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titusquah
2020-07-27 14:57:22 -06:00
parent 90b086b6fe
commit af71a2c208
26 changed files with 499 additions and 203 deletions
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@@ -159,7 +159,6 @@
<span class="kn">from</span> <span class="nn">scipy.optimize</span> <span class="kn">import</span> <span class="n">minimize</span>
<span class="c1"># noinspection PyPep8Naming</span>
<span class="kn">import</span> <span class="nn">xml.etree.ElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
<span class="kn">import</span> <span class="nn">shutil</span>
<span class="kn">import</span> <span class="nn">copy</span>
@@ -169,9 +168,6 @@
<span class="kn">import</span> <span class="nn">pkg_resources</span>
<span class="kn">from</span> <span class="nn">.utils</span> <span class="kn">import</span> <span class="n">set_size</span>
<span class="n">sns</span><span class="o">.</span><span class="n">set</span><span class="p">()</span>
<span class="n">sns</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">font_scale</span><span class="o">=</span><span class="mf">1.6</span><span class="p">)</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>
<span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
@@ -285,7 +281,8 @@
<span class="sd"> :param extracted_species_list: (list) names of extracted species elements.</span>
<span class="sd"> If ``None``, extracted_species_list will be extracted_species_ion_names</span>
<span class="sd"> without &#39;+&#39; i.e. &#39;Nd+++&#39;-&gt;&#39;Nd&#39;</span>
<span class="sd"> without &#39;+&#39; i.e. &#39;Nd+++&#39;-&gt;&#39;Nd&#39;</span>
<span class="sd"> :param aq_solvent_rho: (float) density of solvent (g/L)</span>
<span class="sd"> If ``None``, molar volume/molecular weight is used from xml</span>
@@ -413,12 +410,22 @@
<span class="sd"> &#39;function&#39;, &#39;kwargs&#39;, and &#39;independent_params.</span>
<span class="sd"> &#39;function&#39; is a function of the form</span>
<span class="sd"> ``function(independent_param__value_list, **kwargs)``</span>
<span class="sd"> ``function(independent_param__value_list, custom_objects_dict,</span>
<span class="sd"> **kwargs)``</span>
<span class="sd"> &#39;kwargs&#39; are the extra arguments to pass to function</span>
<span class="sd"> &#39;independent_params&#39; is a list of parameter names in opt_dict that the</span>
<span class="sd"> dependent_param is a function of.</span>
<span class="sd"> &#39;custom_objects_dict&#39; is for accessing the estimator&#39;s internal</span>
<span class="sd"> custom_objects_dict and must be included in the arguments, even if the</span>
<span class="sd"> custom_objects_dict is not set and is None.</span>
<span class="sd"> See example code for usage.</span>
<span class="sd"> :param custom_objects_dict: (dict) dictionary containing custom objects</span>
<span class="sd"> format: {&lt;object_name_string&gt;: &lt;object&gt;,...}</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
@@ -436,12 +443,13 @@
<span class="n">diluant_rho</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">opt_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
<span class="n">objective_function</span><span class="o">=</span><span class="s1">&#39;Log-MSE&#39;</span><span class="p">,</span>
<span class="n">optimizer</span><span class="o">=</span><span class="s1">&#39;SLSQP&#39;</span><span class="p">,</span>
<span class="n">optimizer</span><span class="o">=</span><span class="s1">&#39;scipy_minimize&#39;</span><span class="p">,</span>
<span class="n">temp_xml_file_path</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>
<span class="n">custom_objects_dict</span><span class="o">=</span><span class="kc">None</span>
<span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_built_in_obj_list</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;Log-MSE&#39;</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_built_in_opt_list</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;SLSQP&#39;</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_built_in_opt_list</span> <span class="o">=</span> <span class="p">[</span><span class="s1">&#39;scipy_minimize&#39;</span><span class="p">]</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span> <span class="o">=</span> <span class="n">exp_data</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_phases_xml_filename</span> <span class="o">=</span> <span class="n">phases_xml_filename</span>
<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>
@@ -463,6 +471,7 @@
<span class="n">temp_xml_file_path</span> <span class="o">=</span> <span class="sa">r</span><span class="s1">&#39;</span><span class="si">{0}</span><span class="s1">/temp.xml&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s1">&#39;TEMP&#39;</span><span class="p">))</span>
<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="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="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="c1"># Try and except for adding package data to path.</span>
<span class="c1"># This only works for sdist, not bdist</span>
<span class="c1"># If bdist is needed, research &quot;manifest.in&quot; python setup files</span>
@@ -474,7 +483,7 @@
<span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_phases_xml_filename</span> <span class="o">=</span> \
<span class="n">pkg_resources</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span><span class="s1">&#39;llepe&#39;</span><span class="p">,</span>
<span class="sa">r</span><span class="s1">&#39;..\data\xmls\</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="s1">&#39;../data/xmls/</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">phases_xml_filename</span><span class="p">))</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</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">_temp_xml_file_path</span><span class="p">)</span>
@@ -485,7 +494,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span> <span class="o">=</span> <span class="n">pkg_resources</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span>
<span class="s1">&#39;llepe&#39;</span><span class="p">,</span> <span class="sa">r</span><span class="s1">&#39;..\data\csvs\</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">))</span>
<span class="s1">&#39;llepe&#39;</span><span class="p">,</span> <span class="s1">&#39;../data/csvs/</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
@@ -600,7 +609,7 @@
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span> <span class="o">=</span> <span class="n">pkg_resources</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span>
<span class="s1">&#39;llepe&#39;</span><span class="p">,</span> <span class="sa">r</span><span class="s1">&#39;..\data\csvs\</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">))</span>
<span class="s1">&#39;llepe&#39;</span><span class="p">,</span> <span class="s1">&#39;../data/csvs/</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_exp_data</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_exp_df</span> <span class="o">=</span> <span class="n">exp_data</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
@@ -654,7 +663,7 @@
<span class="k">except</span> <span class="ne">FileNotFoundError</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_phases_xml_filename</span> <span class="o">=</span> \
<span class="n">pkg_resources</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span><span class="s1">&#39;llepe&#39;</span><span class="p">,</span>
<span class="sa">r</span><span class="s1">&#39;..\data\xmls\</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="s1">&#39;../data/xmls/</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">phases_xml_filename</span><span class="p">))</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">copyfile</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">_temp_xml_file_path</span><span class="p">)</span>
@@ -998,7 +1007,7 @@
<span class="s2">&quot;optimizer must be a function &quot;</span>
<span class="s2">&quot;with at least 2 arguments: &quot;</span>
<span class="s2">&quot;f(objective_func,x_guess, kwargs)&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">optimizer</span> <span class="o">==</span> <span class="s1">&#39;SLSQP&#39;</span><span class="p">:</span>
<span class="k">if</span> <span class="n">optimizer</span> <span class="o">==</span> <span class="s1">&#39;scipy_minimize&#39;</span><span class="p">:</span>
<span class="n">optimizer</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">scipy_minimize</span>
<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>
@@ -1037,6 +1046,7 @@
<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>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the dependant_params_dict</span>
<span class="sd"> :return: dependant_params_dict: (dict) dictionary containing</span>
<span class="sd"> information about parameters dependant on opt_dict</span>
<span class="sd"> &quot;&quot;&quot;</span>
@@ -1045,12 +1055,32 @@
<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>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Sets the dependant_params_dict</span>
<span class="sd"> :param dependant_params_dict: (dict) dictionary containing information</span>
<span class="sd"> about parameters dependant on opt_dict</span>
<span class="sd"> about parameters dependant on opt_dict</span>
<span class="sd"> &quot;&quot;&quot;</span>
<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>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Returns the custom_objects_dict</span>
<span class="sd"> :return: custom_objects_dict: (dict) dictionary containing</span>
<span class="sd"> information about custom objects from user</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">_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>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Sets the custom_objects_dict</span>
<span class="sd"> :param custom_objects_dict: (dict) dictionary containing information</span>
<span class="sd"> about about custom objects from user</span>
<span class="sd"> &quot;&quot;&quot;</span>
<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.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>
<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>
@@ -1143,6 +1173,7 @@
<span class="n">objective_function</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_objective_function</span>
<span class="n">opt_dict</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_opt_dict</span><span class="p">)</span>
<span class="n">dep_dict</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_dependant_params_dict</span><span class="p">)</span>
<span class="n">custom_objects_dict</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_custom_objects_dict</span><span class="p">)</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
@@ -1158,6 +1189,8 @@
<span class="n">x</span><span class="p">[</span><span class="n">ind</span><span class="p">]):</span> <span class="c1"># if nan, do not update xml with nan</span>
<span class="n">opt_dict</span><span class="p">[</span><span class="n">param_name</span><span class="p">][</span><span class="s1">&#39;input_value&#39;</span><span class="p">]</span> <span class="o">*=</span> <span class="n">x</span><span class="p">[</span><span class="n">ind</span><span class="p">]</span>
<span class="k">if</span> <span class="n">custom_objects_dict</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">update_custom_objects_dict</span><span class="p">(</span><span class="n">opt_dict</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">update_xml</span><span class="p">(</span><span class="n">opt_dict</span><span class="p">,</span>
<span class="n">temp_xml_file_path</span><span class="p">,</span>
<span class="n">dependant_params_dict</span><span class="o">=</span><span class="n">dep_dict</span><span class="p">)</span>
@@ -1228,8 +1261,8 @@
<span class="n">dependant_params_dict</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;updates xml file with info_dict</span>
<span class="sd"> :param info_dict: (dict) info in {species_names:{thermo_prop:val}}</span>
<span class="sd"> Requires an identical structure to opt_dict</span>
<span class="sd"> :param info_dict: (dict) Requires an identical structure to opt_dict</span>
<span class="sd"> Ignores items with keys containing &quot;custom_object_name&quot;</span>
<span class="sd"> :param phases_xml_filename: (str) xml filename if editing other xml</span>
<span class="sd"> If ``None``, the current xml will be modified and the internal</span>
<span class="sd"> Cantera phases will be refreshed to the new values.</span>
@@ -1239,7 +1272,8 @@
<span class="k">if</span> <span class="n">phases_xml_filename</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">phases_xml_filename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phases_xml_filename</span>
<span class="n">new_dict</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">info_dict</span><span class="p">)</span>
<span class="n">dep_dict</span> <span class="o">=</span> <span class="n">dependant_params_dict</span>
<span class="n">dep_dict</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="n">dependant_params_dict</span><span class="p">)</span>
<span class="n">custom_objects_dict</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_custom_objects_dict</span><span class="p">)</span>
<span class="k">if</span> <span class="n">dep_dict</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">new_dict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">dep_dict</span><span class="p">)</span>
@@ -1257,10 +1291,12 @@
<span class="n">ind_vals</span> <span class="o">=</span> <span class="p">[</span><span class="n">new_dict</span><span class="p">[</span><span class="n">ind_param_name</span><span class="p">][</span><span class="s1">&#39;input_value&#39;</span><span class="p">]</span>
<span class="k">for</span> <span class="n">ind_param_name</span> <span class="ow">in</span> <span class="n">ind_param_names</span><span class="p">]</span>
<span class="k">if</span> <span class="n">mod_kwargs</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">param_name</span><span class="p">][</span><span class="s1">&#39;input_value&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">mod_func</span><span class="p">(</span><span class="n">ind_vals</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">param_name</span><span class="p">][</span><span class="s1">&#39;input_value&#39;</span><span class="p">]</span> <span class="o">=</span> \
<span class="n">mod_func</span><span class="p">(</span><span class="n">ind_vals</span><span class="p">,</span>
<span class="n">custom_objects_dict</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">new_dict</span><span class="p">[</span><span class="n">param_name</span><span class="p">][</span><span class="s1">&#39;input_value&#39;</span><span class="p">]</span> <span class="o">=</span> \
<span class="n">mod_func</span><span class="p">(</span><span class="n">ind_vals</span><span class="p">,</span> <span class="n">custom_objects_dict</span><span class="p">,</span>
<span class="o">**</span><span class="n">mod_kwargs</span><span class="p">)</span>
<span class="n">tree</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">phases_xml_filename</span><span class="p">)</span>
<span class="n">root</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span>
@@ -1268,6 +1304,8 @@
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">new_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">new_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="n">now</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span>
<span class="k">if</span> <span class="s1">&#39;custom_object_name&#39;</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
<span class="k">continue</span>
<span class="k">if</span> <span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;upper_attrib_name&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
<span class="ow">and</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;lower_attrib_name&#39;</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">):</span>
<span class="k">for</span> <span class="n">child1</span> <span class="ow">in</span> <span class="n">root</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="s1">&#39;upper_element_name&#39;</span><span class="p">]):</span>
@@ -1324,6 +1362,31 @@
<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>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> updates internal custom_objects_dict with info_dict</span>
<span class="sd"> :param info_dict: Requires an identical structure to opt_dict</span>
<span class="sd"> Ignores items with keys containing &quot;custom_object_name&quot;</span>
<span class="sd"> :return: None</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">custom_objects_dict</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_custom_objects_dict</span><span class="p">)</span>
<span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">info_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">info_dict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
<span class="k">if</span> <span class="s1">&#39;upper_element_name&#39;</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
<span class="k">continue</span>
<span class="n">func</span> <span class="o">=</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;function&#39;</span><span class="p">]</span>
<span class="n">value</span> <span class="o">=</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;input_value&#39;</span><span class="p">]</span>
<span class="n">kwargs</span> <span class="o">=</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;kwargs&#39;</span><span class="p">]</span>
<span class="n">object_name</span> <span class="o">=</span> <span class="n">d</span><span class="p">[</span><span class="s1">&#39;custom_object_name&#39;</span><span class="p">]</span>
<span class="n">new_object</span> <span class="o">=</span> <span class="n">func</span><span class="p">(</span><span class="n">custom_objects_dict</span><span class="p">[</span><span class="n">object_name</span><span class="p">],</span>
<span class="n">value</span><span class="p">,</span>
<span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="n">custom_objects_dict</span><span class="p">[</span><span class="n">object_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">new_object</span>
<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>
<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>
@@ -1388,6 +1451,11 @@
<span class="s1">&#39;meas&#39;</span><span class="p">:</span> <span class="n">meas</span><span class="p">,</span>
<span class="n">c_data</span><span class="p">:</span> <span class="n">exp_df</span><span class="p">[</span><span class="n">c_data</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">,</span>
<span class="s1">&#39;feed_molarity&#39;</span><span class="p">:</span> <span class="n">feed_molarity</span><span class="p">})</span>
<span class="k">elif</span> <span class="n">c_data</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">combined_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="s1">&#39;pred&#39;</span><span class="p">:</span> <span class="n">pred</span><span class="p">,</span>
<span class="s1">&#39;meas&#39;</span><span class="p">:</span> <span class="n">meas</span><span class="p">,</span>
<span class="s1">&#39;c_data&#39;</span><span class="p">:</span> <span class="n">c_data</span><span class="p">,</span>
<span class="s1">&#39;feed_molarity&#39;</span><span class="p">:</span> <span class="n">feed_molarity</span><span class="p">})</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">combined_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="s1">&#39;pred&#39;</span><span class="p">:</span> <span class="n">pred</span><span class="p">,</span>
<span class="s1">&#39;meas&#39;</span><span class="p">:</span> <span class="n">meas</span><span class="p">,</span>
@@ -1420,35 +1488,36 @@
<span class="n">default_title</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">{0}</span><span class="s1"> complex eq. conc. (mol/L)&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="n">compared_species</span><span class="p">)</span>
<span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">()</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data_labels</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
<span class="n">unique_labels</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">data_labels</span><span class="p">))</span>
<span class="k">for</span> <span class="n">label</span> <span class="ow">in</span> <span class="n">unique_labels</span><span class="p">:</span>
<span class="n">filtered_data</span> <span class="o">=</span> <span class="n">combined_df</span><span class="p">[</span><span class="n">combined_df</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="n">label</span><span class="p">]</span>
<span class="n">filtered_meas</span> <span class="o">=</span> <span class="n">filtered_data</span><span class="p">[</span><span class="s1">&#39;meas&#39;</span><span class="p">]</span>
<span class="n">filtered_pred</span> <span class="o">=</span> <span class="n">filtered_data</span><span class="p">[</span><span class="s1">&#39;pred&#39;</span><span class="p">]</span>
<span class="n">ax</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">filtered_meas</span><span class="p">,</span> <span class="n">filtered_pred</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">filtered_pred</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">ax</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">filtered_meas</span><span class="p">,</span> <span class="n">filtered_pred</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">)</span>
<span class="k">if</span> <span class="n">legend</span><span class="p">:</span>
<span class="n">ax</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s1">&#39;best&#39;</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">c_data</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">c_data</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
<span class="n">c_data</span> <span class="o">=</span> <span class="n">combined_df</span><span class="p">[</span><span class="n">c_data</span><span class="p">]</span><span class="o">.</span><span class="n">values</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">c_data</span> <span class="o">=</span> <span class="n">combined_df</span><span class="p">[</span><span class="s1">&#39;c_data&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">meas</span><span class="p">,</span> <span class="n">pred</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="n">c_data</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="s1">&#39;viridis&#39;</span><span class="p">)</span>
<span class="n">c_bar</span> <span class="o">=</span> <span class="n">fig</span><span class="o">.</span><span class="n">colorbar</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s1">&#39;</span><span class="si">%.2f</span><span class="s1">&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">c_label</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">c_bar</span><span class="o">.</span><span class="n">set_label</span><span class="p">(</span><span class="n">c_label</span><span class="p">,</span> <span class="n">rotation</span><span class="o">=</span><span class="mi">270</span><span class="p">,</span> <span class="n">labelpad</span><span class="o">=</span><span class="mi">20</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">sns</span><span class="o">.</span><span class="n">scatterplot</span><span class="p">(</span><span class="n">meas</span><span class="p">,</span> <span class="n">pred</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;r&quot;</span><span class="p">,</span>
<span class="n">legend</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">meas</span><span class="p">,</span> <span class="n">pred</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="s2">&quot;r&quot;</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">min_max_data</span><span class="p">,</span> <span class="n">min_max_data</span><span class="p">,</span> <span class="n">color</span><span class="o">=</span><span class="s2">&quot;b&quot;</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="s2">&quot;&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">print_r_squared</span><span class="p">:</span>
<span class="n">ax</span><span class="o">.</span><span class="n">text</span><span class="p">(</span><span class="n">min_max_data</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">min_max_data</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="mf">0.9</span><span class="p">,</span>
<span class="s1">&#39;$R^2$=</span><span class="si">{0:.2f}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">r_squared</span><span class="p">(</span><span class="n">compared_value</span><span class="p">)))</span>
<span class="c1"># plt.legend(loc=&#39;lower right&#39;)</span>
<span class="c1"># else:</span>
<span class="c1"># plt.legend()</span>
<span class="n">ax</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">xlabel</span><span class="o">=</span><span class="s1">&#39;Measured&#39;</span><span class="p">,</span> <span class="n">ylabel</span><span class="o">=</span><span class="s1">&#39;Predicted&#39;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">plot_title</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>

2
docs/build/html/_sources/guide/install.rst.txt vendored
View File

@@ -8,7 +8,7 @@ Installation
Prerequisites
=============
REEPS requires python3 (>=3.5) with the development headers.
LLEPE requires python3 (>=3.5) with the development headers.
Stable Release

23
docs/build/html/_sources/guide/quickstart.rst.txt vendored
View File

@@ -9,28 +9,41 @@ Here is a quick example of how to fit an xml thermodynamic model to experimental
This code fits Nd standard enthalpy in the "twophase.xml" cantera file to the
experimental data in "Nd_exp_data.csv".
This code requires that you copy and paste the "elementz.xml" file in the llepe's data folder into
the Cantera's data folder located in your environments site-packages folder.
The code then produces a parity plot of the measured and predicted concentrations of Nd 3+ in the
aqueous phase.
.. code-block:: python
from reeps import REEPS
from llepe import LLEPE
opt_dict = {'Nd(H(A)2)3(org)_h0': {'upper_element_name': 'species',
'upper_attrib_name': 'name',
'upper_attrib_value': 'Nd(H(A)2)3(org)',
'lower_element_name': 'h0',
'lower_attrib_name': None,
'lower_attrib_value': None,
'input_format': '{0}',
'input_value': -4.7e6}}
searcher_parameters = {'exp_csv_filename': 'Nd_exp_data.csv',
searcher_parameters = {'exp_data': 'Nd_exp_data.csv',
'phases_xml_filename': 'twophase.xml',
'opt_dict': {'Nd(H(A)2)3(org)': {'h0': -4.7e6}},
'opt_dict': opt_dict,
'phase_names': ['HCl_electrolyte', 'PC88A_liquid'],
'aq_solvent_name': 'H2O(L)',
'extractant_name': '(HA)2(org)',
'diluant_name': 'dodecane',
'complex_names': ['Nd(H(A)2)3(org)'],
'rare_earth_ion_names': ['Nd+++'],
'extracted_species_ion_names': ['Nd+++'],
'aq_solvent_rho': 1000.0,
'extractant_rho': 960.0,
'diluant_rho': 750.0}
searcher = REEPS(**searcher_parameters)
searcher = LLEPE(**searcher_parameters)
est_enthalpy = searcher.fit()
searcher.update_xml(est_enthalpy)
searcher.parity_plot(print_r_squared=True)
The code should return something like this
.. figure:: ../_static/img/quick_start_output.png

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16
docs/build/html/genindex.html vendored
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@@ -182,6 +182,8 @@
<li><a href="modules/reeps.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>
<li><a href="modules/reeps.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>
@@ -192,11 +194,11 @@
<li><a href="modules/reeps.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>
<li><a href="modules/reeps.html#llepe.LLEPE.get_extractant_rho">get_extractant_rho() (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>
<li><a href="modules/reeps.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>
@@ -280,6 +282,8 @@
<li><a href="modules/reeps.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>
<li><a href="modules/reeps.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>
@@ -288,11 +292,11 @@
<li><a href="modules/reeps.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>
<li><a href="modules/reeps.html#llepe.LLEPE.set_extractant_name">set_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.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>
<li><a href="modules/reeps.html#llepe.LLEPE.set_extracted_species_ion_names">set_extracted_species_ion_names() (llepe.LLEPE method)</a>
@@ -317,10 +321,12 @@
<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_predicted_dict">update_predicted_dict() (llepe.LLEPE method)</a>
<li><a href="modules/reeps.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>
<li><a href="modules/reeps.html#llepe.LLEPE.update_xml">update_xml() (llepe.LLEPE method)</a>
</li>
</ul></td>

2
docs/build/html/guide/install.html vendored
View File

@@ -166,7 +166,7 @@
<span id="install"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline"></a></h1>
<div class="section" id="prerequisites">
<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline"></a></h2>
<p>REEPS requires python3 (&gt;=3.5) with the development headers.</p>
<p>LLEPE requires python3 (&gt;=3.5) with the development headers.</p>
</div>
<div class="section" id="stable-release">
<h2>Stable Release<a class="headerlink" href="#stable-release" title="Permalink to this headline"></a></h2>

23
docs/build/html/guide/quickstart.html vendored
View File

@@ -160,29 +160,42 @@
<p>Here is a quick example of how to fit an xml thermodynamic model to experimental data.</p>
<p>This code fits Nd standard enthalpy in the &quot;twophase.xml&quot; cantera file to the
experimental data in &quot;Nd_exp_data.csv&quot;.</p>
<p>This code requires that you copy and paste the &quot;elementz.xml&quot; file in the llepe's data folder into
the Cantera's data folder located in your environments site-packages folder.</p>
<p>The code then produces a parity plot of the measured and predicted concentrations of Nd 3+ in the
aqueous phase.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">reeps</span> <span class="kn">import</span> <span class="n">REEPS</span>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">llepe</span> <span class="kn">import</span> <span class="n">LLEPE</span>
<span class="n">opt_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;Nd(H(A)2)3(org)_h0&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;upper_element_name&#39;</span><span class="p">:</span> <span class="s1">&#39;species&#39;</span><span class="p">,</span>
<span class="s1">&#39;upper_attrib_name&#39;</span><span class="p">:</span> <span class="s1">&#39;name&#39;</span><span class="p">,</span>
<span class="s1">&#39;upper_attrib_value&#39;</span><span class="p">:</span> <span class="s1">&#39;Nd(H(A)2)3(org)&#39;</span><span class="p">,</span>
<span class="s1">&#39;lower_element_name&#39;</span><span class="p">:</span> <span class="s1">&#39;h0&#39;</span><span class="p">,</span>
<span class="s1">&#39;lower_attrib_name&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s1">&#39;lower_attrib_value&#39;</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
<span class="s1">&#39;input_format&#39;</span><span class="p">:</span> <span class="s1">&#39;</span><span class="si">{0}</span><span class="s1">&#39;</span><span class="p">,</span>
<span class="s1">&#39;input_value&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mf">4.7e6</span><span class="p">}}</span>
<span class="n">searcher_parameters</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;exp_csv_filename&#39;</span><span class="p">:</span> <span class="s1">&#39;Nd_exp_data.csv&#39;</span><span class="p">,</span>
<span class="n">searcher_parameters</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;exp_data&#39;</span><span class="p">:</span> <span class="s1">&#39;Nd_exp_data.csv&#39;</span><span class="p">,</span>
<span class="s1">&#39;phases_xml_filename&#39;</span><span class="p">:</span> <span class="s1">&#39;twophase.xml&#39;</span><span class="p">,</span>
<span class="s1">&#39;opt_dict&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;Nd(H(A)2)3(org)&#39;</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;h0&#39;</span><span class="p">:</span> <span class="o">-</span><span class="mf">4.7e6</span><span class="p">}},</span>
<span class="s1">&#39;opt_dict&#39;</span><span class="p">:</span> <span class="n">opt_dict</span><span class="p">,</span>
<span class="s1">&#39;phase_names&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;HCl_electrolyte&#39;</span><span class="p">,</span> <span class="s1">&#39;PC88A_liquid&#39;</span><span class="p">],</span>
<span class="s1">&#39;aq_solvent_name&#39;</span><span class="p">:</span> <span class="s1">&#39;H2O(L)&#39;</span><span class="p">,</span>
<span class="s1">&#39;extractant_name&#39;</span><span class="p">:</span> <span class="s1">&#39;(HA)2(org)&#39;</span><span class="p">,</span>
<span class="s1">&#39;diluant_name&#39;</span><span class="p">:</span> <span class="s1">&#39;dodecane&#39;</span><span class="p">,</span>
<span class="s1">&#39;complex_names&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Nd(H(A)2)3(org)&#39;</span><span class="p">],</span>
<span class="s1">&#39;rare_earth_ion_names&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Nd+++&#39;</span><span class="p">],</span>
<span class="s1">&#39;extracted_species_ion_names&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;Nd+++&#39;</span><span class="p">],</span>
<span class="s1">&#39;aq_solvent_rho&#39;</span><span class="p">:</span> <span class="mf">1000.0</span><span class="p">,</span>
<span class="s1">&#39;extractant_rho&#39;</span><span class="p">:</span> <span class="mf">960.0</span><span class="p">,</span>
<span class="s1">&#39;diluant_rho&#39;</span><span class="p">:</span> <span class="mf">750.0</span><span class="p">}</span>
<span class="n">searcher</span> <span class="o">=</span> <span class="n">REEPS</span><span class="p">(</span><span class="o">**</span><span class="n">searcher_parameters</span><span class="p">)</span>
<span class="n">searcher</span> <span class="o">=</span> <span class="n">LLEPE</span><span class="p">(</span><span class="o">**</span><span class="n">searcher_parameters</span><span class="p">)</span>
<span class="n">est_enthalpy</span> <span class="o">=</span> <span class="n">searcher</span><span class="o">.</span><span class="n">fit</span><span class="p">()</span>
<span class="n">searcher</span><span class="o">.</span><span class="n">update_xml</span><span class="p">(</span><span class="n">est_enthalpy</span><span class="p">)</span>
<span class="n">searcher</span><span class="o">.</span><span class="n">parity_plot</span><span class="p">(</span><span class="n">print_r_squared</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>
</div>
<p>The code should return something like this</p>
<div class="figure align-default">
<img alt="../_images/quick_start_output.png" src="../_images/quick_start_output.png" />
</div>
</div>

85
docs/build/html/modules/reeps.html vendored
View File

@@ -163,7 +163,7 @@
<h2>Parameters<a class="headerlink" href="#parameters" title="Permalink to this headline"></a></h2>
<dl class="py class">
<dt id="llepe.LLEPE">
<em class="property">class </em><code class="sig-prename descclassname">llepe.</code><code class="sig-name descname">LLEPE</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">exp_data</span></em>, <em class="sig-param"><span class="n">phases_xml_filename</span></em>, <em class="sig-param"><span class="n">phase_names</span></em>, <em class="sig-param"><span class="n">aq_solvent_name</span></em>, <em class="sig-param"><span class="n">extractant_name</span></em>, <em class="sig-param"><span class="n">diluant_name</span></em>, <em class="sig-param"><span class="n">complex_names</span></em>, <em class="sig-param"><span class="n">extracted_species_ion_names</span></em>, <em class="sig-param"><span class="n">extracted_species_list</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">aq_solvent_rho</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">extractant_rho</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">diluant_rho</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">opt_dict</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">objective_function</span><span class="o">=</span><span class="default_value">'Log-MSE'</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="o">=</span><span class="default_value">'SLSQP'</span></em>, <em class="sig-param"><span class="n">temp_xml_file_path</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">dependant_params_dict</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#llepe.LLEPE" title="Permalink to this definition"></a></dt>
<em class="property">class </em><code class="sig-prename descclassname">llepe.</code><code class="sig-name descname">LLEPE</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">exp_data</span></em>, <em class="sig-param"><span class="n">phases_xml_filename</span></em>, <em class="sig-param"><span class="n">phase_names</span></em>, <em class="sig-param"><span class="n">aq_solvent_name</span></em>, <em class="sig-param"><span class="n">extractant_name</span></em>, <em class="sig-param"><span class="n">diluant_name</span></em>, <em class="sig-param"><span class="n">complex_names</span></em>, <em class="sig-param"><span class="n">extracted_species_ion_names</span></em>, <em class="sig-param"><span class="n">extracted_species_list</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">aq_solvent_rho</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">extractant_rho</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">diluant_rho</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">opt_dict</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">objective_function</span><span class="o">=</span><span class="default_value">'Log-MSE'</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="o">=</span><span class="default_value">'scipy_minimize'</span></em>, <em class="sig-param"><span class="n">temp_xml_file_path</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">dependant_params_dict</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">custom_objects_dict</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#llepe.LLEPE" title="Permalink to this definition"></a></dt>
<dd><p>Liquid-Liquid Extraction Parameter estimator</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
@@ -277,10 +277,8 @@ i.e. Nd(H(A)2)3(org), Pr(H(A)2)3(org)</p>
<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>
<dl class="simple">
<dt>If <code class="docutils literal notranslate"><span class="pre">None</span></code>, extracted_species_list will be extracted_species_ion_names</dt><dd><p>without '+' i.e. 'Nd+++'-&gt;'Nd'</p>
</dd>
</dl>
<p>If <code class="docutils literal notranslate"><span class="pre">None</span></code>, extracted_species_list will be extracted_species_ion_names
without '+' i.e. 'Nd+++'-&gt;'Nd'</p>
</p></li>
<li><p><strong>aq_solvent_rho</strong> -- <p>(float) density of solvent (g/L)</p>
<p>If <code class="docutils literal notranslate"><span class="pre">None</span></code>, molar volume/molecular weight is used from xml</p>
@@ -402,13 +400,19 @@ xml file</p>
about parameters dependant on opt_dict. Has a similar structure to
opt_dict except instead of input values, it has 3 other fields:
'function', 'kwargs', and 'independent_params.</p>
<p>'function' is a function of the form
<code class="docutils literal notranslate"><span class="pre">function(independent_param__value_list,</span> <span class="pre">**kwargs)</span></code>
'kwargs' are the extra arguments to pass to function
'independent_params' is a list of parameter names in opt_dict that the
<p>'function' is a function of the form</p>
<p><code class="docutils literal notranslate"><span class="pre">function(independent_param__value_list,</span> <span class="pre">custom_objects_dict,</span>
<span class="pre">**kwargs)</span></code></p>
<p>'kwargs' are the extra arguments to pass to function</p>
<p>'independent_params' is a list of parameter names in opt_dict that the
dependent_param is a function of.</p>
<p>'custom_objects_dict' is for accessing the estimator's internal
custom_objects_dict and must be included in the arguments, even if the
custom_objects_dict is not set and is None.</p>
<p>See example code for usage.</p>
</p></li>
<li><p><strong>custom_objects_dict</strong> -- (dict) dictionary containing custom objects
format: {&lt;object_name_string&gt;: &lt;object&gt;,...}</p></li>
</ul>
</dd>
</dl>
@@ -469,14 +473,28 @@ optimized opt_dict: Has identical structure as opt_dict</p>
</dl>
</dd></dl>
<dl class="py method">
<dt id="llepe.LLEPE.get_custom_objects_dict">
<code class="sig-name descname">get_custom_objects_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE.get_custom_objects_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#llepe.LLEPE.get_custom_objects_dict" title="Permalink to this definition"></a></dt>
<dd><p>Returns the custom_objects_dict</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>custom_objects_dict: (dict) dictionary containing
information about custom objects from user</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="llepe.LLEPE.get_dependant_params_dict">
<code class="sig-name descname">get_dependant_params_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE.get_dependant_params_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#llepe.LLEPE.get_dependant_params_dict" title="Permalink to this definition"></a></dt>
<dd><p>Returns the dependant_params_dict
:return: dependant_params_dict: (dict) dictionary containing</p>
<blockquote>
<div><p>information about parameters dependant on opt_dict</p>
</div></blockquote>
<dd><p>Returns the dependant_params_dict</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>dependant_params_dict: (dict) dictionary containing
information about parameters dependant on opt_dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
@@ -795,12 +813,28 @@ objective_function value</p>
</dl>
</dd></dl>
<dl class="py method">
<dt id="llepe.LLEPE.set_custom_objects_dict">
<code class="sig-name descname">set_custom_objects_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">custom_objects_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE.set_custom_objects_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#llepe.LLEPE.set_custom_objects_dict" title="Permalink to this definition"></a></dt>
<dd><p>Sets the custom_objects_dict</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>custom_objects_dict</strong> -- (dict) dictionary containing information
about about custom objects from user</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="llepe.LLEPE.set_dependant_params_dict">
<code class="sig-name descname">set_dependant_params_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dependant_params_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE.set_dependant_params_dict"><span class="viewcode-link">[source]</span></a><a class="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
<dd><p>Sets the dependant_params_dict</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>dependant_params_dict</strong> -- (dict) dictionary containing information
about parameters dependant on opt_dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
@@ -979,6 +1013,21 @@ xml file.</p>
</dl>
</dd></dl>
<dl class="py method">
<dt id="llepe.LLEPE.update_custom_objects_dict">
<code class="sig-name descname">update_custom_objects_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">info_dict</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE.update_custom_objects_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#llepe.LLEPE.update_custom_objects_dict" title="Permalink to this definition"></a></dt>
<dd><p>updates internal custom_objects_dict with info_dict</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>info_dict</strong> -- Requires an identical structure to opt_dict
Ignores items with keys containing &quot;custom_object_name&quot;</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>None</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="llepe.LLEPE.update_predicted_dict">
<code class="sig-name descname">update_predicted_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">phases_xml_filename</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">phase_names</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/llepe/llepe.html#LLEPE.update_predicted_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#llepe.LLEPE.update_predicted_dict" title="Permalink to this definition"></a></dt>
@@ -1005,8 +1054,8 @@ If <code class="docutils literal notranslate"><span class="pre">None</span></cod
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>info_dict</strong> -- (dict) info in {species_names:{thermo_prop:val}}
Requires an identical structure to opt_dict</p></li>
<li><p><strong>info_dict</strong> -- (dict) Requires an identical structure to opt_dict
Ignores items with keys containing &quot;custom_object_name&quot;</p></li>
<li><p><strong>phases_xml_filename</strong> -- (str) xml filename if editing other xml
If <code class="docutils literal notranslate"><span class="pre">None</span></code>, the current xml will be modified and the internal
Cantera phases will be refreshed to the new values.</p></li>

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