry">
<code class="descname">disable_symmetry</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.disable_symmetry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.disable_symmetry" title="Permalink to this definition">¶</a></dt>
<dd><p>Turn the symmetry off.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.qchem_deprecated.QcTask.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/qchem_deprecated.html#QcTask.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.from_dict" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.qchem_deprecated.QcTask.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/qchem_deprecated.html#QcTask.from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.from_file" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="classmethod">
<dt id="pymatgen.io.qchem_deprecated.QcTask.from_string">
<em class="property">classmethod </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/qchem_deprecated.html#QcTask.from_string"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.from_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates QcInput 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 a QChem input file.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>QcInput object</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcTask.molecule">
<code class="descname">molecule</code><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.molecule" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcTask.optional_keywords_list">
<code class="descname">optional_keywords_list</code><em class="property"> = {'alist', 'aux_basis', 'basis', 'basis2', 'cdft', 'ecp', 'efp_fragments', 'efp_params', 'empirical_dispersion', 'external_charges', 'force_field_params', 'intracule', 'isotopes', 'localized_diabatization', 'multipole_field', 'nbo', 'occupied', 'opt', 'pcm', 'pcm_solvent', 'plots', 'qm_atoms', 'solvent', 'svp', 'svpirf', 'swap_occupied_virtual', 'van_der_waals', 'velocity', 'xc_functional'}</em><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.optional_keywords_list" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.scale_geom_opt_threshold">
<code class="descname">scale_geom_opt_threshold</code><span class="sig-paren">(</span><em>gradient=0.1</em>, <em>displacement=0.1</em>, <em>energy=0.1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.scale_geom_opt_threshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.scale_geom_opt_threshold" title="Permalink to this definition">¶</a></dt>
<dd><p>Adjust the convergence criteria of geometry optimization.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gradient</strong> – the scale factor for gradient criteria. If less than
1.0, you are tightening the threshold. The base value is
300 × 10E−6</p></li>
<li><p><strong>displacement</strong> – the scale factor for atomic displacement. If less
then 1.0, you are tightening the threshold. The base value is
1200 × 10E−6</p></li>
<li><p><strong>energy</strong> – the scale factor for energy change between successive
iterations. If less than 1.0, you are tightening the
threshold. The base value is 100 × 10E−8.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_auxiliary_basis_set">
<code class="descname">set_auxiliary_basis_set</code><span class="sig-paren">(</span><em>aux_basis_set</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_auxiliary_basis_set"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_auxiliary_basis_set" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_basis2">
<code class="descname">set_basis2</code><span class="sig-paren">(</span><em>basis2_basis_set</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_basis2"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_basis2" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_basis_set">
<code class="descname">set_basis_set</code><span class="sig-paren">(</span><em>basis_set</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_basis_set"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_basis_set" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_dft_grid">
<code class="descname">set_dft_grid</code><span class="sig-paren">(</span><em>radical_points=128</em>, <em>angular_points=302</em>, <em>grid_type='Lebedev'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_dft_grid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_dft_grid" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the grid for DFT numerical integrations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>radical_points</strong> – Radical points. (Integer)</p></li>
<li><p><strong>angular_points</strong> – Angular points. (Integer)</p></li>
<li><p><strong>grid_type</strong> – The type of of the grid. There are two standard grids:
SG-1 and SG-0. The other two supported grids are “Lebedev” and
“Gauss-Legendre”</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_ecp">
<code class="descname">set_ecp</code><span class="sig-paren">(</span><em>ecp</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_ecp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_ecp" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_geom_max_iterations">
<code class="descname">set_geom_max_iterations</code><span class="sig-paren">(</span><em>iterations</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_geom_max_iterations"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_geom_max_iterations" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the max iterations of geometry optimization.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>iterations</strong> – the maximum iterations of geometry optimization.</p></li>
<li><p><strong>(</strong><strong>Integer</strong><strong>)</strong> – </p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_geom_opt_coords_type">
<code class="descname">set_geom_opt_coords_type</code><span class="sig-paren">(</span><em>coords_type='internal_switch'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_geom_opt_coords_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_geom_opt_coords_type" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the coordinates system used in geometry optimization.
“cartesian” — always cartesian coordinates.
“internal” — always internal coordinates.
“internal-switch” — try internal coordinates first, if fails, switch
to cartesian coordinates.
“z-matrix” — always z-matrix coordinates.
“z-matrix-switch” — try z-matrix first, if fails, switch to
cartesian coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>coords_type</strong> – The type of the coordinates. (str)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_geom_opt_use_gdiis">
<code class="descname">set_geom_opt_use_gdiis</code><span class="sig-paren">(</span><em>subspace_size=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_geom_opt_use_gdiis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_geom_opt_use_gdiis" title="Permalink to this definition">¶</a></dt>
<dd><p>Use GDIIS algorithm in geometry optimization.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>subspace_size</strong> – The size of the DIIS subsapce. None for default
value. The default value is min(NDEG, NATOMS, 4) NDEG = number
of moleculardegrees of freedom.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_integral_threshold">
<code class="descname">set_integral_threshold</code><span class="sig-paren">(</span><em>thresh=12</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_integral_threshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_integral_threshold" title="Permalink to this definition">¶</a></dt>
<dd><p>Cutoff for neglect of two electron integrals. 10−THRESH (THRESH <= 14).
In QChem, the default values are:
8 For single point energies.
10 For optimizations and frequency calculations.
14 For coupled-cluster calculations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>thresh</strong> – The exponent of the threshold. (Integer)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_max_num_of_scratch_files">
<code class="descname">set_max_num_of_scratch_files</code><span class="sig-paren">(</span><em>num=16</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_max_num_of_scratch_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_max_num_of_scratch_files" title="Permalink to this definition">¶</a></dt>
<dd><p>In QChem, the size of a single scratch is limited 2GB. By default,
the max number of scratich is 16, which is cooresponding to 32GB
scratch space. If you want to use more scratch disk space, you need
to increase the number of scratch files:</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>num</strong> – The max number of the scratch files. (Integer)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_memory">
<code class="descname">set_memory</code><span class="sig-paren">(</span><em>total=None</em>, <em>static=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_memory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_memory" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the maxium allowed memory.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>total</strong> – The total memory. Integer. Unit: MBytes. If set to None,
this parameter will be neglected.</p></li>
<li><p><strong>static</strong> – The static memory. Integer. Unit MBytes. If set to None,
this parameterwill be neglected.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_partial_hessian_atoms">
<code class="descname">set_partial_hessian_atoms</code><span class="sig-paren">(</span><em>alist</em>, <em>phess=1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_partial_hessian_atoms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_partial_hessian_atoms" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_scf_algorithm_and_iterations">
<code class="descname">set_scf_algorithm_and_iterations</code><span class="sig-paren">(</span><em>algorithm='diis'</em>, <em>iterations=50</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_scf_algorithm_and_iterations"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_scf_algorithm_and_iterations" title="Permalink to this definition">¶</a></dt>
<dd><p>Set algorithm used for converging SCF and max number of SCF iterations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>algorithm</strong> – The algorithm used for converging SCF. (str)</p></li>
<li><p><strong>iterations</strong> – The max number of SCF iterations. (Integer)</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_scf_convergence_threshold">
<code class="descname">set_scf_convergence_threshold</code><span class="sig-paren">(</span><em>exponent=8</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_scf_convergence_threshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_scf_convergence_threshold" title="Permalink to this definition">¶</a></dt>
<dd><p>SCF is considered converged when the wavefunction error is less than
10**(-exponent).
In QChem, the default values are:
5 For single point energy calculations.
7 For geometry optimizations and vibrational analysis.
8 For SSG calculations</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>exponent</strong> – The exponent of the threshold. (Integer)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_scf_initial_guess">
<code class="descname">set_scf_initial_guess</code><span class="sig-paren">(</span><em>guess='SAD'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_scf_initial_guess"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_scf_initial_guess" title="Permalink to this definition">¶</a></dt>
<dd><p>Set initial guess method to be used for SCF</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>guess</strong> – The initial guess method. (str)</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.set_velocities">
<code class="descname">set_velocities</code><span class="sig-paren">(</span><em>velocities</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.set_velocities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.set_velocities" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>(</strong><strong>au</strong><strong>)</strong> (<em>velocities</em>) – list of list of atom velocities</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.use_cosmo">
<code class="descname">use_cosmo</code><span class="sig-paren">(</span><em>dielectric_constant=78.4</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.use_cosmo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.use_cosmo" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the solvent model to COSMO.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>dielectric_constant</strong> – the dielectric constant for the solvent.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.use_pcm">
<code class="descname">use_pcm</code><span class="sig-paren">(</span><em>pcm_params=None</em>, <em>solvent_key='solvent'</em>, <em>solvent_params=None</em>, <em>radii_force_field=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/io/qchem_deprecated.html#QcTask.use_pcm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.use_pcm" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the solvent model to PCM. Default parameters are trying to comply to
gaussian default value</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pcm_params</strong> (<em>dict</em>) – The parameters of “$pcm” section.</p></li>
<li><p><strong>solvent_key</strong> (<em>str</em>) – for versions < 4.2 the section name is “pcm_solvent”</p></li>
<li><p><strong>solvent_params</strong> (<em>dict</em>) – The parameters of solvent_key section</p></li>
<li><p><strong>radii_force_field</strong> (<em>str</em>) – The force fied used to set the solute
radii. Default to UFF.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.io.qchem_deprecated.QcTask.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/qchem_deprecated.html#QcTask.write_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.write_file" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcTask.xyz_patt">
<code class="descname">xyz_patt</code><em class="property"> = re.compile('^(\\w+)[\\s,]+([\\d\\.eE\\-]+)[\\s,]+([\\d\\.eE\\-]+)[\\s,]+([\\d\\.eE\\-]+)[\\-\\.\\s,\\w.]*$')</em><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.xyz_patt" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="attribute">
<dt id="pymatgen.io.qchem_deprecated.QcTask.zmat_patt">
<code class="descname">zmat_patt</code><em class="property"> = re.compile('^(\\w+)*([\\s,]+(\\w+)[\\s,]+(\\w+))*[\\-\\.\\s,\\w]*$')</em><a class="headerlink" href="#pymatgen.io.qchem_deprecated.QcTask.zmat_patt" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
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