Changeset 2390 for Tutorials/MerohedralTwins
- Timestamp:
- Jul 28, 2016 2:18:10 PM (7 years ago)
- Location:
- Tutorials/MerohedralTwins
- Files:
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- 10 edited
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Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm
r2294 r2390 25 25 <o:Author>Von Dreele</o:Author> 26 26 <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> 29 29 <o:Created>2016-05-26T15:52:00Z</o:Created> 30 <o:LastSaved>2016-0 5-26T15:52:00Z</o:LastSaved>30 <o:LastSaved>2016-07-28T18:45:00Z</o:LastSaved> 31 31 <o:Pages>1</o:Pages> 32 <o:Words>332 1</o:Words>33 <o:Characters>189 34</o:Characters>32 <o:Words>3323</o:Words> 33 <o:Characters>18947</o:Characters> 34 34 <o:Lines>157</o:Lines> 35 35 <o:Paragraphs>44</o:Paragraphs> 36 <o:CharactersWithSpaces>222 11</o:CharactersWithSpaces>36 <o:CharactersWithSpaces>22226</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 twinning.814 There is a general discussion of twinning in International Tables for813 structure of a few single crystal structures where there is merohedral 814 twinning. 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; … … 892 892 893 893 <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 894 4491(2006). The structure is given in the file <span class=SpellE><b><span 895 style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span 896 style='font-family:"Calibri",sans-serif'>/data/1b.cif</span></b> and the data 897 are in <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span 898 style='font-family:"Calibri",sans-serif'>/data/1b.fcf</span></b>. This example 899 is <span class=SpellE>noncentrosymmetric</span> and the data was collected with 899 900 radiation (<span class=SpellE>MoK</span>α) that gives significant resonant 900 901 scattering from the Ga atoms. </p> … … 918 919 and you will see the General page for this phase</p> 919 920 920 <p class=MsoNormal><span style='mso-no-proof:yes'><img width= 650 height=500921 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=403 height=310 921 922 id="_x0000_i1056" 922 923 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 925 926 Factor/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 directory927 chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>;927 file); a file selection dialog box will appear with the previously selected 928 directory chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>; 928 929 a popup window will appear</p> 929 930 … … 992 993 parameter</span></b> for refinement and do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> 993 994 from 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 <spanclass=SpellE>merohedrally</span> inversion twinned.</p>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> 998 999 999 1000 <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> 1028 1029 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) 1031 1032 and systematic extinctions indicated that the space group was either one of the 1032 1033 <span class=SpellE>enantiomorphic</span> pair P3<sub>1</sub>21 or P3<sub>2</sub>21 … … 1073 1074 o:title=""/> 1074 1075 </v:shape><![endif]--><![if !vml]><img width=495 height=235 1075 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image00 2.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>1076 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.gif" v:shapes="Picture_x0020_39"><![endif]></span></p> 1076 1077 1077 1078 <p class=MsoNormal>There are two significant warnings concerning <span … … 1178 1179 width=9 height=19 id="_x0000_i1039" 1179 1180 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1 1180 Laue data symmetries that there is twinning so dont bother trying to make it better1181 b y refining the structure. To determine the possible twin law we refer to Table1182 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"1181 Laue data symmetries that there is twinning so dont bother trying to make it 1182 better by refining the structure. To determine the possible twin law we refer 1183 to Table 1.3.4.2 of the International Tables for Crystallography Vol C. and see 1184 that indeed Laue <span style='position:relative;top:3pt'><span 1185 style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1038" 1185 1186 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1 1186 1187 as P3<sub>2</sub>21 can be simulated by twinned Laue <span style='position: … … 1283 1284 1284 1285 <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 <2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span1286 eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub> < 1287 2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span 1287 1288 style='font-family:"Calibri",sans-serif'>Controls</span></b> entry from the 1288 1289 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 1317 1318 crystals 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 t he table (m.., ..2/.2.) indicates (perhaps obscurely) the operator1320 specifics;they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr1319 (reproduced above) as either a mirror or a 2-fold. The detailed symbolism in the 1320 table (m.., ..2/.2.) indicates (perhaps obscurely) the operator specifics; 1321 they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr 1321 1322 m:val="̅"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family: 1322 1323 "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" 1334 1335 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'> 1335 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image00 3.png"1336 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image004.png" 1336 1337 o:title="" chromakey="white"/> 1337 1338 </v:shape><![endif]--><![if !vml]><img width=26 height=19 1338 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image00 4.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]> or1339 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]> or 1339 1340 2 as <!--[if gte msEquation 12]><m:oMath><i style='mso-bidi-font-style:normal'><span 1340 1341 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" 1350 1351 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'> 1351 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image00 5.png"1352 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.png" 1352 1353 o:title="" chromakey="white"/> 1353 1354 </v:shape><![endif]--><![if !vml]><img width=26 height=19 1354 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 06.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span1355 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span 1355 1356 style='font-family:"Cambria Math",serif'>; we will use the 2-fold, m and 1356 1357 inversion operators to fully test for presence of the 4 possible twin laws. … … 1381 1382 o:title=""/> 1382 1383 </v:shape><![endif]--><![if !vml]><img width=449 height=500 1383 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 08.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 spacegroup is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>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> 1388 1389 twinned (twin fractions 2 & 4). We can improve it by refining the atom 1389 1390 positions and thermal parameters, but first we need to replace the hydrogen … … 1399 1400 o:title=""/> 1400 1401 </v:shape><![endif]--><![if !vml]><img width=700 height=300 1401 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 10.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>1402 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image021.gif" v:shapes="Picture_x0020_41"><![endif]></span></p> 1402 1403 1403 1404 <p class=MsoNormal>If you scroll down the page, youll see H-atoms with default … … 1434 1435 o:title=""/> 1435 1436 </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: 1437 src="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 1440 H-atom placement. As expected we want 3 H-atoms on the terminal CH<sub>3</sub> 1441 groups on the <span class=SpellE>Cp</span>* ring and one for each C-atom for 1442 the NC<sub>5</sub>H<sub>5</sub> molecule. Press <b style='mso-bidi-font-weight: 1448 1443 normal'><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 1444 minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; you will see the 1445 H-atoms added in turn to the structure and they will be inserted immediately 1446 after their respective C-atom. Their positions and thermal parameters are tied 1447 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 1453 1450 style='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<b1451 mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading and select <b 1455 1452 style='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 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 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> 1456 from the popup; press <b style='mso-bidi-font-weight:normal'><span 1457 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1458 mso-hansi-theme-font:minor-latin'>OK</span></b>. The Atom table will be redrawn 1459 with XU in every entry under Refine. Now do <b style='mso-bidi-font-weight: 1460 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1461 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from 1462 the 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 1462 1464 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1463 1465 mso-hansi-theme-font:minor-latin'>Data</span></b> tab the Twin element … … 1470 1472 o:title=""/> 1471 1473 </v:shape><![endif]--><![if !vml]><img width=449 height=500 1472 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 14.gif" v:shapes="Picture_x0020_43"><![endif]></span><span1474 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_43"><![endif]></span><span 1473 1475 style='mso-spacerun:yes'> </span></p> 1474 1476 … … 1506 1508 o:title=""/> 1507 1509 </v:shape><![endif]--><![if !vml]><img width=360 height=351 1508 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 16.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>1510 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_44"><![endif]></span></p> 1509 1511 1510 1512 <p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span 1511 1513 style='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 m so-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put the inverted1518 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 m so-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot will both1521 be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span1514 mso-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: 1517 minor-latin'>Choose unit cell</span></b> to <b style='mso-bidi-font-weight: 1518 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1519 minor-latin;mso-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put 1520 the inverted structure back inside the unit cell. Press <b style='mso-bidi-font-weight: 1521 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1522 minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot 1523 will both be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span 1522 1524 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1523 1525 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span … … 1533 1535 o:title=""/> 1534 1536 </v:shape><![endif]--><![if !vml]><img width=449 height=500 1535 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image0 18.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>1537 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_46"><![endif]></span></p> 1536 1538 1537 1539 <p class=MsoNormal>Now the identity Twin Law is ~2/3 and the 2-fold Twin Law is 1538 1540 the 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 merohedraltwin exercises. You can save this project if desired.</p>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> 1541 1543 1542 1544 <p class=MsoNormal><o:p> </o:p></p> 1543 1545 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> 1546 1549 </body> 1547 1550 -
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