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

change sphinx docs links; rebuild & fixing minor formatting

File:
1 edited

Legend:

Unmodified
Added
Removed

  • sphinxdocs/build/html/_modules/GSASIIobj.html

    r1513 r1709  
    5252<span class="c">#GSASIIobj - data objects for GSAS-II</span>
    5353<span class="c">########### SVN repository information ###################</span>
    54 <span class="c"># $Date: 2014-09-14 19:48:39 -0500 (Sun, 14 Sep 2014) $</span>
    55 <span class="c"># $Author: vondreele $</span>
    56 <span class="c"># $Revision: 1496 $</span>
     54<span class="c"># $Date: 2015-03-12 17:09:00 -0500 (Thu, 12 Mar 2015) $</span>
     55<span class="c"># $Author: toby $</span>
     56<span class="c"># $Revision: 1698 $</span>
    5757<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIobj.py $</span>
    58 <span class="c"># $Id: GSASIIobj.py 1496 2014-09-15 00:48:39Z vondreele $</span>
     58<span class="c"># $Id: GSASIIobj.py 1698 2015-03-12 22:09:00Z toby $</span>
    5959<span class="c">########### SVN repository information ###################</span>
    6060
    … …  
    441441<span class="sd">cia               ADP flag: Isotropic (&#39;I&#39;) or Anisotropic (&#39;A&#39;)</span>
    442442<span class="sd">cia+1             Uiso (float)</span>
    443 <span class="sd">cia+2...cia+6     U11, U22, U33, U12, U13, U23 (6 floats)</span>
    444 <span class="sd">atom[-1]                unique atom identifier (int)</span>
     443<span class="sd">cia+2...cia+7     U11, U22, U33, U12, U13, U23 (6 floats)</span>
     444<span class="sd">atom[cia+8]       unique atom identifier (int)</span>
     445
    445446<span class="sd">==============   ====================================================</span>
    446447
    … …  
    894895<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
    895896
    896 <span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1496 $&quot;</span><span class="p">)</span>
     897<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1698 $&quot;</span><span class="p">)</span>
    897898
    898899<span class="n">DefaultControls</span> <span class="o">=</span> <span class="p">{</span>
    … …  
    901902    <span class="s">&#39;minF/sig&#39;</span><span class="p">:</span><span class="mi">0</span><span class="p">,</span>
    902903    <span class="s">&#39;Author&#39;</span><span class="p">:</span><span class="s">&#39;no name&#39;</span><span class="p">,</span>
    903     <span class="s">&#39;FreeVar1&#39;</span><span class="p">:</span><span class="s">&#39;Sample humidity (%)&#39;</span><span class="p">,</span>
    904     <span class="s">&#39;FreeVar2&#39;</span><span class="p">:</span><span class="s">&#39;Sample voltage (V)&#39;</span><span class="p">,</span>
    905     <span class="s">&#39;FreeVar3&#39;</span><span class="p">:</span><span class="s">&#39;Applied load (MN)&#39;</span><span class="p">,</span>
     904    <span class="s">&#39;FreePrm1&#39;</span><span class="p">:</span><span class="s">&#39;Sample humidity (%)&#39;</span><span class="p">,</span>
     905    <span class="s">&#39;FreePrm2&#39;</span><span class="p">:</span><span class="s">&#39;Sample voltage (V)&#39;</span><span class="p">,</span>
     906    <span class="s">&#39;FreePrm3&#39;</span><span class="p">:</span><span class="s">&#39;Applied load (MN)&#39;</span><span class="p">,</span>
    906907    <span class="p">}</span>
    907908<span class="sd">&#39;&#39;&#39;Values to be used as defaults for the initial contents of the ``Controls``</span>
    … …  
    10281029        <span class="n">AtomRanIdLookup</span><span class="p">[</span><span class="n">pId</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
    10291030        <span class="k">for</span> <span class="n">iatm</span><span class="p">,</span><span class="n">at</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">Phases</span><span class="p">[</span><span class="n">ph</span><span class="p">][</span><span class="s">&#39;Atoms&#39;</span><span class="p">]):</span>
    1030             <span class="n">ranId</span> <span class="o">=</span> <span class="n">at</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
     1031            <span class="n">ranId</span> <span class="o">=</span> <span class="n">at</span><span class="p">[</span><span class="n">cia</span><span class="o">+</span><span class="mi">8</span><span class="p">]</span>
    10311032            <span class="k">while</span> <span class="n">ranId</span> <span class="ow">in</span> <span class="n">AtomRanIdLookup</span><span class="p">[</span><span class="n">pId</span><span class="p">]:</span> <span class="c"># check for dups</span>
    10321033                <span class="k">print</span> <span class="p">(</span><span class="s">&quot;</span><span class="se">\n\n</span><span class="s">*** Phase &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">ph</span><span class="p">)</span><span class="o">+</span><span class="s">&quot; atom &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">iatm</span><span class="p">)</span><span class="o">+</span><span class="s">&quot; has repeated ranId. Fixing.</span><span class="se">\n</span><span class="s">&quot;</span><span class="p">)</span>
    1033                 <span class="n">at</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">ranId</span> <span class="o">=</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>
     1034                <span class="n">at</span><span class="p">[</span><span class="n">cia</span><span class="o">+</span><span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="n">ranId</span> <span class="o">=</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>
    10341035            <span class="n">AtomRanIdLookup</span><span class="p">[</span><span class="n">pId</span><span class="p">][</span><span class="n">ranId</span><span class="p">]</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">iatm</span><span class="p">)</span>
    10351036            <span class="k">if</span> <span class="n">Phases</span><span class="p">[</span><span class="n">ph</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><span class="p">:</span>
    … …  
    13421343        <span class="s">&#39;RBRTr;.*&#39;</span> <span class="p">:</span> <span class="s">&#39;Residue rigid body torsion parameter&#39;</span><span class="p">,</span>
    13431344        <span class="s">&#39;RBR([TLS])([123AB][123AB])&#39;</span> <span class="p">:</span> <span class="s">&#39;Residue rigid body group disp. param.&#39;</span><span class="p">,</span>
    1344         <span class="c"># Global vars (::&lt;var&gt;)</span>
    13451345        <span class="s">&#39;constr([0-9]*)&#39;</span> <span class="p">:</span> <span class="s">&#39;Parameter from constraint&#39;</span><span class="p">,</span>
     1346        <span class="c"># supersymmetry parameters  p::&lt;var&gt;:a:o &#39;Flen&#39;,&#39;Fcent&#39;?</span>
     1347        <span class="s">&#39;mV([0-2])$&#39;</span> <span class="p">:</span> <span class="s">&#39;Modulation vector component </span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
     1348        <span class="s">&#39;Fsin&#39;</span>  <span class="p">:</span>   <span class="s">&#39;Sin site fraction modulation&#39;</span><span class="p">,</span>
     1349        <span class="s">&#39;Fcos&#39;</span>  <span class="p">:</span>   <span class="s">&#39;Cos site fraction modulation&#39;</span><span class="p">,</span>
     1350        <span class="s">&#39;Fzero&#39;</span>  <span class="p">:</span>   <span class="s">&#39;Crenel function offset&#39;</span><span class="p">,</span>
     1351        <span class="s">&#39;Fwid&#39;</span>   <span class="p">:</span>   <span class="s">&#39;Crenel function width&#39;</span><span class="p">,</span>
     1352        <span class="s">&#39;Tzero&#39;</span>  <span class="p">:</span>   <span class="s">&#39;Sawtooth/ZigZag location&#39;</span><span class="p">,</span>
     1353        <span class="s">&#39;([XYZ])slope&#39;</span><span class="p">:</span> <span class="s">&#39;Sawtooth/ZigZag slope for </span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
     1354        <span class="s">&#39;([XYZ])sin&#39;</span>  <span class="p">:</span> <span class="s">&#39;Sin position wave for </span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
     1355        <span class="s">&#39;([XYZ])cos&#39;</span>  <span class="p">:</span> <span class="s">&#39;Cos position wave for </span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
     1356        <span class="s">&#39;U([123][123])sin$&#39;</span> <span class="p">:</span>  <span class="s">&#39;Sin thermal wave for U</span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
     1357        <span class="s">&#39;U([123][123])cos$&#39;</span> <span class="p">:</span>  <span class="s">&#39;Cos thermal wave for U</span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
     1358        <span class="s">&#39;M([XYZ])sin$&#39;</span> <span class="p">:</span>  <span class="s">&#39;Sin mag. moment wave for </span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
     1359        <span class="s">&#39;M([XYZ])cos$&#39;</span> <span class="p">:</span>  <span class="s">&#39;Cos mag. moment wave for </span><span class="se">\\</span><span class="s">1&#39;</span><span class="p">,</span>
    13461360        <span class="c"># SASD vars (l:&lt;var&gt;;l = component)</span>
    13471361        <span class="s">&#39;Aspect ratio&#39;</span> <span class="p">:</span> <span class="s">&#39;Particle aspect ratio&#39;</span><span class="p">,</span>
    … …  
    13891403        <span class="n">m</span> <span class="o">=</span> <span class="n">key</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
    13901404        <span class="k">if</span> <span class="n">m</span><span class="p">:</span>
     1405            <span class="n">reVarDesc</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
    13911406            <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">expand</span><span class="p">(</span><span class="n">reVarDesc</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
    13921407    <span class="k">return</span> <span class="bp">None</span>
Note: See TracChangeset for help on using the changeset viewer.