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51  <h1>Source code for sas.models.ReflectivityIIModel</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.ReflAdvModel</span> <span class="kn">import</span> <span class="n">ReflAdvModel</span>
55<span class="kn">from</span> <span class="nn">copy</span> <span class="kn">import</span> <span class="n">deepcopy</span>
56<span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">floor</span>
57<span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">fabs</span>
58<span class="n">func_list</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;Erf(|nu|*z)&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">,</span> <span class="s">&#39;RPower(z^|nu|)&#39;</span><span class="p">:</span><span class="mi">1</span><span class="p">,</span> <span class="s">&#39;LPower(z^|nu|)&#39;</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span> \
59                     <span class="s">&#39;RExp(-|nu|*z)&#39;</span><span class="p">:</span><span class="mi">3</span><span class="p">,</span> <span class="s">&#39;LExp(-|nu|*z)&#39;</span><span class="p">:</span><span class="mi">4</span><span class="p">}</span>
60<span class="n">max_nshells</span> <span class="o">=</span> <span class="mi">10</span>
61<div class="viewcode-block" id="ReflectivityIIModel"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel">[docs]</a><span class="k">class</span> <span class="nc">ReflectivityIIModel</span><span class="p">(</span><span class="n">BaseComponent</span><span class="p">):</span>
62    <span class="sd">&quot;&quot;&quot;</span>
63<span class="sd">    This multi-model is based on Parratt formalism and provides the capability</span>
64<span class="sd">    of changing the number of layers between 0 and 10.</span>
65<span class="sd">    &quot;&quot;&quot;</span>
66    <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>
67        <span class="sd">&quot;&quot;&quot;</span>
68<span class="sd">            :param multfactor: number of layers in the model, </span>
69<span class="sd">            assumes 0&lt;= n_layers &lt;=10.</span>
70<span class="sd">        &quot;&quot;&quot;</span>
71        <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>
72
73        <span class="c">## Setting  model name model description</span>
74        <span class="bp">self</span><span class="o">.</span><span class="n">description</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
75        <span class="n">model</span> <span class="o">=</span> <span class="n">ReflAdvModel</span><span class="p">()</span>
76        <span class="bp">self</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">model</span>
77        <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s">&quot;ReflectivityIIModel&quot;</span>
78        <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>
79        <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">multfactor</span><span class="p">)</span>
80        <span class="c">## Define parameters</span>
81        <span class="bp">self</span><span class="o">.</span><span class="n">params</span> <span class="o">=</span> <span class="p">{}</span>
82       
83        <span class="c">## Parameter details [units, min, max]</span>
84        <span class="bp">self</span><span class="o">.</span><span class="n">details</span> <span class="o">=</span> <span class="p">{}</span>
85       
86        <span class="c"># non-fittable parameters</span>
87        <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>
88       
89        <span class="c"># list of function in order of the function number </span>
90        <span class="bp">self</span><span class="o">.</span><span class="n">fun_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_func_list</span><span class="p">()</span>
91        <span class="c">## dispersion</span>
92        <span class="bp">self</span><span class="o">.</span><span class="n">_set_dispersion</span><span class="p">()</span>
93        <span class="c">## Define parameters</span>
94        <span class="bp">self</span><span class="o">.</span><span class="n">_set_params</span><span class="p">()</span>
95       
96        <span class="c">## Parameter details [units, min, max]</span>
97        <span class="bp">self</span><span class="o">.</span><span class="n">_set_details</span><span class="p">()</span>
98       
99        <span class="c">#list of parameter that can be fitted</span>
100        <span class="bp">self</span><span class="o">.</span><span class="n">_set_fixed_params</span><span class="p">()</span> 
101        <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_layers&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span>
102       
103        <span class="c">## functional multiplicity info of the model</span>
104        <span class="c"># [int(maximum no. of functionality),&quot;str(Titl),</span>
105        <span class="c"># [str(name of function0),...], [str(x-asix name of sld),...]]</span>
106        <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 Layers:&quot;</span><span class="p">,</span> <span class="p">[],</span> <span class="p">[</span><span class="s">&#39;Depth&#39;</span><span class="p">]]</span>
107        <span class="c">## independent parameter name and unit [string]</span>
108        <span class="bp">self</span><span class="o">.</span><span class="n">input_name</span> <span class="o">=</span> <span class="s">&quot;Q&quot;</span>
109        <span class="bp">self</span><span class="o">.</span><span class="n">input_unit</span> <span class="o">=</span> <span class="s">&quot;A^{-1}&quot;</span>
110        <span class="c">## output name and unit  [string]</span>
111        <span class="bp">self</span><span class="o">.</span><span class="n">output_name</span> <span class="o">=</span> <span class="s">&quot;Reflectivity&quot;</span>
112        <span class="bp">self</span><span class="o">.</span><span class="n">output_unit</span> <span class="o">=</span> <span class="s">&quot;&quot;</span>
113   
114   
115    <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>
116        <span class="sd">&quot;&quot;&quot;</span>
117<span class="sd">        Internal utility function to copy the internal</span>
118<span class="sd">        data members to a fresh copy.</span>
119<span class="sd">        &quot;&quot;&quot;</span>
120        <span class="n">obj</span><span class="o">.</span><span class="n">params</span>     <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">)</span>
121        <span class="n">obj</span><span class="o">.</span><span class="n">non_fittable</span>     <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">non_fittable</span><span class="p">)</span>
122        <span class="n">obj</span><span class="o">.</span><span class="n">description</span>     <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">description</span><span class="p">)</span>
123        <span class="n">obj</span><span class="o">.</span><span class="n">details</span>    <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">details</span><span class="p">)</span>
124        <span class="n">obj</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span><span class="p">)</span>
125        <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>
126
127        <span class="k">return</span> <span class="n">obj</span>
128   
129   
130    <span class="k">def</span> <span class="nf">_set_dispersion</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
131        <span class="sd">&quot;&quot;&quot;</span>
132<span class="sd">        model dispersions</span>
133<span class="sd">        &quot;&quot;&quot;</span> 
134        <span class="c">##set dispersion from model </span>
135        <span class="bp">self</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="p">{}</span>
136                   
137
138    <span class="k">def</span> <span class="nf">_set_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
139        <span class="sd">&quot;&quot;&quot;</span>
140<span class="sd">        Concatenate the parameters of the model to create</span>
141<span class="sd">        this model parameters </span>
142<span class="sd">        &quot;&quot;&quot;</span>
143        <span class="c"># rearrange the parameters for the given # of shells</span>
144        <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>
145            <span class="n">n</span> <span class="o">=</span> <span class="mi">0</span>
146            <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>
147            <span class="n">first_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
148            <span class="n">last_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="n">pos</span><span class="p">]</span>
149            <span class="k">if</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">&#39;npts&#39;</span><span class="p">:</span>
150                <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>
151                <span class="k">continue</span>
152            <span class="k">elif</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">&#39;sldIM&#39;</span><span class="p">:</span>
153                <span class="k">continue</span>
154            <span class="k">elif</span> <span class="n">first_name</span> <span class="o">==</span> <span class="s">&#39;func&#39;</span><span class="p">:</span>
155                <span class="n">n</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
156                <span class="k">while</span> <span class="n">n</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="p">:</span>
157                    <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span>
158                    <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">&#39;inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span> 
159                        <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>
160                        <span class="k">continue</span>
161           
162                <span class="c">#continue</span>
163            <span class="k">elif</span> <span class="n">last_name</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">5</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;inter&#39;</span><span class="p">:</span>
164                <span class="n">n</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
165                <span class="k">while</span> <span class="n">n</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="p">:</span>
166                    <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span>
167                    <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">&#39;inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
168                        <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>
169                        <span class="k">continue</span>
170            <span class="k">elif</span> <span class="n">last_name</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">4</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;flat&#39;</span><span class="p">:</span>
171                <span class="k">while</span> <span class="n">n</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="p">:</span>
172                    <span class="n">n</span> <span class="o">+=</span> <span class="mi">1</span>
173                    <span class="k">if</span> <span class="n">last_name</span> <span class="o">==</span> <span class="s">&#39;flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="p">):</span>
174                        <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>
175                        <span class="k">continue</span>
176            <span class="k">elif</span> <span class="n">name</span> <span class="o">==</span> <span class="s">&#39;n_layers&#39;</span><span class="p">:</span>
177                <span class="k">continue</span>
178            <span class="k">else</span><span class="p">:</span>
179                <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>
180 
181        <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_layers&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span>   
182 
183        <span class="c"># set constrained values for the original model params</span>
184        <span class="bp">self</span><span class="o">.</span><span class="n">_set_xtra_model_param</span><span class="p">()</span>       
185
186    <span class="k">def</span> <span class="nf">_set_details</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
187        <span class="sd">&quot;&quot;&quot;</span>
188<span class="sd">        Concatenate details of the original model to create</span>
189<span class="sd">        this model details </span>
190<span class="sd">        &quot;&quot;&quot;</span>
191        <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>
192            <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>
193                <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>
194           
195   
196    <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>
197        <span class="sd">&quot;&quot;&quot;</span>
198<span class="sd">        Set params of original model that are hidden from this model</span>
199<span class="sd">        &quot;&quot;&quot;</span>
200        <span class="c"># look for the model parameters that are not in param list</span>
201        <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>
202            <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>
203                <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>
204                    <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>
205                    <span class="k">continue</span>
206                <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> 
207                    <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>
208                    <span class="k">continue</span>
209
210                <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_layers</span><span class="p">,</span><span class="n">max_nshells</span><span class="p">):</span>
211                    <span class="k">if</span> <span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;_&#39;</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">nshell</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
212                        <span class="k">try</span><span class="p">:</span>
213                            <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>
214                                <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_medium&#39;</span><span class="p">]</span>
215                            <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">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;sldIM&#39;</span><span class="p">:</span>
216                                <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;sldIM_medium&#39;</span><span class="p">]</span>
217                            <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>
218                        <span class="k">except</span><span class="p">:</span>
219                            <span class="n">message</span> <span class="o">=</span> <span class="s">&quot;ReflectivityIIModel evaluation problem&quot;</span>
220                            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">message</span>
221   
222    <span class="k">def</span> <span class="nf">_get_func_list</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
223        <span class="sd">&quot;&quot;&quot;</span>
224<span class="sd">            Get the list of functions in each layer (shell) </span>
225<span class="sd">        &quot;&quot;&quot;</span>
226        <span class="k">return</span> <span class="n">func_list</span>
227       
228<div class="viewcode-block" id="ReflectivityIIModel.getProfile"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.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>
229        <span class="sd">&quot;&quot;&quot;</span>
230<span class="sd">        Get SLD profile </span>
231<span class="sd">        </span>
232<span class="sd">        : return: (z, beta) where z is a list of depth of the transition points</span>
233<span class="sd">                beta is a list of the corresponding SLD values </span>
234<span class="sd">        &quot;&quot;&quot;</span>
235        <span class="c"># max_pts for each layers</span>
236        <span class="n">n_sub</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;npts_inter&#39;</span><span class="p">])</span>
237        <span class="n">z</span> <span class="o">=</span> <span class="p">[]</span>
238        <span class="n">beta</span> <span class="o">=</span> <span class="p">[]</span>
239        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
240        <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;sld_bottom0&#39;</span><span class="p">])</span> 
241       
242        <span class="n">z0</span> <span class="o">=</span> <span class="mf">0.0</span>
243        <span class="n">dz</span> <span class="o">=</span> <span class="mf">0.0</span>
244        <span class="c"># for layers from the top</span>
245        <span class="k">for</span> <span class="n">n_lyr</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_layers</span><span class="o">+</span><span class="mi">2</span><span class="p">):</span>
246            <span class="n">i</span> <span class="o">=</span> <span class="n">n_lyr</span>
247            <span class="c"># j=0 for interface, j=1 for flat layer </span>
248            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">):</span>
249                <span class="c"># interation for sub-layers</span>
250                <span class="k">for</span> <span class="n">n_s</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">):</span>
251                    <span class="c"># for flat layer</span>
252                    <span class="k">if</span> <span class="n">j</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
253                        <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span>
254                            <span class="k">break</span>
255                        <span class="c"># shift half sub thickness for the first point</span>
256                        <span class="n">z0</span> <span class="o">-=</span> <span class="n">dz</span><span class="o">/</span><span class="mf">2.0</span>
257                        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span>
258                        <span class="n">sld_i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;sld_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span>
259                        <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_i</span><span class="p">)</span>
260                        <span class="n">dz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;thick_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span>
261                        <span class="n">z0</span> <span class="o">+=</span> <span class="n">dz</span>
262                    <span class="k">else</span><span class="p">:</span>
263                        <span class="n">dz</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;thick_inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span><span class="o">/</span><span class="n">n_sub</span>
264                        <span class="n">nu</span> <span class="o">=</span> <span class="n">fabs</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;nu_inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)])</span>
265                        <span class="k">if</span> <span class="n">n_s</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
266                            <span class="c"># shift half sub thickness for the point</span>
267                            <span class="n">z0</span> <span class="o">+=</span> <span class="n">dz</span><span class="o">/</span><span class="mf">2.0</span>
268                        <span class="c"># decide which sld is which, sld_r or sld_l</span>
269                        <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
270                            <span class="n">sld_l</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;sld_bottom0&#39;</span><span class="p">]</span>
271                        <span class="k">else</span><span class="p">:</span>
272                            <span class="n">sld_l</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;sld_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span>
273                        <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">n_layers</span><span class="o">+</span><span class="mi">1</span><span class="p">:</span>
274                            <span class="n">sld_r</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;sld_medium&#39;</span><span class="p">]</span>
275                        <span class="k">else</span><span class="p">:</span>
276                            <span class="n">sld_r</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;sld_flat</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)]</span>
277                        <span class="k">if</span> <span class="n">sld_r</span> <span class="o">==</span> <span class="n">sld_l</span><span class="p">:</span>
278                            <span class="n">sld_i</span> <span class="o">=</span> <span class="n">sld_r</span>
279                        <span class="k">else</span><span class="p">:</span>
280                            <span class="n">func_idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="s">&#39;func_inter</span><span class="si">%s</span><span class="s">&#39;</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">)]</span>
281                            <span class="c"># calculate the sld</span>
282                            <span class="n">sld_i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_sld</span><span class="p">(</span><span class="n">func_idx</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">,</span> <span class="n">n_s</span><span class="o">+</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">nu</span><span class="p">,</span>
283                                              <span class="n">sld_l</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">)</span>
284                    <span class="c"># append to the list</span>
285                    <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span>
286                    <span class="n">beta</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">sld_i</span><span class="p">)</span>
287                    <span class="k">if</span> <span class="n">j</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> 
288                        <span class="k">break</span>
289                    <span class="k">else</span><span class="p">:</span> 
290                        <span class="n">z0</span> <span class="o">+=</span> <span class="n">dz</span>
291        <span class="c"># put substrate and superstrate profile</span>
292        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="p">)</span>
293        <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_medium&#39;</span><span class="p">])</span> 
294        <span class="n">z_ext</span> <span class="o">=</span> <span class="n">z0</span><span class="o">/</span><span class="mf">5.0</span>
295       
296        <span class="c"># put the extra points for the substrate </span>
297        <span class="c"># and superstrate</span>
298        <span class="n">z</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">z0</span><span class="o">+</span><span class="n">z_ext</span><span class="p">)</span>
299        <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_medium&#39;</span><span class="p">])</span> 
300        <span class="n">z</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="n">z_ext</span><span class="p">)</span>
301        <span class="n">beta</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</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_bottom0&#39;</span><span class="p">])</span> 
302        <span class="c"># rearrange the profile for NR sld profile style</span>
303        <span class="n">z</span> <span class="o">=</span> <span class="p">[</span><span class="n">z0</span> <span class="o">-</span> <span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">z</span><span class="p">]</span>
304        <span class="n">z</span><span class="o">.</span><span class="n">reverse</span><span class="p">()</span>
305        <span class="n">beta</span><span class="o">.</span><span class="n">reverse</span><span class="p">()</span> 
306        <span class="k">return</span> <span class="n">z</span><span class="p">,</span> <span class="n">beta</span>
307    </div>
308    <span class="k">def</span> <span class="nf">_get_sld</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func_idx</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">,</span> <span class="n">n_s</span><span class="p">,</span> <span class="n">nu</span><span class="p">,</span> <span class="n">sld_l</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">):</span>
309        <span class="sd">&quot;&quot;&quot;</span>
310<span class="sd">        Get the function asked to build sld profile</span>
311<span class="sd">        : param func_idx: func type number</span>
312<span class="sd">        : param n_sub: total number of sub_layer</span>
313<span class="sd">        : param n_s: index of sub_layer</span>
314<span class="sd">        : param nu: coefficient of the function</span>
315<span class="sd">        : param sld_l: sld on the left side</span>
316<span class="sd">        : param sld_r: sld on the right side</span>
317<span class="sd">        : return: sld value, float</span>
318<span class="sd">        &quot;&quot;&quot;</span>
319        <span class="kn">from</span> <span class="nn">sas.models.SLDCalFunc</span> <span class="kn">import</span> <span class="n">SLDCalFunc</span>
320        <span class="c"># sld_cal init</span>
321        <span class="n">sld_cal</span> <span class="o">=</span> <span class="n">SLDCalFunc</span><span class="p">()</span>
322        <span class="c"># set params</span>
323        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;fun_type&#39;</span><span class="p">,</span> <span class="n">func_idx</span><span class="p">)</span>
324        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;npts_inter&#39;</span><span class="p">,</span> <span class="n">n_sub</span><span class="p">)</span>
325        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;shell_num&#39;</span><span class="p">,</span> <span class="n">n_s</span><span class="p">)</span>
326        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;nu_inter&#39;</span><span class="p">,</span> <span class="n">nu</span><span class="p">)</span>
327        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;sld_left&#39;</span><span class="p">,</span> <span class="n">sld_l</span><span class="p">)</span>
328        <span class="n">sld_cal</span><span class="o">.</span><span class="n">setParam</span><span class="p">(</span><span class="s">&#39;sld_right&#39;</span><span class="p">,</span> <span class="n">sld_r</span><span class="p">)</span>
329        <span class="c"># return sld value</span>
330        <span class="k">return</span> <span class="n">sld_cal</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
331   
332<div class="viewcode-block" id="ReflectivityIIModel.setParam"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.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>
333        <span class="sd">&quot;&quot;&quot; </span>
334<span class="sd">        Set the value of a model parameter</span>
335<span class="sd">    </span>
336<span class="sd">        : param name: name of the parameter</span>
337<span class="sd">        : param value: value of the parameter</span>
338<span class="sd">        &quot;&quot;&quot;</span>
339        <span class="c"># set param to new model</span>
340        <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>
341       
342        <span class="c">## setParam to model </span>
343        <span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s">&#39;sld_medium&#39;</span><span class="p">:</span>
344            <span class="c"># the sld_*** model.params not in params must set </span>
345            <span class="c"># to value of sld_solv</span>
346            <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>
347                <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>
348                    <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>   
349       
350        <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>
351</div>
352    <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>
353        <span class="sd">&quot;&quot;&quot;</span>
354<span class="sd">        Helper function to setParam</span>
355<span class="sd">        &quot;&quot;&quot;</span>
356
357        <span class="c"># Look for standard parameter</span>
358        <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>
359            <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>
360                <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>
361                <span class="k">return</span>
362       
363        <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>
364             
365   
366    <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>
367        <span class="sd">&quot;&quot;&quot;</span>
368<span class="sd">        Fill the self.fixed list with the model fixed list</span>
369<span class="sd">        &quot;&quot;&quot;</span>
370        <span class="k">pass</span>         
371
372<div class="viewcode-block" id="ReflectivityIIModel.run"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.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>
373        <span class="sd">&quot;&quot;&quot; </span>
374<span class="sd">        Evaluate the model</span>
375<span class="sd">        </span>
376<span class="sd">        :param x: input q, or [q,phi]</span>
377<span class="sd">        </span>
378<span class="sd">        :return: scattering function P(q)</span>
379<span class="sd">        </span>
380<span class="sd">        &quot;&quot;&quot;</span>
381
382        <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>
383</div>
384<div class="viewcode-block" id="ReflectivityIIModel.runXY"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.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>
385        <span class="sd">&quot;&quot;&quot; </span>
386<span class="sd">        Evaluate the model</span>
387<span class="sd">        </span>
388<span class="sd">        : param x: input q-value (float or [float, float] as [qx, qy])</span>
389<span class="sd">        : return: scattering function value</span>
390<span class="sd">        &quot;&quot;&quot;</span> 
391
392        <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>
393   
394    <span class="c">## Now (May27,10) directly uses the model eval function </span>
395    <span class="c">## instead of the for-loop in Base Component.</span></div>
396<div class="viewcode-block" id="ReflectivityIIModel.evalDistribution"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.evalDistribution">[docs]</a>    <span class="k">def</span> <span class="nf">evalDistribution</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">x</span><span class="p">):</span>
397        <span class="sd">&quot;&quot;&quot; </span>
398<span class="sd">        Evaluate the model in cartesian coordinates</span>
399<span class="sd">        </span>
400<span class="sd">        : param x: input q[], or [qx[], qy[]]</span>
401<span class="sd">        : return: scattering function P(q[])</span>
402<span class="sd">        &quot;&quot;&quot;</span>
403        <span class="c"># set effective radius and scaling factor before run</span>
404        <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></div>
405<div class="viewcode-block" id="ReflectivityIIModel.calculate_ER"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.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>
406        <span class="sd">&quot;&quot;&quot;</span>
407<span class="sd">        &quot;&quot;&quot;</span>
408        <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></div>
409<div class="viewcode-block" id="ReflectivityIIModel.set_dispersion"><a class="viewcode-back" href="../../../dev/api/sas.models.html#sas.models.ReflectivityIIModel.ReflectivityIIModel.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>
410        <span class="sd">&quot;&quot;&quot;</span>
411<span class="sd">        Set the dispersion object for a model parameter</span>
412<span class="sd">        </span>
413<span class="sd">        : param parameter: name of the parameter [string]</span>
414<span class="sd">        :dispersion: dispersion object of type DispersionModel</span>
415<span class="sd">        &quot;&quot;&quot;</span>
416        <span class="k">pass</span></div></div>
417</pre></div>
418
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