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51  <h1>Source code for sas.models.SphericalSLDModel</h1><div class="highlight"><pre>
52<span class="sd">&quot;&quot;&quot;</span>
53<span class="sd">    Spherical SLD model</span>
54<span class="sd">&quot;&quot;&quot;</span>
55<span class="kn">from</span> <span class="nn">sas.models.BaseComponent</span> <span class="kn">import</span> <span class="n">BaseComponent</span>
56<span class="kn">from</span> <span class="nn">sas.models.SphereSLDModel</span> <span class="kn">import</span> <span class="n">SphereSLDModel</span>
57<span class="kn">from</span> <span class="nn">copy</span> <span class="kn">import</span> <span class="n">deepcopy</span>
58<span class="n">func_list</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;Erf(|nu|*z)&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">,</span> <span class="s">&#39;RPower(z^|nu|)&#39;</span><span class="p">:</span><span class="mi">1</span><span class="p">,</span> <span class="s">&#39;LPower(z^|nu|)&#39;</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span> \
59                     <span class="s">&#39;RExp(-|nu|*z)&#39;</span><span class="p">:</span><span class="mi">3</span><span class="p">,</span> <span class="s">&#39;LExp(-|nu|*z)&#39;</span><span class="p">:</span><span class="mi">4</span><span class="p">}</span>
60<span class="n">max_nshells</span> <span class="o">=</span> <span class="mi">10</span>
61
62<div class="viewcode-block" id="SphericalSLDModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel">[docs]</a><span class="k">class</span> <span class="nc">SphericalSLDModel</span><span class="p">(</span><span class="n">BaseComponent</span><span class="p">):</span>
63    <span class="sd">&quot;&quot;&quot;</span>
64<span class="sd">    This multi-model is based on Parratt formalism and provides the capability</span>
65<span class="sd">    of changing the number of layers between 0 and 10.</span>
66<span class="sd">    &quot;&quot;&quot;</span>
67    <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>
68        <span class="sd">&quot;&quot;&quot;</span>
69<span class="sd">            :param multfactor: number of layers in the model, </span>
70<span class="sd">            assumes 0&lt;= n_shells &lt;=10.</span>
71<span class="sd">        &quot;&quot;&quot;</span>
72        <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>
73
74        <span class="c">## Setting  model name model description</span>
75        <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
76        <span class="n">model</span> <span class="o">=</span> <span class="n">SphereSLDModel</span><span class="p">()</span>
77        <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span>
78        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;SphericalSLDModel&quot;</span>
79        <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">description</span>
80        <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span> <span class="o">=</span> <span class="n">multfactor</span>
81        <span class="c">## Define parameters</span>
82        <span class="bp">self</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="p">{}</span>
83       
84        <span class="c">## Parameter details [units, min, max]</span>
85        <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span>
86       
87        <span class="c"># non-fittable parameters</span>
88        <span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">non_fittable</span>
89       
90        <span class="c"># list of function in order of the function number </span>
91        <span class="bp">self</span><span class="o">.</span><span class="n">fun_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_func_list</span><span class="p">()</span>
92        <span class="c">## dispersion</span>
93        <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span>
94        <span class="c">## Define parameters</span>
95        <span class="bp">self</span><span class="o">.</span><span class="n">_set_params</span><span class="p">()</span>
96       
97        <span class="c">## Parameter details [units, min, max]</span>
98        <span class="bp">self</span><span class="o">.</span><span class="n">_set_details</span><span class="p">()</span>
99       
100        <span class="c">#list of parameter that can be fitted</span>
101        <span class="bp">self</span><span class="o">.</span><span class="n">_set_fixed_params</span><span class="p">()</span> 
102        <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;n_shells&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span>
103       
104        <span class="c">## functional multiplicity info of the model</span>
105        <span class="c"># [int(maximum no. of functionality),&quot;str(Titl),</span>
106        <span class="c"># [str(name of function0),...], [str(x-asix name of sld),...]]</span>
107        <span class="bp">self</span><span class="o">.</span><span class="n">multiplicity_info</span> <span class="o">=</span> <span class="p">[</span><span class="n">max_nshells</span><span class="p">,</span> <span class="s">&quot;No. of Shells:&quot;</span><span class="p">,</span> <span class="p">[],</span> <span class="p">[</span><span class="s">&#39;Radius&#39;</span><span class="p">]]</span>
108       
109   
110    <span class="k">def</span> <span class="nf">_clone</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">):</span>
111        <span class="sd">&quot;&quot;&quot;</span>
112<span class="sd">        Internal utility function to copy the internal</span>
113<span class="sd">        data members to a fresh copy.</span>
114<span class="sd">        &quot;&quot;&quot;</span>
115        <span class="n">obj</span><span class="o">.</span><span class="n">params</span>     <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">)</span>
116        <span class="n">obj</span><span class="o">.</span><span class="n">non_fittable</span>     <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span><span class="p">)</span>
117        <span class="n">obj</span><span class="o">.</span><span class="n">description</span>     <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">description</span><span class="p">)</span>
118        <span class="n">obj</span><span class="o">.</span><span class="n">details</span>    <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">)</span>
119        <span class="n">obj</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">)</span>
120        <span class="n">obj</span><span class="o">.</span><span class="n">model</span>  <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">clone</span><span class="p">()</span>
121
122        <span class="k">return</span> <span class="n">obj</span>
123   
124   
125    <span class="k">def</span> <span class="nf">_set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
126        <span class="sd">&quot;&quot;&quot;</span>
127<span class="sd">        model dispersions</span>
128<span class="sd">        &quot;&quot;&quot;</span> 
129        <span class="c">##set dispersion from model </span>
130        <span class="k">for</span> <span class="n">name</span> <span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">dispersion</span><span class="o">.</span><span class="n">iteritems</span><span class="p">():</span>   
131             
132            <span class="n">nshell</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
133            <span class="k">if</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;thick&#39;</span><span class="p">:</span>
134                <span class="k">while</span> <span class="n">nshell</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">:</span>
135                    <span class="n">nshell</span> <span class="o">+=</span> <span class="mi">1</span>
136                    <span class="k">if</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">nshell</span><span class="p">):</span>
137                        <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
138                    <span class="k">else</span><span class="p">:</span> 
139                        <span class="k">continue</span>
140            <span class="k">else</span><span class="p">:</span>
141                <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
142
143    <span class="k">def</span> <span class="nf">_set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
144        <span class="sd">&quot;&quot;&quot;</span>
145<span class="sd">        Concatenate the parameters of the model to create</span>
146<span class="sd">        this model parameters </span>
147<span class="sd">        &quot;&quot;&quot;</span>
148        <span class="c"># rearrange the parameters for the given # of shells</span>
149        <span class="k">for</span> <span class="n">name</span> <span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iteritems</span><span class="p">():</span>
150            <span class="n">n</span> <span class="o">=</span> <span class="mi">0</span>
151            <span class="n">pos</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">))</span><span class="o">-</span><span class="mi">1</span>
152            <span class="n">first_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
153            <span class="n">last_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="n">pos</span><span class="p">]</span>
154            <span class="k">if</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">&#39;npts&#39;</span><span class="p">:</span>
155                <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
156                <span class="k">continue</span>
157            <span class="k">elif</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">&#39;func&#39;</span><span class="p">:</span>
158                <span class="n">n</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
159                <span class="k">while</span> <span class="n">n</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span><span class="p">:</span>
160                    <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span>
161                    <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">&#39;inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span> 
162                        <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
163                        <span class="k">continue</span>
164            <span class="k">elif</span> <span class="n">last_name</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">5</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;inter&#39;</span><span class="p">:</span>
165                <span class="n">n</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
166                <span class="k">while</span> <span class="n">n</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span><span class="p">:</span>
167                    <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span>
168                    <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">&#39;inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
169                        <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
170                        <span class="k">continue</span>
171            <span class="k">elif</span> <span class="n">last_name</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;flat&#39;</span><span class="p">:</span>
172                <span class="k">while</span> <span class="n">n</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span><span class="p">:</span>
173                    <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span>
174                    <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">&#39;flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
175                        <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
176                        <span class="k">continue</span>
177            <span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s">&#39;n_shells&#39;</span><span class="p">:</span>
178                <span class="k">continue</span>
179            <span class="k">else</span><span class="p">:</span>
180                <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
181 
182        <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;n_shells&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span>   
183 
184        <span class="c"># set constrained values for the original model params</span>
185        <span class="bp">self</span><span class="o">.</span><span class="n">_set_xtra_model_param</span><span class="p">()</span>       
186
187    <span class="k">def</span> <span class="nf">_set_details</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
188        <span class="sd">&quot;&quot;&quot;</span>
189<span class="sd">        Concatenate details of the original model to create</span>
190<span class="sd">        this model details </span>
191<span class="sd">        &quot;&quot;&quot;</span>
192        <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">detail</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">details</span><span class="o">.</span><span class="n">iteritems</span><span class="p">():</span>
193            <span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iterkeys</span><span class="p">():</span>
194                <span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">detail</span>
195           
196   
197    <span class="k">def</span> <span class="nf">_set_xtra_model_param</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
198        <span class="sd">&quot;&quot;&quot;</span>
199<span class="sd">        Set params of original model that are hidden from this model</span>
200<span class="sd">        &quot;&quot;&quot;</span>
201        <span class="c"># look for the model parameters that are not in param list</span>
202        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iterkeys</span><span class="p">():</span>
203            <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
204                <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;thick&#39;</span><span class="p">:</span>
205                    <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
206                    <span class="k">continue</span>
207                <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;func&#39;</span><span class="p">:</span> 
208                    <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
209                    <span class="k">continue</span>
210
211                <span class="k">for</span> <span class="n">nshell</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span><span class="p">,</span> <span class="n">max_nshells</span><span class="p">):</span>
212                    <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">nshell</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
213                        <span class="k">try</span><span class="p">:</span>
214                            <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;sld&#39;</span><span class="p">:</span>
215                                <span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;sld_solv&#39;</span><span class="p">]</span>
216                            <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
217                        <span class="k">except</span><span class="p">:</span>
218                            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="s">&quot;SphericalSLD model problem&quot;</span>
219   
220    <span class="k">def</span> <span class="nf">_get_func_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
221        <span class="sd">&quot;&quot;&quot;</span>
222<span class="sd">        Get the list of functions in each layer (shell) </span>
223<span class="sd">        &quot;&quot;&quot;</span>
224        <span class="k">return</span> <span class="n">func_list</span>
225       
226<div class="viewcode-block" id="SphericalSLDModel.getProfile"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel.getProfile">[docs]</a>    <span class="k">def</span> <span class="nf">getProfile</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">        Get SLD profile </span>
229<span class="sd">        </span>
230<span class="sd">        : return: (z, beta) where z is a list of depth of the transition points</span>
231<span class="sd">                beta is a list of the corresponding SLD values </span>
232<span class="sd">        &quot;&quot;&quot;</span>
233        <span class="c"># max_pts for each layers</span>
234        <span class="n">n_sub</span> <span class="o">=</span> <span class="nb">int</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="s">&#39;npts_inter&#39;</span><span class="p">])</span>
235        <span class="n">z</span> <span class="o">=</span> <span class="p">[]</span>
236        <span class="n">beta</span> <span class="o">=</span> <span class="p">[]</span>
237        <span class="n">z0</span> <span class="o">=</span> <span class="mi">0</span>
238        <span class="c"># two sld points for core</span>
239        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
240        <span class="n">beta</span><span class="o">.</span><span class="n">append</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="s">&#39;sld_core0&#39;</span><span class="p">])</span> 
241        <span class="n">z</span><span class="o">.</span><span class="n">append</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="s">&#39;rad_core0&#39;</span><span class="p">])</span> 
242        <span class="n">beta</span><span class="o">.</span><span class="n">append</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="s">&#39;sld_core0&#39;</span><span class="p">])</span> 
243        <span class="n">z0</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;rad_core0&#39;</span><span class="p">]</span>
244        <span class="c"># for layers from the core</span>
245        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span><span class="o">+</span><span class="mi">2</span><span class="p">):</span>
246            <span class="n">dz</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;thick_inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span><span class="o">/</span><span class="n">n_sub</span>
247            <span class="c"># j=0 for interface, j=1 for flat layer </span>
248            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">):</span>
249                <span class="c"># interation for sub-layers</span>
250                <span class="k">for</span> <span class="n">n_s</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n_sub</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
251                    <span class="k">if</span> <span class="n">j</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
252                        <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span>
253                            <span class="k">break</span>
254                        <span class="c"># shift half sub thickness for the first point</span>
255                        <span class="n">z0</span> <span class="o">-=</span> <span class="n">dz</span><span class="c">#/2.0</span>
256                        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span>
257                        <span class="c">#z0 -= dz/2.0</span>
258                        <span class="n">z0</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;thick_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span>
259                       
260                        <span class="n">sld_i</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;sld_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span>
261                        <span class="n">beta</span><span class="o">.</span><span class="n">append</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="s">&#39;sld_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)])</span>
262                        <span class="n">dz</span> <span class="o">=</span> <span class="mi">0</span>
263                    <span class="k">else</span><span class="p">:</span>
264                        <span class="n">nu</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;nu_inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span>
265                        <span class="c"># decide which sld is which, sld_r or sld_l</span>
266                        <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
267                            <span class="n">sld_l</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;sld_core0&#39;</span><span class="p">]</span>
268                        <span class="k">else</span><span class="p">:</span>
269                            <span class="n">sld_l</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;sld_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span>
270                        <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span>
271                            <span class="n">sld_r</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;sld_solv&#39;</span><span class="p">]</span>
272                        <span class="k">else</span><span class="p">:</span>
273                            <span class="n">sld_r</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;sld_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span>
274                        <span class="c"># get function type</span>
275                        <span class="n">func_idx</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;func_inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span>
276                        <span class="c"># calculate the sld</span>
277                        <span class="n">sld_i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_sld</span><span class="p">(</span><span class="n">func_idx</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">,</span> <span class="n">n_s</span><span class="p">,</span> <span class="n">nu</span><span class="p">,</span>
278                                              <span class="n">sld_l</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">)</span>
279                    <span class="c"># append to the list</span>
280                    <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span>
281                    <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_i</span><span class="p">)</span>
282                    <span class="n">z0</span> <span class="o">+=</span> <span class="n">dz</span>
283                    <span class="k">if</span> <span class="n">j</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
284                        <span class="k">break</span>
285        <span class="c"># put sld of solvent</span>
286        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span>
287        <span class="n">beta</span><span class="o">.</span><span class="n">append</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="s">&#39;sld_solv&#39;</span><span class="p">])</span> 
288        <span class="n">z_ext</span> <span class="o">=</span> <span class="n">z0</span><span class="o">/</span><span class="mf">5.0</span>
289        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="o">+</span><span class="n">z_ext</span><span class="p">)</span>
290        <span class="n">beta</span><span class="o">.</span><span class="n">append</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="s">&#39;sld_solv&#39;</span><span class="p">])</span> 
291        <span class="c"># return sld profile (r, beta)</span>
292        <span class="k">return</span> <span class="n">z</span><span class="p">,</span> <span class="n">beta</span>
293    </div>
294    <span class="k">def</span> <span class="nf">_get_sld</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func_idx</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">,</span> <span class="n">n_s</span><span class="p">,</span> <span class="n">nu</span><span class="p">,</span> <span class="n">sld_l</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">):</span>
295        <span class="sd">&quot;&quot;&quot;</span>
296<span class="sd">        Get the function asked to build sld profile</span>
297<span class="sd">        : param func_idx: func type number</span>
298<span class="sd">        : param n_sub: total number of sub_layer</span>
299<span class="sd">        : param n_s: index of sub_layer</span>
300<span class="sd">        : param nu: coefficient of the function</span>
301<span class="sd">        : param sld_l: sld on the left side</span>
302<span class="sd">        : param sld_r: sld on the right side</span>
303<span class="sd">        : return: sld value, float</span>
304<span class="sd">        &quot;&quot;&quot;</span>
305        <span class="kn">from</span> <span class="nn">sas.models.SLDCalFunc</span> <span class="kn">import</span> <span class="n">SLDCalFunc</span>
306        <span class="c"># sld_cal init</span>
307        <span class="n">sld_cal</span> <span class="o">=</span> <span class="n">SLDCalFunc</span><span class="p">()</span>
308        <span class="c"># set params</span>
309        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;fun_type&#39;</span><span class="p">,</span> <span class="n">func_idx</span><span class="p">)</span>
310        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;npts_inter&#39;</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">)</span>
311        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;shell_num&#39;</span><span class="p">,</span> <span class="n">n_s</span><span class="p">)</span>
312        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;nu_inter&#39;</span><span class="p">,</span> <span class="n">nu</span><span class="p">)</span>
313        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;sld_left&#39;</span><span class="p">,</span> <span class="n">sld_l</span><span class="p">)</span>
314        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;sld_right&#39;</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">)</span>
315        <span class="c"># return sld value</span>
316        <span class="k">return</span> <span class="n">sld_cal</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
317   
318<div class="viewcode-block" id="SphericalSLDModel.setParam"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel.setParam">[docs]</a>    <span class="k">def</span> <span class="nf">setParam</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
319        <span class="sd">&quot;&quot;&quot; </span>
320<span class="sd">        Set the value of a model parameter</span>
321<span class="sd">    </span>
322<span class="sd">        : param name: name of the parameter</span>
323<span class="sd">        : param value: value of the parameter</span>
324<span class="sd">        &quot;&quot;&quot;</span>
325        <span class="c"># set param to new model</span>
326        <span class="bp">self</span><span class="o">.</span><span class="n">_setParamHelper</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
327       
328        <span class="c">## setParam to model </span>
329        <span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s">&#39;sld_solv&#39;</span><span class="p">:</span>
330            <span class="c"># the sld_*** model.params not in params must set to </span>
331            <span class="c"># value of sld_solv</span>
332            <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">iterkeys</span><span class="p">():</span>
333                <span class="k">if</span> <span class="n">key</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span> <span class="ow">and</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;sld&#39;</span><span class="p">:</span>
334                    <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
335           
336        <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
337</div>
338    <span class="k">def</span> <span class="nf">_setParamHelper</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">value</span><span class="p">):</span>
339        <span class="sd">&quot;&quot;&quot;</span>
340<span class="sd">        Helper function to setParam</span>
341<span class="sd">        &quot;&quot;&quot;</span>
342        <span class="n">toks</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">)</span>
343        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">toks</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
344            <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
345                <span class="k">if</span> <span class="n">item</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="n">toks</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span>
346                    <span class="k">for</span> <span class="n">par</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">[</span><span class="n">item</span><span class="p">]:</span>
347                        <span class="k">if</span> <span class="n">par</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="n">toks</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span>
348                            <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">[</span><span class="n">item</span><span class="p">][</span><span class="n">par</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
349                            <span class="k">return</span>
350        <span class="c"># Look for standard parameter</span>
351        <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
352            <span class="k">if</span> <span class="n">item</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span>
353                <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="n">item</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span>
354                <span class="k">return</span>
355       
356        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="s">&quot;Model does not contain parameter </span><span class="si">%s</span><span class="s">&quot;</span> <span class="o">%</span> <span class="n">name</span>
357             
358   
359    <span class="k">def</span> <span class="nf">_set_fixed_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
360        <span class="sd">&quot;&quot;&quot;</span>
361<span class="sd">        Fill the self.fixed list with the model fixed list</span>
362<span class="sd">        &quot;&quot;&quot;</span>
363        <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">fixed</span><span class="p">:</span>
364            <span class="k">if</span> <span class="n">item</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;.&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span> 
365                <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
366
367        <span class="bp">self</span><span class="o">.</span><span class="n">fixed</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
368
369<div class="viewcode-block" id="SphericalSLDModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel.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>
370        <span class="sd">&quot;&quot;&quot; </span>
371<span class="sd">        Evaluate the model</span>
372<span class="sd">        </span>
373<span class="sd">        :param x: input q, or [q,phi]</span>
374<span class="sd">        </span>
375<span class="sd">        :return: scattering function P(q)</span>
376<span class="sd">        </span>
377<span class="sd">        &quot;&quot;&quot;</span>
378
379        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
380</div>
381<div class="viewcode-block" id="SphericalSLDModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel.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>
382        <span class="sd">&quot;&quot;&quot; </span>
383<span class="sd">        Evaluate the model</span>
384<span class="sd">        </span>
385<span class="sd">        : param x: input q-value (float or [float, float] as [qx, qy])</span>
386<span class="sd">        : return: scattering function value</span>
387<span class="sd">        &quot;&quot;&quot;</span> 
388
389        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">runXY</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
390   
391    <span class="c">## Now (May27,10) directly uses the model eval function </span>
392    <span class="c">## instead of the for-loop in Base Component.</span></div>
393<div class="viewcode-block" id="SphericalSLDModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel.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>
394        <span class="sd">&quot;&quot;&quot; </span>
395<span class="sd">        Evaluate the model in cartesian coordinates</span>
396<span class="sd">        </span>
397<span class="sd">        : param x: input q[], or [qx[], qy[]]</span>
398<span class="sd">        : return: scattering function P(q[])</span>
399<span class="sd">        &quot;&quot;&quot;</span>
400        <span class="c"># set effective radius and scaling factor before run</span>
401        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">evalDistribution</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
402    </div>
403<div class="viewcode-block" id="SphericalSLDModel.calculate_ER"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel.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>
404        <span class="sd">&quot;&quot;&quot;</span>
405<span class="sd">        &quot;&quot;&quot;</span>
406        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">calculate_ER</span><span class="p">()</span>
407    </div>
408<div class="viewcode-block" id="SphericalSLDModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.SphericalSLDModel.SphericalSLDModel.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>
409        <span class="sd">&quot;&quot;&quot;</span>
410<span class="sd">        Set the dispersion object for a model parameter</span>
411<span class="sd">        </span>
412<span class="sd">        : param parameter: name of the parameter [string]</span>
413<span class="sd">        :dispersion: dispersion object of type DispersionModel</span>
414<span class="sd">        &quot;&quot;&quot;</span>
415        <span class="n">value</span> <span class="o">=</span> <span class="bp">None</span>
416        <span class="k">if</span> <span class="n">parameter</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">dispersion</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
417            <span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">set_dispersion</span><span class="p">(</span><span class="n">parameter</span><span class="p">,</span> <span class="n">dispersion</span><span class="p">)</span>
418        <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span>
419        <span class="k">return</span> <span class="n">value</span></div></div>
420</pre></div>
421
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