Changeset 2390 for Tutorials/MCsimanneal


Ignore:
Timestamp:
Jul 28, 2016 2:18:10 PM (5 years ago)
Author:
vondreele
Message:
 
Location:
Tutorials/MCsimanneal
Files:
12 edited

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Added
Removed
  • Tutorials/MCsimanneal/MCSA in GSAS.htm

    r1745 r2390  
    2323  <o:Author>vondreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>3</o:Revision>
    26   <o:TotalTime>767</o:TotalTime>
     25  <o:Revision>4</o:Revision>
     26  <o:TotalTime>768</o:TotalTime>
    2727  <o:Created>2015-03-16T21:14:00Z</o:Created>
    28   <o:LastSaved>2015-03-19T20:13:00Z</o:LastSaved>
     28  <o:LastSaved>2016-07-28T18:42:00Z</o:LastSaved>
    2929  <o:Pages>1</o:Pages>
    30   <o:Words>2432</o:Words>
    31   <o:Characters>13865</o:Characters>
     30  <o:Words>2431</o:Words>
     31  <o:Characters>13861</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>115</o:Lines>
    3434  <o:Paragraphs>32</o:Paragraphs>
    35   <o:CharactersWithSpaces>16265</o:CharactersWithSpaces>
    36   <o:Version>15.00</o:Version>
     35  <o:CharactersWithSpaces>16260</o:CharactersWithSpaces>
     36  <o:Version>16.00</o:Version>
    3737 </o:DocumentProperties>
    3838</xml><![endif]-->
     
    4444<!--[if gte mso 9]><xml>
    4545 <w:WordDocument>
    46   <w:Zoom>116</w:Zoom>
    4746  <w:SpellingState>Clean</w:SpellingState>
    4847  <w:GrammarState>Clean</w:GrammarState>
     
    645644 /* Font Definitions */
    646645 @font-face
    647         {font-family:"Cambria Math";
    648         panose-1:2 4 5 3 5 4 6 3 2 4;
    649         mso-font-charset:0;
    650         mso-generic-font-family:roman;
    651         mso-font-pitch:variable;
    652         mso-font-signature:-536870145 1107305727 0 0 415 0;}
    653 @font-face
    654646        {font-family:Calibri;
    655647        panose-1:2 15 5 2 2 2 4 3 2 4;
     
    960952        mso-hansi-font-family:"Courier New";
    961953        mso-bidi-font-family:"Courier New";}
     954p.msonormal0, li.msonormal0, div.msonormal0
     955        {mso-style-name:msonormal;
     956        mso-style-noshow:yes;
     957        mso-style-priority:99;
     958        mso-style-unhide:no;
     959        mso-margin-top-alt:auto;
     960        margin-right:0in;
     961        mso-margin-bottom-alt:auto;
     962        margin-left:0in;
     963        mso-pagination:widow-orphan;
     964        font-size:12.0pt;
     965        font-family:"Times New Roman",serif;
     966        mso-fareast-font-family:"Times New Roman";
     967        mso-fareast-theme-font:minor-fareast;}
    962968span.TitleChar
    963969        {mso-style-name:"Title Char";
     
    11121118        mso-ansi-font-size:10.0pt;
    11131119        mso-bidi-font-size:10.0pt;
     1120        font-family:"Calibri",sans-serif;
    11141121        mso-ascii-font-family:Calibri;
    11151122        mso-hansi-font-family:Calibri;
     
    12661273<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
    12671274structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
    1268 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
    1269 were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
     1275diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
     1276kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
    12701277and were originally collected on NSLS beam line X3b1. The MC/SA technique is
    12711278needed in these cases because as you will see the data does not extend very far
     
    12891296Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
    12901297data file</span></b> menu item to read the data file into the current GSAS-II
    1291 project. Change the file directory to <b style='mso-bidi-font-weight:normal'><span
    1292 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1293 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1294 minor-latin'>exercises/<span class=SpellE>MCsimanneal</span></span></b><span
     1298project. Change the file directory to <span class=SpellE><b style='mso-bidi-font-weight:
     1299normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1300minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1301mso-bidi-theme-font:minor-latin'>MCsimanneal</span></b></span><b
     1302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1304Calibri;mso-bidi-theme-font:minor-latin'>/data</span></b><span
    12951305style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12961306mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    12971307minor-latin'> to find the file; you may need to change the file type to <b
    1298 style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
    1299 file.</span></p>
     1308style='mso-bidi-font-weight:normal'>All files (<span class=GramE>*.*</span>)</b>
     1309to find the desired file.</span></p>
    13001310
    13011311<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     
    13111321mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    13121322Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1313 Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1323Dialog box asking <b style='mso-bidi-font-weight:normal'><span
    13141324style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13151325mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1316 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1317 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1318 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1319 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    1320 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'>Yes</span></b></span> button to
    1323 proceed.</p>
     1326minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
     1327normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1328minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1329mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
    13241330
    13251331<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     
    13621368 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
    13631369</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1364 src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1370src="MCSA%20in%20GSAS_files/image055.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    13651371
    13661372<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    14211427mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
    14221428cell should almost immediately appear with an M20 ~200 with a=7.748, b=7.651,
    1423 c=12.736, Vol=755.01. NB: your solution may have <span class=GramE>a &amp;</span>
    1424 b switched. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1425 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1426 minor-latin'>Cell Index/Refine/Copy Cell</span></b>; you can then try various
    1427 space groups. Press the <b style='mso-bidi-font-weight:normal'><span
    1428 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1429 mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to see the
    1430 lines with extinctions (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
    1431 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1432 mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub> 2<sub>1</sub> 2<sub>1</sub></span></b>).
    1433 You can then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1434 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1435 minor-latin'>Cell Index/Refine/Refine Cell</span></b> to improve the lattice
    1436 parameters with M20 ~380. Finally do <b style='mso-bidi-font-weight:normal'><span
    1437 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1438 mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Make new phase</span></b>
    1439 to create the phase; I named it <b style='mso-bidi-font-weight:normal'><span
    1440 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1441 mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
     1429c=12.736, Vol=755.01. NB: your solution may have a &amp; b switched. Do <b
     1430style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1431mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cell
     1432Index/Refine/Copy Cell</span></b>; you can then try various space groups. Press
     1433the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1434mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show HKL
     1435positions</span></b> to see the lines with extinctions (Hint: it’s <b
     1436style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1437mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub>
     14382<sub>1</sub> 2<sub>1</sub></span></b>). You can then do <b style='mso-bidi-font-weight:
     1439normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1440minor-latin;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
     1441to improve the lattice parameters with M20 ~380. Finally do <b
     1442style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1443mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cell
     1444Index/Refine/Make new phase</span></b> to create the phase; I named it <b
     1445style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1446mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
    14421447
    14431448<h2>Step 4. Setup for Pawley refinement</h2>
     
    15091514
    15101515<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1511  id="_x0000_i1050" type="#_x0000_t75" style='width:487.5pt;height:375pt;
    1512  visibility:visible;mso-wrap-style:square'>
     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'>
    15131518 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
    15141519</v:shape><![endif]--><![if !vml]><img border=0 width=650 height=500
    1515 src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1050"><![endif]></span></p>
     1520src="MCSA%20in%20GSAS_files/image056.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
    15161521
    15171522<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15301535 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
    15311536</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
    1532 src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
     1537src="MCSA%20in%20GSAS_files/image057.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
    15331538
    15341539<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15421547 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
    15431548</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
    1544 src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
     1549src="MCSA%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
    15451550
    15461551<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15731578 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
    15741579</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
    1575 src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
     1580src="MCSA%20in%20GSAS_files/image059.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
    15761581
    15771582<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15781583
    1579 <p class=MsoNormal>This completes the Pawley refinement setup; be careful that
    1580 you didn’t skip a step as it might not work correctly if you did.</p>
     1584<p class=MsoNormal>This completes the Pawley refinement setup; be careful that you
     1585didn’t skip a step as it might not work correctly if you did.</p>
    15811586
    15821587<h2>Step 5. Pawley refinement</h2>
     
    15981603
    15991604<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1600  id="_x0000_i1046" type="#_x0000_t75" style='width:525pt;height:450pt;
    1601  visibility:visible;mso-wrap-style:square'>
     1605 id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
     1606 height:450pt;visibility:visible;mso-wrap-style:square'>
    16021607 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
    16031608</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1604 src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
     1609src="MCSA%20in%20GSAS_files/image060.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
    16051610
    16061611<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16351640style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16361641mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
    1637 class=SpellE>coeff</span>.</span></b> <span class=GramE>to</span> <b
    1638 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1639 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>;
    1640 the window shows</p>
     1642class=SpellE>coeff</span>.</span></b> to <b style='mso-bidi-font-weight:normal'><span
     1643style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1644mso-hansi-theme-font:minor-latin'>5</span></b>; the window shows</p>
    16411645
    16421646<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    16451649 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
    16461650</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
    1647 src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
     1651src="MCSA%20in%20GSAS_files/image061.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    16481652
    16491653<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16671671normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16681672minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> for refinement; then
    1669 do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1670 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1671 mso-hansi-theme-font:minor-latin'>Calculate</span></b></span><b
    1672 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1673 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> /Refine</span></b>
    1674 again. I got Rwp~7.5% at convergence and the fit looked like</p>
     1673do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1674mso-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>
    16751676
    16761677<p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
    1677  id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
    1678  visibility:visible;mso-wrap-style:square'>
     1678 id="Picture_x0020_8" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
     1679 height:450pt;visibility:visible;mso-wrap-style:square'>
    16791680 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
    16801681</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1681 src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="_x0000_i1044"><![endif]></span></p>
     1682src="MCSA%20in%20GSAS_files/image062.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
    16821683
    16831684<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16971698  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
    16981699</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
    1699 src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
     1700src="MCSA%20in%20GSAS_files/image063.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
    17001701
    17011702<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
     
    17221723minor-latin'>aminoquinoline.xyz</span></b></span>. The <b style='mso-bidi-font-weight:
    17231724normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1724 minor-latin;mso-hansi-theme-font:minor-latin'>Rigid <span class=GramE>bodies</span></span></b>
    1725 window will show</p>
     1725minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b> window
     1726will show</p>
    17261727
    17271728<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    17301731 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
    17311732</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
    1732 src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
     1733src="MCSA%20in%20GSAS_files/image064.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
    17331734
    17341735<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    17361737<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
    17371738style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1738 mso-hansi-theme-font:minor-latin'>Plot?</span></b> <span class=GramE>box</span>
    1739 a drawing will appear</p>
    1740 
    1741 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1742  id="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;height:234pt;
    1743  visibility:visible;mso-wrap-style:square'>
     1739mso-hansi-theme-font:minor-latin'>Plot?</span></b> box a drawing will appear</p>
     1740
     1741<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'>
    17441744 <v:imagedata src="MCSA%20in%20GSAS_files/image021.png" o:title="" croptop="13685f"
    17451745  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
    17461746</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
    1747 src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="_x0000_i1041"><![endif]></span></p>
     1747src="MCSA%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_11"><![endif]></span></p>
    17481748
    17491749<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    17611761  cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
    17621762</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
    1763 src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
     1763src="MCSA%20in%20GSAS_files/image066.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    17641764
    17651765<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    17911791 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
    17921792</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
    1793 src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
     1793src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
    17941794
    17951795<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    18031803  cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
    18041804</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
    1805 src="MCSA%20in%20GSAS_files/image028.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1805src="MCSA%20in%20GSAS_files/image068.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
    18061806
    18071807<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    18101810whose centers fall within the unit cell; the reference one is that in the lower
    18111811left corner with C1 at the origin. You can enter values in the <span
     1812class=SpellE><span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1813style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1814mso-hansi-theme-font:minor-latin'>x,y</span></b></span><b style='mso-bidi-font-weight:
     1815normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1816minor-latin;mso-hansi-theme-font:minor-latin'>,z</span></b></span> boxes and
     1817see how the structure changes. Similarly, you can enter an angle in <span
    18121818class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    18131819"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1814 minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
    1815 the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
    1816 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1817 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
    1818 or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1819 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1820 mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
     1820minor-latin'>Oa</span></b></span> or a vector in the <span class=SpellE><span
     1821class=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:
     1823minor-latin'>Oi,Oj</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1824style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1825mso-hansi-theme-font:minor-latin'>,Ok</span></b></span><span
    18211826style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
    1822 molecule. Each of these parameters has a defined range for the MC/SA
    1823 optimization run we are about to do; they define the multidimensional search
    1824 volume. Within that volume will be a number of correct solutions to the
    1825 structure problem all related by translational and space group symmetry. One
    1826 can limit this volume by choosing more limited ranges, but here we’ll just go
    1827 with the default. We want to optimize the position and orientation of this
    1828 molecule; check the <b style='mso-bidi-font-weight:normal'><span
    1829 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1830 mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
    1831 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1832 minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <b
    1833 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1827molecule. Each of these parameters has a defined range for the MC/SA optimization
     1828run we are about to do; they define the multidimensional search volume. Within
     1829that volume will be a number of correct solutions to the structure problem all
     1830related by translational and space group symmetry. One can limit this volume by
     1831choosing more limited ranges, but here we’ll just go with the default. We want
     1832to optimize the position and orientation of this molecule; check the <b
     1833style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1834mso-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;
     1836mso-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;
    18341838mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>
    18351839boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     
    18381842normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18391843minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
    1840 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1841 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1842 minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
     1844class=SpellE><span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1845style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1846mso-hansi-theme-font:minor-latin'>Oi,Oj</span></b></span><b style='mso-bidi-font-weight:
     1847normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1848minor-latin;mso-hansi-theme-font:minor-latin'>,Ok</span></b></span><b
    18431849style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18441850mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b>
    1845 <span class=GramE>pulldown</span>. The MC/SA window should look like</p>
    1846 
    1847 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1848  id="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;height:193.5pt;
    1849  visibility:visible;mso-wrap-style:square'>
     1851pulldown. The MC/SA window should look like</p>
     1852
     1853<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'>
    18501856 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
    18511857</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
    1852 src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="_x0000_i1037"><![endif]></span><span
     1858src="MCSA%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_15"><![endif]></span><span
    18531859style='mso-spacerun:yes'> </span></p>
    18541860
     
    18701876style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18711877mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
    1872 structure factors will be Pawley model values, <span class=SpellE><span
    1873 class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>)
    1874 in Pawley table, and the covariance matrix developed from the refinement will
    1875 be used for peak overlap effects in the MC/SA calculations. Alternatively, if
    1876 you choose <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1877 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1878 minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span> Bank 1 </span></b>then
    1879 the structure factors will be those, <span class=SpellE>Fosq</span> in
    1880 Reflection table, extracted during the Pawley refinement and the peak FWHMs
     1878structure factors will be Pawley model values, <span class=SpellE>Fsq</span>(<span
     1879class=SpellE>hkl</span>) in Pawley table, and the covariance matrix developed
     1880from the refinement will be used for peak overlap effects in the MC/SA
     1881calculations. Alternatively, if you choose <b style='mso-bidi-font-weight:normal'><span
     1882style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1883mso-hansi-theme-font:minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span>
     1884Bank 1 </span></b>then the structure factors will be those, <span class=SpellE>Fosq</span>
     1885in Reflection table, extracted during the Pawley refinement and the peak FWHMs
    18811886will be used for peak overlap effects in the MC/SA calculations. Notice that
    1882 the Pawley <span class=SpellE><span class=GramE>Fsq</span></span><span
    1883 class=GramE>(</span><span class=SpellE>hkl</span>) values are the same as the <span
    1884 class=SpellE>Fcsq</span> Reflection List values. Here I chose <b
    1885 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1887the Pawley <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) values
     1888are the same as the <span class=SpellE>Fcsq</span> Reflection List values. Here
     1889I chose <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18861890mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR <span
    18871891class=SpellE>Quinoli.gda</span> Bank 1 </span></b>for the <b style='mso-bidi-font-weight:
     
    19171921schedule. I also used <b style='mso-bidi-font-weight:normal'><span
    19181922style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1919 mso-hansi-theme-font:minor-latin'>4 MC/SA runs</span></b> <span class=GramE>When</span>
    1920 done the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1923mso-hansi-theme-font:minor-latin'>4 MC/SA runs</span></b> When done the <b
     1924style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19211925mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    19221926window should look like</p>
     
    19271931 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
    19281932</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
    1929 src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
     1933src="MCSA%20in%20GSAS_files/image070.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
    19301934
    19311935<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    19491953 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
    19501954</v:shape><![endif]--><![if !vml]><img border=0 width=752 height=365
    1951 src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
     1955src="MCSA%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
    19521956
    19531957<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    19621966  cropbottom="21002f" cropleft="39996f" cropright="10456f"/>
    19631967</v:shape><![endif]--><![if !vml]><img border=0 width=486 height=398
    1964 src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1968src="MCSA%20in%20GSAS_files/image072.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
    19651969
    19661970<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    19681972<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
    19691973good solution with a very low Residual (~4.8%). This problem typically gives
    1970 suitable solutions with Residuals of 4-5%. If your cell indexing resulted in <span
    1971 class=GramE>a &amp;</span> b swapped, you should view the structure along b
    1972 (green). If no good solution appears (e.g. molecules clashing), then you should
    1973 just rerun MC/SA perhaps using more runs or more trials. Be sure to set the <b
    1974 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1975 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Keep</span></b>
    1976 box for any solutions you want to retain; the others will be cleared before the
    1977 next MC/SA run starts. When you think you have a good one, <span class=GramE><b
     1974suitable 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
     1976solution appears (e.g. molecules clashing), then you should just rerun MC/SA
     1977perhaps using more runs or more trials. Be sure to set the <b style='mso-bidi-font-weight:
     1978normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1979minor-latin;mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any
     1980solutions you want to retain; the others will be cleared before the next MC/SA
     1981run starts. When you think you have a good one, <span class=GramE><b
    19781982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19791983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span>
     
    20012005 <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/>
    20022006</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=365
    2003 src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
     2007src="MCSA%20in%20GSAS_files/image073.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
    20042008
    20052009<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    20062010
    2007 <p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>2.6%</span>!)
    2008 and the structure</p>
     2011<p class=MsoNormal>This is clearly a good result (R ~ 2.6%!) and the structure</p>
    20092012
    20102013<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    20142017  cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
    20152018</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
    2016 src="MCSA%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
     2019src="MCSA%20in%20GSAS_files/image074.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
    20172020
    20182021<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    20192022
    2020 <p class=MsoNormal><span class=GramE>is</span> identical to the published one</p>
     2023<p class=MsoNormal>is identical to the published one</p>
    20212024
    20222025<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    20262029  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
    20272030</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
    2028 src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
    2029 
    2030 <p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
     2031src="MCSA%20in%20GSAS_files/image075.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
     2032
     2033<p class=MsoNormal>as drawn by the Mercury program </p>
    20312034
    20322035<p class=MsoNormal>(<a
     
    20452048  cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
    20462049</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
    2047 src="MCSA%20in%20GSAS_files/image044.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
     2050src="MCSA%20in%20GSAS_files/image076.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
    20482051
    20492052<p class=MsoNormal>And they will be listed in the Atoms table.</p>
     
    20542057 <v:imagedata src="MCSA%20in%20GSAS_files/image045.png" o:title=""/>
    20552058</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
    2056 src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
     2059src="MCSA%20in%20GSAS_files/image077.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
    20572060
    20582061<p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use
     
    20982101mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
    20992102style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2100 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
    2101 class=GramE>size</span></span></b> &amp; <span class=SpellE><b
    2102 style='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'>mustrain</span></b></span>
    2104 boxes and do another <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'>Calculate/Refine</span></b>; I got an <span
    2107 class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not refined atom
    2108 positions or thermal parameters; to do this we need to describe the structure
    2109 as a rigid body.</p>
     2103mso-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
     2105style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2106mso-hansi-theme-font:minor-latin'>mustrain</span></b></span> boxes and do
     2107another <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2108mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
     2109I got an <span class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not
     2110refined atom positions or thermal parameters; to do this we need to describe
     2111the structure as a rigid body.</p>
    21102112
    21112113<h2>Step 9. Rigid body model</h2>
     
    21462148 <v:imagedata src="MCSA%20in%20GSAS_files/image047.png" o:title=""/>
    21472149</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
    2148 src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
     2150src="MCSA%20in%20GSAS_files/image078.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
    21492151
    21502152<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    21542156corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
    21552157order; the drawing will show the shift of molecular origin and then its
    2156 reorientation as the three atoms are selected. Press <span class=GramE><b
    2157 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2158 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b></span>
    2159 when done; the structure will be drawn with yellow bonds indicating that it is
    2160 now a rigid body and not independent atoms. The <b style='mso-bidi-font-weight:
    2161 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2162 minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows
    2163 the new rigid body</p>
     2158reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight:
     2159normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2160minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b> when done; the
     2161structure will be drawn with yellow bonds indicating that it is now a rigid
     2162body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span
     2163style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2164mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows the new
     2165rigid body</p>
    21642166
    21652167<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21682170 <v:imagedata src="MCSA%20in%20GSAS_files/image049.png" o:title=""/>
    21692171</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
    2170 src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
    2171 
    2172 <p class=MsoNormal>To refine the rigid body parameters check the <b
    2173 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2172src="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>
     2175check the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21742176mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
    2175 <span class=GramE>box</span>, select <b style='mso-bidi-font-weight:normal'><span
    2176 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2177 mso-hansi-theme-font:minor-latin'>AV</span></b> from the pull down, choose <span
    2178 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     2177box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    21792178"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2180 minor-latin'>Uiso</span></b></span> from the thermal parameter model and check
    2181 its <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2182 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
    2183 <span class=GramE>box</span>. Then do <b style='mso-bidi-font-weight:normal'><span
    2184 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2185 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple
    2186 of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
    2187 the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2179minor-latin'>AV</span></b> from the pull down, choose <span class=SpellE><b
     2180style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2181mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Uiso</span></b></span>
     2182from the thermal parameter model and check its <b style='mso-bidi-font-weight:
     2183normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2184minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b> box. Then do <b
     2185style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2186mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
     2187after 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
    21882189style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    21892190mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
     
    21952196 <v:imagedata src="MCSA%20in%20GSAS_files/image051.png" o:title=""/>
    21962197</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
    2197 src="MCSA%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    2198 
    2199 <p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
     2198src="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>
    22002201
    22012202<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    22042205 <v:imagedata src="MCSA%20in%20GSAS_files/image053.png" o:title=""/>
    22052206</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    2206 src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
     2207src="MCSA%20in%20GSAS_files/image081.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
    22072208
    22082209<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
    22092210Next is a more complex case involving some internal degrees of freedom in the
    2210 molecule of a-d-<span class=GramE>lactose.</span></p>
     2211molecule of a-d-lactose.</p>
    22112212
    22122213</div>
  • Tutorials/MCsimanneal/MCSA in GSAS_files/filelist.xml

    r1718 r2390  
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  • Tutorials/MCsimanneal/MCSA in GSAS_files/item0060.xml

    r1718 r2390  
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    r1745 r2390  
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