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51  <h1>Source code for sas.models.StackedDisksModel</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/stacked_disks.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">CStackedDisksModel</span>
79
80<div class="viewcode-block" id="create_StackedDisksModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.create_StackedDisksModel">[docs]</a><span class="k">def</span> <span class="nf">create_StackedDisksModel</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">StackedDisksModel</span><span class="p">()</span>
85    <span class="c"># CStackedDisksModel.__init__(obj) is called by</span>
86    <span class="c"># the StackedDisksModel constructor</span>
87    <span class="k">return</span> <span class="n">obj</span>
88</div>
89<div class="viewcode-block" id="StackedDisksModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel">[docs]</a><span class="k">class</span> <span class="nc">StackedDisksModel</span><span class="p">(</span><span class="n">CStackedDisksModel</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 StackedDisksModel model. </span>
92<span class="sd">    This file was auto-generated from src/sas/models/include/stacked_disks.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           = 0.01 </span>
99<span class="sd">    * core_thick      = 10.0 [A]</span>
100<span class="sd">    * radius          = 3000.0 [A]</span>
101<span class="sd">    * layer_thick     = 15.0 [A]</span>
102<span class="sd">    * core_sld        = 4e-06 [1/A^(2)]</span>
103<span class="sd">    * layer_sld       = -4e-07 [1/A^(2)]</span>
104<span class="sd">    * solvent_sld     = 5e-06 [1/A^(2)]</span>
105<span class="sd">    * n_stacking      = 1.0 </span>
106<span class="sd">    * sigma_d         = 0.0 </span>
107<span class="sd">    * background      = 0.001 [1/cm]</span>
108<span class="sd">    * axis_theta      = 0.0 [rad]</span>
109<span class="sd">    * axis_phi        = 0.0 [rad]</span>
110
111<span class="sd">    &quot;&quot;&quot;</span>
112       
113    <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>
114        <span class="sd">&quot;&quot;&quot; Initialization &quot;&quot;&quot;</span>
115        <span class="bp">self</span><span class="o">.</span><span class="n">__dict__</span> <span class="o">=</span> <span class="p">{}</span>
116       
117        <span class="c"># Initialize BaseComponent first, then sphere</span>
118        <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>
119        <span class="c">#apply(CStackedDisksModel.__init__, (self,)) </span>
120
121        <span class="n">CStackedDisksModel</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
122        <span class="bp">self</span><span class="o">.</span><span class="n">is_multifunc</span> <span class="o">=</span> <span class="bp">False</span>
123                       
124        <span class="c">## Name of the model</span>
125        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;StackedDisksModel&quot;</span>
126        <span class="c">## Model description</span>
127        <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>
128<span class="s">         One layer of disk consists of a core, a top layer, and a bottom layer.</span>
129<span class="s">                radius =  the radius of the disk</span>
130<span class="s">                core_thick = thickness of the core</span>
131<span class="s">                layer_thick = thickness of a layer</span>
132<span class="s">                core_sld = the SLD of the core</span>
133<span class="s">                layer_sld = the SLD of the layers</span>
134<span class="s">                n_stacking = the number of the disks</span>
135<span class="s">                sigma_d =  Gaussian STD of d-spacing</span>
136<span class="s">                solvent_sld = the SLD of the solvent</span>
137<span class="s">        &quot;&quot;&quot;</span>
138       
139        <span class="c">## Parameter details [units, min, max]</span>
140        <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span>
141        <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>
142        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;core_thick&#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>
143        <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>
144        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;layer_thick&#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>
145        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;core_sld&#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>
146        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;layer_sld&#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>
147        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;solvent_sld&#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>
148        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;n_stacking&#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>
149        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;sigma_d&#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;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>
151        <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="s">&#39;axis_theta&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[rad]&#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;axis_phi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;[rad]&#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
154        <span class="c">## fittable parameters</span>
155        <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;core_thick.width&#39;</span><span class="p">,</span>
156                      <span class="s">&#39;layer_thick.width&#39;</span><span class="p">,</span>
157                      <span class="s">&#39;radius.width&#39;</span><span class="p">,</span>
158                      <span class="s">&#39;axis_theta.width&#39;</span><span class="p">,</span>
159                      <span class="s">&#39;axis_phi.width&#39;</span><span class="p">]</span>
160       
161        <span class="c">## non-fittable parameters</span>
162        <span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span> <span class="o">=</span> <span class="p">[]</span>
163       
164        <span class="c">## parameters with orientation</span>
165        <span class="bp">self</span><span class="o">.</span><span class="n">orientation_params</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;axis_phi&#39;</span><span class="p">,</span>
166                                   <span class="s">&#39;axis_theta&#39;</span><span class="p">,</span>
167                                   <span class="s">&#39;axis_phi.width&#39;</span><span class="p">,</span>
168                                   <span class="s">&#39;axis_theta.width&#39;</span><span class="p">]</span>
169
170        <span class="c">## parameters with magnetism</span>
171        <span class="bp">self</span><span class="o">.</span><span class="n">magnetic_params</span> <span class="o">=</span> <span class="p">[]</span>
172
173        <span class="bp">self</span><span class="o">.</span><span class="n">category</span> <span class="o">=</span> <span class="bp">None</span>
174        <span class="bp">self</span><span class="o">.</span><span class="n">multiplicity_info</span> <span class="o">=</span> <span class="bp">None</span>
175       
176    <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>
177        <span class="sd">&quot;&quot;&quot;</span>
178<span class="sd">        restore the state of a model from pickle</span>
179<span class="sd">        &quot;&quot;&quot;</span>
180        <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>
181       
182    <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>
183        <span class="sd">&quot;&quot;&quot;</span>
184<span class="sd">        Overwrite the __reduce_ex__ of PyTypeObject *type call in the init of </span>
185<span class="sd">        c model.</span>
186<span class="sd">        &quot;&quot;&quot;</span>
187        <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>
188        <span class="k">return</span> <span class="p">(</span><span class="n">create_StackedDisksModel</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>
189       
190<div class="viewcode-block" id="StackedDisksModel.clone"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel.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>
191        <span class="sd">&quot;&quot;&quot; Return a identical copy of self &quot;&quot;&quot;</span>
192        <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">StackedDisksModel</span><span class="p">())</span>   
193        </div>
194<div class="viewcode-block" id="StackedDisksModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel.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>
195        <span class="sd">&quot;&quot;&quot; </span>
196<span class="sd">        Evaluate the model</span>
197<span class="sd">        </span>
198<span class="sd">        :param x: input q, or [q,phi]</span>
199<span class="sd">        </span>
200<span class="sd">        :return: scattering function P(q)</span>
201<span class="sd">        </span>
202<span class="sd">        &quot;&quot;&quot;</span>
203        <span class="k">return</span> <span class="n">CStackedDisksModel</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>
204   </div>
205<div class="viewcode-block" id="StackedDisksModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel.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>
206        <span class="sd">&quot;&quot;&quot; </span>
207<span class="sd">        Evaluate the model in cartesian coordinates</span>
208<span class="sd">        </span>
209<span class="sd">        :param x: input q, or [qx, qy]</span>
210<span class="sd">        </span>
211<span class="sd">        :return: scattering function P(q)</span>
212<span class="sd">        </span>
213<span class="sd">        &quot;&quot;&quot;</span>
214        <span class="k">return</span> <span class="n">CStackedDisksModel</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>
215        </div>
216<div class="viewcode-block" id="StackedDisksModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel.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>
217        <span class="sd">&quot;&quot;&quot; </span>
218<span class="sd">        Evaluate the model in cartesian coordinates</span>
219<span class="sd">        </span>
220<span class="sd">        :param x: input q[], or [qx[], qy[]]</span>
221<span class="sd">        </span>
222<span class="sd">        :return: scattering function P(q[])</span>
223<span class="sd">        </span>
224<span class="sd">        &quot;&quot;&quot;</span>
225        <span class="k">return</span> <span class="n">CStackedDisksModel</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>
226        </div>
227<div class="viewcode-block" id="StackedDisksModel.calculate_ER"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel.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>
228        <span class="sd">&quot;&quot;&quot; </span>
229<span class="sd">        Calculate the effective radius for P(q)*S(q)</span>
230<span class="sd">        </span>
231<span class="sd">        :return: the value of the effective radius</span>
232<span class="sd">        </span>
233<span class="sd">        &quot;&quot;&quot;</span>       
234        <span class="k">return</span> <span class="n">CStackedDisksModel</span><span class="o">.</span><span class="n">calculate_ER</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
235        </div>
236<div class="viewcode-block" id="StackedDisksModel.calculate_VR"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel.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>
237        <span class="sd">&quot;&quot;&quot; </span>
238<span class="sd">        Calculate the volf ratio for P(q)*S(q)</span>
239<span class="sd">        </span>
240<span class="sd">        :return: the value of the volf ratio</span>
241<span class="sd">        </span>
242<span class="sd">        &quot;&quot;&quot;</span>       
243        <span class="k">return</span> <span class="n">CStackedDisksModel</span><span class="o">.</span><span class="n">calculate_VR</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
244              </div>
245<div class="viewcode-block" id="StackedDisksModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.StackedDisksModel.StackedDisksModel.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>
246        <span class="sd">&quot;&quot;&quot;</span>
247<span class="sd">        Set the dispersion object for a model parameter</span>
248<span class="sd">        </span>
249<span class="sd">        :param parameter: name of the parameter [string]</span>
250<span class="sd">        :param dispersion: dispersion object of type DispersionModel</span>
251<span class="sd">        </span>
252<span class="sd">        &quot;&quot;&quot;</span>
253        <span class="k">return</span> <span class="n">CStackedDisksModel</span><span class="o">.</span><span class="n">set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
254               <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>
255       
256   
257<span class="c"># End of file</span>
258</pre></div></div></div>
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