Changeset 1435 for trunk/help/Charge Flipping in GSAS.htm
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TabularUnified trunk/help/Charge Flipping in GSAS.htm ¶
r1434 r1435 23 23 <o:Author>vondreele</o:Author> 24 24 <o:LastAuthor>Von Dreele</o:LastAuthor> 25 <o:Revision> 2</o:Revision>26 <o:TotalTime>1 </o:TotalTime>25 <o:Revision>4</o:Revision> 26 <o:TotalTime>14</o:TotalTime> 27 27 <o:Created>2014-07-21T14:56:00Z</o:Created> 28 <o:LastSaved>2014-07-2 1T14:56:00Z</o:LastSaved>28 <o:LastSaved>2014-07-23T17:41:00Z</o:LastSaved> 29 29 <o:Pages>10</o:Pages> 30 <o:Words>22 23</o:Words>31 <o:Characters>12 672</o:Characters>30 <o:Words>2239</o:Words> 31 <o:Characters>12763</o:Characters> 32 32 <o:Company>Argonne National Laboratory</o:Company> 33 <o:Lines>10 5</o:Lines>33 <o:Lines>106</o:Lines> 34 34 <o:Paragraphs>29</o:Paragraphs> 35 <o:CharactersWithSpaces>14 866</o:CharactersWithSpaces>35 <o:CharactersWithSpaces>14973</o:CharactersWithSpaces> 36 36 <o:Version>14.00</o:Version> 37 37 </o:DocumentProperties> … … 45 45 <w:WordDocument> 46 46 <w:Zoom>156</w:Zoom> 47 <w:SpellingState>Clean</w:SpellingState> 48 <w:GrammarState>Clean</w:GrammarState> 47 49 <w:TrackMoves>false</w:TrackMoves> 48 50 <w:TrackFormatting/> … … 786 788 mso-fareast-theme-font:minor-fareast; 787 789 mso-bidi-font-family:Calibri;} 790 span.SpellE 791 {mso-style-name:""; 792 mso-spl-e:yes;} 793 span.GramE 794 {mso-style-name:""; 795 mso-gram-e:yes;} 788 796 .MsoChpDefault 789 797 {mso-style-type:export-only; … … 1226 1234 1227 1235 <h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in 1228 GSAS-II - jadarite<o:p></o:p></span></h1>1236 GSAS-II - <span class=SpellE>jadarite</span><o:p></o:p></span></h1> 1229 1237 1230 1238 <h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1> 1231 1239 1232 1240 <p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure 1233 of jadarite (aka kryptonite) from powder diffraction data via charge flipping.1234 This structure was originally solved by Pam Whitfield from laboratory powder 1235 data in the space group P2<sub>1</sub>/c. </p>1241 of <span class=SpellE>jadarite</span> (aka kryptonite) from powder 1242 diffraction data via charge flipping. This structure was originally solved by 1243 Pam Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p> 1236 1244 1237 1245 <p class=MsoNormal>If you have not done so already, <a 1238 1246 href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file 1239 (I called it jadarite.gpx) you saved from the second part of the <a1240 href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing exercise</a>. 1241 If you didnt do that exercise, do it now.</p>1242 1243 <h2> Step 1.Setup for Pawley refinement</h2>1247 (I called it <span class=SpellE>jadarite.gpx</span>) you saved from the second 1248 part of the <a href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing 1249 exercise</a>. If you didnt do that exercise, do it now.</p> 1250 1251 <h2><span class=GramE>Step 1.</span> Setup for Pawley refinement</h2> 1244 1252 1245 1253 <p class=MsoNormal>There are a number of steps that must be done in preparation … … 1261 1269 set of ~1Å resolution as needed for charge flipping. Enter <b style='mso-bidi-font-weight: 1262 1270 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1263 minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for < b1264 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1265 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Tmax</span></b> 1266 as the upper limit and make a note of the exact d-spacing (0.9945Å) usingthe1267 mouse cursor on the plot.</p>1271 minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for <span 1272 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1273 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1274 minor-latin'>Tmax</span></b></span> as the upper limit and make a note of the 1275 exact d-spacing (0.9945Å) using the mouse cursor on the plot.</p> 1268 1276 1269 1277 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span … … 1289 1297 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Select 1290 1298 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1291 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>1292 and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span 1293 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1294 m so-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>1299 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample 1300 Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight: 1301 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1302 minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p> 1295 1303 1296 1304 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span … … 1306 1314 box and enter the d-spacing (0.9945) into the <b style='mso-bidi-font-weight: 1307 1315 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1308 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b> box.</p> 1316 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b> 1317 box.</p> 1309 1318 1310 1319 <p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span … … 1368 1377 <p class=MsoNormal>Ive stretched the window slightly to see the entire 1369 1378 contents. This is the location for all the phase dependent parameters for this 1370 histogram. Notice that it includes phase fraction, size & mustrain as well 1371 as preferred orientation, elastic strain and extinction corrections. The 1372 Babinet correction is intended for protein work where a significant region of 1373 the structure is disordered solvent. There are buttons for plotting size and 1374 mustrain surfaces</p> 1375 1376 <p class=MsoNormal>and preferred orientation correction curves.</p> 1379 histogram. Notice that it includes phase fraction, size & <span 1380 class=SpellE>mustrain</span> as well as preferred orientation, elastic strain 1381 and extinction corrections. The <span class=SpellE>Babinet</span> correction is 1382 intended for protein work where a significant region of the structure is 1383 disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span> 1384 surfaces</p> 1385 1386 <p class=MsoNormal><span class=GramE>and</span> preferred orientation 1387 correction curves.</p> 1377 1388 1378 1389 <p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span 1379 1390 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1380 1391 mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be 1381 empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span 1382 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1383 mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this 1384 makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight: 1385 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1386 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table 1387 should list reflections 0-629. Select and check the <b style='mso-bidi-font-weight: 1388 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1389 minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column using 1390 the same technique you used for the peak list. </p> 1392 empty except for column headings. <span class=GramE>Do</span> <b 1393 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1394 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley 1395 create</span></b>; this makes the reflection set over the range covered by 1396 setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1397 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span 1398 class=SpellE>dmin</span></span></b>. The table should list reflections 0-629. 1399 Select and check the <b style='mso-bidi-font-weight:normal'><span 1400 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1401 mso-hansi-theme-font:minor-latin'>refine</span></b> column using the same 1402 technique you used for the peak list. </p> 1391 1403 1392 1404 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1408 1420 file is made; the name will be jadarite.bck0.gpx. It can be used to recover 1409 1421 from a bad refinement. A progress dialog box will appear showing the residual 1410 as the refinement proceeds. My refinement completed with Rwp ~15.5%; a dialog1411 box appears asking if you wish to load the result. Press <b style='mso-bidi-font-weight: 1412 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1413 m inor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot1414 select the PWDR line in the GSAS-II data tree (Ive adjusted the width and 1415 height).</p>1422 as the refinement proceeds. My refinement completed with <span class=SpellE>Rwp</span> 1423 ~15.5%; a dialog box appears asking if you wish to load the result. Press <b 1424 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1425 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1426 To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted the 1427 width and height).</p> 1416 1428 1417 1429 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1418 id=" Picture_x0020_7" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;1419 height:450pt;visibility:visible;mso-wrap-style:square'>1430 id="_x0000_i1043" type="#_x0000_t75" style='width:525pt;height:450pt; 1431 visibility:visible;mso-wrap-style:square'> 1420 1432 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/> 1421 1433 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600 1422 src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes=" Picture_x0020_7"><![endif]></span></p>1434 src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="_x0000_i1043"><![endif]></span></p> 1423 1435 1424 1436 <p class=MsoNormal>It is evident from examining the plot that improvement can … … 1444 1456 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> W</span></b>,<b 1445 1457 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1446 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> X </span></b>&<b 1447 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1448 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Y</span></b>. 1449 Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1450 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; 1451 I obtained an improved residual of 9.7% with a much better fit at the high 1452 angle part of the pattern.</p> 1458 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span 1459 class=GramE>X</span> </span></b>&<b style='mso-bidi-font-weight:normal'><span 1460 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1461 mso-hansi-theme-font:minor-latin'> Y</span></b>. Repeat <b style='mso-bidi-font-weight: 1462 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1463 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I 1464 obtained an improved residual of 9.7% with a much better fit at the high angle 1465 part of the pattern.</p> 1453 1466 1454 1467 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1535 1548 1536 1549 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape 1537 id=" _x0000_i1041" type="#_x0000_t75" style='width:337.5pt;height:225pt;1538 visibility:visible;mso-wrap-style:square'>1550 id="Picture_x0020_7" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt; 1551 height:225pt;visibility:visible;mso-wrap-style:square'> 1539 1552 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/> 1540 1553 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300 1541 src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes=" _x0000_i1041"><![endif]></span></p>1554 src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p> 1542 1555 1543 1556 <p class=MsoNormal><o:p> </o:p></p> … … 1584 1597 the map and make atoms out of them. The map peak list is sorted with the 1585 1598 highest peak first; you can change the sorting to be along any of the column 1586 headings in the table by a single click on the desired heading. The <b 1587 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1588 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b> 1589 column gives the distance of each peak from the origin. The menu items under 1590 Map peaks give you several tools to aid in the peak selection process, we will 1591 just use a couple in this example. I have chosen to proceed by sorting the 1592 atoms by <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1593 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b>, 1594 selecting all and then finding the unique ones. </p> 1599 headings in the table by a single click on the desired heading. The <span 1600 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1601 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1602 minor-latin'>dzero</span></b></span> column gives the distance of each peak 1603 from the origin. The menu items under Map peaks give you several tools to aid 1604 in the peak selection <span class=GramE>process,</span> we will just use a 1605 couple in this example. I have chosen to proceed by sorting the atoms by <span 1606 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1607 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1608 minor-latin'>dzero</span></b></span>, selecting all and then finding the unique 1609 ones. </p> 1595 1610 1596 1611 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; 1597 1612 mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family: 1598 1613 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 1599 </span></span></span><![endif]>Do a single click on the < b style='mso-bidi-font-weight:1600 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1601 m inor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b> column heading.1602 This will sort the peaks in increasing distance from the origin.</p>1614 </span></span></span><![endif]>Do a single click on the <span class=SpellE><b 1615 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1616 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b></span> 1617 column heading. This will sort the peaks in increasing distance from the origin.</p> 1603 1618 1604 1619 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1653 1668 identification (M100 for the largest in the <b style='mso-bidi-font-weight: 1654 1669 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1655 minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which 1656 maynot be one of those moved to the <b style='mso-bidi-font-weight:normal'><span1670 minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which may 1671 not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span 1657 1672 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1658 1673 mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort 1659 1674 them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span 1660 1675 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1661 mso-hansi-theme-font:minor-latin'>Alt</span></b> key down and then selecting a 1662 position in the table with the <b style='mso-bidi-font-weight:normal'><span 1663 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1664 mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. My list is now 1665 </p> 1676 mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight: 1677 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1678 minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down 1679 and then selecting a position in the table with the <b style='mso-bidi-font-weight: 1680 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1681 minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On 1682 Linux machines the <b style='mso-bidi-font-weight:normal'><span 1683 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1684 mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by 1685 the operating system; use <b style='mso-bidi-font-weight:normal'><span 1686 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1687 mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. My 1688 list is now </p> 1666 1689 1667 1690 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1739 1762 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1740 1763 mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the 1741 charge flip map (do <b style='mso-bidi-font-weight:normal'><span 1742 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1743 mso-hansi-theme-font:minor-latin'>Clear map</span></b> in the <b 1764 charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span 1765 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1766 mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight: 1767 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1768 minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b 1744 1769 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1745 1770 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> … … 1757 1782 1758 1783 <p class=MsoNormal>Save the project file; the next step is to complete the 1759 structure by finding the Li and H atoms and then doing the Rietveld refinement1760 on the completed structure.</p>1784 structure by finding the Li and H atoms and then doing the <span class=SpellE>Rietveld</span> 1785 refinement on the completed structure.</p> 1761 1786 1762 1787 <h2>Step 5 Complete the structure</h2> 1763 1788 1764 1789 <p class=MsoNormal>To complete the structure you will need to perform a 1765 preliminary Rietveld refinement. This will make the atom positions more1766 a ccurate and prepare a set of calculated structure factors needed to generate a1767 difference Fourier map good enough to reveal the Li atom position and maybe the 1768 H-atom as well. There are a number of steps needed to set all the controls from 1769 the previous Pawley refinement to get a successful start for the Rietveld 1770 refinement.</p>1790 preliminary <span class=SpellE>Rietveld</span> refinement. This will make the 1791 atom positions more accurate and prepare a set of calculated structure factors 1792 needed to generate a difference Fourier map good enough to reveal the Li atom 1793 position and maybe the H-atom as well. There are a number of steps needed to 1794 set all the controls from the previous Pawley refinement to get a successful 1795 start for the <span class=SpellE>Rietveld</span> refinement.</p> 1771 1796 1772 1797 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 1815 1840 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1816 1841 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main 1817 GSAS-II data tree menu; all that was refined is scale and background. I got a1818 Rwp ~31%. The plot shows clear intensity differences; the atom positions 1819 obviously need refinement.</p>1842 GSAS-II data tree menu; all that was refined is scale and background. I got <span 1843 class=GramE>a</span> <span class=SpellE>Rwp</span> ~31%. The plot shows clear 1844 intensity differences; the atom positions obviously need refinement.</p> 1820 1845 1821 1846 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape … … 1853 1878 <p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span 1854 1879 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1855 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my Rwp is 1856 now ~15%. You can now safely refine lattice parameters (in the <b 1857 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1858 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1859 tab for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1880 mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span 1881 class=SpellE>Rwp</span> is now ~15%. You can now safely refine lattice 1882 parameters (in the <b style='mso-bidi-font-weight:normal'><span 1883 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1884 mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b 1885 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1860 1886 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>) 1861 1887 and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; … … 1868 1894 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1869 1895 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>, 1870 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1871 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> 1872 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1896 <span class=GramE><b style='mso-bidi-font-weight:normal'><span 1897 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1898 mso-hansi-theme-font:minor-latin'>X</span></b></span> & <b 1899 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1873 1900 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>. 1874 1901 My refinement improved slightly to Rwp~14.5%. Lets see if a difference Fourier … … 1876 1903 Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1877 1904 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite 1878 General</span></b> tab ; the <b style='mso-bidi-font-weight:normal'><span1879 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1880 m so-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway1881 down the window.</p>1905 General</span></b> <span class=GramE>tab ;</span> the <b style='mso-bidi-font-weight: 1906 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1907 minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> 1908 are midway down the window.</p> 1882 1909 1883 1910 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; 1884 1911 mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family: 1885 1912 "Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> 1886 </span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span 1887 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1888 mso-hansi-theme-font:minor-latin'>delt-F</span></b> for the <b 1889 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1913 </span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight: 1914 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1915 minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b 1916 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1917 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b> 1918 for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1890 1919 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p> 1891 1920 … … 1942 1971 src="Charge%20Flipping%20in%20GSAS_files/image038.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p> 1943 1972 1944 <p class=MsoNormal>What is drawn here are green dots whose size are 1945 proportional to the electron density. These are the Li atom positions. There 1946 are several ways within GSAS-II to add it to the atom list. One is to do <b 1947 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1948 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Search 1949 map</span></b> in the <b style='mso-bidi-font-weight:normal'><span 1950 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 1951 mso-hansi-theme-font:minor-latin'>General</span></b> tab and then find them in 1952 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 1953 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> 1954 tab much the same way we did earlier in this exercise. Another is to get the 1955 atom position directly from the map, we will do that now.</p> 1973 <p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots 1974 whose size are proportional to the electron density. These are the Li atom 1975 positions. There are several ways within GSAS-II to add it to the atom list. 1976 One is to do <b style='mso-bidi-font-weight:normal'><span style='font-family: 1977 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1978 minor-latin'>Compute/Search map</span></b> in the <b style='mso-bidi-font-weight: 1979 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font: 1980 minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab and then 1981 find them in the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1982 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1983 minor-latin'>Map peaks</span></b> tab much the same way we did earlier in this 1984 exercise. Another is to get the atom position directly from the map, we will do 1985 that now.</p> 1956 1986 1957 1987 <p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in; … … 2028 2058 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2029 2059 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main 2030 GSAS-II data tree window. My residual Rwp dropped to ~11.3%. Next set all <b 2031 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2032 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> 2033 flags to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2060 GSAS-II data tree window. My residual <span class=SpellE>Rwp</span> dropped to 2061 ~11.3%. Next set all <b style='mso-bidi-font-weight:normal'><span 2062 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2063 mso-hansi-theme-font:minor-latin'>refine</span></b> flags to <b 2064 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif"; 2034 2065 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>XU</span></b> 2035 2066 and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family: 2036 2067 "Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 2037 minor-latin'>Calculate/Refine</span></b>. My residual is now Rwp ~10.8%. Maybe2038 we can find the H-atom.</p>2068 minor-latin'>Calculate/Refine</span></b>. My residual is now <span 2069 class=SpellE>Rwp</span> ~10.8%. Maybe we can find the H-atom.</p> 2039 2070 2040 2071 <p class=MsoNormal>From the <b style='mso-bidi-font-weight:normal'><span … … 2072 2103 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin; 2073 2104 mso-hansi-theme-font:minor-latin'>UNK</span></b>). Repeat the Calculate/Refine 2074 without varying any of the H-atom parameters; my final Rwp = 10.69% (you dont 2075 get much improvement for adding an H-atom to an oxide structure).</p> 2105 without varying any of the H-atom parameters; my final <span class=SpellE>Rwp</span> 2106 = 10.69% (you dont get much improvement for adding an H-atom to an oxide 2107 structure).</p> 2076 2108 2077 2109 </div>
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