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Updated documentation
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titusquah
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<span id="install"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="prerequisites">
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<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline">¶</a></h2>
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<p>REEPS requires python3 (>=3.5) with the development headers.</p>
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<p>LLEPE requires python3 (>=3.5) with the development headers.</p>
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</div>
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<div class="section" id="stable-release">
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<h2>Stable Release<a class="headerlink" href="#stable-release" title="Permalink to this headline">¶</a></h2>
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<p>Here is a quick example of how to fit an xml thermodynamic model to experimental data.</p>
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<p>This code fits Nd standard enthalpy in the "twophase.xml" cantera file to the
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experimental data in "Nd_exp_data.csv".</p>
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<p>This code requires that you copy and paste the "elementz.xml" file in the llepe's data folder into
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the Cantera's data folder located in your environments site-packages folder.</p>
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<p>The code then produces a parity plot of the measured and predicted concentrations of Nd 3+ in the
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aqueous phase.</p>
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<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>
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<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>
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<span class="n">opt_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'Nd(H(A)2)3(org)_h0'</span><span class="p">:</span> <span class="p">{</span><span class="s1">'upper_element_name'</span><span class="p">:</span> <span class="s1">'species'</span><span class="p">,</span>
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<span class="s1">'upper_attrib_name'</span><span class="p">:</span> <span class="s1">'name'</span><span class="p">,</span>
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<span class="s1">'upper_attrib_value'</span><span class="p">:</span> <span class="s1">'Nd(H(A)2)3(org)'</span><span class="p">,</span>
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<span class="s1">'lower_element_name'</span><span class="p">:</span> <span class="s1">'h0'</span><span class="p">,</span>
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<span class="s1">'lower_attrib_name'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
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<span class="s1">'lower_attrib_value'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
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<span class="s1">'input_format'</span><span class="p">:</span> <span class="s1">'</span><span class="si">{0}</span><span class="s1">'</span><span class="p">,</span>
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<span class="s1">'input_value'</span><span class="p">:</span> <span class="o">-</span><span class="mf">4.7e6</span><span class="p">}}</span>
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<span class="n">searcher_parameters</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'exp_csv_filename'</span><span class="p">:</span> <span class="s1">'Nd_exp_data.csv'</span><span class="p">,</span>
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<span class="n">searcher_parameters</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'exp_data'</span><span class="p">:</span> <span class="s1">'Nd_exp_data.csv'</span><span class="p">,</span>
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<span class="s1">'phases_xml_filename'</span><span class="p">:</span> <span class="s1">'twophase.xml'</span><span class="p">,</span>
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<span class="s1">'opt_dict'</span><span class="p">:</span> <span class="p">{</span><span class="s1">'Nd(H(A)2)3(org)'</span><span class="p">:</span> <span class="p">{</span><span class="s1">'h0'</span><span class="p">:</span> <span class="o">-</span><span class="mf">4.7e6</span><span class="p">}},</span>
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<span class="s1">'opt_dict'</span><span class="p">:</span> <span class="n">opt_dict</span><span class="p">,</span>
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<span class="s1">'phase_names'</span><span class="p">:</span> <span class="p">[</span><span class="s1">'HCl_electrolyte'</span><span class="p">,</span> <span class="s1">'PC88A_liquid'</span><span class="p">],</span>
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<span class="s1">'aq_solvent_name'</span><span class="p">:</span> <span class="s1">'H2O(L)'</span><span class="p">,</span>
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<span class="s1">'extractant_name'</span><span class="p">:</span> <span class="s1">'(HA)2(org)'</span><span class="p">,</span>
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<span class="s1">'diluant_name'</span><span class="p">:</span> <span class="s1">'dodecane'</span><span class="p">,</span>
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<span class="s1">'complex_names'</span><span class="p">:</span> <span class="p">[</span><span class="s1">'Nd(H(A)2)3(org)'</span><span class="p">],</span>
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<span class="s1">'rare_earth_ion_names'</span><span class="p">:</span> <span class="p">[</span><span class="s1">'Nd+++'</span><span class="p">],</span>
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<span class="s1">'extracted_species_ion_names'</span><span class="p">:</span> <span class="p">[</span><span class="s1">'Nd+++'</span><span class="p">],</span>
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<span class="s1">'aq_solvent_rho'</span><span class="p">:</span> <span class="mf">1000.0</span><span class="p">,</span>
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<span class="s1">'extractant_rho'</span><span class="p">:</span> <span class="mf">960.0</span><span class="p">,</span>
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<span class="s1">'diluant_rho'</span><span class="p">:</span> <span class="mf">750.0</span><span class="p">}</span>
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<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>
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<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>
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<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>
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<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>
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<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>
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</pre></div>
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</div>
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<p>The code should return something like this</p>
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<div class="figure align-default">
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<img alt="../_images/quick_start_output.png" src="../_images/quick_start_output.png" />
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</div>
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</div>
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