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51  <h1>Source code for sas.models.PolymerExclVolume</h1><div class="highlight"><pre>
52<span class="c">#!/usr/bin/env python</span>
53
54<span class="c">##############################################################################</span>
55<span class="c">#       This software was developed by the University of Tennessee as part of the</span>
56<span class="c">#       Distributed Data Analysis of Neutron Scattering Experiments (DANSE)</span>
57<span class="c">#       project funded by the US National Science Foundation.</span>
58<span class="c">#</span>
59<span class="c">#       If you use DANSE applications to do scientific research that leads to</span>
60<span class="c">#       publication, we ask that you acknowledge the use of the software with the</span>
61<span class="c">#       following sentence:</span>
62<span class="c">#</span>
63<span class="c">#       &quot;This work benefited from DANSE software developed under NSF award DMR-0520547.&quot;</span>
64<span class="c">#</span>
65<span class="c">#       copyright 2008, University of Tennessee</span>
66<span class="c">##############################################################################</span>
67<span class="kn">from</span> <span class="nn">sas.models.BaseComponent</span> <span class="kn">import</span> <span class="n">BaseComponent</span>
68<span class="kn">from</span> <span class="nn">scipy.special</span> <span class="kn">import</span> <span class="n">gammainc</span><span class="p">,</span><span class="n">gamma</span>
69<span class="kn">import</span> <span class="nn">copy</span>   
70<span class="kn">import</span> <span class="nn">math</span>
71   
72<div class="viewcode-block" id="PolymerExclVolume"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.PolymerExclVolume.PolymerExclVolume">[docs]</a><span class="k">class</span> <span class="nc">PolymerExclVolume</span><span class="p">(</span><span class="n">BaseComponent</span><span class="p">):</span>
73    <span class="sd">&quot;&quot;&quot; </span>
74<span class="sd">    Class that evaluates a PolymerExclVolModel model. </span>
75<span class="sd">    This file was auto-generated from ..\c_extensions\polyexclvol.h.</span>
76<span class="sd">    Refer to that file and the structure it contains</span>
77<span class="sd">    for details of the model.</span>
78
79<span class="sd">    List of default parameters:</span>
80<span class="sd">    </span>
81<span class="sd">    * scale           = 0.01 </span>
82<span class="sd">    * rg              = 100.0 [A]</span>
83<span class="sd">    * m               = 3.0 </span>
84<span class="sd">    * background      = 0.0 [1/cm]</span>
85
86<span class="sd">    &quot;&quot;&quot;</span>
87       
88    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
89        <span class="sd">&quot;&quot;&quot; Initialization &quot;&quot;&quot;</span>
90       
91        <span class="c"># Initialize BaseComponent first, then sphere</span>
92        <span class="n">BaseComponent</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
93       
94        <span class="c">## Name of the model</span>
95        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;PolymerExclVolume&quot;</span>
96        <span class="c">## Model description</span>
97        <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span><span class="s">&quot;&quot;&quot; Compute the scattering intensity from polymers with excluded volume effects.</span>
98<span class="s">                scale: scale factor times volume fraction,</span>
99<span class="s">                or just volume fraction for absolute scale data</span>
100<span class="s">                rg: radius of gyration</span>
101<span class="s">                m = Porod exponent</span>
102<span class="s">                background: incoherent background</span>
103<span class="s">                &quot;&quot;&quot;</span>
104        <span class="c">## Define parameters</span>
105        <span class="bp">self</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="p">{}</span>
106        <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;scale&#39;</span><span class="p">]</span>        <span class="o">=</span> <span class="mf">1.0</span>
107        <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;rg&#39;</span><span class="p">]</span>           <span class="o">=</span> <span class="mf">60.0</span>
108        <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;m&#39;</span><span class="p">]</span>            <span class="o">=</span> <span class="mf">3.0</span>
109        <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;background&#39;</span><span class="p">]</span>   <span class="o">=</span> <span class="mf">0.0</span>
110
111       
112        <span class="c">## Parameter details [units, min, max]</span>
113        <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span>
114        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;scale&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
115        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;rg&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[A]&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
116        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;m&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
117        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;background&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[1/cm]&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
118
119        <span class="c">## fittable parameters</span>
120        <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span><span class="o">=</span><span class="p">[]</span>
121       
122        <span class="c">## non-fittable parameters</span>
123        <span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span><span class="o">=</span><span class="p">[]</span>
124       
125        <span class="c">## parameters with orientation</span>
126        <span class="bp">self</span><span class="o">.</span><span class="n">orientation_params</span> <span class="o">=</span><span class="p">[]</span>
127       
128    <span class="k">def</span> <span class="nf">_polymerexclvol</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
129       
130        <span class="n">sc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;scale&#39;</span><span class="p">]</span>
131        <span class="n">rg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;rg&#39;</span><span class="p">]</span>
132        <span class="n">mm</span>  <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;m&#39;</span><span class="p">]</span>
133        <span class="n">bg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;background&#39;</span><span class="p">]</span>
134   
135        <span class="n">nu</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="n">mm</span>
136   
137        <span class="n">Xx</span> <span class="o">=</span> <span class="n">x</span> <span class="o">*</span> <span class="n">x</span> <span class="o">*</span> <span class="n">rg</span> <span class="o">*</span> <span class="n">rg</span> <span class="o">*</span><span class="p">(</span><span class="mf">2.0</span> <span class="o">*</span> <span class="n">nu</span> <span class="o">+</span> <span class="mf">1.0</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="mf">2.0</span> <span class="o">*</span> <span class="n">nu</span> <span class="o">+</span> <span class="mf">2.0</span><span class="p">)</span> <span class="o">/</span> <span class="mf">6.0</span>
138        <span class="n">onu</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="n">nu</span>
139        <span class="n">o2nu</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span><span class="p">(</span><span class="mf">2.0</span> <span class="o">*</span> <span class="n">nu</span><span class="p">)</span>
140        <span class="n">Ps</span> <span class="o">=</span><span class="p">(</span><span class="mf">1.0</span> <span class="o">/</span> <span class="p">(</span><span class="n">nu</span> <span class="o">*</span> <span class="nb">pow</span><span class="p">(</span><span class="n">Xx</span><span class="p">,</span><span class="n">o2nu</span><span class="p">)))</span> <span class="o">*</span> <span class="p">(</span><span class="n">gamma</span><span class="p">(</span><span class="n">o2nu</span><span class="p">)</span><span class="o">*</span><span class="n">gammainc</span><span class="p">(</span><span class="n">o2nu</span><span class="p">,</span><span class="n">Xx</span><span class="p">)</span> <span class="o">-</span> \
141                        <span class="mf">1.0</span> <span class="o">/</span> <span class="nb">pow</span><span class="p">(</span><span class="n">Xx</span><span class="p">,</span><span class="n">o2nu</span><span class="p">)</span> <span class="o">*</span> <span class="n">gamma</span><span class="p">(</span><span class="n">onu</span><span class="p">)</span><span class="o">*</span><span class="n">gammainc</span><span class="p">(</span><span class="n">onu</span><span class="p">,</span><span class="n">Xx</span><span class="p">))</span>
142
143        <span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
144            <span class="n">Ps</span> <span class="o">=</span> <span class="mf">1.0</span>
145
146        <span class="k">return</span> <span class="p">(</span><span class="n">sc</span> <span class="o">*</span> <span class="n">Ps</span> <span class="o">+</span> <span class="n">bg</span><span class="p">);</span>
147
148<div class="viewcode-block" id="PolymerExclVolume.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.PolymerExclVolume.PolymerExclVolume.run">[docs]</a>    <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">):</span>
149        <span class="sd">&quot;&quot;&quot; Evaluate the model</span>
150<span class="sd">            @param x: input q-value (float or [float, float] as [r, theta])</span>
151<span class="sd">            @return: (guinier value)</span>
152<span class="sd">        &quot;&quot;&quot;</span>
153        <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">&#39;list&#39;</span><span class="p">:</span>
154            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_polymerexclvol</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
155        <span class="k">elif</span> <span class="n">x</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">&#39;tuple&#39;</span><span class="p">:</span>
156            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">&quot;Tuples are not allowed as input to BaseComponent models&quot;</span>
157        <span class="k">else</span><span class="p">:</span>
158            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_polymerexclvol</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
159   </div>
160<div class="viewcode-block" id="PolymerExclVolume.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.PolymerExclVolume.PolymerExclVolume.runXY">[docs]</a>    <span class="k">def</span> <span class="nf">runXY</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">):</span>
161        <span class="sd">&quot;&quot;&quot; Evaluate the model</span>
162<span class="sd">            @param x: input q-value (float or [float, float] as [qx, qy])</span>
163<span class="sd">            @return: guinier value</span>
164<span class="sd">        &quot;&quot;&quot;</span>
165        <span class="k">if</span> <span class="n">x</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">&#39;list&#39;</span><span class="p">:</span>
166            <span class="n">q</span> <span class="o">=</span> <span class="n">math</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">**</span><span class="mi">2</span> <span class="o">+</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span>
167            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_polymerexclvol</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
168        <span class="k">elif</span> <span class="n">x</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span> <span class="o">==</span> <span class="s">&#39;tuple&#39;</span><span class="p">:</span>
169            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">&quot;Tuples are not allowed as input to BaseComponent models&quot;</span>
170        <span class="k">else</span><span class="p">:</span>
171            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_polymerexclvol</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
172       
173
174   
175<span class="c"># End of file</span></div></div>
176</pre></div>
177
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203        <li class="right" style="margin-right: 10px">
204          <a href="../../../genindex.html" title="General Index"
205             >index</a></li>
206        <li class="right" >
207          <a href="../../../py-modindex.html" title="Python Module Index"
208             >modules</a> |</li>
209        <li><a href="../../../index.html">SasView 3.0.0 documentation</a> &raquo;</li>
210          <li><a href="../../index.html" >Module code</a> &raquo;</li>
211          <li><a href="../models.html" >sas.models</a> &raquo;</li> 
212      </ul>
213    </div>
214    <div class="footer">
215        &copy; Copyright 2013, The SasView Project.
216      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
217    </div>
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