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51  <h1>Source code for sas.models.OnionExpShellModel</h1><div class="highlight"><pre>
52   
53<span class="kn">from</span> <span class="nn">sas.models.BaseComponent</span> <span class="kn">import</span> <span class="n">BaseComponent</span>
54<span class="kn">from</span> <span class="nn">sas.models.OnionModel</span> <span class="kn">import</span> <span class="n">OnionModel</span>
55<span class="kn">import</span> <span class="nn">copy</span>
56<span class="n">max_nshells</span> <span class="o">=</span> <span class="mi">10</span>
57<div class="viewcode-block" id="OnionExpShellModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.OnionExpShellModel.OnionExpShellModel">[docs]</a><span class="k">class</span> <span class="nc">OnionExpShellModel</span><span class="p">(</span><span class="n">BaseComponent</span><span class="p">):</span>
58    <span class="sd">&quot;&quot;&quot;</span>
59<span class="sd">    This multi-model is based on CoreMultiShellModel with exponential </span>
60<span class="sd">    func shells and provides the capability</span>
61<span class="sd">    of changing the number of shells between 1 and 10.</span>
62<span class="sd">    &quot;&quot;&quot;</span>
63    <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">n_shells</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
64        <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>
65        <span class="sd">&quot;&quot;&quot;</span>
66<span class="sd">        :param n_shells: number of shells in the model, </span>
67<span class="sd">        assumes 1&lt;= n_shells &lt;=10.</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">OnionModel</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;OnionExpShellModel&quot;</span>
75        <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>
76        <span class="bp">self</span><span class="o">.</span><span class="n">n_shells</span> <span class="o">=</span> <span class="n">n_shells</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">## dispersion</span>
84        <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span>
85        <span class="c">## Define parameters</span>
86        <span class="bp">self</span><span class="o">.</span><span class="n">_set_params</span><span class="p">()</span>
87       
88        <span class="c">## Parameter details [units, min, max]</span>
89        <span class="bp">self</span><span class="o">.</span><span class="n">_set_details</span><span class="p">()</span>
90       
91        <span class="c">#list of parameter that can be fitted</span>
92        <span class="bp">self</span><span class="o">.</span><span class="n">_set_fixed_params</span><span class="p">()</span> 
93        <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>
94        <span class="c">## functional multiplicity info of the model</span>
95        <span class="c"># [int(maximum no. of functionality),&quot;str(Titl),</span>
96        <span class="c"># [str(name of function0),...], [str(x-asix name of sld),...]]</span>
97        <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="s">&#39;Radius&#39;</span><span class="p">]]</span>
98
99        <span class="c">## parameters with orientation: can be removed since there is </span>
100        <span class="c"># no orientational params</span>
101        <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">orientation_params</span><span class="p">:</span>
102            <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">item</span><span class="p">)</span>
103        <span class="bp">self</span><span class="o">.</span><span class="n">getProfile</span><span class="p">()</span>       
104    <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>
105        <span class="sd">&quot;&quot;&quot;</span>
106<span class="sd">        Internal utility function to copy the internal</span>
107<span class="sd">        data members to a fresh copy.</span>
108<span class="sd">        &quot;&quot;&quot;</span>
109        <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>
110        <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>
111        <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>
112        <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>
113        <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>
114
115        <span class="k">return</span> <span class="n">obj</span>
116   
117   
118    <span class="k">def</span> <span class="nf">_set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
119        <span class="sd">&quot;&quot;&quot;</span>
120<span class="sd">        model dispersions</span>
121<span class="sd">        &quot;&quot;&quot;</span> 
122        <span class="c">##set dispersion from model </span>
123        <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>   
124             
125            <span class="n">nshell</span> <span class="o">=</span> <span class="mi">0</span>
126            <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>
127                <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>
128                    <span class="n">nshell</span> <span class="o">+=</span> <span class="mi">1</span>
129                    <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;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>
130                        <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>
131                    <span class="k">else</span><span class="p">:</span> 
132                        <span class="k">continue</span>
133            <span class="k">else</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                   
136
137    <span class="k">def</span> <span class="nf">_set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
138        <span class="sd">&quot;&quot;&quot;</span>
139<span class="sd">        Concatenate the parameters of the model to create</span>
140<span class="sd">        this model parameters </span>
141<span class="sd">        &quot;&quot;&quot;</span>
142        <span class="c"># rearrange the parameters for the given # of shells</span>
143        <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>
144            <span class="n">nshell</span> <span class="o">=</span> <span class="mi">0</span>
145            <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>
146            <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;func&#39;</span><span class="p">:</span>
147                <span class="k">continue</span>
148            <span class="k">elif</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><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;shell&#39;</span><span class="p">:</span>
149                    <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>
150                        <span class="n">nshell</span> <span class="o">+=</span> <span class="mi">1</span>
151                        <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="n">pos</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>
152                            <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>
153                            <span class="k">continue</span>
154            <span class="k">else</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               
157        <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>   
158
159        <span class="c"># set constrained values for the original model params</span>
160        <span class="bp">self</span><span class="o">.</span><span class="n">_set_xtra_model_param</span><span class="p">()</span>       
161 
162    <span class="k">def</span> <span class="nf">_set_details</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
163        <span class="sd">&quot;&quot;&quot;</span>
164<span class="sd">        Concatenate details of the original model to create</span>
165<span class="sd">        this model details </span>
166<span class="sd">        &quot;&quot;&quot;</span>
167        <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>
168            <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>
169                <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>
170           
171   
172    <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>
173        <span class="sd">&quot;&quot;&quot;</span>
174<span class="sd">        Set params of original model that are hidden from this model</span>
175<span class="sd">        &quot;&quot;&quot;</span>
176        <span class="c"># look for the model parameters that are not in param list</span>
177        <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>
178            <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>
179                <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>
180                    <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>
181                    <span class="k">continue</span>
182                <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;A&#39;</span><span class="p">:</span>
183                    <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>
184                    <span class="k">continue</span>
185                <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>
186                    <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">2</span><span class="p">)</span>
187                    <span class="k">continue</span>
188                <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>
189                    <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;sld_in_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>
190                        <span class="k">try</span><span class="p">:</span>
191                            <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>
192                            <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>
193                        <span class="k">except</span><span class="p">:</span> <span class="k">pass</span>
194<div class="viewcode-block" id="OnionExpShellModel.getProfile"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.OnionExpShellModel.OnionExpShellModel.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>
195        <span class="sd">&quot;&quot;&quot;</span>
196<span class="sd">        Get SLD profile </span>
197<span class="sd">        </span>
198<span class="sd">        : return: (r, beta) where r is a list of radius of the transition </span>
199<span class="sd">                points and  beta is a list of the corresponding SLD values </span>
200<span class="sd">        &quot;&quot;&quot;</span>
201        <span class="c"># max_pts for each shells</span>
202        <span class="n">max_pts</span> <span class="o">=</span> <span class="mi">10</span>
203        <span class="n">r</span> <span class="o">=</span> <span class="p">[]</span>
204        <span class="n">beta</span> <span class="o">=</span> <span class="p">[]</span>
205        <span class="c"># for core at r=0</span>
206        <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>
207        <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>
208        <span class="c"># for core at r=rad_core</span>
209        <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>
210        <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>
211       
212        <span class="c"># for shells</span>
213        <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>
214            <span class="c"># Left side of each shells</span>
215            <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>           
216            <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>
217            <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_in_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">n</span><span class="p">)])</span>
218           
219            <span class="n">A</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;A_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">n</span><span class="p">)]</span>
220            <span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">fabs</span>
221            <span class="k">if</span> <span class="n">fabs</span><span class="p">(</span><span class="n">A</span><span class="p">)</span> <span class="o">&lt;</span><span class="mf">1.0e-16</span><span class="p">:</span>
222                <span class="c"># Right side of each shells</span>
223                <span class="n">r0</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_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">n</span><span class="p">)]</span>
224                <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>
225                <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_in_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">n</span><span class="p">)])</span>
226            <span class="k">else</span><span class="p">:</span>
227                <span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">exp</span>
228                <span class="n">rn</span> <span class="o">=</span> <span class="n">r0</span>
229                <span class="k">for</span> <span class="n">n_sub</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">max_pts</span><span class="p">):</span>
230                    <span class="c"># Right side of each sub_shells</span>
231                    <span class="n">rn</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_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">n</span><span class="p">)]</span><span class="o">/</span><span class="mf">10.0</span>
232                    <span class="n">r</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rn</span><span class="p">)</span>
233                    <span class="n">slope</span> <span class="o">=</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_out_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">n</span><span class="p">)]</span> \
234                                    <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_in_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">n</span><span class="p">)])</span> \
235                                     <span class="o">/</span><span class="p">(</span><span class="n">exp</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;A_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">n</span><span class="p">)])</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span>
236                    <span class="n">const</span> <span class="o">=</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_in_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">n</span><span class="p">)]</span><span class="o">-</span><span class="n">slope</span><span class="p">)</span>
237                    <span class="n">beta_n</span> <span class="o">=</span> <span class="n">slope</span><span class="o">*</span><span class="n">exp</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;A_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">n</span><span class="p">)]</span><span class="o">*</span> \
238                        <span class="p">(</span><span class="n">rn</span><span class="o">-</span><span class="n">r0</span><span class="p">)</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_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">n</span><span class="p">)]))</span> <span class="o">+</span> <span class="n">const</span>
239                    <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">beta_n</span><span class="p">)</span>
240           
241        <span class="c"># for solvent</span>
242        <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>           
243        <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>
244        <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>
245        <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>
246        <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>
247        <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>
248       
249        <span class="k">return</span> <span class="n">r</span><span class="p">,</span> <span class="n">beta</span>
250    </div>
251<div class="viewcode-block" id="OnionExpShellModel.setParam"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.OnionExpShellModel.OnionExpShellModel.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>
252        <span class="sd">&quot;&quot;&quot; </span>
253<span class="sd">        Set the value of a model parameter</span>
254<span class="sd">    </span>
255<span class="sd">        : param name: name of the parameter</span>
256<span class="sd">        : param value: value of the parameter</span>
257<span class="sd">        &quot;&quot;&quot;</span>
258        <span class="c"># set param to new model</span>
259        <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>
260       
261        <span class="c">## setParam to model </span>
262        <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>
263            <span class="c"># the sld_*** model.params not in params must set to value </span>
264            <span class="c"># of sld_solv</span>
265            <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>
266                <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>
267                        <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>
268        <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>
269       </div>
270    <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>
271        <span class="sd">&quot;&quot;&quot;</span>
272<span class="sd">        Helper function to setParam</span>
273<span class="sd">        &quot;&quot;&quot;</span>
274        <span class="c">#look for dispersion parameters</span>
275        <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>
276        <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>
277            <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>
278                <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>
279                    <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>
280                        <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>
281                            <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>
282                            <span class="k">return</span>
283        <span class="c"># Look for standard parameter</span>
284        <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>
285            <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>
286                <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>
287                <span class="k">return</span>
288       
289        <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>
290             
291   
292    <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>
293        <span class="sd">&quot;&quot;&quot;</span>
294<span class="sd">        Fill the self.fixed list with the model fixed list</span>
295<span class="sd">        &quot;&quot;&quot;</span>
296        <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>
297            <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> 
298                <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>
299
300        <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>
301        <span class="k">pass</span>         
302               
303<div class="viewcode-block" id="OnionExpShellModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.OnionExpShellModel.OnionExpShellModel.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>
304        <span class="sd">&quot;&quot;&quot; </span>
305<span class="sd">        Evaluate the model</span>
306<span class="sd">        </span>
307<span class="sd">        : param x: input q-value (float or [float, float] as [r, theta])</span>
308<span class="sd">        : return: (I value)</span>
309<span class="sd">        &quot;&quot;&quot;</span>
310
311        <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>
312</div>
313<div class="viewcode-block" id="OnionExpShellModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.OnionExpShellModel.OnionExpShellModel.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>
314        <span class="sd">&quot;&quot;&quot; </span>
315<span class="sd">        Evaluate the model</span>
316<span class="sd">        </span>
317<span class="sd">        : param x: input q-value (float or [float, float] as [qx, qy])</span>
318<span class="sd">        : return: I value</span>
319<span class="sd">        &quot;&quot;&quot;</span> 
320
321        <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>
322   
323    <span class="c">## Now (May27,10) directly uses the model eval function </span>
324    <span class="c">## instead of the for-loop in Base Component.</span></div>
325<div class="viewcode-block" id="OnionExpShellModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.OnionExpShellModel.OnionExpShellModel.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>
326        <span class="sd">&quot;&quot;&quot; </span>
327<span class="sd">        Evaluate the model in cartesian coordinates</span>
328<span class="sd">        </span>
329<span class="sd">        : param x: input q[], or [qx[], qy[]]</span>
330<span class="sd">        : return: scattering function P(q[])</span>
331<span class="sd">        &quot;&quot;&quot;</span>
332        <span class="c"># set effective radius and scaling factor before run</span>
333        <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>
334</div>
335<div class="viewcode-block" id="OnionExpShellModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.OnionExpShellModel.OnionExpShellModel.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>
336        <span class="sd">&quot;&quot;&quot;</span>
337<span class="sd">        Set the dispersion object for a model parameter</span>
338<span class="sd">        </span>
339<span class="sd">        : param parameter: name of the parameter [string]</span>
340<span class="sd">        :dispersion: dispersion object of type DispersionModel</span>
341<span class="sd">        &quot;&quot;&quot;</span>
342        <span class="n">value</span><span class="o">=</span> <span class="bp">None</span>
343        <span class="k">try</span><span class="p">:</span>
344            <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>
345                <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>
346            <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span>
347            <span class="k">return</span> <span class="n">value</span>
348        <span class="k">except</span><span class="p">:</span>
349            <span class="k">raise</span> </div></div>
350</pre></div>
351
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