Ignore:
Timestamp:
Mar 14, 2015 5:35:03 PM (8 years ago)
Author:
toby
Message:

change sphinx docs links; rebuild & fixing minor formatting

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1 edited

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  • sphinxdocs/build/html/_modules/G2phase.html

    r1513 r1709  
    5151<span class="c"># -*- coding: utf-8 -*-</span>
    5252<span class="c">########### SVN repository information ###################</span>
    53 <span class="c"># $Date: 2014-09-26 09:41:33 -0500 (Fri, 26 Sep 2014) $</span>
     53<span class="c"># $Date: 2015-01-08 16:24:32 -0600 (Thu, 08 Jan 2015) $</span>
    5454<span class="c"># $Author: vondreele $</span>
    55 <span class="c"># $Revision: 1506 $</span>
     55<span class="c"># $Revision: 1625 $</span>
    5656<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2phase.py $</span>
    57 <span class="c"># $Id: G2phase.py 1506 2014-09-26 14:41:33Z vondreele $</span>
     57<span class="c"># $Id: G2phase.py 1625 2015-01-08 22:24:32Z vondreele $</span>
    5858<span class="c">########### SVN repository information ###################</span>
    5959<span class="c">#</span>
    … …  
    7878<span class="kn">import</span> <span class="nn">GSASIIlattice</span> <span class="kn">as</span> <span class="nn">G2lat</span>
    7979<span class="kn">import</span> <span class="nn">GSASIIpath</span>
    80 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1506 $&quot;</span><span class="p">)</span>
     80<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1625 $&quot;</span><span class="p">)</span>
    8181
    8282<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>
    … …  
    454454            <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>
    455455                <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 too high; GSAS-II limited to (3+1) supersymmetry&quot;</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>           
    457457                <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>
    458459                <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>
    459460                    <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>
    … …  
    461462                    <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>
    462463                <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>
    463                 <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>
     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>
    464465                <span class="c"># space group processing failed, try to look up name in table</span>
    465466                <span class="k">while</span> <span class="n">E</span><span class="p">:</span>
    … …  
    477478                    <span class="n">dlg</span><span class="o">.</span><span class="n">Destroy</span><span class="p">()</span>
    478479                <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>
    479                 <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>
    480480            <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>
    481481                <span class="k">if</span> <span class="n">nqi</span><span class="p">:</span>
    … …  
    483483                <span class="n">Type</span> <span class="o">=</span> <span class="s">&#39;modulated&#39;</span>
    484484                <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="p">[</span><span class="n">nqi</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">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>
     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>
    486486                <span class="n">nqi</span> <span class="o">+=</span> <span class="mi">1</span>
    487487            <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>
    … …  
    560560                <span class="k">print</span> <span class="n">Sfrac</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
    561561            <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="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>
     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>
    563566                <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>
    564567            <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>
    … …  
    568571            <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>
    569572            <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>
    570576            <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">,</span><span class="s">&#39;Sadp&#39;</span><span class="p">:</span><span class="n">Sadp</span><span class="p">,</span><span class="s">&#39;Smag&#39;</span><span class="p">:</span><span class="n">Smag</span><span class="p">}})</span>    <span class="c">#SS2 is for (3+2), etc.</span>
    571             <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>
    572577            <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>
    573578        <span class="n">file2</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
    … …  
    582587        <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SuperVec&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">SuperVec</span>
    583588        <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SuperSg&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">SuperSg</span>
     589        <span class="k">if</span> <span class="n">SuperSg</span><span class="p">:</span>
     590            <span class="n">Phase</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SSGData&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">SSpcGroup</span><span class="p">(</span><span class="n">SGData</span><span class="p">,</span><span class="n">SuperSg</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
    584591        <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">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>
    585592        <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>
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