Changeset 3078


Ignore:
Timestamp:
Sep 15, 2017 3:57:16 PM (6 years ago)
Author:
vondreele
Message:

Update to 2 frame

Location:
Tutorials/MCsimanneal
Files:
36 added
57 deleted
22 edited

Legend:

Unmodified
Added
Removed

  • Tutorials/MCsimanneal/MCSA in GSAS.htm

    r2390 r3078  
    2222 <o:DocumentProperties>
    2323  <o:Author>vondreele</o:Author>
    24   <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>4</o:Revision>
    26   <o:TotalTime>768</o:TotalTime>
     24  <o:LastAuthor>vondreele</o:LastAuthor>
     25  <o:Revision>7</o:Revision>
     26  <o:TotalTime>1389</o:TotalTime>
    2727  <o:Created>2015-03-16T21:14:00Z</o:Created>
    28   <o:LastSaved>2016-07-28T18:42:00Z</o:LastSaved>
    29   <o:Pages>1</o:Pages>
    30   <o:Words>2431</o:Words>
    31   <o:Characters>13861</o:Characters>
     28  <o:LastSaved>2017-09-15T20:53:00Z</o:LastSaved>
     29  <o:Pages>26</o:Pages>
     30  <o:Words>2658</o:Words>
     31  <o:Characters>15155</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    33   <o:Lines>115</o:Lines>
    34   <o:Paragraphs>32</o:Paragraphs>
    35   <o:CharactersWithSpaces>16260</o:CharactersWithSpaces>
     33  <o:Lines>126</o:Lines>
     34  <o:Paragraphs>35</o:Paragraphs>
     35  <o:CharactersWithSpaces>17778</o:CharactersWithSpaces>
    3636  <o:Version>16.00</o:Version>
    3737 </o:DocumentProperties>
    3838</xml><![endif]-->
    39 <link rel=dataStoreItem href="MCSA%20in%20GSAS_files/item0060.xml"
    40 target="MCSA%20in%20GSAS_files/props061.xml">
     39<link rel=dataStoreItem href="MCSA%20in%20GSAS_files/item0066.xml"
     40target="MCSA%20in%20GSAS_files/props067.xml">
    4141<link rel=themeData href="MCSA%20in%20GSAS_files/themedata.thmx">
    4242<link rel=colorSchemeMapping
    … …  
    4444<!--[if gte mso 9]><xml>
    4545 <w:WordDocument>
     46  <w:View>Print</w:View>
     47  <w:Zoom>124</w:Zoom>
    4648  <w:SpellingState>Clean</w:SpellingState>
    4749  <w:GrammarState>Clean</w:GrammarState>
    … …  
    644646 /* Font Definitions */
    645647 @font-face
     648        {font-family:"Cambria Math";
     649        panose-1:2 4 5 3 5 4 6 3 2 4;
     650        mso-font-charset:0;
     651        mso-generic-font-family:roman;
     652        mso-font-pitch:variable;
     653        mso-font-signature:-536870145 1107305727 0 0 415 0;}
     654@font-face
    646655        {font-family:Calibri;
    647656        panose-1:2 15 5 2 2 2 4 3 2 4;
    … …  
    649658        mso-generic-font-family:swiss;
    650659        mso-font-pitch:variable;
    651         mso-font-signature:-536870145 1073786111 1 0 415 0;}
     660        mso-font-signature:-536859905 -1073732485 9 0 511 0;}
    652661@font-face
    653662        {font-family:Cambria;
    … …  
    11041113        font-family:"Calibri",sans-serif;
    11051114        mso-fareast-font-family:"Times New Roman";
    1106         mso-fareast-theme-font:minor-fareast;
    1107         mso-bidi-font-family:Calibri;}
     1115        mso-fareast-theme-font:minor-fareast;}
    11081116span.SpellE
    11091117        {mso-style-name:"";
    … …  
    12731281<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
    12741282structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
    1275 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
    1276 kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
     1283diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
     1284were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
    12771285and were originally collected on NSLS beam line X3b1. The MC/SA technique is
    12781286needed in these cases because as you will see the data does not extend very far
    … …  
    12931301style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
    12941302the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1295 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1296 Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
    1297 data file</span></b> menu item to read the data file into the current GSAS-II
    1298 project. Change the file directory to <span class=SpellE><b style='mso-bidi-font-weight:
    1299 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1300 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1301 mso-bidi-theme-font:minor-latin'>MCsimanneal</span></b></span><b
    1302 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1303 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1304 Calibri;mso-bidi-theme-font:minor-latin'>/data</span></b><span
    1305 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1306 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1304minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
     1305to read the data file into the current GSAS-II project. Change the file
     1306directory to <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1307style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1308mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>MCsimanneal</span></b></span><b
     1309style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1310mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1311minor-latin'>/data</span></b><span style='font-family:"Calibri",sans-serif;
     1312mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    13071313minor-latin'> to find the file; you may need to change the file type to <b
    1308 style='mso-bidi-font-weight:normal'>All files (<span class=GramE>*.*</span>)</b>
    1309 to find the desired file.</span></p>
     1314style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired file.</span></p>
    13101315
    13111316<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
    … …  
    13141319the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    13151320style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1316 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1317 minor-latin'>Quinoli.gda</span></b></span><span style='font-family:"Calibri",sans-serif;
    1318 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1319 Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog
    1320 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1321 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1322 Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1323 Dialog box asking <b style='mso-bidi-font-weight:normal'><span
    1324 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1325 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1326 minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
    1327 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1328 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1329 mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
     1321mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Quinoli.gda</span></b></span><span
     1322style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1323mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> data</span>
     1324file in the first dialog and press <b style='mso-bidi-font-weight:normal'><span
     1325style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1326mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
     1327There will be a Dialog box asking <b style='mso-bidi-font-weight:normal'><span
     1328style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1329mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is this the
     1330file you want?</span></b> Press <b style='mso-bidi-font-weight:normal'><span
     1331style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1332mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
     1333button to proceed.</p>
    13301334
    13311335<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
    … …  
    13331337style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    13341338the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1335 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1336 Calibri;mso-bidi-theme-font:minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b>
    1337 instrument parameter file in the second dialog and press <b style='mso-bidi-font-weight:
    1338 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1339 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1340 mso-bidi-theme-font:minor-latin'>Open</span></b>. You’ll have to change the
    1341 file type to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1342 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1343 minor-latin'>*.<span class=SpellE>instprm</span></span></b> (GSAS-II instrument
    1344 parameter file). The powder pattern will immediately appear.</p>
     1339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1340minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b> instrument
     1341parameter file in the second dialog and press <b style='mso-bidi-font-weight:
     1342normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1343minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
     1344You’ll have to change the file type to <b style='mso-bidi-font-weight:normal'><span
     1345style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1346mso-hansi-theme-font:minor-latin'>*.<span class=SpellE>instprm</span></span></b>
     1347(GSAS-II instrument parameter file). The powder pattern will immediately
     1348appear.</p>
    13451349
    13461350<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
    … …  
    13641368 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    13651369 <o:lock v:ext="edit" aspectratio="t"/>
    1366 </v:shapetype><v:shape id="Picture_x0020_28" o:spid="_x0000_i1051" type="#_x0000_t75"
    1367  style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
    1368  <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
    1369 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1370 src="MCSA%20in%20GSAS_files/image055.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1370</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75"
     1371 style='width:468pt;height:401.25pt;visibility:visible;mso-wrap-style:square'>
     1372 <v:imagedata src="MCSA%20in%20GSAS_files/image002.png" o:title=""/>
     1373</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1374src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_1"><![endif]></span></p>
    13711375
    13721376<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
    … …  
    13931397picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
    13941398normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1395 minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ <span
    1396 class=SpellE>PeakFit</span> </span></b>to fit them. You will need to vary at
    1397 least <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1399minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span>
     1400</span></b>to fit them (it will ask to save the project; I called it ‘<b
     1401style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1402mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1403minor-latin'>2-amino</span></b>’). You will need to vary at least <b
     1404style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13981405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    13991406&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    … …  
    14261433style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14271434mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
    1428 cell should almost immediately appear with an M20 ~200 with a=7.748, b=7.651,
     1435cell should almost immediately appear with an M20 ~370 with a=7.748, b=7.650,
    14291436c=12.736, Vol=755.01. NB: your solution may have a &amp; b switched. Do <b
    14301437style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    … …  
    14631470"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
    14641471style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>;
    1465 there is a zero point at the end that needs to be excluded. Use the right mouse
    1466 button and pick a point just inside the end avoiding the zero. Make a note of
    1467 the exact d-spacing (for me 1.8133) using the mouse cursor on the plot.</p>
     1472there are a few zero points at the end that need to be excluded. Use the right
     1473mouse button and pick a point just inside the end avoiding the zeros. Make a
     1474note of the exact d-spacing (for me 1.8126) using the mouse cursor on the plot.</p>
    14681475
    14691476<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    … …  
    15041511normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    15051512minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
    1506 box and enter the d-spacing (1.8133) into the <b style='mso-bidi-font-weight:
    1507 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1508 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
    1509 box.</p>
     1513box, enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
     1514style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1515mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1.8126</span></b>)
     1516into the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1517mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
     1518class=SpellE>dmin</span></span></b> box and set the <b style='mso-bidi-font-weight:
     1519normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1520minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Pawley
     1521neg. wt.</span></b><span style='mso-spacerun:yes'>  </span><span class=GramE>to</span>
     1522<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1523mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1524minor-latin'>0.001</span></b>. This will suppress possible negative Pawley
     1525reflection intensities.</p>
    15101526
    15111527<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
    … …  
    15141530
    15151531<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1516  id="Picture_x0020_2" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:487.5pt;
    1517  height:375pt;visibility:visible;mso-wrap-style:square'>
    1518  <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
    1519 </v:shape><![endif]--><![if !vml]><img border=0 width=650 height=500
    1520 src="MCSA%20in%20GSAS_files/image056.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1532 id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:468pt;
     1533 height:263.25pt;visibility:visible;mso-wrap-style:square'>
     1534 <v:imagedata src="MCSA%20in%20GSAS_files/image006.png" o:title=""/>
     1535</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=351
     1536src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
    15211537
    15221538<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    15271543for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
    15281544style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1529 mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
    1530 dialog box will appear</p>
    1531 
    1532 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1533  id="Picture_x0020_3" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;
    1534  height:252pt;visibility:visible;mso-wrap-style:square'>
    1535  <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
    1536 </v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
    1537 src="MCSA%20in%20GSAS_files/image057.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
     1545mso-hansi-theme-font:minor-latin'>Edit Phase/Add powder histograms</span></b>;
     1546a dialog box will appear</p>
     1547
     1548<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1549 id="Picture_x0020_3" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:241.5pt;
     1550 height:228.75pt;visibility:visible;mso-wrap-style:square'>
     1551 <v:imagedata src="MCSA%20in%20GSAS_files/image010.png" o:title=""/>
     1552</v:shape><![endif]--><![if !vml]><img border=0 width=322 height=305
     1553src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
    15381554
    15391555<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15401556
    1541 <p class=MsoNormal>Select either choice; the desired data set will be added to
    1542 this phase for analysis. The data tab now shows the new data set.</p>
    1543 
    1544 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1545  id="Picture_x0020_30" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
    1546  height:375pt;visibility:visible;mso-wrap-style:square'>
    1547  <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
    1548 </v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
    1549 src="MCSA%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
     1557<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
     1558style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1559mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Set All</span></b>
     1560and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1561mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     1562minor-latin'>OK</span></b>; the desired data set will be added to this phase
     1563for analysis. The data tab now shows the new data set.</p>
     1564
     1565<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1566 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
     1567 height:263.25pt;visibility:visible;mso-wrap-style:square'>
     1568 <v:imagedata src="MCSA%20in%20GSAS_files/image014.png" o:title=""/>
     1569</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=351
     1570src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
    15501571
    15511572<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    15741595
    15751596<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1576  id="Picture_x0020_5" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
    1577  height:225pt;visibility:visible;mso-wrap-style:square'>
    1578  <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
    1579 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
    1580 src="MCSA%20in%20GSAS_files/image059.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
     1597 id="Picture_x0020_5" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
     1598 height:345pt;visibility:visible;mso-wrap-style:square'>
     1599 <v:imagedata src="MCSA%20in%20GSAS_files/image018.png" o:title=""/>
     1600</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=460
     1601src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
    15811602
    15821603<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15831604
    1584 <p class=MsoNormal>This completes the Pawley refinement setup; be careful that you
    1585 didn’t skip a step as it might not work correctly if you did.</p>
     1605<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
     1606you didn’t skip a step as it might not work correctly if you did.</p>
    15861607
    15871608<h2>Step 5. Pawley refinement</h2>
    … …  
    15951616mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
    15961617used to recover from a bad refinement. A progress dialog box will appear
    1597 showing the residual as the refinement proceeds. My refinement completed with <span
    1598 class=SpellE>Rwp</span> ~12.9%; a dialog box appears asking if you wish to load
    1599 the result. Press <b style='mso-bidi-font-weight:normal'><span
    1600 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1601 mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
    1602 PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
    1603 
    1604 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1605  id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
    1606  height:450pt;visibility:visible;mso-wrap-style:square'>
    1607  <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
    1608 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1609 src="MCSA%20in%20GSAS_files/image060.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
     1618showing the residual as the refinement proceeds. My refinement (after 2-3
     1619tries) completed with <span class=SpellE>Rwp</span> ~13%; a dialog box appears
     1620asking if you wish to load the result. Press <b style='mso-bidi-font-weight:
     1621normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1622minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot
     1623select the PWDR line in the GSAS-II data tree (I’ve adjusted the width and
     1624height).</p>
     1625
     1626<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1627 id="Picture_x0020_6" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
     1628 height:401.25pt;visibility:visible;mso-wrap-style:square'>
     1629 <v:imagedata src="MCSA%20in%20GSAS_files/image022.png" o:title=""/>
     1630</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1631src="MCSA%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
    16101632
    16111633<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    16341656minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b
    16351657style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1636 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>;
     1658mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>;
    16371659for the peak only refine <b style='mso-bidi-font-weight:normal'><span
    16381660style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    … …  
    16451667
    16461668<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1647  id="Picture_x0020_33" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
    1648  height:197.25pt;visibility:visible;mso-wrap-style:square'>
    1649  <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
    1650 </v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
    1651 src="MCSA%20in%20GSAS_files/image061.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
     1669 id="Picture_x0020_7" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
     1670 height:207.75pt;visibility:visible;mso-wrap-style:square'>
     1671 <v:imagedata src="MCSA%20in%20GSAS_files/image026.png" o:title=""/>
     1672</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=277
     1673src="MCSA%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
    16521674
    16531675<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    16561678style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16571679mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
    1658 class=SpellE>Rwp</span> fell to ~8.5%. In <b style='mso-bidi-font-weight:normal'><span
     1680class=SpellE>Rwp</span> fell to ~10%. In <b style='mso-bidi-font-weight:normal'><span
    16591681style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16601682mso-hansi-theme-font:minor-latin'>Background</span></b> select <span
    … …  
    16731695do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16741696mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate
    1675 /Refine</span></b> again. I got Rwp~7.5% at convergence and the fit looked like</p>
    1676 
    1677 <p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
    1678  id="Picture_x0020_8" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
    1679  height:450pt;visibility:visible;mso-wrap-style:square'>
    1680  <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
    1681 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1682 src="MCSA%20in%20GSAS_files/image062.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
     1697/Refine</span></b> again. I got Rwp~8.3% at convergence and the fit looked like</p>
     1698
     1699<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1700
     1701<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1702 id="Picture_x0020_8" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
     1703 height:401.25pt;visibility:visible;mso-wrap-style:square'>
     1704 <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
     1705</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1706src="MCSA%20in%20GSAS_files/image025.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
    16831707
    16841708<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    16931717
    16941718<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1695  id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:142.5pt;
     1719 id="Picture_x0020_9" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:142.5pt;
    16961720 height:93.75pt;visibility:visible;mso-wrap-style:square'>
    16971721 <v:imagedata src="MCSA%20in%20GSAS_files/image017.png" o:title="" croptop="20629f"
    16981722  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
    16991723</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
    1700 src="MCSA%20in%20GSAS_files/image063.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
     1724src="MCSA%20in%20GSAS_files/image027.jpg" v:shapes="Picture_x0020_9"><![endif]></span></p>
    17011725
    17021726<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
    … …  
    17151739mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
    17161740style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1717 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Body/Import
    1718 XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:normal'><span
    1719 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1720 mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <span
    1721 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1722 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1723 minor-latin'>aminoquinoline.xyz</span></b></span>. The <b style='mso-bidi-font-weight:
    1724 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1725 minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b> window
    1726 will show</p>
    1727 
    1728 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1729  id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:300pt;
    1730  height:320.25pt;visibility:visible;mso-wrap-style:square'>
    1731  <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
    1732 </v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
    1733 src="MCSA%20in%20GSAS_files/image064.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
     1741mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit
     1742Body/Import XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:
     1743normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1744minor-latin;mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and
     1745select <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1746style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1747mso-hansi-theme-font:minor-latin'>aminoquinoline.xyz</span></b></span>. The <b
     1748style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1749mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b>
     1750window will show</p>
     1751
     1752<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1753 id="Picture_x0020_31" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
     1754 height:419.25pt;visibility:visible;mso-wrap-style:square'>
     1755 <v:imagedata src="MCSA%20in%20GSAS_files/image028.png" o:title=""/>
     1756</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=559
     1757src="MCSA%20in%20GSAS_files/image029.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
    17341758
    17351759<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17361760
     1761<p class=MsoNormal>You should change the <b style='mso-bidi-font-weight:normal'><span
     1762style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1763mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
     1764meaningful, I used <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'>amino</span></b>.<o:p></o:p></p>
     1767
    17371768<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
    17381769style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    … …  
    17401771
    17411772<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1742  id="Picture_x0020_11" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;
    1743  height:234pt;visibility:visible;mso-wrap-style:square'>
    1744  <v:imagedata src="MCSA%20in%20GSAS_files/image021.png" o:title="" croptop="13685f"
    1745   cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
    1746 </v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
    1747 src="MCSA%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_11"><![endif]></span></p>
     1773 id="Picture_x0020_32" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
     1774 height:406.5pt;visibility:visible;mso-wrap-style:square'>
     1775 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
     1776</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=542
     1777src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    17481778
    17491779<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    17511781<p class=MsoNormal>The orientation is determined by rotation and translation
    17521782about a coordinate system centered on C1 and defined by the vectors C1-C2 and
    1753 C1-C3; you can change these via the pull downs (you can’t pick the same atom
    1754 for two of these so pick them appropriately; I chose C2, C3 &amp; C6). My new
    1755 model is</p>
    1756 
    1757 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1758  id="Picture_x0020_36" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:4in;
    1759  height:234.75pt;visibility:visible;mso-wrap-style:square'>
    1760  <v:imagedata src="MCSA%20in%20GSAS_files/image023.png" o:title="" croptop="13609f"
    1761   cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
    1762 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
    1763 src="MCSA%20in%20GSAS_files/image066.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
     1783C1-C3. The C1-C2 vector defines the X-axis (red), the cross product of C1-C2 and
     1784C1-C3 defines the Z-axis (blue; default view direction) and the Y-axis is
     1785defined as Z-axis cross X-axis (green; down toward C5). You can change these
     1786via the pull downs (you can’t pick the same atom for two of these so pick them
     1787appropriately; I chose C2, C3 &amp; C6). At each choice the structure will be
     1788transformed accordingly. My new model is</p>
     1789
     1790<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1791 id="_x0000_i1041" type="#_x0000_t75" style='width:468pt;height:404.25pt;
     1792 visibility:visible;mso-wrap-style:square'>
     1793 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
     1794</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
     1795src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="_x0000_i1041"><![endif]></span></p>
    17641796
    17651797<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17661798
    1767 <p class=MsoNormal>Notice that the model includes H-atoms; they are not really
    1768 needed for MC/SA and will just make computation times a bit longer than
    1769 necessary. You should change the <b style='mso-bidi-font-weight:normal'><span
    1770 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1771 mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
    1772 meaningful, I used <b style='mso-bidi-font-weight:normal'><span
    1773 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1774 mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
     1799<p class=MsoNormal>The molecular coordinate system has been changed by you
     1800assignment of reference atoms. The C2-C3 vector is now the X-axis (red), the
     1801C2-C6 vector is ~ the Y-axis (green) and the Z-axis (blue) is ~normal to the
     1802molecular plane. The rigid body coordinates reflect this change</p>
     1803
     1804<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1805 id="_x0000_i1040" type="#_x0000_t75" style='width:468pt;height:420.75pt;
     1806 visibility:visible;mso-wrap-style:square'>
     1807 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title=""/>
     1808</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=561
     1809src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="_x0000_i1040"><![endif]></span></p>
     1810
     1811<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The Cart z values are
     1812all close to zero and C3 has only a nonzero Cart x. Notice that the model
     1813includes H-atoms; they are not really needed for MC/SA and will just make
     1814computation times a bit longer than necessary. They can be removed by selecting
     1815the Strip H-atoms box; for now leave them in. </p>
     1816
     1817<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17751818
    17761819<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
    … …  
    17871830
    17881831<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1789  id="Picture_x0020_37" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:448.5pt;
    1790  height:251.25pt;visibility:visible;mso-wrap-style:square'>
    1791  <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
    1792 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
    1793 src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
     1832 id="_x0000_i1039" type="#_x0000_t75" style='width:468pt;height:212.25pt;
     1833 visibility:visible;mso-wrap-style:square'>
     1834 <v:imagedata src="MCSA%20in%20GSAS_files/image042.png" o:title=""/>
     1835</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=283
     1836src="MCSA%20in%20GSAS_files/image044.gif" v:shapes="_x0000_i1039"><![endif]></span></p>
    17941837
    17951838<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17961839
    1797 <p class=MsoNormal>And the plot shows the arbitrarily positioned molecules.</p>
    1798 
    1799 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1800  id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in;
    1801  height:232.5pt;visibility:visible;mso-wrap-style:square'>
    1802  <v:imagedata src="MCSA%20in%20GSAS_files/image027.png" o:title="" croptop="17592f"
    1803   cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
    1804 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
    1805 src="MCSA%20in%20GSAS_files/image068.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1840<p class=MsoNormal>And the plot shows the molecular XYZ-axes lined up along the
     1841crystal <span class=SpellE>abc</span>-axes; this is expected from our choice of
     1842molecular reference atoms (C2, C3 &amp; C6).</p>
     1843
     1844<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1845 id="Picture_x0020_33" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
     1846 height:404.25pt;visibility:visible;mso-wrap-style:square'>
     1847 <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
     1848</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
     1849src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    18061850
    18071851<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    18091853<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
    18101854whose centers fall within the unit cell; the reference one is that in the lower
    1811 left corner with C1 at the origin. You can enter values in the <span
    1812 class=SpellE><span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1813 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1814 mso-hansi-theme-font:minor-latin'>x,y</span></b></span><b style='mso-bidi-font-weight:
    1815 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1816 minor-latin;mso-hansi-theme-font:minor-latin'>,z</span></b></span> boxes and
    1817 see how the structure changes. Similarly, you can enter an angle in <span
     1855right corner with C2 at the origin. You can enter values in the <span
    18181856class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    18191857"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1820 minor-latin'>Oa</span></b></span> or a vector in the <span class=SpellE><span
    1821 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1822 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1823 minor-latin'>Oi,Oj</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1824 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1825 mso-hansi-theme-font:minor-latin'>,Ok</span></b></span><span
     1858minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
     1859the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
     1860style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1861mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
     1862or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1863style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1864mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
    18261865style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
    1827 molecule. Each of these parameters has a defined range for the MC/SA optimization
    1828 run we are about to do; they define the multidimensional search volume. Within
    1829 that volume will be a number of correct solutions to the structure problem all
    1830 related by translational and space group symmetry. One can limit this volume by
    1831 choosing more limited ranges, but here we’ll just go with the default. We want
    1832 to optimize the position and orientation of this molecule; check the <b
    1833 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1834 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>x</span></b>,
    1835 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1836 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b>
    1837 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1866molecule. Each of these parameters has a defined range for the MC/SA
     1867optimization run we are about to do; they define the multidimensional search
     1868volume. Within that volume will be a number of correct solutions to the
     1869structure problem all related by translational and space group symmetry. One
     1870can limit this volume by choosing more limited ranges, but here we’ll just go
     1871with the default. We want to optimize the position and orientation of this
     1872molecule; check the <b style='mso-bidi-font-weight:normal'><span
     1873style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1874mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
     1875normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1876minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <b
     1877style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18381878mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>
    18391879boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    … …  
    18421882normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18431883minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
    1844 class=SpellE><span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1845 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1846 mso-hansi-theme-font:minor-latin'>Oi,Oj</span></b></span><b style='mso-bidi-font-weight:
    1847 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1848 minor-latin;mso-hansi-theme-font:minor-latin'>,Ok</span></b></span><b
     1884class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1885"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1886minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
    18491887style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18501888mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b>
    … …  
    18521890
    18531891<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1854  id="Picture_x0020_15" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;
    1855  height:193.5pt;visibility:visible;mso-wrap-style:square'>
    1856  <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
    1857 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
    1858 src="MCSA%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_15"><![endif]></span><span
     1892 id="Picture_x0020_34" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
     1893 height:204.75pt;visibility:visible;mso-wrap-style:square'>
     1894 <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
     1895</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=273
     1896src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_34"><![endif]></span><span
    18591897style='mso-spacerun:yes'> </span></p>
    18601898
    … …  
    18921930normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18931931minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it
    1894 give slightly better performance in MC/SA.</p>
     1932gives slightly better performance in MC/SA.</p>
    18951933
    18961934<p class=MsoNormal>Next, you need to set the minimum d-spacing (<b
    … …  
    19181956for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19191957mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
    1920 this is the number of random tries at each “temperature” in the annealing
    1921 schedule. I also used <b style='mso-bidi-font-weight:normal'><span
    1922 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1923 mso-hansi-theme-font:minor-latin'>4 MC/SA runs</span></b> When done the <b
    1924 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1925 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    1926 window should look like</p>
    1927 
    1928 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1929  id="Picture_x0020_38" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
    1930  height:375pt;visibility:visible;mso-wrap-style:square'>
    1931  <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
    1932 </v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
    1933 src="MCSA%20in%20GSAS_files/image070.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
     1958this is the number of random tries at each “temperature” in the annealing schedule.
     1959I also used <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1960"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1961minor-latin'>4 MC/SA runs</span></b> When done the <b style='mso-bidi-font-weight:
     1962normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1963minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> window should
     1964look like</p>
     1965
     1966<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1967 id="Picture_x0020_35" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
     1968 height:223.5pt;visibility:visible;mso-wrap-style:square'>
     1969 <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
     1970</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=298
     1971src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
    19341972
    19351973<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    19491987
    19501988<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1951  id="Picture_x0020_39" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:564pt;
    1952  height:273.75pt;visibility:visible;mso-wrap-style:square'>
    1953  <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
    1954 </v:shape><![endif]--><![if !vml]><img border=0 width=752 height=365
    1955 src="MCSA%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
     1989 id="Picture_x0020_36" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
     1990 height:253.5pt;visibility:visible;mso-wrap-style:square'>
     1991 <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
     1992</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=338
     1993src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
    19561994
    19571995<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    19611999
    19622000<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1963  id="Picture_x0020_1" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:364.5pt;
    1964  height:298.5pt;visibility:visible;mso-wrap-style:square'>
    1965  <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="8643f"
    1966   cropbottom="21002f" cropleft="39996f" cropright="10456f"/>
    1967 </v:shape><![endif]--><![if !vml]><img border=0 width=486 height=398
    1968 src="MCSA%20in%20GSAS_files/image072.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     2001 id="Picture_x0020_37" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
     2002 height:405pt;visibility:visible;mso-wrap-style:square'>
     2003 <v:imagedata src="MCSA%20in%20GSAS_files/image082.png" o:title=""/>
     2004</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=540
     2005src="MCSA%20in%20GSAS_files/image083.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
    19692006
    19702007<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    19712008
    19722009<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
    1973 good solution with a very low Residual (~4.8%). This problem typically gives
    1974 suitable solutions with Residuals of 4-5%. If your cell indexing resulted in a
    1975 &amp; b swapped, you should view the structure along b (green). If no good
    1976 solution appears (e.g. molecules clashing), then you should just rerun MC/SA
    1977 perhaps using more runs or more trials. Be sure to set the <b style='mso-bidi-font-weight:
    1978 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1979 minor-latin;mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any
    1980 solutions you want to retain; the others will be cleared before the next MC/SA
    1981 run starts. When you think you have a good one, <span class=GramE><b
    1982 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1983 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span>
    1984 it; the parameters will be copied to the appropriate boxes in the upper part of
    1985 the MC/SA window and the structure is drawn again. Next we want to refine this
     2010good solution with a very low Residual (~7.2%). This problem typically gives
     2011suitable solutions with Residuals of 7%; if you had stripped the H-atoms, the
     2012best residual is ~10%. If your cell indexing resulted in <span class=GramE>a
     2013&amp;</span> b swapped, you should view the structure along a (red). If no good
     2014solution appears (e.g. molecules clashing &amp; high residuals), then you
     2015should just rerun MC/SA perhaps using more runs or more trials.</p>
     2016
     2017<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
     2018
     2019<p class=MsoNormal>The MC/SA calculations can take advantage of multicore
     2020machines. First set the number of cores by doing <b style='mso-bidi-font-weight:
     2021normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2022minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Preferences</span></b>;
     2023select <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2024style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2025mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Multiprocessing_cores</span></b></span>
     2026from the pulldown and enter the number you wish to use (I suggest Maxcores-1).
     2027Then press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     2028style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2029mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b></span><b
     2030style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2031mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
     2032minor-latin'> current settings</span></b>; your choice becomes available immediately
     2033and is then set for all your future uses of GSAS-II. <span
     2034style='mso-spacerun:yes'> </span>Do <b style='mso-bidi-font-weight:normal'><span
     2035style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2036mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Compute/Multi
     2037MC/SA</span></b> to use it.</p>
     2038
     2039<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     2040
     2041<p class=MsoNormal>Be sure to set the <b style='mso-bidi-font-weight:normal'><span
     2042style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2043mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
     2044want to retain; the others will be cleared before the next MC/SA run starts.
     2045When you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
     2046normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2047minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span> it; the
     2048parameters will be copied to the appropriate boxes in the upper part of the
     2049MC/SA window and the structure is drawn again. Next we want to refine this
    19862050solution so go back to the <b style='mso-bidi-font-weight:normal'><span
    19872051style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    … …  
    19962060style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19972061mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
    1998 be sure to select the best one before starting. The residual should drop to a
     2062be sure to select the best one before starting. The residual might drop to a
    19992063much lower level. This refinement can be repeated with tighter restriction on
    2000 the ranges; I used 5% for a final run and got</p>
    2001 
    2002 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2003  id="Picture_x0020_40" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:448.5pt;
    2004  height:273.75pt;visibility:visible;mso-wrap-style:square'>
    2005  <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/>
    2006 </v:shape><![endif]--><![if !vml]><img border=0 width=598 height=365
    2007 src="MCSA%20in%20GSAS_files/image073.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
     2064the ranges. My result (no improvement on 7%) was</p>
     2065
     2066<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2067 id="Picture_x0020_38" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
     2068 height:257.25pt;visibility:visible;mso-wrap-style:square'>
     2069 <v:imagedata src="MCSA%20in%20GSAS_files/image084.png" o:title=""/>
     2070</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=343
     2071src="MCSA%20in%20GSAS_files/image085.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
    20082072
    20092073<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    20102074
    2011 <p class=MsoNormal>This is clearly a good result (R ~ 2.6%!) and the structure</p>
    2012 
    2013 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2014  id="Picture_x0020_23" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:288.75pt;
    2015  height:248.25pt;visibility:visible;mso-wrap-style:square'>
    2016  <v:imagedata src="MCSA%20in%20GSAS_files/image039.png" o:title="" croptop="11555f"
    2017   cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
    2018 </v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
    2019 src="MCSA%20in%20GSAS_files/image074.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
     2075<p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>7.2%</span>!)
     2076and the structure</p>
     2077
     2078<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2079 id="Picture_x0020_39" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
     2080 height:402.75pt;visibility:visible;mso-wrap-style:square'>
     2081 <v:imagedata src="MCSA%20in%20GSAS_files/image086.png" o:title=""/>
     2082</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=537
     2083src="MCSA%20in%20GSAS_files/image087.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
    20202084
    20212085<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    20222086
    2023 <p class=MsoNormal>is identical to the published one</p>
     2087<p class=MsoNormal>Has a different origin choice (a &amp; b might also be
     2088switched) than the published one </p>
    20242089
    20252090<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    20292094  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
    20302095</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
    2031 src="MCSA%20in%20GSAS_files/image075.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
     2096src="MCSA%20in%20GSAS_files/image088.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
    20322097
    20332098<p class=MsoNormal>as drawn by the Mercury program </p>
    … …  
    20432108
    20442109<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2045  id="Picture_x0020_25" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:4in;
    2046  height:243.75pt;visibility:visible;mso-wrap-style:square'>
    2047  <v:imagedata src="MCSA%20in%20GSAS_files/image043.png" o:title="" croptop="12581f"
    2048   cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
    2049 </v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
    2050 src="MCSA%20in%20GSAS_files/image076.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
     2110 id="Picture_x0020_40" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
     2111 height:402.75pt;visibility:visible;mso-wrap-style:square'>
     2112 <v:imagedata src="MCSA%20in%20GSAS_files/image089.png" o:title=""/>
     2113</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=537
     2114src="MCSA%20in%20GSAS_files/image090.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
    20512115
    20522116<p class=MsoNormal>And they will be listed in the Atoms table.</p>
    20532117
    20542118<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2055  id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
    2056  height:225pt;visibility:visible;mso-wrap-style:square'>
    2057  <v:imagedata src="MCSA%20in%20GSAS_files/image045.png" o:title=""/>
    2058 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
    2059 src="MCSA%20in%20GSAS_files/image077.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
     2119 id="Picture_x0020_41" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
     2120 height:288.75pt;visibility:visible;mso-wrap-style:square'>
     2121 <v:imagedata src="MCSA%20in%20GSAS_files/image091.png" o:title=""/>
     2122</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=385
     2123src="MCSA%20in%20GSAS_files/image095.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
    20602124
    20612125<p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use
    … …  
    20872151minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
    20882152the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
    2089 was ~9%. Next check the <b style='mso-bidi-font-weight:normal'><span
     2153was ~12%. Next check the <b style='mso-bidi-font-weight:normal'><span
    20902154style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    20912155mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b
    … …  
    21012165mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
    21022166style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2103 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. size</span></b>
    2104 &amp; <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    2105 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2106 mso-hansi-theme-font:minor-latin'>mustrain</span></b></span> boxes and do
    2107 another <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2108 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    2109 I got an <span class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not
    2110 refined atom positions or thermal parameters; to do this we need to describe
    2111 the structure as a rigid body.</p>
     2167mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
     2168class=GramE>size</span></span></b> &amp; <span class=SpellE><b
     2169style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
     2171boxes and do another <b style='mso-bidi-font-weight:normal'><span
     2172style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2173mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice) I got an <span
     2174class=SpellE>R<sub>wp</sub></span> ~8.2% for this. We’ve not refined atom
     2175positions or thermal parameters; to do this we need to describe the structure
     2176as a rigid body.</p>
    21122177
    21132178<h2>Step 9. Rigid body model</h2>
    … …  
    21322197minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
    21332198style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2134 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign
     2199mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Body/Assign
    21352200atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
    21362201normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    … …  
    21442209
    21452210<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2146  id="Picture_x0020_27" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:337.5pt;
    2147  height:218.25pt;visibility:visible;mso-wrap-style:square'>
    2148  <v:imagedata src="MCSA%20in%20GSAS_files/image047.png" o:title=""/>
    2149 </v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
    2150 src="MCSA%20in%20GSAS_files/image078.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
     2211 id="Picture_x0020_42" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
     2212 height:195.75pt;visibility:visible;mso-wrap-style:square'>
     2213 <v:imagedata src="MCSA%20in%20GSAS_files/image096.png" o:title=""/>
     2214</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=261
     2215src="MCSA%20in%20GSAS_files/image097.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
    21512216
    21522217<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    21582223reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight:
    21592224normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2160 minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b> when done; the
    2161 structure will be drawn with yellow bonds indicating that it is now a rigid
     2225minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b> when done; the
     2226structure will be drawn with orange bonds indicating that it is now a rigid
    21622227body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span
    21632228style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    … …  
    21662231
    21672232<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2168  id="Picture_x0020_29" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:474.75pt;
    2169  height:210pt;visibility:visible;mso-wrap-style:square'>
    2170  <v:imagedata src="MCSA%20in%20GSAS_files/image049.png" o:title=""/>
    2171 </v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
    2172 src="MCSA%20in%20GSAS_files/image079.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
    2173 
    2174 <p class=MsoNormal>To refine the rigid body <span class=GramE>parameters</span>
    2175 check the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2233 id="Picture_x0020_43" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
     2234 height:207pt;visibility:visible;mso-wrap-style:square'>
     2235 <v:imagedata src="MCSA%20in%20GSAS_files/image098.png" o:title=""/>
     2236</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=276
     2237src="MCSA%20in%20GSAS_files/image099.gif" v:shapes="Picture_x0020_43"><![endif]></span></p>
     2238
     2239<p class=MsoNormal>To refine the rigid body origin position check the <b
     2240style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21762241mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
    21772242box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    … …  
    21862251mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    21872252after a couple of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span>
    2188 ~7.9% and the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    2189 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2190 mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
    2191 new parameters</p>
    2192 
    2193 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2194  id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:474.75pt;
    2195  height:225.75pt;visibility:visible;mso-wrap-style:square'>
    2196  <v:imagedata src="MCSA%20in%20GSAS_files/image051.png" o:title=""/>
    2197 </v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
    2198 src="MCSA%20in%20GSAS_files/image080.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    2199 
    2200 <p class=MsoNormal>and the profile shows the fit</p>
    2201 
    2202 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2203  id="Picture_x0020_31" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
    2204  height:450pt;visibility:visible;mso-wrap-style:square'>
    2205  <v:imagedata src="MCSA%20in%20GSAS_files/image053.png" o:title=""/>
    2206 </v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    2207 src="MCSA%20in%20GSAS_files/image081.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
     2253~7.9% and the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2254"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2255minor-latin'>RB Models</span></b> window shows the new parameters</p>
     2256
     2257<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2258 id="Picture_x0020_44" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
     2259 height:3in;visibility:visible;mso-wrap-style:square'>
     2260 <v:imagedata src="MCSA%20in%20GSAS_files/image100.png" o:title=""/>
     2261</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=288
     2262src="MCSA%20in%20GSAS_files/image101.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
     2263
     2264<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
     2265
     2266<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     2267 id="Picture_x0020_45" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
     2268 height:401.25pt;visibility:visible;mso-wrap-style:square'>
     2269 <v:imagedata src="MCSA%20in%20GSAS_files/image102.png" o:title=""/>
     2270</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     2271src="MCSA%20in%20GSAS_files/image103.gif" v:shapes="Picture_x0020_45"><![endif]></span></p>
    22082272
    22092273<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.

  • Tutorials/MCsimanneal/MCSA in GSAS_files/filelist.xml

    r2390 r3078  
    11<xml xmlns:o="urn:schemas-microsoft-com:office:office">
    22 <o:MainFile HRef="../MCSA%20in%20GSAS.htm"/>
    3  <o:File HRef="item0060.xml"/>
    4  <o:File HRef="props061.xml"/>
     3 <o:File HRef="item0066.xml"/>
     4 <o:File HRef="props067.xml"/>
    55 <o:File HRef="themedata.thmx"/>
    66 <o:File HRef="colorschememapping.xml"/>
    7  <o:File HRef="image001.png"/>
    8  <o:File HRef="image055.gif"/>
    9  <o:File HRef="image003.png"/>
    10  <o:File HRef="image056.gif"/>
    11  <o:File HRef="image005.png"/>
    12  <o:File HRef="image057.gif"/>
    13  <o:File HRef="image007.png"/>
    14  <o:File HRef="image058.gif"/>
    15  <o:File HRef="image009.png"/>
    16  <o:File HRef="image059.gif"/>
    17  <o:File HRef="image011.png"/>
    18  <o:File HRef="image060.gif"/>
    19  <o:File HRef="image013.png"/>
    20  <o:File HRef="image061.gif"/>
    21  <o:File HRef="image015.png"/>
    22  <o:File HRef="image062.gif"/>
     7 <o:File HRef="image002.png"/>
     8 <o:File HRef="image004.gif"/>
     9 <o:File HRef="image006.png"/>
     10 <o:File HRef="image008.gif"/>
     11 <o:File HRef="image010.png"/>
     12 <o:File HRef="image012.gif"/>
     13 <o:File HRef="image014.png"/>
     14 <o:File HRef="image016.gif"/>
     15 <o:File HRef="image018.png"/>
     16 <o:File HRef="image020.gif"/>
     17 <o:File HRef="image022.png"/>
     18 <o:File HRef="image023.gif"/>
     19 <o:File HRef="image026.png"/>
     20 <o:File HRef="image024.gif"/>
     21 <o:File HRef="image030.png"/>
     22 <o:File HRef="image025.gif"/>
    2323 <o:File HRef="image017.png"/>
    24  <o:File HRef="image063.jpg"/>
    25  <o:File HRef="image019.png"/>
    26  <o:File HRef="image064.gif"/>
    27  <o:File HRef="image021.png"/>
    28  <o:File HRef="image065.jpg"/>
    29  <o:File HRef="image023.png"/>
    30  <o:File HRef="image066.jpg"/>
    31  <o:File HRef="image025.png"/>
    32  <o:File HRef="image067.gif"/>
    33  <o:File HRef="image027.png"/>
    34  <o:File HRef="image068.jpg"/>
    35  <o:File HRef="image029.png"/>
    36  <o:File HRef="image069.gif"/>
     24 <o:File HRef="image027.jpg"/>
     25 <o:File HRef="image028.png"/>
     26 <o:File HRef="image029.gif"/>
    3727 <o:File HRef="image031.png"/>
    38  <o:File HRef="image070.gif"/>
     28 <o:File HRef="image032.gif"/>
    3929 <o:File HRef="image033.png"/>
    40  <o:File HRef="image071.gif"/>
     30 <o:File HRef="image034.gif"/>
    4131 <o:File HRef="image035.png"/>
    42  <o:File HRef="image072.jpg"/>
    43  <o:File HRef="image037.png"/>
    44  <o:File HRef="image073.gif"/>
    45  <o:File HRef="image039.png"/>
    46  <o:File HRef="image074.jpg"/>
     32 <o:File HRef="image038.gif"/>
     33 <o:File HRef="image042.png"/>
     34 <o:File HRef="image044.gif"/>
     35 <o:File HRef="image066.png"/>
     36 <o:File HRef="image046.gif"/>
     37 <o:File HRef="image068.png"/>
     38 <o:File HRef="image048.gif"/>
     39 <o:File HRef="image070.png"/>
     40 <o:File HRef="image050.gif"/>
     41 <o:File HRef="image052.png"/>
     42 <o:File HRef="image054.gif"/>
     43 <o:File HRef="image082.png"/>
     44 <o:File HRef="image083.gif"/>
     45 <o:File HRef="image084.png"/>
     46 <o:File HRef="image085.gif"/>
     47 <o:File HRef="image086.png"/>
     48 <o:File HRef="image087.gif"/>
    4749 <o:File HRef="image041.png"/>
    48  <o:File HRef="image075.jpg"/>
    49  <o:File HRef="image043.png"/>
    50  <o:File HRef="image076.jpg"/>
    51  <o:File HRef="image045.png"/>
    52  <o:File HRef="image077.gif"/>
    53  <o:File HRef="image047.png"/>
    54  <o:File HRef="image078.gif"/>
    55  <o:File HRef="image049.png"/>
    56  <o:File HRef="image079.gif"/>
    57  <o:File HRef="image051.png"/>
    58  <o:File HRef="image080.gif"/>
    59  <o:File HRef="image053.png"/>
    60  <o:File HRef="image081.gif"/>
     50 <o:File HRef="image088.jpg"/>
     51 <o:File HRef="image089.png"/>
     52 <o:File HRef="image090.gif"/>
     53 <o:File HRef="image091.png"/>
     54 <o:File HRef="image095.gif"/>
     55 <o:File HRef="image096.png"/>
     56 <o:File HRef="image097.gif"/>
     57 <o:File HRef="image098.png"/>
     58 <o:File HRef="image099.gif"/>
     59 <o:File HRef="image100.png"/>
     60 <o:File HRef="image101.gif"/>
     61 <o:File HRef="image102.png"/>
     62 <o:File HRef="image103.gif"/>
    6163 <o:File HRef="filelist.xml"/>
    6264</xml>
Note: See TracChangeset for help on using the changeset viewer.