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update self-docs, start work on constraints object

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57  <div class="section" id="module-GSASIIstrMain">
58<span id="gsas-ii-structure-submodules"></span><h1><em>GSAS-II Structure  Submodules</em><a class="headerlink" href="#module-GSASIIstrMain" title="Permalink to this headline">¶</a></h1>
59<div class="section" id="gsasiistrmain-main-structure-routine">
60<h2><em>GSASIIstrMain: main structure routine</em><a class="headerlink" href="#gsasiistrmain-main-structure-routine" title="Permalink to this headline">¶</a></h2>
61<dl class="function">
62<dt id="GSASIIstrMain.BestPlane">
63<tt class="descclassname">GSASIIstrMain.</tt><tt class="descname">BestPlane</tt><big>(</big><em>PlaneData</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMain.html#BestPlane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMain.BestPlane" title="Permalink to this definition">¶</a></dt>
64<dd><p>Needs a doc string</p>
65</dd></dl>
66
67<dl class="function">
68<dt id="GSASIIstrMain.DisAglTor">
69<tt class="descclassname">GSASIIstrMain.</tt><tt class="descname">DisAglTor</tt><big>(</big><em>DATData</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMain.html#DisAglTor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMain.DisAglTor" title="Permalink to this definition">¶</a></dt>
70<dd><p>Needs a doc string</p>
71</dd></dl>
72
73<dl class="function">
74<dt id="GSASIIstrMain.DistAngle">
75<tt class="descclassname">GSASIIstrMain.</tt><tt class="descname">DistAngle</tt><big>(</big><em>DisAglCtls</em>, <em>DisAglData</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMain.html#DistAngle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMain.DistAngle" title="Permalink to this definition">¶</a></dt>
76<dd><p>Needs a doc string</p>
77</dd></dl>
78
79<dl class="function">
80<dt id="GSASIIstrMain.Refine">
81<tt class="descclassname">GSASIIstrMain.</tt><tt class="descname">Refine</tt><big>(</big><em>GPXfile</em>, <em>dlg</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMain.html#Refine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMain.Refine" title="Permalink to this definition">¶</a></dt>
82<dd><p>Needs a doc string</p>
83</dd></dl>
84
85<dl class="function">
86<dt id="GSASIIstrMain.SeqRefine">
87<tt class="descclassname">GSASIIstrMain.</tt><tt class="descname">SeqRefine</tt><big>(</big><em>GPXfile</em>, <em>dlg</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMain.html#SeqRefine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMain.SeqRefine" title="Permalink to this definition">¶</a></dt>
88<dd><p>Needs a doc string</p>
89</dd></dl>
90
91<dl class="function">
92<dt id="GSASIIstrMain.main">
93<tt class="descclassname">GSASIIstrMain.</tt><tt class="descname">main</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/GSASIIstrMain.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMain.main" title="Permalink to this definition">¶</a></dt>
94<dd><p>Needs a doc string</p>
95</dd></dl>
96
97</div>
98<span class="target" id="module-GSASIIstrMath"></span><div class="section" id="gsasiistrmath-structure-math-routines">
99<h2><em>GSASIIstrMath - structure math routines</em><a class="headerlink" href="#gsasiistrmath-structure-math-routines" title="Permalink to this headline">¶</a></h2>
100<dl class="function">
101<dt id="GSASIIstrMath.ApplyRBModelDervs">
102<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">ApplyRBModelDervs</tt><big>(</big><em>dFdvDict</em>, <em>parmDict</em>, <em>rigidbodyDict</em>, <em>Phase</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#ApplyRBModelDervs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.ApplyRBModelDervs" title="Permalink to this definition">¶</a></dt>
103<dd><p>Needs a doc string</p>
104</dd></dl>
105
106<dl class="function">
107<dt id="GSASIIstrMath.ApplyRBModels">
108<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">ApplyRBModels</tt><big>(</big><em>parmDict</em>, <em>Phases</em>, <em>rigidbodyDict</em>, <em>Update=False</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#ApplyRBModels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.ApplyRBModels" title="Permalink to this definition">¶</a></dt>
109<dd><p>Takes RB info from RBModels in Phase and RB data in rigidbodyDict along with
110current RB values in parmDict &amp; modifies atom contents (xyz &amp; Uij) of parmDict</p>
111</dd></dl>
112
113<dl class="function">
114<dt id="GSASIIstrMath.ApplyXYZshifts">
115<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">ApplyXYZshifts</tt><big>(</big><em>parmDict</em>, <em>varyList</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#ApplyXYZshifts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.ApplyXYZshifts" title="Permalink to this definition">¶</a></dt>
116<dd><p>takes atom x,y,z shift and applies it to corresponding atom x,y,z value</p>
117<table class="docutils field-list" frame="void" rules="none">
118<col class="field-name" />
119<col class="field-body" />
120<tbody valign="top">
121<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
122<li><strong>parmDict</strong> (<em>dict</em>) &#8211; parameter dictionary</li>
123<li><strong>varyList</strong> (<em>list</em>) &#8211; list of variables</li>
124</ul>
125</td>
126</tr>
127<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">newAtomDict - dictionary of new atomic coordinate names &amp; values; key is parameter shift name</p>
128</td>
129</tr>
130</tbody>
131</table>
132</dd></dl>
133
134<dl class="function">
135<dt id="GSASIIstrMath.Dict2Values">
136<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">Dict2Values</tt><big>(</big><em>parmdict</em>, <em>varylist</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#Dict2Values"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.Dict2Values" title="Permalink to this definition">¶</a></dt>
137<dd><p>Use before call to leastsq to setup list of values for the parameters
138in parmdict, as selected by key in varylist</p>
139</dd></dl>
140
141<dl class="function">
142<dt id="GSASIIstrMath.GetAbsorb">
143<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetAbsorb</tt><big>(</big><em>refl</em>, <em>hfx</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetAbsorb"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetAbsorb" title="Permalink to this definition">¶</a></dt>
144<dd><p>Needs a doc string</p>
145</dd></dl>
146
147<dl class="function">
148<dt id="GSASIIstrMath.GetAbsorbDerv">
149<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetAbsorbDerv</tt><big>(</big><em>refl</em>, <em>hfx</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetAbsorbDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetAbsorbDerv" title="Permalink to this definition">¶</a></dt>
150<dd><p>Needs a doc string</p>
151</dd></dl>
152
153<dl class="function">
154<dt id="GSASIIstrMath.GetAtomFXU">
155<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetAtomFXU</tt><big>(</big><em>pfx</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetAtomFXU"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetAtomFXU" title="Permalink to this definition">¶</a></dt>
156<dd><p>Needs a doc string</p>
157</dd></dl>
158
159<dl class="function">
160<dt id="GSASIIstrMath.GetFobsSq">
161<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetFobsSq</tt><big>(</big><em>Histograms</em>, <em>Phases</em>, <em>parmDict</em>, <em>calcControls</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetFobsSq"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetFobsSq" title="Permalink to this definition">¶</a></dt>
162<dd><p>Needs a doc string</p>
163</dd></dl>
164
165<dl class="function">
166<dt id="GSASIIstrMath.GetHStrainShift">
167<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetHStrainShift</tt><big>(</big><em>refl</em>, <em>SGData</em>, <em>phfx</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetHStrainShift"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetHStrainShift" title="Permalink to this definition">¶</a></dt>
168<dd><p>Needs a doc string</p>
169</dd></dl>
170
171<dl class="function">
172<dt id="GSASIIstrMath.GetHStrainShiftDerv">
173<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetHStrainShiftDerv</tt><big>(</big><em>refl</em>, <em>SGData</em>, <em>phfx</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetHStrainShiftDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetHStrainShiftDerv" title="Permalink to this definition">¶</a></dt>
174<dd><p>Needs a doc string</p>
175</dd></dl>
176
177<dl class="function">
178<dt id="GSASIIstrMath.GetIntensityCorr">
179<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetIntensityCorr</tt><big>(</big><em>refl</em>, <em>G</em>, <em>g</em>, <em>pfx</em>, <em>phfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetIntensityCorr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetIntensityCorr" title="Permalink to this definition">¶</a></dt>
180<dd><p>Needs a doc string</p>
181</dd></dl>
182
183<dl class="function">
184<dt id="GSASIIstrMath.GetIntensityDerv">
185<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetIntensityDerv</tt><big>(</big><em>refl</em>, <em>G</em>, <em>g</em>, <em>pfx</em>, <em>phfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetIntensityDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetIntensityDerv" title="Permalink to this definition">¶</a></dt>
186<dd><p>Needs a doc string</p>
187</dd></dl>
188
189<dl class="function">
190<dt id="GSASIIstrMath.GetNewCellParms">
191<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetNewCellParms</tt><big>(</big><em>parmDict</em>, <em>varyList</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetNewCellParms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetNewCellParms" title="Permalink to this definition">¶</a></dt>
192<dd><p>Needs a doc string</p>
193</dd></dl>
194
195<dl class="function">
196<dt id="GSASIIstrMath.GetPrefOri">
197<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetPrefOri</tt><big>(</big><em>refl</em>, <em>G</em>, <em>g</em>, <em>phfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetPrefOri"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetPrefOri" title="Permalink to this definition">¶</a></dt>
198<dd><p>Needs a doc string</p>
199</dd></dl>
200
201<dl class="function">
202<dt id="GSASIIstrMath.GetPrefOriDerv">
203<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetPrefOriDerv</tt><big>(</big><em>refl</em>, <em>G</em>, <em>g</em>, <em>phfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetPrefOriDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetPrefOriDerv" title="Permalink to this definition">¶</a></dt>
204<dd><p>Needs a doc string</p>
205</dd></dl>
206
207<dl class="function">
208<dt id="GSASIIstrMath.GetReflPos">
209<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetReflPos</tt><big>(</big><em>refl</em>, <em>wave</em>, <em>G</em>, <em>hfx</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetReflPos"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetReflPos" title="Permalink to this definition">¶</a></dt>
210<dd><p>Needs a doc string</p>
211</dd></dl>
212
213<dl class="function">
214<dt id="GSASIIstrMath.GetReflPosDerv">
215<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetReflPosDerv</tt><big>(</big><em>refl</em>, <em>wave</em>, <em>A</em>, <em>hfx</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetReflPosDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetReflPosDerv" title="Permalink to this definition">¶</a></dt>
216<dd><p>Needs a doc string</p>
217</dd></dl>
218
219<dl class="function">
220<dt id="GSASIIstrMath.GetSampleSigGam">
221<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetSampleSigGam</tt><big>(</big><em>refl</em>, <em>wave</em>, <em>G</em>, <em>GB</em>, <em>phfx</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetSampleSigGam"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetSampleSigGam" title="Permalink to this definition">¶</a></dt>
222<dd><p>Needs a doc string</p>
223</dd></dl>
224
225<dl class="function">
226<dt id="GSASIIstrMath.GetSampleSigGamDerv">
227<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">GetSampleSigGamDerv</tt><big>(</big><em>refl</em>, <em>wave</em>, <em>G</em>, <em>GB</em>, <em>phfx</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#GetSampleSigGamDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.GetSampleSigGamDerv" title="Permalink to this definition">¶</a></dt>
228<dd><p>Needs a doc string</p>
229</dd></dl>
230
231<dl class="function">
232<dt id="GSASIIstrMath.HessRefine">
233<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">HessRefine</tt><big>(</big><em>values</em>, <em>HistoPhases</em>, <em>parmDict</em>, <em>varylist</em>, <em>calcControls</em>, <em>pawleyLookup</em>, <em>dlg</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#HessRefine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.HessRefine" title="Permalink to this definition">¶</a></dt>
234<dd><p>Needs a doc string</p>
235</dd></dl>
236
237<dl class="function">
238<dt id="GSASIIstrMath.SCExtinction">
239<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">SCExtinction</tt><big>(</big><em>ref</em>, <em>phfx</em>, <em>hfx</em>, <em>pfx</em>, <em>calcControls</em>, <em>parmDict</em>, <em>varyList</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#SCExtinction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.SCExtinction" title="Permalink to this definition">¶</a></dt>
240<dd><p>Single crystal extinction function; puts correction in ref[13] and returns
241corrections needed for derivatives</p>
242</dd></dl>
243
244<dl class="function">
245<dt id="GSASIIstrMath.SHPOcal">
246<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">SHPOcal</tt><big>(</big><em>refl</em>, <em>g</em>, <em>phfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#SHPOcal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.SHPOcal" title="Permalink to this definition">¶</a></dt>
247<dd><p>spherical harmonics preferred orientation (cylindrical symmetry only)</p>
248</dd></dl>
249
250<dl class="function">
251<dt id="GSASIIstrMath.SHPOcalDerv">
252<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">SHPOcalDerv</tt><big>(</big><em>refl</em>, <em>g</em>, <em>phfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#SHPOcalDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.SHPOcalDerv" title="Permalink to this definition">¶</a></dt>
253<dd><p>spherical harmonics preferred orientation derivatives (cylindrical symmetry only)</p>
254</dd></dl>
255
256<dl class="function">
257<dt id="GSASIIstrMath.SHTXcal">
258<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">SHTXcal</tt><big>(</big><em>refl</em>, <em>g</em>, <em>pfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#SHTXcal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.SHTXcal" title="Permalink to this definition">¶</a></dt>
259<dd><p>Spherical harmonics texture</p>
260</dd></dl>
261
262<dl class="function">
263<dt id="GSASIIstrMath.SHTXcalDerv">
264<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">SHTXcalDerv</tt><big>(</big><em>refl</em>, <em>g</em>, <em>pfx</em>, <em>hfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#SHTXcalDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.SHTXcalDerv" title="Permalink to this definition">¶</a></dt>
265<dd><p>Spherical harmonics texture derivatives</p>
266</dd></dl>
267
268<dl class="function">
269<dt id="GSASIIstrMath.StructureFactor">
270<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">StructureFactor</tt><big>(</big><em>refList</em>, <em>G</em>, <em>hfx</em>, <em>pfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#StructureFactor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.StructureFactor" title="Permalink to this definition">¶</a></dt>
271<dd><p>Compute structure factors for all h,k,l for phase
272puts the result, F^2, in each ref[8] in refList
273input:</p>
274<table class="docutils field-list" frame="void" rules="none">
275<col class="field-name" />
276<col class="field-body" />
277<tbody valign="top">
278<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
279<li><strong>refList</strong> (<em>list</em>) &#8211; [ref] where each ref = h,k,l,m,d,...,[equiv h,k,l],phase[equiv]</li>
280<li><strong>G</strong> (<em>np.array</em>) &#8211; reciprocal metric tensor</li>
281<li><strong>pfx</strong> (<em>str</em>) &#8211; phase id string</li>
282<li><strong>SGData</strong> (<em>dict</em>) &#8211; space group info. dictionary output from SpcGroup</li>
283<li><strong>calcControls</strong> (<em>dict</em>) &#8211; </li>
284<li><strong>ParmDict</strong> (<em>dict</em>) &#8211; </li>
285</ul>
286</td>
287</tr>
288</tbody>
289</table>
290</dd></dl>
291
292<dl class="function">
293<dt id="GSASIIstrMath.StructureFactorDerv">
294<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">StructureFactorDerv</tt><big>(</big><em>refList</em>, <em>G</em>, <em>hfx</em>, <em>pfx</em>, <em>SGData</em>, <em>calcControls</em>, <em>parmDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#StructureFactorDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.StructureFactorDerv" title="Permalink to this definition">¶</a></dt>
295<dd><p>Needs a doc string</p>
296</dd></dl>
297
298<dl class="function">
299<dt id="GSASIIstrMath.Values2Dict">
300<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">Values2Dict</tt><big>(</big><em>parmdict</em>, <em>varylist</em>, <em>values</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#Values2Dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.Values2Dict" title="Permalink to this definition">¶</a></dt>
301<dd><p>Use after call to leastsq to update the parameter dictionary with
302values corresponding to keys in varylist</p>
303</dd></dl>
304
305<dl class="function">
306<dt id="GSASIIstrMath.dervRefine">
307<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">dervRefine</tt><big>(</big><em>values</em>, <em>HistoPhases</em>, <em>parmDict</em>, <em>varylist</em>, <em>calcControls</em>, <em>pawleyLookup</em>, <em>dlg</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#dervRefine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.dervRefine" title="Permalink to this definition">¶</a></dt>
308<dd><p>Needs a doc string</p>
309</dd></dl>
310
311<dl class="function">
312<dt id="GSASIIstrMath.errRefine">
313<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">errRefine</tt><big>(</big><em>values</em>, <em>HistoPhases</em>, <em>parmDict</em>, <em>varylist</em>, <em>calcControls</em>, <em>pawleyLookup</em>, <em>dlg</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#errRefine"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.errRefine" title="Permalink to this definition">¶</a></dt>
314<dd><p>Needs a doc string</p>
315</dd></dl>
316
317<dl class="function">
318<dt id="GSASIIstrMath.getPowderProfile">
319<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">getPowderProfile</tt><big>(</big><em>parmDict</em>, <em>x</em>, <em>varylist</em>, <em>Histogram</em>, <em>Phases</em>, <em>calcControls</em>, <em>pawleyLookup</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#getPowderProfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.getPowderProfile" title="Permalink to this definition">¶</a></dt>
320<dd><p>Needs a doc string</p>
321</dd></dl>
322
323<dl class="function">
324<dt id="GSASIIstrMath.getPowderProfileDerv">
325<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">getPowderProfileDerv</tt><big>(</big><em>parmDict</em>, <em>x</em>, <em>varylist</em>, <em>Histogram</em>, <em>Phases</em>, <em>rigidbodyDict</em>, <em>calcControls</em>, <em>pawleyLookup</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#getPowderProfileDerv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.getPowderProfileDerv" title="Permalink to this definition">¶</a></dt>
326<dd><p>Needs a doc string</p>
327</dd></dl>
328
329<dl class="function">
330<dt id="GSASIIstrMath.penaltyDeriv">
331<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">penaltyDeriv</tt><big>(</big><em>pNames</em>, <em>pVal</em>, <em>HistoPhases</em>, <em>parmDict</em>, <em>varyList</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#penaltyDeriv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.penaltyDeriv" title="Permalink to this definition">¶</a></dt>
332<dd><p>Needs a doc string</p>
333</dd></dl>
334
335<dl class="function">
336<dt id="GSASIIstrMath.penaltyFxn">
337<tt class="descclassname">GSASIIstrMath.</tt><tt class="descname">penaltyFxn</tt><big>(</big><em>HistoPhases</em>, <em>parmDict</em>, <em>varyList</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrMath.html#penaltyFxn"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrMath.penaltyFxn" title="Permalink to this definition">¶</a></dt>
338<dd><p>Needs a doc string</p>
339</dd></dl>
340
341</div>
342<span class="target" id="module-GSASIIstrIO"></span><div class="section" id="gsasiistrio-structure-i-o-routines">
343<h2><em>GSASIIstrIO: structure I/O routines</em><a class="headerlink" href="#gsasiistrio-structure-i-o-routines" title="Permalink to this headline">¶</a></h2>
344<dl class="function">
345<dt id="GSASIIstrIO.CheckConstraints">
346<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">CheckConstraints</tt><big>(</big><em>GPXfile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#CheckConstraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.CheckConstraints" title="Permalink to this definition">¶</a></dt>
347<dd><p>Load constraints and related info and return any error or warning messages</p>
348</dd></dl>
349
350<dl class="function">
351<dt id="GSASIIstrIO.GPXBackup">
352<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GPXBackup</tt><big>(</big><em>GPXfile</em>, <em>makeBack=True</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GPXBackup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GPXBackup" title="Permalink to this definition">¶</a></dt>
353<dd><p>makes a backup of the current .gpx file (?)</p>
354<table class="docutils field-list" frame="void" rules="none">
355<col class="field-name" />
356<col class="field-body" />
357<tbody valign="top">
358<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
359<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
360<li><strong>makeBack</strong> (<em>bool</em>) &#8211; if True (default), the backup is written to
361a new file; if False, the last backup is overwritten</li>
362</ul>
363</td>
364</tr>
365<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">the name of the backup file that was written</p>
366</td>
367</tr>
368</tbody>
369</table>
370</dd></dl>
371
372<dl class="function">
373<dt id="GSASIIstrIO.GetAllPhaseData">
374<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetAllPhaseData</tt><big>(</big><em>GPXfile</em>, <em>PhaseName</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetAllPhaseData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetAllPhaseData" title="Permalink to this definition">¶</a></dt>
375<dd><p>Returns the entire dictionary for PhaseName from GSASII gpx file</p>
376<table class="docutils field-list" frame="void" rules="none">
377<col class="field-name" />
378<col class="field-body" />
379<tbody valign="top">
380<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
381<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
382<li><strong>PhaseName</strong> (<em>str</em>) &#8211; phase name</li>
383</ul>
384</td>
385</tr>
386<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">phase dictionary</p>
387</td>
388</tr>
389</tbody>
390</table>
391</dd></dl>
392
393<dl class="function">
394<dt id="GSASIIstrIO.GetConstraints">
395<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetConstraints</tt><big>(</big><em>GPXfile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetConstraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetConstraints" title="Permalink to this definition">¶</a></dt>
396<dd><p>Read the constraints from the GPX file and interpret them</p>
397</dd></dl>
398
399<dl class="function">
400<dt id="GSASIIstrIO.GetControls">
401<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetControls</tt><big>(</big><em>GPXfile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetControls"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetControls" title="Permalink to this definition">¶</a></dt>
402<dd><p>Returns dictionary of control items found in GSASII gpx file</p>
403<table class="docutils field-list" frame="void" rules="none">
404<col class="field-name" />
405<col class="field-body" />
406<tbody valign="top">
407<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</td>
408</tr>
409<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">dictionary of control items</td>
410</tr>
411</tbody>
412</table>
413</dd></dl>
414
415<dl class="function">
416<dt id="GSASIIstrIO.GetFprime">
417<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetFprime</tt><big>(</big><em>controlDict</em>, <em>Histograms</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetFprime"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetFprime" title="Permalink to this definition">¶</a></dt>
418<dd><p>Needs a doc string</p>
419</dd></dl>
420
421<dl class="function">
422<dt id="GSASIIstrIO.GetHistogramData">
423<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetHistogramData</tt><big>(</big><em>Histograms</em>, <em>Print=True</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetHistogramData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetHistogramData" title="Permalink to this definition">¶</a></dt>
424<dd><p>needs a doc string</p>
425</dd></dl>
426
427<dl class="function">
428<dt id="GSASIIstrIO.GetHistogramNames">
429<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetHistogramNames</tt><big>(</big><em>GPXfile</em>, <em>hType</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetHistogramNames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetHistogramNames" title="Permalink to this definition">¶</a></dt>
430<dd><p>Returns a list of histogram names found in GSASII gpx file</p>
431<table class="docutils field-list" frame="void" rules="none">
432<col class="field-name" />
433<col class="field-body" />
434<tbody valign="top">
435<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
436<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
437<li><strong>hNames</strong> (<em>str</em>) &#8211; list of histogram names</li>
438</ul>
439</td>
440</tr>
441<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">list of histogram names (types = PWDR &amp; HKLF)</p>
442</td>
443</tr>
444</tbody>
445</table>
446</dd></dl>
447
448<dl class="function">
449<dt id="GSASIIstrIO.GetHistogramPhaseData">
450<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetHistogramPhaseData</tt><big>(</big><em>Phases</em>, <em>Histograms</em>, <em>Print=True</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetHistogramPhaseData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetHistogramPhaseData" title="Permalink to this definition">¶</a></dt>
451<dd><p>needs a doc string</p>
452</dd></dl>
453
454<dl class="function">
455<dt id="GSASIIstrIO.GetHistograms">
456<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetHistograms</tt><big>(</big><em>GPXfile</em>, <em>hNames</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetHistograms"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetHistograms" title="Permalink to this definition">¶</a></dt>
457<dd><p>Returns a dictionary of histograms found in GSASII gpx file</p>
458<table class="docutils field-list" frame="void" rules="none">
459<col class="field-name" />
460<col class="field-body" />
461<tbody valign="top">
462<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
463<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
464<li><strong>hNames</strong> (<em>str</em>) &#8211; list of histogram names</li>
465</ul>
466</td>
467</tr>
468<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">dictionary of histograms (types = PWDR &amp; HKLF)</p>
469</td>
470</tr>
471</tbody>
472</table>
473</dd></dl>
474
475<dl class="function">
476<dt id="GSASIIstrIO.GetPawleyConstr">
477<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetPawleyConstr</tt><big>(</big><em>SGLaue</em>, <em>PawleyRef</em>, <em>pawleyVary</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetPawleyConstr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetPawleyConstr" title="Permalink to this definition">¶</a></dt>
478<dd><p>needs a doc string</p>
479</dd></dl>
480
481<dl class="function">
482<dt id="GSASIIstrIO.GetPhaseData">
483<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetPhaseData</tt><big>(</big><em>PhaseData</em>, <em>RestraintDict={}</em>, <em>rbIds={}</em>, <em>Print=True</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetPhaseData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetPhaseData" title="Permalink to this definition">¶</a></dt>
484<dd><p>needs a doc string</p>
485</dd></dl>
486
487<dl class="function">
488<dt id="GSASIIstrIO.GetPhaseNames">
489<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetPhaseNames</tt><big>(</big><em>GPXfile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetPhaseNames"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetPhaseNames" title="Permalink to this definition">¶</a></dt>
490<dd><p>Returns a list of phase names found under &#8216;Phases&#8217; in GSASII gpx file</p>
491<table class="docutils field-list" frame="void" rules="none">
492<col class="field-name" />
493<col class="field-body" />
494<tbody valign="top">
495<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</td>
496</tr>
497<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">list of phase names</td>
498</tr>
499</tbody>
500</table>
501</dd></dl>
502
503<dl class="function">
504<dt id="GSASIIstrIO.GetRestraints">
505<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetRestraints</tt><big>(</big><em>GPXfile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetRestraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetRestraints" title="Permalink to this definition">¶</a></dt>
506<dd><p>Read the restraints from the GPX file.
507Throws an exception if not found in the .GPX file</p>
508</dd></dl>
509
510<dl class="function">
511<dt id="GSASIIstrIO.GetRigidBodies">
512<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetRigidBodies</tt><big>(</big><em>GPXfile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetRigidBodies"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetRigidBodies" title="Permalink to this definition">¶</a></dt>
513<dd><p>Read the rigid body models from the GPX file</p>
514</dd></dl>
515
516<dl class="function">
517<dt id="GSASIIstrIO.GetRigidBodyModels">
518<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetRigidBodyModels</tt><big>(</big><em>rigidbodyDict</em>, <em>Print=True</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetRigidBodyModels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetRigidBodyModels" title="Permalink to this definition">¶</a></dt>
519<dd><p>needs a doc string</p>
520</dd></dl>
521
522<dl class="function">
523<dt id="GSASIIstrIO.GetUsedHistogramsAndPhases">
524<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">GetUsedHistogramsAndPhases</tt><big>(</big><em>GPXfile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#GetUsedHistogramsAndPhases"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.GetUsedHistogramsAndPhases" title="Permalink to this definition">¶</a></dt>
525<dd><p>Returns all histograms that are found in any phase
526and any phase that uses a histogram</p>
527<table class="docutils field-list" frame="void" rules="none">
528<col class="field-name" />
529<col class="field-body" />
530<tbody valign="top">
531<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</td>
532</tr>
533<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">(Histograms,Phases)<ul class="simple">
534<li>Histograms = dictionary of histograms as {name:data,...}</li>
535<li>Phases = dictionary of phases that use histograms</li>
536</ul>
537</td>
538</tr>
539</tbody>
540</table>
541</dd></dl>
542
543<dl class="function">
544<dt id="GSASIIstrIO.PrintRestraints">
545<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">PrintRestraints</tt><big>(</big><em>cell</em>, <em>SGData</em>, <em>AtPtrs</em>, <em>Atoms</em>, <em>AtLookup</em>, <em>textureData</em>, <em>phaseRest</em>, <em>pFile</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#PrintRestraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.PrintRestraints" title="Permalink to this definition">¶</a></dt>
546<dd><p>needs a doc string</p>
547</dd></dl>
548
549<dl class="function">
550<dt id="GSASIIstrIO.ProcessConstraints">
551<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">ProcessConstraints</tt><big>(</big><em>constList</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#ProcessConstraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.ProcessConstraints" title="Permalink to this definition">¶</a></dt>
552<dd><p>interpret constraints</p>
553</dd></dl>
554
555<dl class="function">
556<dt id="GSASIIstrIO.SetHistogramData">
557<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">SetHistogramData</tt><big>(</big><em>parmDict</em>, <em>sigDict</em>, <em>Histograms</em>, <em>Print=True</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#SetHistogramData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.SetHistogramData" title="Permalink to this definition">¶</a></dt>
558<dd><p>needs a doc string</p>
559</dd></dl>
560
561<dl class="function">
562<dt id="GSASIIstrIO.SetHistogramPhaseData">
563<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">SetHistogramPhaseData</tt><big>(</big><em>parmDict</em>, <em>sigDict</em>, <em>Phases</em>, <em>Histograms</em>, <em>Print=True</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#SetHistogramPhaseData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.SetHistogramPhaseData" title="Permalink to this definition">¶</a></dt>
564<dd><p>needs a doc string</p>
565</dd></dl>
566
567<dl class="function">
568<dt id="GSASIIstrIO.SetPhaseData">
569<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">SetPhaseData</tt><big>(</big><em>parmDict</em>, <em>sigDict</em>, <em>Phases</em>, <em>RBIds</em>, <em>covData</em>, <em>RestraintDict=None</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#SetPhaseData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.SetPhaseData" title="Permalink to this definition">¶</a></dt>
570<dd><p>needs a doc string</p>
571</dd></dl>
572
573<dl class="function">
574<dt id="GSASIIstrIO.SetRigidBodyModels">
575<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">SetRigidBodyModels</tt><big>(</big><em>parmDict</em>, <em>sigDict</em>, <em>rigidbodyDict</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#SetRigidBodyModels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.SetRigidBodyModels" title="Permalink to this definition">¶</a></dt>
576<dd><p>needs a doc string</p>
577</dd></dl>
578
579<dl class="function">
580<dt id="GSASIIstrIO.SetSeqResult">
581<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">SetSeqResult</tt><big>(</big><em>GPXfile</em>, <em>Histograms</em>, <em>SeqResult</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#SetSeqResult"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.SetSeqResult" title="Permalink to this definition">¶</a></dt>
582<dd><p>Needs doc string</p>
583<table class="docutils field-list" frame="void" rules="none">
584<col class="field-name" />
585<col class="field-body" />
586<tbody valign="top">
587<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</td>
588</tr>
589</tbody>
590</table>
591</dd></dl>
592
593<dl class="function">
594<dt id="GSASIIstrIO.SetUsedHistogramsAndPhases">
595<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">SetUsedHistogramsAndPhases</tt><big>(</big><em>GPXfile</em>, <em>Histograms</em>, <em>Phases</em>, <em>RigidBodies</em>, <em>CovData</em>, <em>makeBack=True</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#SetUsedHistogramsAndPhases"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.SetUsedHistogramsAndPhases" title="Permalink to this definition">¶</a></dt>
596<dd><p>Updates gpxfile from all histograms that are found in any phase
597and any phase that used a histogram. Also updates rigid body definitions.</p>
598<table class="docutils field-list" frame="void" rules="none">
599<col class="field-name" />
600<col class="field-body" />
601<tbody valign="top">
602<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
603<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
604<li><strong>Histograms</strong> (<em>dict</em>) &#8211; dictionary of histograms as {name:data,...}</li>
605<li><strong>Phases</strong> (<em>dict</em>) &#8211; dictionary of phases that use histograms</li>
606<li><strong>RigidBodies</strong> (<em>dict</em>) &#8211; dictionary of rigid bodies</li>
607<li><strong>CovData</strong> (<em>dict</em>) &#8211; dictionary of refined variables, varyList, &amp; covariance matrix</li>
608<li><strong>makeBack</strong> (<em>bool</em>) &#8211; True if new backup of .gpx file is to be made; else use the last one made</li>
609</ul>
610</td>
611</tr>
612</tbody>
613</table>
614</dd></dl>
615
616<dl class="function">
617<dt id="GSASIIstrIO.ShowBanner">
618<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">ShowBanner</tt><big>(</big><em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#ShowBanner"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.ShowBanner" title="Permalink to this definition">¶</a></dt>
619<dd><p>Print authorship, copyright and citation notice</p>
620</dd></dl>
621
622<dl class="function">
623<dt id="GSASIIstrIO.ShowControls">
624<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">ShowControls</tt><big>(</big><em>Controls</em>, <em>pFile=None</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#ShowControls"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.ShowControls" title="Permalink to this definition">¶</a></dt>
625<dd><p>Print controls information</p>
626</dd></dl>
627
628<dl class="function">
629<dt id="GSASIIstrIO.cellFill">
630<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">cellFill</tt><big>(</big><em>pfx</em>, <em>SGData</em>, <em>parmDict</em>, <em>sigDict</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#cellFill"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.cellFill" title="Permalink to this definition">¶</a></dt>
631<dd><p>needs a doc string</p>
632</dd></dl>
633
634<dl class="function">
635<dt id="GSASIIstrIO.cellVary">
636<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">cellVary</tt><big>(</big><em>pfx</em>, <em>SGData</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#cellVary"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.cellVary" title="Permalink to this definition">¶</a></dt>
637<dd><p>needs a doc string</p>
638</dd></dl>
639
640<dl class="function">
641<dt id="GSASIIstrIO.getBackupName">
642<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">getBackupName</tt><big>(</big><em>GPXfile</em>, <em>makeBack</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#getBackupName"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.getBackupName" title="Permalink to this definition">¶</a></dt>
643<dd><p>Get the name for the backup .gpx file name</p>
644<table class="docutils field-list" frame="void" rules="none">
645<col class="field-name" />
646<col class="field-body" />
647<tbody valign="top">
648<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
649<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
650<li><strong>makeBack</strong> (<em>bool</em>) &#8211; if True the name of a new file is returned, if
651False the name of the last file that exists is returned</li>
652</ul>
653</td>
654</tr>
655<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">the name of a backup file</p>
656</td>
657</tr>
658</tbody>
659</table>
660</dd></dl>
661
662<dl class="function">
663<dt id="GSASIIstrIO.getCellEsd">
664<tt class="descclassname">GSASIIstrIO.</tt><tt class="descname">getCellEsd</tt><big>(</big><em>pfx</em>, <em>SGData</em>, <em>A</em>, <em>covData</em><big>)</big><a class="reference internal" href="_modules/GSASIIstrIO.html#getCellEsd"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#GSASIIstrIO.getCellEsd" title="Permalink to this definition">¶</a></dt>
665<dd><p>needs a doc string</p>
666</dd></dl>
667
668</div>
669</div>
670
671
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674      </div>
675      <div class="sphinxsidebar">
676        <div class="sphinxsidebarwrapper">
677  <h3><a href="index.html">Table Of Contents</a></h3>
678  <ul>
679<li><a class="reference internal" href="#"><em>GSAS-II Structure  Submodules</em></a><ul>
680<li><a class="reference internal" href="#gsasiistrmain-main-structure-routine"><em>GSASIIstrMain: main structure routine</em></a></li>
681<li><a class="reference internal" href="#gsasiistrmath-structure-math-routines"><em>GSASIIstrMath - structure math routines</em></a></li>
682<li><a class="reference internal" href="#gsasiistrio-structure-i-o-routines"><em>GSASIIstrIO: structure I/O routines</em></a></li>
683</ul>
684</li>
685</ul>
686
687  <h4>Previous topic</h4>
688  <p class="topless"><a href="GSASIIGUI.html"
689                        title="previous chapter"><em>GSAS-II GUI Submodules</em></a></p>
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691  <p class="topless"><a href="GSASIImapvars.html"
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