Update write_thermo_yaml docs

VlachosGroup · Apr 21, 2024 · 1cee0e2 · 1cee0e2
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diff --git a/.doctrees/api/constants/constants.doctree b/.doctrees/api/constants/constants.doctree
diff --git a/.doctrees/api/constants/constants/pmutt.constants.Na.doctree b/.doctrees/api/constants/constants/pmutt.constants.Na.doctree
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diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.einstein_to_debye.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.einstein_to_debye.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.energy_to_freq.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.energy_to_freq.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.energy_to_temp.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.energy_to_temp.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.energy_to_wavenumber.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.energy_to_wavenumber.doctree
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diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.freq_to_temp.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.freq_to_temp.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.freq_to_wavenumber.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.freq_to_wavenumber.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.inertia_to_temp.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.inertia_to_temp.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.temp_to_energy.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.temp_to_energy.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.temp_to_freq.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.temp_to_freq.doctree
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diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_energy.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_energy.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_freq.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_freq.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_inertia.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_inertia.doctree
diff --git a/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_temp.doctree b/.doctrees/api/constants/unit_conv/pmutt.constants.wavenumber_to_temp.doctree
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diff --git a/.doctrees/api/kinetic_models/omkm_phases/pmutt.omkm.phase.IdealGas.doctree b/.doctrees/api/kinetic_models/omkm_phases/pmutt.omkm.phase.IdealGas.doctree
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diff --git a/.doctrees/api/statmech/misc/pmutt.statmech.ConstantMode.doctree b/.doctrees/api/statmech/misc/pmutt.statmech.ConstantMode.doctree
diff --git a/.doctrees/api/statmech/misc/pmutt.statmech.EmptyMode.doctree b/.doctrees/api/statmech/misc/pmutt.statmech.EmptyMode.doctree
diff --git a/.doctrees/api/statmech/nucl/pmutt.statmech.nucl.EmptyNucl.doctree b/.doctrees/api/statmech/nucl/pmutt.statmech.nucl.EmptyNucl.doctree
diff --git a/.doctrees/api/statmech/rot/pmutt.statmech.rot.RigidRotor.doctree b/.doctrees/api/statmech/rot/pmutt.statmech.rot.RigidRotor.doctree
diff --git a/.doctrees/api/statmech/statmech.doctree b/.doctrees/api/statmech/statmech.doctree
diff --git a/.doctrees/api/statmech/statmech/pmutt.statmech.StatMech.doctree b/.doctrees/api/statmech/statmech/pmutt.statmech.StatMech.doctree
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diff --git a/.doctrees/api/statmech/vib/pmutt.statmech.vib.DebyeVib.doctree b/.doctrees/api/statmech/vib/pmutt.statmech.vib.DebyeVib.doctree
diff --git a/.doctrees/api/statmech/vib/pmutt.statmech.vib.EinsteinVib.doctree b/.doctrees/api/statmech/vib/pmutt.statmech.vib.EinsteinVib.doctree
diff --git a/.doctrees/api/statmech/vib/pmutt.statmech.vib.HarmonicVib.doctree b/.doctrees/api/statmech/vib/pmutt.statmech.vib.HarmonicVib.doctree
diff --git a/.doctrees/api/statmech/vib/pmutt.statmech.vib.QRRHOVib.doctree b/.doctrees/api/statmech/vib/pmutt.statmech.vib.QRRHOVib.doctree
diff --git a/.doctrees/api/visualization/visual.doctree b/.doctrees/api/visualization/visual.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/examples_jupyter/examples.doctree b/.doctrees/examples_jupyter/examples.doctree
diff --git a/.doctrees/includeme.doctree b/.doctrees/includeme.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/install.doctree b/.doctrees/install.doctree
diff --git a/.doctrees/publications.doctree b/.doctrees/publications.doctree
diff --git a/.doctrees/referencing.doctree b/.doctrees/referencing.doctree
diff --git a/.doctrees/release_notes.doctree b/.doctrees/release_notes.doctree
diff --git a/.doctrees/workshops/aiche_2019.doctree b/.doctrees/workshops/aiche_2019.doctree
diff --git a/.doctrees/workshops/nam_2019.doctree b/.doctrees/workshops/nam_2019.doctree
diff --git a/.doctrees/workshops/polimi_2020.doctree b/.doctrees/workshops/polimi_2020.doctree
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diff --git a/_sources/api/io/io.rst.txt b/_sources/api/io/io.rst.txt
@@ -338,6 +338,7 @@ OpenMKM
 
    omkm.write_cti
    omkm.write_yaml
+   omkm.write_thermo_yaml
    omkm.get_species_phases
    omkm.get_reactions_phases
    omkm.get_interactions_phases

diff --git a/_sources/api/io/omkm/pmutt.io.omkm.write_thermo_yaml.rst.txt b/_sources/api/io/omkm/pmutt.io.omkm.write_thermo_yaml.rst.txt
@@ -0,0 +1,6 @@
+pmutt.io.omkm.write\_thermo\_yaml
+=================================
+
+.. currentmodule:: pmutt.io.omkm
+
+.. autofunction:: write_thermo_yaml
diff --git a/api/io/io.html b/api/io/io.html
@@ -131,6 +131,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#openmkm">OpenMKM</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="omkm/pmutt.io.omkm.write_cti.html">pmutt.io.omkm.write_cti</a></li>
 <li class="toctree-l3"><a class="reference internal" href="omkm/pmutt.io.omkm.write_yaml.html">pmutt.io.omkm.write_yaml</a></li>
+<li class="toctree-l3"><a class="reference internal" href="omkm/pmutt.io.omkm.write_thermo_yaml.html">pmutt.io.omkm.write_thermo_yaml</a></li>
 <li class="toctree-l3"><a class="reference internal" href="omkm/pmutt.io.omkm.get_species_phases.html">pmutt.io.omkm.get_species_phases</a></li>
 <li class="toctree-l3"><a class="reference internal" href="omkm/pmutt.io.omkm.get_reactions_phases.html">pmutt.io.omkm.get_reactions_phases</a></li>
 <li class="toctree-l3"><a class="reference internal" href="omkm/pmutt.io.omkm.get_interactions_phases.html">pmutt.io.omkm.get_interactions_phases</a></li>
@@ -546,16 +547,19 @@ <h2>OpenMKM<a class="headerlink" href="#openmkm" title="Permalink to this headin
 <tr class="row-even"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.write_yaml.html#pmutt.io.omkm.write_yaml" title="pmutt.io.omkm.write_yaml"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.write_yaml</span></code></a></p></td>
 <td><p>Writes the reactor options in a YAML file for OpenMKM.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.get_species_phases.html#pmutt.io.omkm.get_species_phases" title="pmutt.io.omkm.get_species_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.get_species_phases</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="omkm/pmutt.io.omkm.write_thermo_yaml.html#pmutt.io.omkm.write_thermo_yaml" title="pmutt.io.omkm.write_thermo_yaml"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.write_thermo_yaml</span></code></a></p></td>
+<td><p>Writes the units, phases, species, lateral interactions, reactions and additional options in the CTI format for OpenMKM</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.get_species_phases.html#pmutt.io.omkm.get_species_phases" title="pmutt.io.omkm.get_species_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.get_species_phases</span></code></a></p></td>
 <td><p>Helper method to organize species into its phases</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.get_reactions_phases.html#pmutt.io.omkm.get_reactions_phases" title="pmutt.io.omkm.get_reactions_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.get_reactions_phases</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.get_reactions_phases.html#pmutt.io.omkm.get_reactions_phases" title="pmutt.io.omkm.get_reactions_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.get_reactions_phases</span></code></a></p></td>
 <td><p>Helper method to organize reaction into its phases</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.get_interactions_phases.html#pmutt.io.omkm.get_interactions_phases" title="pmutt.io.omkm.get_interactions_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.get_interactions_phases</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.get_interactions_phases.html#pmutt.io.omkm.get_interactions_phases" title="pmutt.io.omkm.get_interactions_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.get_interactions_phases</span></code></a></p></td>
 <td><p>Helper method to organize reaction into its phases</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.organize_phases.html#pmutt.io.omkm.organize_phases" title="pmutt.io.omkm.organize_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.organize_phases</span></code></a></p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="../kinetic_models/omkm/pmutt.io.omkm.organize_phases.html#pmutt.io.omkm.organize_phases" title="pmutt.io.omkm.organize_phases"><code class="xref py py-obj docutils literal notranslate"><span class="pre">omkm.organize_phases</span></code></a></p></td>
 <td><p>Helper method to organize phase data for OpenMKM</p></td>
 </tr>
 </tbody>