Changeset 2394


Ignore:
Timestamp:
Jul 28, 2016 2:27:34 PM (5 years ago)
Author:
vondreele
Message:
 
Location:
Tutorials/MerohedralTwins
Files:
9 edited

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  • Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm

    r2390 r2394  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>3</o:Revision>
    28   <o:TotalTime>2</o:TotalTime>
     27  <o:Revision>4</o:Revision>
     28  <o:TotalTime>3</o:TotalTime>
    2929  <o:Created>2016-05-26T15:52:00Z</o:Created>
    30   <o:LastSaved>2016-07-28T18:45:00Z</o:LastSaved>
     30  <o:LastSaved>2016-07-28T19:27:00Z</o:LastSaved>
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    811811
    812812<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
    813 structure of a few single crystal structures where there is merohedral
    814 twinning. There is a general discussion of twinning in International Tables for
     813structure of a few single crystal structures where there is merohedral twinning.
     814There is a general discussion of twinning in International Tables for
    815815Crystallography (2006), Vol. C, Chapter 1.3, pp 10-14. Merohedral twinning
    816816occurs when the twin operation (2, m or <span style='position:relative;
    817 top:3pt'><span style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1058"
     817top:3pt'><span style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1057"
    818818src="Merohedral%20twin%20refinement%20in%20GSAS_files/image015.png"></span>)
    819819belongs to the point group of the vector lattice but not of the crystal
     
    910910style='font-family:"Calibri",sans-serif'>1b.cif</span></b>) and select it. A
    911911popup window will appear. Press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>;
    912 a new popup will appear</p>
    913 
    914 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=336 height=137
    915 id="_x0000_i1057"
    916 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.png"></span></p>
    917 
    918 <p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>,
     912a new popup will appear; Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>,
    919913and you will see the General page for this phase</p>
    920914
     
    993987parameter</span></b> for refinement and do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
    994988from the main GSAS-II data tree menu. The structure will quickly refine to give
    995 <span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable improvement
    996 on Scale factor alone. The Flack parameter is now 0.452, meaning that both
    997 hands somehow exist in the structure. This can happen if the crystal is <span
    998 class=SpellE>merohedrally</span> inversion twinned.</p>
     989<span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable
     990improvement on Scale factor alone. The Flack parameter is now 0.452, meaning
     991that both hands somehow exist in the structure. This can happen if the crystal
     992is <span class=SpellE>merohedrally</span> inversion twinned.</p>
    999993
    1000994<p class=MsoNormal>To introduce this twin, press the <b><span style='font-family:
     
    10281022[NC<sub>7</sub>H<sub>8</sub>]<sup>+</sup><o:p></o:p></span></h2>
    10291023
    1030 <p class=MsoNormal>In this case the data collection Laue statistics (very nearly
    1031 <span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m)
     1024<p class=MsoNormal>In this case the data collection Laue statistics (very
     1025nearly <span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m)
    10321026and systematic extinctions indicated that the space group was either one of the
    10331027<span class=SpellE>enantiomorphic</span> pair P3<sub>1</sub>21 or P3<sub>2</sub>21
     
    10741068  o:title=""/>
    10751069</v:shape><![endif]--><![if !vml]><img width=495 height=235
    1076 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
     1070src="Merohedral%20twin%20refinement%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
    10771071
    10781072<p class=MsoNormal>There are two significant warnings concerning <span
     
    13531347  o:title="" chromakey="white"/>
    13541348</v:shape><![endif]--><![if !vml]><img width=26 height=19
    1355 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     1349src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    13561350style='font-family:"Cambria Math",serif'>; we will use the 2-fold, m and
    13571351inversion operators to fully test for presence of the 4 possible twin laws.
     
    13821376  o:title=""/>
    13831377</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1384 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
    1385 
    1386 <p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is nonphysical
    1387 and the 1<sup>st</sup> twin fraction is small. It is likely that the true space
    1388 group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
     1378src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
     1379
     1380<p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is
     1381nonphysical and the 1<sup>st</sup> twin fraction is small. It is likely that
     1382the true space group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
    13891383twinned (twin fractions 2 &amp; 4). We can improve it by refining the atom
    13901384positions and thermal parameters, but first we need to replace the hydrogen
     
    14001394  o:title=""/>
    14011395</v:shape><![endif]--><![if !vml]><img width=700 height=300
    1402 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image021.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
     1396src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
    14031397
    14041398<p class=MsoNormal>If you scroll down the page, you’ll see H-atoms with default
     
    14351429  o:title=""/>
    14361430</v:shape><![endif]--><![if !vml]><img width=400 height=485
    1437 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
     1431src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
    14381432
    14391433<p class=MsoNormal>It specifies the expected geometry around each C-atom for
     
    14461440after their respective C-atom. Their positions and thermal parameters are tied
    14471441to the C-atoms so that after refinement of the structure they can be shifted to
    1448 the <span class=SpellE>stereochemically</span> best positions. For the
    1449 refinement, double click the <b style='mso-bidi-font-weight:normal'><span
    1450 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1451 mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading and select <b
     1442the <span class=SpellE>stereochemically</span> best positions. For the refinement,
     1443double click the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1444"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1445minor-latin'>Refine</span></b> column heading and select <b style='mso-bidi-font-weight:
     1446normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1447minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> and <b
    14521448style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1453 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    1454 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14551449mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
    14561450from the popup; press <b style='mso-bidi-font-weight:normal'><span
     
    14721466  o:title=""/>
    14731467</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1474 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
     1468src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
    14751469style='mso-spacerun:yes'> </span></p>
    14761470
     
    14891483you’ll see the Operators popup (press <b style='mso-bidi-font-weight:normal'><span
    14901484style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1491 mso-hansi-theme-font:minor-latin'>Ok</span></b>) and the General tab will be
    1492 redrawn. Next select the <b style='mso-bidi-font-weight:normal'><span
     1485mso-hansi-theme-font:minor-latin'>Ok</span></b>) and the General tab will be redrawn.
     1486Next select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1487"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1488minor-latin'>Atoms</span></b> tab; do <b style='mso-bidi-font-weight:normal'><span
    14931489style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1494 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab; do <b style='mso-bidi-font-weight:
     1490mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b> to put them in
     1491their best positions.<span style='mso-spacerun:yes'>  </span>Next select all
     1492the atoms by double clicking the empty box in upper left corner of the table;
     1493all atoms will be highlighted &amp; plotted green. Do <b style='mso-bidi-font-weight:
    14951494normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1496 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b> to
    1497 put them in their best positions.<span style='mso-spacerun:yes'>  </span>Next
    1498 select all the atoms by double clicking the empty box in upper left corner of
    1499 the table; all atoms will be highlighted &amp; plotted green. Do <b
    1500 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1501 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Transform
    1502 atoms</span></b>; a popup will appear.</p>
     1495minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>;
     1496a popup will appear.</p>
    15031497
    15041498<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15081502  o:title=""/>
    15091503</v:shape><![endif]--><![if !vml]><img width=360 height=351
    1510 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
     1504src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
    15111505
    15121506<p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span
     
    15351529  o:title=""/>
    15361530</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1537 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
     1531src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
    15381532
    15391533<p class=MsoNormal>Now the identity Twin Law is ~2/3 and the 2-fold Twin Law is
    15401534the other ~1/3 while the other two are ~zero. You can delete them and repeat
    1541 the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the merohedral
    1542 twin exercises. You can save this project if desired.</p>
     1535the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the
     1536merohedral twin exercises. You can save this project if desired.</p>
    15431537
    15441538<p class=MsoNormal><o:p>&nbsp;</o:p></p>
  • Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS_files/filelist.xml

    r2390 r2394  
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