<listdefault="true"id="f4439dc0-6756-4612-8f7d-596d8949f300"name="Default Changelist"comment="Edited parity plot to allow color to represent 3rd dimension. Still need to improve colorbar axis name.">
<taskid="LOCAL-00011"summary="Included package data in data/csvs and data/xmls. Note this only works for sdists. If bdist is needed, research "manifest.in" python setup files.">
<created>1592321239574</created>
<optionname="number"value="00011"/>
<optionname="presentableId"value="LOCAL-00011"/>
<optionname="project"value="LOCAL"/>
<updated>1592321239574</updated>
</task>
<optionname="localTasksCounter"value="12"/>
<servers/>
</component>
<componentname="Vcs.Log.Tabs.Properties">
@ -269,8 +303,8 @@
<MESSAGEvalue="Completed one composition parameter estimation"/>
<MESSAGEvalue="Modified reeps to grab charge from REE in xml file for initial chlorine moles calculation"/>
<MESSAGEvalue="Allow user to change optimizer and objective function. Also added r-squared evaluator. Changed temp file location to user temp folder. Added a prediction dictionary to access the values predicted by model."/>
<MESSAGEvalue="Included package data in data/csvs and data/xmls. Note this only works for sdists. If bdist is needed, research "manifest.in" python setup files." />
<optionname="LAST_COMMIT_MESSAGE"value="Included package data in data/csvs and data/xmls. Note this only works for sdists. If bdist is needed, research "manifest.in" python setup files." />
<MESSAGEvalue="Edited parity plot to allow color to represent 3rd dimension. Still need to improve colorbar axis name." />
<optionname="LAST_COMMIT_MESSAGE"value="Edited parity plot to allow color to represent 3rd dimension. Still need to improve colorbar axis name." />
<h1>Welcome to reeps's docs! - the Rare earth element parameter searcher<aclass="headerlink"href="#welcome-to-reeps-s-docs-the-rare-earth-element-parameter-searcher"title="Permalink to this headline">¶</a></h1>
<p>REEPS is a package for thermodynamic parameter estimation specifically
for rare earth element extraction modeling.</p>
<p>REEPS takes experimental data in a csv and system data in a xml.</p>
<h1>Welcome to llepe's docs! - the Liquid-Liquid Extraction Parameter Estimator<aclass="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>
<p>Error between predicted and experimental data is then minimized.</p>
<divclass="toctree-wrapper compound">
@ -178,7 +177,7 @@ for rare earth element extraction modeling.</p>
<li><p><strong>phase_names</strong> -- <p>(list) names of phases in xml file</p>
@ -272,18 +273,14 @@ i.e. Nd(H(A)2)3(org), Pr(H(A)2)3(org)</p>
<li><p><strong>aq_solvent_name</strong> -- (str) name of aqueous solvent in xml file</p></li>
<li><p><strong>extractant_name</strong> -- (str) name of extractant in xml file</p></li>
<li><p><strong>diluant_name</strong> -- (str) name of diluant in xml file</p></li>
<li><p><strong>complex_names</strong> -- <p>(list) names of complexes in xml file.</p>
<p>Ensure the ordering is correct</p>
</p></li>
<li><p><strong>rare_earth_ion_names</strong> -- <p>(list) names of rare earth ions in xml file</p>
<p>Ensure the ordering is correct</p>
</p></li>
<li><p><strong>re_species_list</strong> -- <p>(list) names of rare earth elements.</p>
<li><p><strong>complex_names</strong> -- (list) names of complexes in xml file.</p></li>
<li><p><strong>extracted_species_ion_names</strong> -- (list) names of extracted species ions
in xml file</p></li>
<li><p><strong>extracted_species_list</strong> -- <p>(list) names of extracted species elements.</p>
<dlclass="simple">
<dt>If <codeclass="docutils literal notranslate"><spanclass="pre">None</span></code>, re_species_list will be rare_earth_ion_names without '+'</dt><dd><p>i.e. 'Nd+++'->'Nd'</p>
<dt>If <codeclass="docutils literal notranslate"><spanclass="pre">None</span></code>, extracted_species_list will be extracted_species_ion_names</dt><dd><p>without '+' i.e. 'Nd+++'->'Nd'</p>
</dd>
</dl>
<p>Ensure the ordering is correct</p>
</p></li>
<li><p><strong>aq_solvent_rho</strong> -- <p>(float) density of solvent (g/L)</p>
<p>If <codeclass="docutils literal notranslate"><spanclass="pre">None</span></code>, molar volume/molecular weight is used from xml</p>
@ -296,26 +293,26 @@ i.e. Nd(H(A)2)3(org), Pr(H(A)2)3(org)</p>
</p></li>
<li><p><strong>opt_dict</strong> -- <p>(dict) dictionary containing info about which
species parameters are updated to fit model to experimental data</p>
'kwargs' are the extra arguments to pass to function
'independent_params' is a list of parameter names in opt_dict that the
dependent_param is a function of.</p>
<p>See example code for usage.</p>
</p></li>
</ul>
</dd>
</dl>
<dlclass="py method">
<dtid="reeps.REEPS.fit">
<codeclass="sig-name descname">fit</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">objective_function</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">optimizer</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">objective_kwargs</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">optimizer_kwargs</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span>→ dict<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.fit"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.fit"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.fit">
<codeclass="sig-name descname">fit</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">objective_function</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">optimizer</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">objective_kwargs</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">optimizer_kwargs</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span>→ tuple<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.fit"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.fit" title="Permalink to this definition">¶</a></dt>
<dd><p>Fits experimental to modeled data by minimizing objective function
with optimizer. Returns dictionary with opt_dict structure</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><ulclass="simple">
<li><p><strong>objective_function</strong> -- (function) function to compute objective</p></li>
<li><p><strong>optimizer</strong> -- (function) function to perform optimization</p></li>
<li><p><strong>optimizer_kwargs</strong> -- (dict) arguments for optimizer</p></li>
<li><p><strong>objective_kwargs</strong> -- (dict) arguments for objective function</p></li>
<li><p><strong>objective_function</strong> -- (function) function to compute objective
If 'None', last set objective or default function is used</p></li>
<li><p><strong>optimizer</strong> -- (function) function to perform optimization
If 'None', last set optimizer or default is used</p></li>
<li><p><strong>optimizer_kwargs</strong> -- (dict) optional arguments for optimizer</p></li>
optimized opt_dict: Has identical structure as opt_dict</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_aq_solvent_name">
<codeclass="sig-name descname">get_aq_solvent_name</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_aq_solvent_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_aq_solvent_name" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_aq_solvent_name">
<codeclass="sig-name descname">get_aq_solvent_name</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_aq_solvent_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_aq_solvent_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns aq_solvent_name</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -438,8 +448,8 @@ as opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_aq_solvent_rho">
<codeclass="sig-name descname">get_aq_solvent_rho</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_aq_solvent_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_aq_solvent_rho" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_aq_solvent_rho">
<codeclass="sig-name descname">get_aq_solvent_rho</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_aq_solvent_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_aq_solvent_rho" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns aqueous solvent density (g/L)</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -449,8 +459,8 @@ as opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_complex_names">
<codeclass="sig-name descname">get_complex_names</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_complex_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_complex_names" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_complex_names">
<codeclass="sig-name descname">get_complex_names</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_complex_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_complex_names" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns list of complex names</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -460,15 +470,25 @@ as opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_diluant_name">
<codeclass="sig-name descname">get_diluant_name</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_diluant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_diluant_name"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_dependant_params_dict">
<codeclass="sig-name descname">get_dependant_params_dict</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_dependant_params_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_dependant_params_dict"title="Permalink to this definition">¶</a></dt>
<div><p>information about parameters dependant on opt_dict</p>
</div></blockquote>
</dd></dl>
<dlclass="py method">
<dtid="llepe.LLEPE.get_diluant_name">
<codeclass="sig-name descname">get_diluant_name</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_diluant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_diluant_name"title="Permalink to this definition">¶</a></dt>
<dd><p>Returns diluant name
:return: diluant_name: (str) name of diluant in xml file</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_diluant_rho">
<codeclass="sig-name descname">get_diluant_rho</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_diluant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_diluant_rho"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_diluant_rho">
<codeclass="sig-name descname">get_diluant_rho</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_diluant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_diluant_rho" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns diluant density (g/L)</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -478,8 +498,8 @@ as opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_exp_df">
<codeclass="sig-name descname">get_exp_df</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ pandas.core.frame.DataFrame<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_exp_df"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_exp_df" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_exp_df">
<codeclass="sig-name descname">get_exp_df</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ pandas.core.frame.DataFrame<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_exp_df"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_exp_df" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the experimental DataFrame</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -489,8 +509,8 @@ as opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_extractant_name">
<codeclass="sig-name descname">get_extractant_name</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_extractant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_extractant_name" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_extractant_name">
<codeclass="sig-name descname">get_extractant_name</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_extractant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_extractant_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns extractant name</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -500,8 +520,8 @@ as opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_extractant_rho">
<codeclass="sig-name descname">get_extractant_rho</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_extractant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_extractant_rho" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_extractant_rho">
<codeclass="sig-name descname">get_extractant_rho</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ str<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_extractant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_extractant_rho" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns extractant density (g/L)</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -511,8 +531,32 @@ as opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_in_moles">
<codeclass="sig-name descname">get_in_moles</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ pandas.core.frame.DataFrame<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_in_moles"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_in_moles"title="Permalink to this definition">¶</a></dt>
<codeclass="sig-name descname">get_extracted_species_ion_names</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_extracted_species_ion_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_extracted_species_ion_names"title="Permalink to this definition">¶</a></dt>
<dd><p>Returns list of extracted species ion names</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
<ddclass="field-odd"><p>extracted_species_ion_names: (list) names of
extracted species ions in xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="llepe.LLEPE.get_extracted_species_list">
<codeclass="sig-name descname">get_extracted_species_list</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_extracted_species_list"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_extracted_species_list"title="Permalink to this definition">¶</a></dt>
<dd><p>Returns list of extracted species names</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
<ddclass="field-odd"><p>extracted_species_list: (list) names of extracted species in
xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="llepe.LLEPE.get_in_moles">
<codeclass="sig-name descname">get_in_moles</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ pandas.core.frame.DataFrame<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_in_moles"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_in_moles"title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the in_moles DataFrame which contains the initial mole
fractions of each species for each experiment</p>
<dlclass="field-list simple">
@ -523,8 +567,8 @@ fractions of each species for each experiment</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_objective_function">
<codeclass="sig-name descname">get_objective_function</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_objective_function"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_objective_function" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_objective_function">
<codeclass="sig-name descname">get_objective_function</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_objective_function"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_objective_function" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns objective function</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -535,8 +579,8 @@ error between model and experimental data</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_opt_dict">
<codeclass="sig-name descname">get_opt_dict</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ dict<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_opt_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_opt_dict" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_opt_dict">
<codeclass="sig-name descname">get_opt_dict</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ dict<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_opt_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_opt_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the dictionary containing optimization information</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -547,8 +591,8 @@ species parameters are updated to fit model to experimental data</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_optimizer">
<codeclass="sig-name descname">get_optimizer</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_optimizer"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_optimizer" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_optimizer">
<codeclass="sig-name descname">get_optimizer</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_optimizer"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_optimizer" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns objective function</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -559,8 +603,8 @@ function</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_phases">
<codeclass="sig-name descname">get_phases</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_phases"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_phases" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_phases">
<codeclass="sig-name descname">get_phases</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_phases"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_phases" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the list of Cantera solutions</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
@ -570,8 +614,8 @@ function</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_predicted_dict">
<codeclass="sig-name descname">get_predicted_dict</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_predicted_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_predicted_dict" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_predicted_dict">
<codeclass="sig-name descname">get_predicted_dict</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_predicted_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_predicted_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns predicted dictionary of species concentrations
that xml parameters predicts given current in_moles</p>
<dlclass="field-list simple">
@ -582,32 +626,8 @@ that xml parameters predicts given current in_moles</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_rare_earth_ion_names">
<codeclass="sig-name descname">get_rare_earth_ion_names</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_rare_earth_ion_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_rare_earth_ion_names"title="Permalink to this definition">¶</a></dt>
<dd><p>Returns list of rare earth ion names</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
<ddclass="field-odd"><p>rare_earth_ion_names: (list) names of rare earth ions in
xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_re_species_list">
<codeclass="sig-name descname">get_re_species_list</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span>→ list<aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_re_species_list"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_re_species_list"title="Permalink to this definition">¶</a></dt>
<dd><p>Returns list of rare earth element names</p>
<dlclass="field-list simple">
<dtclass="field-odd">Returns</dt>
<ddclass="field-odd"><p>re_species_list: (list) names of rare earth elements in
xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.get_temp_xml_file_path">
<codeclass="sig-name descname">get_temp_xml_file_path</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.get_temp_xml_file_path"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.get_temp_xml_file_path"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.get_temp_xml_file_path">
<codeclass="sig-name descname">get_temp_xml_file_path</code><spanclass="sig-paren">(</span><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.get_temp_xml_file_path"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.get_temp_xml_file_path"title="Permalink to this definition">¶</a></dt>
<dd><p>Returns path to temporary xml file.</p>
<p>This xml file is a duplicate of the phases_xml_file name and is
modified during the optimization process to avoid changing the original
@ -620,9 +640,9 @@ xml file.</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.log_mean_squared_error">
<codeclass="sig-name descname">log_mean_squared_error</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">predicted_dict</span></em>, <emclass="sig-param"><spanclass="n">meas_df</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.log_mean_squared_error"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.log_mean_squared_error" title="Permalink to this definition">¶</a></dt>
<dd><p>Default objective function for REEPS</p>
<dtid="llepe.LLEPE.log_mean_squared_error">
<codeclass="sig-name descname">log_mean_squared_error</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">predicted_dict</span></em>, <emclass="sig-param"><spanclass="n">meas_df</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.log_mean_squared_error"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.log_mean_squared_error" title="Permalink to this definition">¶</a></dt>
<dd><p>Default objective function for LLEPE</p>
<p>Returns the log mean squared error of
predicted distribution ratios (d=n_org/n_aq)
to measured d.</p>
@ -641,41 +661,110 @@ to measured d.</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.parity_plot">
<codeclass="sig-name descname">parity_plot</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">compared_value</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">save_path</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">print_r_squared</span><spanclass="o">=</span><spanclass="default_value">False</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.parity_plot"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.parity_plot" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.parity_plot">
<codeclass="sig-name descname">parity_plot</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">compared_value</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">c_data</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">c_label</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">plot_title</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">save_path</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">print_r_squared</span><spanclass="o">=</span><spanclass="default_value">False</span></em>, <emclass="sig-param"><spanclass="n">data_labels</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">legend</span><spanclass="o">=</span><spanclass="default_value">True</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.parity_plot"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.parity_plot" title="Permalink to this definition">¶</a></dt>
<dd><p>Parity plot between measured and predicted compared_value.
Default compared value is {RE_1}_aq_eq</p>
Default compared value is {ES_1}_aq_eq</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><ulclass="simple">
<li><p><strong>compared_value</strong> -- (str) Quantity to compare predicted and
experimental data. Can be any column containing "eq" in exp_df i.e.
h_eq, z_eq, {RE}_d_eq, etc.</p></li>
h_eq, z_eq, {ES}_d_eq, etc.</p></li>
<li><p><strong>plot_title</strong> -- <p>(str or boolean)</p>
<dlclass="simple">
<dt>If None (default): Plot title will be generated from compared_value</dt><dd><p>Recommend to just explore. If h_eq, plot_title is
"H^+ eq conc".</p>
</dd>
</dl>
<p>If str: Plot title will be plot_title string</p>
<p>If "False": No plot title</p>
</p></li>
<li><p><strong>c_data</strong> -- (list or np.ndarray) data for color axis</p></li>
<li><p><strong>c_label</strong> -- (str) label for color axis</p></li>
<li><p><strong>save_path</strong> -- (str) save path for parity plot</p></li>
<li><p><strong>print_r_squared</strong> -- (boolean) To plot or not to plot r-squared
value. Prints 2 places past decimal</p></li>
<li><p><strong>data_labels</strong> -- labels for the data such as paper's name where
experiment is pulled from.</p></li>
<li><p><strong>legend</strong> -- whether to display legend for data_labels. Has no
effect if data_labels is None</p></li>
</ul>
</dd>
<dtclass="field-even">Return fig, ax</dt>
<ddclass="field-even"><p>returns the figure and axes objects</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="llepe.LLEPE.plot_3d_data">
<emclass="property">static </em><codeclass="sig-name descname">plot_3d_data</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">x_data</span></em>, <emclass="sig-param"><spanclass="n">y_data</span></em>, <emclass="sig-param"><spanclass="n">z_data</span></em>, <emclass="sig-param"><spanclass="n">c_data</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">x_label</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">y_label</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">z_label</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">c_label</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.plot_3d_data"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.plot_3d_data"title="Permalink to this definition">¶</a></dt>
<dd><dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><ulclass="simple">
<li><p><strong>x_data</strong> -- (list) list of data for x axis</p></li>
<li><p><strong>y_data</strong> -- (list) list of data for y axis</p></li>
<li><p><strong>z_data</strong> -- (list) list of data for z axis</p></li>
<li><p><strong>c_data</strong> -- (list) list of data for color axis</p></li>
<li><p><strong>x_label</strong> -- (str) label for x axis</p></li>
<li><p><strong>y_label</strong> -- (str) label for y axis</p></li>
<li><p><strong>z_label</strong> -- (str) label for z axis</p></li>
<li><p><strong>c_label</strong> -- (str) label for color axis</p></li>
</ul>
</dd>
<dtclass="field-even">Returns</dt>
<ddclass="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.r_squared">
<codeclass="sig-name descname">r_squared</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">compared_value</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.r_squared"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.r_squared"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.r_squared">
<codeclass="sig-name descname">r_squared</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">compared_value</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.r_squared"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.r_squared" title="Permalink to this definition">¶</a></dt>
<dd><p>r-squared value comparing measured and predicted compared value</p>
<p>Closer to 1, the better the model's predictions.</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><p><strong>compared_value</strong> -- (str) Quantity to compare predicted and
experimental data. Can be any column containing "eq" in exp_df i.e.
h_eq, z_eq, {RE}_d_eq, etc.</p>
h_eq, z_eq, {ES}_d_eq, etc. default is {ES}_aq_eq</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_aq_solvent_name">
<codeclass="sig-name descname">set_aq_solvent_name</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">aq_solvent_name</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_aq_solvent_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_aq_solvent_name"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.scipy_minimize">
<emclass="property">static </em><codeclass="sig-name descname">scipy_minimize</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">objective</span></em>, <emclass="sig-param"><spanclass="n">x_guess</span></em>, <emclass="sig-param"><spanclass="n">optimizer_kwargs</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.scipy_minimize"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.scipy_minimize"title="Permalink to this definition">¶</a></dt>
<codeclass="sig-name descname">set_aq_solvent_name</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">aq_solvent_name</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_aq_solvent_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_aq_solvent_name"title="Permalink to this definition">¶</a></dt>
<dd><p>Change aq_solvent_name to input aq_solvent_name</p>
<codeclass="sig-name descname">set_aq_solvent_rho</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">aq_solvent_rho</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_aq_solvent_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_aq_solvent_rho" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_aq_solvent_rho">
<codeclass="sig-name descname">set_aq_solvent_rho</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">aq_solvent_rho</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_aq_solvent_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_aq_solvent_rho" title="Permalink to this definition">¶</a></dt>
<dd><p>Changes aqueous solvent density (g/L) to input aq_solvent_rho</p>
<codeclass="sig-name descname">set_complex_names</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">complex_names</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_complex_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_complex_names" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_complex_names">
<codeclass="sig-name descname">set_complex_names</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">complex_names</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_complex_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_complex_names" title="Permalink to this definition">¶</a></dt>
<dd><p>Change complex names list to input complex_names</p>
<codeclass="sig-name descname">set_diluant_name</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">diluant_name</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_diluant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_diluant_name"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_dependant_params_dict">
<codeclass="sig-name descname">set_dependant_params_dict</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">dependant_params_dict</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_dependant_params_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_dependant_params_dict"title="Permalink to this definition">¶</a></dt>
<dd><p>Sets the dependant_params_dict
:param dependant_params_dict: (dict) dictionary containing information
about parameters dependant on opt_dict</p>
</dd></dl>
<dlclass="py method">
<dtid="llepe.LLEPE.set_diluant_name">
<codeclass="sig-name descname">set_diluant_name</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">diluant_name</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_diluant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_diluant_name"title="Permalink to this definition">¶</a></dt>
<dd><p>Change diluant_name to input diluant_name</p>
<codeclass="sig-name descname">set_diluant_rho</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">diluant_rho</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_diluant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_diluant_rho" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_diluant_rho">
<codeclass="sig-name descname">set_diluant_rho</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">diluant_rho</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_diluant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_diluant_rho" title="Permalink to this definition">¶</a></dt>
<dd><p>Changes diluant density (g/L) to input diluant_rho</p>
<codeclass="sig-name descname">set_exp_df</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">exp_csv_filename</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_exp_df"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_exp_df" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_exp_df">
<codeclass="sig-name descname">set_exp_df</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">exp_data</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_exp_df"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_exp_df" title="Permalink to this definition">¶</a></dt>
<dd><p>Changes the experimental DataFrame to input exp_csv_filename data
<p>See class docstring on "exp_csv_filename" for further explanations.</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><p><strong>exp_csv_filename</strong> -- (str) file name/path for experimental data csv</p>
<ddclass="field-odd"><p><strong>exp_data</strong> -- (str or pd.DataFrame)
file name/path or DataFrame for experimental data csv</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_extractant_name">
<codeclass="sig-name descname">set_extractant_name</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">extractant_name</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_extractant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_extractant_name" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_extractant_name">
<codeclass="sig-name descname">set_extractant_name</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">extractant_name</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_extractant_name"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_extractant_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Change extractant_name to input extractant_name
:param extractant_name: (str) name of extractant in xml file</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_extractant_rho">
<codeclass="sig-name descname">set_extractant_rho</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">extractant_rho</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_extractant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_extractant_rho" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_extractant_rho">
<codeclass="sig-name descname">set_extractant_rho</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">extractant_rho</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_extractant_rho"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_extractant_rho" title="Permalink to this definition">¶</a></dt>
<dd><p>Changes extractant density (g/L) to input extractant_rho</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
@ -761,8 +859,38 @@ and renames columns to internal REEPS names</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_in_moles">
<codeclass="sig-name descname">set_in_moles</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">feed_vol</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_in_moles"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_in_moles"title="Permalink to this definition">¶</a></dt>
<codeclass="sig-name descname">set_extracted_species_ion_names</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">extracted_species_ion_names</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_extracted_species_ion_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_extracted_species_ion_names"title="Permalink to this definition">¶</a></dt>
<dd><dlclass="simple">
<dt>Change list of extracted species ion names to input</dt><dd><p>extracted_species_ion_names</p>
</dd>
</dl>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><p><strong>extracted_species_ion_names</strong> -- (list) names of extracted species
ions in xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="llepe.LLEPE.set_extracted_species_list">
<codeclass="sig-name descname">set_extracted_species_list</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">extracted_species_list</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_extracted_species_list"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_extracted_species_list"title="Permalink to this definition">¶</a></dt>
<dd><dlclass="simple">
<dt>Change list of extracted species ion names to input</dt><dd><p>extracted_species_ion_names</p>
</dd>
</dl>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><p><strong>extracted_species_list</strong> -- (list) names of extracted species in
xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="llepe.LLEPE.set_in_moles">
<codeclass="sig-name descname">set_in_moles</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">feed_vol</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_in_moles"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_in_moles"title="Permalink to this definition">¶</a></dt>
<dd><p>Function that initializes mole fractions to input feed_vol</p>
<p>This function is called at initialization</p>
<p>Sets in_moles to a pd.DataFrame containing initial mole fractions</p>
@ -770,14 +898,14 @@ and renames columns to internal REEPS names</p>
<p>This function also calls update_predicted_dict</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><p><strong>feed_vol</strong> -- (float) feed volume of mixture (g/L)</p>
<ddclass="field-odd"><p><strong>feed_vol</strong> -- (float) feed volume of mixture (L)</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_objective_function">
<codeclass="sig-name descname">set_objective_function</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">objective_function</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_objective_function"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_objective_function" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_objective_function">
<codeclass="sig-name descname">set_objective_function</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">objective_function</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_objective_function"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_objective_function" title="Permalink to this definition">¶</a></dt>
<dd><p>Change objective function to input objective_function.</p>
<blockquote>
<div><p>See class docstring on "objective_function" for instructions</p>
@ -791,8 +919,8 @@ error between model and experimental data</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_opt_dict">
<codeclass="sig-name descname">set_opt_dict</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">opt_dict</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_opt_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_opt_dict" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_opt_dict">
<codeclass="sig-name descname">set_opt_dict</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">opt_dict</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_opt_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_opt_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the dictionary to input opt_dict.</p>
<p>opt_dict specifies species parameters to be updated to
fit model to data</p>
@ -806,8 +934,8 @@ species parameters are updated to fit model to experimental data</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_optimizer">
<codeclass="sig-name descname">set_optimizer</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">optimizer</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_optimizer"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_optimizer" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_optimizer">
<codeclass="sig-name descname">set_optimizer</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">optimizer</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_optimizer"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_optimizer" title="Permalink to this definition">¶</a></dt>
<dd><p>Change optimizer function to input optimizer.</p>
<blockquote>
<div><p>See class docstring on "optimizer" for instructions</p>
@ -821,11 +949,11 @@ function</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_phases">
<codeclass="sig-name descname">set_phases</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">phases_xml_filename</span></em>, <emclass="sig-param"><spanclass="n">phase_names</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_phases"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_phases" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_phases">
<codeclass="sig-name descname">set_phases</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">phases_xml_filename</span></em>, <emclass="sig-param"><spanclass="n">phase_names</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_phases"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_phases" title="Permalink to this definition">¶</a></dt>
<dd><p>Change list of Cantera solutions by inputting
new xml file name and phase names</p>
<p>Also runs set_in_moles to set initial molality to 1 g/L</p>
<p>Also runs set_in_moles to set feed volume to 1 L</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><ulclass="simple">
@ -838,38 +966,8 @@ for equilibrium calc</p></li>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_rare_earth_ion_names">
<codeclass="sig-name descname">set_rare_earth_ion_names</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">rare_earth_ion_names</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_rare_earth_ion_names"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_rare_earth_ion_names"title="Permalink to this definition">¶</a></dt>
<dd><dlclass="simple">
<dt>Change list of rare earth ion names to input</dt><dd><p>rare_earth_ion_names</p>
</dd>
</dl>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><p><strong>rare_earth_ion_names</strong> -- (list) names of rare earth ions in
xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_re_species_list">
<codeclass="sig-name descname">set_re_species_list</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">re_species_list</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_re_species_list"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_re_species_list"title="Permalink to this definition">¶</a></dt>
<dd><dlclass="simple">
<dt>Change list of rare earth ion names to input</dt><dd><p>rare_earth_ion_names</p>
</dd>
</dl>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
<ddclass="field-odd"><p><strong>re_species_list</strong> -- (list) names of rare earth elements in
xml file</p>
</dd>
</dl>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.set_temp_xml_file_path">
<codeclass="sig-name descname">set_temp_xml_file_path</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">temp_xml_file_path</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.set_temp_xml_file_path"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.set_temp_xml_file_path"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.set_temp_xml_file_path">
<codeclass="sig-name descname">set_temp_xml_file_path</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">temp_xml_file_path</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.set_temp_xml_file_path"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.set_temp_xml_file_path"title="Permalink to this definition">¶</a></dt>
<dd><p>Changes temporary xml file path to input temp_xml_file_path.</p>
<p>This xml file is a duplicate of the phases_xml_file name and is
modified during the optimization process to avoid changing the original
@ -882,34 +980,8 @@ xml file.</p>
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.slsqp_optimizer">
<emclass="property">static </em><codeclass="sig-name descname">slsqp_optimizer</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">objective</span></em>, <emclass="sig-param"><spanclass="n">x_guess</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.slsqp_optimizer"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.slsqp_optimizer"title="Permalink to this definition">¶</a></dt>
<codeclass="sig-name descname">update_predicted_dict</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">phases_xml_filename</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">phase_names</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.update_predicted_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.update_predicted_dict"title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.update_predicted_dict">
<codeclass="sig-name descname">update_predicted_dict</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">phases_xml_filename</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">phase_names</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.update_predicted_dict"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.update_predicted_dict"title="Permalink to this definition">¶</a></dt>
<dd><p>Function that computes the predicted equilibrium concentrations
the fed phases_xml_filename parameters predicts given the initial
mole fractions set by in_moles()</p>
@ -927,8 +999,8 @@ If <code class="docutils literal notranslate"><span class="pre">None</span></cod
</dd></dl>
<dlclass="py method">
<dtid="reeps.REEPS.update_xml">
<codeclass="sig-name descname">update_xml</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">info_dict</span></em>, <emclass="sig-param"><spanclass="n">phases_xml_filename</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/reeps/reeps.html#REEPS.update_xml"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#reeps.REEPS.update_xml" title="Permalink to this definition">¶</a></dt>
<dtid="llepe.LLEPE.update_xml">
<codeclass="sig-name descname">update_xml</code><spanclass="sig-paren">(</span><emclass="sig-param"><spanclass="n">info_dict</span></em>, <emclass="sig-param"><spanclass="n">phases_xml_filename</span><spanclass="o">=</span><spanclass="default_value">None</span></em>, <emclass="sig-param"><spanclass="n">dependant_params_dict</span><spanclass="o">=</span><spanclass="default_value">None</span></em><spanclass="sig-paren">)</span><aclass="reference internal"href="../_modules/llepe/llepe.html#LLEPE.update_xml"><spanclass="viewcode-link">[source]</span></a><aclass="headerlink"href="#llepe.LLEPE.update_xml" title="Permalink to this definition">¶</a></dt>
<dd><p>updates xml file with info_dict</p>
<dlclass="field-list simple">
<dtclass="field-odd">Parameters</dt>
@ -938,6 +1010,8 @@ Requires an identical structure to opt_dict</p></li>
<li><p><strong>phases_xml_filename</strong> -- (str) xml filename if editing other xml
If <codeclass="docutils literal notranslate"><spanclass="pre">None</span></code>, the current xml will be modified and the internal
Cantera phases will be refreshed to the new values.</p></li>
<li><p><strong>dependant_params_dict</strong> -- (dict) dictionary containing information
titusquah
5 years ago