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<title>specie — Cortix 0.1.0 documentation</title>
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<h1>Source code for specie</h1><div class="highlight"><pre>
<span></span><span class="ch">#!/usr/bin/env python</span>
<span class="c1"># -*- coding: utf-8 -*-</span>
<span class="c1"># This file is part of the Cortix toolkit environment</span>
<span class="c1"># https://cortix.org</span>
<span class="c1">#</span>
<span class="c1"># All rights reserved, see COPYRIGHT for full restrictions.</span>
<span class="c1"># https://github.com/dpploy/cortix/blob/master/COPYRIGHT.txt</span>
<span class="c1">#</span>
<span class="c1"># Licensed under the University of Massachusetts Lowell LICENSE:</span>
<span class="c1"># https://github.com/dpploy/cortix/blob/master/LICENSE.txt</span>
<span class="sd">'''</span>
<span class="sd">Author: Valmor de Almeida dealmeidav@ornl.gov; vfda</span>
<span class="sd">This Specie class is to be used with other classes in plant-level process modules.</span>
<span class="sd">NB: Species is always used either in singular or plural cases, the class</span>
<span class="sd"> named here reflects one species. If many species are used in an external</span>
<span class="sd"> context, the species object name can be used without conflict.</span>
<span class="sd">For unit testing do at the linux command prompt:</span>
<span class="sd"> python specie.py</span>
<span class="sd">NB: The Specie() class encapsulates either the molecular or empirical chemical</span>
<span class="sd"> formula of a compound.</span>
<span class="sd"> This is done as follows. Say MAO2 is either a molecular or empirical chemical</span>
<span class="sd"> formula of a ficticious compound denoting minor actinides dioxide. The list</span>
<span class="sd"> of atoms is given as follows:</span>
<span class="sd"> ['0.49*Np-237', '0.42*Am-241', '0.08*Am-243', '0.01*Cm-244', '2.0*O-16']</span>
<span class="sd"> note the MA forming nuclides add to 1 = 0.49 + 0.42 + 0.08 + 0.01. Therefore</span>
<span class="sd"> the number of atoms in this compound is 3. 1 MA "atom" and 2 O.</span>
<span class="sd"> Note that the total number of "atoms" is obtained by summing all multipliers:</span>
<span class="sd"> 0.49 + 0.42 + 0.08 + 0.01 + 2.0.</span>
<span class="sd"> The nuclide is indicated by the element symbol followed by a dash and the</span>
<span class="sd"> atomic mass number. Here the number of nuclide types is 5 (self._nNuclideTypes).</span>
<span class="sd"> The numbers preceeding the nuclide symbol before the * will be referred to as</span>
<span class="sd"> multipliers. The sum of the multipliers will add to the number of "atoms" in</span>
<span class="sd"> the formula. WARNING: a multiplier could be in the format 0.00e-00. In this</span>
<span class="sd"> case a hiphen may appear twice, e.g.: 1.549e-09*U-233</span>
<span class="sd"> Other forms can be used for common true species</span>
<span class="sd"> ['Np-237', '2.0*O-16'] or ['Np-237', 'O-16', 'O-16'] or [ '2*H', 'O' ] or</span>
<span class="sd"> [ 'H', 'O', 'H' ] etc...</span>
<span class="sd"> This code will calculate the molar mass of any species with a given valid</span>
<span class="sd"> atom list using a provided periodic table of chemical elements. The user</span>
<span class="sd"> can also reset the value of the molar mass with a setter method.</span>
<span class="sd">Sat May 9 21:40:48 EDT 2015 created; vfda</span>
<span class="sd">'''</span>
<span class="c1">#*********************************************************************************</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">from</span> <span class="nn">cortix.support.periodictable</span> <span class="k">import</span> <span class="n">ELEMENTS</span>
<span class="c1">#*********************************************************************************</span>
<div class="viewcode-block" id="Specie"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie">[docs]</a><span class="k">class</span> <span class="nc">Specie</span><span class="p">:</span>
<span class="sd">'''</span>
<span class="sd"> todo: phase should not be here; concentrations should not be here</span>
<span class="sd"> only molar quantities should be here</span>
<span class="sd"> see the Phase container</span>
<span class="sd"> '''</span>
<span class="c1">#*********************************************************************************</span>
<span class="c1"># Construction</span>
<span class="c1">#*********************************************************************************</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
<span class="n">name</span><span class="o">=</span><span class="s1">'null'</span><span class="p">,</span>
<span class="n">formula_name</span><span class="o">=</span><span class="s1">'null'</span><span class="p">,</span>
<span class="n">phase</span><span class="o">=</span><span class="s1">'null'</span><span class="p">,</span>
<span class="n">atoms</span><span class="o">=</span><span class="nb">list</span><span class="p">(),</span>
<span class="n">molarCC</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="c1"># default unit: M (mole/L)</span>
<span class="n">massCC</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span> <span class="c1"># default unit: g/L</span>
<span class="n">flag</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops not string.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_name</span> <span class="o">=</span> <span class="n">name</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">formula_name</span><span class="p">,</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops not string.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__formula_name</span> <span class="o">=</span> <span class="n">formula_name</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">phase</span><span class="p">,</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops not string.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_phase</span> <span class="o">=</span> <span class="n">phase</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="nb">list</span><span class="p">),</span> <span class="s1">'oops not list.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="o">=</span> <span class="n">atoms</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_flag</span> <span class="o">=</span> <span class="n">flag</span> <span class="c1"># flag can be any type</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarHeatPwr</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarGammaPwr</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivity</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarMassUnit</span> <span class="o">=</span> <span class="s1">'g/mole'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarHeatPwrUnit</span> <span class="o">=</span> <span class="s1">'W/mole'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarGammaPwrUnit</span> <span class="o">=</span> <span class="s1">'W/mole'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivityUnit</span> <span class="o">=</span> <span class="s1">'Ci/mole'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivityFractions</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCCUnit</span> <span class="o">=</span> <span class="s1">'mole/L'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_massCCUnit</span> <span class="o">=</span> <span class="s1">'g/L'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__UpdateMolarMass</span><span class="p">()</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCC</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_massCC</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="k">return</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">molarCC</span><span class="p">,</span> <span class="nb">float</span><span class="p">),</span> <span class="s1">'oops not a float.'</span>
<span class="k">assert</span> <span class="n">molarCC</span> <span class="o">>=</span> <span class="mf">0.0</span><span class="p">,</span> <span class="s1">'oops negative value.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCC</span> <span class="o">=</span> <span class="n">molarCC</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_massCC</span> <span class="o">=</span> <span class="n">molarCC</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">massCC</span><span class="p">,</span> <span class="nb">float</span><span class="p">),</span> <span class="s1">'oops not a float.'</span>
<span class="k">assert</span> <span class="n">massCC</span> <span class="o">>=</span> <span class="mf">0.0</span><span class="p">,</span> <span class="s1">'oops negative value.'</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_massCC</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_massCC</span> <span class="o">=</span> <span class="n">massCC</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCC</span> <span class="o">=</span> <span class="n">massCC</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span>
<span class="k">return</span>
<span class="c1">#*********************************************************************************</span>
<span class="c1"># Public Member Functions</span>
<span class="c1">#*********************************************************************************</span>
<div class="viewcode-block" id="Specie.GetName"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetName">[docs]</a> <span class="k">def</span> <span class="nf">GetName</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the empirical name of the species. For example, "water".</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> name: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_name</span></div>
<div class="viewcode-block" id="Specie.SetName"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetName">[docs]</a> <span class="k">def</span> <span class="nf">SetName</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">n</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the empirical name of the species to n.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> n: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_name</span> <span class="o">=</span> <span class="n">n</span></div>
<span class="n">name</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetName</span><span class="p">,</span> <span class="n">SetName</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetFormulaName"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetFormulaName">[docs]</a> <span class="k">def</span> <span class="nf">GetFormulaName</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the formulaic name of the compound. For example, "Dihydrogen</span>
<span class="sd"> monoxide".</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> self.__formula_name: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__formula_name</span></div>
<div class="viewcode-block" id="Specie.SetFormulaName"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetFormulaName">[docs]</a> <span class="k">def</span> <span class="nf">SetFormulaName</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">f</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the formulaic name to f.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> self.__formula_name: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__formula_name</span> <span class="o">=</span> <span class="n">f</span></div>
<span class="n">formula_name</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetFormulaName</span><span class="p">,</span> <span class="n">SetFormulaName</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetPhase"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetPhase">[docs]</a> <span class="k">def</span> <span class="nf">GetPhase</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the phase history of the species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> phase: dataFrame</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_phase</span></div>
<div class="viewcode-block" id="Specie.SetPhase"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetPhase">[docs]</a> <span class="k">def</span> <span class="nf">SetPhase</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">p</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the phase history to p.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> p: dataFrame</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_mass</span> <span class="o">=</span> <span class="n">p</span></div>
<span class="n">phase</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetPhase</span><span class="p">,</span> <span class="n">SetPhase</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarMass"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarMass">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarMass</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the numerical value for the molar mass of the species. Units</span>
<span class="sd"> are given by molarMassUnit.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarMass: float</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span></div>
<div class="viewcode-block" id="Specie.SetMolarMass"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarMass">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarMass</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the molar mass of the species equal to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: float</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarMass</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMolarMass</span><span class="p">,</span> <span class="n">SetMolarMass</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarMassUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarMassUnit">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarMassUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the unit used to measure the molar mass of the species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarMassUnit: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMassUnit</span></div>
<div class="viewcode-block" id="Specie.SetMolarMassUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarMassUnit">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarMassUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the unit used to measure the molar mass of the species to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarMassUnit</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarMassUnit</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMolarMassUnit</span><span class="p">,</span> <span class="n">SetMolarMassUnit</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarRadioactivity"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarRadioactivity">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarRadioactivity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the numerical value for molar radioactivity of the species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarRadioactivity: float</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivity</span></div>
<div class="viewcode-block" id="Specie.SetMolarRadioactivity"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarRadioactivity">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarRadioactivity</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the molar radioactivity of the species equal to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: float</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivity</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarRadioactivity</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span> <span class="n">GetMolarRadioactivity</span><span class="p">,</span> <span class="n">SetMolarRadioactivity</span><span class="p">,</span>
<span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarRadioactivityFractions"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarRadioactivityFractions">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarRadioactivityFractions</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns a list of numbers that speciefies the % of molar reactivity</span>
<span class="sd"> that comes from each type of atom in the species. For example, a</span>
<span class="sd"> molarRadioactivityFraction of [0.65, 0.35] for water means that 65%</span>
<span class="sd"> of the molar radioactivity comes from the hydrogen atoms and 35% comes</span>
<span class="sd"> from the oxygen atom.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarRadioactivityFractions: list</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivityFractions</span></div>
<div class="viewcode-block" id="Specie.SetMolarRadioactivityFractions"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarRadioactivityFractions">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarRadioactivityFractions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fracs</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets molarRadioactivityFractions equal to fracs. Fracs must be a list</span>
<span class="sd"> of floatswith the same length as there are different atoms in the</span>
<span class="sd"> species, or the function call will fail. (e.g. self._atoms and fracs</span>
<span class="sd"> must be of the same length). Take care to ensure that the elements of</span>
<span class="sd"> fracs match with the elements of self._atoms! (65% is in the same</span>
<span class="sd"> position in fracs as hydrogen is in self._atoms, following the above</span>
<span class="sd"> example).</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> fracs: list</span>
<span class="sd"> '''</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fracs</span><span class="p">,</span> <span class="nb">list</span><span class="p">),</span> <span class="s1">'oops not list.'</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fracs</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">fracs</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">),</span> <span class="s1">'oops not right length,'</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">fracs</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">fracs</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="nb">float</span><span class="p">),</span> <span class="s1">'oops not float.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivityFractions</span> <span class="o">=</span> <span class="n">fracs</span></div>
<span class="n">molarRadioactivityFractions</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span> <span class="n">GetMolarRadioactivityFractions</span><span class="p">,</span>
<span class="n">SetMolarRadioactivityFractions</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarRadioactivityUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarRadioactivityUnit">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarRadioactivityUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the unit used to measure molar radioactivity.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarRadioactivityUnit: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivityUnit</span></div>
<div class="viewcode-block" id="Specie.SetMolarRadioactivityUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarRadioactivityUnit">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarRadioactivityUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the unit used to measure molar radioactivity to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarRadioactivityUnit</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarRadioactivityUnit</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span> <span class="n">GetMolarRadioactivityUnit</span><span class="p">,</span>
<span class="n">SetMolarRadioactivityUnit</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarHeatPwr"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarHeatPwr">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarHeatPwr</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the amount of heat generated per mole of this species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarHeatPwr: float</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarHeatPwr</span></div>
<div class="viewcode-block" id="Specie.SetMolarHeatPwr"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarHeatPwr">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarHeatPwr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the amount of heat generated per mole of this species to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: float</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarHeatPwr</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarHeatPwr</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMolarHeatPwr</span><span class="p">,</span> <span class="n">SetMolarHeatPwr</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarHeatPwrUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarHeatPwrUnit">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarHeatPwrUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the unit used to measure the amount of heat generated per mole</span>
<span class="sd"> of this species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarHeatPwrUnit: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarHeatPwrUnit</span></div>
<div class="viewcode-block" id="Specie.SetMolarHeatPwrUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarHeatPwrUnit">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarHeatPwrUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the unit used to measure the amount of heat generated per mole of</span>
<span class="sd"> this species to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarHeatPwrUnit</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarHeatPwrUnit</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span> <span class="n">GetMolarHeatPwrUnit</span><span class="p">,</span> <span class="n">SetMolarHeatPwrUnit</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarGammaPwr"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarGammaPwr">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarGammaPwr</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the amount of gamma radiation produced per mole of this species</span>
<span class="sd"> (measured in units of power).</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarGammaPwr: float</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarGammaPwr</span></div>
<div class="viewcode-block" id="Specie.SetMolarGammaPwr"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarGammaPwr">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarGammaPwr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the amount of gamma radiation produced per mole of this species to</span>
<span class="sd"> v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: float</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarGammaPwr</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarGammaPwr</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMolarGammaPwr</span><span class="p">,</span> <span class="n">SetMolarGammaPwr</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarGammaPwrUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarGammaPwrUnit">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarGammaPwrUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the unit used to measure the amount of gamma radiation produced</span>
<span class="sd"> per mole of this species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarGammaPwrUnit: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarGammaPwrUnit</span></div>
<div class="viewcode-block" id="Specie.SetMolarGammaPwrUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarGammaPwrUnit">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarGammaPwrUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the unit used to measure the amount of gamma radiation produced</span>
<span class="sd"> per mole of this species to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarGammaPwrUnit</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarGammaPwrUnit</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span> <span class="n">GetMolarGammaPwrUnit</span><span class="p">,</span> <span class="n">SetMolarGammaPwrUnit</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span>
<span class="kc">None</span><span class="p">)</span>
<span class="c1"># Deprecated; see new interface below as GetFormula</span>
<div class="viewcode-block" id="Specie.GetAtoms"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetAtoms">[docs]</a> <span class="k">def</span> <span class="nf">GetAtoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span></div>
<div class="viewcode-block" id="Specie.SetAtoms"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetAtoms">[docs]</a> <span class="k">def</span> <span class="nf">SetAtoms</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atoms</span><span class="p">):</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="nb">list</span><span class="p">),</span> <span class="s1">'oops not list.'</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops not string.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="o">=</span> <span class="n">atoms</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__UpdateMolarMass</span><span class="p">()</span></div>
<span class="n">atoms</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetAtoms</span><span class="p">,</span> <span class="n">SetAtoms</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="c1"># New interface</span>
<div class="viewcode-block" id="Specie.GetFormula"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetFormula">[docs]</a> <span class="k">def</span> <span class="nf">GetFormula</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the molecular or empirical formula of the species. It is</span>
<span class="sd"> usually a list, for example, of the form ['2*H', 'O'].</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> formula: list</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span></div>
<div class="viewcode-block" id="Specie.SetFormula"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetFormula">[docs]</a> <span class="k">def</span> <span class="nf">SetFormula</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atoms</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the species' formula equal to atoms. Will automatically update</span>
<span class="sd"> the molar mass of the species, and will also fail if atoms is not a</span>
<span class="sd"> list of strings.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> atoms: list</span>
<span class="sd"> '''</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="nb">list</span><span class="p">),</span> <span class="s1">'oops not list.'</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">atoms</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops not string.'</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span> <span class="o">=</span> <span class="n">atoms</span>
<span class="bp">self</span><span class="o">.</span><span class="n">__UpdateMolarMass</span><span class="p">()</span></div>
<span class="n">formula</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetFormula</span><span class="p">,</span> <span class="n">SetFormula</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetNAtoms"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetNAtoms">[docs]</a> <span class="k">def</span> <span class="nf">GetNAtoms</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span> <span class="c1"># number of ficticious atoms in the species (see NB above)</span>
<span class="sd">'''</span>
<span class="sd"> Returns the total number of atoms comprising the species. For example,</span>
<span class="sd"> water is comprised of three atoms.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> nAtoms: int</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nAtoms</span></div>
<span class="n">nAtoms</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetNAtoms</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="c1"># number of nuclide types involved in the species definition</span>
<div class="viewcode-block" id="Specie.GetNNuclideTypes"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetNNuclideTypes">[docs]</a> <span class="k">def</span> <span class="nf">GetNNuclideTypes</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the number of different types of atoms comprising the species.</span>
<span class="sd"> For example, water is composed of two different types of atoms,</span>
<span class="sd"> hydrogen and oxygen.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> nNuclideTypes: int</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_nNuclideTypes</span></div>
<span class="n">nNuclideTypes</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetNNuclideTypes</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.SetFlag"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetFlag">[docs]</a> <span class="k">def</span> <span class="nf">SetFlag</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">f</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the flag associated with the species to f.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> f: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_flag</span> <span class="o">=</span> <span class="n">f</span></div>
<div class="viewcode-block" id="Specie.GetFlag"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetFlag">[docs]</a> <span class="k">def</span> <span class="nf">GetFlag</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the flag associated with the species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> flag: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_flag</span></div>
<span class="n">flag</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetFlag</span><span class="p">,</span> <span class="n">SetFlag</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarCC"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarCC">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarCC</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the numerical value for the number (molar) density of the</span>
<span class="sd"> species (moles/volume).</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarCC: float</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarCC</span></div>
<div class="viewcode-block" id="Specie.SetMolarCC"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarCC">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarCC</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the numerical value for the molar density of the species to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: float</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCC</span> <span class="o">=</span> <span class="n">v</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_massCC</span> <span class="o">=</span> <span class="n">v</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span></div>
<span class="n">molarCC</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMolarCC</span><span class="p">,</span> <span class="n">SetMolarCC</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMolarCCUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMolarCCUnit">[docs]</a> <span class="k">def</span> <span class="nf">GetMolarCCUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the unit used to measure molar density of the species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> molarCCUnit: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarCCUnit</span></div>
<div class="viewcode-block" id="Specie.SetMolarCCUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMolarCCUnit">[docs]</a> <span class="k">def</span> <span class="nf">SetMolarCCUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the unit used to measure the molar density of the species to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCCUnit</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">molarCCUnit</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMolarCCUnit</span><span class="p">,</span> <span class="n">SetMolarCCUnit</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMassCC"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMassCC">[docs]</a> <span class="k">def</span> <span class="nf">GetMassCC</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the numerical value of the mass density of the species</span>
<span class="sd"> (mass/volume).</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> massCC: float</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_massCC</span></div>
<div class="viewcode-block" id="Specie.SetMassCC"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMassCC">[docs]</a> <span class="k">def</span> <span class="nf">SetMassCC</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the numerical value of the mass density equal to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: float</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_massCC</span> <span class="o">=</span> <span class="n">v</span>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span> <span class="o">==</span> <span class="mf">0.0</span> <span class="ow">and</span> <span class="n">v</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCC</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarCC</span> <span class="o">=</span> <span class="n">v</span> <span class="o">/</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span></div>
<span class="n">massCC</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMassCC</span><span class="p">,</span> <span class="n">SetMassCC</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<div class="viewcode-block" id="Specie.GetMassCCUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.GetMassCCUnit">[docs]</a> <span class="k">def</span> <span class="nf">GetMassCCUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Returns the unit used to measure the mass density of the species.</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> massCCUnit: str</span>
<span class="sd"> '''</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_massCCUnit</span></div>
<div class="viewcode-block" id="Specie.SetMassCCUnit"><a class="viewcode-back" href="../support_rst/specie.html#specie.Specie.SetMassCCUnit">[docs]</a> <span class="k">def</span> <span class="nf">SetMassCCUnit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">v</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Sets the units used to measure mass density to v.</span>
<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> v: str</span>
<span class="sd"> '''</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_massCCUnit</span> <span class="o">=</span> <span class="n">v</span></div>
<span class="n">massCCUnit</span> <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">GetMassCCUnit</span><span class="p">,</span> <span class="n">SetMassCCUnit</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">s</span> <span class="o">=</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> Specie(): name=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' formula_name=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' phase=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> formula=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> # atoms=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' # nuclide types=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' molar mass=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">' molar cc=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">' mass cc=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> flag=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar radioactivity=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> \
<span class="s1">'</span><span class="se">\n\t</span><span class="s1"> radioactivity dens.=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar heat pwr=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> heat pwr dens.=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> \
<span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar gamma pwr=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> gamma pwr dens.=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> \
<span class="s1">'</span><span class="se">\n\t</span><span class="s1"> atoms=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar radioactivity fractions=</span><span class="si">%s</span><span class="s1">'</span>
<span class="k">return</span> <span class="n">s</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">__formula_name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">phase</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">__ReorderFormula</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">nAtoms</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">nNuclideTypes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarMass</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarMassUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCCUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">massCC</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">massCCUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">flag</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivity</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivityUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivity</span> <span class="o">*</span>
<span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="s1">'[Ci/cc]'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarHeatPwr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarHeatPwrUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarHeatPwr</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="s1">'[W/cc]'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarGammaPwr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarGammaPwrUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarGammaPwr</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="s1">'[W/cc]'</span><span class="p">,</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'*'</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">formula</span><span class="p">],</span> <span class="p">[</span><span class="s1">'</span><span class="si">%9.3e</span><span class="s1">'</span> <span class="o">%</span> <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivityFractions</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="n">s</span> <span class="o">=</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> Specie(): name=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' formula_name=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' phase=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> formula=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> # atoms=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' # nuclide types=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">' molar mass=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">' molar cc=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">' mass cc=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> flag=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar radioactivity=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> \
<span class="s1">'</span><span class="se">\n\t</span><span class="s1"> radioactivity dens.=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar heat pwr=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> heat pwr dens.=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> \
<span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar gamma pwr=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> gamma pwr dens.=</span><span class="si">%9.3e</span><span class="s1">[</span><span class="si">%s</span><span class="s1">];'</span> <span class="o">+</span> \
<span class="s1">'</span><span class="se">\n\t</span><span class="s1"> atoms=</span><span class="si">%s</span><span class="s1">;'</span> <span class="o">+</span> <span class="s1">'</span><span class="se">\n\t</span><span class="s1"> molar radioactivity fractions=</span><span class="si">%s</span><span class="s1">'</span>
<span class="k">return</span> <span class="n">s</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">__formula_name</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">phase</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">__ReorderFormula</span><span class="p">(),</span> <span class="bp">self</span><span class="o">.</span><span class="n">nAtoms</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">nNuclideTypes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarMass</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarMassUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCCUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">massCC</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">massCCUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">flag</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivity</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivityUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivity</span> <span class="o">*</span>
<span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="s1">'[Ci/cc]'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarHeatPwr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarHeatPwrUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarHeatPwr</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="s1">'[W/cc]'</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarGammaPwr</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarGammaPwrUnit</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarGammaPwr</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarCC</span><span class="p">,</span> <span class="s1">'[W/cc]'</span><span class="p">,</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'*'</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">formula</span><span class="p">],</span> <span class="p">[</span><span class="s1">'</span><span class="si">%9.3e</span><span class="s1">'</span> <span class="o">%</span> <span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">molarRadioactivityFractions</span><span class="p">])</span>
<span class="c1">#*********************************************************************************</span>
<span class="c1"># Private Helper Functions (Internal use: __)</span>
<span class="c1">#*********************************************************************************</span>
<span class="k">def</span> <span class="nf">__UpdateMolarMass</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Updates the molar mass of the species after the molecular formula has</span>
<span class="sd"> been changed.</span>
<span class="sd"> '''</span>
<span class="c1">#if len(self._atoms) == 0:</span>
<span class="c1"># self._nAtoms = 0</span>
<span class="c1"># return</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops'</span>
<span class="n">tmp</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'*'</span><span class="p">)</span>
<span class="n">nuclide</span> <span class="o">=</span> <span class="n">tmp</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="n">element</span> <span class="o">=</span> <span class="n">nuclide</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'-'</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">assert</span> <span class="n">element</span> <span class="ow">in</span> <span class="n">ELEMENTS</span><span class="p">,</span> <span class="s1">'element = </span><span class="si">%r</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">element</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_nAtoms</span> <span class="o">=</span> <span class="mi">0</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_nNuclideTypes</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">nuclides</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="n">nAtoms</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">summ</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops'</span>
<span class="c1"># format example: 3.2*O-18, or 3*O or O or O-16</span>
<span class="n">tmp</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'*'</span><span class="p">)</span>
<span class="n">multiple</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="c1"># single nuclide</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">nuclide</span> <span class="o">=</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="c1"># multiple nuclide</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">multiple</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">nuclide</span> <span class="o">=</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">assert</span> <span class="kc">False</span>
<span class="n">nuclides</span><span class="p">[</span><span class="n">nuclide</span><span class="p">]</span> <span class="o">=</span> <span class="n">multiple</span>
<span class="n">nAtoms</span> <span class="o">+=</span> <span class="n">multiple</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">tmp</span> <span class="o">=</span> <span class="n">nuclide</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'-'</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">element</span> <span class="o">=</span> <span class="n">ELEMENTS</span><span class="p">[</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
<span class="n">molarMass</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">exactmass</span> <span class="c1"># from isotopic composition</span>
<span class="k">if</span> <span class="n">molarMass</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">:</span>
<span class="n">molarMass</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">mass</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">element</span> <span class="o">=</span> <span class="n">ELEMENTS</span><span class="p">[</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">isotopes</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(</span><span class="s1">'m'</span><span class="p">))]</span>
<span class="n">molarMass</span> <span class="o">=</span> <span class="n">element</span><span class="o">.</span><span class="n">mass</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">assert</span> <span class="kc">False</span>
<span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="n">summ</span> <span class="o">+=</span> <span class="n">multiple</span> <span class="o">*</span> <span class="mf">0.0</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">summ</span> <span class="o">+=</span> <span class="n">multiple</span> <span class="o">*</span> <span class="n">molarMass</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_molarMass</span> <span class="o">=</span> <span class="n">summ</span>
<span class="c1"># print( summ )</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_nAtoms</span> <span class="o">=</span> <span class="n">nAtoms</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_nNuclideTypes</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">nuclides</span><span class="p">)</span>
<span class="k">return</span>
<span class="k">def</span> <span class="nf">__ReorderFormula</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Takes a list of atoms for a molecular or empirical formula and places</span>
<span class="sd"> it in order of decreasing magnitude of stoichiometric coefficient. For</span>
<span class="sd"> example, [O, 2*H] will be returned as [2*H, O].</span>
<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> atoms2: list</span>
<span class="sd"> '''</span>
<span class="n">atoms1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">[:]</span> <span class="c1"># shallow copy</span>
<span class="n">atoms2</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">)</span> <span class="o"><=</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">return</span> <span class="n">atoms1</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
<span class="c1"># save the multiplier value as a string type of scientific notation</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="p">:</span>
<span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">entry</span><span class="p">,</span> <span class="nb">str</span><span class="p">),</span> <span class="s1">'oops'</span>
<span class="c1"># format example: 3.2*O-18, or 3*O or O or O-16</span>
<span class="n">tmp</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'*'</span><span class="p">)</span>
<span class="n">multiplier</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">continue</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">multiplier</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">assert</span> <span class="kc">False</span>
<span class="k">assert</span> <span class="n">multiplier</span> <span class="o">!=</span> <span class="mf">0.0</span><span class="p">,</span> <span class="s1">'multiplier = </span><span class="si">%r</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">multiplier</span><span class="p">)</span>
<span class="n">multiplier</span> <span class="o">=</span> <span class="s1">'</span><span class="si">{0:9.3e}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">multiplier</span><span class="p">)</span>
<span class="n">atoms1</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_atoms</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">entry</span><span class="p">)]</span> <span class="o">=</span> <span class="n">multiplier</span> <span class="o">+</span> <span class="s1">'*'</span> <span class="o">+</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="c1"># order in decreasing order of multiplier magnitude</span>
<span class="n">multipliers_lst</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">entry</span> <span class="ow">in</span> <span class="n">atoms1</span><span class="p">:</span>
<span class="n">tmp</span> <span class="o">=</span> <span class="n">entry</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'*'</span><span class="p">)</span>
<span class="n">multiplier</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
<span class="k">continue</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">multiplier</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">assert</span> <span class="kc">False</span>
<span class="n">multipliers_lst</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">multiplier</span><span class="p">))</span>
<span class="n">sortedAtoms_lst</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span> <span class="k">for</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">a</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">multipliers_lst</span><span class="p">,</span> <span class="n">atoms1</span><span class="p">),</span>
<span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">pair</span><span class="p">:</span> <span class="n">pair</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
<span class="n">reverse</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>
<span class="n">atoms2</span> <span class="o">=</span> <span class="n">sortedAtoms_lst</span>
<span class="k">return</span> <span class="n">atoms2</span></div>
<span class="c1">#============================= end class Specie ==================================</span>
</pre></div>
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Cortix is a Python library for network modeling and HPC simulation.
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<a href="https://www.uml.edu/Engineering/Chemical/faculty/de-Almeida-Valmor.aspx">Prof. V. F. de Almeida, Ph.D.</a></br>
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<a href="https://www.uml.edu/">UMass Lowell</a><br>
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