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Jul 28, 2016 2:18:10 PM (5 years ago)
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vondreele
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Tutorials/MerohedralTwins
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  • Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm

    r2294 r2390  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>2</o:Revision>
    28   <o:TotalTime>0</o:TotalTime>
     27  <o:Revision>3</o:Revision>
     28  <o:TotalTime>2</o:TotalTime>
    2929  <o:Created>2016-05-26T15:52:00Z</o:Created>
    30   <o:LastSaved>2016-05-26T15:52:00Z</o:LastSaved>
     30  <o:LastSaved>2016-07-28T18:45:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    32   <o:Words>3321</o:Words>
    33   <o:Characters>18934</o:Characters>
     32  <o:Words>3323</o:Words>
     33  <o:Characters>18947</o:Characters>
    3434  <o:Lines>157</o:Lines>
    3535  <o:Paragraphs>44</o:Paragraphs>
    36   <o:CharactersWithSpaces>22211</o:CharactersWithSpaces>
     36  <o:CharactersWithSpaces>22226</o:CharactersWithSpaces>
    3737  <o:Version>16.00</o:Version>
    3838 </o:DocumentProperties>
     
    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 twinning.
    814 There is a general discussion of twinning in International Tables for
     813structure of a few single crystal structures where there is merohedral
     814twinning. There 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;
     
    892892
    893893<p class=MsoNormal>This example was taken from Luo, et al., Dalton Trans.
    894 4491(2006). The structure is given in the file <b><span style='font-family:
    895 "Calibri",sans-serif'>/exercises/<span class=SpellE>MerohedralTwins</span>/1b.cif</span></b>
    896 and the data are in <b><span style='font-family:"Calibri",sans-serif'>/exercises/<span
    897 class=SpellE>MerohedralTwins</span>/1b.fcf</span></b>. This example is <span
    898 class=SpellE>noncentrosymmetric</span> and the data was collected with
     8944491(2006). The structure is given in the file <span class=SpellE><b><span
     895style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span
     896style='font-family:"Calibri",sans-serif'>/data/1b.cif</span></b> and the data
     897are in <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span
     898style='font-family:"Calibri",sans-serif'>/data/1b.fcf</span></b>. This example
     899is <span class=SpellE>noncentrosymmetric</span> and the data was collected with
    899900radiation (<span class=SpellE>MoK</span>&#945;) that gives significant resonant
    900901scattering from the Ga atoms. </p>
     
    918919and you will see the General page for this phase</p>
    919920
    920 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=650 height=500
     921<p class=MsoNormal><span style='mso-no-proof:yes'><img width=403 height=310
    921922id="_x0000_i1056"
    922923src="Merohedral%20twin%20refinement%20in%20GSAS_files/image007.png"></span></p>
     
    924925<p class=MsoNormal>Next do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
    925926Factor/from CIF file</span></b> (that is the format of a “<span class=SpellE>fcf</span>”
    926 file); a file selection dialog box will appear with the previously selected directory
    927 chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>;
     927file); a file selection dialog box will appear with the previously selected
     928directory chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>;
    928929a popup window will appear</p>
    929930
     
    992993parameter</span></b> for refinement and do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
    993994from the main GSAS-II data tree menu. The structure will quickly refine to give
    994 <span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable
    995 improvement on Scale factor alone. The Flack parameter is now 0.452, meaning
    996 that both hands somehow exist in the structure. This can happen if the crystal
    997 is <span class=SpellE>merohedrally</span> inversion twinned.</p>
     995<span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable improvement
     996on Scale factor alone. The Flack parameter is now 0.452, meaning that both
     997hands somehow exist in the structure. This can happen if the crystal is <span
     998class=SpellE>merohedrally</span> inversion twinned.</p>
    998999
    9991000<p class=MsoNormal>To introduce this twin, press the <b><span style='font-family:
     
    10271028[NC<sub>7</sub>H<sub>8</sub>]<sup>+</sup><o:p></o:p></span></h2>
    10281029
    1029 <p class=MsoNormal>In this case the data collection Laue statistics (very
    1030 nearly <span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m)
     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)
    10311032and systematic extinctions indicated that the space group was either one of the
    10321033<span class=SpellE>enantiomorphic</span> pair P3<sub>1</sub>21 or P3<sub>2</sub>21
     
    10731074  o:title=""/>
    10741075</v:shape><![endif]--><![if !vml]><img width=495 height=235
    1075 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
     1076src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
    10761077
    10771078<p class=MsoNormal>There are two significant warnings concerning <span
     
    11781179width=9 height=19 id="_x0000_i1039"
    11791180src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1
    1180 Laue data symmetries that there is twinning so don’t bother trying to make it better
    1181 by refining the structure. To determine the possible twin law we refer to Table
    1182 1.3.4.2 of the International Tables for Crystallography Vol C. and see that
    1183 indeed Laue <span style='position:relative;top:3pt'><span style='mso-no-proof:
    1184 yes'><img width=9 height=19 id="_x0000_i1038"
     1181Laue data symmetries that there is twinning so don’t bother trying to make it
     1182better by refining the structure. To determine the possible twin law we refer
     1183to Table 1.3.4.2 of the International Tables for Crystallography Vol C. and see
     1184that indeed Laue <span style='position:relative;top:3pt'><span
     1185style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1038"
    11851186src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1
    11861187as P3<sub>2</sub>21 can be simulated by twinned Laue <span style='position:
     
    12831284
    12841285<p class=MsoNormal>Before beginning the refinement, it usually the practice to
    1285 eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub>
    1286 &lt; 2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span
     1286eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub> &lt;
     12872<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span
    12871288style='font-family:"Calibri",sans-serif'>Controls</span></b> entry from the
    12881289GSAS-II data tree.</p>
     
    13161317that indeed Laue 6/mmm as P6<sub>1</sub>22 can be simulated by twinned Laue 6/m
    13171318crystals in P6<sub>1</sub>; the possible operator is shown in Table 1.3.4.1
    1318 (reproduced above) as either a mirror or a 2-fold. The detailed symbolism in
    1319 the table (‘m.., ..2/.2.’) indicates (perhaps obscurely) the operator
    1320 specifics; they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr
     1319(reproduced above) as either a mirror or a 2-fold. The detailed symbolism in the
     1320table (‘m.., ..2/.2.’) indicates (perhaps obscurely) the operator specifics;
     1321they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr
    13211322    m:val="&#773;"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family:
    13221323   "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic;
     
    13331334EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    13341335 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'>
    1335  <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.png"
     1336 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image004.png"
    13361337  o:title="" chromakey="white"/>
    13371338</v:shape><![endif]--><![if !vml]><img width=26 height=19
    1338 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;or
     1339src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;or
    133913402 as <!--[if gte msEquation 12]><m:oMath><i style='mso-bidi-font-style:normal'><span
    13401341 style='font-family:"Cambria Math",serif'><span style='position:relative;
     
    13491350EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    13501351 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'>
    1351  <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.png"
     1352 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.png"
    13521353  o:title="" chromakey="white"/>
    13531354</v:shape><![endif]--><![if !vml]><img width=26 height=19
    1354 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     1355src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    13551356style='font-family:"Cambria Math",serif'>; we will use the 2-fold, m and
    13561357inversion operators to fully test for presence of the 4 possible twin laws.
     
    13811382  o:title=""/>
    13821383</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1383 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
    1384 
    1385 <p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is
    1386 nonphysical and the 1<sup>st</sup> twin fraction is small. It is likely that
    1387 the true space group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
     1384src="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
     1387and the 1<sup>st</sup> twin fraction is small. It is likely that the true space
     1388group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
    13881389twinned (twin fractions 2 &amp; 4). We can improve it by refining the atom
    13891390positions and thermal parameters, but first we need to replace the hydrogen
     
    13991400  o:title=""/>
    14001401</v:shape><![endif]--><![if !vml]><img width=700 height=300
    1401 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
     1402src="Merohedral%20twin%20refinement%20in%20GSAS_files/image021.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
    14021403
    14031404<p class=MsoNormal>If you scroll down the page, you’ll see H-atoms with default
     
    14341435  o:title=""/>
    14351436</v:shape><![endif]--><![if !vml]><img width=400 height=485
    1436 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
    1437 
    1438 <p class=MsoNormal>It specifies the expected geometry around each C-atom for H-atom
    1439 placement. As expected we want 3 H-atoms on the terminal CH<sub>3</sub> groups
    1440 on the <span class=SpellE>Cp</span>* ring and one for each C-atom for the NC<sub>5</sub>H<sub>5</sub>
    1441 molecule. Press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1442 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1443 minor-latin'>Ok</span></b>; you will see the H-atoms added in turn to the
    1444 structure and they will be inserted immediately after their respective C-atom.
    1445 Their positions and thermal parameters are tied to the C-atoms so that after
    1446 refinement of the structure they can be shifted to the <span class=SpellE>stereochemically</span>
    1447 best positions. For the refinement, double click the <b style='mso-bidi-font-weight:
     1437src="Merohedral%20twin%20refinement%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
     1438
     1439<p class=MsoNormal>It specifies the expected geometry around each C-atom for
     1440H-atom placement. As expected we want 3 H-atoms on the terminal CH<sub>3</sub>
     1441groups on the <span class=SpellE>Cp</span>* ring and one for each C-atom for
     1442the NC<sub>5</sub>H<sub>5</sub> molecule. Press <b style='mso-bidi-font-weight:
    14481443normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1449 minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading
    1450 and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1451 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1452 minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1444minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; you will see the
     1445H-atoms added in turn to the structure and they will be inserted immediately
     1446after their respective C-atom. Their positions and thermal parameters are tied
     1447to the C-atoms so that after refinement of the structure they can be shifted to
     1448the <span class=SpellE>stereochemically</span> best positions. For the
     1449refinement, double click the <b style='mso-bidi-font-weight:normal'><span
    14531450style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1454 mso-hansi-theme-font:minor-latin'>U</span></b> from the popup; press <b
     1451mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading and select <b
    14551452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1456 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1457 The Atom table will be redrawn with XU in every entry under Refine. Now do <b
    1458 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1459 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1460 from the main GSASII data tree window; the <span class=SpellE>Rw</span> will
    1461 drop to ~1.92%. If you look at the <b style='mso-bidi-font-weight:normal'><span
     1453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
     1454and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1455mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
     1456from the popup; press <b style='mso-bidi-font-weight:normal'><span
     1457style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1458mso-hansi-theme-font:minor-latin'>OK</span></b>. The Atom table will be redrawn
     1459with XU in every entry under Refine. Now do <b style='mso-bidi-font-weight:
     1460normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1461minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
     1462the main GSASII data tree window; the <span class=SpellE>Rw</span> will drop to
     1463~1.92%. If you look at the <b style='mso-bidi-font-weight:normal'><span
    14621464style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14631465mso-hansi-theme-font:minor-latin'>Data</span></b> tab the Twin element
     
    14701472  o:title=""/>
    14711473</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1472 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
     1474src="Merohedral%20twin%20refinement%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
    14731475style='mso-spacerun:yes'> </span></p>
    14741476
     
    15061508  o:title=""/>
    15071509</v:shape><![endif]--><![if !vml]><img width=360 height=351
    1508 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
     1510src="Merohedral%20twin%20refinement%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
    15091511
    15101512<p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span
    15111513style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1512 mso-hansi-theme-font:minor-latin'>Choose inversion</span></b> box and (important)
    1513 set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1514 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Choose unit
    1515 cell</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1516 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1517 mso-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put the inverted
    1518 structure back inside the unit cell. Press <b style='mso-bidi-font-weight:normal'><span
    1519 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1520 mso-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot will both
    1521 be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span
     1514mso-hansi-theme-font:minor-latin'>Choose inversion</span></b> box and
     1515(important) set <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1516"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1517minor-latin'>Choose unit cell</span></b> to <b style='mso-bidi-font-weight:
     1518normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1519minor-latin;mso-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put
     1520the inverted structure back inside the unit cell. Press <b style='mso-bidi-font-weight:
     1521normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1522minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot
     1523will both be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span
    15221524style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15231525mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
     
    15331535  o:title=""/>
    15341536</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1535 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
     1537src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
    15361538
    15371539<p class=MsoNormal>Now the identity Twin Law is ~2/3 and the 2-fold Twin Law is
    15381540the other ~1/3 while the other two are ~zero. You can delete them and repeat
    1539 the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the
    1540 merohedral twin exercises. You can save this project if desired.</p>
     1541the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the merohedral
     1542twin exercises. You can save this project if desired.</p>
    15411543
    15421544<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15431545
    1544 </span></span></span></span></span></span></span></span></span></span></span></div>
    1545 
     1546</span></div>
     1547
     1548</span></span></span></span></span></span></span></span></span></span>
    15461549</body>
    15471550
  • Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS_files/filelist.xml

    r2292 r2390  
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