Ignore:
Timestamp:
Aug 25, 2014 4:47:28 PM (9 years ago)
Author:
vondreele
Message:

Fix CW & TOF hydrostatic strain calculations & change disply formats
work on TOF size/mustrain calcs.

File:
1 edited

Legend:

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  • trunk/help/MCSA in GSAS.htm

    r1475 r1478  
    2323  <o:Author>vondreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>14</o:Revision>
    26   <o:TotalTime>579</o:TotalTime>
     25  <o:Revision>15</o:Revision>
     26  <o:TotalTime>580</o:TotalTime>
    2727  <o:Created>2014-08-19T14:01:00Z</o:Created>
    28   <o:LastSaved>2014-08-22T13:42:00Z</o:LastSaved>
     28  <o:LastSaved>2014-08-25T14:05:00Z</o:LastSaved>
    2929  <o:Pages>9</o:Pages>
    3030  <o:Words>2418</o:Words>
    … …  
    955955<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
    956956structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
    957 diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
    958 kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
    959 and were originally collected on NSLS beam line X17b. The MC/SA technique is
     957diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
     958were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
     959and were originally collected on NSLS beam line X3b1. The MC/SA technique is
    960960needed in these cases because as you will see the data does not extend very far
    961961in 2&#920; so one cannot use charge flipping to solve them. The steps for each
    … …  
    10511051 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
    10521052</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1053 src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
     1053src="MCSA%20in%20GSAS_files/image031.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
    10541054
    10551055<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
    … …  
    11721172style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    11731173<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
    1174 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
    1175 Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
    1176 normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
    1177 minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
     1174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b>
     1175and uncheck refinement of <b style='mso-bidi-font-weight:normal'><span
     1176style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
     1177mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
    11781178
    11791179<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
    … …  
    12011201 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
    12021202</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
    1203 src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1203src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
    12041204
    12051205<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    12181218 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
    12191219</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
    1220 src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
     1220src="MCSA%20in%20GSAS_files/image033.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
    12211221
    12221222<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    12331233 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
    12341234</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
    1235 src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1235src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    12361236
    12371237<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    12651265 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
    12661266</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
    1267 src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
     1267src="MCSA%20in%20GSAS_files/image035.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
    12681268
    12691269<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    12941294 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
    12951295</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1296 src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
     1296src="MCSA%20in%20GSAS_files/image036.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
    12971297
    12981298<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    13371337 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
    13381338</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
    1339 src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1339src="MCSA%20in%20GSAS_files/image037.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
    13401340
    13411341<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    13711371 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
    13721372</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1373 src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
     1373src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    13741374
    13751375<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    13801380<h2><span class=GramE>Step 6.</span> Setup for Monte Carlo/Simulated Annealing</h2>
    13811381
    1382 <p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
    1383 rings with one N-substituted position and an amino side group</p>
     1382<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic rings
     1383with one N-substituted position and an amino side group</p>
    13841384
    13851385<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    13891389  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
    13901390</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
    1391 src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
     1391src="MCSA%20in%20GSAS_files/image039.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
    13921392
    13931393<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
    … …  
    14231423 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
    14241424</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
    1425 src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
     1425src="MCSA%20in%20GSAS_files/image040.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
    14261426
    14271427<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    14381438  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
    14391439</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
    1440 src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1440src="MCSA%20in%20GSAS_files/image041.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
    14411441
    14421442<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    14541454  cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
    14551455</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
    1456 src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
     1456src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
    14571457
    14581458<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    14621462necessary. You should change the <b style='mso-bidi-font-weight:normal'><span
    14631463style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1464 mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
    1465 meaningful, I used <b style='mso-bidi-font-weight:normal'><span
    1466 style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
    1467 mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
     1464mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something meaningful,
     1465I used <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
     1466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
    14681467
    14691468<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
    … …  
    14841483 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
    14851484</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
    1486 src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
     1485src="MCSA%20in%20GSAS_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
    14871486
    14881487<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    14961495  cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
    14971496</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
    1498 src="MCSA%20in%20GSAS_files/image027.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
     1497src="MCSA%20in%20GSAS_files/image045.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
    14991498
    15001499<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    15441543 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
    15451544</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
    1546 src="MCSA%20in%20GSAS_files/image028.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
     1545src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
    15471546style='mso-spacerun:yes'> </span></p>
    15481547
    … …  
    16181617 <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
    16191618</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
    1620 src="MCSA%20in%20GSAS_files/image047.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1619src="MCSA%20in%20GSAS_files/image058.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
    16211620
    16221621<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    16401639 <v:imagedata src="MCSA%20in%20GSAS_files/image048.png" o:title=""/>
    16411640</v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
    1642 src="MCSA%20in%20GSAS_files/image049.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
     1641src="MCSA%20in%20GSAS_files/image059.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
    16431642
    16441643<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    16531652  cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
    16541653</v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
    1655 src="MCSA%20in%20GSAS_files/image051.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
     1654src="MCSA%20in%20GSAS_files/image060.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
    16561655
    16571656<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    16911690 <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
    16921691</v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
    1693 src="MCSA%20in%20GSAS_files/image053.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
     1692src="MCSA%20in%20GSAS_files/image061.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
    16941693
    16951694<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    17041703  cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
    17051704</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
    1706 src="MCSA%20in%20GSAS_files/image055.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
     1705src="MCSA%20in%20GSAS_files/image062.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
    17071706
    17081707<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    17161715  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
    17171716</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
    1718 src="MCSA%20in%20GSAS_files/image057.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
     1717src="MCSA%20in%20GSAS_files/image063.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
    17191718
    17201719<p class=MsoNormal><span class=GramE>as</span> drawn by the Mercury program </p>
    … …  
    17351734  cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
    17361735</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
    1737 src="MCSA%20in%20GSAS_files/image072.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
     1736src="MCSA%20in%20GSAS_files/image065.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
    17381737
    17391738<p class=MsoNormal>And they will be listed in the Atoms table.</p>
    … …  
    17441743 <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
    17451744</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
    1746 src="MCSA%20in%20GSAS_files/image076.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
     1745src="MCSA%20in%20GSAS_files/image067.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
    17471746
    17481747<p class=MsoNormal>It is now ready for <span class=SpellE>Rietveld</span>
    … …  
    18371836 <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
    18381837</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
    1839 src="MCSA%20in%20GSAS_files/image077.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
     1838src="MCSA%20in%20GSAS_files/image069.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
    18401839
    18411840<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    18591858 <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
    18601859</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
    1861 src="MCSA%20in%20GSAS_files/image078.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
     1860src="MCSA%20in%20GSAS_files/image071.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
    18621861
    18631862<p class=MsoNormal>To refine the rigid body parameters check the <b
    … …  
    18861885 <v:imagedata src="MCSA%20in%20GSAS_files/image073.png" o:title=""/>
    18871886</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
    1888 src="MCSA%20in%20GSAS_files/image079.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
     1887src="MCSA%20in%20GSAS_files/image075.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    18891888
    18901889<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
    … …  
    18951894 <v:imagedata src="MCSA%20in%20GSAS_files/image074.png" o:title=""/>
    18961895</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
    1897 src="MCSA%20in%20GSAS_files/image080.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
     1896src="MCSA%20in%20GSAS_files/image081.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
    18981897
    18991898<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
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