Changeset 3451

Timestamp:

Jun 25, 2018 4:23:51 PM (5 years ago)

Author:

toby

Message:

seq refine: update tutorial, Py3 bug

Files:

• Tutorials/SeqRefine/SequentialTutorial.htm (modified) (10 diffs)
• trunk/GSASIIdataGUI.py (modified) (1 diff)

Tutorials/SeqRefine/SequentialTutorial.htm

@@ -1609 +1609 @@
 the<b> </b></span><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 major-latin;mso-hansi-theme-font:major-latin'>Constraints</span> </b><span
-style='mso-bidi-font-weight:bold'>item</span> in the data tree and the <b><span
-style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
-mso-hansi-theme-font:major-latin'>Select tab/Histogram/Phase</span> </b><span
+style='mso-bidi-font-weight:bold'>item</span> in the data tree and
+then in the <b>Select tab</b> menu use the <b>Histogram/Phase</b> <span
 style='mso-bidi-font-weight:bold'>menu item</span>, and then <span
 style='mso-bidi-font-weight:bold'>click on the<b> </b></span><b><span
@@ -1812 +1811 @@
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>There
 are several additional variables that should now be added. One should always
-refine a sample displacement parameter or rarely a zero correction. In this
+refine a sample displacement parameter (or rarely one refines a zero correction.) In this
 case, the best choice is to <span style='mso-bidi-font-weight:bold'>add the<b> </b></span><b><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
@@ -2042 +2041 @@
 style='mso-bidi-font-weight:bold'> terms</span> to refine the lattice strain
 terms. While here, to simplify convergence for the sequential refinement, where
-lattice constants change significantly, <span style='mso-bidi-font-weight:bold'>turn
-off the refinement of the three size and mustrain terms and the phase fraction</span>.
+lattice constants change significantly, <B>turn
+off</B> the refinement of the <b>three size and mustrain terms and the phase fraction</b>.
 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Data</span></b>
@@ -2734 +2733 @@
 <p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l1 level1 lfo16'><![if !supportLists]><span
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
-style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Likewise,
+style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+</span></span></span><![endif]>Likewise, in the Sample Parameters tree item
 <span style='mso-bidi-font-weight:bold'>include the<b> </b></span><b><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
@@ -2747 +2747 @@
 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
 style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>For
-Phase parameters <span style='mso-bidi-font-weight:bold'>add the three
+Phase parameters <span style='mso-bidi-font-weight:bold'> in the Data
+section, add the three
 broadening terms</span> for the CuCr<sub>2</sub>O<sub>4</sub> phase and do <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin;mso-bidi-theme-font:
 major-latin'>Edit Phase/Copy flags</span></b>. (Important: not Copy!) For the <span
-style='mso-bidi-font-weight:bold'>CuO phase, add the single sample broadening
+style='mso-bidi-font-weight:bold'>CuO phase, add refinement of the single sample broadening
 term and the remaining lattice parameter</span> via the <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
@@ -2773 +2774 @@
 values between 13.8 and 17.</p>
 
+<h1>Step 8: Further sequential refinements. </h1>
+
 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
 
@@ -2781 +2784 @@
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Phase
-fraction</span></b> checkbox and do <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
-mso-hansi-theme-font:major-latin;mso-bidi-theme-font:major-latin'>Edit Phase/C</span></b><b
+fraction</span></b> checkbox in the Phase/Data tab. Do this for each
+Phase followed by use of <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
+mso-hansi-theme-font:major-latin;mso-bidi-theme-font:major-latin'>Edit Phase/</span></b><b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>opy Flags</span></b>
-from the menu for both phases. However, if the refinement is attempted it will
-proceed but will not constrain the two phase fractions to sum to one for all
-but the 1<sup>st</sup> histogram. See <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
-mso-hansi-theme-font:major-latin;mso-bidi-theme-font:major-latin'>::constr0</span></b>,
-<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin;mso-bidi-theme-font:
-major-latin'>1:*:Scale</span></b> and <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
-mso-hansi-theme-font:major-latin;mso-bidi-theme-font:major-latin'>0:*:Scale</span></b>
-below.</p>
-
-<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
-mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_82" o:spid="_x0000_i1032"
- type="#_x0000_t75" style='width:6in;height:247.5pt;visibility:visible;
- mso-wrap-style:square'>
- <v:imagedata src="SequentialTutorial_files/image048.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img width=576 height=330
-src="SequentialTutorial_files/image080.png" v:shapes="Picture_x0020_82"><![endif]></span></p>
-
-<p class=MsoListParagraphCxSpLast><o:p>&nbsp;</o:p></p>
-
-<p class=MsoNormal style='margin-left:.5in'>To fix this, one additional step is
-needed to switch the constraints to work properly. Note that constraint we
-defined before (on <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
-mso-hansi-theme-font:major-latin'>0:0:Scale</span></b> and <b style='mso-bidi-font-weight:
-normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
-major-latin;mso-hansi-theme-font:major-latin'>1:0:Scale</span></b>) pertains
-only to the first histogram. Also a constraint is ignored if none of the
-variables in it are included in the refinement, so this constraint only affects
-the first histogram. We could set up a constraint for each histogram that has
-been added, but this would be rather tedious to set up. The alternate is to set
-up a constraint where a wildcard (<span style='font-family:Courier'>*</span>)
-is used. Wildcards only apply to sequential fits and causes the current
-histogram number to be inserted for the <span style='font-family:Courier'>*</span>
-when each histogram is used. </p>
+mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Copy
+Flags</span></b>. However, a constraint is still needed as before, but
+to be applied to each histogram. Constraints entered with a specific histogram
+number, as was done before, will be ignored. For sequential
+refinements, only constraints where the histogram number is specified
+as "*" are used. 
 
 <p class=MsoListParagraphCxSpFirst><o:p>&nbsp;</o:p></p>
@@ -2879 +2851 @@
 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
 
-<p class=MsoListParagraphCxSpMiddle>These two constraints will interfere when
-refining the with first histogram, so <span style='mso-bidi-font-weight:bold'>press
-the </span><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
+<p class=MsoListParagraphCxSpMiddle>These two constraints do not
+interfere, since the first will be used during a non-sequential
+refinement and the second is used only for sequential fits, but if
+desired the first constraint can be deleted by pressing the </span><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 major-latin;mso-hansi-theme-font:major-latin'>Delete</span></b><span
 style='mso-bidi-font-weight:bold'> button for the first</span> one to remove
-it.</p>
-
-<p class=MsoListParagraphCxSpMiddle><span style='mso-spacerun:yes'> </span><span
-style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
- id="Picture_x0020_86" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:6in;
- height:137.25pt;visibility:visible;mso-wrap-style:square'>
- <v:imagedata src="SequentialTutorial_files/image055.png" o:title=""/>
-</v:shape><![endif]--><![if !vml]><img width=576 height=183
-src="SequentialTutorial_files/image083.png" v:shapes="Picture_x0020_86"><![endif]></span></p>
+it, but this is optional.</p>
 
 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
@@ -2902 +2867 @@
 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Calculate/Sequential
 refine</span> </b><span style='mso-bidi-font-weight:bold'>menu item<b>.</b></span>
-Three new columns appear at the end of the table for <b style='mso-bidi-font-weight:
+Five new columns appear at the end of the table for <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 major-latin;mso-hansi-theme-font:major-latin'>::constr0</span></b> (generated
-by the constraint) and the initial variables, <b style='mso-bidi-font-weight:
+by the constraint) and the selected variables, <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
 major-latin;mso-hansi-theme-font:major-latin'>0:*:Scale</span></b> and <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>1:*:Scale</span></b>.
+mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>1:*:Scale</span></b>. Also
+included are the weight fractions for each phase. Note that the phase
+fractions all add to one.
 Changes to the R<sub>wp</sub> values are quite small, even though the value for
 the minor phase changes significantly. This indicates that the refinement is
-relatively insensitive to these values. There are now values for all three
-columns and the two scales add to one.</p>
+relatively insensitive to these values. 
+</p>
 
 <p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
@@ -2922 +2889 @@
 </v:shape><![endif]--><![if !vml]><img width=576 height=264
 src="SequentialTutorial_files/image084.png" v:shapes="Picture_x0020_88"><![endif]></span></p>
+
+<h1>Step 9: Complete the sequential refinement. </h1>
+
+<p class=MsoListParagraphCxSpFirst><o:p>&nbsp;</o:p></p>
 
 <p class=MsoListParagraphCxSpMiddle>The last thing we will add to the

trunk/GSASIIdataGUI.py

@@ -6924 +6924 @@
     for phase in Phases:
         var = str(Phases[phase]['pId'])+':*:Scale'
-        if var not in combinedVaryList+depValDict.keys(): continue
+        if var not in combinedVaryList+list(depValDict.keys()): continue
         wtFrList = []
         sigwtFrList = []