Changeset 2394 for Tutorials/MerohedralTwins

Timestamp:

Jul 28, 2016 2:27:34 PM (7 years ago)

Author:

vondreele

Message:

 

Location:

Tutorials/MerohedralTwins

Files:

• Merohedral twin refinement in GSAS.htm (modified) (15 diffs)
• Merohedral twin refinement in GSAS_files/filelist.xml (modified) (1 diff)
• Merohedral twin refinement in GSAS_files/image008.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image010.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image012.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image014.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image016.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image018.gif (modified) (previous)
• Merohedral twin refinement in GSAS_files/image019.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>3</o:Revision>
-  <o:TotalTime>2</o:TotalTime>
+  <o:Revision>4</o:Revision>
+  <o:TotalTime>3</o:TotalTime>
   <o:Created>2016-05-26T15:52:00Z</o:Created>
-  <o:LastSaved>2016-07-28T18:45:00Z</o:LastSaved>
+  <o:LastSaved>2016-07-28T19:27:00Z</o:LastSaved>
   <o:Pages>1</o:Pages>
-  <o:Words>3323</o:Words>
-  <o:Characters>18947</o:Characters>
-  <o:Lines>157</o:Lines>
+  <o:Words>3302</o:Words>
+  <o:Characters>18828</o:Characters>
+  <o:Lines>156</o:Lines>
   <o:Paragraphs>44</o:Paragraphs>
-  <o:CharactersWithSpaces>22226</o:CharactersWithSpaces>
+  <o:CharactersWithSpaces>22086</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;
-top:3pt'><span style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1058"
+top:3pt'><span style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1057"
 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image015.png"></span>)
 belongs to the point group of the vector lattice but not of the crystal
@@ -910 +910 @@
 style='font-family:"Calibri",sans-serif'>1b.cif</span></b>) and select it. A
 popup window will appear. Press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>;
-a new popup will appear</p>
-
-<p class=MsoNormal><span style='mso-no-proof:yes'><img width=336 height=137
-id="_x0000_i1057"
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.png"></span></p>
-
-<p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>,
+a new popup will appear; Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>,
 and you will see the General page for this phase</p>
 
@@ -993 +987 @@
 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:
@@ -1028 +1022 @@
 [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
@@ -1074 +1068 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=495 height=235
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
 
 <p class=MsoNormal>There are two significant warnings concerning <span
@@ -1353 +1347 @@
   o:title="" chromakey="white"/>
 </v:shape><![endif]--><![if !vml]><img width=26 height=19
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.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.
@@ -1382 +1376 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=449 height=500
-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>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.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
@@ -1400 +1394 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=700 height=300
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image021.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.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
@@ -1435 +1429 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=400 height=485
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
 
 <p class=MsoNormal>It specifies the expected geometry around each C-atom for
@@ -1446 +1440 @@
 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'>Refine</span></b> column heading and select <b
+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'>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 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 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
@@ -1472 +1466 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=449 height=500
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
 style='mso-spacerun:yes'> </span></p>
 
@@ -1489 +1483 @@
 you’ll see the Operators 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>) and the General tab will be
-redrawn. Next select the <b style='mso-bidi-font-weight:normal'><span
+mso-hansi-theme-font:minor-latin'>Ok</span></b>) and the General tab will be redrawn.
+Next select 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'>Atoms</span></b> tab; 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'>Atoms</span></b> tab; do <b style='mso-bidi-font-weight:
+mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b> to put them in
+their best positions.<span style='mso-spacerun:yes'>  </span>Next select all
+the atoms by double clicking the empty box in upper left corner of the table;
+all atoms will be highlighted &amp; plotted green. 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'>Edit/Update H atoms</span></b> to
-put them in their best positions.<span style='mso-spacerun:yes'>  </span>Next
-select all the atoms by double clicking the empty box in upper left corner of
-the table; all atoms will be highlighted &amp; plotted green. 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'>Edit/Transform
-atoms</span></b>; a popup will appear.</p>
+minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>;
+a popup will appear.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
@@ -1508 +1502 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=360 height=351
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
 
 <p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span
@@ -1535 +1529 @@
   o:title=""/>
 </v:shape><![endif]--><![if !vml]><img width=449 height=500
-src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
+src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.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>

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