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Timestamp:
Oct 10, 2015 9:59:34 PM (7 years ago)
Author:
toby
Message:

rebuild docs

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1 edited

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  • sphinxdocs/build/html/_modules/G2phase_CIF.html

    r1832 r1998  
    5151<span class="c"># -*- coding: utf-8 -*-</span>
    5252<span class="c">########### SVN repository information ###################</span>
    53 <span class="c"># $Date: 2015-03-25 15:42:15 -0500 (Wed, 25 Mar 2015) $</span>
    54 <span class="c"># $Author: vondreele $</span>
    55 <span class="c"># $Revision: 1762 $</span>
     53<span class="c"># $Date: 2015-10-05 14:05:04 -0500 (Mon, 05 Oct 2015) $</span>
     54<span class="c"># $Author: toby $</span>
     55<span class="c"># $Revision: 1985 $</span>
    5656<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2phase_CIF.py $</span>
    57 <span class="c"># $Id: G2phase_CIF.py 1762 2015-03-25 20:42:15Z vondreele $</span>
     57<span class="c"># $Id: G2phase_CIF.py 1985 2015-10-05 19:05:04Z toby $</span>
    5858<span class="c">########### SVN repository information ###################</span>
    5959<span class="sd">&#39;&#39;&#39;</span>
    … …  
    8080<span class="kn">import</span> <span class="nn">GSASIIpy3</span> <span class="kn">as</span> <span class="nn">G2p3</span>
    8181<span class="kn">import</span> <span class="nn">GSASIIpath</span>
    82 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1762 $&quot;</span><span class="p">)</span>
     82<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1985 $&quot;</span><span class="p">)</span>
    8383<span class="kn">import</span> <span class="nn">CifFile</span> <span class="kn">as</span> <span class="nn">cif</span> <span class="c"># PyCifRW from James Hester</span>
    8484
    … …  
    224224                <span class="n">atomkeys</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">atomloop</span><span class="o">.</span><span class="n">keys</span><span class="p">()]</span>
    225225                <span class="k">if</span> <span class="ow">not</span> <span class="n">blk</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;_atom_site_type_symbol&#39;</span><span class="p">):</span>
    226                     <span class="bp">self</span><span class="o">.</span><span class="n">isodistort_warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">lack of atom types prevents ISODISTORT processing&#39;</span>
     226                    <span class="bp">self</span><span class="o">.</span><span class="n">isodistort_warnings</span> <span class="o">+=</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">atom types are missing. </span><span class="se">\n</span><span class="s"> Check &amp; revise atom types as needed&#39;</span>
    227227                <span class="k">if</span> <span class="n">blk</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;_atom_site_aniso_label&#39;</span><span class="p">):</span>
    228228                    <span class="n">anisoloop</span> <span class="o">=</span> <span class="n">blk</span><span class="o">.</span><span class="n">GetLoop</span><span class="p">(</span><span class="s">&#39;_atom_site_aniso_label&#39;</span><span class="p">)</span>
    229229                    <span class="n">anisokeys</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">anisoloop</span><span class="o">.</span><span class="n">keys</span><span class="p">()]</span>
     230                    <span class="n">anisolabels</span> <span class="o">=</span> <span class="n">blk</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;_atom_site_aniso_label&#39;</span><span class="p">)</span>
    230231                <span class="k">else</span><span class="p">:</span>
    231232                    <span class="n">anisoloop</span> <span class="o">=</span> <span class="bp">None</span>
    232233                    <span class="n">anisokeys</span> <span class="o">=</span> <span class="p">[]</span>
     234                    <span class="n">anisolabels</span> <span class="o">=</span> <span class="p">[]</span>
    233235                <span class="bp">self</span><span class="o">.</span><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="p">[]</span>
    234236                <span class="n">G2AtomDict</span> <span class="o">=</span> <span class="p">{</span>  <span class="s">&#39;_atom_site_type_symbol&#39;</span> <span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
    … …  
    254256                        <span class="k">if</span> <span class="n">col</span> <span class="o">&gt;=</span> <span class="mi">3</span><span class="p">:</span>
    255257                            <span class="n">atomlist</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="o">=</span> <span class="n">cif</span><span class="o">.</span><span class="n">get_number_with_esd</span><span class="p">(</span><span class="n">val</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     258                            <span class="k">if</span> <span class="n">col</span> <span class="o">&gt;=</span> <span class="mi">11</span><span class="p">:</span> <span class="n">atomlist</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="c"># if any Aniso term is defined, set flag</span>
    256259                        <span class="k">elif</span> <span class="n">col</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
    257260                            <span class="n">atomlist</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="o">=</span> <span class="n">val</span>
    … …  
    261264                                <span class="n">atomlist</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>
    262265                        <span class="k">elif</span> <span class="n">key</span> <span class="o">==</span> <span class="s">&#39;_atom_site_u_iso_or_equiv&#39;</span><span class="p">:</span>
    263                             <span class="n">atomlist</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span><span class="n">cif</span><span class="o">.</span><span class="n">get_number_with_esd</span><span class="p">(</span><span class="n">val</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     266                            <span class="n">uisoval</span> <span class="o">=</span><span class="n">cif</span><span class="o">.</span><span class="n">get_number_with_esd</span><span class="p">(</span><span class="n">val</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
     267                            <span class="k">if</span> <span class="n">uisoval</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="n">uisoval</span>
    264268                    <span class="k">if</span> <span class="ow">not</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">and</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
    265                         <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">2</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>
    266                             <span class="n">typ</span> <span class="o">=</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()[:</span><span class="n">i</span><span class="p">]</span>
    267                             <span class="k">if</span> <span class="n">G2elem</span><span class="o">.</span><span class="n">CheckElement</span><span class="p">(</span><span class="n">typ</span><span class="p">):</span>
    268                                 <span class="n">atomlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">typ</span>
    269                             <span class="k">if</span> <span class="ow">not</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;Xe&#39;</span>
    270                     <span class="n">ulbl</span> <span class="o">=</span> <span class="s">&#39;_atom_site_aniso_label&#39;</span>
    271                     <span class="k">if</span>  <span class="n">atomlist</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="ow">and</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">blk</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ulbl</span><span class="p">):</span>
    272                         <span class="k">for</span> <span class="n">val</span><span class="p">,</span><span class="n">key</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">anisoloop</span><span class="o">.</span><span class="n">GetKeyedPacket</span><span class="p">(</span><span class="n">ulbl</span><span class="p">,</span><span class="n">atomlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
    273                                            <span class="n">anisokeys</span><span class="p">):</span>
     269                        <span class="n">typ</span> <span class="o">=</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">rstrip</span><span class="p">(</span><span class="s">&#39;0123456789-+&#39;</span><span class="p">)</span>
     270                        <span class="k">if</span> <span class="n">G2elem</span><span class="o">.</span><span class="n">CheckElement</span><span class="p">(</span><span class="n">typ</span><span class="p">):</span>
     271                            <span class="n">atomlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">typ</span>
     272                        <span class="k">if</span> <span class="ow">not</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
     273                            <span class="n">atomlist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="s">&#39;Xe&#39;</span>
     274                            <span class="bp">self</span><span class="o">.</span><span class="n">warnings</span> <span class="o">+=</span> <span class="s">&#39; Atom type &#39;</span><span class="o">+</span><span class="n">typ</span><span class="o">+</span><span class="s">&#39; not recognized; Xe assumed</span><span class="se">\n</span><span class="s">&#39;</span>
     275                    <span class="k">if</span> <span class="n">atomlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">anisolabels</span><span class="p">:</span> <span class="c"># does this atom have aniso values in separate loop?</span>
     276                        <span class="n">atomlist</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="c"># set the aniso flag</span>
     277                        <span class="k">for</span> <span class="n">val</span><span class="p">,</span><span class="n">key</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span> <span class="c"># load the values</span>
     278                                <span class="n">anisoloop</span><span class="o">.</span><span class="n">GetKeyedPacket</span><span class="p">(</span><span class="s">&#39;_atom_site_aniso_label&#39;</span><span class="p">,</span><span class="n">atomlist</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
     279                                <span class="n">anisokeys</span><span class="p">):</span>
    274280                            <span class="n">col</span> <span class="o">=</span> <span class="n">G2AtomDict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key</span><span class="p">)</span>
    275281                            <span class="k">if</span> <span class="n">col</span><span class="p">:</span>
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