Changeset 2986 for Tutorials/CFjadarite


Ignore:
Timestamp:
Aug 9, 2017 4:12:27 PM (4 years ago)
Author:
vondreele
Message:

update to 2 frame

Location:
Tutorials/CFjadarite
Files:
45 added
43 deleted
4 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/CFjadarite/Charge Flipping in GSAS.htm

    r1728 r2986  
    2222 <o:DocumentProperties>
    2323  <o:Author>vondreele</o:Author>
    24   <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>7</o:Revision>
    26   <o:TotalTime>127</o:TotalTime>
     24  <o:LastAuthor>vondreele</o:LastAuthor>
     25  <o:Revision>8</o:Revision>
     26  <o:TotalTime>340</o:TotalTime>
    2727  <o:Created>2014-07-21T14:56:00Z</o:Created>
    28   <o:LastSaved>2015-03-17T17:47:00Z</o:LastSaved>
    29   <o:Pages>1</o:Pages>
    30   <o:Words>2225</o:Words>
    31   <o:Characters>12684</o:Characters>
     28  <o:LastSaved>2017-08-09T21:07:00Z</o:LastSaved>
     29  <o:Pages>20</o:Pages>
     30  <o:Words>2291</o:Words>
     31  <o:Characters>13062</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    33   <o:Lines>105</o:Lines>
    34   <o:Paragraphs>29</o:Paragraphs>
    35   <o:CharactersWithSpaces>14880</o:CharactersWithSpaces>
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    15511566<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
    15521567of <span class=SpellE>jadarite</span> (aka “kryptonite”) from powder
    1553 diffraction data via charge flipping. This structure was originally solved by Pam
    1554 Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>
     1568diffraction data via charge flipping. This structure was originally solved by
     1569Pam Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>
    15551570
    15561571<p class=MsoNormal>If you have not done so already, start GSAS-II and open the
     
    16221637normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16231638minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
    1624 box and enter the d-spacing (0.9945) into the <b style='mso-bidi-font-weight:
    1625 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1626 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
    1627 box.</p>
     1639box and enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
     1640style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1641mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.9945</span></b>)
     1642into the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1643mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1644class=SpellE>dmin</span></span></b> box.</p>
     1645
     1646<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
     1647style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
     1648style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Also
     1649set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1651minor-latin'>Pawley neg. wt.</span></b> to <b style='mso-bidi-font-weight:normal'><span
     1652style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1653mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.001;</span></b>
     1654this will force all Pawley reflection intensities to be &gt; 0.</p>
    16281655
    16291656<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
     
    16511678 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
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    1655  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image001.png" o:title=""/>
    1656 </v:shape><![endif]--><![if !vml]><img width=723 height=500
    1657 src="Charge%20Flipping%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1047"><![endif]></span></p>
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     1681 style='width:468pt;height:179.25pt;visibility:visible;mso-wrap-style:square'>
     1682 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image047.png" o:title=""/>
     1683</v:shape><![endif]--><![if !vml]><img width=624 height=239
     1684src="Charge%20Flipping%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    16581685
    16591686<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
     
    16621689for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
    16631690style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1664 mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
    1665 dialog box will appear</p>
     1691mso-hansi-theme-font:minor-latin'>Edit Phase/Add powder histograms</span></b>;
     1692a dialog box will appear</p>
    16661693
    16671694<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1668  id="Picture_x0020_2" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:259.5pt;
    1669  height:252pt;visibility:visible;mso-wrap-style:square'>
    1670  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image003.png" o:title=""/>
    1671 </v:shape><![endif]--><![if !vml]><img width=346 height=336
    1672 src="Charge%20Flipping%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
    1673 
    1674 <p class=MsoNormal>Select either choice; the desired data set will be added to
    1675 this phase for analysis. The data tab now shows the new data set; check the <b
    1676 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1695 id="_x0000_i1047" type="#_x0000_t75" style='width:241.5pt;height:228.75pt;
     1696 visibility:visible;mso-wrap-style:square'>
     1697 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image049.png" o:title=""/>
     1698</v:shape><![endif]--><![if !vml]><img width=322 height=305
     1699src="Charge%20Flipping%20in%20GSAS_files/image050.gif" v:shapes="_x0000_i1047"><![endif]></span></p>
     1700
     1701<p class=MsoNormal>Select the one possibility; the desired data set will be
     1702added to this phase for analysis. The data tab now shows the new data set;
     1703check the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16771704mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
    16781705button to see the full information</p>
    16791706
    16801707<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1681  id="Picture_x0020_25" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:359.25pt;
    1682  height:375pt;visibility:visible;mso-wrap-style:square'>
    1683  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image005.png" o:title=""/>
    1684 </v:shape><![endif]--><![if !vml]><img width=479 height=500
    1685 src="Charge%20Flipping%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
     1708 id="_x0000_i1046" type="#_x0000_t75" style='width:442.5pt;height:378.75pt;
     1709 visibility:visible;mso-wrap-style:square'>
     1710 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image051.png" o:title=""/>
     1711</v:shape><![endif]--><![if !vml]><img width=590 height=505
     1712src="Charge%20Flipping%20in%20GSAS_files/image052.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
    16861713
    16871714<p class=MsoNormal>I’ve stretched the window slightly to see the entire
     
    16921719intended for protein work where a significant region of the structure is
    16931720disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
    1694 surfaces</p>
    1695 
    1696 <p class=MsoNormal><span class=GramE>and</span> preferred orientation
    1697 correction curves.</p>
     1721surfaces and preferred orientation correction curves.</p>
    16981722
    16991723<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
     
    17121736
    17131737<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1714  id="Picture_x0020_4" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:375pt;
    1715  height:225pt;visibility:visible;mso-wrap-style:square'>
    1716  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image007.png" o:title=""/>
    1717 </v:shape><![endif]--><![if !vml]><img width=500 height=300
    1718 src="Charge%20Flipping%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
     1738 id="Picture_x0020_28" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
     1739 height:246.75pt;visibility:visible;mso-wrap-style:square'>
     1740 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image053.png" o:title=""/>
     1741</v:shape><![endif]--><![if !vml]><img width=624 height=329
     1742src="Charge%20Flipping%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    17191743
    17201744<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
     
    17301754from a bad refinement. A progress dialog box will appear showing the residual
    17311755as the refinement proceeds. My refinement completed with <span class=SpellE>Rwp</span>
    1732 ~15.5%; a dialog box appears asking if you wish to load the result. Press <b
     1756~15.0%; a dialog box appears asking if you wish to load the result. Press <b
    17331757style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17341758mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1735 To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted the
    1736 width and height).</p>
     1759To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
     1760the width and height).</p>
    17371761
    17381762<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1739  id="Picture_x0020_26" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
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    17401764 height:450pt;visibility:visible;mso-wrap-style:square'>
    17411765 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/>
    17421766</v:shape><![endif]--><![if !vml]><img width=700 height=600
    1743 src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
     1767src="Charge%20Flipping%20in%20GSAS_files/image055.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
    17441768
    17451769<p class=MsoNormal>It is evident from examining the plot that improvement can
     
    17751799
    17761800<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1777  id="Picture_x0020_27" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
     1801 id="Picture_x0020_27" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
    17781802 height:450pt;visibility:visible;mso-wrap-style:square'>
    17791803 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image011.png" o:title=""/>
    17801804</v:shape><![endif]--><![if !vml]><img width=700 height=600
    1781 src="Charge%20Flipping%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
     1805src="Charge%20Flipping%20in%20GSAS_files/image056.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
    17821806
    17831807<p class=MsoNormal>This may be good enough to try charge flipping.</p>
     
    18061830set to be used those in <b style='mso-bidi-font-weight:normal'><span
    18071831style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1808 mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
    1809 data set; these should match the Pawley reflection set.</p>
     1832mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR data
     1833set; these should match the Pawley reflection set.</p>
    18101834
    18111835<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    18571881
    18581882<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1859  id="Picture_x0020_7" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt;
    1860  height:225pt;visibility:visible;mso-wrap-style:square'>
    1861  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/>
    1862 </v:shape><![endif]--><![if !vml]><img width=450 height=300
    1863 src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1883 id="Picture_x0020_40" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
     1884 height:240pt;visibility:visible;mso-wrap-style:square'>
     1885 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image057.png" o:title=""/>
     1886</v:shape><![endif]--><![if !vml]><img width=624 height=320
     1887src="Charge%20Flipping%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
    18641888
    18651889<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    18661890
    18671891<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1868  id="Picture_x0020_1" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:338.25pt;
    1869  height:289.5pt;visibility:visible;mso-wrap-style:square'>
    1870  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image015.png" o:title=""
    1871   croptop="2431f" cropbottom="25578f" cropleft="38673f" cropright="11746f"/>
    1872 </v:shape><![endif]--><![if !vml]><img width=451 height=386
    1873 src="Charge%20Flipping%20in%20GSAS_files/image016.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1892 id="Picture_x0020_41" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:352.5pt;
     1893 height:304.5pt;visibility:visible;mso-wrap-style:square'>
     1894 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image059.png" o:title=""/>
     1895</v:shape><![endif]--><![if !vml]><img width=470 height=406
     1896src="Charge%20Flipping%20in%20GSAS_files/image060.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
    18741897
    18751898<p class=MsoNormal>The result looks very promising! Charge flipping operates
     
    19381961style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19391962mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
    1940 should select (grey) 13 out of 52 peak positions in the table and all should be
    1941 near the top of the list. They will be colored green in the plot. If more are
    1942 selected then check the map offset – it may need a slight correction.</p>
     1963should select (grey) 13-14 out of 52 peak positions in the table and all should
     1964be near the top of the list. They will be colored green in the plot. If more
     1965are selected then check the map offset – it may need a slight correction.</p>
    19431966
    19441967<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1945  id="Picture_x0020_28" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:375pt;
    1946  height:369.75pt;visibility:visible;mso-wrap-style:square'>
    1947  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image017.png" o:title=""/>
    1948 </v:shape><![endif]--><![if !vml]><img width=500 height=493
    1949 src="Charge%20Flipping%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1968 id="Picture_x0020_42" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
     1969 height:327.75pt;visibility:visible;mso-wrap-style:square'>
     1970 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image061.png" o:title=""/>
     1971</v:shape><![endif]--><![if !vml]><img width=624 height=437
     1972src="Charge%20Flipping%20in%20GSAS_files/image062.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
    19501973
    19511974<p class=MsoNormal>These are now ready to turn into atoms. Do <b
     
    19551978selected positions and the <b style='mso-bidi-font-weight:normal'><span
    19561979style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1957 mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 14 new H
     1980mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 13 new H
    19581981atoms. We are looking for heavier atoms in the formula NaSiO<sub>8</sub>B<sub>3</sub>LiH
    1959 so 14 atoms should correspond to all but the H atoms.</p>
     1982so 13 atoms should correspond to all but the Li &amp; H atoms.</p>
    19601983
    19611984<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1962  id="Picture_x0020_10" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:338.25pt;
    1963  height:291.75pt;visibility:visible;mso-wrap-style:square'>
    1964  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image019.png" o:title=""
    1965   croptop="3527f" cropbottom="24386f" cropleft="38043f" cropright="12462f"/>
    1966 </v:shape><![endif]--><![if !vml]><img width=451 height=389
    1967 src="Charge%20Flipping%20in%20GSAS_files/image020.jpg" v:shapes="Picture_x0020_10"><![endif]></span></p>
     1985 id="Picture_x0020_43" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:282.75pt;
     1986 height:244.5pt;visibility:visible;mso-wrap-style:square'>
     1987 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image063.png" o:title=""/>
     1988</v:shape><![endif]--><![if !vml]><img width=377 height=326
     1989src="Charge%20Flipping%20in%20GSAS_files/image064.gif" v:shapes="Picture_x0020_43"><![endif]></span></p>
    19681990
    19691991<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1970  id="Picture_x0020_29" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:532.5pt;
    1971  height:306pt;visibility:visible;mso-wrap-style:square'>
    1972  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image021.png" o:title=""/>
    1973 </v:shape><![endif]--><![if !vml]><img width=710 height=408
    1974 src="Charge%20Flipping%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
     1992 id="Picture_x0020_44" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
     1993 height:327.75pt;visibility:visible;mso-wrap-style:square'>
     1994 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image065.png" o:title=""/>
     1995</v:shape><![endif]--><![if !vml]><img width=624 height=437
     1996src="Charge%20Flipping%20in%20GSAS_files/image066.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
    19751997
    19761998<p class=MsoNormal>The atom names indicate the peak magnitude to aid
     
    19942016the operating system; use <b style='mso-bidi-font-weight:normal'><span
    19952017style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1996 mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms. My
    1997 list is now </p>
     2018mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> instead to move atoms.
     2019My list is now </p>
    19982020
    19992021<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2000  id="Picture_x0020_30" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:450pt;
    2001  height:300pt;visibility:visible;mso-wrap-style:square'>
    2002  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image023.png" o:title=""/>
    2003 </v:shape><![endif]--><![if !vml]><img width=600 height=400
    2004 src="Charge%20Flipping%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
     2022 id="Picture_x0020_45" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
     2023 height:327.75pt;visibility:visible;mso-wrap-style:square'>
     2024 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image067.png" o:title=""/>
     2025</v:shape><![endif]--><![if !vml]><img width=624 height=437
     2026src="Charge%20Flipping%20in%20GSAS_files/image068.gif" v:shapes="Picture_x0020_45"><![endif]></span></p>
    20052027
    20062028<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
     
    20092031style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20102032mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
    2011 menu to make the drawing reflect the change in atom ordering.</p>
    2012 
    2013 <p class=MsoNormal>To proceed, one could select an atom and see its bonding pattern
    2014 with its neighbors to identify it. Then pick its neighbors and identify them
    2015 continuing on until all atoms are identified. In my case this would be:</p>
     2033menu to make the drawing reflect the change in atom ordering. Go to Draw Atoms
     2034and double click the upper left box (empty); the entire table will be selected
     2035(gray). Then do Edit Figure/Fill Unit Cell; the structure will be redrawn with
     2036all the equivalent positions shown.</p>
     2037
     2038<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2039 id="Picture_x0020_46" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:306.75pt;
     2040 height:266.25pt;visibility:visible;mso-wrap-style:square'>
     2041 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image069.png" o:title=""/>
     2042</v:shape><![endif]--><![if !vml]><img width=409 height=355
     2043src="Charge%20Flipping%20in%20GSAS_files/image070.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
     2044
     2045<p class=MsoNormal>To proceed, one could select an atom and see its bonding
     2046pattern with its neighbors to identify it. Then pick its neighbors and identify
     2047them continuing on until all atoms are identified. In my case this would be:</p>
    20162048
    20172049<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
    20182050mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
    20192051"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    2020 </span></span></span><![endif]>Pick M50; it is bonded to 4 neighbors (one is in
    2021 next cell) as a tetrahedron. Probably Si. Change its Type. The plot will change
    2022 the green (as selected) ball to a gold colored one (the color assigned to Si).
    2023 You may have to rock the structure slightly to make the change happen.</p>
     2052</span></span></span><![endif]>Go to the Atoms tab and pick M83; it is bonded
     2053to 4 neighbors (two are in next cell) as a tetrahedron. Probably Si. Change its
     2054Type. The plot will change the green (as selected) ball to a gold colored one
     2055(the color assigned to Si). You may have to rock the structure slightly to make
     2056the change happen. The equivalent ones are also shown; some show the four
     2057neighbors as a tetrahedron.</p>
    20242058
    20252059<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    20442078
    20452079<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2046  id="Picture_x0020_13" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:526.5pt;
    2047  height:6in;visibility:visible;mso-wrap-style:square'>
    2048  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image025.png" o:title=""
    2049   croptop="2450f" cropbottom="26950f" cropleft="39199f" cropright="11167f"/>
    2050 </v:shape><![endif]--><![if !vml]><img width=702 height=576
    2051 src="Charge%20Flipping%20in%20GSAS_files/image026.jpg" v:shapes="Picture_x0020_13"><![endif]></span></p>
     2080 id="Picture_x0020_47" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:366.75pt;
     2081 height:318.75pt;visibility:visible;mso-wrap-style:square'>
     2082 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image071.png" o:title=""/>
     2083</v:shape><![endif]--><![if !vml]><img width=489 height=425
     2084src="Charge%20Flipping%20in%20GSAS_files/image072.gif" v:shapes="Picture_x0020_47"><![endif]></span></p>
    20522085
    20532086<p class=MsoNormal>The original charge flipping solution is still visible and
     
    20552088
    20562089<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2057  id="Picture_x0020_18" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
    2058  height:290.25pt;visibility:visible;mso-wrap-style:square'>
    2059  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image027.png" o:title=""/>
    2060 </v:shape><![endif]--><![if !vml]><img width=700 height=387
    2061 src="Charge%20Flipping%20in%20GSAS_files/image028.gif" v:shapes="Picture_x0020_18"><![endif]></span></p>
    2062 
    2063 <p class=MsoNormal>Interestingly the atoms identified exactly matched with the
    2064 magnitudes of the charge flip map peaks with Si &amp; Na at the top and B at
    2065 the bottom.</p>
     2090 id="Picture_x0020_48" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
     2091 height:228.75pt;visibility:visible;mso-wrap-style:square'>
     2092 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image073.png" o:title=""/>
     2093</v:shape><![endif]--><![if !vml]><img width=624 height=305
     2094src="Charge%20Flipping%20in%20GSAS_files/image074.gif" v:shapes="Picture_x0020_48"><![endif]></span></p>
     2095
     2096<p class=MsoNormal>Interestingly the atoms identified exactly matched with the magnitudes
     2097of the charge flip map peaks with Si &amp; Na near the top and B at the bottom.</p>
    20662098
    20672099<p class=MsoNormal>Now one can safely remove the map peaks (do <b
     
    20832115
    20842116<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2085  id="Picture_x0020_15" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525.75pt;
    2086  height:398.25pt;visibility:visible;mso-wrap-style:square'>
    2087  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image029.png" o:title=""
    2088   croptop="2054f" cropbottom="23166f" cropleft="37518f" cropright="9679f"/>
    2089 </v:shape><![endif]--><![if !vml]><img width=701 height=531
    2090 src="Charge%20Flipping%20in%20GSAS_files/image030.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
     2117 id="Picture_x0020_49" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:395.25pt;
     2118 height:341.25pt;visibility:visible;mso-wrap-style:square'>
     2119 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image075.png" o:title=""/>
     2120</v:shape><![endif]--><![if !vml]><img width=527 height=455
     2121src="Charge%20Flipping%20in%20GSAS_files/image076.gif" v:shapes="Picture_x0020_49"><![endif]></span></p>
    20912122
    20922123<p class=MsoNormal>Save the project file; the next step is to complete the
     
    20972128
    20982129<p class=MsoNormal>To complete the structure you will need to perform a
    2099 preliminary Rietveld refinement. This will make the atom positions more
    2100 accurate and prepare a set of calculated structure factors needed to generate a
     2130preliminary Rietveld refinement. This will make the atom positions more accurate
     2131and prepare a set of calculated structure factors needed to generate a
    21012132difference Fourier map good enough to reveal the Li atom position and maybe the
    21022133H-atom as well. There are a number of steps needed to set all the controls from
     
    21542185
    21552186<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2156  id="Picture_x0020_32" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
    2157  height:383.25pt;visibility:visible;mso-wrap-style:square'>
    2158  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image031.png" o:title=""/>
    2159 </v:shape><![endif]--><![if !vml]><img width=700 height=511
    2160 src="Charge%20Flipping%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
     2187 id="Picture_x0020_50" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:425.25pt;
     2188 height:364.5pt;visibility:visible;mso-wrap-style:square'>
     2189 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image077.png" o:title=""/>
     2190</v:shape><![endif]--><![if !vml]><img width=567 height=486
     2191src="Charge%20Flipping%20in%20GSAS_files/image078.gif" v:shapes="Picture_x0020_50"><![endif]></span></p>
    21612192
    21622193<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
     
    21792210
    21802211<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2181  id="Picture_x0020_17" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
    2182  height:225pt;visibility:visible;mso-wrap-style:square'>
    2183  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image033.png" o:title=""/>
    2184 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    2185 src="Charge%20Flipping%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_17"><![endif]></span></p>
     2212 id="Picture_x0020_51" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
     2213 height:228.75pt;visibility:visible;mso-wrap-style:square'>
     2214 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image079.png" o:title=""/>
     2215</v:shape><![endif]--><![if !vml]><img width=624 height=305
     2216src="Charge%20Flipping%20in%20GSAS_files/image080.gif" v:shapes="Picture_x0020_51"><![endif]></span></p>
    21862217
    21872218<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
     
    22122243Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    22132244mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite
    2214 General</span></b> <span class=GramE>tab ;</span> the <b style='mso-bidi-font-weight:
    2215 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2216 minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b>
    2217 are midway down the window.</p>
     2245General</span></b> tab; the <b style='mso-bidi-font-weight:normal'><span
     2246style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2247mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> are midway
     2248down the window.</p>
    22182249
    22192250<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    22662297
    22672298<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2268  id="Picture_x0020_19" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:274.5pt;
    2269  height:337.5pt;visibility:visible;mso-wrap-style:square'>
    2270  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image035.png" o:title=""/>
    2271 </v:shape><![endif]--><![if !vml]><img width=366 height=450
    2272 src="Charge%20Flipping%20in%20GSAS_files/image036.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
     2299 id="Picture_x0020_52" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
     2300 height:228.75pt;visibility:visible;mso-wrap-style:square'>
     2301 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image081.png" o:title=""/>
     2302</v:shape><![endif]--><![if !vml]><img width=624 height=305
     2303src="Charge%20Flipping%20in%20GSAS_files/image082.gif" v:shapes="Picture_x0020_52"><![endif]></span></p>
    22732304
    22742305<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2275  id="Picture_x0020_20" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:349.5pt;
    2276  height:299.25pt;visibility:visible;mso-wrap-style:square'>
    2277  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image037.png" o:title=""
    2278   croptop="5231f" cropbottom="8930f" cropleft="11448f" cropright="20374f"/>
    2279 </v:shape><![endif]--><![if !vml]><img width=466 height=399
    2280 src="Charge%20Flipping%20in%20GSAS_files/image038.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     2306 id="Picture_x0020_53" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:392.25pt;
     2307 height:340.5pt;visibility:visible;mso-wrap-style:square'>
     2308 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image083.png" o:title=""/>
     2309</v:shape><![endif]--><![if !vml]><img width=523 height=454
     2310src="Charge%20Flipping%20in%20GSAS_files/image084.gif" v:shapes="Picture_x0020_53"><![endif]></span></p>
    22812311
    22822312<p class=MsoNormal>What is drawn here are green dots whose size are
     
    22902320the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    22912321mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b>
    2292 tab much the same way we did earlier in this exercise. Another is to get the
    2293 atom position directly from the map, we will do that now.</p>
     2322tab much the same way we did earlier in this exercise. Another is to get the atom
     2323position directly from the map, we will do that now.</p>
    22942324
    22952325<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    23152345
    23162346<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2317  id="Picture_x0020_21" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:350.25pt;
    2318  height:302.25pt;visibility:visible;mso-wrap-style:square'>
    2319  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image039.png" o:title=""
    2320   cropbottom="13787f" cropleft="10923f" cropright="20900f"/>
    2321 </v:shape><![endif]--><![if !vml]><img width=467 height=403
    2322 src="Charge%20Flipping%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_21"><![endif]></span></p>
     2347 id="Picture_x0020_54" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:342pt;
     2348 height:294.75pt;visibility:visible;mso-wrap-style:square'>
     2349 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image085.png" o:title=""/>
     2350</v:shape><![endif]--><![if !vml]><img width=456 height=393
     2351src="Charge%20Flipping%20in%20GSAS_files/image086.gif" v:shapes="Picture_x0020_54"><![endif]></span></p>
    23232352
    23242353<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
     
    23272356</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
    23282357style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2329 mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>, a white
    2330 ball will appear at the selected position and an H-atom (name = <b
     2358mso-hansi-theme-font:minor-latin'>Edit Atoms/Insert view point</span></b>, a
     2359white ball will appear at the selected position and an H-atom (name = <b
    23312360style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23322361mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
     
    23442373
    23452374<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2346  id="Picture_x0020_22" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:348pt;
    2347  height:297pt;visibility:visible;mso-wrap-style:square'>
    2348  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image041.png" o:title=""
    2349   croptop="374f" cropbottom="13600f" cropleft="10817f" cropright="20795f"/>
    2350 </v:shape><![endif]--><![if !vml]><img width=464 height=396
    2351 src="Charge%20Flipping%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_22"><![endif]></span></p>
     2375 id="Picture_x0020_55" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:306.75pt;
     2376 height:264.75pt;visibility:visible;mso-wrap-style:square'>
     2377 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image087.png" o:title=""/>
     2378</v:shape><![endif]--><![if !vml]><img width=409 height=353
     2379src="Charge%20Flipping%20in%20GSAS_files/image088.gif" v:shapes="Picture_x0020_55"><![endif]></span></p>
    23522380
    23532381<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2354  id="Picture_x0020_23" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
    2355  height:225pt;visibility:visible;mso-wrap-style:square'>
    2356  <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image043.png" o:title=""/>
    2357 </v:shape><![endif]--><![if !vml]><img width=700 height=300
    2358 src="Charge%20Flipping%20in%20GSAS_files/image044.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
     2382 id="Picture_x0020_56" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
     2383 height:228.75pt;visibility:visible;mso-wrap-style:square'>
     2384 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image089.png" o:title=""/>
     2385</v:shape><![endif]--><![if !vml]><img width=624 height=305
     2386src="Charge%20Flipping%20in%20GSAS_files/image090.gif" v:shapes="Picture_x0020_56"><![endif]></span></p>
    23592387
    23602388<p class=MsoNormal>Change the <b style='mso-bidi-font-weight:normal'><span
     
    23952423  cropbottom="13413f" cropleft="10818f" cropright="21005f"/>
    23962424</v:shape><![endif]--><![if !vml]><img width=464 height=403
    2397 src="Charge%20Flipping%20in%20GSAS_files/image046.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
     2425src="Charge%20Flipping%20in%20GSAS_files/image091.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
    23982426
    23992427<p class=MsoNormal>I moved the cross to a very interesting feature of the map
  • Tutorials/CFjadarite/Charge Flipping in GSAS_files/filelist.xml

    r1718 r2986  
    55 <o:File HRef="themedata.thmx"/>
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    5456</xml>
  • Tutorials/CFjadarite/Charge Flipping in GSAS_files/item0052.xml

    r1718 r2986  
    1 <b:Sources SelectedStyle="\HarvardIUCrIT.XSL" StyleName="IUCr Int. Tables*" xmlns:b="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" xmlns="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"></b:Sources>
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  • Tutorials/CFjadarite/Charge Flipping in GSAS_files/props053.xml

    r1728 r2986  
    11<?xml version="1.0" encoding="UTF-8" standalone="no"?>
    2 <ds:datastoreItem ds:itemID="{A7432F61-DED9-4BD8-B9BE-DE86CEEDA0F5}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>
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