Changeset 1745 for Tutorials/MCsimanneal


Ignore:
Timestamp:
Mar 20, 2015 8:49:59 AM (7 years ago)
Author:
vondreele
Message:

changes to various tutorials - mostly getting file references correct & removing hyperlinks

Location:
Tutorials/MCsimanneal
Files:
22 edited

Legend:

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

    r1718 r1745  
    2323  <o:Author>vondreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>2</o:Revision>
    26   <o:TotalTime>581</o:TotalTime>
     25  <o:Revision>3</o:Revision>
     26  <o:TotalTime>767</o:TotalTime>
    2727  <o:Created>2015-03-16T21:14:00Z</o:Created>
    28   <o:LastSaved>2015-03-16T21:14:00Z</o:LastSaved>
     28  <o:LastSaved>2015-03-19T20:13:00Z</o:LastSaved>
    2929  <o:Pages>1</o:Pages>
    30   <o:Words>2420</o:Words>
    31   <o:Characters>13797</o:Characters>
     30  <o:Words>2432</o:Words>
     31  <o:Characters>13865</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    33   <o:Lines>114</o:Lines>
     33  <o:Lines>115</o:Lines>
    3434  <o:Paragraphs>32</o:Paragraphs>
    35   <o:CharactersWithSpaces>16185</o:CharactersWithSpaces>
     35  <o:CharactersWithSpaces>16265</o:CharactersWithSpaces>
    3636  <o:Version>15.00</o:Version>
    3737 </o:DocumentProperties>
     
    4444<!--[if gte mso 9]><xml>
    4545 <w:WordDocument>
     46  <w:Zoom>116</w:Zoom>
     47  <w:SpellingState>Clean</w:SpellingState>
     48  <w:GrammarState>Clean</w:GrammarState>
    4649  <w:TrackMoves>false</w:TrackMoves>
    4750  <w:TrackFormatting/>
     
    644647        {font-family:"Cambria Math";
    645648        panose-1:2 4 5 3 5 4 6 3 2 4;
    646         mso-font-charset:1;
     649        mso-font-charset:0;
    647650        mso-generic-font-family:roman;
    648         mso-font-format:other;
    649651        mso-font-pitch:variable;
    650         mso-font-signature:0 0 0 0 0 0;}
     652        mso-font-signature:-536870145 1107305727 0 0 415 0;}
    651653@font-face
    652654        {font-family:Calibri;
     
    10981100        mso-fareast-theme-font:minor-fareast;
    10991101        mso-bidi-font-family:Calibri;}
     1102span.SpellE
     1103        {mso-style-name:"";
     1104        mso-spl-e:yes;}
     1105span.GramE
     1106        {mso-style-name:"";
     1107        mso-gram-e:yes;}
    11001108.MsoChpDefault
    11011109        {mso-style-type:export-only;
     
    11041112        mso-ansi-font-size:10.0pt;
    11051113        mso-bidi-font-size:10.0pt;
    1106         font-family:"Calibri",sans-serif;
    11071114        mso-ascii-font-family:Calibri;
    11081115        mso-hansi-font-family:Calibri;
     
    12591266<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
    12601267structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
    1261 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
    1262 kindly provided by Peter Stephens (SUNY StonyBrook) and were originally
    1263 collected on NSLS beam line X3b1. The MC/SA technique is needed in these cases
    1264 because as you will see the data does not extend very far in 2&#920; so one
    1265 cannot use charge flipping to solve them. The steps for each begin with peak
    1266 selection and fitting, then indexing to identify the lattice parameters. A
    1267 Pawley refinement is used to obtain a set of structure factors needed for the
    1268 MC/SA runs. We will use previously developed models for the two molecules; I
    1269 used the freeware program Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
     1268diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
     1269were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
     1270and were originally collected on NSLS beam line X3b1. The MC/SA technique is
     1271needed in these cases because as you will see the data does not extend very far
     1272in 2&#920; so one cannot use charge flipping to solve them. The steps for each
     1273begin with peak selection and fitting, then indexing to identify the lattice
     1274parameters. A Pawley refinement is used to obtain a set of structure factors
     1275needed for the MC/SA runs. We will use previously developed models for the two
     1276molecules; I used the freeware program Avogadro (<a
     1277href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
    12701278to create them.</p>
    12711279
    1272 <p class=MsoNormal>If you have not done so already, <a
    1273 href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a>.</p>
     1280<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
    12741281
    12751282<h2>Step 1. Import powder data for 3-aminoquinoline</h2>
     
    12851292style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12861293mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1287 minor-latin'>Exercises/MCSA</span></b><span style='font-family:"Calibri",sans-serif;
    1288 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1289 Calibri;mso-bidi-theme-font:minor-latin'> to find the file; you may need to
    1290 change the file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b>
    1291 to find the desired file.</span></p>
     1294minor-latin'>exercises/<span class=SpellE>MCsimanneal</span></span></b><span
     1295style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1296mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1297minor-latin'> to find the file; you may need to change the file type to <b
     1298style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
     1299file.</span></p>
    12921300
    12931301<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
    12941302style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    12951303style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    1296 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1304the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1305style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1306mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1307minor-latin'>Quinoli.gda</span></b></span><span style='font-family:"Calibri",sans-serif;
    12971308mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1298 Calibri;mso-bidi-theme-font:minor-latin'>Quinoli.gda</span></b><span
    1299 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1300 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1301 minor-latin'> data</span> file in the first dialog and press <b
    1302 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1309Calibri;mso-bidi-theme-font:minor-latin'> data</span> file in the first dialog
     1310and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13031311mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    13041312Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1305 Dialog box asking <b style='mso-bidi-font-weight:normal'><span
     1313Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    13061314style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13071315mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1308 minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
    1309 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1310 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1311 mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
     1316minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1317style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1318mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
     1319minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
     1320style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1321mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1322Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
     1323proceed.</p>
    13121324
    13131325<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
     
    13161328the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13171329mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1318 Calibri;mso-bidi-theme-font:minor-latin'>BNL-I.instprm</span></b> instrument
    1319 parameter file in the second dialog and press <b style='mso-bidi-font-weight:
     1330Calibri;mso-bidi-theme-font:minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b>
     1331instrument parameter file in the second dialog and press <b style='mso-bidi-font-weight:
    13201332normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    13211333minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     
    13231335file type to <b style='mso-bidi-font-weight:normal'><span style='font-family:
    13241336"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1325 minor-latin'>*.instprm</span></b> (GSAS-II instrument parameter file). The
    1326 powder pattern will immediately appear.</p>
     1337minor-latin'>*.<span class=SpellE>instprm</span></span></b> (GSAS-II instrument
     1338parameter file). The powder pattern will immediately appear.</p>
    13271339
    13281340<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     
    13461358 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
    13471359 <o:lock v:ext="edit" aspectratio="t"/>
    1348 </v:shapetype><v:shape id="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
    1349  height:450pt;visibility:visible;mso-wrap-style:square'>
     1360</v:shapetype><v:shape id="Picture_x0020_28" o:spid="_x0000_i1051" type="#_x0000_t75"
     1361 style='width:525pt;height:450pt;visibility:visible;mso-wrap-style:square'>
    13501362 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
    13511363</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1352 src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
     1364src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    13531365
    13541366<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
     
    13751387picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
    13761388normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1377 minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ PeakFit </span></b>to
    1378 fit them. You will need to vary at least <b style='mso-bidi-font-weight:normal'><span
    1379 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1380 mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
    1381 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1382 minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> in <b
    1383 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1389minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ <span
     1390class=SpellE>PeakFit</span> </span></b>to fit them. You will need to vary at
     1391least <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1392mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
     1393&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1394mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
     1395in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    13841396mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
    1385 Parameters</span></b> along with <b style='mso-bidi-font-weight:normal'><span
    1386 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1387 mso-hansi-theme-font:minor-latin'>pos</span></b> &amp; <b style='mso-bidi-font-weight:
    1388 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1389 minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> in the <b
    1390 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1391 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
    1392 to get a reasonable fit suitable for indexing.</p>
     1397Parameters</span></b> along with <span class=SpellE><b style='mso-bidi-font-weight:
     1398normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1399minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span> &amp; <span
     1400class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1401"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1402minor-latin'>int</span></b></span> in the <b style='mso-bidi-font-weight:normal'><span
     1403style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1404mso-hansi-theme-font:minor-latin'>Peak List</span></b> to get a reasonable fit
     1405suitable for indexing.</p>
    13931406
    13941407<h2>Step 3. Indexing</h2>
     
    14021415normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    14031416minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
    1404 indexing. The most likely Bravais lattice for these small organic molecules is
    1405 either Orthorhombic-P or Monoclinic-P; you can try both and see what comes out
    1406 (Hint: it’s <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1407 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1408 minor-latin'>Orthorhombic-P</span></b>). The correct unit cell should almost
    1409 immediately appear with an M20 ~330 with a=7.748, b=7.651, c=12.736,
    1410 Vol=755.01. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1417indexing. The most likely <span class=SpellE>Bravais</span> lattice for these
     1418small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try
     1419both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
     1420style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1421mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>). The correct unit
     1422cell should almost immediately appear with an M20 ~200 with a=7.748, b=7.651,
     1423c=12.736, Vol=755.01. NB: your solution may have <span class=GramE>a &amp;</span>
     1424b switched. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
    14111425"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    14121426minor-latin'>Cell Index/Refine/Copy Cell</span></b>; you can then try various
     
    14871501box and enter the d-spacing (1.8133) into the <b style='mso-bidi-font-weight:
    14881502normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1489 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b> box.</p>
     1503minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
     1504box.</p>
    14901505
    14911506<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
     
    14941509
    14951510<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1496  id="Picture_x0020_2" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;
    1497  height:375pt;visibility:visible;mso-wrap-style:square'>
     1511 id="_x0000_i1050" type="#_x0000_t75" style='width:487.5pt;height:375pt;
     1512 visibility:visible;mso-wrap-style:square'>
    14981513 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
    1499 </v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
    1500 src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1514</v:shape><![endif]--><![if !vml]><img border=0 width=650 height=500
     1515src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1050"><![endif]></span></p>
    15011516
    15021517<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    15201535
    15211536<p class=MsoNormal>Select either choice; the desired data set will be added to
    1522 this phase for analysis. The data tab now shows the new data set; check the <b
    1523 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1524 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
    1525 button to see the full information</p>
    1526 
    1527 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1528  id="Picture_x0020_28" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
     1537this phase for analysis. The data tab now shows the new data set.</p>
     1538
     1539<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1540 id="Picture_x0020_30" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
    15291541 height:375pt;visibility:visible;mso-wrap-style:square'>
    15301542 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
    15311543</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
    1532 src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1544src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
    15331545
    15341546<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15351547
    15361548<p class=MsoNormal>This is the location for all the phase dependent parameters
    1537 for this histogram. Notice that it includes phase fraction, size &amp; mustrain
    1538 as well as preferred orientation, elastic strain and extinction corrections.
    1539 The Babinet correction is intended for protein work where a significant region
    1540 of the structure is disordered solvent. There are buttons for plotting size and
    1541 mustrain surfaces and preferred orientation correction curves.</p>
     1549for this histogram. Notice that it includes phase fraction, size &amp; <span
     1550class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
     1551and extinction corrections. The <span class=SpellE>Babinet</span> correction is
     1552intended for protein work where a significant region of the structure is
     1553disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
     1554surfaces and preferred orientation correction curves.</p>
    15421555
    15431556<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
     
    15491562makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
    15501563normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1551 minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
    1552 should list reflections 0-91. Select and check the <b style='mso-bidi-font-weight:
    1553 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1554 minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column using
    1555 the same technique you used for the peak list. </p>
     1564minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
     1565The table should list reflections 0-91. Select and check the <b
     1566style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1567mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
     1568column using the same technique you used for the peak list. </p>
    15561569
    15571570<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    15771590mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
    15781591used to recover from a bad refinement. A progress dialog box will appear
    1579 showing the residual as the refinement proceeds. My refinement completed with
    1580 Rwp ~12.9%; a dialog box appears asking if you wish to load the result. Press <b
    1581 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1582 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1583 To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
    1584 the width and height).</p>
    1585 
    1586 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1587  id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
    1588  height:450pt;visibility:visible;mso-wrap-style:square'>
     1592showing the residual as the refinement proceeds. My refinement completed with <span
     1593class=SpellE>Rwp</span> ~12.9%; a dialog box appears asking if you wish to load
     1594the result. Press <b style='mso-bidi-font-weight:normal'><span
     1595style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1596mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot select the
     1597PWDR line in the GSAS-II data tree (I’ve adjusted the width and height).</p>
     1598
     1599<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'>
    15891602 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
    15901603</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1591 src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
     1604src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
    15921605
    15931606<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16031616to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16041617mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>,
    1605 then change <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1618then change <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1619style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1620mso-hansi-theme-font:minor-latin'>pos</span></b></span> to <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'>19</span></b>, <span
     1623class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    16061624"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1607 minor-latin'>pos</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1608 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1609 mso-hansi-theme-font:minor-latin'>19</span></b>, <b style='mso-bidi-font-weight:
    1610 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1611 minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> to <b
    1612 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1613 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
    1614 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1615 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
    1616 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1625minor-latin'>int</span></b></span> to <b style='mso-bidi-font-weight:normal'><span
     1626style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1627mso-hansi-theme-font:minor-latin'>100000</span></b> and <b style='mso-bidi-font-weight:
     1628normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1629minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b
     1630style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16171631mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>;
    16181632for the peak only refine <b style='mso-bidi-font-weight:normal'><span
     
    16201634mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b
    16211635style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1622 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b>
    1623 to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1636mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
     1637class=SpellE>coeff</span>.</span></b> <span class=GramE>to</span> <b
     1638style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16241639mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>;
    16251640the window shows</p>
    16261641
    16271642<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1628  id="Picture_x0020_7" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
     1643 id="Picture_x0020_33" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
    16291644 height:197.25pt;visibility:visible;mso-wrap-style:square'>
    16301645 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
    16311646</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
    1632 src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1647src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    16331648
    16341649<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16361651<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
    16371652style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1638 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my Rwp fell to
    1639 ~8.5%. In <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1640 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>
    1641 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1642 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>
    1643 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1644 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
    1645 for refinement and in <b style='mso-bidi-font-weight:normal'><span
    1646 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1647 mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> select <b
    1648 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1649 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
    1650 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1651 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
    1652 for refinement; then do <b style='mso-bidi-font-weight:normal'><span
    1653 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1654 mso-hansi-theme-font:minor-latin'>Calculate /Refine</span></b> again. I got
    1655 Rwp~7.5% at convergence and the fit looked like</p>
     1653mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
     1654class=SpellE>Rwp</span> fell to ~8.5%. In <b style='mso-bidi-font-weight:normal'><span
     1655style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1656mso-hansi-theme-font:minor-latin'>Background</span></b> select <span
     1657class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1658"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1659minor-latin'>pos</span></b></span> &amp; <b style='mso-bidi-font-weight:normal'><span
     1660style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1661mso-hansi-theme-font:minor-latin'>sig</span></b> for refinement and in <b
     1662style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
     1664Parameters</span></b> select <b style='mso-bidi-font-weight:normal'><span
     1665style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1666mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
     1667normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1668minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> for refinement; then
     1669do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1670style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1671mso-hansi-theme-font:minor-latin'>Calculate</span></b></span><b
     1672style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1673mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> /Refine</span></b>
     1674again. I got Rwp~7.5% at convergence and the fit looked like</p>
    16561675
    16571676<p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
    1658  id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
    1659  height:450pt;visibility:visible;mso-wrap-style:square'>
     1677 id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
     1678 visibility:visible;mso-wrap-style:square'>
    16601679 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
    16611680</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1662 src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
     1681src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="_x0000_i1044"><![endif]></span></p>
    16631682
    16641683<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    16951714mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
    16961715style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1697 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Import
     1716mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Body/Import
    16981717XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:normal'><span
    16991718style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1700 mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <b
    1701 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1702 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>aminoquinoline.xyz</span></b>.
    1703 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1704 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b>
     1719mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <span
     1720class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1721"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1722minor-latin'>aminoquinoline.xyz</span></b></span>. The <b style='mso-bidi-font-weight:
     1723normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1724minor-latin;mso-hansi-theme-font:minor-latin'>Rigid <span class=GramE>bodies</span></span></b>
    17051725window will show</p>
    17061726
     
    17161736<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
    17171737style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1718 mso-hansi-theme-font:minor-latin'>Plot?</span></b> box a drawing will appear</p>
    1719 
    1720 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1721  id="Picture_x0020_1" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;
    1722  height:234pt;visibility:visible;mso-wrap-style:square'>
     1738mso-hansi-theme-font:minor-latin'>Plot?</span></b> <span class=GramE>box</span>
     1739a 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'>
    17231744 <v:imagedata src="MCSA%20in%20GSAS_files/image021.png" o:title="" croptop="13685f"
    17241745  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
    17251746</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
    1726 src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1747src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="_x0000_i1041"><![endif]></span></p>
    17271748
    17281749<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    17881809<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
    17891810whose centers fall within the unit cell; the reference one is that in the lower
    1790 left corner with C1 at the origin. You can enter values in the <b
    1791 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1792 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>x,y,z</span></b>
    1793 boxes and see how the structure changes. Similarly, you can enter an angle in <b
    1794 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1795 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b>
    1796 or a vector in the <b style='mso-bidi-font-weight:normal'><span
    1797 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1798 mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok</span></b><span
     1811left corner with C1 at the origin. You can enter values in the <span
     1812class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1813"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1814minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
     1815the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
     1816style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1817mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
     1818or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1819style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1820mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
    17991821style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
    18001822molecule. Each of these parameters has a defined range for the MC/SA
     
    18131835boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    18141836"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1815 minor-latin'>AV</span></b> from the <b style='mso-bidi-font-weight:normal'><span
    1816 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1817 mso-hansi-theme-font:minor-latin'>Oa</span></b>, <b style='mso-bidi-font-weight:
    1818 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1819 minor-latin;mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok Vary?</span></b>
    1820 pulldown. The MC/SA window should look like</p>
    1821 
    1822 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1823  id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;
    1824  height:193.5pt;visibility:visible;mso-wrap-style:square'>
     1837minor-latin'>AV</span></b> from the <span class=SpellE><b style='mso-bidi-font-weight:
     1838normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1839minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
     1840class=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:
     1842minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
     1843style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1844mso-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'>
    18251850 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
    18261851</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
    1827 src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
     1852src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="_x0000_i1037"><![endif]></span><span
    18281853style='mso-spacerun:yes'> </span></p>
    18291854
     
    18451870style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18461871mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
    1847 structure factors will be Pawley model values, Fsq(hkl) in Pawley table, and
    1848 the covariance matrix developed from the refinement will be used for peak
    1849 overlap effects in the MC/SA calculations. Alternatively, if you choose <b
    1850 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1851 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
    1852 Quinoli.gda Bank 1 </span></b>then the structure factors will be those, Fosq in
     1872structure factors will be Pawley model values, <span class=SpellE><span
     1873class=GramE>Fsq</span></span><span class=GramE>(</span><span class=SpellE>hkl</span>)
     1874in Pawley table, and the covariance matrix developed from the refinement will
     1875be used for peak overlap effects in the MC/SA calculations. Alternatively, if
     1876you 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:
     1878minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span> Bank 1 </span></b>then
     1879the structure factors will be those, <span class=SpellE>Fosq</span> in
    18531880Reflection table, extracted during the Pawley refinement and the peak FWHMs
    18541881will be used for peak overlap effects in the MC/SA calculations. Notice that
    1855 the Pawley Fsq(hkl) values are the same as the Fcsq Reflection List values.
    1856 Here I chose <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1857 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1858 minor-latin'>Pawley reflections</span></b> for the <b style='mso-bidi-font-weight:
     1882the Pawley <span class=SpellE><span class=GramE>Fsq</span></span><span
     1883class=GramE>(</span><span class=SpellE>hkl</span>) values are the same as the <span
     1884class=SpellE>Fcsq</span> Reflection List values. Here I chose <b
     1885style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR <span
     1887class=SpellE>Quinoli.gda</span> Bank 1 </span></b>for the <b style='mso-bidi-font-weight:
    18591888normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18601889minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it
     
    18861915mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
    18871916this is the number of random tries at each “temperature” in the annealing
    1888 schedule. When done the <b style='mso-bidi-font-weight:normal'><span
    1889 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1890 mso-hansi-theme-font:minor-latin'>General</span></b> window should look like</p>
    1891 
    1892 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1893  id="Picture_x0020_16" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
     1917schedule. I also used <b style='mso-bidi-font-weight:normal'><span
     1918style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1919mso-hansi-theme-font:minor-latin'>4 MC/SA runs</span></b> <span class=GramE>When</span>
     1920done the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1921mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     1922window should look like</p>
     1923
     1924<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1925 id="Picture_x0020_38" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
    18941926 height:375pt;visibility:visible;mso-wrap-style:square'>
    18951927 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
    18961928</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
    1897 src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1929src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
    18981930
    18991931<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    19131945
    19141946<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1915  id="Picture_x0020_19" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:560.25pt;
     1947 id="Picture_x0020_39" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:564pt;
    19161948 height:273.75pt;visibility:visible;mso-wrap-style:square'>
    19171949 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
    1918 </v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
    1919 src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
     1950</v:shape><![endif]--><![if !vml]><img border=0 width=752 height=365
     1951src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
    19201952
    19211953<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    19251957
    19261958<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1927  id="Picture_x0020_20" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:279.75pt;
    1928  height:243.75pt;visibility:visible;mso-wrap-style:square'>
    1929  <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="11773f"
    1930   cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
    1931 </v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
    1932 src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1959 id="Picture_x0020_1" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:364.5pt;
     1960 height:298.5pt;visibility:visible;mso-wrap-style:square'>
     1961 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="8643f"
     1962  cropbottom="21002f" cropleft="39996f" cropright="10456f"/>
     1963</v:shape><![endif]--><![if !vml]><img border=0 width=486 height=398
     1964src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
    19331965
    19341966<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     
    19361968<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
    19371969good solution with a very low Residual (~4.8%). This problem typically gives
    1938 suitable solutions with Residuals of 4-5%. If no good solution appears (e.g.
    1939 molecules clashing), then you should just rerun MC/SA perhaps using more runs
    1940 or more trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
    1941 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1942 mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
    1943 want to retain; the others will be cleared before the next MC/SA run starts.
    1944 When you think you have a good one, <b style='mso-bidi-font-weight:normal'><span
    1945 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1946 mso-hansi-theme-font:minor-latin'>Select</span></b> it; the parameters will be
    1947 copied to the appropriate boxes in the upper part of the MC/SA window and the
    1948 structure is drawn again. Next we want to refine this solution so go back to
    1949 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1950 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
    1951 tab.</p>
     1970suitable solutions with Residuals of 4-5%. If your cell indexing resulted in <span
     1971class=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
     1973just rerun MC/SA perhaps using more runs or more trials. Be sure to set the <b
     1974style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1975mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Keep</span></b>
     1976box for any solutions you want to retain; the others will be cleared before the
     1977next MC/SA run starts. When you think you have a good one, <span class=GramE><b
     1978style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1979mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span>
     1980it; the parameters will be copied to the appropriate boxes in the upper part of
     1981the MC/SA window and the structure is drawn again. Next we want to refine this
     1982solution so go back to the <b style='mso-bidi-font-weight:normal'><span
     1983style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1984mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
    19521985
    19531986<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
     
    19641997
    19651998<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1966  id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:569.25pt;
    1967  height:285pt;visibility:visible;mso-wrap-style:square'>
     1999 id="Picture_x0020_40" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:448.5pt;
     2000 height:273.75pt;visibility:visible;mso-wrap-style:square'>
    19682001 <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/>
    1969 </v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
    1970 src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
     2002</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=365
     2003src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
    19712004
    19722005<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    19732006
    1974 <p class=MsoNormal>This is clearly a good result (R ~ 0.4%!) and the structure</p>
     2007<p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>2.6%</span>!)
     2008and the structure</p>
    19752009
    19762010<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19842018<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    19852019
    1986 <p class=MsoNormal>is identical to the published one</p>
     2020<p class=MsoNormal><span class=GramE>is</span> identical to the published one</p>
    19872021
    19882022<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    19942028src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
    19952029
    1996 <p class=MsoNormal>as drawn by the Mercury program </p>
     2030<p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
    19972031
    19982032<p class=MsoNormal>(<a
     
    20492083normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    20502084minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
    2051 the main GSAS-II data tree window; my R<sub>wp</sub> was ~9%. Next check the <b
    2052 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2053 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
    2054 cell</span></b> in the <b style='mso-bidi-font-weight:normal'><span
    2055 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2056 mso-hansi-theme-font:minor-latin'>General</span></b> window and in the <b
    2057 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2058 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
    2059 window, using the <b style='mso-bidi-font-weight:normal'><span
    2060 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2061 mso-hansi-theme-font:minor-latin'>uniaxial</span></b> model for mustrain, check
    2062 both <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2063 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst. size</span></b>
    2064 &amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2065 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b>
     2085the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
     2086was ~9%. Next check the <b style='mso-bidi-font-weight:normal'><span
     2087style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2088mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b
     2089style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2090mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
     2091window and in the <b style='mso-bidi-font-weight:normal'><span
     2092style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2093mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b
     2094style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2095mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b>
     2096model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
     2097style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2098mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
     2099style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2100mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
     2101class=GramE>size</span></span></b> &amp; <span class=SpellE><b
     2102style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2103mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
    20662104boxes and do another <b style='mso-bidi-font-weight:normal'><span
    20672105style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2068 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an R<sub>wp</sub>
    2069 ~8.5% for this. We’ve not refined atom positions or thermal parameters; to do
    2070 this we need to describe the structure as a rigid body.</p>
     2106mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an <span
     2107class=SpellE>R<sub>wp</sub></span> ~8.5% for this. We’ve not refined atom
     2108positions or thermal parameters; to do this we need to describe the structure
     2109as a rigid body.</p>
    20712110
    20722111<h2>Step 9. Rigid body model</h2>
     
    21152154corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
    21162155order; the drawing will show the shift of molecular origin and then its
    2117 reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight:
    2118 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2119 minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b> when done; the
    2120 structure will be drawn with yellow bonds indicating that it is now a rigid
    2121 body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span
    2122 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2123 mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows the new
    2124 rigid body</p>
     2156reorientation as the three atoms are selected. Press <span class=GramE><b
     2157style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2158mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b></span>
     2159when done; the structure will be drawn with yellow bonds indicating that it is
     2160now a rigid body and not independent atoms. The <b style='mso-bidi-font-weight:
     2161normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2162minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows
     2163the new rigid body</p>
    21252164
    21262165<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21342173style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    21352174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
    2136 box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2175<span class=GramE>box</span>, select <b style='mso-bidi-font-weight:normal'><span
     2176style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2177mso-hansi-theme-font:minor-latin'>AV</span></b> from the pull down, choose <span
     2178class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    21372179"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2138 minor-latin'>AV</span></b> from the pull down, choose <b style='mso-bidi-font-weight:
    2139 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2140 minor-latin;mso-hansi-theme-font:minor-latin'>Uiso</span></b> from the thermal
    2141 parameter model and check its <b style='mso-bidi-font-weight:normal'><span
    2142 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2143 mso-hansi-theme-font:minor-latin'>Refine?</span></b> box. Then do <b
    2144 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2145 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
    2146 after a couple of refinement runs I got an R<sub>wp</sub> ~7.9% and the <b
    2147 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2148 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RBModels</span></b>
    2149 window shows the new parameters</p>
     2180minor-latin'>Uiso</span></b></span> from the thermal parameter model and check
     2181its <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2182mso-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
     2184style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2185mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; after a couple
     2186of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span> ~7.9% and
     2187the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2188style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2189mso-hansi-theme-font:minor-latin'>RBModels</span></b></span> window shows the
     2190new parameters</p>
    21502191
    21512192<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21562197src="MCSA%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    21572198
    2158 <p class=MsoNormal>and the profile shows the fit</p>
     2199<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
    21592200
    21602201<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     
    21672208<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
    21682209Next is a more complex case involving some internal degrees of freedom in the
    2169 molecule of a-d-lactose.</p>
     2210molecule of a-d-<span class=GramE>lactose.</span></p>
    21702211
    21712212</div>
  • Tutorials/MCsimanneal/MCSA in GSAS_files/props061.xml

    r1718 r1745  
    11<?xml version="1.0" encoding="UTF-8" standalone="no"?>
    2 <ds:datastoreItem ds:itemID="{912881B4-24FC-4C17-8C86-27AE205F2E8C}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>
     2<ds:datastoreItem ds:itemID="{1E488168-A1CB-44C1-823D-66A014A41372}" xmlns:ds="http://schemas.openxmlformats.org/officeDocument/2006/customXml"><ds:schemaRefs><ds:schemaRef ds:uri="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"/></ds:schemaRefs></ds:datastoreItem>
Note: See TracChangeset for help on using the changeset viewer.