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51  <h1>Source code for sas.models.LamellarPSHGModel</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/lamellarPS_HG.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">CLamellarPSHGModel</span>
79
80<div class="viewcode-block" id="create_LamellarPSHGModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.create_LamellarPSHGModel">[docs]</a><span class="k">def</span> <span class="nf">create_LamellarPSHGModel</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">LamellarPSHGModel</span><span class="p">()</span>
85    <span class="c"># CLamellarPSHGModel.__init__(obj) is called by</span>
86    <span class="c"># the LamellarPSHGModel constructor</span>
87    <span class="k">return</span> <span class="n">obj</span>
88</div>
89<div class="viewcode-block" id="LamellarPSHGModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel">[docs]</a><span class="k">class</span> <span class="nc">LamellarPSHGModel</span><span class="p">(</span><span class="n">CLamellarPSHGModel</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 LamellarPSHGModel model. </span>
92<span class="sd">    This file was auto-generated from src/sas/models/include/lamellarPS_HG.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">    * spacing         = 40.0 [A]</span>
100<span class="sd">    * deltaT          = 10.0 [A]</span>
101<span class="sd">    * deltaH          = 2.0 [A]</span>
102<span class="sd">    * sld_tail        = 4e-07 [1/A^(2)]</span>
103<span class="sd">    * sld_head        = 2e-06 [1/A^(2)]</span>
104<span class="sd">    * sld_solvent     = 6e-06 [1/A^(2)]</span>
105<span class="sd">    * n_plates        = 30.0 </span>
106<span class="sd">    * caille          = 0.001 </span>
107<span class="sd">    * background      = 0.001 [1/cm]</span>
108
109<span class="sd">    &quot;&quot;&quot;</span>
110       
111    <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>
112        <span class="sd">&quot;&quot;&quot; Initialization &quot;&quot;&quot;</span>
113        <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span> <span class="o">=</span> <span class="p">{}</span>
114       
115        <span class="c"># Initialize BaseComponent first, then sphere</span>
116        <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>
117        <span class="c">#apply(CLamellarPSHGModel.__init__, (self,)) </span>
118
119        <span class="n">CLamellarPSHGModel</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
120        <span class="bp">self</span><span class="o">.</span><span class="n">is_multifunc</span> <span class="o">=</span> <span class="bp">False</span>
121                       
122        <span class="c">## Name of the model</span>
123        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;LamellarPSHGModel&quot;</span>
124        <span class="c">## Model description</span>
125        <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>
126<span class="s">        [Concentrated Lamellar (head+tail) Form Factor]: Calculates the</span>
127<span class="s">                intensity from a lyotropic lamellar phase.</span>
128<span class="s">                The intensity (form factor and structure factor)</span>
129<span class="s">                calculated is for lamellae of two-layer scattering</span>
130<span class="s">                length density that are randomly distributed in</span>
131<span class="s">                solution (a powder average). The scattering</span>
132<span class="s">                length density of the tail region, headgroup</span>
133<span class="s">                region, and solvent are taken to be different.</span>
134<span class="s">                The model can also be applied to large,</span>
135<span class="s">                multi-lamellar vesicles.</span>
136<span class="s">                No resolution smeared version is included</span>
137<span class="s">                in the structure factor of this model.</span>
138<span class="s">                *Parameters: spacing = repeat spacing,</span>
139<span class="s">                deltaT = tail length,</span>
140<span class="s">                deltaH = headgroup thickness,</span>
141<span class="s">                n_plates = # of Lamellar plates</span>
142<span class="s">                caille = Caille parameter (&lt;0.8 or &lt;1)</span>
143<span class="s">                background = incoherent bgd</span>
144<span class="s">                scale = scale factor ...</span>
145<span class="s">        &quot;&quot;&quot;</span>
146       
147        <span class="c">## Parameter details [units, min, max]</span>
148        <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</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;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>
150        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;spacing&#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>
151        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;deltaT&#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>
152        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;deltaH&#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;sld_tail&#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>
154        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;sld_head&#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>
155        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;sld_solvent&#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;n_plates&#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>
157        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;caille&#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        <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>
159
160        <span class="c">## fittable parameters</span>
161        <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;deltaT.width&#39;</span><span class="p">,</span>
162                      <span class="s">&#39;deltaH.width&#39;</span><span class="p">,</span>
163                      <span class="s">&#39;spacing.width&#39;</span><span class="p">]</span>
164       
165        <span class="c">## non-fittable parameters</span>
166        <span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span> <span class="o">=</span> <span class="p">[]</span>
167       
168        <span class="c">## parameters with orientation</span>
169        <span class="bp">self</span><span class="o">.</span><span class="n">orientation_params</span> <span class="o">=</span> <span class="p">[]</span>
170
171        <span class="c">## parameters with magnetism</span>
172        <span class="bp">self</span><span class="o">.</span><span class="n">magnetic_params</span> <span class="o">=</span> <span class="p">[]</span>
173
174        <span class="bp">self</span><span class="o">.</span><span class="n">category</span> <span class="o">=</span> <span class="bp">None</span>
175        <span class="bp">self</span><span class="o">.</span><span class="n">multiplicity_info</span> <span class="o">=</span> <span class="bp">None</span>
176       
177    <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>
178        <span class="sd">&quot;&quot;&quot;</span>
179<span class="sd">        restore the state of a model from pickle</span>
180<span class="sd">        &quot;&quot;&quot;</span>
181        <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>
182       
183    <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>
184        <span class="sd">&quot;&quot;&quot;</span>
185<span class="sd">        Overwrite the __reduce_ex__ of PyTypeObject *type call in the init of </span>
186<span class="sd">        c model.</span>
187<span class="sd">        &quot;&quot;&quot;</span>
188        <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>
189        <span class="k">return</span> <span class="p">(</span><span class="n">create_LamellarPSHGModel</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>
190       
191<div class="viewcode-block" id="LamellarPSHGModel.clone"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel.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>
192        <span class="sd">&quot;&quot;&quot; Return a identical copy of self &quot;&quot;&quot;</span>
193        <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">LamellarPSHGModel</span><span class="p">())</span>   
194        </div>
195<div class="viewcode-block" id="LamellarPSHGModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel.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>
196        <span class="sd">&quot;&quot;&quot; </span>
197<span class="sd">        Evaluate the model</span>
198<span class="sd">        </span>
199<span class="sd">        :param x: input q, or [q,phi]</span>
200<span class="sd">        </span>
201<span class="sd">        :return: scattering function P(q)</span>
202<span class="sd">        </span>
203<span class="sd">        &quot;&quot;&quot;</span>
204        <span class="k">return</span> <span class="n">CLamellarPSHGModel</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>
205   </div>
206<div class="viewcode-block" id="LamellarPSHGModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel.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>
207        <span class="sd">&quot;&quot;&quot; </span>
208<span class="sd">        Evaluate the model in cartesian coordinates</span>
209<span class="sd">        </span>
210<span class="sd">        :param x: input q, or [qx, qy]</span>
211<span class="sd">        </span>
212<span class="sd">        :return: scattering function P(q)</span>
213<span class="sd">        </span>
214<span class="sd">        &quot;&quot;&quot;</span>
215        <span class="k">return</span> <span class="n">CLamellarPSHGModel</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>
216        </div>
217<div class="viewcode-block" id="LamellarPSHGModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel.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>
218        <span class="sd">&quot;&quot;&quot; </span>
219<span class="sd">        Evaluate the model in cartesian coordinates</span>
220<span class="sd">        </span>
221<span class="sd">        :param x: input q[], or [qx[], qy[]]</span>
222<span class="sd">        </span>
223<span class="sd">        :return: scattering function P(q[])</span>
224<span class="sd">        </span>
225<span class="sd">        &quot;&quot;&quot;</span>
226        <span class="k">return</span> <span class="n">CLamellarPSHGModel</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>
227        </div>
228<div class="viewcode-block" id="LamellarPSHGModel.calculate_ER"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel.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>
229        <span class="sd">&quot;&quot;&quot; </span>
230<span class="sd">        Calculate the effective radius for P(q)*S(q)</span>
231<span class="sd">        </span>
232<span class="sd">        :return: the value of the effective radius</span>
233<span class="sd">        </span>
234<span class="sd">        &quot;&quot;&quot;</span>       
235        <span class="k">return</span> <span class="n">CLamellarPSHGModel</span><span class="o">.</span><span class="n">calculate_ER</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
236        </div>
237<div class="viewcode-block" id="LamellarPSHGModel.calculate_VR"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel.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>
238        <span class="sd">&quot;&quot;&quot; </span>
239<span class="sd">        Calculate the volf ratio for P(q)*S(q)</span>
240<span class="sd">        </span>
241<span class="sd">        :return: the value of the volf ratio</span>
242<span class="sd">        </span>
243<span class="sd">        &quot;&quot;&quot;</span>       
244        <span class="k">return</span> <span class="n">CLamellarPSHGModel</span><span class="o">.</span><span class="n">calculate_VR</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
245              </div>
246<div class="viewcode-block" id="LamellarPSHGModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.LamellarPSHGModel.LamellarPSHGModel.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>
247        <span class="sd">&quot;&quot;&quot;</span>
248<span class="sd">        Set the dispersion object for a model parameter</span>
249<span class="sd">        </span>
250<span class="sd">        :param parameter: name of the parameter [string]</span>
251<span class="sd">        :param dispersion: dispersion object of type DispersionModel</span>
252<span class="sd">        </span>
253<span class="sd">        &quot;&quot;&quot;</span>
254        <span class="k">return</span> <span class="n">CLamellarPSHGModel</span><span class="o">.</span><span class="n">set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
255               <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>
256       
257   
258<span class="c"># End of file</span>
259</pre></div></div></div>
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