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Jul 23, 2014 12:46:23 PM (11 years ago)
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vondreele
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modify comments about use of Alt key

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  • TabularUnified trunk/help/Charge Flipping in GSAS.htm

    r1434 r1435  
    2323  <o:Author>vondreele</o:Author>
    2424  <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>
    2727  <o:Created>2014-07-21T14:56:00Z</o:Created>
    28   <o:LastSaved>2014-07-21T14:56:00Z</o:LastSaved>
     28  <o:LastSaved>2014-07-23T17:41:00Z</o:LastSaved>
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     30  <o:Words>2239</o:Words>
     31  <o:Characters>12763</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    33   <o:Lines>105</o:Lines>
     33  <o:Lines>106</o:Lines>
    3434  <o:Paragraphs>29</o:Paragraphs>
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     47  <w:SpellingState>Clean</w:SpellingState>
     48  <w:GrammarState>Clean</w:GrammarState>
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    4850  <w:TrackFormatting/>
     
    786788        mso-fareast-theme-font:minor-fareast;
    787789        mso-bidi-font-family:Calibri;}
     790span.SpellE
     791        {mso-style-name:"";
     792        mso-spl-e:yes;}
     793span.GramE
     794        {mso-style-name:"";
     795        mso-gram-e:yes;}
    788796.MsoChpDefault
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    12261234
    12271235<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
    1228 GSAS-II - jadarite<o:p></o:p></span></h1>
     1236GSAS-II - <span class=SpellE>jadarite</span><o:p></o:p></span></h1>
    12291237
    12301238<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
    12311239
    12321240<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>
     1241of <span class=SpellE>jadarite</span> (aka “kryptonite”) from powder
     1242diffraction data via charge flipping. This structure was originally solved by
     1243Pam Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>
    12361244
    12371245<p class=MsoNormal>If you have not done so already, <a
    12381246href="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 <a
    1240 href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing exercise</a>.
    1241 If you didn’t 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
     1248part of the <a href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing
     1249exercise</a>. If you didn’t do that exercise, do it now.</p>
     1250
     1251<h2><span class=GramE>Step 1.</span> Setup for Pawley refinement</h2>
    12441252
    12451253<p class=MsoNormal>There are a number of steps that must be done in preparation
     
    12611269set of ~1Å resolution as needed for charge flipping. Enter <b style='mso-bidi-font-weight:
    12621270normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1263 minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for <b
    1264 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) using the
    1267 mouse cursor on the plot.</p>
     1271minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for <span
     1272class=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:
     1274minor-latin'>Tmax</span></b></span> as the upper limit and make a note of the
     1275exact d-spacing (0.9945Å) using the mouse cursor on the plot.</p>
    12681276
    12691277<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
     
    12891297style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    12901298<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 mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
     1299mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
     1300Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
     1301normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1302minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
    12951303
    12961304<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
     
    13061314box and enter the d-spacing (0.9945) into the <b style='mso-bidi-font-weight:
    13071315normal'><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>
     1316minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
     1317box.</p>
    13091318
    13101319<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
     
    13681377<p class=MsoNormal>I’ve stretched the window slightly to see the entire
    13691378contents. This is the location for all the phase dependent parameters for this
    1370 histogram. Notice that it includes phase fraction, size &amp; 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>
     1379histogram. Notice that it includes phase fraction, size &amp; <span
     1380class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
     1381and extinction corrections. The <span class=SpellE>Babinet</span> correction is
     1382intended for protein work where a significant region of the structure is
     1383disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
     1384surfaces</p>
     1385
     1386<p class=MsoNormal><span class=GramE>and</span> preferred orientation
     1387correction curves.</p>
    13771388
    13781389<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
    13791390style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    13801391mso-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>
     1392empty except for column headings. <span class=GramE>Do</span> <b
     1393style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
     1395create</span></b>; this makes the reflection set over the range covered by
     1396setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1397mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1398class=SpellE>dmin</span></span></b>. The table should list reflections 0-629.
     1399Select and check the <b style='mso-bidi-font-weight:normal'><span
     1400style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1401mso-hansi-theme-font:minor-latin'>refine</span></b> column using the same
     1402technique you used for the peak list. </p>
    13911403
    13921404<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    14081420file is made; the name will be jadarite.bck0.gpx. It can be used to recover
    14091421from 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 dialog
    1411 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 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot
    1414 select the PWDR line in the GSAS-II data tree (I’ve adjusted the width and
    1415 height).</p>
     1422as 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
     1424style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1425mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
     1426To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted the
     1427width and height).</p>
    14161428
    14171429<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'>
    14201432 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/>
    14211433</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>
     1434src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="_x0000_i1043"><![endif]></span></p>
    14231435
    14241436<p class=MsoNormal>It is evident from examining the plot that improvement can
     
    14441456mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> W</span></b>,<b
    14451457style='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>&amp;<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>
     1458mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
     1459class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
     1460style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1461mso-hansi-theme-font:minor-latin'> Y</span></b>. Repeat <b style='mso-bidi-font-weight:
     1462normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1463minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I
     1464obtained an improved residual of 9.7% with a much better fit at the high angle
     1465part of the pattern.</p>
    14531466
    14541467<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15351548
    15361549<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'>
    15391552 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/>
    15401553</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>
     1554src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
    15421555
    15431556<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15841597the map and make atoms out of them. The map peak list is sorted with the
    15851598highest 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>
     1599headings in the table by a single click on the desired heading. The <span
     1600class=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:
     1602minor-latin'>dzero</span></b></span> column gives the distance of each peak
     1603from the origin. The menu items under Map peaks give you several tools to aid
     1604in the peak selection <span class=GramE>process,</span> we will just use a
     1605couple in this example. I have chosen to proceed by sorting the atoms by <span
     1606class=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:
     1608minor-latin'>dzero</span></b></span>, selecting all and then finding the unique
     1609ones. </p>
    15951610
    15961611<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    15971612mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
    15981613"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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 minor-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
     1615style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1616mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b></span>
     1617column heading. This will sort the peaks in increasing distance from the origin.</p>
    16031618
    16041619<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    16531668identification (M100 for the largest in the <b style='mso-bidi-font-weight:
    16541669normal'><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 may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
     1670minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which may
     1671not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
    16571672style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    16581673mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
    16591674them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
    16601675style='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>
     1676mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
     1677normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1678minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
     1679and then selecting a position in the table with the <b style='mso-bidi-font-weight:
     1680normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1681minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
     1682Linux machines the <b style='mso-bidi-font-weight:normal'><span
     1683style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1684mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
     1685the operating system; use <b style='mso-bidi-font-weight:normal'><span
     1686style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1687mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. My
     1688list is now </p>
    16661689
    16671690<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17391762style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    17401763mso-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
     1764charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1765style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1766mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
     1767normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1768minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
    17441769style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    17451770mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     
    17571782
    17581783<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 refinement
    1760 on the completed structure.</p>
     1784structure by finding the Li and H atoms and then doing the <span class=SpellE>Rietveld</span>
     1785refinement on the completed structure.</p>
    17611786
    17621787<h2>Step 5 Complete the structure</h2>
    17631788
    17641789<p class=MsoNormal>To complete the structure you will need to perform a
    1765 preliminary Rietveld refinement. This will make the atom positions more
    1766 accurate and prepare a set of calculated structure factors needed to generate a
    1767 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>
     1790preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
     1791atom positions more accurate and prepare a set of calculated structure factors
     1792needed to generate a difference Fourier map good enough to reveal the Li atom
     1793position and maybe the H-atom as well. There are a number of steps needed to
     1794set all the controls from the previous Pawley refinement to get a successful
     1795start for the <span class=SpellE>Rietveld</span> refinement.</p>
    17711796
    17721797<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18151840style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    18161841mso-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 a
    1818 Rwp ~31%. The plot shows clear intensity differences; the atom positions
    1819 obviously need refinement.</p>
     1842GSAS-II data tree menu; all that was refined is scale and background. I got <span
     1843class=GramE>a</span> <span class=SpellE>Rwp</span> ~31%. The plot shows clear
     1844intensity differences; the atom positions obviously need refinement.</p>
    18201845
    18211846<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    18531878<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
    18541879style='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";
     1880mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
     1881class=SpellE>Rwp</span> is now ~15%. You can now safely refine lattice
     1882parameters (in the <b style='mso-bidi-font-weight:normal'><span
     1883style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1884mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
     1885style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18601886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>)
    18611887and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     
    18681894style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18691895mso-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 &amp; <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
     1897style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1898mso-hansi-theme-font:minor-latin'>X</span></b></span> &amp; <b
     1899style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18731900mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>.
    18741901My refinement improved slightly to Rwp~14.5%. Let’s see if a difference Fourier
     
    18761903Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18771904mso-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'><span
    1879 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1880 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
    1881 down the window.</p>
     1905General</span></b> <span class=GramE>tab ;</span> the <b style='mso-bidi-font-weight:
     1906normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1907minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b>
     1908are midway down the window.</p>
    18821909
    18831910<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    18841911mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
    18851912"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    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:
     1914normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1915minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
     1916style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1917mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
     1918for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    18901919mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
    18911920
     
    19421971src="Charge%20Flipping%20in%20GSAS_files/image038.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    19431972
    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
     1974whose size are proportional to the electron density. These are the Li atom
     1975positions. There are several ways within GSAS-II to add it to the atom list.
     1976One 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:
     1978minor-latin'>Compute/Search map</span></b> in the <b style='mso-bidi-font-weight:
     1979normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
     1980minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab and then
     1981find 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:
     1983minor-latin'>Map peaks</span></b> tab much the same way we did earlier in this
     1984exercise. Another is to get the atom position directly from the map, we will do
     1985that now.</p>
    19561986
    19571987<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20282058style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    20292059mso-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";
     2060GSAS-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
     2062style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     2063mso-hansi-theme-font:minor-latin'>refine</span></b> flags to <b
     2064style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    20342065mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>XU</span></b>
    20352066and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
    20362067"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%. Maybe
    2038 we can find the H-atom.</p>
     2068minor-latin'>Calculate/Refine</span></b>. My residual is now <span
     2069class=SpellE>Rwp</span> ~10.8%. Maybe we can find the H-atom.</p>
    20392070
    20402071<p class=MsoNormal>From the <b style='mso-bidi-font-weight:normal'><span
     
    20722103style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    20732104mso-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 don’t
    2075 get much improvement for adding an H-atom to an oxide structure).</p>
     2105without varying any of the H-atom parameters; my final <span class=SpellE>Rwp</span>
     2106= 10.69% (you don’t get much improvement for adding an H-atom to an oxide
     2107structure).</p>
    20762108
    20772109</div>
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