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50  <h1>Source code for G2export_shelx</h1><div class="highlight"><pre>
51<span class="c">#!/usr/bin/env python</span>
52<span class="c"># -*- coding: utf-8 -*-</span>
53<span class="c">########### SVN repository information ###################</span>
54<span class="c"># $Date: 2014-12-26 21:08:45 -0600 (Fri, 26 Dec 2014) $</span>
55<span class="c"># $Author: vondreele $</span>
56<span class="c"># $Revision: 1618 $</span>
57<span class="c"># $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/exports/G2export_shelx.py $</span>
58<span class="c"># $Id: G2export_shelx.py 1618 2014-12-27 03:08:45Z vondreele $</span>
59<span class="c">########### SVN repository information ###################</span>
60<span class="sd">&#39;&#39;&#39;</span>
61<span class="sd">*Module G2export_shelx: Examples*</span>
62<span class="sd">-------------------------------------------</span>
63
64<span class="sd">Code to export coordinates in the SHELX .ins format</span>
65<span class="sd">(as best as I can makes sense of it).</span>
66
67<span class="sd">&#39;&#39;&#39;</span>
68<span class="kn">import</span> <span class="nn">os.path</span>
69<span class="kn">import</span> <span class="nn">GSASIIpath</span>
70<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1618 $&quot;</span><span class="p">)</span>
71<span class="kn">import</span> <span class="nn">GSASIIIO</span> <span class="kn">as</span> <span class="nn">G2IO</span>
72<span class="kn">import</span> <span class="nn">GSASIIstrIO</span> <span class="kn">as</span> <span class="nn">G2stIO</span>
73<span class="kn">import</span> <span class="nn">GSASIIlattice</span> <span class="kn">as</span> <span class="nn">G2lat</span>
74<span class="kn">import</span> <span class="nn">GSASIIspc</span> <span class="kn">as</span> <span class="nn">G2spc</span>
75
76<div class="viewcode-block" id="ExportPhaseShelx"><a class="viewcode-back" href="../exports.html#G2export_shelx.ExportPhaseShelx">[docs]</a><span class="k">class</span> <span class="nc">ExportPhaseShelx</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ExportBaseclass</span><span class="p">):</span>
77    <span class="sd">&#39;&#39;&#39;Used to create a SHELX .ins file for a phase</span>
78
79<span class="sd">    :param wx.Frame G2frame: reference to main GSAS-II frame</span>
80<span class="sd">    &#39;&#39;&#39;</span>
81    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">G2frame</span><span class="p">):</span>
82        <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 &lt;parentclass&gt;.__init__</span>
83            <span class="n">G2frame</span><span class="o">=</span><span class="n">G2frame</span><span class="p">,</span>
84            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;SHELX .ins&#39;</span><span class="p">,</span>
85            <span class="n">extension</span><span class="o">=</span><span class="s">&#39;.ins&#39;</span><span class="p">,</span>
86            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Export phase as SHELX .ins file&#39;</span>
87            <span class="p">)</span>
88        <span class="bp">self</span><span class="o">.</span><span class="n">exporttype</span> <span class="o">=</span> <span class="p">[</span><span class="s">&#39;phase&#39;</span><span class="p">]</span>
89        <span class="bp">self</span><span class="o">.</span><span class="n">multiple</span> <span class="o">=</span> <span class="bp">True</span>
90
91<div class="viewcode-block" id="ExportPhaseShelx.Exporter"><a class="viewcode-back" href="../exports.html#G2export_shelx.ExportPhaseShelx.Exporter">[docs]</a>    <span class="k">def</span> <span class="nf">Exporter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">event</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
92        <span class="sd">&#39;&#39;&#39;Export as a SHELX .ins file</span>
93<span class="sd">        &#39;&#39;&#39;</span>
94        <span class="kn">import</span> <span class="nn">re</span>
95        <span class="c"># the export process starts here</span>
96        <span class="bp">self</span><span class="o">.</span><span class="n">InitExport</span><span class="p">(</span><span class="n">event</span><span class="p">)</span>
97        <span class="c"># load all of the tree into a set of dicts</span>
98        <span class="bp">self</span><span class="o">.</span><span class="n">loadTree</span><span class="p">()</span>
99        <span class="c"># create a dict with refined values and their uncertainties</span>
100        <span class="bp">self</span><span class="o">.</span><span class="n">loadParmDict</span><span class="p">()</span>
101        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ExportSelect</span><span class="p">():</span> <span class="k">return</span>  <span class="c"># set export parameters; </span>
102        <span class="n">filename</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span>
103        <span class="k">for</span> <span class="n">phasenam</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">phasenam</span><span class="p">:</span>
104            <span class="n">phasedict</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">Phases</span><span class="p">[</span><span class="n">phasenam</span><span class="p">]</span> <span class="c"># pointer to current phase info            </span>
105            <span class="n">i</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">Phases</span><span class="p">[</span><span class="n">phasenam</span><span class="p">][</span><span class="s">&#39;pId&#39;</span><span class="p">]</span>
106            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">phasenam</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span> <span class="c"># if more than one filename is included, add a phase #</span>
107                <span class="bp">self</span><span class="o">.</span><span class="n">filename</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">1</span><span class="p">]</span> <span class="o">+</span> <span class="s">&quot;_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">extension</span>
108            <span class="n">fp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">OpenFile</span><span class="p">()</span>
109            <span class="c"># title line</span>
110            <span class="bp">self</span><span class="o">.</span><span class="n">Write</span><span class="p">(</span><span class="s">&quot;TITL from &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">G2frame</span><span class="o">.</span><span class="n">GSASprojectfile</span><span class="p">)</span><span class="o">+</span><span class="s">&quot;, phase &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">phasenam</span><span class="p">))</span>
111            <span class="c"># get &amp; write cell parameters</span>
112            <span class="n">cell</span><span class="p">,</span><span class="n">sig</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">GetCell</span><span class="p">(</span><span class="n">phasenam</span><span class="p">)</span>
113            <span class="bp">self</span><span class="o">.</span><span class="n">Write</span><span class="p">(</span><span class="s">&quot;CELL 0.5 {:.5f} {:.5f} {:.5f} {:.3f} {:.3f} {:.3f}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="n">cell</span><span class="p">[:</span><span class="mi">6</span><span class="p">]))</span>
114            <span class="c"># Shelx lattice number</span>
115            <span class="n">lattnum</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;P&#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="mi">2</span><span class="p">,</span><span class="s">&#39;R&#39;</span><span class="p">:</span><span class="mi">2</span><span class="p">,</span><span class="s">&#39;F&#39;</span><span class="p">:</span><span class="mi">3</span><span class="p">,</span><span class="s">&#39;A&#39;</span><span class="p">:</span><span class="mi">4</span><span class="p">,</span><span class="s">&#39;B&#39;</span><span class="p">:</span><span class="mi">5</span><span class="p">,</span><span class="s">&#39;C&#39;</span><span class="p">:</span><span class="mi">6</span><span class="p">}</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">phasedict</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SGData&#39;</span><span class="p">][</span><span class="s">&#39;SGLatt&#39;</span><span class="p">],</span><span class="mi">0</span><span class="p">)</span>
116            <span class="k">if</span> <span class="ow">not</span> <span class="n">phasedict</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SGData&#39;</span><span class="p">][</span><span class="s">&#39;SGInv&#39;</span><span class="p">]:</span> <span class="n">lattnum</span> <span class="o">*=</span> <span class="o">-</span><span class="mi">1</span>
117            <span class="bp">self</span><span class="o">.</span><span class="n">Write</span><span class="p">(</span><span class="s">&quot;LATT &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">lattnum</span><span class="p">))</span>
118            <span class="c"># generate symmetry operations not including centering and center of symmetry</span>
119            <span class="k">for</span> <span class="n">Opr</span> <span class="ow">in</span> <span class="n">phasedict</span><span class="p">[</span><span class="s">&#39;General&#39;</span><span class="p">][</span><span class="s">&#39;SGData&#39;</span><span class="p">][</span><span class="s">&#39;SGOps&#39;</span><span class="p">]:</span>
120                <span class="n">sym</span> <span class="o">=</span> <span class="n">G2spc</span><span class="o">.</span><span class="n">MT2text</span><span class="p">(</span><span class="n">Opr</span><span class="p">)</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">&quot; ,&quot;</span><span class="p">,</span><span class="s">&quot;, &quot;</span><span class="p">)</span>
121                <span class="bp">self</span><span class="o">.</span><span class="n">Write</span><span class="p">(</span><span class="s">&#39;SYMM &#39;</span><span class="o">+</span><span class="n">G2IO</span><span class="o">.</span><span class="n">trim</span><span class="p">(</span><span class="n">sym</span><span class="p">))</span>
122            <span class="c"># scan through atom types, count the number of times that each element occurs</span>
123            <span class="n">AtomsList</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">GetAtoms</span><span class="p">(</span><span class="n">phasenam</span><span class="p">)</span>
124            <span class="n">maxmult</span> <span class="o">=</span> <span class="mi">0</span>
125            <span class="n">elemtypes</span> <span class="o">=</span> <span class="p">{}</span>
126            <span class="k">for</span> <span class="n">lbl</span><span class="p">,</span><span class="n">typ</span><span class="p">,</span><span class="n">mult</span><span class="p">,</span><span class="n">xyz</span><span class="p">,</span><span class="n">td</span> <span class="ow">in</span> <span class="n">AtomsList</span><span class="p">:</span>
127                <span class="n">maxmult</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">maxmult</span><span class="p">,</span><span class="n">mult</span><span class="p">)</span>
128                <span class="n">typ</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="s">&#39;[A-Za-z]+&#39;</span><span class="p">,</span><span class="n">typ</span><span class="p">)</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
129                <span class="n">typ</span> <span class="o">=</span> <span class="n">typ</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
130                <span class="n">typ</span> <span class="o">=</span> <span class="n">typ</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="o">+</span><span class="n">typ</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
131                <span class="k">if</span> <span class="n">elemtypes</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">typ</span><span class="p">)</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
132                    <span class="n">elemtypes</span><span class="p">[</span><span class="n">typ</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
133                <span class="k">else</span><span class="p">:</span>
134                    <span class="n">elemtypes</span><span class="p">[</span><span class="n">typ</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
135            <span class="c"># create scattering factor record</span>
136            <span class="n">s</span> <span class="o">=</span> <span class="s">&quot;SFAC&quot;</span>
137            <span class="n">elemlist</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">elemtypes</span><span class="p">)</span>
138            <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">elemlist</span><span class="p">:</span>
139                <span class="n">s</span> <span class="o">+=</span> <span class="s">&quot; &quot;</span> <span class="o">+</span> <span class="n">elem</span>
140            <span class="bp">self</span><span class="o">.</span><span class="n">Write</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
141            <span class="c"># handle atom records</span>
142            <span class="n">count</span> <span class="o">=</span> <span class="p">{}</span>
143            <span class="k">for</span> <span class="n">lbl</span><span class="p">,</span><span class="n">typ</span><span class="p">,</span><span class="n">mult</span><span class="p">,</span><span class="n">xyz</span><span class="p">,</span><span class="n">td</span> <span class="ow">in</span> <span class="n">AtomsList</span><span class="p">:</span>
144                <span class="n">typ</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="s">&#39;[A-Za-z]+&#39;</span><span class="p">,</span><span class="n">typ</span><span class="p">)</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
145                <span class="n">typ</span> <span class="o">=</span> <span class="n">typ</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
146                <span class="n">typ</span> <span class="o">=</span> <span class="n">typ</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="o">+</span><span class="n">typ</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
147                <span class="k">if</span> <span class="n">count</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">typ</span><span class="p">)</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
148                    <span class="n">count</span><span class="p">[</span><span class="n">typ</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
149                <span class="k">else</span><span class="p">:</span>
150                    <span class="n">count</span><span class="p">[</span><span class="n">typ</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
151                <span class="c"># make a unique &lt;=4 character label, if possible</span>
152                <span class="k">if</span> <span class="n">elemtypes</span><span class="p">[</span><span class="n">typ</span><span class="p">]</span> <span class="o">&lt;=</span> <span class="mi">99</span><span class="p">:</span>
153                    <span class="n">lbl</span> <span class="o">=</span> <span class="s">&quot;{:s}{:d}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">typ</span><span class="p">,</span><span class="n">count</span><span class="p">[</span><span class="n">typ</span><span class="p">])</span>
154                <span class="k">else</span><span class="p">:</span> <span class="c"># more than 99 atoms, use hexadecimal notation</span>
155                    <span class="n">lbl</span> <span class="o">=</span> <span class="n">typ</span> <span class="o">+</span> <span class="s">&quot;{:X}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">count</span><span class="p">[</span><span class="n">typ</span><span class="p">])[</span><span class="o">-</span><span class="mi">2</span><span class="p">:]</span>
156                <span class="n">sfnum</span> <span class="o">=</span> <span class="n">elemlist</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">typ</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span> <span class="c"># element number in scattering factor list</span>
157                <span class="n">l</span> <span class="o">=</span> <span class="n">lbl</span><span class="o">+</span><span class="s">&quot; &quot;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">sfnum</span><span class="p">)</span>
158                <span class="n">l</span> <span class="o">+=</span> <span class="s">&quot; {:.5f} {:.5f} {:.5f}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">xyz</span><span class="p">[:</span><span class="mi">3</span><span class="p">]])</span>
159                <span class="k">if</span> <span class="n">mult</span> <span class="o">==</span> <span class="n">maxmult</span><span class="p">:</span>
160                    <span class="n">m</span> <span class="o">=</span> <span class="mi">1</span>
161                <span class="k">else</span><span class="p">:</span>
162                    <span class="n">m</span> <span class="o">=</span> <span class="mf">1.</span><span class="o">*</span><span class="n">mult</span><span class="o">/</span><span class="n">maxmult</span>
163                <span class="k">if</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">3</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="c"># frac</span>
164                    <span class="n">occ</span> <span class="o">=</span> <span class="mi">10</span> <span class="o">+</span> <span class="n">m</span>
165                <span class="k">else</span><span class="p">:</span>
166                    <span class="n">occ</span> <span class="o">=</span> <span class="n">m</span> <span class="o">*</span> <span class="n">xyz</span><span class="p">[</span><span class="mi">3</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
167                <span class="n">l</span> <span class="o">+=</span> <span class="s">&quot; {:.3f}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">occ</span><span class="p">)</span>
168                <span class="k">for</span> <span class="n">val</span><span class="p">,</span><span class="n">sig</span> <span class="ow">in</span> <span class="n">td</span><span class="p">:</span>
169                    <span class="n">l</span> <span class="o">+=</span> <span class="s">&quot; {:.3f}&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">val</span><span class="p">)</span>                   
170                <span class="bp">self</span><span class="o">.</span><span class="n">Write</span><span class="p">(</span><span class="n">l</span><span class="p">)</span>
171            <span class="bp">self</span><span class="o">.</span><span class="n">Write</span><span class="p">(</span><span class="s">&#39;END&#39;</span><span class="p">)</span>
172            <span class="bp">self</span><span class="o">.</span><span class="n">CloseFile</span><span class="p">()</span>
173            <span class="k">print</span><span class="p">(</span><span class="s">&#39;Phase &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">phasenam</span><span class="p">)</span><span class="o">+</span><span class="s">&#39; written to file &#39;</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">fullpath</span><span class="p">))</span></div></div>
174</pre></div>
175
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