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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.</p>
61<div class="section" id="constraints-tree-item">
62<h2>Constraints Tree Item<a class="headerlink" href="#constraints-tree-item" title="Permalink to this headline">¶</a></h2>
63<span class="target" id="constraints-table"></span><p id="index-0">Constraints are stored in a dict, separated into groups.
64Note that parameter are named in the following pattern,
65p:h:&lt;var&gt;:n, where p is the phase number, h is the histogram number
66&lt;var&gt; is a variable name and n is the parameter number.
67If a parameter does not depend on a histogram or phase or is unnumbered, that
68number is omitted.
69Note that the contents of each dict item is a List where each element in the
70list is a <a class="reference internal" href="#constraint-definitions-table"><em>constraint definition objects</em></a>.</p>
71<p>The keys in the Constraints dict are:</p>
72<table border="1" class="docutils">
73<colgroup>
74<col width="16%" />
75<col width="84%" />
76</colgroup>
77<thead valign="bottom">
78<tr class="row-odd"><th class="head">key</th>
79<th class="head">explanation</th>
80</tr>
81</thead>
82<tbody valign="top">
83<tr class="row-even"><td>Hist</td>
84<td>This specifies a list of constraints on
85histogram-related parameters,
86which will be of form :h:&lt;var&gt;:n.</td>
87</tr>
88<tr class="row-odd"><td>HAP</td>
89<td>This specifies a list of constraints on parameters
90that are defined for every histogram in each phase
91and are of form p:h:&lt;var&gt;:n.</td>
92</tr>
93<tr class="row-even"><td>Phase</td>
94<td>This specifies a list of constraints on phase
95parameters,
96which will be of form p::&lt;var&gt;:n.</td>
97</tr>
98<tr class="row-odd"><td>Global</td>
99<td>This specifies a list of constraints on parameters
100that are not tied to a histogram or phase and
101are of form ::&lt;var&gt;:n</td>
102</tr>
103</tbody>
104</table>
105<span class="target" id="constraint-definitions-table"></span><p id="index-1">Each constraint is defined as a list using a series of terms of form</p>
106<div class="highlight-python"><pre>[[&lt;mult1&gt;, &lt;var1&gt;], [&lt;mult2&gt;, &lt;var2&gt;],..., &lt;fixed val&gt;, &lt;vary flag&gt;, &lt;cons type&gt;]</pre>
107</div>
108<p>Where the variable pair list item containing two values [&lt;mult&gt;, &lt;var&gt;],</p>
109<blockquote>
110<div><ul class="simple">
111<li>&lt;mult&gt; is a multiplier for the constraint (float)</li>
112<li>&lt;var&gt; is the name of the variable (str) (or to be implemented a <a class="reference internal" href="#GSASIIobj.VarName" title="GSASIIobj.VarName"><tt class="xref py py-class docutils literal"><span class="pre">VarName</span></tt></a> object.)</li>
113</ul>
114</div></blockquote>
115<p>Note that the last three items in the list play a special role:</p>
116<blockquote>
117<div><ul>
118<li><p class="first">&lt;fixed val&gt; is the fixed value for a constraint equation or is None</p>
119</li>
120<li><p class="first">&lt;vary flag&gt; is True, False or None and is intended to use to indicate if new variables
121should be refined.</p>
122</li>
123<li><p class="first">&lt;cons type&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>
124<blockquote>
125<div><ul class="simple">
126<li>&#8216;e&#8217; defines a set of equivalent variables. Only the first variable is refined (if the
127appropriate refine flag is set) and and all other equivalent variables in the list
128are generated from that variable. The vary flag for those variables is ignored.</li>
129<li>&#8216;c&#8217; defines a constraint equation of form, <span class="math">\(m_1 \times var_1 + m_2 \times var_2 + ... = c\)</span></li>
130<li>&#8216;h&#8217; defines a variable to hold (not vary). Any variable on this list is not varied, even if its refinement
131flag is set. This is of particular value when needing to hold one or more variables in a set such as
132the reciprocal metric tensor or anisotropic displacement parameter.</li>
133<li>&#8216;f&#8217; defines a relationship to define a new variable according to relationship
134<span class="math">\(newvar = m_1 \times var_1 + m_2 \times var_2 + ...\)</span></li>
135</ul>
136</div></blockquote>
137</li>
138</ul>
139</div></blockquote>
140</div>
141<div class="section" id="covariance-tree-item">
142<h2>Covariance Tree Item<a class="headerlink" href="#covariance-tree-item" title="Permalink to this headline">¶</a></h2>
143<span class="target" id="covariance-table"></span><p id="index-2">The Covariance tree item has results from the last least-squares run. They
144are stored in a dict with these keys:</p>
145<table border="1" class="docutils">
146<colgroup>
147<col width="16%" />
148<col width="19%" />
149<col width="65%" />
150</colgroup>
151<thead valign="bottom">
152<tr class="row-odd"><th class="head">key</th>
153<th class="head">sub-key</th>
154<th class="head">explanation</th>
155</tr>
156</thead>
157<tbody valign="top">
158<tr class="row-even"><td>newCellDict</td>
159<td></td>
160<td>dict with lattice parameters computed by
161<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>
162</tr>
163<tr class="row-odd"><td>title</td>
164<td></td>
165<td>Name of gpx file(?) (str)</td>
166</tr>
167<tr class="row-even"><td>variables</td>
168<td></td>
169<td>Values for all N refined variables
170(list of float values, length N,
171ordered to match varyList)</td>
172</tr>
173<tr class="row-odd"><td>sig</td>
174<td></td>
175<td>Uncertainty values for all N refined variables
176(list of float values, length N,
177ordered to match varyList)</td>
178</tr>
179<tr class="row-even"><td>varyList</td>
180<td></td>
181<td>List of directly refined variables
182(list of str values, length N)</td>
183</tr>
184<tr class="row-odd"><td>newAtomDict</td>
185<td></td>
186<td>dict with atom position values computed in
187<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>
188</tr>
189<tr class="row-even"><td>Rvals</td>
190<td></td>
191<td>R-factors, GOF, Marquardt value for last
192refinement cycle (dict)</td>
193</tr>
194<tr class="row-odd"><td></td>
195<td>Nobs</td>
196<td>Number of observed data points (int)</td>
197</tr>
198<tr class="row-even"><td></td>
199<td>Rwp</td>
200<td>overall weighted profile R-factor (%, float)</td>
201</tr>
202<tr class="row-odd"><td></td>
203<td>chisq</td>
204<td>sum[w*(Iobs-Icalc)**2] for all data
205note this is not the reduced chi squared (float)</td>
206</tr>
207<tr class="row-even"><td></td>
208<td>lamMax</td>
209<td>Marquardt value applied to Hessian diagonal
210(float)</td>
211</tr>
212<tr class="row-odd"><td></td>
213<td>GOF</td>
214<td>The goodness-of-fit, aka square root of
215the reduced chi squared. (float)</td>
216</tr>
217<tr class="row-even"><td>covMatrix</td>
218<td></td>
219<td>The (NxN) covVariance matrix (np.array)</td>
220</tr>
221</tbody>
222</table>
223</div>
224<div class="section" id="phase-tree-items">
225<h2>Phase Tree Items<a class="headerlink" href="#phase-tree-items" title="Permalink to this headline">¶</a></h2>
226<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
227Phases item in a dict with keys:</p>
228<table border="1" class="docutils">
229<colgroup>
230<col width="10%" />
231<col width="15%" />
232<col width="75%" />
233</colgroup>
234<thead valign="bottom">
235<tr class="row-odd"><th class="head">key</th>
236<th class="head">sub-key</th>
237<th class="head">explanation</th>
238</tr>
239</thead>
240<tbody valign="top">
241<tr class="row-even"><td>General</td>
242<td></td>
243<td>Overall information for the phase (dict)</td>
244</tr>
245<tr class="row-odd"><td></td>
246<td>AtomPtrs</td>
247<td>list of four locations to use to pull info
248from the atom records (list)</td>
249</tr>
250<tr class="row-even"><td></td>
251<td>F000X</td>
252<td>x-ray F(000) intensity (float)</td>
253</tr>
254<tr class="row-odd"><td></td>
255<td>F000N</td>
256<td>neutron F(000) intensity (float)</td>
257</tr>
258<tr class="row-even"><td></td>
259<td>Mydir</td>
260<td>directory of current .gpx file (str)</td>
261</tr>
262<tr class="row-odd"><td></td>
263<td>MCSA controls</td>
264<td>?</td>
265</tr>
266<tr class="row-even"><td></td>
267<td>Cell</td>
268<td>List with 7 items: cell refinement flag (bool)
269a, b, c, (Angstrom, float)
270alpha, beta &amp; gamma (degrees, float)</td>
271</tr>
272<tr class="row-odd"><td></td>
273<td>Type</td>
274<td>for now &#8216;nuclear&#8217; (str)</td>
275</tr>
276<tr class="row-even"><td></td>
277<td>Map</td>
278<td>dict of map parameters</td>
279</tr>
280<tr class="row-odd"><td></td>
281<td>SH Texture</td>
282<td>dict of spherical harmonic preferred orientation
283parameters</td>
284</tr>
285<tr class="row-even"><td></td>
286<td>Isotope</td>
287<td>dict of isotopes for each atom type</td>
288</tr>
289<tr class="row-odd"><td></td>
290<td>Isotopes</td>
291<td>dict of scattering lengths for each isotope
292combination for each element in phase</td>
293</tr>
294<tr class="row-even"><td></td>
295<td>Name</td>
296<td>phase name (str)</td>
297</tr>
298<tr class="row-odd"><td></td>
299<td>SGData</td>
300<td>Space group details as a <a class="reference internal" href="#sgdata-table"><em>space group (SGData) object</em></a>
301as 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>
302</tr>
303<tr class="row-even"><td></td>
304<td>Pawley neg wt</td>
305<td>Restraint value for negative Pawley intensities
306(float)</td>
307</tr>
308<tr class="row-odd"><td></td>
309<td>Flip</td>
310<td>Charge flip controls dict?</td>
311</tr>
312<tr class="row-even"><td></td>
313<td>Data plot type</td>
314<td>?</td>
315</tr>
316<tr class="row-odd"><td></td>
317<td>Mass</td>
318<td>Mass of unit cell contents in g/mol</td>
319</tr>
320<tr class="row-even"><td></td>
321<td>POhkl</td>
322<td>March-Dollase preferred orientation direction</td>
323</tr>
324<tr class="row-odd"><td></td>
325<td>Z</td>
326<td>?</td>
327</tr>
328<tr class="row-even"><td></td>
329<td>vdWRadii</td>
330<td>?</td>
331</tr>
332<tr class="row-odd"><td></td>
333<td>Color</td>
334<td>Colors for atoms (list of (r,b,g) triplets)</td>
335</tr>
336<tr class="row-even"><td></td>
337<td>AtomTypes</td>
338<td>List of atom types</td>
339</tr>
340<tr class="row-odd"><td></td>
341<td>AtomMass</td>
342<td>List of masses for atoms</td>
343</tr>
344<tr class="row-even"><td></td>
345<td>doPawley</td>
346<td>Flag for Pawley intensity extraction (bool)</td>
347</tr>
348<tr class="row-odd"><td></td>
349<td>NoAtoms</td>
350<td>Number of atoms per unit cell of each type (dict)</td>
351</tr>
352<tr class="row-even"><td></td>
353<td>Pawley dmin</td>
354<td>maximum Q (as d-space) to use for Pawley
355extraction (float)</td>
356</tr>
357<tr class="row-odd"><td></td>
358<td>BondRadii</td>
359<td>Radius for each atom used to compute
360interatomic distances (list of floats)</td>
361</tr>
362<tr class="row-even"><td></td>
363<td>AngleRadii</td>
364<td>Radius for each atom used to compute
365interatomic angles (list of floats)</td>
366</tr>
367<tr class="row-odd"><td>ranId</td>
368<td></td>
369<td>unique random number Id for phase (int)</td>
370</tr>
371<tr class="row-even"><td>pId</td>
372<td></td>
373<td>Phase Id number for current project (int).</td>
374</tr>
375<tr class="row-odd"><td>Atoms</td>
376<td></td>
377<td>Atoms in phase as a list of lists. The outer list
378is for each atom, the inner list contains varying
379items depending on the type of phase, see
380the <a class="reference internal" href="#atoms-table"><em>Atom Records</em></a> description.
381(list of lists)</td>
382</tr>
383<tr class="row-even"><td>Drawing</td>
384<td></td>
385<td>Display parameters (dict)</td>
386</tr>
387<tr class="row-odd"><td></td>
388<td>ballScale</td>
389<td>Size of spheres in ball-and-stick display (float)</td>
390</tr>
391<tr class="row-even"><td></td>
392<td>bondList</td>
393<td>dict with bonds</td>
394</tr>
395<tr class="row-odd"><td></td>
396<td>contourLevel</td>
397<td>? (float)</td>
398</tr>
399<tr class="row-even"><td></td>
400<td>showABC</td>
401<td>Flag to show view point triplet (bool). True=show.</td>
402</tr>
403<tr class="row-odd"><td></td>
404<td>viewDir</td>
405<td>cartesian viewing direction (np.array with three
406elements)</td>
407</tr>
408<tr class="row-even"><td></td>
409<td>Zclip</td>
410<td>clipping distance in A (float)</td>
411</tr>
412<tr class="row-odd"><td></td>
413<td>backColor</td>
414<td>background for plot as and R,G,B triplet
415(default = [0, 0, 0], black).
416(list with three atoms)</td>
417</tr>
418<tr class="row-even"><td></td>
419<td>selectedAtoms</td>
420<td>List of selected atoms (list of int values)</td>
421</tr>
422<tr class="row-odd"><td></td>
423<td>showRigidBodies</td>
424<td>Flag to highlight rigid body placement</td>
425</tr>
426<tr class="row-even"><td></td>
427<td>sizeH</td>
428<td>Size ratio for H atoms (float)</td>
429</tr>
430<tr class="row-odd"><td></td>
431<td>bondRadius</td>
432<td>Size of binds in A (float)</td>
433</tr>
434<tr class="row-even"><td></td>
435<td>atomPtrs</td>
436<td>? (list)</td>
437</tr>
438<tr class="row-odd"><td></td>
439<td>viewPoint</td>
440<td>list of lists. First item in list is [x,y,z]
441in fractional coordinates for the center of
442the plot. Second item ?.</td>
443</tr>
444<tr class="row-even"><td></td>
445<td>showHydrogen</td>
446<td>Flag to control plotting of H atoms.</td>
447</tr>
448<tr class="row-odd"><td></td>
449<td>unitCellBox</td>
450<td>Flag to control display of the unit cell.</td>
451</tr>
452<tr class="row-even"><td></td>
453<td>ellipseProb</td>
454<td>Probability limit for display of thermal
455ellipsoids in % (float).</td>
456</tr>
457<tr class="row-odd"><td></td>
458<td>vdwScale</td>
459<td>Multiplier of van der Waals radius for
460display of vdW spheres.</td>
461</tr>
462<tr class="row-even"><td></td>
463<td>Atoms</td>
464<td>A list of lists with an entry for each atom
465that is plotted.</td>
466</tr>
467<tr class="row-odd"><td></td>
468<td>Zstep</td>
469<td>Step to de/increase Z-clip (float)</td>
470</tr>
471<tr class="row-even"><td></td>
472<td>Quaternion</td>
473<td>Viewing quaternion (4 element np.array)</td>
474</tr>
475<tr class="row-odd"><td></td>
476<td>radiusFactor</td>
477<td>Distance ratio for searching for bonds. ? Bonds
478are located that are within r(Ra+Rb) and (Ra+Rb)/r
479where Ra and Rb are the atomic radii.</td>
480</tr>
481<tr class="row-even"><td></td>
482<td>oldxy</td>
483<td>? (list with two floats)</td>
484</tr>
485<tr class="row-odd"><td></td>
486<td>cameraPos</td>
487<td>Viewing position in A for plot (float)</td>
488</tr>
489<tr class="row-even"><td></td>
490<td>depthFog</td>
491<td>? (bool)</td>
492</tr>
493<tr class="row-odd"><td>RBModels</td>
494<td></td>
495<td>Rigid body assignments (note Rigid body definitions
496are stored in their own main top-level tree entry.)</td>
497</tr>
498<tr class="row-even"><td>Pawley ref</td>
499<td></td>
500<td>Pawley reflections</td>
501</tr>
502<tr class="row-odd"><td>Histograms</td>
503<td></td>
504<td>A dict of dicts. The key for the outer dict is
505the histograms tied to this phase. The inner
506dict contains the combined phase/histogram
507parameters for items such as scale factors,
508size and strain parameters. (dict)</td>
509</tr>
510<tr class="row-even"><td>MCSA</td>
511<td></td>
512<td>Monte-Carlo simulated annealing parameters</td>
513</tr>
514</tbody>
515</table>
516</div>
517<div class="section" id="space-group-objects">
518<h2>Space Group Objects<a class="headerlink" href="#space-group-objects" title="Permalink to this headline">¶</a></h2>
519<span class="target" id="sgdata-table"></span><p id="index-4">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> 
520and the information is placed in a SGdata object,
521which is a dict with these keys:</p>
522<table border="1" class="docutils">
523<colgroup>
524<col width="16%" />
525<col width="84%" />
526</colgroup>
527<thead valign="bottom">
528<tr class="row-odd"><th class="head">key</th>
529<th class="head">explanation</th>
530</tr>
531</thead>
532<tbody valign="top">
533<tr class="row-even"><td>SpGrp</td>
534<td>space group symbol (str)</td>
535</tr>
536<tr class="row-odd"><td>Laue</td>
537<td>one of the following 14 Laue classes:
538-1, 2/m, mmm, 4/m, 4/mmm, 3R,
5393mR, 3, 3m1, 31m, 6/m, 6/mmm, m3, m3m (str)</td>
540</tr>
541<tr class="row-even"><td>SGInv</td>
542<td>True if centrosymmetric, False if not (bool)</td>
543</tr>
544<tr class="row-odd"><td>SGLatt</td>
545<td>Lattice centering type. Will be one of
546P, A, B, C, I, F, R (str)</td>
547</tr>
548<tr class="row-even"><td>SGUniq</td>
549<td>unique axis if monoclinic. Will be
550a, b, or c for monoclinic space groups.
551Will be blank for non-monoclinic. (str)</td>
552</tr>
553<tr class="row-odd"><td>SGCen</td>
554<td>Symmetry cell centering vectors. A (n,3) np.array
555of centers. Will always have at least one row:
556<tt class="docutils literal"><span class="pre">np.array([[0,</span> <span class="pre">0,</span> <span class="pre">0]])</span></tt></td>
557</tr>
558<tr class="row-even"><td>SGOps</td>
559<td>symmetry operations as a list of form
560<tt class="docutils literal"><span class="pre">[[M1,T1],</span> <span class="pre">[M2,T2],...]</span></tt>
561where <span class="math">\(M_n\)</span> is a 3x3 np.array
562and <span class="math">\(T_n\)</span> is a length 3 np.array.
563Atom coordinates are transformed where the
564Asymmetric unit coordinates [X is (x,y,z)]
565are transformed using
566<span class="math">\(X^\prime = M_n*X+T_n\)</span></td>
567</tr>
568<tr class="row-odd"><td>SGSys</td>
569<td>symmetry unit cell: type one of
570&#8216;triclinic&#8217;, &#8216;monoclinic&#8217;, &#8216;orthorhombic&#8217;,
571&#8216;tetragonal&#8217;, &#8216;rhombohedral&#8217;, &#8216;trigonal&#8217;,
572&#8216;hexagonal&#8217;, &#8216;cubic&#8217; (str)</td>
573</tr>
574<tr class="row-even"><td>SGPolax</td>
575<td>Axes for space group polarity. Will be one of
576&#8216;&#8217;, &#8216;x&#8217;, &#8216;y&#8217;, &#8216;x y&#8217;, &#8216;z&#8217;, &#8216;x z&#8217;, &#8216;y z&#8217;,
577&#8216;xyz&#8217;. In the case where axes are arbitrary
578&#8216;111&#8217; is used (P 1, and ?).</td>
579</tr>
580</tbody>
581</table>
582</div>
583<div class="section" id="atom-records">
584<h2>Atom Records<a class="headerlink" href="#atom-records" title="Permalink to this headline">¶</a></h2>
585<span class="target" id="atoms-table"></span><p id="index-5">If <tt class="docutils literal"><span class="pre">phasedict</span></tt> points to the phase information in the data tree, then
586atoms are contained in a list of atom records (list) in
587<tt class="docutils literal"><span class="pre">phasedict['Atoms']</span></tt>. Also needed to read atom information
588are 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>,
589which define locations in the atom record, as shown below.</p>
590<table border="1" class="docutils">
591<colgroup>
592<col width="21%" />
593<col width="79%" />
594</colgroup>
595<thead valign="bottom">
596<tr class="row-odd"><th class="head">location</th>
597<th class="head">explanation</th>
598</tr>
599</thead>
600<tbody valign="top">
601<tr class="row-even"><td>cx,cx+1,cx+2</td>
602<td>the x,y and z coordinates</td>
603</tr>
604<tr class="row-odd"><td>cx+3</td>
605<td>fractional occupancy (also cs-1)</td>
606</tr>
607<tr class="row-even"><td>ct-1</td>
608<td>atom label</td>
609</tr>
610<tr class="row-odd"><td>ct</td>
611<td>atom type</td>
612</tr>
613<tr class="row-even"><td>ct+1</td>
614<td>refinement flags</td>
615</tr>
616<tr class="row-odd"><td>cs</td>
617<td>site symmetry string</td>
618</tr>
619<tr class="row-even"><td>cs+1</td>
620<td>site multiplicity</td>
621</tr>
622<tr class="row-odd"><td>cia</td>
623<td>ADP flag: Isotropic (&#8216;I&#8217;) or Anisotropic (&#8216;A&#8217;)</td>
624</tr>
625<tr class="row-even"><td>cia+1</td>
626<td>Uiso</td>
627</tr>
628<tr class="row-odd"><td>cia+2...cia+6</td>
629<td>U11, U22, U33, U12, U13, U23</td>
630</tr>
631</tbody>
632</table>
633</div>
634<div class="section" id="powder-diffraction-tree-items">
635<h2>Powder Diffraction Tree Items<a class="headerlink" href="#powder-diffraction-tree-items" title="Permalink to this headline">¶</a></h2>
636<span class="target" id="powder-table"></span><p id="index-6">Every powder diffraction histogram is stored in the GSAS-II data tree
637with a top-level entry named beginning with the string &#8220;PWDR &#8221;. The
638diffraction data for that information are directly associated with
639that tree item and there are a series of children to that item. The
640routine <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">GetUsedHistogramsAndPhasesfromTree()</span></tt></a> will
641load this information into a dictionary where the child tree name is
642used as a key, and the information in the main entry is assigned
643a key of <tt class="docutils literal"><span class="pre">Data</span></tt>, as outlined below.</p>
644<table border="1" class="docutils">
645<colgroup>
646<col width="25%" />
647<col width="17%" />
648<col width="58%" />
649</colgroup>
650<thead valign="bottom">
651<tr class="row-odd"><th class="head">key</th>
652<th class="head">sub-key</th>
653<th class="head">explanation</th>
654</tr>
655</thead>
656<tbody valign="top">
657<tr class="row-even"><td>Limits</td>
658<td></td>
659<td>A list of two two element lists, as [[Ld,Hd],[L,H]]
660where L and Ld are the current and default lowest
661two-theta value to be used and
662where H and Hd are the current and default highest
663two-theta value to be used.</td>
664</tr>
665<tr class="row-odd"><td>Reflection Lists</td>
666<td></td>
667<td>A dict with an entry for each phase in the
668histogram. The contents of each dict item
669is a list or reflections as described in the
670<a class="reference internal" href="#powderrefl-table"><em>Powder Reflections</em></a>
671description.</td>
672</tr>
673<tr class="row-even"><td>Instrument Parameters</td>
674<td></td>
675<td>A list containing two dicts where the possible
676keys in each dict are listed below. The value
677for each item is a list containing three values:
678the initial value, the current value and a
679refinement flag which can have a value of
680True, False or 0 where 0 indicates a value that
681cannot be refined. The first and second
682values are floats unless otherwise noted.
683Items in the first dict are noted as [1]</td>
684</tr>
685<tr class="row-odd"><td></td>
686<td>Lam</td>
687<td>Specifies a wavelength in Angstroms [1]</td>
688</tr>
689<tr class="row-even"><td></td>
690<td>Lam1</td>
691<td>Specifies the primary wavelength in
692Angstrom, when an alpha1, alpha2
693source is used [1]</td>
694</tr>
695<tr class="row-odd"><td></td>
696<td><p class="first">Lam2</p>
697<p class="last">I(L2)/I(L1)</p>
698</td>
699<td>Specifies the secondary wavelength in
700Angstrom, when an alpha1, alpha2
701source is used [1]
702Ratio of Lam2 to Lam1 [1]</td>
703</tr>
704<tr class="row-even"><td></td>
705<td>Type</td>
706<td><dl class="first last docutils">
707<dt>Histogram type (str) [1]:</dt>
708<dd><ul class="first last simple">
709<li>&#8216;PXC&#8217; for constant wavelength x-ray</li>
710<li>&#8216;PNC&#8217; for constant wavelength neutron</li>
711<li>&#8216;PNT&#8217; for time of flight neutron</li>
712</ul>
713</dd>
714</dl>
715</td>
716</tr>
717<tr class="row-odd"><td></td>
718<td>Zero</td>
719<td>Two-theta zero correction in <em>degrees</em> [1]</td>
720</tr>
721<tr class="row-even"><td></td>
722<td>Azimuth</td>
723<td>Azimuthal setting angle for data recorded
724with differing setting angles [1]</td>
725</tr>
726<tr class="row-odd"><td></td>
727<td>U, V, W</td>
728<td>Cagliotti profile coefficients
729for Gaussian instrumental broadening, where the
730FWHM goes as
731<span class="math">\(U \tan^2\theta + V \tan\theta + W\)</span> [1]</td>
732</tr>
733<tr class="row-even"><td></td>
734<td>X, Y</td>
735<td>Cauchy (Lorentzian) instrumental broadening
736coefficients [1]</td>
737</tr>
738<tr class="row-odd"><td></td>
739<td>SH/L</td>
740<td>Variant of the Finger-Cox-Jephcoat asymmetric
741peak broadening ratio. Note that this is the
742average between S/L and H/L where S is
743sample height, H is the slit height and
744L is the goniometer diameter. [1]</td>
745</tr>
746<tr class="row-even"><td></td>
747<td>Polariz.</td>
748<td>Polarization coefficient. [1]</td>
749</tr>
750<tr class="row-odd"><td>wtFactor</td>
751<td></td>
752<td>A weighting factor to increase or decrease
753the leverage of data in the histogram (float).
754A value of 1.0 weights the data with their
755standard uncertainties and a larger value
756increases the weighting of the data (equivalent
757to decreasing the uncertainties).</td>
758</tr>
759<tr class="row-even"><td>Sample Parameters</td>
760<td></td>
761<td>Specifies a dict with parameters that describe how
762the data were collected, as listed
763below. Refinable parameters are a list containing
764a float and a bool, where the second value
765specifies if the value is refined, otherwise
766the value is a float unless otherwise noted.</td>
767</tr>
768<tr class="row-odd"><td></td>
769<td>Scale</td>
770<td>The histogram scale factor (refinable)</td>
771</tr>
772<tr class="row-even"><td></td>
773<td>Absorption</td>
774<td>The sample absorption coefficient as
775<span class="math">\(\mu r\)</span> where r is the radius
776(refinable).</td>
777</tr>
778<tr class="row-odd"><td></td>
779<td>DisplaceX,
780DisplaceY</td>
781<td>Sample displacement from goniometer center
782where Y is along the beam direction and
783X is perpendicular. Units are <span class="math">\(\mu m\)</span>
784(refinable).</td>
785</tr>
786<tr class="row-even"><td></td>
787<td>Phi, Chi,
788Omega</td>
789<td>Goniometer sample setting angles, in degrees.</td>
790</tr>
791<tr class="row-odd"><td></td>
792<td>Gonio. radius</td>
793<td>Radius of the diffractometer in mm</td>
794</tr>
795<tr class="row-even"><td></td>
796<td>InstrName</td>
797<td>A name for the instrument, used in preparing
798a CIF (str).</td>
799</tr>
800<tr class="row-odd"><td></td>
801<td>Force,
802Temperature,
803Humidity,
804Pressure,
805Voltage</td>
806<td>Variables that describe how the measurement
807was performed. Not used directly in
808any computations.</td>
809</tr>
810<tr class="row-even"><td></td>
811<td>ranId</td>
812<td>The random-number Id for the histogram
813(same value as where top-level key is ranId)</td>
814</tr>
815<tr class="row-odd"><td></td>
816<td>Type</td>
817<td>Type of diffraction data, may be &#8216;Debye-Scherrer&#8217;
818or &#8216;Bragg-Brentano&#8217; (str).</td>
819</tr>
820<tr class="row-even"><td></td>
821<td>Diffuse</td>
822<td>not in use?</td>
823</tr>
824<tr class="row-odd"><td>hId</td>
825<td></td>
826<td>The number assigned to the histogram when
827the project is loaded or edited (can change)</td>
828</tr>
829<tr class="row-even"><td>ranId</td>
830<td></td>
831<td>A random number id for the histogram
832that does not change</td>
833</tr>
834<tr class="row-odd"><td>Background</td>
835<td></td>
836<td>The background is stored as a list with where
837the first item in the list is list and the second
838item is a dict. The list contains the background
839function and its coefficients; the dict contains
840Debye diffuse terms and background peaks.
841(TODO: this needs to be expanded.)</td>
842</tr>
843<tr class="row-even"><td>Data</td>
844<td></td>
845<td><p class="first">The data consist of a list of 6 np.arrays
846containing in order:</p>
847<blockquote class="last">
848<div><ol class="arabic simple">
849<li>the x-postions (two-theta in degrees),</li>
850<li>the intensity values (Yobs),</li>
851<li>the weights for each Yobs value</li>
852<li>the computed intensity values (Ycalc)</li>
853<li>the background values</li>
854<li>Yobs-Ycalc</li>
855</ol>
856</div></blockquote>
857</td>
858</tr>
859</tbody>
860</table>
861</div>
862<div class="section" id="powder-reflection-data-structure">
863<h2>Powder Reflection Data Structure<a class="headerlink" href="#powder-reflection-data-structure" title="Permalink to this headline">¶</a></h2>
864<span class="target" id="powderrefl-table"></span><p id="index-7">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 list of
865reflections. The items in that list are documented below.</p>
866<table border="1" class="docutils">
867<colgroup>
868<col width="16%" />
869<col width="84%" />
870</colgroup>
871<thead valign="bottom">
872<tr class="row-odd"><th class="head">index</th>
873<th class="head">explanation</th>
874</tr>
875</thead>
876<tbody valign="top">
877<tr class="row-even"><td>0,1,2</td>
878<td>h,k,l (float)</td>
879</tr>
880<tr class="row-odd"><td>3</td>
881<td>multiplicity</td>
882</tr>
883<tr class="row-even"><td>4</td>
884<td>d-space, Angstrom</td>
885</tr>
886<tr class="row-odd"><td>5</td>
887<td>pos, two-theta</td>
888</tr>
889<tr class="row-even"><td>6</td>
890<td>sig, Gaussian width</td>
891</tr>
892<tr class="row-odd"><td>7</td>
893<td>gam, Lorenzian width</td>
894</tr>
895<tr class="row-even"><td>8</td>
896<td>Fobs**2</td>
897</tr>
898<tr class="row-odd"><td>9</td>
899<td>Fcalc**2</td>
900</tr>
901<tr class="row-even"><td>10</td>
902<td>reflection phase, in degrees</td>
903</tr>
904<tr class="row-odd"><td>11</td>
905<td>the equivalent reflections as a (m x 3)
906np.array, where m is 0.5 * multiplicity. Note
907that Freidel pairs, (-h,-k-,l), are not
908included.</td>
909</tr>
910<tr class="row-even"><td>12</td>
911<td>phase shift for each of the equivalent
912reflections as a length (m) array</td>
913</tr>
914<tr class="row-odd"><td>13</td>
915<td>intensity correction for reflection, this times
916Fobs**2 or Fcalc**2 gives Iobs or Icalc</td>
917</tr>
918<tr class="row-even"><td>14</td>
919<td>dict with the form factor (f or b) by atom type
920symbol at the reflection position.</td>
921</tr>
922</tbody>
923</table>
924</div>
925<div class="section" id="classes-and-routines">
926<h2><em>Classes and routines</em><a class="headerlink" href="#classes-and-routines" title="Permalink to this headline">¶</a></h2>
927<dl class="function">
928<dt id="GSASIIobj.LoadHistogramIDs">
929<tt class="descclassname">GSASIIobj.</tt><tt class="descname">LoadHistogramIDs</tt><big>(</big><em>histList</em>, <em>idList</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#LoadHistogramIDs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.LoadHistogramIDs" title="Permalink to this definition">¶</a></dt>
930<dd><p>Save the Id values for a series of histograms</p>
931</dd></dl>
932
933<dl class="class">
934<dt id="GSASIIobj.VarName">
935<em class="property">class </em><tt class="descclassname">GSASIIobj.</tt><tt class="descname">VarName</tt><big>(</big><em>*args</em><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#VarName"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.VarName" title="Permalink to this definition">¶</a></dt>
936<dd><p>Defines a GSAS-II variable either using the phase/atom/histogram
937unique Id numbers or using a character string that specifies
938variables by phase/atom/histogram number (which can change).
939Note that <tt class="xref py py-func docutils literal"><span class="pre">LoadID()</span></tt> should be used to (re)load the current Ids
940before creating or later using the VarName object.</p>
941<p>A <a class="reference internal" href="#GSASIIobj.VarName" title="GSASIIobj.VarName"><tt class="xref py py-class docutils literal"><span class="pre">VarName</span></tt></a> object can be created with a single parameter:</p>
942<table class="docutils field-list" frame="void" rules="none">
943<col class="field-name" />
944<col class="field-body" />
945<tbody valign="top">
946<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>varname</strong> (<em>str</em>) &#8211; <dl class="docutils">
947<dt>a single value can be used to create a <a class="reference internal" href="#GSASIIobj.VarName" title="GSASIIobj.VarName"><tt class="xref py py-class docutils literal"><span class="pre">VarName</span></tt></a></dt>
948<dd>object. The string must be of form &#8220;p:h:var&#8221; or &#8220;p:h:var:a&#8221;, where</dd>
949</dl>
950<ul class="simple">
951<li>p is the phase number (which may be left blank);</li>
952<li>h is the histogram number (which may be left blank);</li>
953<li>a is the atom number (which may be left blank in which case the third colon is omitted).</li>
954</ul>
955</td>
956</tr>
957</tbody>
958</table>
959<p>Alternately, a <a class="reference internal" href="#GSASIIobj.VarName" title="GSASIIobj.VarName"><tt class="xref py py-class docutils literal"><span class="pre">VarName</span></tt></a> object can be created with exactly four positional parameters:</p>
960<table class="docutils field-list" frame="void" rules="none">
961<col class="field-name" />
962<col class="field-body" />
963<tbody valign="top">
964<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
965<li><strong>phasenum</strong> (<em>int</em>) &#8211; The number for the phase</li>
966<li><strong>histnum</strong> (<em>int</em>) &#8211; The number for the histogram</li>
967<li><strong>varname</strong> (<em>str</em>) &#8211; a single value can be used to create a <a class="reference internal" href="#GSASIIobj.VarName" title="GSASIIobj.VarName"><tt class="xref py py-class docutils literal"><span class="pre">VarName</span></tt></a></li>
968<li><strong>atomnum</strong> (<em>int</em>) &#8211; The number for the atom</li>
969</ul>
970</td>
971</tr>
972</tbody>
973</table>
974<dl class="method">
975<dt id="GSASIIobj.VarName.fullDescr">
976<tt class="descname">fullDescr</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#VarName.fullDescr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.VarName.fullDescr" title="Permalink to this definition">¶</a></dt>
977<dd><p>Return a longer description for a GSAS-II variable</p>
978<table class="docutils field-list" frame="void" rules="none">
979<col class="field-name" />
980<col class="field-body" />
981<tbody valign="top">
982<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a short description or &#8216;no definition&#8217; if not found</td>
983</tr>
984</tbody>
985</table>
986</dd></dl>
987
988<dl class="method">
989<dt id="GSASIIobj.VarName.getDescr">
990<tt class="descname">getDescr</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#VarName.getDescr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.VarName.getDescr" title="Permalink to this definition">¶</a></dt>
991<dd><p>Return a short description for a GSAS-II variable</p>
992<table class="docutils field-list" frame="void" rules="none">
993<col class="field-name" />
994<col class="field-body" />
995<tbody valign="top">
996<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">a short description or &#8216;no definition&#8217; if not found</td>
997</tr>
998</tbody>
999</table>
1000</dd></dl>
1001
1002<dl class="method">
1003<dt id="GSASIIobj.VarName.name">
1004<tt class="descname">name</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIobj.html#VarName.name"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIobj.VarName.name" title="Permalink to this definition">¶</a></dt>
1005<dd><p>Formats the GSAS-II variable name as a &#8220;traditional&#8221; string (p:h:&lt;var&gt;:a)</p>
1006<table class="docutils field-list" frame="void" rules="none">
1007<col class="field-name" />
1008<col class="field-body" />
1009<tbody valign="top">
1010<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">the variable name as a str</td>
1011</tr>
1012</tbody>
1013</table>
1014</dd></dl>
1015
1016</dd></dl>
1017
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1020
1021
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1030  <h3><a href="index.html">Table Of Contents</a></h3>
1031  <ul>
1032<li><a class="reference internal" href="#"><em>GSASIIobj: Data objects</em></a><ul>
1033<li><a class="reference internal" href="#constraints-tree-item">Constraints Tree Item</a></li>
1034<li><a class="reference internal" href="#covariance-tree-item">Covariance Tree Item</a></li>
1035<li><a class="reference internal" href="#phase-tree-items">Phase Tree Items</a></li>
1036<li><a class="reference internal" href="#space-group-objects">Space Group Objects</a></li>
1037<li><a class="reference internal" href="#atom-records">Atom Records</a></li>
1038<li><a class="reference internal" href="#powder-diffraction-tree-items">Powder Diffraction Tree Items</a></li>
1039<li><a class="reference internal" href="#powder-reflection-data-structure">Powder Reflection Data Structure</a></li>
1040<li><a class="reference internal" href="#classes-and-routines"><em>Classes and routines</em></a></li>
1041</ul>
1042</li>
1043</ul>
1044
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