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51  <h1>Source code for sas.models.LinearPearlsModel</h1><div class="highlight"><pre>
52<span class="c">##############################################################################</span>
53<span class="c"># This software was developed by the University of Tennessee as part of the</span>
54<span class="c"># Distributed Data Analysis of Neutron Scattering Experiments (DANSE)</span>
55<span class="c"># project funded by the US National Science Foundation.</span>
56<span class="c">#</span>
57<span class="c"># If you use DANSE applications to do scientific research that leads to</span>
58<span class="c"># publication, we ask that you acknowledge the use of the software with the</span>
59<span class="c"># following sentence:</span>
60<span class="c">#</span>
61<span class="c"># This work benefited from DANSE software developed under NSF award DMR-0520547</span>
62<span class="c">#</span>
63<span class="c"># Copyright 2008-2011, University of Tennessee</span>
64<span class="c">##############################################################################</span>
65
66<span class="sd">&quot;&quot;&quot; </span>
67<span class="sd">Provide functionality for a C extension model</span>
68
69<span class="sd">.. WARNING::</span>
70
71<span class="sd">   THIS FILE WAS GENERATED BY WRAPPERGENERATOR.PY</span>
72<span class="sd">   DO NOT MODIFY THIS FILE, MODIFY</span>
73<span class="sd">   src/sas/models/include/linearpearls.h</span>
74<span class="sd">   AND RE-RUN THE GENERATOR SCRIPT</span>
75<span class="sd">&quot;&quot;&quot;</span>
76
77<span class="kn">from</span> <span class="nn">sas.models.BaseComponent</span> <span class="kn">import</span> <span class="n">BaseComponent</span>
78<span class="kn">from</span> <span class="nn">sas.models.sas_extension.c_models</span> <span class="kn">import</span> <span class="n">CLinearPearlsModel</span>
79
80<div class="viewcode-block" id="create_LinearPearlsModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.create_LinearPearlsModel">[docs]</a><span class="k">def</span> <span class="nf">create_LinearPearlsModel</span><span class="p">():</span>
81    <span class="sd">&quot;&quot;&quot;</span>
82<span class="sd">       Create a model instance</span>
83<span class="sd">    &quot;&quot;&quot;</span>
84    <span class="n">obj</span> <span class="o">=</span> <span class="n">LinearPearlsModel</span><span class="p">()</span>
85    <span class="c"># CLinearPearlsModel.__init__(obj) is called by</span>
86    <span class="c"># the LinearPearlsModel constructor</span>
87    <span class="k">return</span> <span class="n">obj</span>
88</div>
89<div class="viewcode-block" id="LinearPearlsModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel">[docs]</a><span class="k">class</span> <span class="nc">LinearPearlsModel</span><span class="p">(</span><span class="n">CLinearPearlsModel</span><span class="p">,</span> <span class="n">BaseComponent</span><span class="p">):</span>
90    <span class="sd">&quot;&quot;&quot; </span>
91<span class="sd">    Class that evaluates a LinearPearlsModel model. </span>
92<span class="sd">    This file was auto-generated from src/sas/models/include/linearpearls.h.</span>
93<span class="sd">    Refer to that file and the structure it contains</span>
94<span class="sd">    for details of the model.</span>
95<span class="sd">    </span>
96<span class="sd">    List of default parameters:</span>
97
98<span class="sd">    * scale           = 1.0 </span>
99<span class="sd">    * radius          = 80.0 [A]</span>
100<span class="sd">    * edge_separation = 350.0 [A]</span>
101<span class="sd">    * num_pearls      = 3.0 </span>
102<span class="sd">    * sld_pearl       = 1e-06 [1/A^(2)]</span>
103<span class="sd">    * sld_solv        = 6.3e-06 [1/A^(2)]</span>
104<span class="sd">    * background      = 0.0 </span>
105<span class="sd">    * scale           = 1.0 </span>
106<span class="sd">    * radius          = 80.0 [A]</span>
107<span class="sd">    * edge_separation = 350.0 [A]</span>
108<span class="sd">    * num_pearls      = 3.0 </span>
109<span class="sd">    * sld_pearl       = 1e-06 [1/A^(2)]</span>
110<span class="sd">    * sld_solv        = 6.3e-06 [1/A^(2)]</span>
111<span class="sd">    * background      = 0.0 </span>
112
113<span class="sd">    &quot;&quot;&quot;</span>
114       
115    <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">multfactor</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
116        <span class="sd">&quot;&quot;&quot; Initialization &quot;&quot;&quot;</span>
117        <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span> <span class="o">=</span> <span class="p">{}</span>
118       
119        <span class="c"># Initialize BaseComponent first, then sphere</span>
120        <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>
121        <span class="c">#apply(CLinearPearlsModel.__init__, (self,)) </span>
122
123        <span class="n">CLinearPearlsModel</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
124        <span class="bp">self</span><span class="o">.</span><span class="n">is_multifunc</span> <span class="o">=</span> <span class="bp">False</span>
125                       
126        <span class="c">## Name of the model</span>
127        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;LinearPearlsModel&quot;</span>
128        <span class="c">## Model description</span>
129        <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="s">&quot;&quot;&quot;</span>
130<span class="s">        Calculate form factor for Pearl Necklace Model</span>
131<span class="s">                [Macromol. 1996, 29, 2974-2979]</span>
132<span class="s">                Parameters:</span>
133<span class="s">                background:background</span>
134<span class="s">                scale: scale factor</span>
135<span class="s">                sld_pearl: the SLD of the pearl spheres</span>
136<span class="s">                sld_solv: the SLD of the solvent</span>
137<span class="s">                num_pearls: number of the pearls</span>
138<span class="s">                radius: the radius of a pearl</span>
139<span class="s">                edge_separation: the length of string segment; surface to surface</span>
140<span class="s">        &quot;&quot;&quot;</span>
141       
142        <span class="c">## Parameter details [units, min, max]</span>
143        <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span>
144        <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>
145        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;radius&#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>
146        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;edge_separation&#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>
147        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;num_pearls&#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>
148        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;sld_pearl&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[1/A^(2)]&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
149        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;sld_solv&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[1/A^(2)]&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
150        <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;&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
151        <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>
152        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;radius&#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>
153        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;edge_separation&#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>
154        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;num_pearls&#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>
155        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;sld_pearl&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[1/A^(2)]&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
156        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;sld_solv&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[1/A^(2)]&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
157        <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;&#39;</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">]</span>
158
159        <span class="c">## fittable parameters</span>
160        <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;radius.width&#39;</span><span class="p">,</span>
161                      <span class="s">&#39;edge_separation.width&#39;</span><span class="p">]</span>
162       
163        <span class="c">## non-fittable parameters</span>
164        <span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span> <span class="o">=</span> <span class="p">[]</span>
165       
166        <span class="c">## parameters with orientation</span>
167        <span class="bp">self</span><span class="o">.</span><span class="n">orientation_params</span> <span class="o">=</span> <span class="p">[]</span>
168
169        <span class="c">## parameters with magnetism</span>
170        <span class="bp">self</span><span class="o">.</span><span class="n">magnetic_params</span> <span class="o">=</span> <span class="p">[]</span>
171
172        <span class="bp">self</span><span class="o">.</span><span class="n">category</span> <span class="o">=</span> <span class="bp">None</span>
173        <span class="bp">self</span><span class="o">.</span><span class="n">multiplicity_info</span> <span class="o">=</span> <span class="bp">None</span>
174       
175    <span class="k">def</span> <span class="nf">__setstate__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">state</span><span class="p">):</span>
176        <span class="sd">&quot;&quot;&quot;</span>
177<span class="sd">        restore the state of a model from pickle</span>
178<span class="sd">        &quot;&quot;&quot;</span>
179        <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="n">state</span>
180       
181    <span class="k">def</span> <span class="nf">__reduce_ex__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">proto</span><span class="p">):</span>
182        <span class="sd">&quot;&quot;&quot;</span>
183<span class="sd">        Overwrite the __reduce_ex__ of PyTypeObject *type call in the init of </span>
184<span class="sd">        c model.</span>
185<span class="sd">        &quot;&quot;&quot;</span>
186        <span class="n">state</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">)</span>
187        <span class="k">return</span> <span class="p">(</span><span class="n">create_LinearPearlsModel</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(),</span> <span class="n">state</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
188       
189<div class="viewcode-block" id="LinearPearlsModel.clone"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel.clone">[docs]</a>    <span class="k">def</span> <span class="nf">clone</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
190        <span class="sd">&quot;&quot;&quot; Return a identical copy of self &quot;&quot;&quot;</span>
191        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_clone</span><span class="p">(</span><span class="n">LinearPearlsModel</span><span class="p">())</span>   
192        </div>
193<div class="viewcode-block" id="LinearPearlsModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel.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>
194        <span class="sd">&quot;&quot;&quot; </span>
195<span class="sd">        Evaluate the model</span>
196<span class="sd">        </span>
197<span class="sd">        :param x: input q, or [q,phi]</span>
198<span class="sd">        </span>
199<span class="sd">        :return: scattering function P(q)</span>
200<span class="sd">        </span>
201<span class="sd">        &quot;&quot;&quot;</span>
202        <span class="k">return</span> <span class="n">CLinearPearlsModel</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
203   </div>
204<div class="viewcode-block" id="LinearPearlsModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel.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>
205        <span class="sd">&quot;&quot;&quot; </span>
206<span class="sd">        Evaluate the model in cartesian coordinates</span>
207<span class="sd">        </span>
208<span class="sd">        :param x: input q, or [qx, qy]</span>
209<span class="sd">        </span>
210<span class="sd">        :return: scattering function P(q)</span>
211<span class="sd">        </span>
212<span class="sd">        &quot;&quot;&quot;</span>
213        <span class="k">return</span> <span class="n">CLinearPearlsModel</span><span class="o">.</span><span class="n">runXY</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
214        </div>
215<div class="viewcode-block" id="LinearPearlsModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel.evalDistribution">[docs]</a>    <span class="k">def</span> <span class="nf">evalDistribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
216        <span class="sd">&quot;&quot;&quot; </span>
217<span class="sd">        Evaluate the model in cartesian coordinates</span>
218<span class="sd">        </span>
219<span class="sd">        :param x: input q[], or [qx[], qy[]]</span>
220<span class="sd">        </span>
221<span class="sd">        :return: scattering function P(q[])</span>
222<span class="sd">        </span>
223<span class="sd">        &quot;&quot;&quot;</span>
224        <span class="k">return</span> <span class="n">CLinearPearlsModel</span><span class="o">.</span><span class="n">evalDistribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
225        </div>
226<div class="viewcode-block" id="LinearPearlsModel.calculate_ER"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel.calculate_ER">[docs]</a>    <span class="k">def</span> <span class="nf">calculate_ER</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
227        <span class="sd">&quot;&quot;&quot; </span>
228<span class="sd">        Calculate the effective radius for P(q)*S(q)</span>
229<span class="sd">        </span>
230<span class="sd">        :return: the value of the effective radius</span>
231<span class="sd">        </span>
232<span class="sd">        &quot;&quot;&quot;</span>       
233        <span class="k">return</span> <span class="n">CLinearPearlsModel</span><span class="o">.</span><span class="n">calculate_ER</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
234        </div>
235<div class="viewcode-block" id="LinearPearlsModel.calculate_VR"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel.calculate_VR">[docs]</a>    <span class="k">def</span> <span class="nf">calculate_VR</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
236        <span class="sd">&quot;&quot;&quot; </span>
237<span class="sd">        Calculate the volf ratio for P(q)*S(q)</span>
238<span class="sd">        </span>
239<span class="sd">        :return: the value of the volf ratio</span>
240<span class="sd">        </span>
241<span class="sd">        &quot;&quot;&quot;</span>       
242        <span class="k">return</span> <span class="n">CLinearPearlsModel</span><span class="o">.</span><span class="n">calculate_VR</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
243              </div>
244<div class="viewcode-block" id="LinearPearlsModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LinearPearlsModel.LinearPearlsModel.set_dispersion">[docs]</a>    <span class="k">def</span> <span class="nf">set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parameter</span><span class="p">,</span> <span class="n">dispersion</span><span class="p">):</span>
245        <span class="sd">&quot;&quot;&quot;</span>
246<span class="sd">        Set the dispersion object for a model parameter</span>
247<span class="sd">        </span>
248<span class="sd">        :param parameter: name of the parameter [string]</span>
249<span class="sd">        :param dispersion: dispersion object of type DispersionModel</span>
250<span class="sd">        </span>
251<span class="sd">        &quot;&quot;&quot;</span>
252        <span class="k">return</span> <span class="n">CLinearPearlsModel</span><span class="o">.</span><span class="n">set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
253               <span class="n">parameter</span><span class="p">,</span> <span class="n">dispersion</span><span class="o">.</span><span class="n">cdisp</span><span class="p">)</span>
254       
255   
256<span class="c"># End of file</span>
257</pre></div></div></div>
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