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Added license and updated docs

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titusquah
2021-03-24 16:34:41 -06:00
parent 70706c05c8
commit ac4f480fd6
60 changed files with 4034 additions and 192 deletions
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@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 64e91a3bc75e7eda68c23d7400e11773
config: fdde7da710e99305b2f90b2ffb8f91ce
tags: 645f666f9bcd5a90fca523b33c5a78b7

5
docs/build/html/_modules/index.html vendored
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@@ -85,10 +85,11 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../guide/install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../guide/quickstart.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="../guide/about.html">About</a></li>
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../modules/LLEPE.html">LLEPE</a></li>
</ul>
@@ -163,7 +164,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

99
docs/build/html/_modules/llepe/llepe.html vendored
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@@ -85,10 +85,11 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../guide/install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../guide/quickstart.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../guide/about.html">About</a></li>
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../modules/LLEPE.html">LLEPE</a></li>
</ul>
@@ -169,7 +170,7 @@
<span class="kn">from</span> <span class="nn">.utils</span> <span class="kn">import</span> <span class="n">set_size</span>
<div class="viewcode-block" id="LLEPE"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE">[docs]</a><span class="k">class</span> <span class="nc">LLEPE</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE">[docs]</a><span class="k">class</span> <span class="nc">LLEPE</span><span class="p">:</span>
<span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Liquid-Liquid Extraction Parameter estimator</span>
@@ -527,7 +528,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">update_predicted_dict</span><span class="p">()</span>
<span class="c1"># TODO: move scipy_minimize to optimizers</span>
<div class="viewcode-block" id="LLEPE.scipy_minimize"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.scipy_minimize">[docs]</a> <span class="nd">@staticmethod</span>
<div class="viewcode-block" id="LLEPE.scipy_minimize"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.scipy_minimize">[docs]</a> <span class="nd">@staticmethod</span>
<span class="k">def</span> <span class="nf">scipy_minimize</span><span class="p">(</span><span class="n">objective</span><span class="p">,</span> <span class="n">x_guess</span><span class="p">,</span> <span class="n">optimizer_kwargs</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot; The default optimizer for LLEPE</span>
@@ -562,7 +563,7 @@
<span class="k">return</span> <span class="n">est_parameters</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">fun</span></div>
<span class="c1"># TODO: move log_mean_squared_error to objectives</span>
<div class="viewcode-block" id="LLEPE.log_mean_squared_error"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.log_mean_squared_error">[docs]</a> <span class="k">def</span> <span class="nf">log_mean_squared_error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">predicted_dict</span><span class="p">,</span> <span class="n">meas_df</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.log_mean_squared_error"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.log_mean_squared_error">[docs]</a> <span class="k">def</span> <span class="nf">log_mean_squared_error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">predicted_dict</span><span class="p">,</span> <span class="n">meas_df</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Default objective function for LLEPE</span>
<span class="sd"> Returns the log mean squared error of</span>
@@ -586,14 +587,14 @@
<span class="n">obj</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">log_diff</span><span class="p">)</span>
<span class="k">return</span> <span class="n">obj</span></div>
<div class="viewcode-block" id="LLEPE.get_exp_df"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_exp_df">[docs]</a> <span class="k">def</span> <span class="nf">get_exp_df</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_exp_df"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_exp_df">[docs]</a> <span class="k">def</span> <span class="nf">get_exp_df</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns the experimental DataFrame</span>
<span class="sd"> :return: (pd.DataFrame) Experimental data</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_exp_df</span></div>
<div class="viewcode-block" id="LLEPE.set_exp_df"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_exp_df">[docs]</a> <span class="k">def</span> <span class="nf">set_exp_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">exp_data</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_exp_df"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_exp_df">[docs]</a> <span class="k">def</span> <span class="nf">set_exp_df</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">exp_data</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Changes the experimental DataFrame to input exp_csv_filename data</span>
<span class="sd"> and renames columns to internal LLEPE names</span>
@@ -634,7 +635,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">update_predicted_dict</span><span class="p">()</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_phases"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_phases">[docs]</a> <span class="k">def</span> <span class="nf">get_phases</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_phases"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_phases">[docs]</a> <span class="k">def</span> <span class="nf">get_phases</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the list of Cantera solutions</span>
@@ -642,7 +643,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phases</span></div>
<div class="viewcode-block" id="LLEPE.set_phases"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_phases">[docs]</a> <span class="k">def</span> <span class="nf">set_phases</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">phases_xml_filename</span><span class="p">,</span> <span class="n">phase_names</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_phases"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_phases">[docs]</a> <span class="k">def</span> <span class="nf">set_phases</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">phases_xml_filename</span><span class="p">,</span> <span class="n">phase_names</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Change list of Cantera solutions by inputting</span>
<span class="sd"> new xml file name and phase names</span>
@@ -675,7 +676,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">update_predicted_dict</span><span class="p">()</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_opt_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_opt_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_opt_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_opt_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_opt_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_opt_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the dictionary containing optimization information</span>
@@ -684,7 +685,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_opt_dict</span></div>
<div class="viewcode-block" id="LLEPE.set_opt_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_opt_dict">[docs]</a> <span class="k">def</span> <span class="nf">set_opt_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">opt_dict</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_opt_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_opt_dict">[docs]</a> <span class="k">def</span> <span class="nf">set_opt_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">opt_dict</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Change the dictionary to input opt_dict.</span>
@@ -700,14 +701,14 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_opt_dict</span> <span class="o">=</span> <span class="n">opt_dict</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_aq_solvent_name"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_aq_solvent_name">[docs]</a> <span class="k">def</span> <span class="nf">get_aq_solvent_name</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_aq_solvent_name"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_aq_solvent_name">[docs]</a> <span class="k">def</span> <span class="nf">get_aq_solvent_name</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns aq_solvent_name</span>
<span class="sd"> :return: aq_solvent_name: (str) name of aqueous solvent in xml file</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_aq_solvent_name</span></div>
<div class="viewcode-block" id="LLEPE.set_aq_solvent_name"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_aq_solvent_name">[docs]</a> <span class="k">def</span> <span class="nf">set_aq_solvent_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aq_solvent_name</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_aq_solvent_name"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_aq_solvent_name">[docs]</a> <span class="k">def</span> <span class="nf">set_aq_solvent_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aq_solvent_name</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot; Change aq_solvent_name to input aq_solvent_name</span>
<span class="sd"> :param aq_solvent_name: (str) name of aqueous solvent in xml file</span>
@@ -715,14 +716,14 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_aq_solvent_name</span> <span class="o">=</span> <span class="n">aq_solvent_name</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_extractant_name"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_extractant_name">[docs]</a> <span class="k">def</span> <span class="nf">get_extractant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_extractant_name"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_extractant_name">[docs]</a> <span class="k">def</span> <span class="nf">get_extractant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns extractant name</span>
<span class="sd"> :return: extractant_name: (str) name of extractant in xml file</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_extractant_name</span></div>
<div class="viewcode-block" id="LLEPE.set_extractant_name"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_extractant_name">[docs]</a> <span class="k">def</span> <span class="nf">set_extractant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extractant_name</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_extractant_name"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_extractant_name">[docs]</a> <span class="k">def</span> <span class="nf">set_extractant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extractant_name</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Change extractant_name to input extractant_name</span>
<span class="sd"> :param extractant_name: (str) name of extractant in xml file</span>
@@ -730,13 +731,13 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_extractant_name</span> <span class="o">=</span> <span class="n">extractant_name</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_diluant_name"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_diluant_name">[docs]</a> <span class="k">def</span> <span class="nf">get_diluant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_diluant_name"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_diluant_name">[docs]</a> <span class="k">def</span> <span class="nf">get_diluant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot; Returns diluant name</span>
<span class="sd"> :return: diluant_name: (str) name of diluant in xml file</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_diluant_name</span></div>
<div class="viewcode-block" id="LLEPE.set_diluant_name"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_diluant_name">[docs]</a> <span class="k">def</span> <span class="nf">set_diluant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">diluant_name</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_diluant_name"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_diluant_name">[docs]</a> <span class="k">def</span> <span class="nf">set_diluant_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">diluant_name</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Change diluant_name to input diluant_name</span>
@@ -745,14 +746,14 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_diluant_name</span> <span class="o">=</span> <span class="n">diluant_name</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_complex_names"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_complex_names">[docs]</a> <span class="k">def</span> <span class="nf">get_complex_names</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_complex_names"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_complex_names">[docs]</a> <span class="k">def</span> <span class="nf">get_complex_names</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns list of complex names</span>
<span class="sd"> :return: complex_names: (list) names of complexes in xml file.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_complex_names</span></div>
<div class="viewcode-block" id="LLEPE.set_complex_names"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_complex_names">[docs]</a> <span class="k">def</span> <span class="nf">set_complex_names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">complex_names</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_complex_names"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_complex_names">[docs]</a> <span class="k">def</span> <span class="nf">set_complex_names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">complex_names</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Change complex names list to input complex_names</span>
<span class="sd"> :param complex_names: (list) names of complexes in xml file.</span>
@@ -760,7 +761,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_complex_names</span> <span class="o">=</span> <span class="n">complex_names</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_extracted_species_ion_names"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_extracted_species_ion_names">[docs]</a> <span class="k">def</span> <span class="nf">get_extracted_species_ion_names</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_extracted_species_ion_names"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_extracted_species_ion_names">[docs]</a> <span class="k">def</span> <span class="nf">get_extracted_species_ion_names</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns list of extracted species ion names</span>
<span class="sd"> :return: extracted_species_ion_names: (list) names of</span>
@@ -768,7 +769,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_extracted_species_ion_names</span></div>
<div class="viewcode-block" id="LLEPE.set_extracted_species_ion_names"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_extracted_species_ion_names">[docs]</a> <span class="k">def</span> <span class="nf">set_extracted_species_ion_names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extracted_species_ion_names</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_extracted_species_ion_names"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_extracted_species_ion_names">[docs]</a> <span class="k">def</span> <span class="nf">set_extracted_species_ion_names</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extracted_species_ion_names</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Change list of extracted species ion names to input</span>
<span class="sd"> extracted_species_ion_names</span>
@@ -778,7 +779,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_extracted_species_ion_names</span> <span class="o">=</span> <span class="n">extracted_species_ion_names</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_extracted_species_list"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_extracted_species_list">[docs]</a> <span class="k">def</span> <span class="nf">get_extracted_species_list</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_extracted_species_list"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_extracted_species_list">[docs]</a> <span class="k">def</span> <span class="nf">get_extracted_species_list</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns list of extracted species names</span>
<span class="sd"> :return: extracted_species_list: (list) names of extracted species in</span>
@@ -786,7 +787,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_extracted_species_list</span></div>
<div class="viewcode-block" id="LLEPE.set_extracted_species_list"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_extracted_species_list">[docs]</a> <span class="k">def</span> <span class="nf">set_extracted_species_list</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extracted_species_list</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_extracted_species_list"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_extracted_species_list">[docs]</a> <span class="k">def</span> <span class="nf">set_extracted_species_list</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extracted_species_list</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Change list of extracted species ion names to input</span>
<span class="sd"> extracted_species_ion_names</span>
@@ -796,14 +797,14 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_extracted_species_list</span> <span class="o">=</span> <span class="n">extracted_species_list</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_aq_solvent_rho"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_aq_solvent_rho">[docs]</a> <span class="k">def</span> <span class="nf">get_aq_solvent_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_aq_solvent_rho"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_aq_solvent_rho">[docs]</a> <span class="k">def</span> <span class="nf">get_aq_solvent_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns aqueous solvent density (g/L)</span>
<span class="sd"> :return: aq_solvent_rho: (float) density of aqueous solvent</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_aq_solvent_rho</span></div>
<div class="viewcode-block" id="LLEPE.set_aq_solvent_rho"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_aq_solvent_rho">[docs]</a> <span class="k">def</span> <span class="nf">set_aq_solvent_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aq_solvent_rho</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_aq_solvent_rho"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_aq_solvent_rho">[docs]</a> <span class="k">def</span> <span class="nf">set_aq_solvent_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aq_solvent_rho</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Changes aqueous solvent density (g/L) to input aq_solvent_rho</span>
<span class="sd"> :param aq_solvent_rho: (float) density of aqueous solvent</span>
@@ -811,14 +812,14 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_aq_solvent_rho</span> <span class="o">=</span> <span class="n">aq_solvent_rho</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_extractant_rho"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_extractant_rho">[docs]</a> <span class="k">def</span> <span class="nf">get_extractant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_extractant_rho"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_extractant_rho">[docs]</a> <span class="k">def</span> <span class="nf">get_extractant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns extractant density (g/L)</span>
<span class="sd"> :return: extractant_rho: (float) density of extractant</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_extractant_rho</span></div>
<div class="viewcode-block" id="LLEPE.set_extractant_rho"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_extractant_rho">[docs]</a> <span class="k">def</span> <span class="nf">set_extractant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extractant_rho</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_extractant_rho"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_extractant_rho">[docs]</a> <span class="k">def</span> <span class="nf">set_extractant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">extractant_rho</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Changes extractant density (g/L) to input extractant_rho</span>
<span class="sd"> :param extractant_rho: (float) density of extractant</span>
@@ -826,14 +827,14 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_extractant_rho</span> <span class="o">=</span> <span class="n">extractant_rho</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_diluant_rho"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_diluant_rho">[docs]</a> <span class="k">def</span> <span class="nf">get_diluant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_diluant_rho"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_diluant_rho">[docs]</a> <span class="k">def</span> <span class="nf">get_diluant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns diluant density (g/L)</span>
<span class="sd"> :return: diluant_rho: (float) density of diluant</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_diluant_rho</span></div>
<div class="viewcode-block" id="LLEPE.set_diluant_rho"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_diluant_rho">[docs]</a> <span class="k">def</span> <span class="nf">set_diluant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">diluant_rho</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_diluant_rho"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_diluant_rho">[docs]</a> <span class="k">def</span> <span class="nf">set_diluant_rho</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">diluant_rho</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Changes diluant density (g/L) to input diluant_rho</span>
<span class="sd"> :param diluant_rho: (float) density of diluant</span>
@@ -846,7 +847,7 @@
<span class="c1"># TODO: Change DataFrame structure to contain info about O/A ratio</span>
<span class="c1"># TODO: Generalize code to more than just org and aq phase (3+ phases)</span>
<span class="c1"># TODO: Handle multiple electrolytes ie. NO3- with Cl-</span>
<div class="viewcode-block" id="LLEPE.set_in_moles"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_in_moles">[docs]</a> <span class="k">def</span> <span class="nf">set_in_moles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">feed_vol</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_in_moles"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_in_moles">[docs]</a> <span class="k">def</span> <span class="nf">set_in_moles</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">feed_vol</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Function that initializes mole fractions to input feed_vol</span>
<span class="sd"> This function is called at initialization</span>
@@ -953,7 +954,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">update_predicted_dict</span><span class="p">()</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_in_moles"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_in_moles">[docs]</a> <span class="k">def</span> <span class="nf">get_in_moles</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
<div class="viewcode-block" id="LLEPE.get_in_moles"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_in_moles">[docs]</a> <span class="k">def</span> <span class="nf">get_in_moles</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
<span class="sd">&quot;&quot;&quot;Returns the in_moles DataFrame which contains the initial mole</span>
<span class="sd"> fractions of each species for each experiment</span>
@@ -961,7 +962,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_in_moles</span></div>
<div class="viewcode-block" id="LLEPE.set_objective_function"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_objective_function">[docs]</a> <span class="k">def</span> <span class="nf">set_objective_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">objective_function</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_objective_function"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_objective_function">[docs]</a> <span class="k">def</span> <span class="nf">set_objective_function</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">objective_function</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Change objective function to input objective_function.</span>
<span class="sd"> See class docstring on &quot;objective_function&quot; for instructions</span>
@@ -986,7 +987,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_objective_function</span> <span class="o">=</span> <span class="n">objective_function</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_objective_function"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_objective_function">[docs]</a> <span class="k">def</span> <span class="nf">get_objective_function</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.get_objective_function"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_objective_function">[docs]</a> <span class="k">def</span> <span class="nf">get_objective_function</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Returns objective function</span>
<span class="sd"> :return: objective_function: (func) Objective function to quantify</span>
@@ -994,7 +995,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objective_function</span></div>
<div class="viewcode-block" id="LLEPE.set_optimizer"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_optimizer">[docs]</a> <span class="k">def</span> <span class="nf">set_optimizer</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">optimizer</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_optimizer"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_optimizer">[docs]</a> <span class="k">def</span> <span class="nf">set_optimizer</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">optimizer</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Change optimizer function to input optimizer.</span>
<span class="sd"> See class docstring on &quot;optimizer&quot; for instructions</span>
@@ -1019,7 +1020,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_optimizer</span> <span class="o">=</span> <span class="n">optimizer</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_optimizer"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_optimizer">[docs]</a> <span class="k">def</span> <span class="nf">get_optimizer</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.get_optimizer"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_optimizer">[docs]</a> <span class="k">def</span> <span class="nf">get_optimizer</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Returns objective function</span>
<span class="sd"> :return: optimizer: (func) Optimizer function to minimize objective</span>
@@ -1027,7 +1028,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_optimizer</span></div>
<div class="viewcode-block" id="LLEPE.get_temp_xml_file_path"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_temp_xml_file_path">[docs]</a> <span class="k">def</span> <span class="nf">get_temp_xml_file_path</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.get_temp_xml_file_path"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_temp_xml_file_path">[docs]</a> <span class="k">def</span> <span class="nf">get_temp_xml_file_path</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Returns path to temporary xml file.</span>
<span class="sd"> This xml file is a duplicate of the phases_xml_file name and is</span>
@@ -1038,7 +1039,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_temp_xml_file_path</span></div>
<div class="viewcode-block" id="LLEPE.set_temp_xml_file_path"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_temp_xml_file_path">[docs]</a> <span class="k">def</span> <span class="nf">set_temp_xml_file_path</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">temp_xml_file_path</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_temp_xml_file_path"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_temp_xml_file_path">[docs]</a> <span class="k">def</span> <span class="nf">set_temp_xml_file_path</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">temp_xml_file_path</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Changes temporary xml file path to input temp_xml_file_path.</span>
<span class="sd"> This xml file is a duplicate of the phases_xml_file name and is</span>
@@ -1050,7 +1051,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_temp_xml_file_path</span> <span class="o">=</span> <span class="n">temp_xml_file_path</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_dependant_params_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_dependant_params_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_dependant_params_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.get_dependant_params_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_dependant_params_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_dependant_params_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the dependant_params_dict</span>
@@ -1059,7 +1060,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_dependant_params_dict</span></div>
<div class="viewcode-block" id="LLEPE.set_dependant_params_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_dependant_params_dict">[docs]</a> <span class="k">def</span> <span class="nf">set_dependant_params_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dependant_params_dict</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_dependant_params_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_dependant_params_dict">[docs]</a> <span class="k">def</span> <span class="nf">set_dependant_params_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">dependant_params_dict</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Sets the dependant_params_dict</span>
@@ -1069,7 +1070,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_dependant_params_dict</span> <span class="o">=</span> <span class="n">dependant_params_dict</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_custom_objects_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_custom_objects_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_custom_objects_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.get_custom_objects_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_custom_objects_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_custom_objects_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the custom_objects_dict</span>
@@ -1078,7 +1079,7 @@
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_custom_objects_dict</span></div>
<div class="viewcode-block" id="LLEPE.set_custom_objects_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.set_custom_objects_dict">[docs]</a> <span class="k">def</span> <span class="nf">set_custom_objects_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">custom_objects_dict</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.set_custom_objects_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.set_custom_objects_dict">[docs]</a> <span class="k">def</span> <span class="nf">set_custom_objects_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">custom_objects_dict</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Sets the custom_objects_dict</span>
@@ -1092,7 +1093,7 @@
<span class="c1"># equilibrium pH to measured value. Will be useful for saponification</span>
<span class="c1"># TODO: Find way to add saponification to model.</span>
<span class="c1"># Maybe use fsolve to match experimental equilibrium pH</span>
<div class="viewcode-block" id="LLEPE.update_predicted_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.update_predicted_dict">[docs]</a> <span class="k">def</span> <span class="nf">update_predicted_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<div class="viewcode-block" id="LLEPE.update_predicted_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.update_predicted_dict">[docs]</a> <span class="k">def</span> <span class="nf">update_predicted_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">phases_xml_filename</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">phase_names</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Function that computes the predicted equilibrium concentrations</span>
@@ -1159,7 +1160,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_predicted_dict</span> <span class="o">=</span> <span class="n">predicted_dict</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.get_predicted_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.get_predicted_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_predicted_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.get_predicted_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.get_predicted_dict">[docs]</a> <span class="k">def</span> <span class="nf">get_predicted_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Returns predicted dictionary of species concentrations</span>
<span class="sd"> that xml parameters predicts given current in_moles</span>
@@ -1223,7 +1224,7 @@
<span class="n">objective_values</span> <span class="o">=</span> <span class="n">objective_values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">return</span> <span class="n">objective_values</span>
<div class="viewcode-block" id="LLEPE.fit"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.fit">[docs]</a> <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<div class="viewcode-block" id="LLEPE.fit"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.fit">[docs]</a> <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">objective_function</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">optimizer</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">objective_kwargs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -1266,7 +1267,7 @@
<span class="k">return</span> <span class="n">opt_dict</span><span class="p">,</span> <span class="n">obj_value</span></div>
<div class="viewcode-block" id="LLEPE.update_xml"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.update_xml">[docs]</a> <span class="k">def</span> <span class="nf">update_xml</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<div class="viewcode-block" id="LLEPE.update_xml"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.update_xml">[docs]</a> <span class="k">def</span> <span class="nf">update_xml</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">info_dict</span><span class="p">,</span>
<span class="n">phases_xml_filename</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">dependant_params_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
@@ -1373,7 +1374,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">set_phases</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_phases_xml_filename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phase_names</span><span class="p">)</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.update_custom_objects_dict"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.update_custom_objects_dict">[docs]</a> <span class="k">def</span> <span class="nf">update_custom_objects_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">info_dict</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.update_custom_objects_dict"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.update_custom_objects_dict">[docs]</a> <span class="k">def</span> <span class="nf">update_custom_objects_dict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">info_dict</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> updates internal custom_objects_dict with info_dict</span>
@@ -1398,7 +1399,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_custom_objects_dict</span> <span class="o">=</span> <span class="n">custom_objects_dict</span>
<span class="k">return</span> <span class="kc">None</span></div>
<div class="viewcode-block" id="LLEPE.parity_plot"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.parity_plot">[docs]</a> <span class="k">def</span> <span class="nf">parity_plot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<div class="viewcode-block" id="LLEPE.parity_plot"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.parity_plot">[docs]</a> <span class="k">def</span> <span class="nf">parity_plot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">compared_value</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">c_data</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">c_label</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -1544,7 +1545,7 @@
<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">save_path</span><span class="p">,</span> <span class="n">bbox_inches</span><span class="o">=</span><span class="s1">&#39;tight&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">fig</span><span class="p">,</span> <span class="n">ax</span></div>
<div class="viewcode-block" id="LLEPE.r_squared"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.r_squared">[docs]</a> <span class="k">def</span> <span class="nf">r_squared</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">compared_value</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<div class="viewcode-block" id="LLEPE.r_squared"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.r_squared">[docs]</a> <span class="k">def</span> <span class="nf">r_squared</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">compared_value</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;r-squared value comparing measured and predicted compared value</span>
<span class="sd"> Closer to 1, the better the model&#39;s predictions.</span>
@@ -1584,7 +1585,7 @@
<span class="n">r_2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">num</span> <span class="o">/</span> <span class="n">den</span><span class="p">)</span>
<span class="k">return</span> <span class="n">r_2</span></div>
<div class="viewcode-block" id="LLEPE.plot_3d_data"><a class="viewcode-back" href="../../modules/reeps.html#llepe.LLEPE.plot_3d_data">[docs]</a> <span class="nd">@staticmethod</span>
<div class="viewcode-block" id="LLEPE.plot_3d_data"><a class="viewcode-back" href="../../modules/LLEPE.html#llepe.LLEPE.plot_3d_data">[docs]</a> <span class="nd">@staticmethod</span>
<span class="k">def</span> <span class="nf">plot_3d_data</span><span class="p">(</span><span class="n">x_data</span><span class="p">,</span>
<span class="n">y_data</span><span class="p">,</span>
<span class="n">z_data</span><span class="p">,</span>
@@ -1646,7 +1647,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

61
docs/build/html/_sources/guide/about.rst.txt vendored Normal file
View File

@@ -0,0 +1,61 @@
.. _about:
************
About
************
Authors
=============
Titus Quah, University of Utah, <titus{dot}quah{at}gmail{dot}com>
Nwike Iloeje, Argonne National Laboratory, <ciloeje{at}anl{dot}gov>
Acknowledgements
================
Based upon work supported by funding from Argonne National Laboratory provided by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy (EERE), under contract DE-AC02-06CH11357
References
==========
If you use LLEPE in your research , we kindly request that you cite the package as follows:
T. Quah and C. O. Iloeje, “Liquid--Liquid Extraction Thermodynamic Parameter Estimator (LLEPE) for Multicomponent Separation Systems,” in Materials Processing Fundamentals 2021, 2021, pp. 107–120, doi: https://doi.org/10.1007/978-3-030-65253-1_9.
License
=======
::
Copyright © 2020, UChicago Argonne, LLC
All Rights Reserved
Software Name: LLEPE
By: Argonne National Laboratory, University of Utah
OPEN SOURCE LICENSE
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software without
specific prior written permission.
******************************************************************************************************
DISCLAIMER
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
OF SUCH DAMAGE.
***************************************************************************************************

6
docs/build/html/_sources/guide/install.rst.txt vendored
View File

@@ -24,17 +24,17 @@ To install the latest master version:
.. code-block:: bash
pip install git+https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git
pip install git+https://github.com/ANL-CEEESA/LLEPE.git
Development version
===================
To contribute to Stable-Baselines, with support for running tests and building the documentation.
To contribute to LLEPE, with support for running tests and building the documentation.
.. code-block:: bash
git clone https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git && cd parameter-estimation
git clone https://github.com/ANL-CEEESA/LLEPE.git
pip install -e .[docs,tests]

12
docs/build/html/_sources/index.rst.txt vendored
View File

@@ -1,9 +1,8 @@
.. reeps documentation master file, created by Titus Quah
sphinx-quickstart on Tue Jun 9 10:13:23 2020.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
.. LLEPE: Liquid-Liquid Equilibrium Parameter Estimator
Copyright (C) 2020, UChicago Argonne, LLC. All rights reserved.
Released under the modified BSD license. See LICENSE for more details.
Welcome to llepe's docs! - the Liquid-Liquid Extraction Parameter Estimator
Welcome to LLEPE's docs! - the Liquid-Liquid Extraction Parameter Estimator
===========================================================================
LLEPE is a package for thermodynamic parameter estimation for liquid-liquid extraction modeling
@@ -19,12 +18,13 @@ Error between predicted and experimental data is then minimized.
guide/install
guide/quickstart
guide/about
.. toctree::
:maxdepth: 1
:caption: Searchers
modules/reeps
modules/LLEPE

15
docs/build/html/_sources/modules/LLEPE.rst.txt vendored Normal file
View File

@@ -0,0 +1,15 @@
.. _LLEPE:
.. automodule:: llepe
LLEPE
=====
Parameters
----------
.. autoclass:: LLEPE
:members:
:inherited-members:

2
docs/build/html/_sources/modules/reeps.rst.txt vendored
View File

@@ -1,4 +1,4 @@
.. _reeps:
.. _LLEPE:
.. automodule:: llepe

103
docs/build/html/genindex.html vendored
View File

@@ -86,10 +86,11 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="guide/install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/quickstart.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/about.html">About</a></li>
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/LLEPE.html">LLEPE</a></li>
</ul>
@@ -169,7 +170,7 @@
<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.fit">fit() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.fit">fit() (llepe.LLEPE method)</a>
</li>
</ul></td>
</tr></table>
@@ -177,45 +178,45 @@
<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.get_aq_solvent_name">get_aq_solvent_name() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_aq_solvent_name">get_aq_solvent_name() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_aq_solvent_rho">get_aq_solvent_rho() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_aq_solvent_rho">get_aq_solvent_rho() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_complex_names">get_complex_names() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_complex_names">get_complex_names() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_custom_objects_dict">get_custom_objects_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_custom_objects_dict">get_custom_objects_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_dependant_params_dict">get_dependant_params_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_dependant_params_dict">get_dependant_params_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_diluant_name">get_diluant_name() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_diluant_name">get_diluant_name() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_diluant_rho">get_diluant_rho() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_diluant_rho">get_diluant_rho() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_exp_df">get_exp_df() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_exp_df">get_exp_df() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_extractant_name">get_extractant_name() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_extractant_name">get_extractant_name() (llepe.LLEPE method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.get_extractant_rho">get_extractant_rho() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_extractant_rho">get_extractant_rho() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_extracted_species_ion_names">get_extracted_species_ion_names() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_extracted_species_ion_names">get_extracted_species_ion_names() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_extracted_species_list">get_extracted_species_list() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_extracted_species_list">get_extracted_species_list() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_in_moles">get_in_moles() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_in_moles">get_in_moles() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_objective_function">get_objective_function() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_objective_function">get_objective_function() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_opt_dict">get_opt_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_opt_dict">get_opt_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_optimizer">get_optimizer() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_optimizer">get_optimizer() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_phases">get_phases() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_phases">get_phases() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_predicted_dict">get_predicted_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_predicted_dict">get_predicted_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.get_temp_xml_file_path">get_temp_xml_file_path() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.get_temp_xml_file_path">get_temp_xml_file_path() (llepe.LLEPE method)</a>
</li>
</ul></td>
</tr></table>
@@ -227,14 +228,14 @@
llepe
<ul>
<li><a href="modules/reeps.html#module-llepe">module</a>
<li><a href="modules/LLEPE.html#module-llepe">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE">LLEPE (class in llepe)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE">LLEPE (class in llepe)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.log_mean_squared_error">log_mean_squared_error() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.log_mean_squared_error">log_mean_squared_error() (llepe.LLEPE method)</a>
</li>
</ul></td>
</tr></table>
@@ -246,7 +247,7 @@
module
<ul>
<li><a href="modules/reeps.html#module-llepe">llepe</a>
<li><a href="modules/LLEPE.html#module-llepe">llepe</a>
</li>
</ul></li>
</ul></td>
@@ -255,11 +256,11 @@
<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.parity_plot">parity_plot() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.parity_plot">parity_plot() (llepe.LLEPE method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.plot_3d_data">plot_3d_data() (llepe.LLEPE static method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.plot_3d_data">plot_3d_data() (llepe.LLEPE static method)</a>
</li>
</ul></td>
</tr></table>
@@ -267,7 +268,7 @@
<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.r_squared">r_squared() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.r_squared">r_squared() (llepe.LLEPE method)</a>
</li>
</ul></td>
</tr></table>
@@ -275,45 +276,45 @@
<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.scipy_minimize">scipy_minimize() (llepe.LLEPE static method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.scipy_minimize">scipy_minimize() (llepe.LLEPE static method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_aq_solvent_name">set_aq_solvent_name() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_aq_solvent_name">set_aq_solvent_name() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_aq_solvent_rho">set_aq_solvent_rho() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_aq_solvent_rho">set_aq_solvent_rho() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_complex_names">set_complex_names() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_complex_names">set_complex_names() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_custom_objects_dict">set_custom_objects_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_custom_objects_dict">set_custom_objects_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_dependant_params_dict">set_dependant_params_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_dependant_params_dict">set_dependant_params_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_diluant_name">set_diluant_name() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_diluant_name">set_diluant_name() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_diluant_rho">set_diluant_rho() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_diluant_rho">set_diluant_rho() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_exp_df">set_exp_df() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_exp_df">set_exp_df() (llepe.LLEPE method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.set_extractant_name">set_extractant_name() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_extractant_name">set_extractant_name() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_extractant_rho">set_extractant_rho() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_extractant_rho">set_extractant_rho() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_extracted_species_ion_names">set_extracted_species_ion_names() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_extracted_species_ion_names">set_extracted_species_ion_names() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_extracted_species_list">set_extracted_species_list() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_extracted_species_list">set_extracted_species_list() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_in_moles">set_in_moles() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_in_moles">set_in_moles() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_objective_function">set_objective_function() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_objective_function">set_objective_function() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_opt_dict">set_opt_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_opt_dict">set_opt_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_optimizer">set_optimizer() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_optimizer">set_optimizer() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_phases">set_phases() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_phases">set_phases() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.set_temp_xml_file_path">set_temp_xml_file_path() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.set_temp_xml_file_path">set_temp_xml_file_path() (llepe.LLEPE method)</a>
</li>
</ul></td>
</tr></table>
@@ -321,13 +322,13 @@
<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.update_custom_objects_dict">update_custom_objects_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.update_custom_objects_dict">update_custom_objects_dict() (llepe.LLEPE method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="modules/reeps.html#llepe.LLEPE.update_predicted_dict">update_predicted_dict() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.update_predicted_dict">update_predicted_dict() (llepe.LLEPE method)</a>
</li>
<li><a href="modules/reeps.html#llepe.LLEPE.update_xml">update_xml() (llepe.LLEPE method)</a>
<li><a href="modules/LLEPE.html#llepe.LLEPE.update_xml">update_xml() (llepe.LLEPE method)</a>
</li>
</ul></td>
</tr></table>
@@ -344,7 +345,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

272
docs/build/html/guide/about.html vendored Normal file
View File

@@ -0,0 +1,272 @@
<!DOCTYPE html>
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<title>About &mdash; LLEPE 1.0.0 documentation</title>
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<p class="caption"><span class="caption-text">User Guide</span></p>
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<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
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<div class="section" id="about">
<span id="id1"></span><h1>About<a class="headerlink" href="#about" title="Permalink to this headline"></a></h1>
<div class="section" id="authors">
<h2>Authors<a class="headerlink" href="#authors" title="Permalink to this headline"></a></h2>
<p>Titus Quah, University of Utah, &lt;titus{dot}quah{at}gmail{dot}com&gt;</p>
<p>Nwike Iloeje, Argonne National Laboratory, &lt;ciloeje{at}anl{dot}gov&gt;</p>
</div>
<div class="section" id="acknowledgements">
<h2>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permalink to this headline"></a></h2>
<p>Based upon work supported by funding from Argonne National Laboratory provided by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy (EERE), under contract DE-AC02-06CH11357</p>
</div>
<div class="section" id="references">
<h2>References<a class="headerlink" href="#references" title="Permalink to this headline"></a></h2>
<p>If you use LLEPE in your research , we kindly request that you cite the package as follows:</p>
<ol class="upperalpha simple" start="20">
<li><p>Quah and C. O. Iloeje, “Liquid--Liquid Extraction Thermodynamic Parameter Estimator (LLEPE) for Multicomponent Separation Systems,” in Materials Processing Fundamentals 2021, 2021, pp. 107–120, doi: <a class="reference external" href="https://doi.org/10.1007/978-3-030-65253-1_9">https://doi.org/10.1007/978-3-030-65253-1_9</a>.</p></li>
</ol>
</div>
<div class="section" id="license">
<h2>License<a class="headerlink" href="#license" title="Permalink to this headline"></a></h2>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>Copyright © 2020, UChicago Argonne, LLC
All Rights Reserved
Software Name: LLEPE
By: Argonne National Laboratory, University of Utah
OPEN SOURCE LICENSE
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software without
specific prior written permission.
******************************************************************************************************
DISCLAIMER
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
OF SUCH DAMAGE.
***************************************************************************************************
</pre></div>
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14
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@@ -36,7 +36,7 @@
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Getting Started" href="quickstart.html" />
<link rel="prev" title="Welcome to llepe&#39;s docs! - the Liquid-Liquid Extraction Parameter Estimator" href="../index.html" />
<link rel="prev" title="Welcome to LLEPE&#39;s docs! - the Liquid-Liquid Extraction Parameter Estimator" href="../index.html" />
</head>
<body class="wy-body-for-nav">
@@ -97,7 +97,7 @@
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="../modules/LLEPE.html">LLEPE</a></li>
</ul>
@@ -175,14 +175,14 @@
<div class="section" id="bleeding-edge-version">
<h2>Bleeding-edge version<a class="headerlink" href="#bleeding-edge-version" title="Permalink to this headline"></a></h2>
<p>To install the latest master version:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip install git+https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip install git+https://github.com/ANL-CEEESA/LLEPE.git
</pre></div>
</div>
</div>
<div class="section" id="development-version">
<h2>Development version<a class="headerlink" href="#development-version" title="Permalink to this headline"></a></h2>
<p>To contribute to Stable-Baselines, with support for running tests and building the documentation.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone https://xgitlab.cels.anl.gov/summer-2020/parameter-estimation.git <span class="o">&amp;&amp;</span> <span class="nb">cd</span> parameter-estimation
<p>To contribute to LLEPE, with support for running tests and building the documentation.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone https://github.com/ANL-CEEESA/LLEPE.git
pip install -e .<span class="o">[</span>docs,tests<span class="o">]</span>
</pre></div>
</div>
@@ -204,7 +204,7 @@ pip install -e .<span class="o">[</span>docs,tests<span class="o">]</span>
<a href="quickstart.html" class="btn btn-neutral float-right" title="Getting Started" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
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</div>
@@ -213,7 +213,7 @@ pip install -e .<span class="o">[</span>docs,tests<span class="o">]</span>
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

2
docs/build/html/guide/quickstart.html vendored
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@@ -218,7 +218,7 @@ aqueous phase.</p>
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

20
docs/build/html/index.html vendored
View File

@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Welcome to llepe&#39;s docs! - the Liquid-Liquid Extraction Parameter Estimator &mdash; LLEPE 1.0.0 documentation</title>
<title>Welcome to LLEPE&#39;s docs! - the Liquid-Liquid Extraction Parameter Estimator &mdash; LLEPE 1.0.0 documentation</title>
@@ -86,10 +86,11 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="guide/install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/quickstart.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/about.html">About</a></li>
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/LLEPE.html">LLEPE</a></li>
</ul>
@@ -135,7 +136,7 @@
<li><a href="#">Docs</a> &raquo;</li>
<li>Welcome to llepe's docs! - the Liquid-Liquid Extraction Parameter Estimator</li>
<li>Welcome to LLEPE's docs! - the Liquid-Liquid Extraction Parameter Estimator</li>
<li class="wy-breadcrumbs-aside">
@@ -155,7 +156,7 @@
<div itemprop="articleBody">
<div class="section" id="welcome-to-llepe-s-docs-the-liquid-liquid-extraction-parameter-estimator">
<h1>Welcome to llepe's docs! - the Liquid-Liquid Extraction Parameter Estimator<a class="headerlink" href="#welcome-to-llepe-s-docs-the-liquid-liquid-extraction-parameter-estimator" title="Permalink to this headline"></a></h1>
<h1>Welcome to LLEPE's docs! - the Liquid-Liquid Extraction Parameter Estimator<a class="headerlink" href="#welcome-to-llepe-s-docs-the-liquid-liquid-extraction-parameter-estimator" title="Permalink to this headline"></a></h1>
<p>LLEPE is a package for thermodynamic parameter estimation for liquid-liquid extraction modeling</p>
<p>LLEPE takes experimental data in a csv and system data in a xml.</p>
<p>The package then uses Cantera, another python package, to simulate equilibrium.</p>
@@ -172,12 +173,19 @@
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="guide/quickstart.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/about.html">About</a><ul>
<li class="toctree-l2"><a class="reference internal" href="guide/about.html#authors">Authors</a></li>
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<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/LLEPE.html">LLEPE</a></li>
</ul>
</div>
</div>
@@ -208,7 +216,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

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docs/build/html/modules/reeps.html vendored
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@@ -34,8 +34,7 @@
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="prev" title="Getting Started" href="../guide/quickstart.html" />
<link rel="search" title="Search" href="../search.html" />
</head>
<body class="wy-body-for-nav">
@@ -87,13 +86,6 @@
<li class="toctree-l1"><a class="reference internal" href="../guide/install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../guide/quickstart.html">Getting Started</a></li>
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">LLEPE</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#parameters">Parameters</a></li>
</ul>
</li>
</ul>
@@ -157,8 +149,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<span class="target" id="module-llepe"><span id="reeps"></span></span><div class="section" id="llepe">
<h1>LLEPE<a class="headerlink" href="#llepe" title="Permalink to this headline"></a></h1>
<span class="target" id="module-llepe"><span id="llepe"></span></span><div class="section" id="id1">
<h1>LLEPE<a class="headerlink" href="#id1" title="Permalink to this headline"></a></h1>
<div class="section" id="parameters">
<h2>Parameters<a class="headerlink" href="#parameters" title="Permalink to this headline"></a></h2>
<dl class="py class">
@@ -1079,19 +1071,12 @@ about parameters dependant on info_dict</p></li>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="../guide/quickstart.html" class="btn btn-neutral float-left" title="Getting Started" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

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@@ -92,10 +92,11 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="guide/install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/quickstart.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/about.html">About</a></li>
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/LLEPE.html">LLEPE</a></li>
</ul>
@@ -170,7 +171,7 @@
<tr>
<td></td>
<td>
<a href="modules/reeps.html#module-llepe"><code class="xref">llepe</code></a></td><td>
<a href="modules/LLEPE.html#module-llepe"><code class="xref">llepe</code></a></td><td>
<em></em></td></tr>
</table>
@@ -185,7 +186,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

5
docs/build/html/search.html vendored
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@@ -86,10 +86,11 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="guide/install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/quickstart.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="guide/about.html">About</a></li>
</ul>
<p class="caption"><span class="caption-text">Searchers</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules/reeps.html">LLEPE</a></li>
<li class="toctree-l1"><a class="reference internal" href="modules/LLEPE.html">LLEPE</a></li>
</ul>
@@ -176,7 +177,7 @@
<div role="contentinfo">
<p>
&copy; Copyright 2020, Argonne National Laboratory
&copy; Copyright 2020, UChicago Argonne, LLC.
</p>
</div>

2
docs/build/html/searchindex.js vendored
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