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58  <span class="target" id="module-GSASIIobj"></span><div class="section" id="gsasiiobj-data-objects">
59<h1><em>GSASIIobj: Data objects</em><a class="headerlink" href="#gsasiiobj-data-objects" title="Permalink to this headline">¶</a></h1>
60<p>This module defines and/or documents the data structures used in GSAS-II, as well
61as provides misc. support routines.</p>
62<div class="section" id="constraints-tree-item">
63<h2>Constraints Tree Item<a class="headerlink" href="#constraints-tree-item" title="Permalink to this headline">¶</a></h2>
64<span class="target" id="constraints-table"></span><p id="index-0">Constraints are stored in a dict, separated into groups.
65Note that parameter are named in the following pattern,
66p:h:&lt;var&gt;:n, where p is the phase number, h is the histogram number
67&lt;var&gt; is a variable name and n is the parameter number.
68If a parameter does not depend on a histogram or phase or is unnumbered, that
69number is omitted.
70Note that the contents of each dict item is a List where each element in the
71list is a <a class="reference internal" href="#constraint-definitions-table"><em>constraint definition objects</em></a>.
72The constraints in this form are converted in
73<a class="reference internal" href="GSASIIstruc.html#GSASIIstrIO.ProcessConstraints" title="GSASIIstrIO.ProcessConstraints"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrIO.ProcessConstraints()</span></tt></a> to the form used in <a class="reference internal" href="GSASIImapvars.html#module-GSASIImapvars" title="GSASIImapvars"><tt class="xref py py-mod docutils literal"><span class="pre">GSASIImapvars</span></tt></a></p>
74<p>The keys in the Constraints dict are:</p>
75<table border="1" class="docutils">
76<colgroup>
77<col width="16%" />
78<col width="84%" />
79</colgroup>
80<thead valign="bottom">
81<tr class="row-odd"><th class="head">key</th>
82<th class="head">explanation</th>
83</tr>
84</thead>
85<tbody valign="top">
86<tr class="row-even"><td>Hist</td>
87<td>This specifies a list of constraints on
88histogram-related parameters,
89which will be of form :h:&lt;var&gt;:n.</td>
90</tr>
91<tr class="row-odd"><td>HAP</td>
92<td>This specifies a list of constraints on parameters
93that are defined for every histogram in each phase
94and are of form p:h:&lt;var&gt;:n.</td>
95</tr>
96<tr class="row-even"><td>Phase</td>
97<td>This specifies a list of constraints on phase
98parameters,
99which will be of form p::&lt;var&gt;:n.</td>
100</tr>
101<tr class="row-odd"><td>Global</td>
102<td>This specifies a list of constraints on parameters
103that are not tied to a histogram or phase and
104are of form ::&lt;var&gt;:n</td>
105</tr>
106</tbody>
107</table>
108<span class="target" id="constraint-definitions-table"></span><p id="index-1">Each constraint is defined as an item in a list. Each constraint is of form:</p>
109<div class="highlight-python"><pre>[[&lt;mult1&gt;, &lt;var1&gt;], [&lt;mult2&gt;, &lt;var2&gt;],..., &lt;fixedval&gt;, &lt;varyflag&gt;, &lt;constype&gt;]</pre>
110</div>
111<p>Where the variable pair list item containing two values [&lt;mult&gt;, &lt;var&gt;], where:</p>
112<blockquote>
113<div><ul>
114<li><p class="first">&lt;mult&gt; is a multiplier for the constraint (float)</p>
115</li>
116<li><dl class="first docutils">
117<dt>&lt;var&gt; a <a class="reference internal" href="#GSASIIobj.G2VarObj" title="GSASIIobj.G2VarObj"><tt class="xref py py-class docutils literal"><span class="pre">G2VarObj</span></tt></a> object (previously a str variable name of form</dt>
118<dd><p class="first last">&#8216;p:h:name[:at]&#8217;)</p>
119</dd>
120</dl>
121</li>
122</ul>
123</div></blockquote>
124<p>Note that the last three items in the list play a special role:</p>
125<blockquote>
126<div><ul>
127<li><p class="first">&lt;fixedval&gt; is the fixed value for a <cite>constant equation</cite> (<tt class="docutils literal"><span class="pre">constype=c</span></tt>)
128constraint or is None. For a <cite>New variable</cite> (<tt class="docutils literal"><span class="pre">constype=f</span></tt>) constraint,
129a variable name can be specified as a str (used for externally
130generated constraints)</p>
131</li>
132<li><p class="first">&lt;varyflag&gt; is True or False for <cite>New variable</cite> (<tt class="docutils literal"><span class="pre">constype=f</span></tt>) constraints
133or is None. This will be implemented in the future to indicate if these variables
134should be refined.</p>
135</li>
136<li><p class="first">&lt;constype&gt; is one of four letters, &#8216;e&#8217;, &#8216;c&#8217;, &#8216;h&#8217;, &#8216;f&#8217; that determines the type of constraint:</p>
137<blockquote>
138<div><ul class="simple">
139<li>&#8216;e&#8217; defines a set of equivalent variables. Only the first variable is refined (if the
140appropriate refine flag is set) and and all other equivalent variables in the list
141are generated from that variable, using the appropriate multipliers.</li>
142<li>&#8216;c&#8217; defines a constraint equation of form,
143<span class="math">\(m_1 \times var_1 + m_2 \times var_2 + ... = c\)</span></li>
144<li>&#8216;h&#8217; defines a variable to hold (not vary). Any variable on this list is not varied,
145even if its refinement flag is set. Only one [mult,var] pair is allowed in a hold
146constraint and the mult value is ignored.
147This is of particular value when needing to hold one or more variables where a
148single flag controls a set of variables such as, coordinates,
149the reciprocal metric tensor or anisotropic displacement parameter.</li>
150<li>&#8216;f&#8217; defines a new variable (function) according to relationship
151<span class="math">\(newvar = m_1 \times var_1 + m_2 \times var_2 + ...\)</span></li>
152</ul>
153</div></blockquote>
154</li>
155</ul>
156</div></blockquote>
157</div>
158<div class="section" id="covariance-tree-item">
159<h2>Covariance Tree Item<a class="headerlink" href="#covariance-tree-item" title="Permalink to this headline">¶</a></h2>
160<span class="target" id="covariance-table"></span><p id="index-2">The Covariance tree item has results from the last least-squares run. They
161are stored in a dict with these keys:</p>
162<table border="1" class="docutils">
163<colgroup>
164<col width="16%" />
165<col width="19%" />
166<col width="65%" />
167</colgroup>
168<thead valign="bottom">
169<tr class="row-odd"><th class="head">key</th>
170<th class="head">sub-key</th>
171<th class="head">explanation</th>
172</tr>
173</thead>
174<tbody valign="top">
175<tr class="row-even"><td>newCellDict</td>
176<td></td>
177<td>dict with lattice parameters computed by
178<a class="reference internal" href="GSASIIstruc.html#GSASIIstrMath.GetNewCellParms" title="GSASIIstrMath.GetNewCellParms"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrMath.GetNewCellParms()</span></tt></a> (dict)</td>
179</tr>
180<tr class="row-odd"><td>title</td>
181<td></td>
182<td>Name of gpx file(?) (str)</td>
183</tr>
184<tr class="row-even"><td>variables</td>
185<td></td>
186<td>Values for all N refined variables
187(list of float values, length N,
188ordered to match varyList)</td>
189</tr>
190<tr class="row-odd"><td>sig</td>
191<td></td>
192<td>Uncertainty values for all N refined variables
193(list of float values, length N,
194ordered to match varyList)</td>
195</tr>
196<tr class="row-even"><td>varyList</td>
197<td></td>
198<td>List of directly refined variables
199(list of str values, length N)</td>
200</tr>
201<tr class="row-odd"><td>newAtomDict</td>
202<td></td>
203<td>dict with atom position values computed in
204<a class="reference internal" href="GSASIIstruc.html#GSASIIstrMath.ApplyXYZshifts" title="GSASIIstrMath.ApplyXYZshifts"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrMath.ApplyXYZshifts()</span></tt></a> (dict)</td>
205</tr>
206<tr class="row-even"><td>Rvals</td>
207<td></td>
208<td>R-factors, GOF, Marquardt value for last
209refinement cycle (dict)</td>
210</tr>
211<tr class="row-odd"><td></td>
212<td>Nobs</td>
213<td>Number of observed data points (int)</td>
214</tr>
215<tr class="row-even"><td></td>
216<td>Rwp</td>
217<td>overall weighted profile R-factor (%, float)</td>
218</tr>
219<tr class="row-odd"><td></td>
220<td>chisq</td>
221<td>sum[w*(Iobs-Icalc)**2] for all data
222note this is not the reduced chi squared (float)</td>
223</tr>
224<tr class="row-even"><td></td>
225<td>lamMax</td>
226<td>Marquardt value applied to Hessian diagonal
227(float)</td>
228</tr>
229<tr class="row-odd"><td></td>
230<td>GOF</td>
231<td>The goodness-of-fit, aka square root of
232the reduced chi squared. (float)</td>
233</tr>
234<tr class="row-even"><td>covMatrix</td>
235<td></td>
236<td>The (NxN) covVariance matrix (np.array)</td>
237</tr>
238</tbody>
239</table>
240</div>
241<div class="section" id="phase-tree-items">
242<h2>Phase Tree Items<a class="headerlink" href="#phase-tree-items" title="Permalink to this headline">¶</a></h2>
243<span class="target" id="phase-table"></span><p id="index-3">Phase information is stored in the GSAS-II data tree as children of the
244Phases item in a dict with keys:</p>
245<table border="1" class="docutils">
246<colgroup>
247<col width="10%" />
248<col width="15%" />
249<col width="75%" />
250</colgroup>
251<thead valign="bottom">
252<tr class="row-odd"><th class="head">key</th>
253<th class="head">sub-key</th>
254<th class="head">explanation</th>
255</tr>
256</thead>
257<tbody valign="top">
258<tr class="row-even"><td>General</td>
259<td></td>
260<td>Overall information for the phase (dict)</td>
261</tr>
262<tr class="row-odd"><td></td>
263<td>AtomPtrs</td>
264<td>list of four locations to use to pull info
265from the atom records (list)</td>
266</tr>
267<tr class="row-even"><td></td>
268<td>F000X</td>
269<td>x-ray F(000) intensity (float)</td>
270</tr>
271<tr class="row-odd"><td></td>
272<td>F000N</td>
273<td>neutron F(000) intensity (float)</td>
274</tr>
275<tr class="row-even"><td></td>
276<td>Mydir</td>
277<td>directory of current .gpx file (str)</td>
278</tr>
279<tr class="row-odd"><td></td>
280<td>MCSA controls</td>
281<td>Monte Carlo-Simulated Annealing controls (dict)</td>
282</tr>
283<tr class="row-even"><td></td>
284<td>Cell</td>
285<td>List with 8 items: cell refinement flag (bool)
286a, b, c, (Angstrom, float)
287alpha, beta &amp; gamma (degrees, float)
288volume (A^3, float)</td>
289</tr>
290<tr class="row-odd"><td></td>
291<td>Type</td>
292<td>&#8216;nuclear&#8217; or &#8216;macromolecular&#8217; for now (str)</td>
293</tr>
294<tr class="row-even"><td></td>
295<td>Map</td>
296<td>dict of map parameters</td>
297</tr>
298<tr class="row-odd"><td></td>
299<td>SH Texture</td>
300<td>dict of spherical harmonic preferred orientation
301parameters</td>
302</tr>
303<tr class="row-even"><td></td>
304<td>Isotope</td>
305<td>dict of isotopes for each atom type</td>
306</tr>
307<tr class="row-odd"><td></td>
308<td>Isotopes</td>
309<td>dict of scattering lengths for each isotope
310combination for each element in phase</td>
311</tr>
312<tr class="row-even"><td></td>
313<td>Name</td>
314<td>phase name (str)</td>
315</tr>
316<tr class="row-odd"><td></td>
317<td>SGData</td>
318<td>Space group details as a <a class="reference internal" href="#sgdata-table"><em>space group (SGData) object</em></a>
319as defined in <a class="reference internal" href="GSASIIutil.html#GSASIIspc.SpcGroup" title="GSASIIspc.SpcGroup"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIspc.SpcGroup()</span></tt></a>.</td>
320</tr>
321<tr class="row-even"><td></td>
322<td>Pawley neg wt</td>
323<td>Restraint value for negative Pawley intensities
324(float)</td>
325</tr>
326<tr class="row-odd"><td></td>
327<td>Flip</td>
328<td>dict of Charge flip controls</td>
329</tr>
330<tr class="row-even"><td></td>
331<td>Data plot type</td>
332<td>data plot type (&#8216;Mustrain&#8217;, &#8216;Size&#8217; or
333&#8216;Preferred orientation&#8217;) for powder data (str)</td>
334</tr>
335<tr class="row-odd"><td></td>
336<td>Mass</td>
337<td>Mass of unit cell contents in g/mol</td>
338</tr>
339<tr class="row-even"><td></td>
340<td>POhkl</td>
341<td>March-Dollase preferred orientation direction</td>
342</tr>
343<tr class="row-odd"><td></td>
344<td>Z</td>
345<td>dict of atomic numbers for each atom type</td>
346</tr>
347<tr class="row-even"><td></td>
348<td>vdWRadii</td>
349<td>dict of van der Waals radii for each atom type</td>
350</tr>
351<tr class="row-odd"><td></td>
352<td>Color</td>
353<td>Colors for atoms (list of (r,b,g) triplets)</td>
354</tr>
355<tr class="row-even"><td></td>
356<td>AtomTypes</td>
357<td>List of atom types</td>
358</tr>
359<tr class="row-odd"><td></td>
360<td>AtomMass</td>
361<td>List of masses for atoms</td>
362</tr>
363<tr class="row-even"><td></td>
364<td>doPawley</td>
365<td>Flag for Pawley intensity extraction (bool)</td>
366</tr>
367<tr class="row-odd"><td></td>
368<td>NoAtoms</td>
369<td>Number of atoms per unit cell of each type (dict)</td>
370</tr>
371<tr class="row-even"><td></td>
372<td>Pawley dmin</td>
373<td>maximum Q (as d-space) to use for Pawley
374extraction (float)</td>
375</tr>
376<tr class="row-odd"><td></td>
377<td>BondRadii</td>
378<td>Default radius for each atom used to compute
379interatomic distances (list of floats)</td>
380</tr>
381<tr class="row-even"><td></td>
382<td>AngleRadii</td>
383<td>Default radius for each atom used to compute
384interatomic angles (list of floats)</td>
385</tr>
386<tr class="row-odd"><td></td>
387<td>DisAglCtls</td>
388<td>Dict with distance/angle search controls,
389which has keys &#8216;Name&#8217;, &#8216;AtomTypes&#8217;,
390&#8216;BondRadii&#8217;, &#8216;AngleRadii&#8217; which are as above
391except are possibly edited. Also contains
392&#8216;Factors&#8217;, which is a 2 element list with
393a multiplier for bond and angle search range
394[typically (0.85,0.85)].</td>
395</tr>
396<tr class="row-even"><td>ranId</td>
397<td></td>
398<td>unique random number Id for phase (int)</td>
399</tr>
400<tr class="row-odd"><td>pId</td>
401<td></td>
402<td>Phase Id number for current project (int).</td>
403</tr>
404<tr class="row-even"><td>Atoms</td>
405<td></td>
406<td>Atoms in phase as a list of lists. The outer list
407is for each atom, the inner list contains varying
408items depending on the type of phase, see
409the <a class="reference internal" href="#atoms-table"><em>Atom Records</em></a> description.
410(list of lists)</td>
411</tr>
412<tr class="row-odd"><td>Drawing</td>
413<td></td>
414<td>Display parameters (dict)</td>
415</tr>
416<tr class="row-even"><td></td>
417<td>ballScale</td>
418<td>Size of spheres in ball-and-stick display (float)</td>
419</tr>
420<tr class="row-odd"><td></td>
421<td>bondList</td>
422<td>dict with bonds</td>
423</tr>
424<tr class="row-even"><td></td>
425<td>contourLevel</td>
426<td>map contour level in e/A^3 (float)</td>
427</tr>
428<tr class="row-odd"><td></td>
429<td>showABC</td>
430<td>Flag to show view point triplet (bool). True=show.</td>
431</tr>
432<tr class="row-even"><td></td>
433<td>viewDir</td>
434<td>cartesian viewing direction (np.array with three
435elements)</td>
436</tr>
437<tr class="row-odd"><td></td>
438<td>Zclip</td>
439<td>clipping distance in A (float)</td>
440</tr>
441<tr class="row-even"><td></td>
442<td>backColor</td>
443<td>background for plot as and R,G,B triplet
444(default = [0, 0, 0], black).
445(list with three atoms)</td>
446</tr>
447<tr class="row-odd"><td></td>
448<td>selectedAtoms</td>
449<td>List of selected atoms (list of int values)</td>
450</tr>
451<tr class="row-even"><td></td>
452<td>showRigidBodies</td>
453<td>Flag to highlight rigid body placement</td>
454</tr>
455<tr class="row-odd"><td></td>
456<td>sizeH</td>
457<td>Size ratio for H atoms (float)</td>
458</tr>
459<tr class="row-even"><td></td>
460<td>bondRadius</td>
461<td>Size of binds in A (float)</td>
462</tr>
463<tr class="row-odd"><td></td>
464<td>atomPtrs</td>
465<td>positions of x, type, site sym, ADP flag in Draw Atoms (list)</td>
466</tr>
467<tr class="row-even"><td></td>
468<td>viewPoint</td>
469<td>list of lists. First item in list is [x,y,z]
470in fractional coordinates for the center of
471the plot. Second item list of previous &amp; current
472atom number viewed (may be [0,0])</td>
473</tr>
474<tr class="row-odd"><td></td>
475<td>showHydrogen</td>
476<td>Flag to control plotting of H atoms.</td>
477</tr>
478<tr class="row-even"><td></td>
479<td>unitCellBox</td>
480<td>Flag to control display of the unit cell.</td>
481</tr>
482<tr class="row-odd"><td></td>
483<td>ellipseProb</td>
484<td>Probability limit for display of thermal
485ellipsoids in % (float).</td>
486</tr>
487<tr class="row-even"><td></td>
488<td>vdwScale</td>
489<td>Multiplier of van der Waals radius for
490display of vdW spheres.</td>
491</tr>
492<tr class="row-odd"><td></td>
493<td>Atoms</td>
494<td>A list of lists with an entry for each atom
495that is plotted.</td>
496</tr>
497<tr class="row-even"><td></td>
498<td>Zstep</td>
499<td>Step to de/increase Z-clip (float)</td>
500</tr>
501<tr class="row-odd"><td></td>
502<td>Quaternion</td>
503<td>Viewing quaternion (4 element np.array)</td>
504</tr>
505<tr class="row-even"><td></td>
506<td>radiusFactor</td>
507<td>Distance ratio for searching for bonds. ? Bonds
508are located that are within r(Ra+Rb) and (Ra+Rb)/r
509where Ra and Rb are the atomic radii.</td>
510</tr>
511<tr class="row-odd"><td></td>
512<td>oldxy</td>
513<td>previous view point (list with two floats)</td>
514</tr>
515<tr class="row-even"><td></td>
516<td>cameraPos</td>
517<td>Viewing position in A for plot (float)</td>
518</tr>
519<tr class="row-odd"><td></td>
520<td>depthFog</td>
521<td>True if use depthFog on plot - set currently as False (bool)</td>
522</tr>
523<tr class="row-even"><td>RBModels</td>
524<td></td>
525<td>Rigid body assignments (note Rigid body definitions
526are stored in their own main top-level tree entry.)</td>
527</tr>
528<tr class="row-odd"><td>Pawley ref</td>
529<td></td>
530<td>Pawley reflections</td>
531</tr>
532<tr class="row-even"><td>Histograms</td>
533<td></td>
534<td>A dict of dicts. The key for the outer dict is
535the histograms tied to this phase. The inner
536dict contains the combined phase/histogram
537parameters for items such as scale factors,
538size and strain parameters. (dict)</td>
539</tr>
540<tr class="row-odd"><td>MCSA</td>
541<td></td>
542<td>Monte-Carlo simulated annealing parameters (dict)</td>
543</tr>
544<tr class="row-even"><td></td>
545<td>&nbsp;</td>
546<td>&nbsp;</td>
547</tr>
548</tbody>
549</table>
550</div>
551<div class="section" id="rigid-body-objects">
552<h2>Rigid Body Objects<a class="headerlink" href="#rigid-body-objects" title="Permalink to this headline">¶</a></h2>
553<span class="target" id="rbdata-table"></span><p id="index-4">Rigid body descriptions are available for two types of rigid bodies: &#8216;Vector&#8217; 
554and &#8216;Residue&#8217;. Vector rigid bodies are developed by a sequence of translations each
555with a refinable magnitude and Residue rigid bodies are described as Cartesian coordinates
556with defined refinable torsion angles.</p>
557<table border="1" class="docutils">
558<colgroup>
559<col width="10%" />
560<col width="14%" />
561<col width="76%" />
562</colgroup>
563<thead valign="bottom">
564<tr class="row-odd"><th class="head">key</th>
565<th class="head">sub-key</th>
566<th class="head">explanation</th>
567</tr>
568</thead>
569<tbody valign="top">
570<tr class="row-even"><td>Vector</td>
571<td>RBId</td>
572<td>vector rigid bodies (dict of dict)</td>
573</tr>
574<tr class="row-odd"><td></td>
575<td>AtInfo</td>
576<td>Drad, Color: atom drawing radius &amp; color for each atom type (dict)</td>
577</tr>
578<tr class="row-even"><td></td>
579<td>RBname</td>
580<td>Name assigned by user to rigid body (str)</td>
581</tr>
582<tr class="row-odd"><td></td>
583<td>VectMag</td>
584<td>vector magnitudes in A (list)</td>
585</tr>
586<tr class="row-even"><td></td>
587<td>rbXYZ</td>
588<td>Cartesian coordinates for Vector rigid body (list of 3 float)</td>
589</tr>
590<tr class="row-odd"><td></td>
591<td>rbRef</td>
592<td>3 assigned reference atom nos. in rigid body for origin
593definition, use center of atoms flag (list of 3 int &amp; 1 bool)</td>
594</tr>
595<tr class="row-even"><td></td>
596<td>VectRef</td>
597<td>refinement flags for VectMag values (list of bool)</td>
598</tr>
599<tr class="row-odd"><td></td>
600<td>rbTypes</td>
601<td>Atom types for each atom in rigid body (list of str)</td>
602</tr>
603<tr class="row-even"><td></td>
604<td>rbVect</td>
605<td>Cartesian vectors for each translation used to build rigid body (list of lists)</td>
606</tr>
607<tr class="row-odd"><td></td>
608<td>useCount</td>
609<td>Number of times rigid body is used in any structure (int)</td>
610</tr>
611<tr class="row-even"><td>Residue</td>
612<td>RBId</td>
613<td>residue rigid bodies (dict of dict)</td>
614</tr>
615<tr class="row-odd"><td></td>
616<td>AtInfo</td>
617<td>Drad, Color: atom drawing radius &amp; color for each atom type(dict)</td>
618</tr>
619<tr class="row-even"><td></td>
620<td>RBname</td>
621<td>Name assigned by user to rigid body (str)</td>
622</tr>
623<tr class="row-odd"><td></td>
624<td>rbXYZ</td>
625<td>Cartesian coordinates for Residue rigid body (list of 3 float)</td>
626</tr>
627<tr class="row-even"><td></td>
628<td>rbTypes</td>
629<td>Atom types for each atom in rigid body (list of str)</td>
630</tr>
631<tr class="row-odd"><td></td>
632<td>atNames</td>
633<td>Names of each atom in rigid body (e.g. C1,N2...) (list of str)</td>
634</tr>
635<tr class="row-even"><td></td>
636<td>rbRef</td>
637<td>3 assigned reference atom nos. in rigid body for origin
638definition, use center of atoms flag (list of 3 int &amp; 1 bool)</td>
639</tr>
640<tr class="row-odd"><td></td>
641<td>rbSeq</td>
642<td>Orig,Piv,angle,Riding (list): definition of internal rigid body
643torsion; origin atom (int), pivot atom (int), torsion angle (float),
644riding atoms (list of int)</td>
645</tr>
646<tr class="row-even"><td></td>
647<td>SelSeq</td>
648<td>[int,int] used by SeqSizer to identify objects</td>
649</tr>
650<tr class="row-odd"><td></td>
651<td>useCount</td>
652<td>Number of times rigid body is used in any structure (int)</td>
653</tr>
654<tr class="row-even"><td>RBIds</td>
655<td></td>
656<td>unique Ids generated upon creation of each rigid body (dict)</td>
657</tr>
658<tr class="row-odd"><td></td>
659<td>Vector</td>
660<td>Ids for each Vector rigid body (list)</td>
661</tr>
662<tr class="row-even"><td></td>
663<td>Residue</td>
664<td>Ids for each Residue rigid body (list)</td>
665</tr>
666</tbody>
667</table>
668</div>
669<div class="section" id="space-group-objects">
670<h2>Space Group Objects<a class="headerlink" href="#space-group-objects" title="Permalink to this headline">¶</a></h2>
671<span class="target" id="sgdata-table"></span><p id="index-5">Space groups are interpreted by <a class="reference internal" href="GSASIIutil.html#GSASIIspc.SpcGroup" title="GSASIIspc.SpcGroup"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIspc.SpcGroup()</span></tt></a> 
672and the information is placed in a SGdata object
673which is a dict with these keys:</p>
674<table border="1" class="docutils">
675<colgroup>
676<col width="16%" />
677<col width="84%" />
678</colgroup>
679<thead valign="bottom">
680<tr class="row-odd"><th class="head">key</th>
681<th class="head">explanation</th>
682</tr>
683</thead>
684<tbody valign="top">
685<tr class="row-even"><td>SpGrp</td>
686<td>space group symbol (str)</td>
687</tr>
688<tr class="row-odd"><td>Laue</td>
689<td>one of the following 14 Laue classes:
690-1, 2/m, mmm, 4/m, 4/mmm, 3R,
6913mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)</td>
692</tr>
693<tr class="row-even"><td>SGInv</td>
694<td>True if centrosymmetric, False if not (bool)</td>
695</tr>
696<tr class="row-odd"><td>SGLatt</td>
697<td>Lattice centering type. Will be one of
698P, A, B, C, I, F, R (str)</td>
699</tr>
700<tr class="row-even"><td>SGUniq</td>
701<td>unique axis if monoclinic. Will be
702a, b, or c for monoclinic space groups.
703Will be blank for non-monoclinic. (str)</td>
704</tr>
705<tr class="row-odd"><td>SGCen</td>
706<td>Symmetry cell centering vectors. A (n,3) np.array
707of centers. Will always have at least one row:
708<tt class="docutils literal"><span class="pre">np.array([[0,</span> <span class="pre">0,</span> <span class="pre">0]])</span></tt></td>
709</tr>
710<tr class="row-even"><td>SGOps</td>
711<td>symmetry operations as a list of form
712<tt class="docutils literal"><span class="pre">[[M1,T1],</span> <span class="pre">[M2,T2],...]</span></tt>
713where <span class="math">\(M_n\)</span> is a 3x3 np.array
714and <span class="math">\(T_n\)</span> is a length 3 np.array.
715Atom coordinates are transformed where the
716Asymmetric unit coordinates [X is (x,y,z)]
717are transformed using
718<span class="math">\(X^\prime = M_n*X+T_n\)</span></td>
719</tr>
720<tr class="row-odd"><td>SGSys</td>
721<td>symmetry unit cell: type one of
722&#8216;triclinic&#8217;, &#8216;monoclinic&#8217;, &#8216;orthorhombic&#8217;,
723&#8216;tetragonal&#8217;, &#8216;rhombohedral&#8217;, &#8216;trigonal&#8217;,
724&#8216;hexagonal&#8217;, &#8216;cubic&#8217; (str)</td>
725</tr>
726<tr class="row-even"><td>SGPolax</td>
727<td>Axes for space group polarity. Will be one of
728&#8216;&#8217;, &#8216;x&#8217;, &#8216;y&#8217;, &#8216;x y&#8217;, &#8216;z&#8217;, &#8216;x z&#8217;, &#8216;y z&#8217;,
729&#8216;xyz&#8217;. In the case where axes are arbitrary
730&#8216;111&#8217; is used (P 1, and ?).</td>
731</tr>
732</tbody>
733</table>
734</div>
735<div class="section" id="atom-records">
736<h2>Atom Records<a class="headerlink" href="#atom-records" title="Permalink to this headline">¶</a></h2>
737<span class="target" id="atoms-table"></span><p id="index-6">If <tt class="docutils literal"><span class="pre">phasedict</span></tt> points to the phase information in the data tree, then
738atoms are contained in a list of atom records (list) in
739<tt class="docutils literal"><span class="pre">phasedict['Atoms']</span></tt>. Also needed to read atom information
740are four pointers, <tt class="docutils literal"><span class="pre">cx,ct,cs,cia</span> <span class="pre">=</span> <span class="pre">phasedict['General']['atomPtrs']</span></tt>,
741which define locations in the atom record, as shown below. Items shown are
742always present; additional ones for macromolecular phases are marked &#8216;mm&#8217;</p>
743<table border="1" class="docutils">
744<colgroup>
745<col width="21%" />
746<col width="79%" />
747</colgroup>
748<thead valign="bottom">
749<tr class="row-odd"><th class="head">location</th>
750<th class="head">explanation</th>
751</tr>
752</thead>
753<tbody valign="top">
754<tr class="row-even"><td>ct-4</td>
755<td>mm - residue number (str)</td>
756</tr>
757<tr class="row-odd"><td>ct-3</td>
758<td>mm - residue name (e.g. ALA) (str)</td>
759</tr>
760<tr class="row-even"><td>ct-2</td>
761<td>mm - chain label (str)</td>
762</tr>
763<tr class="row-odd"><td>ct-1</td>
764<td>atom label (str)</td>
765</tr>
766<tr class="row-even"><td>ct</td>
767<td>atom type (str)</td>
768</tr>
769<tr class="row-odd"><td>ct+1</td>
770<td>refinement flags; combination of &#8216;F&#8217;, &#8216;X&#8217;, &#8216;U&#8217; (str)</td>
771</tr>
772<tr class="row-even"><td>cx,cx+1,cx+2</td>
773<td>the x,y and z coordinates (3 floats)</td>
774</tr>
775<tr class="row-odd"><td>cs</td>
776<td>site symmetry (str)</td>
777</tr>
778<tr class="row-even"><td>cs+1</td>
779<td>site multiplicity (int)</td>
780</tr>
781<tr class="row-odd"><td>cia</td>
782<td>ADP flag: Isotropic (&#8216;I&#8217;) or Anisotropic (&#8216;A&#8217;)</td>
783</tr>
784<tr class="row-even"><td>cia+1</td>
785<td>Uiso (float)</td>
786</tr>
787<tr class="row-odd"><td>cia+2...cia+6</td>
788<td>U11, U22, U33, U12, U13, U23 (6 floats)</td>
789</tr>
790<tr class="row-even"><td>atom[-1]</td>
791<td>unique atom identifier (int)</td>
792</tr>
793</tbody>
794</table>
795</div>
796<div class="section" id="drawing-atom-records">
797<h2>Drawing Atom Records<a class="headerlink" href="#drawing-atom-records" title="Permalink to this headline">¶</a></h2>
798<span class="target" id="drawing-atoms-table"></span><p id="index-7">If <tt class="docutils literal"><span class="pre">phasedict</span></tt> points to the phase information in the data tree, then
799drawing atoms are contained in a list of drawing atom records (list) in
800<tt class="docutils literal"><span class="pre">phasedict['Drawing']['Atoms']</span></tt>. Also needed to read atom information
801are four pointers, <tt class="docutils literal"><span class="pre">cx,ct,cs,ci</span> <span class="pre">=</span> <span class="pre">phasedict['Drawing']['AtomPtrs']</span></tt>,
802which define locations in the atom record, as shown below. Items shown are
803always present; additional ones for macromolecular phases are marked &#8216;mm&#8217;</p>
804<table border="1" class="docutils">
805<colgroup>
806<col width="17%" />
807<col width="83%" />
808</colgroup>
809<thead valign="bottom">
810<tr class="row-odd"><th class="head">location</th>
811<th class="head">explanation</th>
812</tr>
813</thead>
814<tbody valign="top">
815<tr class="row-even"><td>ct-4</td>
816<td>mm - residue number (str)</td>
817</tr>
818<tr class="row-odd"><td>ct-3</td>
819<td>mm - residue name (e.g. ALA) (str)</td>
820</tr>
821<tr class="row-even"><td>ct-2</td>
822<td>mm - chain label (str)</td>
823</tr>
824<tr class="row-odd"><td>ct-1</td>
825<td>atom label (str)</td>
826</tr>
827<tr class="row-even"><td>ct</td>
828<td>atom type (str)</td>
829</tr>
830<tr class="row-odd"><td>cx,cx+1,cx+2</td>
831<td>the x,y and z coordinates (3 floats)</td>
832</tr>
833<tr class="row-even"><td>cs-1</td>
834<td>Sym Op symbol; sym. op number + unit cell id (e.g. &#8216;1,0,-1&#8217;) (str)</td>
835</tr>
836<tr class="row-odd"><td>cs</td>
837<td>atom drawing style; e.g. &#8216;balls &amp; sticks&#8217; (str)</td>
838</tr>
839<tr class="row-even"><td>cs+1</td>
840<td>atom label style (e.g. &#8216;name&#8217;) (str)</td>
841</tr>
842<tr class="row-odd"><td>cs+2</td>
843<td>atom color (RBG triplet) (int)</td>
844</tr>
845<tr class="row-even"><td>cs+3</td>
846<td>ADP flag: Isotropic (&#8216;I&#8217;) or Anisotropic (&#8216;A&#8217;)</td>
847</tr>
848<tr class="row-odd"><td>cs+4</td>
849<td>Uiso (float)</td>
850</tr>
851<tr class="row-even"><td>cs+5...cs+11</td>
852<td>U11, U22, U33, U12, U13, U23 (6 floats)</td>
853</tr>
854<tr class="row-odd"><td>ci</td>
855<td>unique atom identifier; matches source atom Id in Atom Records (int)</td>
856</tr>
857</tbody>
858</table>
859</div>
860<div class="section" id="powder-diffraction-tree-items">
861<h2>Powder Diffraction Tree Items<a class="headerlink" href="#powder-diffraction-tree-items" title="Permalink to this headline">¶</a></h2>
862<span class="target" id="powder-table"></span><p id="index-8">Every powder diffraction histogram is stored in the GSAS-II data tree
863with a top-level entry named beginning with the string &#8220;PWDR &#8221;. The
864diffraction data for that information are directly associated with
865that tree item and there are a series of children to that item. The
866routines <a class="reference internal" href="GSASII.html#GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree" title="GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree"><tt class="xref py py-func docutils literal"><span class="pre">GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree()</span></tt></a>
867and <a class="reference internal" href="GSASIIstruc.html#GSASIIstrIO.GetUsedHistogramsAndPhases" title="GSASIIstrIO.GetUsedHistogramsAndPhases"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrIO.GetUsedHistogramsAndPhases()</span></tt></a> will
868load this information into a dictionary where the child tree name is
869used as a key, and the information in the main entry is assigned
870a key of <tt class="docutils literal"><span class="pre">Data</span></tt>, as outlined below.</p>
871<table border="1" class="docutils">
872<colgroup>
873<col width="24%" />
874<col width="17%" />
875<col width="59%" />
876</colgroup>
877<thead valign="bottom">
878<tr class="row-odd"><th class="head">key</th>
879<th class="head">sub-key</th>
880<th class="head">explanation</th>
881</tr>
882</thead>
883<tbody valign="top">
884<tr class="row-even"><td>Comments</td>
885<td></td>
886<td>Text strings extracted from the original powder
887data header. These cannot be changed by the user;
888it may be empty.</td>
889</tr>
890<tr class="row-odd"><td>Limits</td>
891<td></td>
892<td>A list of two two element lists, as [[Ld,Hd],[L,H]]
893where L and Ld are the current and default lowest
894two-theta value to be used and
895where H and Hd are the current and default highest
896two-theta value to be used.</td>
897</tr>
898<tr class="row-even"><td>Reflection Lists</td>
899<td></td>
900<td>A dict with an entry for each phase in the
901histogram. The contents of each dict item
902is a dict containing reflections, as described in
903the <a class="reference internal" href="#powderrefl-table"><em>Powder Reflections</em></a>
904description.</td>
905</tr>
906<tr class="row-odd"><td>Instrument Parameters</td>
907<td></td>
908<td>A list containing two dicts where the possible
909keys in each dict are listed below. The value
910for each item is a list containing three values:
911the initial value, the current value and a
912refinement flag which can have a value of
913True, False or 0 where 0 indicates a value that
914cannot be refined. The first and second
915values are floats unless otherwise noted.
916Items in the first dict are noted as [1]</td>
917</tr>
918<tr class="row-even"><td></td>
919<td>Lam</td>
920<td>Specifies a wavelength in Angstroms [1]</td>
921</tr>
922<tr class="row-odd"><td></td>
923<td>Lam1</td>
924<td>Specifies the primary wavelength in
925Angstrom, when an alpha1, alpha2
926source is used [1]</td>
927</tr>
928<tr class="row-even"><td></td>
929<td><p class="first">Lam2</p>
930<p class="last">I(L2)/I(L1)</p>
931</td>
932<td>Specifies the secondary wavelength in
933Angstrom, when an alpha1, alpha2
934source is used [1]
935Ratio of Lam2 to Lam1 [1]</td>
936</tr>
937<tr class="row-odd"><td></td>
938<td>Type</td>
939<td><dl class="first last docutils">
940<dt>Histogram type (str) [1]:</dt>
941<dd><ul class="first last simple">
942<li>&#8216;PXC&#8217; for constant wavelength x-ray</li>
943<li>&#8216;PNC&#8217; for constant wavelength neutron</li>
944<li>&#8216;PNT&#8217; for time of flight neutron</li>
945</ul>
946</dd>
947</dl>
948</td>
949</tr>
950<tr class="row-even"><td></td>
951<td>Zero</td>
952<td>Two-theta zero correction in <em>degrees</em> [1]</td>
953</tr>
954<tr class="row-odd"><td></td>
955<td>Azimuth</td>
956<td>Azimuthal setting angle for data recorded
957with differing setting angles [1]</td>
958</tr>
959<tr class="row-even"><td></td>
960<td>U, V, W</td>
961<td>Cagliotti profile coefficients
962for Gaussian instrumental broadening, where the
963FWHM goes as
964<span class="math">\(U \tan^2\theta + V \tan\theta + W\)</span> [1]</td>
965</tr>
966<tr class="row-odd"><td></td>
967<td>X, Y</td>
968<td>Cauchy (Lorentzian) instrumental broadening
969coefficients [1]</td>
970</tr>
971<tr class="row-even"><td></td>
972<td>SH/L</td>
973<td>Variant of the Finger-Cox-Jephcoat asymmetric
974peak broadening ratio. Note that this is the
975average between S/L and H/L where S is
976sample height, H is the slit height and
977L is the goniometer diameter. [1]</td>
978</tr>
979<tr class="row-odd"><td></td>
980<td>Polariz.</td>
981<td>Polarization coefficient. [1]</td>
982</tr>
983<tr class="row-even"><td>wtFactor</td>
984<td></td>
985<td>A weighting factor to increase or decrease
986the leverage of data in the histogram (float).
987A value of 1.0 weights the data with their
988standard uncertainties and a larger value
989increases the weighting of the data (equivalent
990to decreasing the uncertainties).</td>
991</tr>
992<tr class="row-odd"><td>Sample Parameters</td>
993<td></td>
994<td>Specifies a dict with parameters that describe how
995the data were collected, as listed
996below. Refinable parameters are a list containing
997a float and a bool, where the second value
998specifies if the value is refined, otherwise
999the value is a float unless otherwise noted.</td>
1000</tr>
1001<tr class="row-even"><td></td>
1002<td>Scale</td>
1003<td>The histogram scale factor (refinable)</td>
1004</tr>
1005<tr class="row-odd"><td></td>
1006<td>Absorption</td>
1007<td>The sample absorption coefficient as
1008<span class="math">\(\mu r\)</span> where r is the radius
1009(refinable). Only valid for Debye-Scherrer geometry.</td>
1010</tr>
1011<tr class="row-even"><td></td>
1012<td>SurfaceRoughA</td>
1013<td>Surface roughness parameter A as defined by
1014Surotti,J. Appl. Cryst, 5,325-331, 1972.(refinable -
1015only valid for Bragg-Brentano geometry)</td>
1016</tr>
1017<tr class="row-odd"><td></td>
1018<td>SurfaceRoughB</td>
1019<td>Surface roughness parameter B (refinable -
1020only valid for Bragg-Brentano geometry)</td>
1021</tr>
1022<tr class="row-even"><td></td>
1023<td>DisplaceX,
1024DisplaceY</td>
1025<td>Sample displacement from goniometer center
1026where Y is along the beam direction and
1027X is perpendicular. Units are <span class="math">\(\mu m\)</span>
1028(refinable).</td>
1029</tr>
1030<tr class="row-odd"><td></td>
1031<td>Phi, Chi,
1032Omega</td>
1033<td>Goniometer sample setting angles, in degrees.</td>
1034</tr>
1035<tr class="row-even"><td></td>
1036<td>Gonio. radius</td>
1037<td>Radius of the diffractometer in mm</td>
1038</tr>
1039<tr class="row-odd"><td></td>
1040<td>InstrName</td>
1041<td>A name for the instrument, used in preparing
1042a CIF (str).</td>
1043</tr>
1044<tr class="row-even"><td></td>
1045<td>Force,
1046Temperature,
1047Humidity,
1048Pressure,
1049Voltage</td>
1050<td>Variables that describe how the measurement
1051was performed. Not used directly in
1052any computations.</td>
1053</tr>
1054<tr class="row-odd"><td></td>
1055<td>ranId</td>
1056<td>The random-number Id for the histogram
1057(same value as where top-level key is ranId)</td>
1058</tr>
1059<tr class="row-even"><td></td>
1060<td>Type</td>
1061<td>Type of diffraction data, may be &#8216;Debye-Scherrer&#8217;
1062or &#8216;Bragg-Brentano&#8217; (str).</td>
1063</tr>
1064<tr class="row-odd"><td></td>
1065<td>Diffuse</td>
1066<td>not in use?</td>
1067</tr>
1068<tr class="row-even"><td>hId</td>
1069<td></td>
1070<td>The number assigned to the histogram when
1071the project is loaded or edited (can change)</td>
1072</tr>
1073<tr class="row-odd"><td>ranId</td>
1074<td></td>
1075<td>A random number id for the histogram
1076that does not change</td>
1077</tr>
1078<tr class="row-even"><td>Background</td>
1079<td></td>
1080<td>The background is stored as a list with where
1081the first item in the list is list and the second
1082item is a dict. The list contains the background
1083function and its coefficients; the dict contains
1084Debye diffuse terms and background peaks.
1085(TODO: this needs to be expanded.)</td>
1086</tr>
1087<tr class="row-odd"><td>Data</td>
1088<td></td>
1089<td><p class="first">The data consist of a list of 6 np.arrays
1090containing in order:</p>
1091<blockquote class="last">
1092<div><ol class="arabic simple">
1093<li>the x-postions (two-theta in degrees),</li>
1094<li>the intensity values (Yobs),</li>
1095<li>the weights for each Yobs value</li>
1096<li>the computed intensity values (Ycalc)</li>
1097<li>the background values</li>
1098<li>Yobs-Ycalc</li>
1099</ol>
1100</div></blockquote>
1101</td>
1102</tr>
1103</tbody>
1104</table>
1105</div>
1106<div class="section" id="powder-reflection-data-structure">
1107<h2>Powder Reflection Data Structure<a class="headerlink" href="#powder-reflection-data-structure" title="Permalink to this headline">¶</a></h2>
1108<span class="target" id="powderrefl-table"></span><p id="index-9">For every phase in a histogram, the <tt class="docutils literal"><span class="pre">Reflection</span> <span class="pre">Lists</span></tt> value is a dict
1109one element of which is <cite>&#8216;RefList&#8217;</cite>, which is a np.array containing
1110reflections. The columns in that array are documented below.</p>
1111<table border="1" class="docutils">
1112<colgroup>
1113<col width="14%" />
1114<col width="86%" />
1115</colgroup>
1116<thead valign="bottom">
1117<tr class="row-odd"><th class="head">index</th>
1118<th class="head">explanation</th>
1119</tr>
1120</thead>
1121<tbody valign="top">
1122<tr class="row-even"><td>0,1,2</td>
1123<td>h,k,l (float)</td>
1124</tr>
1125<tr class="row-odd"><td>3</td>
1126<td>multiplicity</td>
1127</tr>
1128<tr class="row-even"><td>4</td>
1129<td>d-space, Angstrom</td>
1130</tr>
1131<tr class="row-odd"><td>5</td>
1132<td>pos, two-theta</td>
1133</tr>
1134<tr class="row-even"><td>6</td>
1135<td>sig, Gaussian width</td>
1136</tr>
1137<tr class="row-odd"><td>7</td>
1138<td>gam, Lorenzian width</td>
1139</tr>
1140<tr class="row-even"><td>8</td>
1141<td><span class="math">\(F_{obs}^2\)</span></td>
1142</tr>
1143<tr class="row-odd"><td>9</td>
1144<td><span class="math">\(F_{calc}^2\)</span></td>
1145</tr>
1146<tr class="row-even"><td>10</td>
1147<td>reflection phase, in degrees</td>
1148</tr>
1149<tr class="row-odd"><td>11</td>
1150<td>intensity correction for reflection, this times
1151<span class="math">\(F_{obs}^2\)</span> or <span class="math">\(F_{calc}^2\)</span> gives Iobs or Icalc</td>
1152</tr>
1153</tbody>
1154</table>
1155</div>
1156<div class="section" id="single-crystal-tree-items">
1157<h2>Single Crystal Tree Items<a class="headerlink" href="#single-crystal-tree-items" title="Permalink to this headline">¶</a></h2>
1158<span class="target" id="xtal-table"></span><p id="index-10">Every single crystal diffraction histogram is stored in the GSAS-II data tree
1159with a top-level entry named beginning with the string &#8220;HKLF &#8221;. The
1160diffraction data for that information are directly associated with
1161that tree item and there are a series of children to that item. The
1162routines <a class="reference internal" href="GSASII.html#GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree" title="GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree"><tt class="xref py py-func docutils literal"><span class="pre">GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree()</span></tt></a>
1163and <a class="reference internal" href="GSASIIstruc.html#GSASIIstrIO.GetUsedHistogramsAndPhases" title="GSASIIstrIO.GetUsedHistogramsAndPhases"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrIO.GetUsedHistogramsAndPhases()</span></tt></a> will
1164load this information into a dictionary where the child tree name is
1165used as a key, and the information in the main entry is assigned
1166a key of <tt class="docutils literal"><span class="pre">Data</span></tt>, as outlined below.</p>
1167<table border="1" class="docutils">
1168<colgroup>
1169<col width="25%" />
1170<col width="17%" />
1171<col width="58%" />
1172</colgroup>
1173<thead valign="bottom">
1174<tr class="row-odd"><th class="head">key</th>
1175<th class="head">sub-key</th>
1176<th class="head">explanation</th>
1177</tr>
1178</thead>
1179<tbody valign="top">
1180<tr class="row-even"><td>Data</td>
1181<td></td>
1182<td>A dict that contains the
1183reflection table,
1184as described in the
1185<a class="reference internal" href="#xtalrefl-table"><em>Single Crystal Reflections</em></a>
1186description.</td>
1187</tr>
1188<tr class="row-odd"><td>Instrument Parameters</td>
1189<td></td>
1190<td>A list containing two dicts where the possible
1191keys in each dict are listed below. The value
1192for most items is a list containing two values:
1193the initial value, the current value.
1194The first and second
1195values are floats unless otherwise noted.</td>
1196</tr>
1197<tr class="row-even"><td></td>
1198<td>Lam</td>
1199<td>Specifies a wavelength in Angstroms (two floats)</td>
1200</tr>
1201<tr class="row-odd"><td></td>
1202<td>Type</td>
1203<td><dl class="first last docutils">
1204<dt>Histogram type (two str values):</dt>
1205<dd><ul class="first last simple">
1206<li>&#8216;SXC&#8217; for constant wavelength x-ray</li>
1207<li>&#8216;SNC&#8217; for constant wavelength neutron</li>
1208<li>&#8216;SNT&#8217; for time of flight neutron</li>
1209</ul>
1210</dd>
1211</dl>
1212</td>
1213</tr>
1214<tr class="row-even"><td></td>
1215<td>InstrName</td>
1216<td>A name for the instrument, used in preparing
1217a CIF (str).</td>
1218</tr>
1219<tr class="row-odd"><td>wtFactor</td>
1220<td></td>
1221<td>A weighting factor to increase or decrease
1222the leverage of data in the histogram (float).
1223A value of 1.0 weights the data with their
1224standard uncertainties and a larger value
1225increases the weighting of the data (equivalent
1226to decreasing the uncertainties).</td>
1227</tr>
1228<tr class="row-even"><td>hId</td>
1229<td></td>
1230<td>The number assigned to the histogram when
1231the project is loaded or edited (can change)</td>
1232</tr>
1233<tr class="row-odd"><td>ranId</td>
1234<td></td>
1235<td>A random number id for the histogram
1236that does not change</td>
1237</tr>
1238</tbody>
1239</table>
1240</div>
1241<div class="section" id="single-crystal-reflection-data-structure">
1242<h2>Single Crystal Reflection Data Structure<a class="headerlink" href="#single-crystal-reflection-data-structure" title="Permalink to this headline">¶</a></h2>
1243<span class="target" id="xtalrefl-table"></span><p id="index-11">For every single crystal a histogram, the <tt class="docutils literal"><span class="pre">'Data'</span></tt> item contains
1244the structure factors as an np.array in item <cite>&#8216;RefList&#8217;</cite>.
1245The columns in that array are documented below.</p>
1246<table border="1" class="docutils">
1247<colgroup>
1248<col width="16%" />
1249<col width="84%" />
1250</colgroup>
1251<thead valign="bottom">
1252<tr class="row-odd"><th class="head">index</th>
1253<th class="head">explanation</th>
1254</tr>
1255</thead>
1256<tbody valign="top">
1257<tr class="row-even"><td>0,1,2</td>
1258<td>h,k,l (float)</td>
1259</tr>
1260<tr class="row-odd"><td>3</td>
1261<td>multiplicity</td>
1262</tr>
1263<tr class="row-even"><td>4</td>
1264<td>d-space, Angstrom</td>
1265</tr>
1266<tr class="row-odd"><td>5</td>
1267<td><span class="math">\(F_{obs}^2\)</span></td>
1268</tr>
1269<tr class="row-even"><td>6</td>
1270<td><span class="math">\(\sigma(F_{obs}^2)\)</span></td>
1271</tr>
1272<tr class="row-odd"><td>7</td>
1273<td><span class="math">\(F_{calc}^2\)</span></td>
1274</tr>
1275<tr class="row-even"><td>8</td>
1276<td><span class="math">\(F_{obs}^2T\)</span></td>
1277</tr>
1278<tr class="row-odd"><td>9</td>
1279<td><span class="math">\(F_{calc}^2T\)</span></td>
1280</tr>
1281<tr class="row-even"><td>10</td>
1282<td>reflection phase, in degrees</td>
1283</tr>
1284<tr class="row-odd"><td>11</td>
1285<td>intensity correction for reflection, this times
1286<span class="math">\(F_{obs}^2\)</span> or <span class="math">\(F_{calc}^2\)</span>
1287gives Iobs or Icalc</td>
1288</tr>
1289</tbody>
1290</table>
1291</div>
1292<div class="section" id="image-data-structure">
1293<h2>Image Data Structure<a class="headerlink" href="#image-data-structure" title="Permalink to this headline">¶</a></h2>
1294<span class="target" id="image-table"></span><p id="index-12">Every 2-dimensional image is stored in the GSAS-II data tree
1295with a top-level entry named beginning with the string &#8220;IMG &#8221;. The
1296image data are directly associated with that tree item and there
1297are a series of children to that item. The routines <a class="reference internal" href="GSASII.html#GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree" title="GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree"><tt class="xref py py-func docutils literal"><span class="pre">GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree()</span></tt></a>
1298and <a class="reference internal" href="GSASIIstruc.html#GSASIIstrIO.GetUsedHistogramsAndPhases" title="GSASIIstrIO.GetUsedHistogramsAndPhases"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrIO.GetUsedHistogramsAndPhases()</span></tt></a> will
1299load this information into a dictionary where the child tree name is
1300used as a key, and the information in the main entry is assigned
1301a key of <tt class="docutils literal"><span class="pre">Data</span></tt>, as outlined below.</p>
1302<table border="1" class="docutils">
1303<colgroup>
1304<col width="12%" />
1305<col width="12%" />
1306<col width="76%" />
1307</colgroup>
1308<thead valign="bottom">
1309<tr class="row-odd"><th class="head">key</th>
1310<th class="head">sub-key</th>
1311<th class="head">explanation</th>
1312</tr>
1313</thead>
1314<tbody valign="top">
1315<tr class="row-even"><td>Comments</td>
1316<td></td>
1317<td>Text strings extracted from the original image data
1318header or a metafile. These cannot be changed by
1319the user; it may be empty.</td>
1320</tr>
1321<tr class="row-odd"><td>Image Controls</td>
1322<td>azmthOff</td>
1323<td>(float) The offset to be applied to an azimuthal
1324value. Accomodates
1325detector orientations other than with the detector
1326X-axis
1327horizontal.</td>
1328</tr>
1329<tr class="row-even"><td></td>
1330<td>background image</td>
1331<td>(list:str,float) The name of a tree item (&#8220;IMG ...&#8221;) that is to be subtracted
1332during image integration multiplied by value. It must have the same size/shape as
1333the integrated image. NB: value &lt; 0 for subtraction.</td>
1334</tr>
1335<tr class="row-odd"><td></td>
1336<td>calibrant</td>
1337<td>(str) The material used for determining the position/orientation
1338of the image. The data is obtained from <a class="reference internal" href="GSASIIutil.html#module-ImageCalibrants" title="ImageCalibrants"><tt class="xref py py-func docutils literal"><span class="pre">ImageCalibrants()</span></tt></a>
1339and UserCalibrants.py (supplied by user).</td>
1340</tr>
1341<tr class="row-even"><td></td>
1342<td>calibdmin</td>
1343<td>(float) The minimum d-spacing used during the last calibration run.</td>
1344</tr>
1345<tr class="row-odd"><td></td>
1346<td>calibskip</td>
1347<td>(int) The number of expected diffraction lines skipped during the last
1348calibration run.</td>
1349</tr>
1350<tr class="row-even"><td></td>
1351<td>center</td>
1352<td>(list:floats) The [X,Y] point in detector coordinates (mm) where the direct beam
1353strikes the detector plane as determined by calibration. This point
1354does not have to be within the limits of the detector boundaries.</td>
1355</tr>
1356<tr class="row-odd"><td></td>
1357<td>centerAzm</td>
1358<td>(bool) If True then the azimuth reported for the integrated slice
1359of the image is at the center line otherwise it is at the leading edge.</td>
1360</tr>
1361<tr class="row-even"><td></td>
1362<td>color</td>
1363<td>(str) The name of the colormap used to display the image. Default = &#8216;Paired&#8217;.</td>
1364</tr>
1365<tr class="row-odd"><td></td>
1366<td>cutoff</td>
1367<td>(float) The minimum value of I/Ib for a point selected in a diffraction ring for
1368calibration calculations. See pixLimit for details as how point is found.</td>
1369</tr>
1370<tr class="row-even"><td></td>
1371<td>DetDepth</td>
1372<td>(float) Coefficient for penetration correction to distance; accounts for diffraction
1373ring offset at higher angles. Optionally determined by calibration.</td>
1374</tr>
1375<tr class="row-odd"><td></td>
1376<td>DetDepthRef</td>
1377<td>(bool) If True then refine DetDepth during calibration/recalibration calculation.</td>
1378</tr>
1379<tr class="row-even"><td></td>
1380<td>distance</td>
1381<td>(float) The distance (mm) from sample to detector plane.</td>
1382</tr>
1383<tr class="row-odd"><td></td>
1384<td>ellipses</td>
1385<td>(list:lists) Each object in ellipses is a list [center,phi,radii,color] where
1386center (list) is location (mm) of the ellipse center on the detector plane, phi is the
1387rotation of the ellipse minor axis from the x-axis, and radii are the minor &amp; major
1388radii of the ellipse. If radii[0] is negative then parameters describe a hyperbola. Color
1389is the selected drawing color (one of &#8216;b&#8217;, &#8216;g&#8217; ,&#8217;r&#8217;) for the ellipse/hyperbola.</td>
1390</tr>
1391<tr class="row-even"><td></td>
1392<td>edgemin</td>
1393<td>(float) Not used;  parameter in EdgeFinder code.</td>
1394</tr>
1395<tr class="row-odd"><td></td>
1396<td>fullIntegrate</td>
1397<td>(bool) If True then integrate over full 360 deg azimuthal range.</td>
1398</tr>
1399<tr class="row-even"><td></td>
1400<td>GonioAngles</td>
1401<td>(list:floats) The &#8216;Omega&#8217;,&#8217;Chi&#8217;,&#8217;Phi&#8217; goniometer angles used for this image.
1402Required for texture calculations.</td>
1403</tr>
1404<tr class="row-odd"><td></td>
1405<td>invert_x</td>
1406<td>(bool) If True display the image with the x-axis inverted.</td>
1407</tr>
1408<tr class="row-even"><td></td>
1409<td>invert_y</td>
1410<td>(bool) If True display the image with the y-axis inverted.</td>
1411</tr>
1412<tr class="row-odd"><td></td>
1413<td>IOtth</td>
1414<td>(list:floats) The minimum and maximum 2-theta values to be used for integration.</td>
1415</tr>
1416<tr class="row-even"><td></td>
1417<td>LRazimuth</td>
1418<td>(list:floats) The minimum and maximum azimuth values to be used for integration.</td>
1419</tr>
1420<tr class="row-odd"><td></td>
1421<td>Oblique</td>
1422<td>(list:float,bool) If True apply a detector absorption correction using the value to the
1423intensities obtained during integration.</td>
1424</tr>
1425<tr class="row-even"><td></td>
1426<td>outAzimuths</td>
1427<td>(int) The number of azimuth pie slices.</td>
1428</tr>
1429<tr class="row-odd"><td></td>
1430<td>outChannels</td>
1431<td>(int) The number of 2-theta steps.</td>
1432</tr>
1433<tr class="row-even"><td></td>
1434<td>pixelSize</td>
1435<td>(list:ints) The X,Y dimensions (microns) of each pixel.</td>
1436</tr>
1437<tr class="row-odd"><td></td>
1438<td>pixLimit</td>
1439<td>(int) A box in the image with 2*pixLimit+1 edges is searched to find the maximum.
1440This value (I) along with the minimum (Ib) in the box is reported by <a class="reference internal" href="GSASIIimage.html#GSASIIimage.ImageLocalMax" title="GSASIIimage.ImageLocalMax"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIimage.ImageLocalMax()</span></tt></a>
1441and subject to cutoff in <a class="reference internal" href="GSASIIimage.html#GSASIIimage.makeRing" title="GSASIIimage.makeRing"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIimage.makeRing()</span></tt></a>.
1442Locations are used to construct rings of points for calibration calcualtions.</td>
1443</tr>
1444<tr class="row-even"><td></td>
1445<td>PolaVal</td>
1446<td>(list:float,bool) If type=&#8217;SASD&#8217; and if True, apply polarization correction to intensities from
1447integration using value.</td>
1448</tr>
1449<tr class="row-odd"><td></td>
1450<td>rings</td>
1451<td>(list:lists) Each entry is [X,Y,dsp] where X &amp; Y are lists of x,y coordinates around a
1452diffraction ring with the same d-spacing (dsp)</td>
1453</tr>
1454<tr class="row-even"><td></td>
1455<td>ring</td>
1456<td>(list) The x,y coordinates of the &gt;5 points on an inner ring
1457selected by the user,</td>
1458</tr>
1459<tr class="row-odd"><td></td>
1460<td>Range</td>
1461<td>(list) The minimum &amp; maximum values of the image</td>
1462</tr>
1463<tr class="row-even"><td></td>
1464<td>rotation</td>
1465<td>(float) The angle between the x-axis and the vector about which the
1466detector is tilted. Constrained to -180 to 180 deg.</td>
1467</tr>
1468<tr class="row-odd"><td></td>
1469<td>SampleShape</td>
1470<td>(str) Currently only &#8216;Cylinder&#8217;. Sample shape for Debye-Scherrer experiments; used for absorption
1471calculations.</td>
1472</tr>
1473<tr class="row-even"><td></td>
1474<td>SampleAbs</td>
1475<td>(list: float,bool) Value of absorption coefficient for Debye-Scherrer experimnents, flag if True
1476to cause correction to be applied.</td>
1477</tr>
1478<tr class="row-odd"><td></td>
1479<td>setDefault</td>
1480<td>(bool) If True the use the image controls values for all new images to be read. (might be removed)</td>
1481</tr>
1482<tr class="row-even"><td></td>
1483<td>setRings</td>
1484<td>(bool) If True then display all the selected x,y ring positions (vida supra rings) used in the calibration.</td>
1485</tr>
1486<tr class="row-odd"><td></td>
1487<td>showLines</td>
1488<td>(bool) If True then isplay the integration limits to be used.</td>
1489</tr>
1490<tr class="row-even"><td></td>
1491<td>size</td>
1492<td>(list:int) The number of pixels on the image x &amp; y axes</td>
1493</tr>
1494<tr class="row-odd"><td></td>
1495<td>type</td>
1496<td>(str) One of &#8216;PWDR&#8217;, &#8216;SASD&#8217; or &#8216;REFL&#8217; for powder, small angle or reflectometry data, respectively.</td>
1497</tr>
1498<tr class="row-even"><td></td>
1499<td>tilt</td>
1500<td>(float) The angle the detector normal makes with the incident beam; range -90 to 90.</td>
1501</tr>
1502<tr class="row-odd"><td></td>
1503<td>wavelength</td>
1504<td>(float) Tha radiation wavelength (Angstroms) as entered by the user (or someday obtained from the image header).</td>
1505</tr>
1506<tr class="row-even"><td>Masks</td>
1507<td>Arcs</td>
1508<td>(list: lists) Each entry [2-theta,[azimuth[0],azimuth[1]],thickness] describes an arc mask
1509to be excluded from integration</td>
1510</tr>
1511<tr class="row-odd"><td></td>
1512<td>Frames</td>
1513<td>(list:lists) Each entry describes the x,y points (3 or more - mm) that describe a frame outside
1514of which is excluded from recalibration and integration. Only one frame is allowed.</td>
1515</tr>
1516<tr class="row-even"><td></td>
1517<td>Points</td>
1518<td>(list:lists) Each entry [x,y,radius] (mm) describes an excluded spot on the image to be excluded
1519from integration.</td>
1520</tr>
1521<tr class="row-odd"><td></td>
1522<td>Polygons</td>
1523<td>(list:lists) Each entry is a list of 3+ [x,y] points (mm) that describe a polygon on the image
1524to be excluded from integration.</td>
1525</tr>
1526<tr class="row-even"><td></td>
1527<td>Rings</td>
1528<td>(list: lists) Each entry [2-theta,thickness] describes a ring mask
1529to be excluded from integration.</td>
1530</tr>
1531<tr class="row-odd"><td></td>
1532<td>Thresholds</td>
1533<td>(list:[tuple,list]) [(Imin,Imax),[Imin,Imax]] This gives lower and upper limits for points on the image to be included
1534in integrsation. The tuple is the image intensity limits and the list are those set by the user.</td>
1535</tr>
1536<tr class="row-even"><td>Stress/Strain</td>
1537<td>Sample phi</td>
1538<td>(float) Sample rotation about vertical axis.</td>
1539</tr>
1540<tr class="row-odd"><td></td>
1541<td>Sample z</td>
1542<td>(float) Sample translation from the calibration sample position (for Sample phi = 0)</td>
1543</tr>
1544<tr class="row-even"><td></td>
1545<td>strain</td>
1546<td>(list: 3x3 array of float) The strain tensor coefficients [[&#8216; e11&#8217;,&#8217;e12&#8217;,&#8217;e13&#8217;],[&#8216; e21&#8217;,&#8217;e22&#8217;,&#8217;e23&#8217;],[&#8216; e31&#8217;,&#8217;e32&#8217;,&#8217;e33&#8217;]].
1547These will be restricted by space group symmetry; result of strain fit refinement.</td>
1548</tr>
1549<tr class="row-odd"><td></td>
1550<td>Type</td>
1551<td>(str) &#8216;True&#8217; or &#8216;Conventional&#8217;: The strain model used for the calculation.</td>
1552</tr>
1553<tr class="row-even"><td></td>
1554<td>d-zero</td>
1555<td>(list:dict) Each item is for a diffraction ring on the image; all items are from the same phase and are used to determine the strain tensor.
1556The dictionary items are:
1557&#8216;Dset&#8217;: (float) True d-spacing for the diffraction ring; entered by the user.
1558&#8216;Dcalc&#8217;: (float) d-spacing...
1559&#8216;pixLimit&#8217;: (int) Search range to find highest point on ring for each data point
1560&#8216;cutoff&#8217;: (float) I/Ib cutoff for searching.
1561&#8216;ImxyObs&#8217;: (list:lists) [[X],[Y]] observed points to be used for strain calculations.
1562&#8216;ImxyCalc&#8217;:(list:lists) [[X],[Y]] calculated points based on refined strain.</td>
1563</tr>
1564</tbody>
1565</table>
1566</div>
1567<div class="section" id="parameter-dictionary">
1568<h2>Parameter Dictionary<a class="headerlink" href="#parameter-dictionary" title="Permalink to this headline">¶</a></h2>
1569<span class="target" id="parmdict-table"></span><p id="index-13">The parameter dictionary contains all of the variable parameters for the refinement.
1570The dictionary keys are the name of the parameter (&lt;phase&gt;:&lt;hist&gt;:&lt;name&gt;:&lt;atom&gt;).
1571It is prepared in two ways. When loaded from the tree
1572(in <a class="reference internal" href="GSASII.html#GSASII.GSASII.MakeLSParmDict" title="GSASII.GSASII.MakeLSParmDict"><tt class="xref py py-meth docutils literal"><span class="pre">GSASII.GSASII.MakeLSParmDict()</span></tt></a> and
1573<a class="reference internal" href="GSASIIGUIr.html#GSASIIIO.ExportBaseclass.loadParmDict" title="GSASIIIO.ExportBaseclass.loadParmDict"><tt class="xref py py-meth docutils literal"><span class="pre">GSASIIIO.ExportBaseclass.loadParmDict()</span></tt></a>),
1574the values are lists with two elements: <tt class="docutils literal"><span class="pre">[value,</span> <span class="pre">refine</span> <span class="pre">flag]</span></tt></p>
1575<p>When loaded from the GPX file (in
1576<a class="reference internal" href="GSASIIstruc.html#GSASIIstrMain.Refine" title="GSASIIstrMain.Refine"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrMain.Refine()</span></tt></a> and <a class="reference internal" href="GSASIIstruc.html#GSASIIstrMain.SeqRefine" title="GSASIIstrMain.SeqRefine"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrMain.SeqRefine()</span></tt></a>), the value in the
1577dict is the actual parameter value (usually a float, but sometimes a
1578letter or string flag value (such as I or A for iso/anisotropic).</p>
1579</div>
1580<div class="section" id="classes-and-routines">
1581<h2><em>Classes and routines</em><a class="headerlink" href="#classes-and-routines" title="Permalink to this headline">¶</a></h2>
1582<dl class="data">
1583<dt id="GSASIIobj.AtomIdLookup">
1584<tt class="descclassname">GSASIIobj.</tt><tt class="descname">AtomIdLookup</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.AtomIdLookup" title="Permalink to this definition">¶</a></dt>
1585<dd><p>dict listing for each phase index as a str, the atom label and atom random Id,
1586keyed by atom sequential index as a str;
1587best to access this using <a class="reference internal" href="#GSASIIobj.LookupAtomLabel" title="GSASIIobj.LookupAtomLabel"><tt class="xref py py-func docutils literal"><span class="pre">LookupAtomLabel()</span></tt></a></p>
1588</dd></dl>
1589
1590<dl class="data">
1591<dt id="GSASIIobj.AtomRanIdLookup">
1592<tt class="descclassname">GSASIIobj.</tt><tt class="descname">AtomRanIdLookup</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.AtomRanIdLookup" title="Permalink to this definition">¶</a></dt>
1593<dd><p>dict listing for each phase the atom sequential index keyed by atom random Id;
1594best to access this using <a class="reference internal" href="#GSASIIobj.LookupAtomId" title="GSASIIobj.LookupAtomId"><tt class="xref py py-func docutils literal"><span class="pre">LookupAtomId()</span></tt></a></p>
1595</dd></dl>
1596
1597<dl class="function">
1598<dt id="GSASIIobj.CompileVarDesc">
1599<tt class="descclassname">GSASIIobj.</tt><tt class="descname">CompileVarDesc</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#CompileVarDesc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.CompileVarDesc" title="Permalink to this definition">¶</a></dt>
1600<dd><p>Set the values in the variable description lookup table (<a class="reference internal" href="#GSASIIobj.VarDesc" title="GSASIIobj.VarDesc"><tt class="xref py py-attr docutils literal"><span class="pre">VarDesc</span></tt></a>)
1601into <a class="reference internal" href="#GSASIIobj.reVarDesc" title="GSASIIobj.reVarDesc"><tt class="xref py py-attr docutils literal"><span class="pre">reVarDesc</span></tt></a>. This is called in <a class="reference internal" href="#GSASIIobj.getDescr" title="GSASIIobj.getDescr"><tt class="xref py py-func docutils literal"><span class="pre">getDescr()</span></tt></a> so the initialization
1602is always done before use.</p>
1603<p>Note that keys may contain regular expressions, where &#8216;[xyz]&#8217;
1604matches &#8216;x&#8217; &#8216;y&#8217; or &#8216;z&#8217; (equivalently &#8216;[x-z]&#8217; describes this as range of values).
1605&#8216;.*&#8217; matches any string. For example:</p>
1606<div class="highlight-python"><pre>'AUiso':'Atomic isotropic displacement parameter',</pre>
1607</div>
1608<p>will match variable <tt class="docutils literal"><span class="pre">'p::AUiso:a'</span></tt>.
1609If parentheses are used in the key, the contents of those parentheses can be
1610used in the value, such as:</p>
1611<div class="highlight-python"><pre>'AU([123][123])':'Atomic anisotropic displacement parameter U\1',</pre>
1612</div>
1613<p>will match <tt class="docutils literal"><span class="pre">AU11</span></tt>, <tt class="docutils literal"><span class="pre">AU23</span></tt>,.. and <cite>U11</cite>, <cite>U23</cite> etc will be displayed
1614in the value when used.</p>
1615</dd></dl>
1616
1617<dl class="data">
1618<dt id="GSASIIobj.DefaultControls">
1619<tt class="descclassname">GSASIIobj.</tt><tt class="descname">DefaultControls</tt><em class="property"> = {'F**2': True, 'shift factor': 1.0, 'deriv type': 'analytic Hessian', 'max cyc': 3, 'minF/sig': 0, 'FreeVar1': 'Sample humidity (%)', 'Author': 'no name', 'FreeVar2': 'Sample voltage (V)', 'FreeVar3': 'Applied load (MN)', 'min dM/M': 0.0001}</em><a class="headerlink" href="#GSASIIobj.DefaultControls" title="Permalink to this definition">¶</a></dt>
1620<dd><p>Values to be used as defaults for the initial contents of the <tt class="docutils literal"><span class="pre">Controls</span></tt>
1621data tree item.</p>
1622</dd></dl>
1623
1624<dl class="class">
1625<dt id="GSASIIobj.G2VarObj">
1626<em class="property">class </em><tt class="descclassname">GSASIIobj.</tt><tt class="descname">G2VarObj</tt><big>(</big><em>*args</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#G2VarObj"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.G2VarObj" title="Permalink to this definition">¶</a></dt>
1627<dd><p>Defines a GSAS-II variable either using the phase/atom/histogram
1628unique Id numbers or using a character string that specifies
1629variables by phase/atom/histogram number (which can change).
1630Note that <tt class="xref py py-func docutils literal"><span class="pre">LoadID()</span></tt> should be used to (re)load the current Ids
1631before creating or later using the G2VarObj object.</p>
1632<p>A <a class="reference internal" href="#GSASIIobj.G2VarObj" title="GSASIIobj.G2VarObj"><tt class="xref py py-class docutils literal"><span class="pre">G2VarObj</span></tt></a> object can be created with a single parameter:</p>
1633<table class="docutils field-list" frame="void" rules="none">
1634<col class="field-name" />
1635<col class="field-body" />
1636<tbody valign="top">
1637<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>varname</strong> (<em>str/tuple</em>) &#8211; <dl class="docutils">
1638<dt>a single value can be used to create a <a class="reference internal" href="#GSASIIobj.G2VarObj" title="GSASIIobj.G2VarObj"><tt class="xref py py-class docutils literal"><span class="pre">G2VarObj</span></tt></a></dt>
1639<dd>object. If a string, it must be of form &#8220;p:h:var&#8221; or &#8220;p:h:var:a&#8221;, where</dd>
1640</dl>
1641<ul class="simple">
1642<li>p is the phase number (which may be left blank);</li>
1643<li>h is the histogram number (which may be left blank);</li>
1644<li>a is the atom number (which may be left blank in which case the third colon is omitted).</li>
1645</ul>
1646<blockquote>
1647<div>Alternately a single tuple of form (Phase,Histogram,VarName,AtomID) can be used, where
1648Phase, Histogram, and AtomID are None or are ranId values and VarName is a string.</div></blockquote>
1649</td>
1650</tr>
1651</tbody>
1652</table>
1653<p>If four positional arguments are supplied, they are:</p>
1654<table class="docutils field-list" frame="void" rules="none">
1655<col class="field-name" />
1656<col class="field-body" />
1657<tbody valign="top">
1658<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
1659<li><strong>phasenum</strong> (<em>str/int</em>) &#8211; The number for the phase</li>
1660<li><strong>histnum</strong> (<em>str/int</em>) &#8211; The number for the histogram</li>
1661<li><strong>varname</strong> (<em>str</em>) &#8211; a single value can be used to create a <a class="reference internal" href="#GSASIIobj.G2VarObj" title="GSASIIobj.G2VarObj"><tt class="xref py py-class docutils literal"><span class="pre">G2VarObj</span></tt></a></li>
1662<li><strong>atomnum</strong> (<em>str/int</em>) &#8211; The number for the atom</li>
1663</ul>
1664</td>
1665</tr>
1666</tbody>
1667</table>
1668<dl class="method">
1669<dt id="GSASIIobj.G2VarObj.varname">
1670<tt class="descname">varname</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#G2VarObj.varname"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.G2VarObj.varname" title="Permalink to this definition">¶</a></dt>
1671<dd><p>Formats the GSAS-II variable name as a &#8220;traditional&#8221; GSAS-II variable
1672string (p:h:&lt;var&gt;:a) or (p:h:&lt;var&gt;)</p>
1673<table class="docutils field-list" frame="void" rules="none">
1674<col class="field-name" />
1675<col class="field-body" />
1676<tbody valign="top">
1677<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">the variable name as a str</td>
1678</tr>
1679</tbody>
1680</table>
1681</dd></dl>
1682
1683</dd></dl>
1684
1685<dl class="data">
1686<dt id="GSASIIobj.HistIdLookup">
1687<tt class="descclassname">GSASIIobj.</tt><tt class="descname">HistIdLookup</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.HistIdLookup" title="Permalink to this definition">¶</a></dt>
1688<dd><p>dict listing histogram name and random Id, keyed by sequential histogram index as a str;
1689best to access this using <a class="reference internal" href="#GSASIIobj.LookupHistName" title="GSASIIobj.LookupHistName"><tt class="xref py py-func docutils literal"><span class="pre">LookupHistName()</span></tt></a></p>
1690</dd></dl>
1691
1692<dl class="data">
1693<dt id="GSASIIobj.HistRanIdLookup">
1694<tt class="descclassname">GSASIIobj.</tt><tt class="descname">HistRanIdLookup</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.HistRanIdLookup" title="Permalink to this definition">¶</a></dt>
1695<dd><p>dict listing histogram sequential index keyed by histogram random Id;
1696best to access this using <a class="reference internal" href="#GSASIIobj.LookupHistId" title="GSASIIobj.LookupHistId"><tt class="xref py py-func docutils literal"><span class="pre">LookupHistId()</span></tt></a></p>
1697</dd></dl>
1698
1699<dl class="function">
1700<dt id="GSASIIobj.IndexAllIds">
1701<tt class="descclassname">GSASIIobj.</tt><tt class="descname">IndexAllIds</tt><big>(</big><em>Histograms</em>, <em>Phases</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#IndexAllIds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.IndexAllIds" title="Permalink to this definition">¶</a></dt>
1702<dd><p>Scan through the used phases &amp; histograms and create an index
1703to the random numbers of phases, histograms and atoms. While doing this,
1704confirm that assigned random numbers are unique &#8211; just in case lightning
1705strikes twice in the same place.</p>
1706<p>Note: this code assumes that the atom random Id (ranId) is the last
1707element each atom record.</p>
1708<p>This is called in two places (only) <a class="reference internal" href="GSASIIstruc.html#GSASIIstrIO.GetUsedHistogramsAndPhases" title="GSASIIstrIO.GetUsedHistogramsAndPhases"><tt class="xref py py-func docutils literal"><span class="pre">GSASIIstrIO.GetUsedHistogramsAndPhases()</span></tt></a>
1709(which loads the histograms and phases from a GPX file) and
1710<a class="reference internal" href="GSASII.html#GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree" title="GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree"><tt class="xref py py-meth docutils literal"><span class="pre">GSASII.GSASII.GetUsedHistogramsAndPhasesfromTree()</span></tt></a>
1711(which loads the histograms and phases from the data tree.)</p>
1712<p>TODO: do we need a lookup for rigid body variables?</p>
1713</dd></dl>
1714
1715<dl class="function">
1716<dt id="GSASIIobj.LookupAtomId">
1717<tt class="descclassname">GSASIIobj.</tt><tt class="descname">LookupAtomId</tt><big>(</big><em>pId</em>, <em>ranId</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#LookupAtomId"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.LookupAtomId" title="Permalink to this definition">¶</a></dt>
1718<dd><p>Get the atom number from a phase and atom random Id</p>
1719<table class="docutils field-list" frame="void" rules="none">
1720<col class="field-name" />
1721<col class="field-body" />
1722<tbody valign="top">
1723<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
1724<li><strong>pId</strong> (<em>int/str</em>) &#8211; the sequential number of the phase</li>
1725<li><strong>ranId</strong> (<em>int</em>) &#8211; the random Id assigned to an atom</li>
1726</ul>
1727</td>
1728</tr>
1729<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">the index number of the atom (str)</p>
1730</td>
1731</tr>
1732</tbody>
1733</table>
1734</dd></dl>
1735
1736<dl class="function">
1737<dt id="GSASIIobj.LookupAtomLabel">
1738<tt class="descclassname">GSASIIobj.</tt><tt class="descname">LookupAtomLabel</tt><big>(</big><em>pId</em>, <em>index</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#LookupAtomLabel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.LookupAtomLabel" title="Permalink to this definition">¶</a></dt>
1739<dd><p>Get the atom label from a phase and atom index number</p>
1740<table class="docutils field-list" frame="void" rules="none">
1741<col class="field-name" />
1742<col class="field-body" />
1743<tbody valign="top">
1744<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
1745<li><strong>pId</strong> (<em>int/str</em>) &#8211; the sequential number of the phase</li>
1746<li><strong>index</strong> (<em>int</em>) &#8211; the index of the atom in the list of atoms</li>
1747</ul>
1748</td>
1749</tr>
1750<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">the label for the atom (str) and the random Id of the atom (int)</p>
1751</td>
1752</tr>
1753</tbody>
1754</table>
1755</dd></dl>
1756
1757<dl class="function">
1758<dt id="GSASIIobj.LookupHistId">
1759<tt class="descclassname">GSASIIobj.</tt><tt class="descname">LookupHistId</tt><big>(</big><em>ranId</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#LookupHistId"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.LookupHistId" title="Permalink to this definition">¶</a></dt>
1760<dd><p>Get the histogram number and name from a histogram random Id</p>
1761<table class="docutils field-list" frame="void" rules="none">
1762<col class="field-name" />
1763<col class="field-body" />
1764<tbody valign="top">
1765<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ranId</strong> (<em>int</em>) &#8211; the random Id assigned to a histogram</td>
1766</tr>
1767<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">the sequential Id (hId) number for the histogram (str)</td>
1768</tr>
1769</tbody>
1770</table>
1771</dd></dl>
1772
1773<dl class="function">
1774<dt id="GSASIIobj.LookupHistName">
1775<tt class="descclassname">GSASIIobj.</tt><tt class="descname">LookupHistName</tt><big>(</big><em>hId</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#LookupHistName"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.LookupHistName" title="Permalink to this definition">¶</a></dt>
1776<dd><p>Get the histogram number and name from a histogram Id</p>
1777<table class="docutils field-list" frame="void" rules="none">
1778<col class="field-name" />
1779<col class="field-body" />
1780<tbody valign="top">
1781<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>hId</strong> (<em>int/str</em>) &#8211; the sequential assigned to a histogram</td>
1782</tr>
1783<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">(hist,ranId) where hist is the name of the histogram (str)
1784and ranId is the random # id for the histogram (int)</td>
1785</tr>
1786</tbody>
1787</table>
1788</dd></dl>
1789
1790<dl class="function">
1791<dt id="GSASIIobj.LookupPhaseId">
1792<tt class="descclassname">GSASIIobj.</tt><tt class="descname">LookupPhaseId</tt><big>(</big><em>ranId</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#LookupPhaseId"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.LookupPhaseId" title="Permalink to this definition">¶</a></dt>
1793<dd><p>Get the phase number and name from a phase random Id</p>
1794<table class="docutils field-list" frame="void" rules="none">
1795<col class="field-name" />
1796<col class="field-body" />
1797<tbody valign="top">
1798<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ranId</strong> (<em>int</em>) &#8211; the random Id assigned to a phase</td>
1799</tr>
1800<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">the sequential Id (pId) number for the phase (str)</td>
1801</tr>
1802</tbody>
1803</table>
1804</dd></dl>
1805
1806<dl class="function">
1807<dt id="GSASIIobj.LookupPhaseName">
1808<tt class="descclassname">GSASIIobj.</tt><tt class="descname">LookupPhaseName</tt><big>(</big><em>pId</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#LookupPhaseName"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.LookupPhaseName" title="Permalink to this definition">¶</a></dt>
1809<dd><p>Get the phase number and name from a phase Id</p>
1810<table class="docutils field-list" frame="void" rules="none">
1811<col class="field-name" />
1812<col class="field-body" />
1813<tbody valign="top">
1814<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>pId</strong> (<em>int/str</em>) &#8211; the sequential assigned to a phase</td>
1815</tr>
1816<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">(phase,ranId) where phase is the name of the phase (str)
1817and ranId is the random # id for the phase (int)</td>
1818</tr>
1819</tbody>
1820</table>
1821</dd></dl>
1822
1823<dl class="function">
1824<dt id="GSASIIobj.MakeUniqueLabel">
1825<tt class="descclassname">GSASIIobj.</tt><tt class="descname">MakeUniqueLabel</tt><big>(</big><em>lbl</em>, <em>labellist</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#MakeUniqueLabel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.MakeUniqueLabel" title="Permalink to this definition">¶</a></dt>
1826<dd><p>Make sure that every a label is unique against a list by adding
1827digits at the end until it is not found in list.</p>
1828<table class="docutils field-list" frame="void" rules="none">
1829<col class="field-name" />
1830<col class="field-body" />
1831<tbody valign="top">
1832<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
1833<li><strong>lbl</strong> (<em>str</em>) &#8211; the input label</li>
1834<li><strong>labellist</strong> (<em>list</em>) &#8211; the labels that have already been encountered</li>
1835</ul>
1836</td>
1837</tr>
1838<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">lbl if not found in labellist or lbl with <tt class="docutils literal"><span class="pre">_1-9</span></tt> (or
1839<tt class="docutils literal"><span class="pre">_10-99</span></tt>, etc.) appended at the end</p>
1840</td>
1841</tr>
1842</tbody>
1843</table>
1844</dd></dl>
1845
1846<dl class="data">
1847<dt id="GSASIIobj.PhaseIdLookup">
1848<tt class="descclassname">GSASIIobj.</tt><tt class="descname">PhaseIdLookup</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.PhaseIdLookup" title="Permalink to this definition">¶</a></dt>
1849<dd><p>dict listing phase name and random Id keyed by sequential phase index as a str;
1850best to access this using <a class="reference internal" href="#GSASIIobj.LookupPhaseName" title="GSASIIobj.LookupPhaseName"><tt class="xref py py-func docutils literal"><span class="pre">LookupPhaseName()</span></tt></a></p>
1851</dd></dl>
1852
1853<dl class="data">
1854<dt id="GSASIIobj.PhaseRanIdLookup">
1855<tt class="descclassname">GSASIIobj.</tt><tt class="descname">PhaseRanIdLookup</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.PhaseRanIdLookup" title="Permalink to this definition">¶</a></dt>
1856<dd><p>dict listing phase sequential index keyed by phase random Id;
1857best to access this using <a class="reference internal" href="#GSASIIobj.LookupPhaseId" title="GSASIIobj.LookupPhaseId"><tt class="xref py py-func docutils literal"><span class="pre">LookupPhaseId()</span></tt></a></p>
1858</dd></dl>
1859
1860<dl class="data">
1861<dt id="GSASIIobj.ShortHistNames">
1862<tt class="descclassname">GSASIIobj.</tt><tt class="descname">ShortHistNames</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.ShortHistNames" title="Permalink to this definition">¶</a></dt>
1863<dd><p>a dict containing a possibly shortened and when non-unique numbered
1864version of the histogram name. Keyed by the histogram sequential index.</p>
1865</dd></dl>
1866
1867<dl class="data">
1868<dt id="GSASIIobj.ShortPhaseNames">
1869<tt class="descclassname">GSASIIobj.</tt><tt class="descname">ShortPhaseNames</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.ShortPhaseNames" title="Permalink to this definition">¶</a></dt>
1870<dd><p>a dict containing a possibly shortened and when non-unique numbered
1871version of the phase name. Keyed by the phase sequential index.</p>
1872</dd></dl>
1873
1874<dl class="data">
1875<dt id="GSASIIobj.VarDesc">
1876<tt class="descclassname">GSASIIobj.</tt><tt class="descname">VarDesc</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.VarDesc" title="Permalink to this definition">¶</a></dt>
1877<dd><p>This dictionary lists descriptions for GSAS-II variables,
1878as set in <a class="reference internal" href="#GSASIIobj.CompileVarDesc" title="GSASIIobj.CompileVarDesc"><tt class="xref py py-func docutils literal"><span class="pre">CompileVarDesc()</span></tt></a>. See that function for a description
1879for how keys and values are written.</p>
1880</dd></dl>
1881
1882<dl class="function">
1883<dt id="GSASIIobj.fmtVarDescr">
1884<tt class="descclassname">GSASIIobj.</tt><tt class="descname">fmtVarDescr</tt><big>(</big><em>varname</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#fmtVarDescr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.fmtVarDescr" title="Permalink to this definition">¶</a></dt>
1885<dd><p>Return a string with a more complete description for a GSAS-II variable</p>
1886<p>TODO: This will not handle rigid body parameters yet</p>
1887<table class="docutils field-list" frame="void" rules="none">
1888<col class="field-name" />
1889<col class="field-body" />
1890<tbody valign="top">
1891<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>name</strong> (<em>str</em>) &#8211; A full G2 variable name with 2 or 3
1892colons (&lt;p&gt;:&lt;h&gt;:name[:&lt;a&gt;])</td>
1893</tr>
1894<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a string with the description</td>
1895</tr>
1896</tbody>
1897</table>
1898</dd></dl>
1899
1900<dl class="function">
1901<dt id="GSASIIobj.getDescr">
1902<tt class="descclassname">GSASIIobj.</tt><tt class="descname">getDescr</tt><big>(</big><em>name</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#getDescr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.getDescr" title="Permalink to this definition">¶</a></dt>
1903<dd><p>Return a short description for a GSAS-II variable</p>
1904<table class="docutils field-list" frame="void" rules="none">
1905<col class="field-name" />
1906<col class="field-body" />
1907<tbody valign="top">
1908<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>name</strong> (<em>str</em>) &#8211; The descriptive part of the variable name without colons (:)</td>
1909</tr>
1910<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a short description or None if not found</td>
1911</tr>
1912</tbody>
1913</table>
1914</dd></dl>
1915
1916<dl class="function">
1917<dt id="GSASIIobj.getVarDescr">
1918<tt class="descclassname">GSASIIobj.</tt><tt class="descname">getVarDescr</tt><big>(</big><em>varname</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#getVarDescr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.getVarDescr" title="Permalink to this definition">¶</a></dt>
1919<dd><p>Return a short description for a GSAS-II variable</p>
1920<table class="docutils field-list" frame="void" rules="none">
1921<col class="field-name" />
1922<col class="field-body" />
1923<tbody valign="top">
1924<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>name</strong> (<em>str</em>) &#8211; A full G2 variable name with 2 or 3
1925colons (&lt;p&gt;:&lt;h&gt;:name[:&lt;a&gt;])</td>
1926</tr>
1927<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a five element list as [<cite>p</cite>,`h`,`name`,`a`,`description`],
1928where <cite>p</cite>, <cite>h</cite>, <cite>a</cite> are str values or <cite>None</cite>, for the phase number,
1929the histogram number and the atom number; <cite>name</cite> will always be
1930an str; and <cite>description</cite> is str or <cite>None</cite>.
1931If the variable name is incorrectly formed (for example, wrong
1932number of colons), <cite>None</cite> is returned instead of a list.</td>
1933</tr>
1934</tbody>
1935</table>
1936</dd></dl>
1937
1938<dl class="data">
1939<dt id="GSASIIobj.reVarDesc">
1940<tt class="descclassname">GSASIIobj.</tt><tt class="descname">reVarDesc</tt><em class="property"> = {}</em><a class="headerlink" href="#GSASIIobj.reVarDesc" title="Permalink to this definition">¶</a></dt>
1941<dd><p>This dictionary lists descriptions for GSAS-II variables with
1942the same values as <a class="reference internal" href="#GSASIIobj.VarDesc" title="GSASIIobj.VarDesc"><tt class="xref py py-attr docutils literal"><span class="pre">VarDesc</span></tt></a> except that keys have been compiled as
1943regular expressions. Initialized in <a class="reference internal" href="#GSASIIobj.CompileVarDesc" title="GSASIIobj.CompileVarDesc"><tt class="xref py py-func docutils literal"><span class="pre">CompileVarDesc()</span></tt></a>.</p>
1944</dd></dl>
1945
1946</div>
1947</div>
1948
1949
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1958  <h3><a href="index.html">Table Of Contents</a></h3>
1959  <ul>
1960<li><a class="reference internal" href="#"><em>GSASIIobj: Data objects</em></a><ul>
1961<li><a class="reference internal" href="#constraints-tree-item">Constraints Tree Item</a></li>
1962<li><a class="reference internal" href="#covariance-tree-item">Covariance Tree Item</a></li>
1963<li><a class="reference internal" href="#phase-tree-items">Phase Tree Items</a></li>
1964<li><a class="reference internal" href="#rigid-body-objects">Rigid Body Objects</a></li>
1965<li><a class="reference internal" href="#space-group-objects">Space Group Objects</a></li>
1966<li><a class="reference internal" href="#atom-records">Atom Records</a></li>
1967<li><a class="reference internal" href="#drawing-atom-records">Drawing Atom Records</a></li>
1968<li><a class="reference internal" href="#powder-diffraction-tree-items">Powder Diffraction Tree Items</a></li>
1969<li><a class="reference internal" href="#powder-reflection-data-structure">Powder Reflection Data Structure</a></li>
1970<li><a class="reference internal" href="#single-crystal-tree-items">Single Crystal Tree Items</a></li>
1971<li><a class="reference internal" href="#single-crystal-reflection-data-structure">Single Crystal Reflection Data Structure</a></li>
1972<li><a class="reference internal" href="#image-data-structure">Image Data Structure</a></li>
1973<li><a class="reference internal" href="#parameter-dictionary">Parameter Dictionary</a></li>
1974<li><a class="reference internal" href="#classes-and-routines"><em>Classes and routines</em></a></li>
1975</ul>
1976</li>
1977</ul>
1978
1979  <h4>Previous topic</h4>
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1981                        title="previous chapter"><em>GSAS-II Main Module</em></a></p>
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