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58  <div class="section" id="module-GSASIIstrMain">
59<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>
60<div class="section" id="gsasiistrmain-main-structure-routine">
61<h2><em>GSASIIstrMain: main structure routine</em><a class="headerlink" href="#gsasiistrmain-main-structure-routine" title="Permalink to this headline">¶</a></h2>
62<dl class="function">
63<dt id="GSASIIstrMain.BestPlane">
64<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>
65<dd><p>Needs a doc string</p>
66</dd></dl>
67
68<dl class="function">
69<dt id="GSASIIstrMain.DisAglTor">
70<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>
71<dd><p>Needs a doc string</p>
72</dd></dl>
73
74<dl class="function">
75<dt id="GSASIIstrMain.DistAngle">
76<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>
77<dd><p>Needs a doc string</p>
78</dd></dl>
79
80<dl class="function">
81<dt id="GSASIIstrMain.Refine">
82<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>
83<dd><p>Needs a doc string</p>
84</dd></dl>
85
86<dl class="function">
87<dt id="GSASIIstrMain.SeqRefine">
88<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>
89<dd><p>Needs a doc string</p>
90</dd></dl>
91
92<dl class="function">
93<dt id="GSASIIstrMain.main">
94<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>
95<dd><p>Needs a doc string</p>
96</dd></dl>
97
98</div>
99<span class="target" id="module-GSASIIstrMath"></span><div class="section" id="gsasiistrmath-structure-math-routines">
100<h2><em>GSASIIstrMath - structure math routines</em><a class="headerlink" href="#gsasiistrmath-structure-math-routines" title="Permalink to this headline">¶</a></h2>
101<dl class="function">
102<dt id="GSASIIstrMath.ApplyRBModelDervs">
103<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>
104<dd><p>Needs a doc string</p>
105</dd></dl>
106
107<dl class="function">
108<dt id="GSASIIstrMath.ApplyRBModels">
109<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>
110<dd><p>Takes RB info from RBModels in Phase and RB data in rigidbodyDict along with
111current RB values in parmDict &amp; modifies atom contents (xyz &amp; Uij) of parmDict</p>
112</dd></dl>
113
114<dl class="function">
115<dt id="GSASIIstrMath.ApplyXYZshifts">
116<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>
117<dd><p>takes atom x,y,z shift and applies it to corresponding atom x,y,z value</p>
118<table class="docutils field-list" frame="void" rules="none">
119<col class="field-name" />
120<col class="field-body" />
121<tbody valign="top">
122<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
123<li><strong>parmDict</strong> (<em>dict</em>) &#8211; parameter dictionary</li>
124<li><strong>varyList</strong> (<em>list</em>) &#8211; list of variables</li>
125</ul>
126</td>
127</tr>
128<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>
129</td>
130</tr>
131</tbody>
132</table>
133</dd></dl>
134
135<dl class="function">
136<dt id="GSASIIstrMath.Dict2Values">
137<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>
138<dd><p>Use before call to leastsq to setup list of values for the parameters
139in parmdict, as selected by key in varylist</p>
140</dd></dl>
141
142<dl class="function">
143<dt id="GSASIIstrMath.GetAbsorb">
144<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>
145<dd><p>Needs a doc string</p>
146</dd></dl>
147
148<dl class="function">
149<dt id="GSASIIstrMath.GetAbsorbDerv">
150<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>
151<dd><p>Needs a doc string</p>
152</dd></dl>
153
154<dl class="function">
155<dt id="GSASIIstrMath.GetAtomFXU">
156<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>
157<dd><p>Needs a doc string</p>
158</dd></dl>
159
160<dl class="function">
161<dt id="GSASIIstrMath.GetFobsSq">
162<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>
163<dd><p>Needs a doc string</p>
164</dd></dl>
165
166<dl class="function">
167<dt id="GSASIIstrMath.GetHStrainShift">
168<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>
169<dd><p>Needs a doc string</p>
170</dd></dl>
171
172<dl class="function">
173<dt id="GSASIIstrMath.GetHStrainShiftDerv">
174<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>
175<dd><p>Needs a doc string</p>
176</dd></dl>
177
178<dl class="function">
179<dt id="GSASIIstrMath.GetIntensityCorr">
180<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>
181<dd><p>Needs a doc string</p>
182</dd></dl>
183
184<dl class="function">
185<dt id="GSASIIstrMath.GetIntensityDerv">
186<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>
187<dd><p>Needs a doc string</p>
188</dd></dl>
189
190<dl class="function">
191<dt id="GSASIIstrMath.GetNewCellParms">
192<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>
193<dd><p>Needs a doc string</p>
194</dd></dl>
195
196<dl class="function">
197<dt id="GSASIIstrMath.GetPrefOri">
198<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>
199<dd><p>Needs a doc string</p>
200</dd></dl>
201
202<dl class="function">
203<dt id="GSASIIstrMath.GetPrefOriDerv">
204<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>
205<dd><p>Needs a doc string</p>
206</dd></dl>
207
208<dl class="function">
209<dt id="GSASIIstrMath.GetReflPos">
210<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>
211<dd><p>Needs a doc string</p>
212</dd></dl>
213
214<dl class="function">
215<dt id="GSASIIstrMath.GetReflPosDerv">
216<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>
217<dd><p>Needs a doc string</p>
218</dd></dl>
219
220<dl class="function">
221<dt id="GSASIIstrMath.GetSampleSigGam">
222<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>
223<dd><p>Needs a doc string</p>
224</dd></dl>
225
226<dl class="function">
227<dt id="GSASIIstrMath.GetSampleSigGamDerv">
228<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>
229<dd><p>Needs a doc string</p>
230</dd></dl>
231
232<dl class="function">
233<dt id="GSASIIstrMath.HessRefine">
234<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>
235<dd><p>Loop over histograms and compute derivatives of the fitting
236model (M) with respect to all parameters.  For each histogram, the
237Jacobian matrix, dMdv, with dimensions (n by m) where n is the
238number of parameters and m is the number of data points <em>in the
239histogram</em>. The (n by n) Hessian is computed from each Jacobian
240and it is returned.  This routine is used when refinement
241derivatives are selected as &#8220;analtytic Hessian&#8221; in Controls.</p>
242<table class="docutils field-list" frame="void" rules="none">
243<col class="field-name" />
244<col class="field-body" />
245<tbody valign="top">
246<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Vec,Hess where Vec is the least-squares vector and Hess is the Hessian</td>
247</tr>
248</tbody>
249</table>
250</dd></dl>
251
252<dl class="function">
253<dt id="GSASIIstrMath.SCExtinction">
254<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>
255<dd><p>Single crystal extinction function; puts correction in ref[13] and returns
256corrections needed for derivatives</p>
257</dd></dl>
258
259<dl class="function">
260<dt id="GSASIIstrMath.SHPOcal">
261<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>
262<dd><p>spherical harmonics preferred orientation (cylindrical symmetry only)</p>
263</dd></dl>
264
265<dl class="function">
266<dt id="GSASIIstrMath.SHPOcalDerv">
267<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>
268<dd><p>spherical harmonics preferred orientation derivatives (cylindrical symmetry only)</p>
269</dd></dl>
270
271<dl class="function">
272<dt id="GSASIIstrMath.SHTXcal">
273<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>
274<dd><p>Spherical harmonics texture</p>
275</dd></dl>
276
277<dl class="function">
278<dt id="GSASIIstrMath.SHTXcalDerv">
279<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>
280<dd><p>Spherical harmonics texture derivatives</p>
281</dd></dl>
282
283<dl class="function">
284<dt id="GSASIIstrMath.StructureFactor">
285<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>
286<dd><p>Compute structure factors for all h,k,l for phase
287puts the result, F^2, in each ref[8] in refList
288input:</p>
289<table class="docutils field-list" frame="void" rules="none">
290<col class="field-name" />
291<col class="field-body" />
292<tbody valign="top">
293<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
294<li><strong>refList</strong> (<em>list</em>) &#8211; [ref] where each ref = h,k,l,m,d,...,[equiv h,k,l],phase[equiv]</li>
295<li><strong>G</strong> (<em>np.array</em>) &#8211; reciprocal metric tensor</li>
296<li><strong>pfx</strong> (<em>str</em>) &#8211; phase id string</li>
297<li><strong>SGData</strong> (<em>dict</em>) &#8211; space group info. dictionary output from SpcGroup</li>
298<li><strong>calcControls</strong> (<em>dict</em>) &#8211; </li>
299<li><strong>ParmDict</strong> (<em>dict</em>) &#8211; </li>
300</ul>
301</td>
302</tr>
303</tbody>
304</table>
305</dd></dl>
306
307<dl class="function">
308<dt id="GSASIIstrMath.StructureFactorDerv">
309<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>
310<dd><p>Needs a doc string</p>
311</dd></dl>
312
313<dl class="function">
314<dt id="GSASIIstrMath.Values2Dict">
315<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>
316<dd><p>Use after call to leastsq to update the parameter dictionary with
317values corresponding to keys in varylist</p>
318</dd></dl>
319
320<dl class="function">
321<dt id="GSASIIstrMath.dervRefine">
322<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>
323<dd><p>Loop over histograms and compute derivatives of the fitting
324model (M) with respect to all parameters.  Results are returned in
325a Jacobian matrix (aka design matrix) of dimensions (n by m) where
326n is the number of parameters and m is the number of data
327points. This can exceed memory when m gets large. This routine is
328used when refinement derivatives are selected as &#8220;analtytic
329Jacobian&#8221; in Controls.</p>
330<table class="docutils field-list" frame="void" rules="none">
331<col class="field-name" />
332<col class="field-body" />
333<tbody valign="top">
334<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Jacobian numpy.array dMdv for all histograms concatinated</td>
335</tr>
336</tbody>
337</table>
338</dd></dl>
339
340<dl class="function">
341<dt id="GSASIIstrMath.errRefine">
342<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>
343<dd><p>Needs a doc string</p>
344</dd></dl>
345
346<dl class="function">
347<dt id="GSASIIstrMath.getPowderProfile">
348<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>
349<dd><p>Needs a doc string</p>
350</dd></dl>
351
352<dl class="function">
353<dt id="GSASIIstrMath.getPowderProfileDerv">
354<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>
355<dd><p>Needs a doc string</p>
356</dd></dl>
357
358<dl class="function">
359<dt id="GSASIIstrMath.penaltyDeriv">
360<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>
361<dd><p>Needs a doc string</p>
362</dd></dl>
363
364<dl class="function">
365<dt id="GSASIIstrMath.penaltyFxn">
366<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>
367<dd><p>Needs a doc string</p>
368</dd></dl>
369
370</div>
371<span class="target" id="module-GSASIIstrIO"></span><div class="section" id="gsasiistrio-structure-i-o-routines">
372<h2><em>GSASIIstrIO: structure I/O routines</em><a class="headerlink" href="#gsasiistrio-structure-i-o-routines" title="Permalink to this headline">¶</a></h2>
373<dl class="function">
374<dt id="GSASIIstrIO.CheckConstraints">
375<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>
376<dd><p>Load constraints and related info and return any error or warning messages</p>
377</dd></dl>
378
379<dl class="function">
380<dt id="GSASIIstrIO.GPXBackup">
381<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>
382<dd><p>makes a backup of the current .gpx file (?)</p>
383<table class="docutils field-list" frame="void" rules="none">
384<col class="field-name" />
385<col class="field-body" />
386<tbody valign="top">
387<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
388<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
389<li><strong>makeBack</strong> (<em>bool</em>) &#8211; if True (default), the backup is written to
390a new file; if False, the last backup is overwritten</li>
391</ul>
392</td>
393</tr>
394<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>
395</td>
396</tr>
397</tbody>
398</table>
399</dd></dl>
400
401<dl class="function">
402<dt id="GSASIIstrIO.GetAllPhaseData">
403<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>
404<dd><p>Returns the entire dictionary for PhaseName from GSASII gpx file</p>
405<table class="docutils field-list" frame="void" rules="none">
406<col class="field-name" />
407<col class="field-body" />
408<tbody valign="top">
409<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
410<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
411<li><strong>PhaseName</strong> (<em>str</em>) &#8211; phase name</li>
412</ul>
413</td>
414</tr>
415<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">phase dictionary</p>
416</td>
417</tr>
418</tbody>
419</table>
420</dd></dl>
421
422<dl class="function">
423<dt id="GSASIIstrIO.GetConstraints">
424<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>
425<dd><p>Read the constraints from the GPX file and interpret them</p>
426</dd></dl>
427
428<dl class="function">
429<dt id="GSASIIstrIO.GetControls">
430<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>
431<dd><p>Returns dictionary of control items found in GSASII gpx file</p>
432<table class="docutils field-list" frame="void" rules="none">
433<col class="field-name" />
434<col class="field-body" />
435<tbody valign="top">
436<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>
437</tr>
438<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">dictionary of control items</td>
439</tr>
440</tbody>
441</table>
442</dd></dl>
443
444<dl class="function">
445<dt id="GSASIIstrIO.GetFprime">
446<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>
447<dd><p>Needs a doc string</p>
448</dd></dl>
449
450<dl class="function">
451<dt id="GSASIIstrIO.GetHistogramData">
452<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>
453<dd><p>needs a doc string</p>
454</dd></dl>
455
456<dl class="function">
457<dt id="GSASIIstrIO.GetHistogramNames">
458<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>
459<dd><p>Returns a list of histogram names found in GSASII gpx file</p>
460<table class="docutils field-list" frame="void" rules="none">
461<col class="field-name" />
462<col class="field-body" />
463<tbody valign="top">
464<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
465<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
466<li><strong>hNames</strong> (<em>str</em>) &#8211; list of histogram names</li>
467</ul>
468</td>
469</tr>
470<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>
471</td>
472</tr>
473</tbody>
474</table>
475</dd></dl>
476
477<dl class="function">
478<dt id="GSASIIstrIO.GetHistogramPhaseData">
479<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>, <em>resetRefList=True</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>
480<dd><p>Loads the HAP histogram/phase information into dicts</p>
481<table class="docutils field-list" frame="void" rules="none">
482<col class="field-name" />
483<col class="field-body" />
484<tbody valign="top">
485<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
486<li><strong>Phases</strong> (<em>dict</em>) &#8211; phase information</li>
487<li><strong>Histograms</strong> (<em>dict</em>) &#8211; Histogram information</li>
488<li><strong>Print</strong> (<em>bool</em>) &#8211; prints information as it is read</li>
489<li><strong>pFile</strong> (<em>file</em>) &#8211; file object to print to (the default, None causes printing to the console)</li>
490<li><strong>resetRefList</strong> (<em>bool</em>) &#8211; Should the contents of the Reflection List be initialized
491on loading. The default, True, initializes the Reflection List as it is loaded.</li>
492</ul>
493</td>
494</tr>
495<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(hapVary,hapDict,controlDict)
496* hapVary: list of refined variables
497* hapDict: dict with refined variables and their values
498* controlDict: dict with computation controls (?)</p>
499</td>
500</tr>
501</tbody>
502</table>
503</dd></dl>
504
505<dl class="function">
506<dt id="GSASIIstrIO.GetHistograms">
507<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>
508<dd><p>Returns a dictionary of histograms found in GSASII gpx file</p>
509<table class="docutils field-list" frame="void" rules="none">
510<col class="field-name" />
511<col class="field-body" />
512<tbody valign="top">
513<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
514<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
515<li><strong>hNames</strong> (<em>str</em>) &#8211; list of histogram names</li>
516</ul>
517</td>
518</tr>
519<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>
520</td>
521</tr>
522</tbody>
523</table>
524</dd></dl>
525
526<dl class="function">
527<dt id="GSASIIstrIO.GetPawleyConstr">
528<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>
529<dd><p>needs a doc string</p>
530</dd></dl>
531
532<dl class="function">
533<dt id="GSASIIstrIO.GetPhaseData">
534<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>
535<dd><p>needs a doc string</p>
536</dd></dl>
537
538<dl class="function">
539<dt id="GSASIIstrIO.GetPhaseNames">
540<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>
541<dd><p>Returns a list of phase names found under &#8216;Phases&#8217; in GSASII gpx file</p>
542<table class="docutils field-list" frame="void" rules="none">
543<col class="field-name" />
544<col class="field-body" />
545<tbody valign="top">
546<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>
547</tr>
548<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">list of phase names</td>
549</tr>
550</tbody>
551</table>
552</dd></dl>
553
554<dl class="function">
555<dt id="GSASIIstrIO.GetRestraints">
556<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>
557<dd><p>Read the restraints from the GPX file.
558Throws an exception if not found in the .GPX file</p>
559</dd></dl>
560
561<dl class="function">
562<dt id="GSASIIstrIO.GetRigidBodies">
563<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>
564<dd><p>Read the rigid body models from the GPX file</p>
565</dd></dl>
566
567<dl class="function">
568<dt id="GSASIIstrIO.GetRigidBodyModels">
569<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>
570<dd><p>needs a doc string</p>
571</dd></dl>
572
573<dl class="function">
574<dt id="GSASIIstrIO.GetUsedHistogramsAndPhases">
575<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>
576<dd><p>Returns all histograms that are found in any phase
577and any phase that uses a histogram</p>
578<table class="docutils field-list" frame="void" rules="none">
579<col class="field-name" />
580<col class="field-body" />
581<tbody valign="top">
582<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>
583</tr>
584<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">(Histograms,Phases)<ul class="simple">
585<li>Histograms = dictionary of histograms as {name:data,...}</li>
586<li>Phases = dictionary of phases that use histograms</li>
587</ul>
588</td>
589</tr>
590</tbody>
591</table>
592</dd></dl>
593
594<dl class="function">
595<dt id="GSASIIstrIO.PrintRestraints">
596<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>
597<dd><p>needs a doc string</p>
598</dd></dl>
599
600<dl class="function">
601<dt id="GSASIIstrIO.ProcessConstraints">
602<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>
603<dd><p>Interpret the constraints in the constList input into a dictionary, etc.</p>
604<table class="docutils field-list" frame="void" rules="none">
605<col class="field-name" />
606<col class="field-body" />
607<tbody valign="top">
608<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>constList</strong> (<em>list</em>) &#8211; <p>a list of lists where each item in the outer list
609specifies a constraint of some form. The last item in each inner list
610determines which of the four constraints types has been input:</p>
611<blockquote>
612<div><ul class="simple">
613<li>h (hold): a single variable that will not be varied. It
614will be removed from the varyList later.</li>
615<li>c (constraint): specifies a linear relationship that
616can be varied as a new grouped variable
617a fixed value.</li>
618<li>f (fixed): specifies a linear relationship that is assigned
619a fixed value.</li>
620<li>e (equivalence): specifies a series of variables where the
621first variable in the last can be used to generate the
622values for all the remaining variables.</li>
623</ul>
624</div></blockquote>
625</td>
626</tr>
627<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">a tuple of (constDict,fixedList,ignored) where:<ul class="simple">
628<li>constDict (list) contains the constraint relationships</li>
629<li>fixedList (list) contains the fixed values for type
630of constraint.</li>
631<li>ignored (int) counts the number of invalid constraint items
632(should always be zero!)</li>
633</ul>
634</td>
635</tr>
636</tbody>
637</table>
638</dd></dl>
639
640<dl class="function">
641<dt id="GSASIIstrIO.SetHistogramData">
642<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>
643<dd><p>needs a doc string</p>
644</dd></dl>
645
646<dl class="function">
647<dt id="GSASIIstrIO.SetHistogramPhaseData">
648<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>
649<dd><p>needs a doc string</p>
650</dd></dl>
651
652<dl class="function">
653<dt id="GSASIIstrIO.SetPhaseData">
654<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>
655<dd><p>needs a doc string</p>
656</dd></dl>
657
658<dl class="function">
659<dt id="GSASIIstrIO.SetRigidBodyModels">
660<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>
661<dd><p>needs a doc string</p>
662</dd></dl>
663
664<dl class="function">
665<dt id="GSASIIstrIO.SetSeqResult">
666<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>
667<dd><p>Needs doc string</p>
668<table class="docutils field-list" frame="void" rules="none">
669<col class="field-name" />
670<col class="field-body" />
671<tbody valign="top">
672<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>
673</tr>
674</tbody>
675</table>
676</dd></dl>
677
678<dl class="function">
679<dt id="GSASIIstrIO.SetUsedHistogramsAndPhases">
680<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>
681<dd><p>Updates gpxfile from all histograms that are found in any phase
682and any phase that used a histogram. Also updates rigid body definitions.</p>
683<table class="docutils field-list" frame="void" rules="none">
684<col class="field-name" />
685<col class="field-body" />
686<tbody valign="top">
687<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
688<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
689<li><strong>Histograms</strong> (<em>dict</em>) &#8211; dictionary of histograms as {name:data,...}</li>
690<li><strong>Phases</strong> (<em>dict</em>) &#8211; dictionary of phases that use histograms</li>
691<li><strong>RigidBodies</strong> (<em>dict</em>) &#8211; dictionary of rigid bodies</li>
692<li><strong>CovData</strong> (<em>dict</em>) &#8211; dictionary of refined variables, varyList, &amp; covariance matrix</li>
693<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>
694</ul>
695</td>
696</tr>
697</tbody>
698</table>
699</dd></dl>
700
701<dl class="function">
702<dt id="GSASIIstrIO.ShowBanner">
703<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>
704<dd><p>Print authorship, copyright and citation notice</p>
705</dd></dl>
706
707<dl class="function">
708<dt id="GSASIIstrIO.ShowControls">
709<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>
710<dd><p>Print controls information</p>
711</dd></dl>
712
713<dl class="function">
714<dt id="GSASIIstrIO.cellFill">
715<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>
716<dd><p>Returns the filled-out reciprocal cell (A) terms and their uncertainties
717from the parameter and sig dictionaries.</p>
718<table class="docutils field-list" frame="void" rules="none">
719<col class="field-name" />
720<col class="field-body" />
721<tbody valign="top">
722<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
723<li><strong>pfx</strong> (<em>str</em>) &#8211; parameter prefix (&#8220;n::&#8221;, where n is a phase number)</li>
724<li><strong>SGdata</strong> (<em>dict</em>) &#8211; a symmetry object</li>
725<li><strong>parmDict</strong> (<em>dict</em>) &#8211; a dictionary of parameters</li>
726<li><strong>sigDict</strong> (<em>dict</em>) &#8211; a dictionary of uncertainties on parameters</li>
727</ul>
728</td>
729</tr>
730<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A,sigA where each is a list of six terms with the A terms</p>
731</td>
732</tr>
733</tbody>
734</table>
735</dd></dl>
736
737<dl class="function">
738<dt id="GSASIIstrIO.cellVary">
739<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>
740<dd><p>needs a doc string</p>
741</dd></dl>
742
743<dl class="function">
744<dt id="GSASIIstrIO.getBackupName">
745<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>
746<dd><p>Get the name for the backup .gpx file name</p>
747<table class="docutils field-list" frame="void" rules="none">
748<col class="field-name" />
749<col class="field-body" />
750<tbody valign="top">
751<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
752<li><strong>GPXfile</strong> (<em>str</em>) &#8211; full .gpx file name</li>
753<li><strong>makeBack</strong> (<em>bool</em>) &#8211; if True the name of a new file is returned, if
754False the name of the last file that exists is returned</li>
755</ul>
756</td>
757</tr>
758<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>
759</td>
760</tr>
761</tbody>
762</table>
763</dd></dl>
764
765<dl class="function">
766<dt id="GSASIIstrIO.getCellEsd">
767<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>
768<dd><p>needs a doc string</p>
769</dd></dl>
770
771</div>
772</div>
773
774
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783  <h3><a href="index.html">Table Of Contents</a></h3>
784  <ul>
785<li><a class="reference internal" href="#"><em>GSAS-II Structure  Submodules</em></a><ul>
786<li><a class="reference internal" href="#gsasiistrmain-main-structure-routine"><em>GSASIIstrMain: main structure routine</em></a></li>
787<li><a class="reference internal" href="#gsasiistrmath-structure-math-routines"><em>GSASIIstrMath - structure math routines</em></a></li>
788<li><a class="reference internal" href="#gsasiistrio-structure-i-o-routines"><em>GSASIIstrIO: structure I/O routines</em></a></li>
789</ul>
790</li>
791</ul>
792
793  <h4>Previous topic</h4>
794  <p class="topless"><a href="GSASIIGUI.html"
795                        title="previous chapter"><em>GSAS-II GUI Submodules</em></a></p>
796  <h4>Next topic</h4>
797  <p class="topless"><a href="GSASIImapvars.html"
798                        title="next chapter"><em>GSASIImapvars: Parameter constraints</em></a></p>
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