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50  <h1>Source code for G2phase</h1><div class="highlight"><pre>
51<span class="c"># -*- coding: utf-8 -*-</span>
52<span class="c">########### SVN repository information ###################</span>
53<span class="c"># $Date: 2015-01-08 16:24:32 -0600 (Thu, 08 Jan 2015) $</span>
54<span class="c"># $Author: vondreele $</span>
55<span class="c"># $Revision: 1625 $</span>
56<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2phase.py $</span>
57<span class="c"># $Id: G2phase.py 1625 2015-01-08 22:24:32Z vondreele $</span>
58<span class="c">########### SVN repository information ###################</span>
59<span class="c">#</span>
60<span class="sd">&#39;&#39;&#39;</span>
61<span class="sd">*Module G2phase: PDB, .EXP &amp; JANA m40,m50*</span>
62<span class="sd">-------------------------------------------</span>
63
64<span class="sd">A set of short routines to read in phases using routines that were</span>
65<span class="sd">previously implemented in GSAS-II: PDB, GSAS .EXP and JANA m40-m50 file formats</span>
66
67<span class="sd">&#39;&#39;&#39;</span>
68
69<span class="kn">import</span> <span class="nn">sys</span>
70<span class="kn">import</span> <span class="nn">os.path</span>
71<span class="kn">import</span> <span class="nn">math</span>
72<span class="kn">import</span> <span class="nn">random</span> <span class="kn">as</span> <span class="nn">ran</span>
73<span class="kn">import</span> <span class="nn">traceback</span>
74<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
75<span class="kn">import</span> <span class="nn">wx</span>
76<span class="kn">import</span> <span class="nn">GSASIIIO</span> <span class="kn">as</span> <span class="nn">G2IO</span>
77<span class="kn">import</span> <span class="nn">GSASIIspc</span> <span class="kn">as</span> <span class="nn">G2spc</span>
78<span class="kn">import</span> <span class="nn">GSASIIlattice</span> <span class="kn">as</span> <span class="nn">G2lat</span>
79<span class="kn">import</span> <span class="nn">GSASIIpath</span>
80<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1625 $&quot;</span><span class="p">)</span>
81
82<div class="viewcode-block" id="PDB_ReaderClass"><a class="viewcode-back" href="../imports.html#G2phase.PDB_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">PDB_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportPhase</span><span class="p">):</span>
83    <span class="s">&#39;Routine to import Phase information from a PDB file&#39;</span>
84    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
85        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to say ImportPhase.__init__</span>
86            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.pdb&#39;</span><span class="p">,</span><span class="s">&#39;.ent&#39;</span><span class="p">,</span><span class="s">&#39;.PDB&#39;</span><span class="p">,</span><span class="s">&#39;.ENT&#39;</span><span class="p">),</span>
87            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
88            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;PDB&#39;</span><span class="p">,</span>
89            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Original Protein Data Bank (.pdb file) import&#39;</span>
90            <span class="p">)</span>
91<div class="viewcode-block" id="PDB_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2phase.PDB_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
92        <span class="sd">&#39;&#39;&#39;Taking a stab a validating a PDB file</span>
93<span class="sd">        (look for cell &amp; at least one atom)</span>
94<span class="sd">        &#39;&#39;&#39;</span>
95        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
96            <span class="k">if</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;CRYST1&#39;</span><span class="p">):</span>
97                <span class="k">break</span>
98        <span class="k">else</span><span class="p">:</span>
99            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;no CRYST1 record found&#39;</span>
100            <span class="k">return</span> <span class="bp">False</span>
101        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
102            <span class="k">if</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;ATOM&#39;</span><span class="p">):</span>
103                <span class="k">return</span> <span class="bp">True</span>
104        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;no ATOM records found after CRYST1 record&#39;</span>
105        <span class="k">return</span> <span class="bp">False</span>
106</div>
107<div class="viewcode-block" id="PDB_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2phase.PDB_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
108        <span class="s">&#39;Read a PDF file using :meth:`ReadPDBPhase`&#39;</span>
109        <span class="k">try</span><span class="p">:</span>
110            <span class="bp">self</span><span class="o">.</span><span class="n">Phase</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ReadPDBPhase</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="p">)</span>
111            <span class="k">return</span> <span class="bp">True</span>
112        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
113            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
114            <span class="k">print</span> <span class="s">&#39;PDB read error:&#39;</span><span class="p">,</span><span class="n">detail</span> <span class="c"># for testing</span>
115            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
116            <span class="k">return</span> <span class="bp">False</span>
117        </div>
118<div class="viewcode-block" id="PDB_ReaderClass.ReadPDBPhase"><a class="viewcode-back" href="../imports.html#G2phase.PDB_ReaderClass.ReadPDBPhase">[docs]</a>    <span class="k">def</span> <span class="nf">ReadPDBPhase</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">parent</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
119        <span class="sd">&#39;&#39;&#39;Read a phase from a PDB file.</span>
120<span class="sd">        &#39;&#39;&#39;</span>
121        <span class="n">EightPiSq</span> <span class="o">=</span> <span class="mf">8.</span><span class="o">*</span><span class="n">math</span><span class="o">.</span><span class="n">pi</span><span class="o">**</span><span class="mi">2</span>
122        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error opening file&#39;</span>
123        <span class="nb">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">&#39;Ur&#39;</span><span class="p">)</span>
124        <span class="n">Phase</span> <span class="o">=</span> <span class="p">{}</span>
125        <span class="n">Title</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
126        <span class="n">Compnd</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
127        <span class="n">Atoms</span> <span class="o">=</span> <span class="p">[]</span>
128        <span class="n">A</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">shape</span><span class="o">=</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span><span class="mi">3</span><span class="p">))</span>
129        <span class="n">S</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
130        <span class="n">line</span> <span class="o">=</span> <span class="mi">1</span>
131        <span class="n">SGData</span> <span class="o">=</span> <span class="bp">None</span>
132        <span class="n">cell</span> <span class="o">=</span> <span class="bp">None</span>
133        <span class="k">while</span> <span class="n">S</span><span class="p">:</span>
134            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error reading at line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
135            <span class="n">Atom</span> <span class="o">=</span> <span class="p">[]</span>
136            <span class="k">if</span> <span class="s">&#39;TITLE&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">5</span><span class="p">]:</span>
137                <span class="n">Title</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">10</span><span class="p">:</span><span class="mi">72</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
138            <span class="k">elif</span> <span class="s">&#39;COMPND    &#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">10</span><span class="p">]:</span>
139                <span class="n">Compnd</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">10</span><span class="p">:</span><span class="mi">72</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
140            <span class="k">elif</span> <span class="s">&#39;CRYST&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">5</span><span class="p">]:</span>
141                <span class="n">abc</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">7</span><span class="p">:</span><span class="mi">34</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
142                <span class="n">angles</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">34</span><span class="p">:</span><span class="mi">55</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
143                <span class="n">cell</span><span class="o">=</span><span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">abc</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">abc</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">abc</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
144                    <span class="nb">float</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="mi">2</span><span class="p">])]</span>
145                <span class="n">Volume</span> <span class="o">=</span> <span class="n">G2lat</span><span class="o">.</span><span class="n">calc_V</span><span class="p">(</span><span class="n">G2lat</span><span class="o">.</span><span class="n">cell2A</span><span class="p">(</span><span class="n">cell</span><span class="p">))</span>
146                <span class="n">AA</span><span class="p">,</span><span class="n">AB</span> <span class="o">=</span> <span class="n">G2lat</span><span class="o">.</span><span class="n">cell2AB</span><span class="p">(</span><span class="n">cell</span><span class="p">)</span>
147                <span class="n">SpGrp</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">55</span><span class="p">:</span><span class="mi">65</span><span class="p">]</span>
148                <span class="n">E</span><span class="p">,</span><span class="n">SGData</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SpcGroup</span><span class="p">(</span><span class="n">SpGrp</span><span class="p">)</span>
149                <span class="c"># space group processing failed, try to look up name in table</span>
150                <span class="k">if</span> <span class="n">E</span><span class="p">:</span>
151                    <span class="n">SpGrpNorm</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">StandardizeSpcName</span><span class="p">(</span><span class="n">SpGrp</span><span class="p">)</span>
152                    <span class="k">if</span> <span class="n">SpGrpNorm</span><span class="p">:</span>
153                        <span class="n">E</span><span class="p">,</span><span class="n">SGData</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SpcGroup</span><span class="p">(</span><span class="n">SpGrpNorm</span><span class="p">)</span>
154                <span class="k">while</span> <span class="n">E</span><span class="p">:</span>
155                    <span class="k">print</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SGErrors</span><span class="p">(</span><span class="n">E</span><span class="p">)</span>
156                    <span class="n">dlg</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">TextEntryDialog</span><span class="p">(</span><span class="n">parent</span><span class="p">,</span>
157                        <span class="n">SpGrp</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="s">&#39; is invalid </span><span class="se">\n</span><span class="s">N.B.: make sure spaces separate axial fields in symbol&#39;</span><span class="p">,</span>
158                        <span class="s">&#39;ERROR in space group symbol&#39;</span><span class="p">,</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="n">style</span><span class="o">=</span><span class="n">wx</span><span class="o">.</span><span class="n">OK</span><span class="p">)</span>
159                    <span class="k">if</span> <span class="n">dlg</span><span class="o">.</span><span class="n">ShowModal</span><span class="p">()</span> <span class="o">==</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_OK</span><span class="p">:</span>
160                        <span class="n">SpGrp</span> <span class="o">=</span> <span class="n">dlg</span><span class="o">.</span><span class="n">GetValue</span><span class="p">()</span>
161                        <span class="n">E</span><span class="p">,</span><span class="n">SGData</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SpcGroup</span><span class="p">(</span><span class="n">SpGrp</span><span class="p">)</span>
162                    <span class="k">else</span><span class="p">:</span>
163                        <span class="n">SGData</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">SGData</span> <span class="c"># P 1</span>
164                        <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">The space group was not interpreted and has been set to &quot;P 1&quot;.&#39;</span>
165                        <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&quot;Change this in phase&#39;s General tab.&quot;</span>           
166                    <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
167                <span class="n">SGlines</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SGPrint</span><span class="p">(</span><span class="n">SGData</span><span class="p">)</span>
168                <span class="k">for</span> <span class="n">l</span> <span class="ow">in</span> <span class="n">SGlines</span><span class="p">:</span> <span class="k">print</span> <span class="n">l</span>
169            <span class="k">elif</span> <span class="s">&#39;SCALE&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">5</span><span class="p">]:</span>
170                <span class="n">V</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">10</span><span class="p">:</span><span class="mi">41</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
171                <span class="n">A</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">V</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">V</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">V</span><span class="p">[</span><span class="mi">2</span><span class="p">])]</span>
172            <span class="k">elif</span> <span class="s">&#39;ATOM&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span> <span class="ow">or</span> <span class="s">&#39;HETATM&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">6</span><span class="p">]:</span>
173                <span class="k">if</span> <span class="ow">not</span> <span class="n">SGData</span><span class="p">:</span>
174                    <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">The space group was not read before atoms and has been set to &quot;P 1&quot;. &#39;</span>
175                    <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&quot;Change this in phase&#39;s General tab.&quot;</span>
176                    <span class="n">SGData</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">SGData</span> <span class="c"># P 1</span>
177                <span class="n">XYZ</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">31</span><span class="p">:</span><span class="mi">39</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">39</span><span class="p">:</span><span class="mi">47</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">47</span><span class="p">:</span><span class="mi">55</span><span class="p">])]</span>
178                <span class="n">XYZ</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">inner</span><span class="p">(</span><span class="n">AB</span><span class="p">,</span><span class="n">XYZ</span><span class="p">)</span>
179                <span class="n">XYZ</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="nb">abs</span><span class="p">(</span><span class="n">XYZ</span><span class="p">)</span><span class="o">&lt;</span><span class="mf">0.00001</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">XYZ</span><span class="p">)</span>
180                <span class="n">SytSym</span><span class="p">,</span><span class="n">Mult</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SytSym</span><span class="p">(</span><span class="n">XYZ</span><span class="p">,</span><span class="n">SGData</span><span class="p">)</span>
181                <span class="n">Uiso</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">61</span><span class="p">:</span><span class="mi">67</span><span class="p">])</span><span class="o">/</span><span class="n">EightPiSq</span>
182                <span class="n">Type</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="mi">14</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
183                <span class="k">if</span> <span class="n">Type</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="s">&#39;123456789&#39;</span><span class="p">:</span>
184                    <span class="n">Type</span> <span class="o">=</span> <span class="n">Type</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
185                <span class="n">Atom</span> <span class="o">=</span> <span class="p">[</span><span class="n">S</span><span class="p">[</span><span class="mi">22</span><span class="p">:</span><span class="mi">27</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span><span class="n">S</span><span class="p">[</span><span class="mi">17</span><span class="p">:</span><span class="mi">20</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">(),</span><span class="n">S</span><span class="p">[</span><span class="mi">20</span><span class="p">:</span><span class="mi">22</span><span class="p">],</span>
186                    <span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="mi">17</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span><span class="n">Type</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="n">XYZ</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">XYZ</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="n">XYZ</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span>
187                    <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">55</span><span class="p">:</span><span class="mi">61</span><span class="p">]),</span><span class="n">SytSym</span><span class="p">,</span><span class="n">Mult</span><span class="p">,</span><span class="s">&#39;I&#39;</span><span class="p">,</span><span class="n">Uiso</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span>
188                <span class="n">S</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
189                <span class="n">line</span> <span class="o">+=</span> <span class="mi">1</span>
190                <span class="k">if</span> <span class="s">&#39;ANISOU&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">6</span><span class="p">]:</span>
191                    <span class="n">Uij</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">30</span><span class="p">:</span><span class="mi">72</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
192                    <span class="n">Uij</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">Uij</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">/</span><span class="mf">10000.</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">Uij</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">/</span><span class="mf">10000.</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">Uij</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span><span class="o">/</span><span class="mf">10000.</span><span class="p">,</span>
193                        <span class="nb">float</span><span class="p">(</span><span class="n">Uij</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span><span class="o">/</span><span class="mf">10000.</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">Uij</span><span class="p">[</span><span class="mi">4</span><span class="p">])</span><span class="o">/</span><span class="mf">10000.</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">Uij</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span><span class="o">/</span><span class="mf">10000.</span><span class="p">]</span>
194                    <span class="n">Atom</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">[:</span><span class="mi">14</span><span class="p">]</span><span class="o">+</span><span class="n">Uij</span>
195                    <span class="n">Atom</span><span class="p">[</span><span class="mi">12</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;A&#39;</span>
196                <span class="n">Atom</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ran</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">maxint</span><span class="p">))</span>
197                <span class="n">Atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Atom</span><span class="p">)</span>
198            <span class="n">S</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
199            <span class="n">line</span> <span class="o">+=</span> <span class="mi">1</span>
200        <span class="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
201        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error after read complete&#39;</span>
202        <span class="k">if</span> <span class="n">Title</span><span class="p">:</span>
203            <span class="n">PhaseName</span> <span class="o">=</span> <span class="n">Title</span>
204        <span class="k">elif</span> <span class="n">Compnd</span><span class="p">:</span>
205            <span class="n">PhaseName</span> <span class="o">=</span> <span class="n">Compnd</span>
206        <span class="k">else</span><span class="p">:</span>
207            <span class="n">PhaseName</span> <span class="o">=</span> <span class="s">&#39;None&#39;</span>
208        <span class="k">if</span> <span class="ow">not</span> <span class="n">SGData</span><span class="p">:</span>
209            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No space group (CRYST entry) found&quot;</span><span class="p">)</span>
210        <span class="k">if</span> <span class="ow">not</span> <span class="n">cell</span><span class="p">:</span>
211            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No cell (CRYST entry) found&quot;</span><span class="p">)</span>
212        <span class="n">Phase</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">SetNewPhase</span><span class="p">(</span><span class="n">Name</span><span class="o">=</span><span class="n">PhaseName</span><span class="p">,</span><span class="n">SGData</span><span class="o">=</span><span class="n">SGData</span><span class="p">,</span><span class="n">cell</span><span class="o">=</span><span class="n">cell</span><span class="o">+</span><span class="p">[</span><span class="n">Volume</span><span class="p">,])</span>
213        <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;macromolecular&#39;</span>
214        <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;AtomPtrs&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">6</span><span class="p">,</span><span class="mi">4</span><span class="p">,</span><span class="mi">10</span><span class="p">,</span><span class="mi">12</span><span class="p">]</span>
215        <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;Atoms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">Atoms</span>
216        <span class="k">return</span> <span class="n">Phase</span>
217</div></div>
218<div class="viewcode-block" id="EXP_ReaderClass"><a class="viewcode-back" href="../imports.html#G2phase.EXP_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">EXP_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportPhase</span><span class="p">):</span>
219    <span class="s">&#39;Routine to import Phase information from GSAS .EXP files&#39;</span>
220    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
221        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to say ImportPhase.__init__</span>
222            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.EXP&#39;</span><span class="p">,</span><span class="s">&#39;.exp&#39;</span><span class="p">),</span>
223            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
224            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;GSAS .EXP&#39;</span><span class="p">,</span>
225            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;GSAS Experiment (.EXP file) import&#39;</span>
226            <span class="p">)</span>
227       
228<div class="viewcode-block" id="EXP_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2phase.EXP_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
229        <span class="s">&#39;Look for a VERSION tag in 1st line&#39;</span> 
230        <span class="k">if</span> <span class="n">filepointer</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">13</span><span class="p">)</span> <span class="o">==</span> <span class="s">&#39;     VERSION &#39;</span><span class="p">:</span>
231            <span class="k">return</span> <span class="bp">True</span>
232        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;File does not begin with VERSION tag&#39;</span>
233        <span class="k">return</span> <span class="bp">False</span>
234</div>
235<div class="viewcode-block" id="EXP_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2phase.EXP_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
236        <span class="s">&#39;Read a phase from a GSAS .EXP file using :meth:`ReadEXPPhase`&#39;</span>
237        <span class="k">try</span><span class="p">:</span>
238            <span class="bp">self</span><span class="o">.</span><span class="n">Phase</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ReadEXPPhase</span><span class="p">(</span><span class="n">ParentFrame</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">)</span>
239            <span class="k">return</span> <span class="bp">True</span>
240        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
241            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
242            <span class="k">print</span> <span class="s">&#39;GSAS .EXP read error:&#39;</span><span class="p">,</span><span class="n">detail</span> <span class="c"># for testing</span>
243            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
244            <span class="k">return</span> <span class="bp">False</span>
245</div>
246<div class="viewcode-block" id="EXP_ReaderClass.ReadEXPPhase"><a class="viewcode-back" href="../imports.html#G2phase.EXP_ReaderClass.ReadEXPPhase">[docs]</a>    <span class="k">def</span> <span class="nf">ReadEXPPhase</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">G2frame</span><span class="p">,</span><span class="n">filepointer</span><span class="p">):</span>
247        <span class="sd">&#39;&#39;&#39;Read a phase from a GSAS .EXP file.</span>
248<span class="sd">        &#39;&#39;&#39;</span>
249        <span class="n">shModels</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;cylindrical&#39;</span><span class="p">,</span><span class="s">&#39;none&#39;</span><span class="p">,</span><span class="s">&#39;shear - 2/m&#39;</span><span class="p">,</span><span class="s">&#39;rolling - mmm&#39;</span><span class="p">]</span>
250        <span class="n">textureData</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;Order&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">,</span><span class="s">&#39;Model&#39;</span><span class="p">:</span><span class="s">&#39;cylindrical&#39;</span><span class="p">,</span><span class="s">&#39;Sample omega&#39;</span><span class="p">:[</span><span class="bp">False</span><span class="p">,</span><span class="mf">0.0</span><span class="p">],</span>
251            <span class="s">&#39;Sample chi&#39;</span><span class="p">:[</span><span class="bp">False</span><span class="p">,</span><span class="mf">0.0</span><span class="p">],</span><span class="s">&#39;Sample phi&#39;</span><span class="p">:[</span><span class="bp">False</span><span class="p">,</span><span class="mf">0.0</span><span class="p">],</span><span class="s">&#39;SH Coeff&#39;</span><span class="p">:[</span><span class="bp">False</span><span class="p">,{}],</span>
252            <span class="s">&#39;SHShow&#39;</span><span class="p">:</span><span class="bp">False</span><span class="p">,</span><span class="s">&#39;PFhkl&#39;</span><span class="p">:[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">],</span><span class="s">&#39;PFxyz&#39;</span><span class="p">:[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">],</span><span class="s">&#39;PlotType&#39;</span><span class="p">:</span><span class="s">&#39;Pole figure&#39;</span><span class="p">}</span>
253        <span class="n">shNcof</span> <span class="o">=</span> <span class="mi">0</span>
254        <span class="n">S</span> <span class="o">=</span> <span class="mi">1</span>
255        <span class="n">NPhas</span> <span class="o">=</span> <span class="p">[]</span>
256        <span class="n">Expr</span> <span class="o">=</span> <span class="p">[{},{},{},{},{},{},{},{},{}]</span> <span class="c"># GSAS can have at most 9 phases</span>
257        <span class="k">for</span> <span class="n">line</span><span class="p">,</span><span class="n">S</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
258            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error reading at line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
259            <span class="k">if</span> <span class="s">&#39;EXPR NPHAS&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">12</span><span class="p">]:</span>
260                <span class="n">Num</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">&#39;0&#39;</span><span class="p">)</span>
261                <span class="n">NPhas</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
262            <span class="k">if</span> <span class="s">&#39;CRS&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">3</span><span class="p">]:</span>
263                <span class="n">N</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">3</span><span class="p">:</span><span class="mi">4</span><span class="p">])</span><span class="o">-</span><span class="mi">1</span>
264                <span class="n">Expr</span><span class="p">[</span><span class="n">N</span><span class="p">][</span><span class="n">S</span><span class="p">[:</span><span class="mi">12</span><span class="p">]]</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">12</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
265        <span class="n">PNames</span> <span class="o">=</span> <span class="p">[]</span>
266        <span class="k">if</span> <span class="ow">not</span> <span class="n">NPhas</span><span class="p">:</span>
267            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No EXPR NPHAS record found&quot;</span><span class="p">)</span>
268        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error interpreting file&#39;</span>
269        <span class="k">for</span> <span class="n">n</span><span class="p">,</span><span class="n">N</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">NPhas</span><span class="p">):</span>
270            <span class="k">if</span> <span class="n">N</span> <span class="o">!=</span> <span class="s">&#39;0&#39;</span><span class="p">:</span>
271                <span class="n">result</span> <span class="o">=</span> <span class="n">n</span>
272                <span class="n">key</span> <span class="o">=</span> <span class="s">&#39;CRS&#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">n</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span><span class="o">+</span><span class="s">&#39;    PNAM&#39;</span>
273                <span class="n">PNames</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Expr</span><span class="p">[</span><span class="n">n</span><span class="p">][</span><span class="n">key</span><span class="p">])</span>
274        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">PNames</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
275            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No phases found&quot;</span><span class="p">)</span>           
276        <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">PNames</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
277            <span class="n">dlg</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">SingleChoiceDialog</span><span class="p">(</span><span class="n">G2frame</span><span class="p">,</span> <span class="s">&#39;Which phase to read?&#39;</span><span class="p">,</span> <span class="s">&#39;Read phase data&#39;</span><span class="p">,</span> <span class="n">PNames</span><span class="p">,</span> <span class="n">wx</span><span class="o">.</span><span class="n">CHOICEDLG_STYLE</span><span class="p">)</span>
278            <span class="k">try</span><span class="p">:</span>
279                <span class="k">if</span> <span class="n">dlg</span><span class="o">.</span><span class="n">ShowModal</span><span class="p">()</span> <span class="o">==</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_OK</span><span class="p">:</span>
280                    <span class="n">result</span> <span class="o">=</span> <span class="n">dlg</span><span class="o">.</span><span class="n">GetSelection</span><span class="p">()</span> <span class="c"># I think this breaks is there are skipped phases. Cant this happen?</span>
281            <span class="k">finally</span><span class="p">:</span>
282                <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>       
283        <span class="n">EXPphase</span> <span class="o">=</span> <span class="n">Expr</span><span class="p">[</span><span class="n">result</span><span class="p">]</span>
284        <span class="n">keyList</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
285        <span class="n">keyList</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
286        <span class="n">SGData</span> <span class="o">=</span> <span class="p">{}</span>
287        <span class="k">if</span> <span class="n">NPhas</span><span class="p">[</span><span class="n">result</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;1&#39;</span><span class="p">:</span>
288            <span class="n">Ptype</span> <span class="o">=</span> <span class="s">&#39;nuclear&#39;</span>
289        <span class="k">elif</span> <span class="n">NPhas</span><span class="p">[</span><span class="n">result</span><span class="p">]</span> <span class="ow">in</span> <span class="p">[</span><span class="s">&#39;2&#39;</span><span class="p">,</span><span class="s">&#39;3&#39;</span><span class="p">]:</span>
290            <span class="n">Ptype</span> <span class="o">=</span> <span class="s">&#39;magnetic&#39;</span>
291        <span class="k">elif</span> <span class="n">NPhas</span><span class="p">[</span><span class="n">result</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;4&#39;</span><span class="p">:</span>
292            <span class="n">Ptype</span> <span class="o">=</span> <span class="s">&#39;macromolecular&#39;</span>
293        <span class="k">elif</span> <span class="n">NPhas</span><span class="p">[</span><span class="n">result</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;10&#39;</span><span class="p">:</span>
294            <span class="n">Ptype</span> <span class="o">=</span> <span class="s">&#39;Pawley&#39;</span>
295        <span class="k">else</span><span class="p">:</span>
296            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;Phase type not recognized&quot;</span><span class="p">)</span>           
297        <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keyList</span><span class="p">:</span>
298            <span class="k">if</span> <span class="s">&#39;PNAM&#39;</span> <span class="ow">in</span> <span class="n">key</span><span class="p">:</span>
299               <span class="n">PhaseName</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
300            <span class="k">elif</span> <span class="s">&#39;ABC   &#39;</span> <span class="ow">in</span> <span class="n">key</span><span class="p">:</span>
301                <span class="n">abc</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">][:</span><span class="mi">10</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">10</span><span class="p">:</span><span class="mi">20</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">20</span><span class="p">:</span><span class="mi">30</span><span class="p">])]</span>                       
302            <span class="k">elif</span> <span class="s">&#39;ANGLES&#39;</span> <span class="ow">in</span> <span class="n">key</span><span class="p">:</span>
303                <span class="n">angles</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">][:</span><span class="mi">10</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">10</span><span class="p">:</span><span class="mi">20</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="mi">20</span><span class="p">:</span><span class="mi">30</span><span class="p">])]</span>                                               
304            <span class="k">elif</span> <span class="s">&#39;SG SYM&#39;</span> <span class="ow">in</span> <span class="n">key</span><span class="p">:</span>
305                <span class="n">SpGrp</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">][:</span><span class="mi">15</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
306                <span class="n">E</span><span class="p">,</span><span class="n">SGData</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SpcGroup</span><span class="p">(</span><span class="n">SpGrp</span><span class="p">)</span>
307                <span class="k">if</span> <span class="n">E</span><span class="p">:</span>
308                    <span class="n">SGData</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">SGData</span> <span class="c"># P 1 -- unlikely to need this!</span>
309                    <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">The GSAS space group was not interpreted(!) and has been set to &quot;P 1&quot;.&#39;</span>
310                    <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&quot;Change this in phase&#39;s General tab.&quot;</span>                       
311            <span class="k">elif</span> <span class="s">&#39;OD    &#39;</span> <span class="ow">in</span> <span class="n">key</span><span class="p">:</span>
312                <span class="n">SHdata</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span> <span class="c"># may not have all 9 values</span>
313                <span class="n">SHvals</span> <span class="o">=</span> <span class="mi">9</span><span class="o">*</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
314                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">9</span><span class="p">):</span>
315                    <span class="k">try</span><span class="p">:</span>
316                        <span class="nb">float</span><span class="p">(</span><span class="n">SHdata</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
317                        <span class="n">SHvals</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">SHdata</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
318                    <span class="k">except</span><span class="p">:</span>
319                        <span class="k">pass</span>
320                <span class="n">textureData</span><span class="p">[</span><span class="s">&#39;Order&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">SHvals</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
321                <span class="n">textureData</span><span class="p">[</span><span class="s">&#39;Model&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">shModels</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">SHvals</span><span class="p">[</span><span class="mi">2</span><span class="p">])]</span>
322                <span class="n">textureData</span><span class="p">[</span><span class="s">&#39;Sample omega&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">False</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">SHvals</span><span class="p">[</span><span class="mi">6</span><span class="p">])]</span>
323                <span class="n">textureData</span><span class="p">[</span><span class="s">&#39;Sample chi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">False</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">SHvals</span><span class="p">[</span><span class="mi">7</span><span class="p">])]</span>
324                <span class="n">textureData</span><span class="p">[</span><span class="s">&#39;Sample phi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">False</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">SHvals</span><span class="p">[</span><span class="mi">8</span><span class="p">])]</span>
325                <span class="n">shNcof</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">SHvals</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
326        <span class="n">Atoms</span> <span class="o">=</span> <span class="p">[]</span>
327        <span class="k">if</span> <span class="n">Ptype</span> <span class="o">==</span> <span class="s">&#39;nuclear&#39;</span><span class="p">:</span>
328            <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keyList</span><span class="p">:</span>
329                <span class="k">if</span> <span class="s">&#39;AT&#39;</span> <span class="ow">in</span> <span class="n">key</span><span class="p">:</span>
330                    <span class="k">if</span> <span class="n">key</span><span class="p">[</span><span class="mi">11</span><span class="p">:]</span> <span class="o">==</span> <span class="s">&#39;A&#39;</span><span class="p">:</span>
331                        <span class="n">S</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
332                    <span class="k">elif</span> <span class="n">key</span><span class="p">[</span><span class="mi">11</span><span class="p">:]</span> <span class="o">==</span> <span class="s">&#39;B&#39;</span><span class="p">:</span>
333                        <span class="n">S</span> <span class="o">+=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
334                        <span class="n">Atom</span> <span class="o">=</span> <span class="p">[</span><span class="n">S</span><span class="p">[</span><span class="mi">50</span><span class="p">:</span><span class="mi">58</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span><span class="n">S</span><span class="p">[:</span><span class="mi">10</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span><span class="s">&#39;&#39;</span><span class="p">,</span>
335                            <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">10</span><span class="p">:</span><span class="mi">20</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">20</span><span class="p">:</span><span class="mi">30</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">30</span><span class="p">:</span><span class="mi">40</span><span class="p">]),</span>
336                            <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">40</span><span class="p">:</span><span class="mi">50</span><span class="p">]),</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="nb">int</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">60</span><span class="p">:</span><span class="mi">62</span><span class="p">]),</span><span class="n">S</span><span class="p">[</span><span class="mi">130</span><span class="p">:</span><span class="mi">131</span><span class="p">]]</span>
337                        <span class="k">if</span> <span class="n">Atom</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;I&#39;</span><span class="p">:</span>
338                            <span class="n">Atom</span> <span class="o">+=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">68</span><span class="p">:</span><span class="mi">78</span><span class="p">]),</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">]</span>
339                        <span class="k">elif</span> <span class="n">Atom</span><span class="p">[</span><span class="mi">9</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;A&#39;</span><span class="p">:</span>
340                            <span class="n">Atom</span> <span class="o">+=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">68</span><span class="p">:</span><span class="mi">78</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">78</span><span class="p">:</span><span class="mi">88</span><span class="p">]),</span>
341                                <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">88</span><span class="p">:</span><span class="mi">98</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">98</span><span class="p">:</span><span class="mi">108</span><span class="p">]),</span>
342                                <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">108</span><span class="p">:</span><span class="mi">118</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">118</span><span class="p">:</span><span class="mi">128</span><span class="p">])]</span>
343                        <span class="n">XYZ</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">[</span><span class="mi">3</span><span class="p">:</span><span class="mi">6</span><span class="p">]</span>
344                        <span class="n">Atom</span><span class="p">[</span><span class="mi">7</span><span class="p">],</span><span class="n">Atom</span><span class="p">[</span><span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SytSym</span><span class="p">(</span><span class="n">XYZ</span><span class="p">,</span><span class="n">SGData</span><span class="p">)</span>
345                        <span class="n">Atom</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ran</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">maxint</span><span class="p">))</span>
346                        <span class="n">Atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Atom</span><span class="p">)</span>
347        <span class="k">elif</span> <span class="n">Ptype</span> <span class="o">==</span> <span class="s">&#39;macromolecular&#39;</span><span class="p">:</span>
348            <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">keyList</span><span class="p">:</span>
349                <span class="k">if</span> <span class="s">&#39;AT&#39;</span> <span class="ow">in</span> <span class="n">key</span><span class="p">[</span><span class="mi">6</span><span class="p">:</span><span class="mi">8</span><span class="p">]:</span>
350                    <span class="n">S</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
351                    <span class="n">Atom</span> <span class="o">=</span> <span class="p">[</span><span class="n">S</span><span class="p">[</span><span class="mi">56</span><span class="p">:</span><span class="mi">60</span><span class="p">],</span><span class="n">S</span><span class="p">[</span><span class="mi">50</span><span class="p">:</span><span class="mi">54</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">upper</span><span class="p">(),</span><span class="n">S</span><span class="p">[</span><span class="mi">54</span><span class="p">:</span><span class="mi">56</span><span class="p">],</span>
352                        <span class="n">S</span><span class="p">[</span><span class="mi">46</span><span class="p">:</span><span class="mi">51</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span><span class="n">S</span><span class="p">[:</span><span class="mi">8</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span><span class="s">&#39;&#39;</span><span class="p">,</span>
353                        <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">16</span><span class="p">:</span><span class="mi">24</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">24</span><span class="p">:</span><span class="mi">32</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">32</span><span class="p">:</span><span class="mi">40</span><span class="p">]),</span>
354                        <span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">8</span><span class="p">:</span><span class="mi">16</span><span class="p">]),</span><span class="s">&#39;1&#39;</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="s">&#39;I&#39;</span><span class="p">,</span><span class="nb">float</span><span class="p">(</span><span class="n">S</span><span class="p">[</span><span class="mi">40</span><span class="p">:</span><span class="mi">46</span><span class="p">]),</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span>
355                    <span class="n">XYZ</span> <span class="o">=</span> <span class="n">Atom</span><span class="p">[</span><span class="mi">6</span><span class="p">:</span><span class="mi">9</span><span class="p">]</span>
356                    <span class="n">Atom</span><span class="p">[</span><span class="mi">10</span><span class="p">],</span><span class="n">Atom</span><span class="p">[</span><span class="mi">11</span><span class="p">]</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SytSym</span><span class="p">(</span><span class="n">XYZ</span><span class="p">,</span><span class="n">SGData</span><span class="p">)</span>
357                    <span class="n">Atom</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ran</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">maxint</span><span class="p">))</span>
358                    <span class="n">Atoms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Atom</span><span class="p">)</span>
359        <span class="n">Volume</span> <span class="o">=</span> <span class="n">G2lat</span><span class="o">.</span><span class="n">calc_V</span><span class="p">(</span><span class="n">G2lat</span><span class="o">.</span><span class="n">cell2A</span><span class="p">(</span><span class="n">abc</span><span class="o">+</span><span class="n">angles</span><span class="p">))</span>
360        <span class="k">if</span> <span class="n">shNcof</span><span class="p">:</span>
361            <span class="n">shCoef</span> <span class="o">=</span> <span class="p">{}</span>
362            <span class="n">nRec</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">((</span><span class="n">shNcof</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">/</span><span class="mi">6</span><span class="o">+</span><span class="mi">1</span><span class="p">)]</span>
363            <span class="k">for</span> <span class="n">irec</span> <span class="ow">in</span> <span class="n">nRec</span><span class="p">:</span>
364                <span class="n">ODkey</span> <span class="o">=</span> <span class="n">keyList</span><span class="p">[</span><span class="mi">0</span><span class="p">][:</span><span class="mi">6</span><span class="p">]</span><span class="o">+</span><span class="s">&#39;OD&#39;</span><span class="o">+</span><span class="s">&#39;</span><span class="si">%3d</span><span class="s">A&#39;</span><span class="o">%</span><span class="p">(</span><span class="n">irec</span><span class="p">)</span>
365                <span class="n">indx</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">ODkey</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
366                <span class="n">ODkey</span> <span class="o">=</span> <span class="n">ODkey</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="s">&#39;B&#39;</span>
367                <span class="n">vals</span> <span class="o">=</span> <span class="n">EXPphase</span><span class="p">[</span><span class="n">ODkey</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
368                <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">val</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">vals</span><span class="p">):</span>
369                    <span class="n">key</span> <span class="o">=</span> <span class="s">&#39;C(</span><span class="si">%s</span><span class="s">,</span><span class="si">%s</span><span class="s">,</span><span class="si">%s</span><span class="s">)&#39;</span><span class="o">%</span><span class="p">(</span><span class="n">indx</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="p">],</span><span class="n">indx</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">],</span><span class="n">indx</span><span class="p">[</span><span class="mi">3</span><span class="o">*</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">])</span>
370                    <span class="n">shCoef</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>
371            <span class="n">textureData</span><span class="p">[</span><span class="s">&#39;SH Coeff&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="bp">False</span><span class="p">,</span><span class="n">shCoef</span><span class="p">]</span>
372        <span class="k">if</span> <span class="ow">not</span> <span class="n">SGData</span><span class="p">:</span>
373            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No space group found in phase&quot;</span><span class="p">)</span>
374        <span class="k">if</span> <span class="ow">not</span> <span class="n">abc</span><span class="p">:</span>
375            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No cell lengths found in phase&quot;</span><span class="p">)</span>
376        <span class="k">if</span> <span class="ow">not</span> <span class="n">angles</span><span class="p">:</span>
377            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No cell angles found in phase&quot;</span><span class="p">)</span>
378        <span class="k">if</span> <span class="ow">not</span> <span class="n">Atoms</span><span class="p">:</span>
379            <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;No atoms found in phase&quot;</span><span class="p">)</span>
380        <span class="n">Phase</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">SetNewPhase</span><span class="p">(</span><span class="n">Name</span><span class="o">=</span><span class="n">PhaseName</span><span class="p">,</span><span class="n">SGData</span><span class="o">=</span><span class="n">SGData</span><span class="p">,</span><span class="n">cell</span><span class="o">=</span><span class="n">abc</span><span class="o">+</span><span class="n">angles</span><span class="o">+</span><span class="p">[</span><span class="n">Volume</span><span class="p">,])</span>
381        <span class="n">general</span> <span class="o">=</span> <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">]</span>
382        <span class="n">general</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ptype</span>
383        <span class="k">if</span> <span class="n">general</span><span class="p">[</span><span class="s">&#39;Type&#39;</span><span class="p">]</span> <span class="o">==</span><span class="s">&#39;macromolecular&#39;</span><span class="p">:</span>
384            <span class="n">general</span><span class="p">[</span><span class="s">&#39;AtomPtrs&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">6</span><span class="p">,</span><span class="mi">4</span><span class="p">,</span><span class="mi">10</span><span class="p">,</span><span class="mi">12</span><span class="p">]</span>
385        <span class="k">else</span><span class="p">:</span>
386            <span class="n">general</span><span class="p">[</span><span class="s">&#39;AtomPtrs&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">7</span><span class="p">,</span><span class="mi">9</span><span class="p">]</span>   
387        <span class="n">general</span><span class="p">[</span><span class="s">&#39;SH Texture&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">textureData</span>
388        <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;Atoms&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">Atoms</span>
389        <span class="k">return</span> <span class="n">Phase</span>
390</div></div>
391<div class="viewcode-block" id="JANA_ReaderClass"><a class="viewcode-back" href="../imports.html#G2phase.JANA_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">JANA_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportPhase</span><span class="p">):</span>
392    <span class="s">&#39;Routine to import Phase information from a JANA2006 file&#39;</span>
393    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
394        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to say ImportPhase.__init__</span>
395            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.m50&#39;</span><span class="p">,</span><span class="s">&#39;.M50&#39;</span><span class="p">),</span>
396            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
397            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;JANA m50&#39;</span><span class="p">,</span>
398            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;JANA2006 phase import&#39;</span>
399            <span class="p">)</span>
400<div class="viewcode-block" id="JANA_ReaderClass.ContentsValidator"><a class="viewcode-back" href="../imports.html#G2phase.JANA_ReaderClass.ContentsValidator">[docs]</a>    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
401        <span class="sd">&#39;&#39;&#39;Taking a stab a validating a .m50 file</span>
402<span class="sd">        (look for cell &amp; at least one atom)</span>
403<span class="sd">        &#39;&#39;&#39;</span>
404        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
405            <span class="k">if</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;cell&#39;</span><span class="p">):</span>
406                <span class="k">break</span>
407        <span class="k">else</span><span class="p">:</span>
408            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;no cell record found&#39;</span>
409            <span class="k">return</span> <span class="bp">False</span>
410        <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">l</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">filepointer</span><span class="p">):</span>
411            <span class="k">if</span> <span class="n">l</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">&#39;spgroup&#39;</span><span class="p">):</span>
412                <span class="k">return</span> <span class="bp">True</span>
413        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;no spgroup record found after cell record&#39;</span>
414        <span class="k">return</span> <span class="bp">False</span>
415        </div>
416<div class="viewcode-block" id="JANA_ReaderClass.Reader"><a class="viewcode-back" href="../imports.html#G2phase.JANA_ReaderClass.Reader">[docs]</a>    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
417        <span class="s">&#39;Read a m50 file using :meth:`ReadJANAPhase`&#39;</span>
418        <span class="k">try</span><span class="p">:</span>
419            <span class="bp">self</span><span class="o">.</span><span class="n">Phase</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ReadJANAPhase</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="p">)</span>
420            <span class="k">return</span> <span class="bp">True</span>
421        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
422            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">  &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">detail</span><span class="p">)</span>
423            <span class="k">print</span> <span class="s">&#39;JANA read error:&#39;</span><span class="p">,</span><span class="n">detail</span> <span class="c"># for testing</span>
424            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
425            <span class="k">return</span> <span class="bp">False</span>
426        </div>
427<div class="viewcode-block" id="JANA_ReaderClass.ReadJANAPhase"><a class="viewcode-back" href="../imports.html#G2phase.JANA_ReaderClass.ReadJANAPhase">[docs]</a>    <span class="k">def</span> <span class="nf">ReadJANAPhase</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">parent</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
428        <span class="sd">&#39;&#39;&#39;Read a phase from a JANA2006 m50 &amp; m40 files.</span>
429<span class="sd">        &#39;&#39;&#39;</span>
430        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error opening file&#39;</span>
431        <span class="nb">file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s">&#39;Ur&#39;</span><span class="p">)</span> <span class="c">#contains only cell &amp; spcgroup</span>
432        <span class="n">Phase</span> <span class="o">=</span> <span class="p">{}</span>
433        <span class="n">Title</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
434        <span class="n">Compnd</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
435        <span class="n">Type</span> <span class="o">=</span> <span class="s">&#39;nuclear&#39;</span>
436        <span class="n">Atoms</span> <span class="o">=</span> <span class="p">[]</span>
437        <span class="n">Atypes</span> <span class="o">=</span> <span class="p">[]</span>
438        <span class="n">SuperVec</span> <span class="o">=</span> <span class="p">[[[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">.</span><span class="mi">1</span><span class="p">],</span><span class="bp">False</span><span class="p">,</span><span class="mi">4</span><span class="p">],[[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">.</span><span class="mi">1</span><span class="p">],</span><span class="bp">False</span><span class="p">,</span><span class="mi">4</span><span class="p">],[[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">.</span><span class="mi">1</span><span class="p">],</span><span class="bp">False</span><span class="p">,</span><span class="mi">4</span><span class="p">]]</span>
439        <span class="n">S</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
440        <span class="n">line</span> <span class="o">=</span> <span class="mi">1</span>
441        <span class="n">SGData</span> <span class="o">=</span> <span class="bp">None</span>
442        <span class="n">SuperSg</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
443        <span class="n">cell</span> <span class="o">=</span> <span class="bp">None</span>
444        <span class="n">nqi</span> <span class="o">=</span> <span class="mi">0</span>
445        <span class="k">while</span> <span class="n">S</span><span class="p">:</span>
446            <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error reading at line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
447            <span class="k">if</span> <span class="s">&#39;title&#39;</span> <span class="ow">in</span> <span class="n">S</span> <span class="ow">and</span> <span class="n">S</span> <span class="o">!=</span> <span class="s">&#39;title</span><span class="se">\n</span><span class="s">&#39;</span><span class="p">:</span>
448                <span class="n">Title</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]</span>
449            <span class="k">elif</span> <span class="s">&#39;cell&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">4</span><span class="p">]:</span>
450                <span class="n">cell</span> <span class="o">=</span> <span class="n">S</span><span class="p">[</span><span class="mi">5</span><span class="p">:]</span><span class="o">.</span><span class="n">split</span><span class="p">()</span>
451                <span class="n">cell</span><span class="o">=</span><span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span>
452                    <span class="nb">float</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">3</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">4</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">5</span><span class="p">])]</span>
453                <span class="n">Volume</span> <span class="o">=</span> <span class="n">G2lat</span><span class="o">.</span><span class="n">calc_V</span><span class="p">(</span><span class="n">G2lat</span><span class="o">.</span><span class="n">cell2A</span><span class="p">(</span><span class="n">cell</span><span class="p">))</span>
454            <span class="k">elif</span> <span class="s">&#39;spgroup&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">:</span>
455                <span class="k">if</span> <span class="s">&#39;X&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">:</span>
456                    <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;Supersymmetry &quot;</span><span class="o">+</span><span class="n">S</span><span class="o">+</span><span class="s">&quot; too high; GSAS-II limited to (3+1) supersymmetry&quot;</span><span class="p">)</span>           
457                <span class="n">SpGrp</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">]</span>
458                <span class="n">SuperSg</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
459                <span class="k">if</span> <span class="s">&#39;(&#39;</span> <span class="ow">in</span> <span class="n">SpGrp</span><span class="p">:</span>    <span class="c">#supercell symmetry - split in 2</span>
460                    <span class="n">SuperStr</span> <span class="o">=</span> <span class="n">SpGrp</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">&#39;(&#39;</span><span class="p">)</span>
461                    <span class="n">SpGrp</span> <span class="o">=</span> <span class="n">SuperStr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
462                    <span class="n">SuperSg</span> <span class="o">=</span> <span class="s">&#39;(&#39;</span><span class="o">+</span><span class="n">SuperStr</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
463                <span class="n">SpGrpNorm</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">StandardizeSpcName</span><span class="p">(</span><span class="n">SpGrp</span><span class="p">)</span>
464                <span class="n">E</span><span class="p">,</span><span class="n">SGData</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SpcGroup</span><span class="p">(</span><span class="n">SpGrpNorm</span><span class="p">)</span>
465                <span class="c"># space group processing failed, try to look up name in table</span>
466                <span class="k">while</span> <span class="n">E</span><span class="p">:</span>
467                    <span class="k">print</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SGErrors</span><span class="p">(</span><span class="n">E</span><span class="p">)</span>
468                    <span class="n">dlg</span> <span class="o">=</span> <span class="n">wx</span><span class="o">.</span><span class="n">TextEntryDialog</span><span class="p">(</span><span class="n">parent</span><span class="p">,</span>
469                        <span class="n">SpGrp</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="s">&#39; is invalid </span><span class="se">\n</span><span class="s">N.B.: make sure spaces separate axial fields in symbol&#39;</span><span class="p">,</span>
470                        <span class="s">&#39;ERROR in space group symbol&#39;</span><span class="p">,</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="n">style</span><span class="o">=</span><span class="n">wx</span><span class="o">.</span><span class="n">OK</span><span class="p">)</span>
471                    <span class="k">if</span> <span class="n">dlg</span><span class="o">.</span><span class="n">ShowModal</span><span class="p">()</span> <span class="o">==</span> <span class="n">wx</span><span class="o">.</span><span class="n">ID_OK</span><span class="p">:</span>
472                        <span class="n">SpGrp</span> <span class="o">=</span> <span class="n">dlg</span><span class="o">.</span><span class="n">GetValue</span><span class="p">()</span>
473                        <span class="n">E</span><span class="p">,</span><span class="n">SGData</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SpcGroup</span><span class="p">(</span><span class="n">SpGrp</span><span class="p">)</span>
474                    <span class="k">else</span><span class="p">:</span>
475                        <span class="n">SGData</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">SGData</span> <span class="c"># P 1</span>
476                        <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">The space group was not interpreted and has been set to &quot;P 1&quot;.&#39;</span>
477                        <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&quot;Change this in phase&#39;s General tab.&quot;</span>           
478                    <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
479                <span class="n">SGlines</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SGPrint</span><span class="p">(</span><span class="n">SGData</span><span class="p">)</span>
480            <span class="k">elif</span> <span class="s">&#39;qi&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">2</span><span class="p">]:</span>
481                <span class="k">if</span> <span class="n">nqi</span><span class="p">:</span>
482                    <span class="k">raise</span> <span class="bp">self</span><span class="o">.</span><span class="n">ImportException</span><span class="p">(</span><span class="s">&quot;Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry&quot;</span><span class="p">)</span>           
483                <span class="n">Type</span> <span class="o">=</span> <span class="s">&#39;modulated&#39;</span>
484                <span class="n">vec</span> <span class="o">=</span> <span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">:]</span>
485                <span class="n">SuperVec</span> <span class="o">=</span> <span class="p">[[</span><span class="nb">float</span><span class="p">(</span><span class="n">vec</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">3</span><span class="p">)],</span><span class="bp">False</span><span class="p">,</span><span class="mi">4</span><span class="p">]</span>
486                <span class="n">nqi</span> <span class="o">+=</span> <span class="mi">1</span>
487            <span class="k">elif</span> <span class="s">&#39;atom&#39;</span> <span class="ow">in</span> <span class="n">S</span><span class="p">[:</span><span class="mi">4</span><span class="p">]:</span>
488                <span class="n">Atypes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">1</span><span class="p">])</span>
489            <span class="n">S</span> <span class="o">=</span> <span class="nb">file</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
490            <span class="n">line</span> <span class="o">+=</span> <span class="mi">1</span>
491        <span class="nb">file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
492        <span class="c">#read atoms from m40 file</span>
493        <span class="k">if</span> <span class="ow">not</span> <span class="n">SGData</span><span class="p">:</span>
494            <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">The space group was not read before atoms and has been set to &quot;P 1&quot;. &#39;</span>
495            <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&quot;Change this in phase&#39;s General tab.&quot;</span>
496            <span class="n">SGData</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">SGData</span> <span class="c"># P 1</span>
497        <span class="n">waveTypes</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;Fourier&#39;</span><span class="p">,</span><span class="s">&#39;Sawtooth&#39;</span><span class="p">,</span><span class="s">&#39;ZigZag&#39;</span><span class="p">,]</span>
498        <span class="n">filename2</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="s">&#39;.m40&#39;</span>
499        <span class="n">file2</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename2</span><span class="p">,</span><span class="s">&#39;Ur&#39;</span><span class="p">)</span>
500        <span class="n">S</span> <span class="o">=</span> <span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
501        <span class="n">line</span> <span class="o">=</span> <span class="mi">1</span>
502        <span class="bp">self</span><span class="o">.</span><span class="n">errors</span> <span class="o">=</span> <span class="s">&#39;Error reading at line &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
503        <span class="n">nAtoms</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">S</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="mi">0</span><span class="p">])</span>
504        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">4</span><span class="p">):</span>
505            <span class="n">S</span> <span class="o">=</span> <span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>           
506        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">nAtoms</span><span class="p">):</span>
507            <span class="n">S1</span> <span class="o">=</span> <span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
508            <span class="n">S1N</span> <span class="o">=</span> <span class="n">S1</span><span class="o">.</span><span class="n">split</span><span class="p">()[</span><span class="o">-</span><span class="mi">3</span><span class="p">:]</span>   <span class="c"># no. occ, no. pos waves, no. ADP waves</span>
509            <span class="n">S1N</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">S1N</span><span class="p">]</span>
510            <span class="n">S1T</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">S1</span><span class="p">[</span><span class="mi">60</span><span class="p">:</span><span class="mi">63</span><span class="p">])</span>
511            <span class="n">waveType</span> <span class="o">=</span> <span class="n">waveTypes</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">S1T</span><span class="p">[</span><span class="mi">1</span><span class="p">])]</span>
512            <span class="n">crenelType</span> <span class="o">=</span> <span class="s">&#39;&#39;</span>
513            <span class="n">Spos</span> <span class="o">=</span> <span class="p">[]</span>
514            <span class="n">Sadp</span> <span class="o">=</span> <span class="p">[]</span>
515            <span class="n">Sfrac</span> <span class="o">=</span> <span class="p">[]</span>
516            <span class="n">Smag</span> <span class="o">=</span> <span class="p">[]</span>
517            <span class="n">XYZ</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">S1</span><span class="p">[</span><span class="mi">27</span><span class="p">:</span><span class="mi">36</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S1</span><span class="p">[</span><span class="mi">36</span><span class="p">:</span><span class="mi">45</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S1</span><span class="p">[</span><span class="mi">45</span><span class="p">:</span><span class="mi">54</span><span class="p">])]</span>
518            <span class="n">SytSym</span><span class="p">,</span><span class="n">Mult</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SytSym</span><span class="p">(</span><span class="n">XYZ</span><span class="p">,</span><span class="n">SGData</span><span class="p">)</span>
519            <span class="n">aType</span> <span class="o">=</span> <span class="n">Atypes</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">S1</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">11</span><span class="p">])</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
520            <span class="n">Name</span> <span class="o">=</span> <span class="n">S1</span><span class="p">[:</span><span class="mi">8</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
521            <span class="k">if</span> <span class="n">S1</span><span class="p">[</span><span class="mi">11</span><span class="p">:</span><span class="mi">15</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s">&#39;1&#39;</span><span class="p">:</span>
522                <span class="n">S2</span> <span class="o">=</span> <span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
523                <span class="n">Uiso</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">S2</span><span class="p">[:</span><span class="mi">9</span><span class="p">])</span>
524                <span class="n">Uij</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">]</span>
525                <span class="n">IA</span> <span class="o">=</span> <span class="s">&#39;I&#39;</span>
526            <span class="k">elif</span> <span class="n">S1</span><span class="p">[</span><span class="mi">11</span><span class="p">:</span><span class="mi">15</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">==</span> <span class="s">&#39;2&#39;</span><span class="p">:</span>
527                <span class="n">S2</span> <span class="o">=</span> <span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
528                <span class="n">IA</span> <span class="o">=</span> <span class="s">&#39;A&#39;</span>
529                <span class="n">Uiso</span> <span class="o">=</span> <span class="mf">0.</span>
530                <span class="n">Uij</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">S2</span><span class="p">[:</span><span class="mi">9</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S2</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">18</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S2</span><span class="p">[</span><span class="mi">18</span><span class="p">:</span><span class="mi">27</span><span class="p">]),</span>
531                    <span class="nb">float</span><span class="p">(</span><span class="n">S2</span><span class="p">[</span><span class="mi">27</span><span class="p">:</span><span class="mi">36</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S2</span><span class="p">[</span><span class="mi">36</span><span class="p">:</span><span class="mi">45</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">S2</span><span class="p">[</span><span class="mi">45</span><span class="p">:</span><span class="mi">54</span><span class="p">])]</span>
532            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">S1N</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
533                <span class="k">if</span> <span class="ow">not</span> <span class="n">i</span><span class="p">:</span>
534                    <span class="n">FS</span> <span class="o">=</span> <span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
535                    <span class="n">Sfrac</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">FS</span><span class="p">[:</span><span class="mi">9</span><span class="p">])</span>    <span class="c">#&#39;O&#39; or &#39;delta&#39; = &#39;length&#39; for crenel</span>
536                    <span class="k">if</span> <span class="nb">int</span><span class="p">(</span><span class="n">S1T</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>  <span class="c">#&quot;&quot;, &quot;Legendre&quot; or &quot;Xharm&quot; in 18:27 for &quot;crenel&quot;!</span>
537                        <span class="n">waveType</span> <span class="o">=</span> <span class="s">&#39;Crenel/Fourier&#39;</span> <span class="c">#all waves &#39;Fourier&#39; no other choice</span>
538                        <span class="n">crenelType</span> <span class="o">=</span> <span class="n">FS</span><span class="p">[</span><span class="mi">18</span><span class="p">:</span><span class="mi">27</span><span class="p">]</span>
539                <span class="n">Sfrac</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()[:</span><span class="mi">18</span><span class="p">])</span> <span class="c">#if not crenel = Osin &amp; Ocos</span>
540                <span class="c"># else Osin &amp; Ocos except last one is X40 = &#39;Center&#39;</span>
541            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">S1N</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span> 
542                <span class="n">Spos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()[:</span><span class="mi">54</span><span class="p">])</span>
543            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">S1N</span><span class="p">[</span><span class="mi">2</span><span class="p">]):</span>
544                <span class="n">Sadp</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()[:</span><span class="mi">54</span><span class="p">]</span><span class="o">+</span><span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">())</span>
545            <span class="k">if</span> <span class="nb">sum</span><span class="p">(</span><span class="n">S1N</span><span class="p">):</span>    <span class="c">#if any waves: skip mystery line?</span>
546                <span class="n">file2</span><span class="o">.</span><span class="n">readline</span><span class="p">()</span>
547            <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">it</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">Sfrac</span><span class="p">):</span>
548                <span class="k">print</span> <span class="n">i</span><span class="p">,</span><span class="n">it</span>
549                <span class="k">if</span> <span class="ow">not</span> <span class="n">i</span><span class="p">:</span>
550                    <span class="k">if</span> <span class="s">&#39;Crenel&#39;</span> <span class="ow">in</span> <span class="n">waveType</span><span class="p">:</span>
551                        <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">),</span><span class="nb">float</span><span class="p">(</span><span class="n">Sfrac</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">][:</span><span class="mi">9</span><span class="p">])]</span>
552                    <span class="k">else</span><span class="p">:</span>
553                        <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">),]</span>
554                <span class="k">else</span><span class="p">:</span>
555                    <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[:</span><span class="mi">9</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">18</span><span class="p">])]</span>
556                <span class="k">if</span> <span class="s">&#39;Crenel&#39;</span> <span class="ow">in</span> <span class="n">waveType</span> <span class="ow">and</span> <span class="n">i</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">Sfrac</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
557                    <span class="k">del</span> <span class="n">Sfrac</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
558                    <span class="k">break</span>               
559                <span class="n">Sfrac</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">vals</span><span class="p">,</span><span class="bp">False</span><span class="p">]</span>
560                <span class="k">print</span> <span class="n">Sfrac</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
561            <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">it</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">Spos</span><span class="p">):</span>
562                <span class="k">if</span> <span class="n">waveType</span> <span class="ow">in</span> <span class="p">[</span><span class="s">&#39;ZigZag&#39;</span><span class="p">,</span><span class="s">&#39;Sawtooth&#39;</span><span class="p">]</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">i</span><span class="p">:</span>
563                    <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[:</span><span class="mi">9</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">18</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">18</span><span class="p">:</span><span class="mi">27</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">27</span><span class="p">:</span><span class="mi">36</span><span class="p">])]</span>
564                <span class="k">else</span><span class="p">:</span>
565                    <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[:</span><span class="mi">9</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">18</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">18</span><span class="p">:</span><span class="mi">27</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">27</span><span class="p">:</span><span class="mi">36</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">36</span><span class="p">:</span><span class="mi">45</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">45</span><span class="p">:</span><span class="mi">54</span><span class="p">])]</span>
566                <span class="n">Spos</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">vals</span><span class="p">,</span><span class="bp">False</span><span class="p">]</span>
567            <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">it</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">Sadp</span><span class="p">):</span>
568                <span class="n">vals</span> <span class="o">=</span> <span class="p">[</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[:</span><span class="mi">9</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">9</span><span class="p">:</span><span class="mi">18</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">18</span><span class="p">:</span><span class="mi">27</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">27</span><span class="p">:</span><span class="mi">36</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">36</span><span class="p">:</span><span class="mi">45</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">45</span><span class="p">:</span><span class="mi">54</span><span class="p">]),</span>
569                    <span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">54</span><span class="p">:</span><span class="mi">63</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">63</span><span class="p">:</span><span class="mi">72</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">72</span><span class="p">:</span><span class="mi">81</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">81</span><span class="p">:</span><span class="mi">90</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">90</span><span class="p">:</span><span class="mi">99</span><span class="p">]),</span><span class="nb">float</span><span class="p">(</span><span class="n">it</span><span class="p">[</span><span class="mi">99</span><span class="p">:</span><span class="mi">108</span><span class="p">])]</span>               
570                <span class="n">Sadp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">vals</span><span class="p">,</span><span class="bp">False</span><span class="p">]</span>
571            <span class="n">Atom</span> <span class="o">=</span> <span class="p">[</span><span class="n">Name</span><span class="p">,</span><span class="n">aType</span><span class="p">,</span><span class="s">&#39;&#39;</span><span class="p">,</span><span class="n">XYZ</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">XYZ</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="n">XYZ</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span><span class="mf">1.0</span><span class="p">,</span><span class="n">SytSym</span><span class="p">,</span><span class="n">Mult</span><span class="p">,</span><span class="n">IA</span><span class="p">,</span><span class="n">Uiso</span><span class="p">]</span>
572            <span class="n">Atom</span> <span class="o">+=</span> <span class="n">Uij</span>
573            <span class="n">Atom</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ran</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">sys</span><span class="o">.</span><span class="n">maxint</span><span class="p">))</span>
574            <span class="n">Atom</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
575            <span class="n">Atom</span><span class="o">.</span><span class="n">append</span><span class="p">([])</span>
576            <span class="n">Atom</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s">&#39;SS1&#39;</span><span class="p">:{</span><span class="s">&#39;waveType&#39;</span><span class="p">:</span><span class="n">waveType</span><span class="p">,</span><span class="s">&#39;crenelType&#39;</span><span class="p">:</span><span class="n">crenelType</span><span class="p">,</span><span class="s">&#39;Sfrac&#39;</span><span class="p">:</span><span class="n">Sfrac</span><span class="p">,</span><span class="s">&#39;Spos&#39;</span><span class="p">:</span><span class="n">Spos</span><span class="p">,</