Changeset 2390 for Tutorials/MerohedralTwins

Timestamp:

Jul 28, 2016 2:18:10 PM (7 years ago)

Author:

vondreele

Message:

 

Location:

Tutorials/MerohedralTwins

Files:

• Merohedral twin refinement in GSAS.htm (modified) (19 diffs)
• Merohedral twin refinement in GSAS_files/filelist.xml (modified) (1 diff)
• Merohedral twin refinement in GSAS_files/image003.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image005.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image006.png (modified) (previous)
• Merohedral twin refinement in GSAS_files/image019.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image020.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image021.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image022.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image023.gif (modified) (previous)

Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm

@@ -25 +25 @@
   <o:Author>Von Dreele</o:Author>
   <o:LastAuthor>Von Dreele</o:LastAuthor>
-  <o:Revision>2</o:Revision>
-  <o:TotalTime>0</o:TotalTime>
+  <o:Revision>3</o:Revision>
+  <o:TotalTime>2</o:TotalTime>
   <o:Created>2016-05-26T15:52:00Z</o:Created>
-  <o:LastSaved>2016-05-26T15:52:00Z</o:LastSaved>
+  <o:LastSaved>2016-07-28T18:45:00Z</o:LastSaved>
   <o:Pages>1</o:Pages>
-  <o:Words>3321</o:Words>
-  <o:Characters>18934</o:Characters>
+  <o:Words>3323</o:Words>
+  <o:Characters>18947</o:Characters>
   <o:Lines>157</o:Lines>
   <o:Paragraphs>44</o:Paragraphs>
-  <o:CharactersWithSpaces>22211</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>22226</o:CharactersWithSpaces>
   <o:Version>16.00</o:Version>
  </o:DocumentProperties>
@@ -811 +811 @@
 
 <p class=MsoNormal>In these exercises you will use GSAS-II to refine the
-structure of a few single crystal structures where there is merohedral twinning.
-There is a general discussion of twinning in International Tables for
+structure of a few single crystal structures where there is merohedral
+twinning. There is a general discussion of twinning in International Tables for
 Crystallography (2006), Vol. C, Chapter 1.3, pp 10-14. Merohedral twinning
 occurs when the twin operation (2, m or <span style='position:relative;
@@ -892 +892 @@
 
 <p class=MsoNormal>This example was taken from Luo, et al., Dalton Trans.
-4491(2006). The structure is given in the file <b><span style='font-family:
-"Calibri",sans-serif'>/exercises/<span class=SpellE>MerohedralTwins</span>/1b.cif</span></b>
-and the data are in <b><span style='font-family:"Calibri",sans-serif'>/exercises/<span
-class=SpellE>MerohedralTwins</span>/1b.fcf</span></b>. This example is <span
-class=SpellE>noncentrosymmetric</span> and the data was collected with
+4491(2006). The structure is given in the file <span class=SpellE><b><span
+style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span
+style='font-family:"Calibri",sans-serif'>/data/1b.cif</span></b> and the data
+are in <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span
+style='font-family:"Calibri",sans-serif'>/data/1b.fcf</span></b>. This example
+is <span class=SpellE>noncentrosymmetric</span> and the data was collected with
 radiation (<span class=SpellE>MoK</span>&#945;) that gives significant resonant
 scattering from the Ga atoms. </p>
@@ -918 +919 @@
 and you will see the General page for this phase</p>
 
-<p class=MsoNormal><span style='mso-no-proof:yes'><img width=650 height=500
+<p class=MsoNormal><span style='mso-no-proof:yes'><img width=403 height=310
 id="_x0000_i1056"
 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image007.png"></span></p>
@@ -924 +925 @@
 <p class=MsoNormal>Next do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
 Factor/from CIF file</span></b> (that is the format of a “<span class=SpellE>fcf</span>”
-file); a file selection dialog box will appear with the previously selected directory
-chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>;
+file); a file selection dialog box will appear with the previously selected
+directory chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>;
 a popup window will appear</p>
 
@@ -992 +993 @@
 parameter</span></b> for refinement and do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
 from the main GSAS-II data tree menu. The structure will quickly refine to give
-<span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable
-improvement on Scale factor alone. The Flack parameter is now 0.452, meaning
-that both hands somehow exist in the structure. This can happen if the crystal
-is <span class=SpellE>merohedrally</span> inversion twinned.</p>
+<span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable improvement
+on Scale factor alone. The Flack parameter is now 0.452, meaning that both
+hands somehow exist in the structure. This can happen if the crystal is <span
+class=SpellE>merohedrally</span> inversion twinned.</p>
 
 <p class=MsoNormal>To introduce this twin, press the <b><span style='font-family:
@@ -1027 +1028 @@
 [NC<sub>7</sub>H<sub>8</sub>]<sup>+</sup><o:p></o:p></span></h2>
 
-<p class=MsoNormal>In this case the data collection Laue statistics (very
-nearly <span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m)
+<p class=MsoNormal>In this case the data collection Laue statistics (very nearly
+<span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m)
 and systematic extinctions indicated that the space group was either one of the
 <span class=SpellE>enantiomorphic</span> pair P3<sub>1</sub>21 or P3<sub>2</sub>21
@@ -1073 +1074 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=495 height=235
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
 
 <p class=MsoNormal>There are two significant warnings concerning <span
@@ -1178 +1179 @@
 width=9 height=19 id="_x0000_i1039"
 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1
-Laue data symmetries that there is twinning so don’t bother trying to make it better
-by refining the structure. To determine the possible twin law we refer to Table
-1.3.4.2 of the International Tables for Crystallography Vol C. and see that
-indeed Laue <span style='position:relative;top:3pt'><span style='mso-no-proof:
-yes'><img width=9 height=19 id="_x0000_i1038"
+Laue data symmetries that there is twinning so don’t bother trying to make it
+better by refining the structure. To determine the possible twin law we refer
+to Table 1.3.4.2 of the International Tables for Crystallography Vol C. and see
+that indeed Laue <span style='position:relative;top:3pt'><span
+style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1038"
 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1
 as P3<sub>2</sub>21 can be simulated by twinned Laue <span style='position:
@@ -1283 +1284 @@
 
 <p class=MsoNormal>Before beginning the refinement, it usually the practice to
-eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub>
-&lt; 2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span
+eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub> &lt;
+2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span
 style='font-family:"Calibri",sans-serif'>Controls</span></b> entry from the
 GSAS-II data tree.</p>
@@ -1316 +1317 @@
 that indeed Laue 6/mmm as P6<sub>1</sub>22 can be simulated by twinned Laue 6/m
 crystals in P6<sub>1</sub>; the possible operator is shown in Table 1.3.4.1
-(reproduced above) as either a mirror or a 2-fold. The detailed symbolism in
-the table (‘m.., ..2/.2.’) indicates (perhaps obscurely) the operator
-specifics; they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr
+(reproduced above) as either a mirror or a 2-fold. The detailed symbolism in the
+table (‘m.., ..2/.2.’) indicates (perhaps obscurely) the operator specifics;
+they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr
     m:val="&#773;"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family:
    "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic;
@@ -1333 +1334 @@
 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
  type="#_x0000_t75" style='width:19.5pt;height:14.25pt'>
- <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.png"
+ <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image004.png"
   o:title="" chromakey="white"/>
 </v:shape><![endif]--><![if !vml]><img width=26 height=19
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;or
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;or
 2 as <!--[if gte msEquation 12]><m:oMath><i style='mso-bidi-font-style:normal'><span
  style='font-family:"Cambria Math",serif'><span style='position:relative;
@@ -1349 +1350 @@
 EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
  type="#_x0000_t75" style='width:19.5pt;height:14.25pt'>
- <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.png"
+ <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.png"
   o:title="" chromakey="white"/>
 </v:shape><![endif]--><![if !vml]><img width=26 height=19
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
 style='font-family:"Cambria Math",serif'>; we will use the 2-fold, m and
 inversion operators to fully test for presence of the 4 possible twin laws.
@@ -1381 +1382 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=449 height=500
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
-
-<p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is
-nonphysical and the 1<sup>st</sup> twin fraction is small. It is likely that
-the true space group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
+
+<p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is nonphysical
+and the 1<sup>st</sup> twin fraction is small. It is likely that the true space
+group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
 twinned (twin fractions 2 &amp; 4). We can improve it by refining the atom
 positions and thermal parameters, but first we need to replace the hydrogen
@@ -1399 +1400 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=700 height=300
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image021.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
 
 <p class=MsoNormal>If you scroll down the page, you’ll see H-atoms with default
@@ -1434 +1435 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=400 height=485
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
-
-<p class=MsoNormal>It specifies the expected geometry around each C-atom for H-atom
-placement. As expected we want 3 H-atoms on the terminal CH<sub>3</sub> groups
-on the <span class=SpellE>Cp</span>* ring and one for each C-atom for the NC<sub>5</sub>H<sub>5</sub>
-molecule. Press <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin'>Ok</span></b>; you will see the H-atoms added in turn to the
-structure and they will be inserted immediately after their respective C-atom.
-Their positions and thermal parameters are tied to the C-atoms so that after
-refinement of the structure they can be shifted to the <span class=SpellE>stereochemically</span>
-best positions. For the refinement, double click the <b style='mso-bidi-font-weight:
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
+
+<p class=MsoNormal>It specifies the expected geometry around each C-atom for
+H-atom placement. As expected we want 3 H-atoms on the terminal CH<sub>3</sub>
+groups on the <span class=SpellE>Cp</span>* ring and one for each C-atom for
+the NC<sub>5</sub>H<sub>5</sub> molecule. Press <b style='mso-bidi-font-weight:
 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
-minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading
-and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
-"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
-minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:normal'><span
+minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; you will see the
+H-atoms added in turn to the structure and they will be inserted immediately
+after their respective C-atom. Their positions and thermal parameters are tied
+to the C-atoms so that after refinement of the structure they can be shifted to
+the <span class=SpellE>stereochemically</span> best positions. For the
+refinement, double click the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>U</span></b> from the popup; press <b
+mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading and select <b
 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
-The Atom table will be redrawn with XU in every entry under Refine. Now do <b
-style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
-from the main GSASII data tree window; the <span class=SpellE>Rw</span> will
-drop to ~1.92%. If you look at the <b style='mso-bidi-font-weight:normal'><span
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
+and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
+mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
+from the popup; press <b style='mso-bidi-font-weight:normal'><span
+style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
+mso-hansi-theme-font:minor-latin'>OK</span></b>. The Atom table will be redrawn
+with XU in every entry under Refine. Now do <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
+the main GSASII data tree window; the <span class=SpellE>Rw</span> will drop to
+~1.92%. If you look at the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Data</span></b> tab the Twin element
@@ -1470 +1472 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=449 height=500
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
 
@@ -1506 +1508 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=360 height=351
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
 
 <p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Choose inversion</span></b> box and (important)
-set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
-mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Choose unit
-cell</span></b> to <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put the inverted
-structure back inside the unit cell. Press <b style='mso-bidi-font-weight:normal'><span
-style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
-mso-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot will both
-be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span
+mso-hansi-theme-font:minor-latin'>Choose inversion</span></b> box and
+(important) set <b style='mso-bidi-font-weight:normal'><span style='font-family:
+"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
+minor-latin'>Choose unit cell</span></b> to <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put
+the inverted structure back inside the unit cell. Press <b style='mso-bidi-font-weight:
+normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
+minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot
+will both be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span
 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
@@ -1533 +1535 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=449 height=500
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
 
 <p class=MsoNormal>Now the identity Twin Law is ~2/3 and the 2-fold Twin Law is
 the other ~1/3 while the other two are ~zero. You can delete them and repeat
-the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the
-merohedral twin exercises. You can save this project if desired.</p>
+the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the merohedral
+twin exercises. You can save this project if desired.</p>
 
 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
 
-</span></span></span></span></span></span></span></span></span></span></span></div>
-
+</span></div>
+
+</span></span></span></span></span></span></span></span></span></span>
 </body>
 

Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS_files/filelist.xml

@@ -4 +4 @@
  <o:File HRef="colorschememapping.xml"/>
  <o:File HRef="image001.png"/>
- <o:File HRef="image002.gif"/>
- <o:File HRef="image003.png"/>
- <o:File HRef="image004.gif"/>
- <o:File HRef="image005.png"/>
- <o:File HRef="image006.gif"/>
+ <o:File HRef="image003.gif"/>
+ <o:File HRef="image004.png"/>
+ <o:File HRef="image005.gif"/>
+ <o:File HRef="image006.png"/>
+ <o:File HRef="image019.gif"/>
  <o:File HRef="image007.png"/>
- <o:File HRef="image008.gif"/>
+ <o:File HRef="image020.gif"/>
  <o:File HRef="image009.png"/>
- <o:File HRef="image010.gif"/>
+ <o:File HRef="image021.gif"/>
  <o:File HRef="image011.png"/>
- <o:File HRef="image012.gif"/>
+ <o:File HRef="image022.gif"/>
  <o:File HRef="image013.png"/>
- <o:File HRef="image014.gif"/>
+ <o:File HRef="image023.gif"/>
  <o:File HRef="image015.png"/>
- <o:File HRef="image016.gif"/>
+ <o:File HRef="image024.gif"/>
  <o:File HRef="image017.png"/>
- <o:File HRef="image018.gif"/>
+ <o:File HRef="image026.gif"/>
  <o:File HRef="filelist.xml"/>
 </xml>