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51  <h1>Source code for sas.models.CoreMultiShellModel</h1><div class="highlight"><pre>
52<span class="sd">&quot;&quot;&quot;</span>
53<span class="sd">    Core-Multi-Shell 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.CoreFourShellModel</span> <span class="kn">import</span> <span class="n">CoreFourShellModel</span>
57<span class="kn">import</span> <span class="nn">copy</span>
58<span class="n">max_nshells</span> <span class="o">=</span> <span class="mi">5</span>
59<div class="viewcode-block" id="CoreMultiShellModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel">[docs]</a><span class="k">class</span> <span class="nc">CoreMultiShellModel</span><span class="p">(</span><span class="n">BaseComponent</span><span class="p">):</span>
60    <span class="sd">&quot;&quot;&quot;</span>
61<span class="sd">    This multi-model is based on CoreFourShellModel and provides the capability</span>
62<span class="sd">    of changing the number of shells between 1 and 4.</span>
63<span class="sd">    &quot;&quot;&quot;</span>
64    <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>
65        <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>
66        <span class="sd">&quot;&quot;&quot;</span>
67<span class="sd">        :param n_shells: number of shells in the model, assumes 1&lt;= n_shells &lt;=4.</span>
68<span class="sd">        &quot;&quot;&quot;</span>
69
70        <span class="c">## Setting  model name model description</span>
71        <span class="bp">self</span><span class="o">.</span><span class="n">description</span><span class="o">=</span><span class="s">&quot;&quot;</span>
72        <span class="n">model</span> <span class="o">=</span> <span class="n">CoreFourShellModel</span><span class="p">()</span>
73        <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span>
74        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;CoreMultiShellModel&quot;</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="bp">self</span><span class="o">.</span><span class="n">n_shells</span> <span class="o">=</span> <span class="n">multfactor</span>
77        <span class="c">## Define parameters</span>
78        <span class="bp">self</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="p">{}</span>
79
80        <span class="c">## Parameter details [units, min, max]</span>
81        <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span>
82       
83        <span class="c"># non-fittable parameters</span>
84        <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>
85       
86        <span class="c">## dispersion</span>
87        <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span>
88        <span class="c">## Define parameters</span>
89        <span class="bp">self</span><span class="o">.</span><span class="n">_set_params</span><span class="p">()</span>
90       
91        <span class="c">## Parameter details [units, min, max]</span>
92        <span class="bp">self</span><span class="o">.</span><span class="n">_set_details</span><span class="p">()</span>
93       
94        <span class="c">#list of parameter that can be fitted</span>
95        <span class="bp">self</span><span class="o">.</span><span class="n">_set_fixed_params</span><span class="p">()</span> 
96        <span class="bp">self</span><span class="o">.</span><span class="n">orientation_params</span> <span class="o">=</span> <span class="p">[]</span>
97        <span class="bp">self</span><span class="o">.</span><span class="n">magnetic_params</span> <span class="o">=</span> <span class="p">[]</span>
98       
99        <span class="c">## functional multiplicity info of the model</span>
100        <span class="c"># [int(maximum no. of functionality),&quot;str(Titl),</span>
101        <span class="c"># [str(name of function0),...], [str(x-asix name of sld),...]]</span>
102        <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>
103
104        <span class="c">## parameters with orientation: can be removed since there is no orientational params</span>
105        <span class="bp">self</span><span class="o">.</span><span class="n">_set_orientation_params</span><span class="p">()</span>
106               
107       
108    <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>
109        <span class="sd">&quot;&quot;&quot;</span>
110<span class="sd">        Internal utility function to copy the internal</span>
111<span class="sd">        data members to a fresh copy.</span>
112<span class="sd">        &quot;&quot;&quot;</span>
113        <span class="n">obj</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="n">copy</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>
114        <span class="n">obj</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="n">copy</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>
115        <span class="n">obj</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="n">copy</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>
116        <span class="n">obj</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="n">copy</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>
117        <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>
118
119        <span class="k">return</span> <span class="n">obj</span>
120   
121   
122    <span class="k">def</span> <span class="nf">_set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
123        <span class="sd">&quot;&quot;&quot;</span>
124<span class="sd">        model dispersions</span>
125<span class="sd">        Polydispersion should not be applied to s_model</span>
126<span class="sd">        &quot;&quot;&quot;</span> 
127        <span class="c">##set dispersion from model </span>
128        <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>     
129            <span class="n">nshell</span> <span class="o">=</span> <span class="mi">0</span>
130            <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="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">&#39;thick&#39;</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
131                <span class="k">while</span> <span class="n">nshell</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>
132                    <span class="n">nshell</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="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;shell</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>
134                        <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>
135                    <span class="k">else</span><span class="p">:</span> 
136                        <span class="k">continue</span>
137            <span class="k">else</span><span class="p">:</span>
138                <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>
139               
140    <span class="k">def</span> <span class="nf">_set_orientation_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
141        <span class="sd">&quot;&quot;&quot;</span>
142<span class="sd">        model orientation and magnetic parameters, same params for this model</span>
143<span class="sd">        &quot;&quot;&quot;</span> 
144        <span class="c">##set dispersion from model </span>
145        <span class="k">for</span> <span class="n">param</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">orientation_params</span><span class="p">:</span>     
146            <span class="n">nshell</span> <span class="o">=</span> <span class="mi">0</span>
147            <span class="k">if</span> <span class="n">param</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><span class="p">]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">&#39;shell&#39;</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">:</span>
148                <span class="c">#print &quot;param&quot;, param, param.split(&#39;_&#39;)[-1].count(&#39;shell&#39;)</span>
149                <span class="bp">self</span><span class="o">.</span><span class="n">orientation_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
150                <span class="bp">self</span><span class="o">.</span><span class="n">magnetic_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
151                <span class="k">continue</span>
152            <span class="k">while</span> <span class="n">nshell</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>
153                <span class="n">nshell</span> <span class="o">+=</span> <span class="mi">1</span>
154                <span class="k">if</span> <span class="n">param</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><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;shell</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>
155                    <span class="bp">self</span><span class="o">.</span><span class="n">orientation_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
156                    <span class="bp">self</span><span class="o">.</span><span class="n">magnetic_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
157                    <span class="k">continue</span>                           
158
159    <span class="k">def</span> <span class="nf">_set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
160        <span class="sd">&quot;&quot;&quot;</span>
161<span class="sd">        Concatenate the parameters of the model to create</span>
162<span class="sd">        this model parameters </span>
163<span class="sd">        &quot;&quot;&quot;</span>
164        <span class="c"># rearrange the parameters for the given # of shells</span>
165        <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>
166            <span class="n">nshell</span> <span class="o">=</span> <span class="mi">0</span>
167            <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="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">&#39;thick&#39;</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">or</span> \
168                        <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="n">count</span><span class="p">(</span><span class="s">&#39;sld&#39;</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">or</span> \
169                        <span class="n">name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;M&#39;</span><span class="p">:</span>
170                <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="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;solv&#39;</span> <span class="ow">or</span> \
171                        <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><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;core0&#39;</span><span class="p">:</span>
172                    <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>
173                    <span class="k">continue</span>
174                <span class="k">while</span> <span class="n">nshell</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>
175                    <span class="n">nshell</span> <span class="o">+=</span> <span class="mi">1</span>
176                    <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="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;shell</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>
177                        <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>
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="c"># set constrained values for the original model params</span>
183        <span class="bp">self</span><span class="o">.</span><span class="n">_set_xtra_model_param</span><span class="p">()</span>       
184 
185    <span class="k">def</span> <span class="nf">_set_details</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
186        <span class="sd">&quot;&quot;&quot;</span>
187<span class="sd">        Concatenate details of the original model to create</span>
188<span class="sd">        this model details </span>
189<span class="sd">        &quot;&quot;&quot;</span>
190        <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>
191            <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>
192                <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>
193           
194   
195    <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>
196        <span class="sd">&quot;&quot;&quot;</span>
197<span class="sd">        Set params of original model that are hidden from this model</span>
198<span class="sd">        &quot;&quot;&quot;</span>
199        <span class="c"># look for the model parameters that are not in param list</span>
200        <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>
201            <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>
202                <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="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">&#39;thick&#39;</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
203                    <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>
204                    <span class="k">continue</span>
205
206                <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>
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="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">&#39;sld&#39;</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span> <span class="ow">and</span> \
208                            <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="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;shell</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>
209                        <span class="k">try</span><span class="p">:</span>
210                            <span class="k">if</span> <span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">&#39;M&#39;</span><span class="p">:</span>
211                                <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>
212                                <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>
213                            <span class="k">else</span><span class="p">:</span>
214                                <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="mf">0.0</span><span class="p">)</span>
215                        <span class="k">except</span><span class="p">:</span> <span class="k">pass</span>
216                     
217
218<div class="viewcode-block" id="CoreMultiShellModel.getProfile"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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>
219        <span class="sd">&quot;&quot;&quot;</span>
220<span class="sd">        Get SLD profile </span>
221<span class="sd">        </span>
222<span class="sd">        : return: (r, beta) where r is a list of radius of the transition points</span>
223<span class="sd">                beta is a list of the corresponding SLD values </span>
224<span class="sd">        : Note: This works only for func_shell# = 2.</span>
225<span class="sd">        &quot;&quot;&quot;</span>
226        <span class="n">r</span> <span class="o">=</span> <span class="p">[]</span>
227        <span class="n">beta</span> <span class="o">=</span> <span class="p">[]</span>
228        <span class="c"># for core at r=0</span>
229        <span class="n">r</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
230        <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>
231        <span class="c"># for core at r=rad_core</span>
232        <span class="n">r</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>
233        <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>
234       
235        <span class="c"># for shells</span>
236        <span class="k">for</span> <span class="n">n</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">1</span><span class="p">):</span>
237            <span class="c"># Left side of each shells</span>
238            <span class="n">r0</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>           
239            <span class="n">r</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">r0</span><span class="p">)</span>
240            <span class="k">exec</span> <span class="s">&quot;beta.append(self.params[&#39;sld_shell</span><span class="si">%s</span><span class="s">&#39;</span><span class="si">% s</span><span class="s">tr(n)])&quot;</span>
241
242            <span class="c"># Right side of each shells</span>
243            <span class="k">exec</span> <span class="s">&quot;r0 += self.params[&#39;thick_shell</span><span class="si">%s</span><span class="s">&#39;</span><span class="si">% s</span><span class="s">tr(n)]&quot;</span>
244            <span class="n">r</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">r0</span><span class="p">)</span>
245            <span class="k">exec</span> <span class="s">&quot;beta.append(self.params[&#39;sld_shell</span><span class="si">%s</span><span class="s">&#39;</span><span class="si">% s</span><span class="s">tr(n)])&quot;</span>
246           
247        <span class="c"># for solvent</span>
248        <span class="n">r0</span> <span class="o">=</span> <span class="n">r</span><span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">r</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>           
249        <span class="n">r</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">r0</span><span class="p">)</span>
250        <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>
251        <span class="n">r_solv</span> <span class="o">=</span> <span class="mi">5</span><span class="o">*</span><span class="n">r0</span><span class="o">/</span><span class="mi">4</span>
252        <span class="n">r</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">r_solv</span><span class="p">)</span>
253        <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>
254       
255        <span class="k">return</span> <span class="n">r</span><span class="p">,</span> <span class="n">beta</span>
256</div>
257<div class="viewcode-block" id="CoreMultiShellModel.setParam"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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>
258        <span class="sd">&quot;&quot;&quot; </span>
259<span class="sd">        Set the value of a model parameter</span>
260<span class="sd">    </span>
261<span class="sd">        : param name: name of the parameter</span>
262<span class="sd">        : param value: value of the parameter</span>
263<span class="sd">        &quot;&quot;&quot;</span>
264        <span class="c"># set param to new model</span>
265        <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>
266        <span class="c">## setParam to model </span>
267        <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>
268            <span class="c"># the sld_*** model.params not in params must set to value of sld_solv</span>
269            <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>
270                <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>
271                    <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>
272                        <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>
273                    <span class="k">elif</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;sld&#39;</span><span class="p">:</span>
274                        <span class="c"># mag params</span>
275                        <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="mf">0.0</span><span class="p">)</span>
276        <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>
277</div>
278    <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>
279        <span class="sd">&quot;&quot;&quot;</span>
280<span class="sd">        Helper function to setParam</span>
281<span class="sd">        &quot;&quot;&quot;</span>
282        <span class="c">#look for dispersion parameters</span>
283        <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>
284        <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>
285            <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>
286                <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>
287                    <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>
288                        <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>
289                            <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>
290                            <span class="k">return</span>
291        <span class="c"># Look for standard parameter</span>
292        <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>
293            <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>
294                <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>
295                <span class="k">return</span>
296       
297        <span class="c">#raise ValueError, &quot;Model does not contain parameter %s&quot; % name</span>
298             
299   
300    <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>
301        <span class="sd">&quot;&quot;&quot;</span>
302<span class="sd">        Fill the self.fixed list with the model fixed list</span>
303<span class="sd">        &quot;&quot;&quot;</span>
304        <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>
305            <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> 
306                <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>
307
308        <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>
309               
310<div class="viewcode-block" id="CoreMultiShellModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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>
311        <span class="sd">&quot;&quot;&quot; </span>
312<span class="sd">        Evaluate the model</span>
313<span class="sd">        </span>
314<span class="sd">        : param x: input q-value (float or [float, float] as [r, theta])</span>
315<span class="sd">        : return: (DAB value)</span>
316<span class="sd">        &quot;&quot;&quot;</span>
317        <span class="c"># set effective radius and scaling factor before run</span>
318
319        <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>
320</div>
321<div class="viewcode-block" id="CoreMultiShellModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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>
322        <span class="sd">&quot;&quot;&quot; </span>
323<span class="sd">        Evaluate the model</span>
324<span class="sd">        </span>
325<span class="sd">        : param x: input q-value (float or [float, float] as [qx, qy])</span>
326<span class="sd">        : return: DAB value</span>
327<span class="sd">        &quot;&quot;&quot;</span> 
328        <span class="c"># set effective radius and scaling factor before run</span>
329
330        <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>
331   
332    <span class="c">## Now (May27,10) directly uses the model eval function </span>
333    <span class="c">## instead of the for-loop in Base Component.</span></div>
334<div class="viewcode-block" id="CoreMultiShellModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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="o">=</span> <span class="p">[]):</span>
335        <span class="sd">&quot;&quot;&quot; </span>
336<span class="sd">        Evaluate the model in cartesian coordinates</span>
337<span class="sd">        </span>
338<span class="sd">        : param x: input q[], or [qx[], qy[]]</span>
339<span class="sd">        : return: scattering function P(q[])</span>
340<span class="sd">        &quot;&quot;&quot;</span>
341        <span class="c"># set effective radius and scaling factor before run</span>
342        <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>
343    </div>
344<div class="viewcode-block" id="CoreMultiShellModel.calculate_ER"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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>
345        <span class="sd">&quot;&quot;&quot; </span>
346<span class="sd">        Calculate the effective radius for P(q)*S(q)</span>
347<span class="sd">        </span>
348<span class="sd">        :return: the value of the effective radius</span>
349<span class="sd">        </span>
350<span class="sd">        &quot;&quot;&quot;</span>       
351        <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> 
352    </div>
353<div class="viewcode-block" id="CoreMultiShellModel.calculate_VR"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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>
354        <span class="sd">&quot;&quot;&quot; </span>
355<span class="sd">        Calculate the volf ratio for P(q)*S(q)</span>
356<span class="sd">        </span>
357<span class="sd">        :return: the value of the volf ratio</span>
358<span class="sd">        </span>
359<span class="sd">        &quot;&quot;&quot;</span>       
360        <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_VR</span><span class="p">()</span>
361    </div>
362<div class="viewcode-block" id="CoreMultiShellModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.CoreMultiShellModel.CoreMultiShellModel.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>
363        <span class="sd">&quot;&quot;&quot;</span>
364<span class="sd">        Set the dispersion object for a model parameter</span>
365<span class="sd">        </span>
366<span class="sd">        : param parameter: name of the parameter [string]</span>
367<span class="sd">        :dispersion: dispersion object of type DispersionModel</span>
368<span class="sd">        &quot;&quot;&quot;</span>
369        <span class="n">value</span> <span class="o">=</span> <span class="bp">None</span>
370        <span class="k">try</span><span class="p">:</span>
371            <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>
372                <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>
373            <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span>
374            <span class="k">return</span> <span class="n">value</span>
375        <span class="k">except</span><span class="p">:</span>
376            <span class="k">raise</span> </div></div>
377</pre></div>
378
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