Changeset 2394 for Tutorials/MerohedralTwins
- Timestamp:
- Jul 28, 2016 2:27:34 PM (7 years ago)
- Location:
- Tutorials/MerohedralTwins
- Files:
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- 9 edited
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Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm
r2390 r2394 25 25 <o:Author>Von Dreele</o:Author> 26 26 <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> 29 29 <o:Created>2016-05-26T15:52:00Z</o:Created> 30 <o:LastSaved>2016-07-28T1 8:45:00Z</o:LastSaved>30 <o:LastSaved>2016-07-28T19:27:00Z</o:LastSaved> 31 31 <o:Pages>1</o:Pages> 32 <o:Words>33 23</o:Words>33 <o:Characters>18 947</o:Characters>34 <o:Lines>15 7</o:Lines>32 <o:Words>3302</o:Words> 33 <o:Characters>18828</o:Characters> 34 <o:Lines>156</o:Lines> 35 35 <o:Paragraphs>44</o:Paragraphs> 36 <o:CharactersWithSpaces>22 226</o:CharactersWithSpaces>36 <o:CharactersWithSpaces>22086</o:CharactersWithSpaces> 37 37 <o:Version>16.00</o:Version> 38 38 </o:DocumentProperties> … … 811 811 812 812 <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 for813 structure of a few single crystal structures where there is merohedral twinning. 814 There is a general discussion of twinning in International Tables for 815 815 Crystallography (2006), Vol. C, Chapter 1.3, pp 10-14. Merohedral twinning 816 816 occurs 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_i105 8"817 top:3pt'><span style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1057" 818 818 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image015.png"></span>) 819 819 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 911 911 popup 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>, 912 a new popup will appear; Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>, 919 913 and you will see the General page for this phase</p> 920 914 … … 993 987 parameter</span></b> for refinement and do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> 994 988 from 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 improvement996 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 990 improvement on Scale factor alone. The Flack parameter is now 0.452, meaning 991 that both hands somehow exist in the structure. This can happen if the crystal 992 is <span class=SpellE>merohedrally</span> inversion twinned.</p> 999 993 1000 994 <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> 1029 1023 1030 <p class=MsoNormal>In this case the data collection Laue statistics (very nearly1031 <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 1025 nearly <span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m) 1032 1026 and systematic extinctions indicated that the space group was either one of the 1033 1027 <span class=SpellE>enantiomorphic</span> pair P3<sub>1</sub>21 or P3<sub>2</sub>21 … … 1074 1068 o:title=""/> 1075 1069 </v:shape><![endif]--><![if !vml]><img width=495 height=235 1076 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image00 3.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>1070 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_39"><![endif]></span></p> 1077 1071 1078 1072 <p class=MsoNormal>There are two significant warnings concerning <span … … 1353 1347 o:title="" chromakey="white"/> 1354 1348 </v:shape><![endif]--><![if !vml]><img width=26 height=19 1355 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 19.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span1349 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span 1356 1350 style='font-family:"Cambria Math",serif'>; we will use the 2-fold, m and 1357 1351 inversion operators to fully test for presence of the 4 possible twin laws. … … 1382 1376 o:title=""/> 1383 1377 </v:shape><![endif]--><![if !vml]><img width=449 height=500 1384 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 20.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 nonphysical1387 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>1378 src="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 1381 nonphysical and the 1<sup>st</sup> twin fraction is small. It is likely that 1382 the true space group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span> 1389 1383 twinned (twin fractions 2 & 4). We can improve it by refining the atom 1390 1384 positions and thermal parameters, but first we need to replace the hydrogen … … 1400 1394 o:title=""/> 1401 1395 </v:shape><![endif]--><![if !vml]><img width=700 height=300 1402 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 21.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>1396 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_41"><![endif]></span></p> 1403 1397 1404 1398 <p class=MsoNormal>If you scroll down the page, youll see H-atoms with default … … 1435 1429 o:title=""/> 1436 1430 </v:shape><![endif]--><![if !vml]><img width=400 height=485 1437 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 22.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>1431 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_42"><![endif]></span></p> 1438 1432 1439 1433 <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 1447 1441 to 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 1442 the <span class=SpellE>stereochemically</span> best positions. For the refinement, 1443 double 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: 1445 minor-latin'>Refine</span></b> column heading and select <b style='mso-bidi-font-weight: 1446 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1447 minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> and <b 1452 1448 style='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;1455 1449 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> 1456 1450 from the popup; press <b style='mso-bidi-font-weight:normal'><span … … 1472 1466 o:title=""/> 1473 1467 </v:shape><![endif]--><![if !vml]><img width=449 height=500 1474 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 23.gif" v:shapes="Picture_x0020_43"><![endif]></span><span1468 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_43"><![endif]></span><span 1475 1469 style='mso-spacerun:yes'> </span></p> 1476 1470 … … 1489 1483 youll see the Operators popup (press <b style='mso-bidi-font-weight:normal'><span 1490 1484 style='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 1485 mso-hansi-theme-font:minor-latin'>Ok</span></b>) and the General tab will be redrawn. 1486 Next 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: 1488 minor-latin'>Atoms</span></b> tab; do <b style='mso-bidi-font-weight:normal'><span 1493 1489 style='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: 1490 mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b> to put them in 1491 their best positions.<span style='mso-spacerun:yes'> </span>Next select all 1492 the atoms by double clicking the empty box in upper left corner of the table; 1493 all atoms will be highlighted & plotted green. Do <b style='mso-bidi-font-weight: 1495 1494 normal'><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 & 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> 1495 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Transform atoms</span></b>; 1496 a popup will appear.</p> 1503 1497 1504 1498 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1508 1502 o:title=""/> 1509 1503 </v:shape><![endif]--><![if !vml]><img width=360 height=351 1510 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 24.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>1504 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_44"><![endif]></span></p> 1511 1505 1512 1506 <p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span … … 1535 1529 o:title=""/> 1536 1530 </v:shape><![endif]--><![if !vml]><img width=449 height=500 1537 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 26.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>1531 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="Picture_x0020_46"><![endif]></span></p> 1538 1532 1539 1533 <p class=MsoNormal>Now the identity Twin Law is ~2/3 and the 2-fold Twin Law is 1540 1534 the 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 merohedral1542 twin exercises. You can save this project if desired.</p>1535 the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the 1536 merohedral twin exercises. You can save this project if desired.</p> 1543 1537 1544 1538 <p class=MsoNormal><o:p> </o:p></p> -
Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS_files/filelist.xml
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