Changeset 2390


Ignore:
Timestamp:
Jul 28, 2016 2:18:10 PM (7 years ago)
Author:
vondreele
Message:
 
Location:
Tutorials
Files:
72 edited

Legend:

Unmodified
Added
Removed

  • Tutorials/LabData/Laboratory X.htm

    r1735 r2390  
    2323  <o:Author>Von Dreele</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>20</o:Revision>
     25  <o:Revision>21</o:Revision>
    2626  <o:TotalTime>1666</o:TotalTime>
    2727  <o:Created>2012-05-08T16:04:00Z</o:Created>
    28   <o:LastSaved>2015-03-18T15:35:00Z</o:LastSaved>
     28  <o:LastSaved>2016-07-28T18:40:00Z</o:LastSaved>
    2929  <o:Pages>1</o:Pages>
    30   <o:Words>3164</o:Words>
    31   <o:Characters>18038</o:Characters>
     30  <o:Words>3163</o:Words>
     31  <o:Characters>18034</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>150</o:Lines>
    3434  <o:Paragraphs>42</o:Paragraphs>
    35   <o:CharactersWithSpaces>21160</o:CharactersWithSpaces>
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     36  <o:Version>16.00</o:Version>
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    3838 <o:OfficeDocumentSettings>
    … …  
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    … …  
    12921299Data - Fluroapatite</span><o:p></o:p></strong></h1>
    12931300
    1294 <p class=MsoNormal>In this tutorial you will refine the structure of <span
    1295 class=SpellE>fluoroapatite</span>, <span class=GramE>Ca<sub>5</sub>F(</span>PO<sub>4</sub>)<sub>3</sub>,
    1296 using constant wavelength laboratory X-ray powder diffraction data. At the
    1297 completion of the refinement you will then prepare a drawing of the <span
    1298 class=SpellE>fluoroapatite</span> structure. The structure is hexagonal with
    1299 four different kinds of atoms spread over seven different sites. The data was
    1300 taken on a conventional Bragg-Brentano powder diffractometer using <span
    1301 class=SpellE>CuK</span><sub><span style='font-family:Symbol'>a</span></sub>
     1301<p class=MsoNormal>In this tutorial you will refine the structure of
     1302fluoroapatite, Ca<sub>5</sub>F(PO<sub>4</sub>)<sub>3</sub>, using constant
     1303wavelength laboratory X-ray powder diffraction data. At the completion of the
     1304refinement you will then prepare a drawing of the fluoroapatite structure. The
     1305structure is hexagonal with four different kinds of atoms spread over seven
     1306different sites. The data was taken on a conventional Bragg-Brentano powder
     1307diffractometer using CuK<sub><span style='font-family:Symbol'>a</span></sub>
    13021308radiation.</p>
    13031309
    … …  
    13201326file</span></b> menu item to read the data file into GSAS-II. This read option
    13211327is set to read any of the powder data formats (except neutron TOF time map
    1322 files) defined for GSAS (angles in <span class=SpellE>centidegrees</span>). The
    1323 <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     1328files) defined for GSAS (angles in centidegrees). The <b style='mso-bidi-font-weight:
     1329normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1330minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1331mso-bidi-theme-font:minor-latin'>xye</span></b> format (angles in degrees) used
     1332by Topas, etc. can also be read via the <b style='mso-bidi-font-weight:normal'><span
    13241333style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13251334mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1326 minor-latin'>xye</span></b></span> format (angles in degrees) used by <span
    1327 class=SpellE>Topas</span>, etc. can also be read via the <b style='mso-bidi-font-weight:
    1328 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1329 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1330 mso-bidi-theme-font:minor-latin'>Import/Import Powder Data</span></b>
    1331 menus.<span style='mso-spacerun:yes'>  </span>Change the file directory to <b
    1332 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1333 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1334 Calibri;mso-bidi-theme-font:minor-latin'>exercises/<span class=SpellE>LabData</span></span></b><span
     1335minor-latin'>Import/Import Powder Data</span></b> menus.<span
     1336style='mso-spacerun:yes'>  </span>Change the file directory to <b
     1337style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1338mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1339Calibri;mso-bidi-theme-font:minor-latin'>LabData/data</span></b><span
    13351340style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13361341mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    … …  
    13511356mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    13521357Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1353 Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1358Dialog box asking <b style='mso-bidi-font-weight:normal'><span
    13541359style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    13551360mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1356 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1357 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1358 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1359 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    1360 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1361 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1362 Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
    1363 proceed.</p>
     1361minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
     1362normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1363minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1364mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
    13641365
    13651366<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo2'><![if !supportLists]><span
    … …  
    14091410
    14101411<p class=MsoNormal>For this step we will take advantage of having an old GSAS
    1411 experiment file with all the parameters for <span class=SpellE>fluroapatite</span>
    1412 otherwise you’ll have to follow the steps used for the <a
    1413 href="Neutron%20CW%20Powder%20Data.htm">CW neutron example on garnet</a> with
    1414 the following information:</p>
    1415 
    1416 <p class=MsoNormal>Phase name = ‘<span class=SpellE>fap</span>’, Space group =
    1417 P 63/m, unit cell a = 9.372, c = 6.886</p>
     1412experiment file with all the parameters for fluroapatite otherwise you’ll have
     1413to follow the steps used for the <a href="Neutron%20CW%20Powder%20Data.htm">CW
     1414neutron example on garnet</a> with the following information:</p>
     1415
     1416<p class=MsoNormal>Phase name = ‘fap’, Space group = P 63/m, unit cell a =
     14179.372, c = 6.886</p>
    14181418
    14191419<p class=MsoNormal>Atom coordinates:</p>
    … …  
    16521652</table>
    16531653
    1654 <p class=MsoNormal>To import the <span class=SpellE>fluroapatite</span> phase
    1655 information from the file FAP.EXP use the <b style='mso-bidi-font-weight:normal'><span
     1654<p class=MsoNormal>To import the fluroapatite phase information from the file
     1655FAP.EXP use the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1656"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1657minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Import/Import
     1658Phase menu</span></b> menu to see a pulldown menu. Select <b style='mso-bidi-font-weight:
     1659normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1660minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1661mso-bidi-theme-font:minor-latin'>from GSAS .EXP file. </span></b>The file
     1662selection dialog will still be set to the directory the data was found; click
     1663on <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1664mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1665Calibri;mso-bidi-theme-font:minor-latin'>FAP.EXP</span></b> and <b
     1666style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1668Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b> to open it. You will
     1669see an <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1670mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Is this the
     1671file you want?</span></b> dialog; press <b style='mso-bidi-font-weight:normal'><span
     1672style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1673mso-hansi-theme-font:minor-latin'>Yes</span></b> to proceed. A small dialog box
     1674with a phase name of ‘<b style='mso-bidi-font-weight:normal'><span
    16561675style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16571676mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1658 minor-latin'>Import/Import Phase menu</span></b> <span class=SpellE>menu</span>
    1659 to see a pulldown menu. Select <b style='mso-bidi-font-weight:normal'><span
    1660 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1661 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1662 minor-latin'>from GSAS .EXP file. </span></b>The file selection dialog will
    1663 still be set to the directory the data was found; click on <b style='mso-bidi-font-weight:
    1664 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1665 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1666 mso-bidi-theme-font:minor-latin'>FAP.EXP</span></b> and <b style='mso-bidi-font-weight:
    1667 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1668 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1669 mso-bidi-theme-font:minor-latin'>Open</span></b> to open it. You will see an <span
    1670 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1671 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1672 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1673 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1674 mso-hansi-theme-font:minor-latin'> this the file you want?</span></b> <span
    1675 class=GramE>dialog</span>; press <b style='mso-bidi-font-weight:normal'><span
    1676 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1677 mso-hansi-theme-font:minor-latin'>Yes</span></b> to proceed. A small dialog box
    1678 with a phase name of ‘<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1679 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1680 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1681 minor-latin'>fap</span></b></span>’ will appear. We didn’t change it so press <b
     1677minor-latin'>fap</span></b>’ will appear. We didn’t change it so press <b
    16821678style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16831679mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    … …  
    16991695style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17001696mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1701 Calibri;mso-bidi-theme-font:minor-latin'>Phase</span></b> entry of <span
    1702 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1703 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1704 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>fap</span></b></span>.
    1705 Select it.to view the <span class=SpellE>fap</span> phase information</p>
     1697Calibri;mso-bidi-theme-font:minor-latin'>Phase</span></b> entry of <b
     1698style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1699mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1700Calibri;mso-bidi-theme-font:minor-latin'>fap</span></b>. Select it.to view the
     1701fap phase information</p>
    17061702
    17071703<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    17631759"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    17641760minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>9. </span></b>This
    1765 will put background points at the two limits and at equal spaces in <span
    1766 class=GramE>log(</span>2<span style='font-family:Symbol'>Q</span>) in between
    1767 so there are more where the background is changing most rapidly. A linear
    1768 interpolation is then used to compute the background for all points in the pattern
    1769 during the Rietveld refinement.</p>
     1761will put background points at the two limits and at equal spaces in log(2<span
     1762style='font-family:Symbol'>Q</span>) in between so there are more where the
     1763background is changing most rapidly. A linear interpolation is then used to
     1764compute the background for all points in the pattern during the Rietveld
     1765refinement.</p>
    17701766
    17711767<h2>Step 5 1<sup>st</sup> Rietveld refinement</h2>
    … …  
    17821778mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    17831779Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> menu. You
    1784 will be asked for a project file name, we used ‘<span class=SpellE>f<b
    1785 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1786 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1787 Calibri;mso-bidi-theme-font:minor-latin'>ap</span></b></span>’ and made the
    1788 file <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
    1789 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1790 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1791 minor-latin'>fap.gpx</span></b></span>. The refinement proceeds and when
    1792 complete (<span class=SpellE>Rwp</span> ~45.2%) a small dialog box will appear
    1793 asking <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1780will be asked for a project file name, we used ‘f<b style='mso-bidi-font-weight:
     1781normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1782minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1783mso-bidi-theme-font:minor-latin'>ap</span></b>’ and made the file <b
     1784style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1785mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1786Calibri;mso-bidi-theme-font:minor-latin'>fap.gpx</span></b>. The refinement
     1787proceeds and when complete (Rwp ~45.2%) a small dialog box will appear asking <b
     1788style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17941789mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    17951790Calibri;mso-bidi-theme-font:minor-latin'>Load new result?</span></b> Press <b
    … …  
    18171812style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18181813mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1819 Calibri;mso-bidi-theme-font:minor-latin'>Phase</span></b> <span class=SpellE><b
    1820 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1821 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1822 Calibri;mso-bidi-theme-font:minor-latin'>fap</span></b></span> and the sample displacement
    1823 is found on the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1814Calibri;mso-bidi-theme-font:minor-latin'>Phase</span></b> <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;mso-bidi-font-family:Calibri;
     1817mso-bidi-theme-font:minor-latin'>fap</span></b> and the sample displacement is
     1818found on the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    18241819"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    18251820minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Sample
    … …  
    19151910      cropbottom="8083f" cropleft="21159f" cropright="21533f"/>
    19161911    </v:shape><![endif]--><![if !vml]><img width=167 height=194
    1917     src="Laboratory%20X_files/image007.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
     1912    src="Laboratory%20X_files/image024.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
    19181913    </div>
    19191914    <![if !mso]></td>
    … …  
    19311926src="Laboratory%20X_files/image008.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
    19321927
    1933 <p class=MsoNormal><span class=GramE>noticeably</span> improved (<span
    1934 class=SpellE>Rwp</span> ~14.5%). Close inspection (see inset) shows that most
    1935 of the differences are in the widths of the peaks so we should refine
    1936 crystallite size and <span class=SpellE>mustrain</span> parameters next.</p>
     1928<p class=MsoNormal>noticeably improved (Rwp ~14.5%). Close inspection (see
     1929inset) shows that most of the differences are in the widths of the peaks so we
     1930should refine crystallite size and mustrain parameters next.</p>
    19371931
    19381932<h2>Step 7 3<sup>rd</sup> Rietveld refinement</h2>
    … …  
    19411935style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19421936mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1943 minor-latin'>Phases/<span class=SpellE>fap</span></span></b> item in the <b
    1944 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1945 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1946 Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> and then
    1947 select the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1948 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1949 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Data</span></b>
    1950 tab and set the refine flags for both size and <span class=SpellE>mustrain</span>.
    1951 The window should look like</p>
     1937minor-latin'>Phases/fap</span></b> item in the <b style='mso-bidi-font-weight:
     1938normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1939minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1940mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> and then select
     1941the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1943Calibri;mso-bidi-theme-font:minor-latin'>Data</span></b> tab and set the refine
     1944flags for both size and mustrain. The window should look like</p>
    19521945
    19531946<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    19651958mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    19661959Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window.
    1967 Do not be alarmed about how the <span class=SpellE>Rwp</span> jumps around on
    1968 the progress bar; that is a consequence of how the <span class=SpellE>Levenberg</span>-Marquardt
    1969 algorithm does a least squares minimization. The result in the end is
    1970 noticeably better than before (<span class=SpellE>Rwp</span>=11.2%)</p>
     1960Do not be alarmed about how the Rwp jumps around on the progress bar; that is a
     1961consequence of how the Levenberg-Marquardt algorithm does a least squares
     1962minimization. The result in the end is noticeably better than before
     1963(Rwp=11.2%)</p>
    19711964
    19721965<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    19821975style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19831976mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1984 Calibri;mso-bidi-theme-font:minor-latin'>Phases/<span class=SpellE>fap</span> </span></b>and
    1985 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1977Calibri;mso-bidi-theme-font:minor-latin'>Phases/fap </span></b>and the <b
     1978style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19861979mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    19871980Calibri;mso-bidi-theme-font:minor-latin'>Atoms</span></b> tab; the <b
    19881981style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19891982mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1990 Calibri;mso-bidi-theme-font:minor-latin'>Phase data for <span class=SpellE>fap</span></span></b>
    1991 window will display</p>
     1983Calibri;mso-bidi-theme-font:minor-latin'>Phase data for fap</span></b> window
     1984will display</p>
    19921985
    19931986<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    20442037mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    20452038Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window.
    2046 The result is a bit better (<span class=SpellE>Rwp</span>=10.4%) and the plot
    2047 is pretty much the same as before</p>
     2039The result is a bit better (Rwp=10.4%) and the plot is pretty much the same as
     2040before</p>
    20482041
    20492042<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    20542047src="Laboratory%20X_files/image014.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
    20552048
    2056 <p class=MsoNormal><span class=GramE>and</span> the atom parameters are</p>
     2049<p class=MsoNormal>and the atom parameters are</p>
    20572050
    20582051<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2059  id="_x0000_i1032" type="#_x0000_t75" style='width:525pt;height:225pt;
    2060  visibility:visible;mso-wrap-style:square'>
     2052 id="Picture_x0020_15" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
     2053 height:225pt;visibility:visible;mso-wrap-style:square'>
    20612054 <v:imagedata src="Laboratory%20X_files/image015.png" o:title=""/>
    20622055</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
    2063 src="Laboratory%20X_files/image015.png" v:shapes="_x0000_i1032"><![endif]></span></p>
    2064 
    2065 <p class=MsoNormal>The refinement is now essentially complete. The file <span
    2066 class=SpellE>fap.lst</span> has the result of the last cycle of refinement with
    2067 values and <span class=SpellE>esds</span> for all the parameters</p>
     2056src="Laboratory%20X_files/image015.png" v:shapes="Picture_x0020_15"><![endif]></span></p>
     2057
     2058<p class=MsoNormal>The refinement is now essentially complete. The file fap.lst
     2059has the result of the last cycle of refinement with values and esds for all the
     2060parameters</p>
    20682061
    20692062<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    20752068<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    20762069font-family:"Courier New";font-weight:normal'><span
    2077 style='mso-spacerun:yes'> </span>Number of function calls: <span class=GramE>12<span
    2078 style='mso-spacerun:yes'>  </span>Number</span> of observations:<span
    2079 style='mso-spacerun:yes'>  </span>5751<span style='mso-spacerun:yes'> 
    2080 </span>Number of parameters:<span style='mso-spacerun:yes'>  </span>34<o:p></o:p></span></h2>
     2070style='mso-spacerun:yes'> </span>Number of function calls: 12<span
     2071style='mso-spacerun:yes'>  </span>Number of observations:<span
     2072style='mso-spacerun:yes'>  </span>5751<span style='mso-spacerun:yes'>  </span>Number
     2073of parameters:<span style='mso-spacerun:yes'>  </span>34<o:p></o:p></span></h2>
    20812074
    20822075<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    20882081<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    20892082font-family:"Courier New";font-weight:normal'><span
    2090 style='mso-spacerun:yes'> </span><span class=SpellE><span class=GramE>wR</span></span>
    2091 =<span style='mso-spacerun:yes'>   </span>10.38%, chi**2 =<span
    2092 style='mso-spacerun:yes'>      </span>19687.8, reduced chi**2 =<span
    2093 style='mso-spacerun:yes'>   </span>3.44<o:p></o:p></span></h2>
     2083style='mso-spacerun:yes'> </span>wR =<span style='mso-spacerun:yes'>  
     2084</span>10.38%, chi**2 =<span style='mso-spacerun:yes'>      </span>19687.8,
     2085reduced chi**2 =<span style='mso-spacerun:yes'>   </span>3.44<o:p></o:p></span></h2>
    20942086
    20952087<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    21052097<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    21062098font-family:"Courier New";font-weight:normal'><span
    2107 style='mso-spacerun:yes'> </span><span class=GramE>name<span
    2108 style='mso-spacerun:yes'>  </span>:</span><span
    2109 style='mso-spacerun:yes'>          </span>0::A0<o:p></o:p></span></h2>
    2110 
    2111 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2112 font-family:"Courier New";font-weight:normal'><span
    2113 style='mso-spacerun:yes'> </span><span class=GramE>value :</span><span
    2114 style='mso-spacerun:yes'>         </span>0.0152<o:p></o:p></span></h2>
    2115 
    2116 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2117 font-family:"Courier New";font-weight:normal'><span
    2118 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2119 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>        
    2120 </span>0.0000<o:p></o:p></span></h2>
     2099style='mso-spacerun:yes'> </span>name<span style='mso-spacerun:yes'> 
     2100</span>:<span style='mso-spacerun:yes'>          </span>0::A0<o:p></o:p></span></h2>
     2101
     2102<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2103font-family:"Courier New";font-weight:normal'><span
     2104style='mso-spacerun:yes'> </span>value :<span style='mso-spacerun:yes'>        
     2105</span>0.0152<o:p></o:p></span></h2>
     2106
     2107<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2108font-family:"Courier New";font-weight:normal'><span
     2109style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2110</span>:<span style='mso-spacerun:yes'>         </span>0.0000<o:p></o:p></span></h2>
    21212111
    21222112<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    21302120font-family:"Courier New";font-weight:normal'><span
    21312121style='mso-spacerun:yes'> </span>Result for phase:<span
    2132 style='mso-spacerun:yes'>  </span><span class=SpellE>fap</span><o:p></o:p></span></h2>
     2122style='mso-spacerun:yes'>  </span>fap<o:p></o:p></span></h2>
    21332123
    21342124<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    21382128<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    21392129font-family:"Courier New";font-weight:normal'><span style='mso-spacerun:yes'> 
    2140 </span><span class=GramE>names :</span><span
    2141 style='mso-spacerun:yes'>            </span>A11<span
     2130</span>names :<span style='mso-spacerun:yes'>            </span>A11<span
    21422131style='mso-spacerun:yes'>            </span>A22<span
    21432132style='mso-spacerun:yes'>            </span>A33<span
    2144 style='mso-spacerun:yes'>            </span>A12<span
     2133style='mso-spacerun:yes'>        </span><span
     2134style='mso-spacerun:yes'>    </span>A12<span
    21452135style='mso-spacerun:yes'>            </span>A13<span
    21462136style='mso-spacerun:yes'>            </span>A23<o:p></o:p></span></h2>
    … …  
    21482138<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    21492139font-family:"Courier New";font-weight:normal'><span style='mso-spacerun:yes'> 
    2150 </span><span class=GramE>values</span>:<span style='mso-spacerun:yes'>   
    2151 </span>0.015180436<span style='mso-spacerun:yes'>    </span>0.015180436<span
     2140</span>values:<span style='mso-spacerun:yes'>    </span>0.015180436<span
     2141style='mso-spacerun:yes'>    </span>0.015180436<span
    21522142style='mso-spacerun:yes'>    </span>0.021090011<span
    21532143style='mso-spacerun:yes'>    </span>0.015180436<span
    … …  
    21572147<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    21582148font-family:"Courier New";font-weight:normal'><span style='mso-spacerun:yes'> 
    2159 </span><span class=SpellE><span class=GramE>esds</span></span><span
    2160 class=GramE><span style='mso-spacerun:yes'>  </span>:</span><span
     2149</span>esds<span style='mso-spacerun:yes'>  </span>:<span
    21612150style='mso-spacerun:yes'>    </span>0.000000320<span
    21622151style='mso-spacerun:yes'>                   </span>0.000000255<span
    … …  
    21692158<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    21702159font-family:"Courier New";font-weight:normal'><span style='mso-spacerun:yes'> 
    2171 </span><span class=GramE>names :</span><span
    2172 style='mso-spacerun:yes'>           </span>a<span
     2160</span>names :<span style='mso-spacerun:yes'>           </span>a<span
    21732161style='mso-spacerun:yes'>           </span>b<span
    2174 style='mso-spacerun:yes'>       </span><span
    2175 style='mso-spacerun:yes'>    </span>c<span style='mso-spacerun:yes'>      
    2176 </span>alpha<span style='mso-spacerun:yes'>        </span>beta<span
     2162style='mso-spacerun:yes'>           </span>c<span
     2163style='mso-spacerun:yes'>       </span>alpha<span
     2164style='mso-spacerun:yes'>        </span>beta<span
    21772165style='mso-spacerun:yes'>       </span>gamma<span
    21782166style='mso-spacerun:yes'>      </span>Volume<o:p></o:p></span></h2>
    … …  
    21802168<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    21812169font-family:"Courier New";font-weight:normal'><span style='mso-spacerun:yes'> 
    2182 </span><span class=GramE>values</span>:<span style='mso-spacerun:yes'>   
    2183 </span>9.371891<span style='mso-spacerun:yes'>    </span>9.371891<span
    2184 style='mso-spacerun:yes'>    </span>6.885914<span style='mso-spacerun:yes'>    
    2185 </span>90.0000<span style='mso-spacerun:yes'>     </span>90.0000<span
    2186 style='mso-spacerun:yes'>    </span>120.0000<span style='mso-spacerun:yes'>    
    2187 </span>523.777<o:p></o:p></span></h2>
     2170</span>values:<span style='mso-spacerun:yes'>    </span>9.371891<span
     2171style='mso-spacerun:yes'>    </span>9.371891<span style='mso-spacerun:yes'>   
     2172</span>6.885914<span style='mso-spacerun:yes'>     </span>90.0000<span
     2173style='mso-spacerun:yes'>     </span>90.0000<span style='mso-spacerun:yes'>   
     2174</span>120.0000<span style='mso-spacerun:yes'>     </span>523.777<o:p></o:p></span></h2>
    21882175
    21892176<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    21902177font-family:"Courier New";font-weight:normal'><span style='mso-spacerun:yes'> 
    2191 </span><span class=SpellE><span class=GramE>esds</span></span><span
    2192 class=GramE><span style='mso-spacerun:yes'>  </span>:</span><span
     2178</span>esds<span style='mso-spacerun:yes'>  </span>:<span
    21932179style='mso-spacerun:yes'>    </span>0.000189<span
    21942180style='mso-spacerun:yes'>                </span>0.000042<span
    2195 style='mso-spacerun:yes'>                                          
    2196 </span>0.008<o:p></o:p></span></h2>
     2181style='mso-spacerun:yes'>                         </span><span
     2182style='mso-spacerun:yes'>                  </span>0.008<o:p></o:p></span></h2>
    21972183
    21982184<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    22052191<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    22062192font-family:"Courier New";font-weight:normal'><span style='mso-spacerun:yes'>  
    2207 </span><span class=GramE>name</span><span style='mso-spacerun:yes'>     
    2208 </span>x<span style='mso-spacerun:yes'>         </span>y<span
     2193</span>name<span style='mso-spacerun:yes'>      </span>x<span
     2194style='mso-spacerun:yes'>         </span>y<span
    22092195style='mso-spacerun:yes'>         </span>z<span style='mso-spacerun:yes'>     
    2210 </span><span class=SpellE>frac</span><span style='mso-spacerun:yes'>   </span><span
    2211 class=SpellE>Uiso</span><span style='mso-spacerun:yes'>     </span>U11<span
    2212 style='mso-spacerun:yes'>     </span>U22<span style='mso-spacerun:yes'>    
    2213 </span>U33<span style='mso-spacerun:yes'>     </span>U12<span
    2214 style='mso-spacerun:yes'>     </span>U13<span style='mso-spacerun:yes'>    
    2215 </span>U23<o:p></o:p></span></h2>
     2196</span>frac<span style='mso-spacerun:yes'>   </span>Uiso<span
     2197style='mso-spacerun:yes'>     </span>U11<span style='mso-spacerun:yes'>    
     2198</span>U22<span style='mso-spacerun:yes'>     </span>U33<span
     2199style='mso-spacerun:yes'>     </span>U12<span style='mso-spacerun:yes'>    
     2200</span>U13<span style='mso-spacerun:yes'>     </span>U23<o:p></o:p></span></h2>
    22162201
    22172202<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    22252210<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    22262211font-family:"Courier New";font-weight:normal'><span
    2227 style='mso-spacerun:yes'> </span><span class=GramE>values</span>: <span
    2228 style='mso-spacerun:yes'>  </span>0.33333<span style='mso-spacerun:yes'>  
    2229 </span>0.66667<span style='mso-spacerun:yes'>   </span>0.00202<span
    2230 style='mso-spacerun:yes'>   </span>1.000 0.00840<o:p></o:p></span></h2>
    2231 
    2232 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2233 font-family:"Courier New";font-weight:normal'><span
    2234 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2235 style='mso-spacerun:yes'>   </span>:<span
    2236 style='mso-spacerun:yes'>                       </span>0.00030<span
    2237 style='mso-spacerun:yes'>         </span>0.00036<o:p></o:p></span></h2>
     2212style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>  
     2213</span>0.33333<span style='mso-spacerun:yes'>   </span>0.66667<span
     2214style='mso-spacerun:yes'>   </span>0.00202<span style='mso-spacerun:yes'>  
     2215</span>1.000 0.00840<o:p></o:p></span></h2>
     2216
     2217<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2218font-family:"Courier New";font-weight:normal'><span
     2219style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2220</span>:<span style='mso-spacerun:yes'>                      
     2221</span>0.00030<span style='mso-spacerun:yes'>         </span>0.00036<o:p></o:p></span></h2>
    22382222
    22392223<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    22442228<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    22452229font-family:"Courier New";font-weight:normal'><span
    2246 style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    2247 style='mso-spacerun:yes'>   </span>0.24161<span style='mso-spacerun:yes'>  
    2248 </span>0.99231<span style='mso-spacerun:yes'>   </span>0.25000<span
    2249 style='mso-spacerun:yes'>   </span>1.000 0.00712<o:p></o:p></span></h2>
    2250 
    2251 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2252 font-family:"Courier New";font-weight:normal'><span
    2253 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2254 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>  
    2255 </span>0.00016<span style='mso-spacerun:yes'>   </span>0.00019<span
    2256 style='mso-spacerun:yes'>                   </span>0.00029<o:p></o:p></span></h2>
     2230style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>  
     2231</span>0.24161<span style='mso-spacerun:yes'>   </span>0.99231<span
     2232style='mso-spacerun:yes'>   </span>0.25000<span style='mso-spacerun:yes'>  
     2233</span>1.000 0.00712<o:p></o:p></span></h2>
     2234
     2235<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2236font-family:"Courier New";font-weight:normal'><span
     2237style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2238</span>:<span style='mso-spacerun:yes'>   </span>0.00016<span
     2239style='mso-spacerun:yes'>   </span>0.00019<span
     2240style='mso-spacerun:yes'>                  </span><span
     2241style='mso-spacerun:yes'> </span>0.00029<o:p></o:p></span></h2>
    22572242
    22582243<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    22632248<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    22642249font-family:"Courier New";font-weight:normal'><span
    2265 style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    2266 style='mso-spacerun:yes'>   </span>0.39715<span style='mso-spacerun:yes'>  
    2267 </span>0.36781<span style='mso-spacerun:yes'>   </span>0.25000<span
    2268 style='mso-spacerun:yes'>   </span>1.000 0.00719<o:p></o:p></span></h2>
    2269 
    2270 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2271 font-family:"Courier New";font-weight:normal'><span
    2272 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2273 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>  
    2274 </span>0.00020<span style='mso-spacerun:yes'>   </span>0.00019<span
     2250style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>  
     2251</span>0.39715<span style='mso-spacerun:yes'>   </span>0.36781<span
     2252style='mso-spacerun:yes'>   </span>0.25000<span style='mso-spacerun:yes'>  
     2253</span>1.000 0.00719<o:p></o:p></span></h2>
     2254
     2255<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2256font-family:"Courier New";font-weight:normal'><span
     2257style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2258</span>:<span style='mso-spacerun:yes'>   </span>0.00020<span
     2259style='mso-spacerun:yes'>   </span>0.00019<span
    22752260style='mso-spacerun:yes'>                   </span>0.00040<o:p></o:p></span></h2>
    22762261
    … …  
    22822267<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    22832268font-family:"Courier New";font-weight:normal'><span
    2284 style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    2285 style='mso-spacerun:yes'>   </span>0.00000<span style='mso-spacerun:yes'>  
    2286 </span>0.00000<span style='mso-spacerun:yes'>   </span>0.25000<span
    2287 style='mso-spacerun:yes'>   </span>1.000 0.01746<o:p></o:p></span></h2>
    2288 
    2289 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2290 font-family:"Courier New";font-weight:normal'><span
    2291 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2292 style='mso-spacerun:yes'>   </span>:<span
    2293 style='mso-spacerun:yes'>                                       </span>0.00142<o:p></o:p></span></h2>
     2269style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>  
     2270</span>0.00000<span style='mso-spacerun:yes'>   </span>0.00000<span
     2271style='mso-spacerun:yes'>   </span>0.25000<span style='mso-spacerun:yes'>  
     2272</span>1.000 0.01746<o:p></o:p></span></h2>
     2273
     2274<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2275font-family:"Courier New";font-weight:normal'><span
     2276style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2277</span>:<span style='mso-spacerun:yes'>                                      
     2278</span>0.00142<o:p></o:p></span></h2>
    22942279
    22952280<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    23002285<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    23012286font-family:"Courier New";font-weight:normal'><span
    2302 style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    2303 style='mso-spacerun:yes'>   </span>0.32546<span style='mso-spacerun:yes'>  
    2304 </span>0.48503<span style='mso-spacerun:yes'>   </span>0.25000<span
    2305 style='mso-spacerun:yes'>   </span>1.000 0.00814<o:p></o:p></span></h2>
    2306 
    2307 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2308 font-family:"Courier New";font-weight:normal'><span
    2309 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2310 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>  
    2311 </span>0.00043<span style='mso-spacerun:yes'>   </span>0.00044<span
     2287style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>  
     2288</span>0.32546<span style='mso-spacerun:yes'>   </span>0.48503<span
     2289style='mso-spacerun:yes'>   </span>0.25000<span style='mso-spacerun:yes'>  
     2290</span>1.000 0.00814<o:p></o:p></span></h2>
     2291
     2292<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2293font-family:"Courier New";font-weight:normal'><span
     2294style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2295</span>:<span style='mso-spacerun:yes'>   </span>0.00043<span
     2296style='mso-spacerun:yes'>   </span>0.00044<span
    23122297style='mso-spacerun:yes'>                   </span>0.00105<o:p></o:p></span></h2>
    23132298
    … …  
    23192304<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    23202305font-family:"Courier New";font-weight:normal'><span
    2321 style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    2322 style='mso-spacerun:yes'>   </span>0.59033<span style='mso-spacerun:yes'>  
    2323 </span>0.46939<span style='mso-spacerun:yes'>   </span>0.25000<span
    2324 style='mso-spacerun:yes'>   </span>1.000 0.01114<o:p></o:p></span></h2>
    2325 
    2326 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2327 font-family:"Courier New";font-weight:normal'><span
    2328 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2329 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>  
    2330 </span>0.00045<span style='mso-spacerun:yes'>   </span>0.00048<span
     2306style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>  
     2307</span>0.59033<span style='mso-spacerun:yes'>   </span>0.46939<span
     2308style='mso-spacerun:yes'>   </span>0.25000<span style='mso-spacerun:yes'>  
     2309</span>1.000 0.01114<o:p></o:p></span></h2>
     2310
     2311<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2312font-family:"Courier New";font-weight:normal'><span
     2313style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2314</span>:<span style='mso-spacerun:yes'>   </span>0.00045<span
     2315style='mso-spacerun:yes'>   </span>0.00048<span
    23312316style='mso-spacerun:yes'>                   </span>0.00112<o:p></o:p></span></h2>
    23322317
    … …  
    23382323<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    23392324font-family:"Courier New";font-weight:normal'><span
    2340 style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    2341 style='mso-spacerun:yes'>   </span>0.33975<span style='mso-spacerun:yes'>  
    2342 </span>0.25900<span style='mso-spacerun:yes'>   </span>0.07097<span
    2343 style='mso-spacerun:yes'>   </span>1.000 0.01096<o:p></o:p></span></h2>
    2344 
    2345 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2346 font-family:"Courier New";font-weight:normal'><span
    2347 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2348 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>  
    2349 </span>0.00035<span style='mso-spacerun:yes'>   </span>0.00035<span
    2350 style='mso-spacerun:yes'>   </span>0.00035<span
    2351 style='mso-spacerun:yes'>         </span>0.00079<o:p></o:p></span></h2>
     2325style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>  
     2326</span>0.33975<span style='mso-spacerun:yes'>   </span>0.25900<span
     2327style='mso-spacerun:yes'>   </span>0.07097<span style='mso-spacerun:yes'>  
     2328</span>1.000 0.01096<o:p></o:p></span></h2>
     2329
     2330<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2331font-family:"Courier New";font-weight:normal'><span
     2332style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2333</span>:<span style='mso-spacerun:yes'>   </span>0.00035<span
     2334style='mso-spacerun:yes'>   </span>0.00035<span style='mso-spacerun:yes'>  
     2335</span>0.00035<span style='mso-spacerun:yes'>         </span>0.00079<o:p></o:p></span></h2>
    23522336
    23532337<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    23562340<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    23572341font-family:"Courier New";font-weight:normal'><span
    2358 style='mso-spacerun:yes'> </span>Phase:<span style='mso-spacerun:yes'>  </span><span
    2359 class=SpellE><span class=GramE>fap</span></span><span class=GramE><span
    2360 style='mso-spacerun:yes'>  </span>in</span> histogram:<span
     2342style='mso-spacerun:yes'> </span>Phase:<span style='mso-spacerun:yes'> 
     2343</span>fap<span style='mso-spacerun:yes'>  </span>in histogram:<span
    23612344style='mso-spacerun:yes'>  </span>PWDR FAP.XRA Bank 1<o:p></o:p></span></h2>
    23622345
    … …  
    23802363style='mso-spacerun:yes'> </span>Size model:<span style='mso-spacerun:yes'>    
    23812364</span>isotropic equatorial:<span style='mso-spacerun:yes'>     </span>0.39088,
    2382 sig:<span style='mso-spacerun:yes'>  </span>0.0718 LG mix <span class=SpellE><span
    2383 class=GramE>coeff</span></span><span class=GramE>.:</span><span
     2365sig:<span style='mso-spacerun:yes'>  </span>0.0718 LG mix coeff.:<span
    23842366style='mso-spacerun:yes'>      </span>1.0000<o:p></o:p></span></h2>
    23852367
    … …  
    23892371<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    23902372font-family:"Courier New";font-weight:normal'><span
    2391 style='mso-spacerun:yes'> </span><span class=SpellE>Mustrain</span> model:
    2392 isotropic equatorial:<span style='mso-spacerun:yes'>    </span><span
    2393 style='mso-spacerun:yes'>   </span>961.3, sig:<span
    2394 style='mso-spacerun:yes'>    </span>25.8 LG mix <span class=SpellE><span
    2395 class=GramE>coeff</span></span><span class=GramE>.:</span><span
     2373style='mso-spacerun:yes'> </span>Mustrain model: isotropic equatorial:<span
     2374style='mso-spacerun:yes'>       </span>961.3, sig:<span
     2375style='mso-spacerun:yes'>    </span>25.8 LG mix coeff.:<span
    23962376style='mso-spacerun:yes'>      </span>1.0000<o:p></o:p></span></h2>
    23972377
    … …  
    24022382font-family:"Courier New";font-weight:normal'><span
    24032383style='mso-spacerun:yes'> </span>Histogram:<span style='mso-spacerun:yes'> 
    2404 </span>PWDR FAP.XRA Bank <span class=GramE>1<span style='mso-spacerun:yes'> 
    2405 </span>histogram</span> Id:<span style='mso-spacerun:yes'>  </span>0<o:p></o:p></span></h2>
     2384</span>PWDR FAP.XRA Bank 1<span style='mso-spacerun:yes'>  </span>histogram
     2385Id:<span style='mso-spacerun:yes'>  </span>0<o:p></o:p></span></h2>
    24062386
    24072387<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    24142394<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    24152395font-family:"Courier New";font-weight:normal'><span
    2416 style='mso-spacerun:yes'> </span>Final refinement <span class=SpellE>wR</span>
    2417 = 10.38% on 5751 observations in this histogram<o:p></o:p></span></h2>
    2418 
    2419 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2420 font-family:"Courier New";font-weight:normal'><span
    2421 style='mso-spacerun:yes'> </span>Other residuals: R = 8.12%, <span
    2422 class=SpellE>Rb</span> = 8.36%, <span class=SpellE>wRb</span> = 10.23% <span
    2423 class=SpellE>wRmin</span> = 5.61%<o:p></o:p></span></h2>
     2396style='mso-spacerun:yes'> </span>Final refinement wR = 10.38% on 5751
     2397observations in this histogram<o:p></o:p></span></h2>
     2398
     2399<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2400font-family:"Courier New";font-weight:normal'><span
     2401style='mso-spacerun:yes'> </span>Other residuals: R = 8.12%, Rb = 8.36%, wRb =
     240210.23% wRmin = 5.61%<o:p></o:p></span></h2>
    24242403
    24252404<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    24372416<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    24382417font-family:"Courier New";font-weight:normal'><span
    2439 style='mso-spacerun:yes'> </span><span class=GramE>names :</span><span
    2440 style='mso-spacerun:yes'>         </span>Scale<span
    2441 style='mso-spacerun:yes'>    </span><span
    2442 style='mso-spacerun:yes'>     </span>Shift<span style='mso-spacerun:yes'> 
    2443 </span>Transparency<span style='mso-spacerun:yes'>    </span><span
    2444 class=SpellE>SurfRoughA</span><span style='mso-spacerun:yes'>    </span><span
    2445 class=SpellE>SurfRoughB</span><o:p></o:p></span></h2>
    2446 
    2447 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2448 font-family:"Courier New";font-weight:normal'><span
    2449 style='mso-spacerun:yes'> </span><span class=GramE>values</span>:<span
    2450 style='mso-spacerun:yes'>       </span>42.2873<span
    2451 style='mso-spacerun:yes'>       </span>83.9821<span
     2418style='mso-spacerun:yes'> </span>names :<span style='mso-spacerun:yes'>        
     2419</span>Scale<span style='mso-spacerun:yes'>         </span>Shift<span
     2420style='mso-spacerun:yes'>  </span>Transparency<span
     2421style='mso-spacerun:yes'>    </span>SurfRoughA<span
     2422style='mso-spacerun:yes'>    </span>SurfRoughB<o:p></o:p></span></h2>
     2423
     2424<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2425font-family:"Courier New";font-weight:normal'><span
     2426style='mso-spacerun:yes'> </span>values:<span style='mso-spacerun:yes'>      
     2427</span>42.2873<span style='mso-spacerun:yes'>       </span>83.9821<span
    24522428style='mso-spacerun:yes'>        </span>0.0000<span
    2453 style='mso-spacerun:yes'>        </span>0.0000<span
    2454 style='mso-spacerun:yes'>        </span>0.0000<o:p></o:p></span></h2>
    2455 
    2456 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2457 font-family:"Courier New";font-weight:normal'><span
    2458 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2459 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>       
    2460 </span>0.1442<span style='mso-spacerun:yes'>        </span>0.3609<span
     2429style='mso-spacerun:yes'>        </span>0.0000<span style='mso-spacerun:yes'>  
     2430</span><span style='mso-spacerun:yes'>     </span>0.0000<o:p></o:p></span></h2>
     2431
     2432<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2433font-family:"Courier New";font-weight:normal'><span
     2434style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2435</span>:<span style='mso-spacerun:yes'>        </span>0.1442<span
     2436style='mso-spacerun:yes'>        </span>0.3609<span
    24612437style='mso-spacerun:yes'>                                          </span><o:p></o:p></span></h2>
    24622438
    … …  
    24712447<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    24722448font-family:"Courier New";font-weight:normal'><span
    2473 style='mso-spacerun:yes'> </span><span class=GramE>value :</span><span
    2474 style='mso-spacerun:yes'>      </span>623.5<span style='mso-spacerun:yes'>    
    2475 </span>405.2<span style='mso-spacerun:yes'>     </span>262.1<span
    2476 style='mso-spacerun:yes'>       </span>154<span style='mso-spacerun:yes'>    
    2477 </span>104.5<span style='mso-spacerun:yes'>     </span>71.38<span
    2478 style='mso-spacerun:yes'>     </span>50.48<span style='mso-spacerun:yes'>    
    2479 </span>49.97<span style='mso-spacerun:yes'>     </span>59.71<o:p></o:p></span></h2>
    2480 
    2481 <h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    2482 font-family:"Courier New";font-weight:normal'><span
    2483 style='mso-spacerun:yes'> </span><span class=GramE>sig</span><span
    2484 style='mso-spacerun:yes'>   </span>:<span style='mso-spacerun:yes'>      
    2485 </span>5.36<span style='mso-spacerun:yes'>     </span>3.124<span
    2486 style='mso-spacerun:yes'>     </span>2.364<span style='mso-spacerun:yes'>    
    2487 </span>1.785<span style='mso-spacerun:yes'>     </span>1.334<span
    2488 style='mso-spacerun:yes'>     </span>1.016<span style='mso-spacerun:yes'>   
    2489 </span>0.9211<span style='mso-spacerun:yes'>     </span>1.141<span
    2490 style='mso-spacerun:yes'>     </span>1.451<o:p></o:p></span></h2>
     2449style='mso-spacerun:yes'> </span>value :<span style='mso-spacerun:yes'>     
     2450</span>623.5<span style='mso-spacerun:yes'>     </span>405.2<span
     2451style='mso-spacerun:yes'>     </span>262.1<span style='mso-spacerun:yes'>      
     2452</span>154<span style='mso-spacerun:yes'>     </span>104.5<span
     2453style='mso-spacerun:yes'>     </span>71.38<span style='mso-spacerun:yes'>    
     2454</span>50.48<span style='mso-spacerun:yes'>     </span>49.97<span
     2455style='mso-spacerun:yes'>     </span>59.71<o:p></o:p></span></h2>
     2456
     2457<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
     2458font-family:"Courier New";font-weight:normal'><span
     2459style='mso-spacerun:yes'> </span>sig<span style='mso-spacerun:yes'>  
     2460</span>:<span style='mso-spacerun:yes'>       </span>5.36<span
     2461style='mso-spacerun:yes'>     </span>3.124<span style='mso-spacerun:yes'>    
     2462</span>2.364<span style='mso-spacerun:yes'>     </span>1.785<span
     2463style='mso-spacerun:yes'>     </span>1.334<span style='mso-spacerun:yes'>    
     2464</span>1.016<span style='mso-spacerun:yes'>    </span>0.9211<span
     2465style='mso-spacerun:yes'>     </span>1.141<span style='mso-spacerun:yes'>    
     2466</span>1.451<o:p></o:p></span></h2>
    24912467
    24922468<h2 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:8.0pt;
    … …  
    24982474
    24992475<p class=MsoNormal>What we like to show is the unit cell contents with the PO<sub>4</sub><sup>-3</sup>
    2500 ions as <span class=SpellE>tetrahedra</span> and the Ca and F atoms as balls.
    2501 Begin by finding <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2476ions as tetrahedra and the Ca and F atoms as balls. Begin by finding <b
     2477style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2478mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2479Calibri;mso-bidi-theme-font:minor-latin'>Phases/fap</span></b> in <b
     2480style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2481mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2482Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> and
     2483selecting the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    25022484"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2503 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Phases/<span
    2504 class=SpellE>fap</span></span></b> in <b style='mso-bidi-font-weight:normal'><span
     2485minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Drawing
     2486Options</span></b> tab. The <b style='mso-bidi-font-weight:normal'><span
    25052487style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    25062488mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2507 minor-latin'>GSAS-II data tree</span></b> and selecting the <b
    2508 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2509 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2510 Calibri;mso-bidi-theme-font:minor-latin'>Drawing Options</span></b> tab. The <b
    2511 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2512 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2513 Calibri;mso-bidi-theme-font:minor-latin'>Phase data for <span class=SpellE>fap</span></span></b>
    2514 window shows <b style='mso-bidi-font-weight:normal'><span style='font-family:
    2515 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2516 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Drawing
    2517 controls</span></b></p>
     2489minor-latin'>Phase data for fap</span></b> window shows <b style='mso-bidi-font-weight:
     2490normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2491minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2492mso-bidi-theme-font:minor-latin'>Drawing controls</span></b></p>
    25182493
    25192494<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    2520  id="_x0000_i1031" type="#_x0000_t75" style='width:292.5pt;height:327pt;
    2521  visibility:visible;mso-wrap-style:square'>
     2495 id="Picture_x0020_16" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:292.5pt;
     2496 height:327pt;visibility:visible;mso-wrap-style:square'>
    25222497 <v:imagedata src="Laboratory%20X_files/image016.png" o:title=""/>
    25232498</v:shape><![endif]--><![if !vml]><img border=0 width=390 height=436
    2524 src="Laboratory%20X_files/image016.png" v:shapes="_x0000_i1031"><![endif]></span></p>
    2525 
    2526 <p class=MsoNormal>The plot will show a new tab marked <span class=SpellE><b
    2527 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2528 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2529 Calibri;mso-bidi-theme-font:minor-latin'>fap</span></b></span> showing some
    2530 balls in various colors. A unit cell box is drawn with 3 colored edges (Red,
    2531 Green &amp; Blue for a, b, c axes, respectively). A multicolored (RGB, again) 3D
    2532 cross is at the center of the plot.</p>
     2499src="Laboratory%20X_files/image016.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
     2500
     2501<p class=MsoNormal>The plot will show a new tab marked <b style='mso-bidi-font-weight:
     2502normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2503minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2504mso-bidi-theme-font:minor-latin'>fap</span></b> showing some balls in various
     2505colors. A unit cell box is drawn with 3 colored edges (Red, Green &amp; Blue
     2506for a, b, c axes, respectively). A multicolored (RGB, again) 3D cross is at the
     2507center of the plot.</p>
    25332508
    25342509<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    25382513  cropbottom="18161f" cropleft="42255f" cropright="8056f"/>
    25392514</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=419
    2540 src="Laboratory%20X_files/image018.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
     2515src="Laboratory%20X_files/image025.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
    25412516
    25422517<p class=MsoNormal>Notice the slider controls in <b style='mso-bidi-font-weight:
    … …  
    26182593style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    26192594mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2620 minor-latin'>Draw Atoms</span></b> table will have all of them listed. The <span
    2621 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    2622 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2623 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Sym</span></b></span><b
    2624 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2625 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2626 Calibri;mso-bidi-theme-font:minor-latin'> Op</span></b> column in the table
    2627 shows the symmetry operator number and unit cell translation used to generate
    2628 that position.</p>
     2595minor-latin'>Draw Atoms</span></b> table will have all of them listed. The <b
     2596style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2597mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2598Calibri;mso-bidi-theme-font:minor-latin'>Sym Op</span></b> column in the table shows
     2599the symmetry operator number and unit cell translation used to generate that
     2600position.</p>
    26292601
    26302602<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
    … …  
    26792651Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> menu. A small
    26802652dialog bow will appear with a list of possible atom drawing styles. Notice the
    2681 first one is blank; that will cause the atom to not be drawn. Select <span
    2682 class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    2683 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    2684 minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>polyhedra</span></b></span>
    2685 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2653first one is blank; that will cause the atom to not be drawn. Select <b
     2654style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2655mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2656Calibri;mso-bidi-theme-font:minor-latin'>polyhedra</span></b> and press <b
     2657style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    26862658mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    26872659Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. Each <b
    … …  
    26982670normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    26992671minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    2700 mso-bidi-theme-font:minor-latin'>O</span></b> <span class=GramE>atoms.</span></p>
     2672mso-bidi-theme-font:minor-latin'>O</span></b> atoms.</p>
    27012673
    27022674<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
    … …  
    27092681style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    27102682mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2711 minor-latin'>OK</span></b>; the O atoms will vanish leaving some odd <span
    2712 class=SpellE>polyhedra</span> and the Ca and F atoms.</p>
     2683minor-latin'>OK</span></b>; the O atoms will vanish leaving some odd polyhedra
     2684and the Ca and F atoms.</p>
    27132685
    27142686<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
    … …  
    27272699style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    27282700mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2729 minor-latin'>Enter</span></b>; the odd <span class=SpellE>polyhedra</span> will
    2730 immediately change to tetrahedra.</p>
     2701minor-latin'>Enter</span></b>; the odd polyhedra will immediately change to
     2702tetrahedra.</p>
    27312703
    27322704<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo4'><![if !supportLists]><span
    … …  
    27832755style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    27842756mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2785 Calibri;mso-bidi-theme-font:minor-latin'>Define Custom Colors</span></b>, move the
    2786 cross around on the spectrum display, set the vertical slider for the
    2787 luminosity (<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
     2757Calibri;mso-bidi-theme-font:minor-latin'>Define Custom Colors</span></b>, move
     2758the cross around on the spectrum display, set the vertical slider for the
     2759luminosity (<b style='mso-bidi-font-weight:normal'><span style='font-family:
     2760"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2761minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>ColorSolid</span></b>
     2762will show the result), and then press <b style='mso-bidi-font-weight:normal'><span
    27882763style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    27892764mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2790 minor-latin'>ColorSolid</span></b></span> will show the result), and then press
    2791 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2792 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2793 Calibri;mso-bidi-theme-font:minor-latin'>OK</span></b>. The drawing will now
    2794 show that color for the atoms and the color will appear in the <b
    2795 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2796 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2797 Calibri;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b> table. If you
    2798 don’t like your colors select <b style='mso-bidi-font-weight:normal'><span
     2765minor-latin'>OK</span></b>. The drawing will now show that color for the atoms
     2766and the color will appear in the <b style='mso-bidi-font-weight:normal'><span
    27992767style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    28002768mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    2801 minor-latin'>Edit/Reset atom colors</span></b> to put them back to their
    2802 default colors. In my drawing I’ve made the Ca atoms a medium gray</p>
     2769minor-latin'>Draw Atoms</span></b> table. If you don’t like your colors select <b
     2770style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2771mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     2772Calibri;mso-bidi-theme-font:minor-latin'>Edit/Reset atom colors</span></b> to
     2773put them back to their default colors. In my drawing I’ve made the Ca atoms a
     2774medium gray</p>
    28032775
    28042776<p class=MsoNormal style='margin-left:.25in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    28072779 <v:imagedata src="Laboratory%20X_files/image021.png" o:title=""/>
    28082780</v:shape><![endif]--><![if !vml]><img border=0 width=582 height=496
    2809 src="Laboratory%20X_files/image022.png" v:shapes="Picture_x0020_288"><![endif]></span></p>
     2781src="Laboratory%20X_files/image026.png" v:shapes="Picture_x0020_288"><![endif]></span></p>
    28102782
    28112783<h2>Step 10. Calculate bond distances and angles</h2>
    28122784
    2813 <p class=MsoNormal>GSAS-II will compute all the distances and angles among all
    2814 the atoms you select in the Atoms table with controls on the range of atom-atom
     2785<p class=MsoNormal>GSAS-II will compute all the distances and angles among all the
     2786atoms you select in the Atoms table with controls on the range of atom-atom
    28152787distances to consider either globally or by atom type. </p>
    28162788
    … …  
    28232795tab in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    28242796mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2825 Calibri;mso-bidi-theme-font:minor-latin'>Phases/<span class=SpellE>fap</span></span></b>.</p>
     2797Calibri;mso-bidi-theme-font:minor-latin'>Phases/fap</span></b>.</p>
    28262798
    28272799<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l1 level1 lfo6'><![if !supportLists]><span
    28282800style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
    28292801style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
    2830 the first Ca atoms by clicking on its row label (<span class=GramE>an</span> “<b
    2831 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2832 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    2833 Calibri;mso-bidi-theme-font:minor-latin'>0</span></b>”). Add to the selection
    2834 the other Ca atom and the P atom in the same way with the Ctrl key down; all
    2835 will be highlighted in blue.</p>
     2802the first Ca atoms by clicking on its row label (an “<b style='mso-bidi-font-weight:
     2803normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2804minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     2805mso-bidi-theme-font:minor-latin'>0</span></b>”). Add to the selection the other
     2806Ca atom and the P atom in the same way with the Ctrl key down; all will be
     2807highlighted in blue.</p>
    28362808
    28372809<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo6'><![if !supportLists]><span
    … …  
    28692841mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    28702842minor-latin'>OK</span></b>. GSAS-II will then display on the console formatted
    2871 tables of individual atom distances and angles with <span class=SpellE>esds</span>
    2872 as appropriate for the two Ca atoms and the P atom.</p>
     2843tables of individual atom distances and angles with esds as appropriate for the
     2844two Ca atoms and the P atom.</p>
    28732845
    28742846<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>********************************************************************************<o:p></o:p></span></p>
    28752847
    28762848<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    2877 style='mso-spacerun:yes'>   </span>Interatomic Distances and Angles for phase <span
    2878 class=SpellE>fap</span><o:p></o:p></span></p>
     2849style='mso-spacerun:yes'>   </span>Interatomic Distances and Angles for phase
     2850fap<o:p></o:p></span></p>
    28792851
    28802852<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>********************************************************************************<o:p></o:p></span></p>
    … …  
    28862858
    28872859<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    2888 style='mso-spacerun:yes'> </span>The lattice is centrosymmetric primitive
    2889 hexagonal<o:p></o:p></span></p>
     2860style='mso-spacerun:yes'> </span>The lattice is centrosymmetric primitive hexagonal<o:p></o:p></span></p>
    28902861
    28912862<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    … …  
    28992870
    29002871<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    2901 style='mso-spacerun:yes'> </span>The inversion center is located at 0<span
    2902 class=GramE>,0,0</span><o:p></o:p></span></p>
     2872style='mso-spacerun:yes'> </span>The inversion center is located at 0,0,0<o:p></o:p></span></p>
    29032873
    29042874<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    29102880
    29112881<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    2912 style='mso-spacerun:yes'> </span><span class=GramE>( 1</span>)<span
    2913 style='mso-spacerun:yes'>     </span>X,<span style='mso-spacerun:yes'>    
    2914 </span>Y,<span style='mso-spacerun:yes'>     </span>Z<span
    2915 style='mso-spacerun:yes'>       </span>( 2)<span style='mso-spacerun:yes'>  
    2916 </span>X-Y,<span style='mso-spacerun:yes'>  </span><span
    2917 style='mso-spacerun:yes'>   </span>X, 1/2+Z<o:p></o:p></span></p>
    2918 
    2919 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    2920 style='mso-spacerun:yes'> </span><span class=GramE>( 3</span>)<span
    2921 style='mso-spacerun:yes'>    </span>-Y,<span style='mso-spacerun:yes'>  
    2922 </span>X-Y,<span style='mso-spacerun:yes'>     </span>Z<span
    2923 style='mso-spacerun:yes'>       </span>( 4)<span style='mso-spacerun:yes'>   
    2924 </span>-X,<span style='mso-spacerun:yes'>    </span>-Y, 1/2+Z<o:p></o:p></span></p>
    2925 
    2926 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    2927 style='mso-spacerun:yes'> </span><span class=GramE>( 5</span>)<span
    2928 style='mso-spacerun:yes'>   </span>Y-X,<span style='mso-spacerun:yes'>   
    2929 </span>-X,<span style='mso-spacerun:yes'>     </span>Z<span
    2930 style='mso-spacerun:yes'>       </span>( 6)<span style='mso-spacerun:yes'>    
    2931 </span>Y,<span style='mso-spacerun:yes'>   </span>Y-X, 1/2+Z<o:p></o:p></span></p>
     2882style='mso-spacerun:yes'> </span>( 1)<span style='mso-spacerun:yes'>    
     2883</span>X,<span style='mso-spacerun:yes'>     </span>Y,<span
     2884style='mso-spacerun:yes'>     </span>Z<span style='mso-spacerun:yes'>      
     2885</span>( 2)<span style='mso-spacerun:yes'>   </span>X-Y,<span
     2886style='mso-spacerun:yes'>     </span>X, 1/2+Z<o:p></o:p></span></p>
     2887
     2888<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
     2889style='mso-spacerun:yes'> </span>( 3)<span style='mso-spacerun:yes'>   
     2890</span>-Y,<span style='mso-spacerun:yes'>   </span>X-Y,<span
     2891style='mso-spacerun:yes'>    </span><span
     2892style='mso-spacerun:yes'> </span>Z<span style='mso-spacerun:yes'>      
     2893</span>( 4)<span style='mso-spacerun:yes'>    </span>-X,<span
     2894style='mso-spacerun:yes'>    </span>-Y, 1/2+Z<o:p></o:p></span></p>
     2895
     2896<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
     2897style='mso-spacerun:yes'> </span>( 5)<span style='mso-spacerun:yes'>  
     2898</span>Y-X,<span style='mso-spacerun:yes'>    </span>-X,<span
     2899style='mso-spacerun:yes'>     </span>Z<span style='mso-spacerun:yes'>      
     2900</span>( 6)<span style='mso-spacerun:yes'>     </span>Y,<span
     2901style='mso-spacerun:yes'>   </span>Y-X, 1/2+Z<o:p></o:p></span></p>
    29322902
    29332903<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    29492919<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29502920style='mso-spacerun:yes'>  </span>To<span style='mso-spacerun:yes'>      
    2951 </span>cell <span class=GramE>+(</span>sym. op.)<span
    2952 style='mso-spacerun:yes'>      </span>dist.<span style='mso-spacerun:yes'>     
    2953 </span>CA1<span style='mso-spacerun:yes'>         </span><span class=SpellE>CA1</span><span
    2954 style='mso-spacerun:yes'>         </span><span class=SpellE>CA1</span><span
    2955 style='mso-spacerun:yes'>         </span><span class=SpellE>CA1</span><span
    2956 style='mso-spacerun:yes'>         </span><span class=SpellE>CA1</span><span
    2957 style='mso-spacerun:yes'>         </span><span class=SpellE>CA1</span><o:p></o:p></span></p>
     2921</span>cell +(sym. op.)<span style='mso-spacerun:yes'>      </span>dist.<span
     2922style='mso-spacerun:yes'>      </span>CA1<span
     2923style='mso-spacerun:yes'>         </span>CA1<span
     2924style='mso-spacerun:yes'>         </span>CA1<span
     2925style='mso-spacerun:yes'>         </span>CA1<span
     2926style='mso-spacerun:yes'>         </span>CA1<span
     2927style='mso-spacerun:yes'>         </span>CA1<o:p></o:p></span></p>
    29582928
    29592929<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29602930style='mso-spacerun:yes'>   </span>O6<span style='mso-spacerun:yes'>         
    2961 </span><span class=SpellE>O6</span><o:p></o:p></span></p>
     2931</span>O6<o:p></o:p></span></p>
    29622932
    29632933<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29642934style='mso-spacerun:yes'>  </span>CA1<span style='mso-spacerun:yes'>    
    2965 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    2966 </span>+(<span style='mso-spacerun:yes'>  </span>-2)<span
    2967 style='mso-spacerun:yes'>   </span>3.471(4)<o:p></o:p></span></p>
     2935</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     2936style='mso-spacerun:yes'>  </span>-2)<span style='mso-spacerun:yes'>  
     2937</span>3.471(4)<o:p></o:p></span></p>
    29682938
    29692939<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29702940style='mso-spacerun:yes'>  </span>CA1<span style='mso-spacerun:yes'>    
    2971 </span><span class=GramE>[ 0</span> 1 1]<span style='mso-spacerun:yes'> 
    2972 </span>+(<span style='mso-spacerun:yes'>  </span>-2)<span
    2973 style='mso-spacerun:yes'>   </span>3.415(4)<o:p></o:p></span></p>
     2941</span>[ 0 1 1]<span style='mso-spacerun:yes'>  </span>+(<span
     2942style='mso-spacerun:yes'>  </span>-2)<span style='mso-spacerun:yes'>  
     2943</span>3.415(4)<o:p></o:p></span></p>
    29742944
    29752945<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29762946style='mso-spacerun:yes'>  </span>CA1<span style='mso-spacerun:yes'>    
    2977 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    2978 </span>+(<span style='mso-spacerun:yes'>  </span>-4)<span
    2979 style='mso-spacerun:yes'>   </span>3.471(4)<o:p></o:p></span></p>
     2947</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     2948style='mso-spacerun:yes'>  </span>-4)<span style='mso-spacerun:yes'>  
     2949</span>3.471(4)<o:p></o:p></span></p>
    29802950
    29812951<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29822952style='mso-spacerun:yes'>  </span>CA1<span style='mso-spacerun:yes'>    
    2983 </span><span class=GramE>[ 0</span> 0 1]<span style='mso-spacerun:yes'> 
    2984 </span>+(<span style='mso-spacerun:yes'>  </span>-4)<span
    2985 style='mso-spacerun:yes'>   </span>3.415(4)<o:p></o:p></span></p>
     2953</span>[ 0 0 1]<span style='mso-spacerun:yes'>  </span>+(<span
     2954style='mso-spacerun:yes'>  </span>-4)<span style='mso-spacerun:yes'>  
     2955</span>3.415(4)<o:p></o:p></span></p>
    29862956
    29872957<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29882958style='mso-spacerun:yes'>  </span>CA1<span style='mso-spacerun:yes'>    
    2989 </span><span class=GramE>[ 1</span> 1 0]<span style='mso-spacerun:yes'> 
    2990 </span>+(<span style='mso-spacerun:yes'>  </span>-6)<span
    2991 style='mso-spacerun:yes'>   </span>3.471(4)<o:p></o:p></span></p>
     2959</span>[ 1 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     2960style='mso-spacerun:yes'>  </span>-6)<span style='mso-spacerun:yes'>  
     2961</span>3.471(4)<o:p></o:p></span></p>
    29922962
    29932963<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    29942964style='mso-spacerun:yes'>  </span>CA1<span style='mso-spacerun:yes'>    
    2995 </span><span class=GramE>[ 1</span> 1 1]<span style='mso-spacerun:yes'> 
    2996 </span>+(<span style='mso-spacerun:yes'>  </span>-6)<span
    2997 style='mso-spacerun:yes'>   </span>3.415(4)<o:p></o:p></span></p>
     2965</span>[ 1 1 1]<span style='mso-spacerun:yes'>  </span>+(<span
     2966style='mso-spacerun:yes'>  </span>-6)<span style='mso-spacerun:yes'>  
     2967</span>3.415(4)<o:p></o:p></span></p>
    29982968
    29992969<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30002970style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3001 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3002 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3003 style='mso-spacerun:yes'>  </span>2.3860(28)<o:p></o:p></span></p>
     2971</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     2972style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     2973</span>2.3860(28)<o:p></o:p></span></p>
    30042974
    30052975<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30062976style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3007 </span><span class=GramE>[ 1</span> 1 0]<span style='mso-spacerun:yes'> 
    3008 </span>+(<span style='mso-spacerun:yes'>   </span>3)<span
    3009 style='mso-spacerun:yes'>  </span>2.3860(28)<o:p></o:p></span></p>
     2977</span>[ 1 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     2978style='mso-spacerun:yes'>   </span>3)<span style='mso-spacerun:yes'> 
     2979</span>2.3860(28)<o:p></o:p></span></p>
    30102980
    30112981<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30122982style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3013 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3014 </span>+(<span style='mso-spacerun:yes'>   </span>5)<span
    3015 style='mso-spacerun:yes'>  </span>2.3860(28)<o:p></o:p></span></p>
     2983</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     2984style='mso-spacerun:yes'>   </span>5)<span style='mso-spacerun:yes'> 
     2985</span>2.3860(28)<o:p></o:p></span></p>
    30162986
    30172987<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30182988style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3019 </span><span class=GramE>[ 0</span> 0-1]<span style='mso-spacerun:yes'> 
    3020 </span>+(<span style='mso-spacerun:yes'>   </span>2)<span
    3021 style='mso-spacerun:yes'>  </span>2.4620(31)<o:p></o:p></span></p>
     2989</span>[ 0 0-1]<span style='mso-spacerun:yes'>  </span>+(<span
     2990style='mso-spacerun:yes'>   </span>2)<span style='mso-spacerun:yes'> 
     2991</span>2.4620(31)<o:p></o:p></span></p>
    30222992
    30232993<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30242994style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3025 </span><span class=GramE>[ 1</span> 1-1]<span style='mso-spacerun:yes'> 
    3026 </span>+(<span style='mso-spacerun:yes'>   </span>4)<span
    3027 style='mso-spacerun:yes'>  </span>2.4620(31)<o:p></o:p></span></p>
     2995</span>[ 1 1-1]<span style='mso-spacerun:yes'>  </span>+(<span
     2996style='mso-spacerun:yes'>   </span>4)<span style='mso-spacerun:yes'> 
     2997</span>2.4620(31)<o:p></o:p></span></p>
    30282998
    30292999<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30303000style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3031 </span><span class=GramE>[ 0</span> 1-1]<span style='mso-spacerun:yes'> 
    3032 </span>+(<span style='mso-spacerun:yes'>   </span>6)<span
    3033 style='mso-spacerun:yes'>  </span>2.4620(31)<o:p></o:p></span></p>
     3001</span>[ 0 1-1]<span style='mso-spacerun:yes'>  </span>+(<span
     3002style='mso-spacerun:yes'>   </span>6)<span style='mso-spacerun:yes'> 
     3003</span>2.4620(31)<o:p></o:p></span></p>
    30343004
    30353005<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    30453015<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30463016style='mso-spacerun:yes'>  </span>To<span style='mso-spacerun:yes'>      
    3047 </span>cell <span class=GramE>+(</span>sym. op.)<span
    3048 style='mso-spacerun:yes'>      </span>dist.<span
     3017</span>cell +(sym. op.)<span style='mso-spacerun:yes'>      </span>dist.<span
    30493018style='mso-spacerun:yes'>       </span>F4<span
    30503019style='mso-spacerun:yes'>          </span>O6<span
    30513020style='mso-spacerun:yes'>          </span>O7<span
    3052 style='mso-spacerun:yes'>          </span><span class=SpellE>O7</span><span
    3053 style='mso-spacerun:yes'>          </span><span class=SpellE>O7</span><o:p></o:p></span></p>
     3021style='mso-spacerun:yes'>          </span>O7<span
     3022style='mso-spacerun:yes'>          </span>O7<o:p></o:p></span></p>
    30543023
    30553024<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30563025style='mso-spacerun:yes'>  </span>F4<span style='mso-spacerun:yes'>     
    3057 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3058 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3059 style='mso-spacerun:yes'>  </span>2.3012(11)<o:p></o:p></span></p>
     3026</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3027style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     3028</span>2.3012(11)<o:p></o:p></span></p>
    30603029
    30613030<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30623031style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3063 </span><span class=GramE>[ 1</span> 1 0]<span style='mso-spacerun:yes'> 
    3064 </span>+(<span style='mso-spacerun:yes'>   </span>3)<span
    3065 style='mso-spacerun:yes'>   </span>2.350(4)<o:p></o:p></span></p>
     3032</span>[ 1 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3033style='mso-spacerun:yes'>   </span>3)<span style='mso-spacerun:yes'>  
     3034</span>2.350(4)<o:p></o:p></span></p>
    30663035
    30673036<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30683037style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3069 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3070 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3071 style='mso-spacerun:yes'>  </span>2.5128(30)<o:p></o:p></span></p>
     3038</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3039style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     3040</span>2.5128(30)<o:p></o:p></span></p>
    30723041
    30733042<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30743043style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3075 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3076 </span>+(<span style='mso-spacerun:yes'>   </span>6)<span
    3077 style='mso-spacerun:yes'>  </span>2.3434(24)<o:p></o:p></span></p>
     3044</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3045style='mso-spacerun:yes'>   </span>6)<span style='mso-spacerun:yes'> 
     3046</span>2.3434(24)<o:p></o:p></span></p>
    30783047
    30793048<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30803049style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3081 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3082 </span>+(<span style='mso-spacerun:yes'>  </span>-3)<span
    3083 style='mso-spacerun:yes'>  </span>2.3434(24)<o:p></o:p></span></p>
     3050</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3051style='mso-spacerun:yes'>  </span>-3)<span style='mso-spacerun:yes'> 
     3052</span>2.3434(24)<o:p></o:p></span></p>
    30843053
    30853054<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    30863055style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3087 </span><span class=GramE>[ 0</span> 1 1]<span style='mso-spacerun:yes'> 
    3088 </span>+(<span style='mso-spacerun:yes'>  </span>-4)<span
    3089 style='mso-spacerun:yes'>  </span>2.5128(30)<o:p></o:p></span></p>
     3056</span>[ 0 1 1]<span style='mso-spacerun:yes'>  </span>+(<span
     3057style='mso-spacerun:yes'>  </span>-4)<span style='mso-spacerun:yes'> 
     3058</span>2.5128(30)<o:p></o:p></span></p>
    30903059
    30913060<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    31013070<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    31023071style='mso-spacerun:yes'>  </span>To<span style='mso-spacerun:yes'>      
    3103 </span>cell <span class=GramE>+(</span>sym. op.)<span
    3104 style='mso-spacerun:yes'>      </span>dist.<span
     3072</span>cell +(sym. op.)<span style='mso-spacerun:yes'>      </span>dist.<span
    31053073style='mso-spacerun:yes'>       </span>O5<span
    31063074style='mso-spacerun:yes'>          </span>O6<span
    … …  
    31093077<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    31103078style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3111 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3112 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3113 style='mso-spacerun:yes'>   </span>1.548(4)<o:p></o:p></span></p>
     3079</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3080style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'>  
     3081</span>1.548(4)<o:p></o:p></span></p>
    31143082
    31153083<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    31163084style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3117 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3118 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3119 style='mso-spacerun:yes'>   </span>1.569(4)<span style='mso-spacerun:yes'>  
    3120 </span>110.37(23)<o:p></o:p></span></p>
     3085</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3086style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'>  
     3087</span>1.569(4)<span style='mso-spacerun:yes'>   </span>110.37(23)<o:p></o:p></span></p>
    31213088
    31223089<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    31233090style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3124 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3125 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3126 style='mso-spacerun:yes'>  </span>1.5167(27)<span style='mso-spacerun:yes'> 
    3127 </span>110.07(15)<span style='mso-spacerun:yes'>  </span>108.77(15)<o:p></o:p></span></p>
     3091</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3092style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     3093</span>1.5167(27)<span style='mso-spacerun:yes'>  </span>110.07(15)<span
     3094style='mso-spacerun:yes'>  </span>108.77(15)<o:p></o:p></span></p>
    31283095
    31293096<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    31303097style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3131 </span><span class=GramE>[ 0</span> 0 1]<span style='mso-spacerun:yes'> 
    3132 </span>+(<span style='mso-spacerun:yes'>  </span>-4)<span
    3133 style='mso-spacerun:yes'>  </span>1.5167(27)<span style='mso-spacerun:yes'> 
    3134 </span>110.07(15)<span style='mso-spacerun:yes'>  </span>108.77(15)<span
    3135 style='mso-spacerun:yes'>  </span>108.74(23)<o:p></o:p></span></p>
     3098</span>[ 0 0 1]<span style='mso-spacerun:yes'>  </span>+(<span
     3099style='mso-spacerun:yes'>  </span>-4)<span style='mso-spacerun:yes'> 
     3100</span>1.5167(27)<span style='mso-spacerun:yes'>  </span>110.07(15)<span
     3101style='mso-spacerun:yes'>  </span>108.77(15)<span style='mso-spacerun:yes'> 
     3102</span>108.74(23)<o:p></o:p></span></p>
    31363103
    31373104<p class=MsoNormal>There is probably too many bonds shown for the Ca1 atom and
    … …  
    31573124
    31583125<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3159 style='mso-spacerun:yes'>   </span>Interatomic Distances and Angles for phase <span
    3160 class=SpellE>fap</span><o:p></o:p></span></p>
     3126style='mso-spacerun:yes'>   </span>Interatomic Distances and Angles for phase
     3127fap<o:p></o:p></span></p>
    31613128
    31623129<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'>********************************************************************************<o:p></o:p></span></p>
    … …  
    31813148
    31823149<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3183 style='mso-spacerun:yes'> </span>The inversion center is located at 0<span
    3184 class=GramE>,0,0</span><o:p></o:p></span></p>
     3150style='mso-spacerun:yes'> </span>The inversion center is located at 0,0,0<o:p></o:p></span></p>
    31853151
    31863152<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    31923158
    31933159<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3194 style='mso-spacerun:yes'> </span><span class=GramE>( 1</span>)<span
    3195 style='mso-spacerun:yes'>     </span>X,<span style='mso-spacerun:yes'>    
    3196 </span>Y,<span style='mso-spacerun:yes'>     </span>Z<span
    3197 style='mso-spacerun:yes'>       </span>( 2)<span style='mso-spacerun:yes'>  
    3198 </span>X-Y,<span style='mso-spacerun:yes'>     </span>X, 1/2+Z<o:p></o:p></span></p>
    3199 
    3200 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3201 style='mso-spacerun:yes'> </span><span class=GramE>( 3</span>)<span
    3202 style='mso-spacerun:yes'>    </span>-Y,<span style='mso-spacerun:yes'>  
    3203 </span>X-Y,<span style='mso-spacerun:yes'>     </span>Z<span
    3204 style='mso-spacerun:yes'>       </span>( 4)<span style='mso-spacerun:yes'>   
    3205 </span>-X,<span style='mso-spacerun:yes'>    </span>-Y, 1/2+Z<o:p></o:p></span></p>
    3206 
    3207 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3208 style='mso-spacerun:yes'> </span><span class=GramE>( 5</span>)<span
    3209 style='mso-spacerun:yes'>   </span>Y-X,<span style='mso-spacerun:yes'>   
    3210 </span>-X,<span style='mso-spacerun:yes'>     </span>Z<span
    3211 style='mso-spacerun:yes'>       </span>( 6)<span style='mso-spacerun:yes'>    
    3212 </span>Y,<span style='mso-spacerun:yes'>   </span>Y-X, 1/2+Z<o:p></o:p></span></p>
     3160style='mso-spacerun:yes'> </span>( 1)<span style='mso-spacerun:yes'>    
     3161</span>X,<span style='mso-spacerun:yes'>     </span>Y,<span
     3162style='mso-spacerun:yes'>     </span>Z<span style='mso-spacerun:yes'>      
     3163</span>( 2)<span style='mso-spacerun:yes'>   </span>X-Y,<span
     3164style='mso-spacerun:yes'>     </span>X, 1/2+Z<o:p></o:p></span></p>
     3165
     3166<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
     3167style='mso-spacerun:yes'> </span>( 3)<span style='mso-spacerun:yes'>   
     3168</span>-Y,<span style='mso-spacerun:yes'>   </span>X-Y,<span
     3169style='mso-spacerun:yes'>     </span>Z<span style='mso-spacerun:yes'>      
     3170</span>( 4)<span style='mso-spacerun:yes'>    </span>-X,<span
     3171style='mso-spacerun:yes'>    </span>-Y, 1/2+Z<o:p></o:p></span></p>
     3172
     3173<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
     3174style='mso-spacerun:yes'> </span>( 5)<span style='mso-spacerun:yes'>  
     3175</span>Y-X,<span style='mso-spacerun:yes'>    </span>-X,<span
     3176style='mso-spacerun:yes'>     </span>Z<span style='mso-spacerun:yes'>      
     3177</span>( 6)<span style='mso-spacerun:yes'>     </span>Y,<span
     3178style='mso-spacerun:yes'>   </span>Y-X, 1/2+Z<o:p></o:p></span></p>
    32133179
    32143180<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    32303196<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    32313197style='mso-spacerun:yes'>  </span>To<span style='mso-spacerun:yes'>      
    3232 </span>cell <span class=GramE>+(</span>sym. op.)<span
    3233 style='mso-spacerun:yes'>      </span>dist.<span
     3198</span>cell +(sym. op.)<span style='mso-spacerun:yes'>      </span>dist.<span
    32343199style='mso-spacerun:yes'>       </span>O5<span
    3235 style='mso-spacerun:yes'>          </span><span class=SpellE>O5</span><span
    3236 style='mso-spacerun:yes'>          </span><span class=SpellE>O5</span><span
     3200style='mso-spacerun:yes'>          </span>O5<span
     3201style='mso-spacerun:yes'>          </span>O5<span
    32373202style='mso-spacerun:yes'>          </span>O6<span
    3238 style='mso-spacerun:yes'>          </span><span class=SpellE>O6</span><o:p></o:p></span></p>
     3203style='mso-spacerun:yes'>          </span>O6<o:p></o:p></span></p>
    32393204
    32403205<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    32413206style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3242 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3243 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3244 style='mso-spacerun:yes'>  </span>2.3860(28)<o:p></o:p></span></p>
     3207</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3208style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     3209</span>2.3860(28)<o:p></o:p></span></p>
    32453210
    32463211<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    32473212style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3248 </span><span class=GramE>[ 1</span> 1 0]<span style='mso-spacerun:yes'> 
    3249 </span>+(<span style='mso-spacerun:yes'>   </span>3)<span
    3250 style='mso-spacerun:yes'>  </span>2.3860(28)<span style='mso-spacerun:yes'> 
    3251 </span>74.44(11)<o:p></o:p></span></p>
     3213</span>[ 1 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3214style='mso-spacerun:yes'>   </span>3)<span style='mso-spacerun:yes'> 
     3215</span>2.3860(28)<span style='mso-spacerun:yes'>  </span>74.44(11)<o:p></o:p></span></p>
    32523216
    32533217<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    32543218style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3255 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3256 </span>+(<span style='mso-spacerun:yes'>   </span>5)<span
    3257 style='mso-spacerun:yes'>  </span>2.3860(28)<span style='mso-spacerun:yes'> 
    3258 </span>74.44(11)<span style='mso-spacerun:yes'>   </span>74.44(11)<o:p></o:p></span></p>
    3259 
    3260 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3261 style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3262 </span><span class=GramE>[ 0</span> 0-1]<span style='mso-spacerun:yes'> 
     3219</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3220style='mso-spacerun:yes'>   </span>5)<span style='mso-spacerun:yes'> 
     3221</span>2.3860(28)<span style='mso-spacerun:yes'>  </span>74.44(11)<span
     3222style='mso-spacerun:yes'>   </span>74.44(11)<o:p></o:p></span></p>
     3223
     3224<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
     3225style='mso-spacerun:yes'>  </span>O6 <span
     3226style='mso-spacerun:yes'>     </span>[ 0 0-1]<span style='mso-spacerun:yes'> 
    32633227</span>+(<span style='mso-spacerun:yes'>   </span>2)<span
    32643228style='mso-spacerun:yes'>  </span>2.4620(31)<span style='mso-spacerun:yes'> 
    … …  
    32683232<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    32693233style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3270 </span><span class=GramE>[ 1</span> 1-1]<span style='mso-spacerun:yes'> 
    3271 </span>+(<span style='mso-spacerun:yes'>   </span>4)<span
    3272 style='mso-spacerun:yes'>  </span>2.4620(31)<span style='mso-spacerun:yes'>  
    3273 </span>92.77(9)<span style='mso-spacerun:yes'>   </span>124.40(11)<span
    3274 style='mso-spacerun:yes'>  </span>154.16(12)<span style='mso-spacerun:yes'> 
    3275 </span>75.80(12)<o:p></o:p></span></p>
     3234</span>[ 1 1-1]<span style='mso-spacerun:yes'>  </span>+(<span
     3235style='mso-spacerun:yes'>   </span>4)<span style='mso-spacerun:yes'> 
     3236</span>2.4620(31)<span style='mso-spacerun:yes'>   </span>92.77(9)<span
     3237style='mso-spacerun:yes'>   </span>124.40(11)<span style='mso-spacerun:yes'> 
     3238</span>154.16(12)<span style='mso-spacerun:yes'>  </span>75.80(12)<o:p></o:p></span></p>
    32763239
    32773240<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    32783241style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3279 </span><span class=GramE>[ 0</span> 1-1] <span
    3280 style='mso-spacerun:yes'> </span>+(<span style='mso-spacerun:yes'>  
    3281 </span>6)<span style='mso-spacerun:yes'>  </span>2.4620(31)<span
    3282 style='mso-spacerun:yes'>  </span>154.16(12)<span style='mso-spacerun:yes'>  
    3283 </span>92.77(9)<span style='mso-spacerun:yes'>   </span>124.40(11)<span
    3284 style='mso-spacerun:yes'>  </span>75.80(12)<span style='mso-spacerun:yes'>  
    3285 </span>75.80(12)<o:p></o:p></span></p>
     3242</span>[ 0 1-1]<span style='mso-spacerun:yes'>  </span>+(<span
     3243style='mso-spacerun:yes'>   </span>6)<span style='mso-spacerun:yes'> 
     3244</span>2.4620(31)<span style='mso-spacerun:yes'>  </span>154.16(12)<span
     3245style='mso-spacerun:yes'>   </span>92.77(9)<span style='mso-spacerun:yes'>  
     3246</span>124.40(11)<span style='mso-spacerun:yes'>  </span>75.80(12)<span
     3247style='mso-spacerun:yes'>   </span>75.80(12)<o:p></o:p></span></p>
    32863248
    32873249<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    32973259<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    32983260style='mso-spacerun:yes'>  </span>To<span style='mso-spacerun:yes'>      
    3299 </span>cell <span class=GramE>+(</span>sym. op.)<span
    3300 style='mso-spacerun:yes'>  </span><span
    3301 style='mso-spacerun:yes'>    </span>dist.<span style='mso-spacerun:yes'>      
    3302 </span>F4<span style='mso-spacerun:yes'>          </span>O6<span
     3261</span>cell +(sym. op.)<span style='mso-spacerun:yes'>      </span>dist.<span
     3262style='mso-spacerun:yes'>       </span>F4<span
     3263style='mso-spacerun:yes'>          </span>O6<span
    33033264style='mso-spacerun:yes'>          </span>O7<span
    3304 style='mso-spacerun:yes'>          </span><span class=SpellE>O7</span><span
    3305 style='mso-spacerun:yes'>          </span><span class=SpellE>O7</span><o:p></o:p></span></p>
     3265style='mso-spacerun:yes'>          </span>O7<span
     3266style='mso-spacerun:yes'>          </span>O7<o:p></o:p></span></p>
    33063267
    33073268<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33083269style='mso-spacerun:yes'>  </span>F4<span style='mso-spacerun:yes'>     
    3309 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3310 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3311 style='mso-spacerun:yes'>  </span>2.3012(11)<o:p></o:p></span></p>
     3270</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3271style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     3272</span>2.3012(11)<o:p></o:p></span></p>
    33123273
    33133274<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33143275style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3315 </span><span class=GramE>[ 1</span> 1 0]<span style='mso-spacerun:yes'> 
    3316 </span>+(<span style='mso-spacerun:yes'>   </span>3)<span
    3317 style='mso-spacerun:yes'>   </span>2.350(4)<span style='mso-spacerun:yes'>  
    3318 </span>152.07(12)<o:p></o:p></span></p>
     3276</span>[ 1 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3277style='mso-spacerun:yes'>   </span>3)<span style='mso-spacerun:yes'>  
     3278</span>2.350(4)<span style='mso-spacerun:yes'>   </span>152.07(12)<o:p></o:p></span></p>
    33193279
    33203280<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33213281style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3322 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3323 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3324 style='mso-spacerun:yes'>  </span>2.5128(30)<span style='mso-spacerun:yes'>  
    3325 </span>81.10(7)<span style='mso-spacerun:yes'>   </span>74.63(11)<o:p></o:p></span></p>
     3282</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3283style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     3284</span>2.5128(30)<span style='mso-spacerun:yes'>   </span>81.10(7)<span
     3285style='mso-spacerun:yes'>   </span>74.63(11)<o:p></o:p></span></p>
    33263286
    33273287<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33283288style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3329 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3330 </span>+(<span style='mso-spacerun:yes'>   </span>6)<span
    3331 style='mso-spacerun:yes'>  </span>2.3434(24)<span style='mso-spacerun:yes'> 
    3332 </span>102.85(8)<span style='mso-spacerun:yes'>    </span>85.36(8)<span
     3289</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3290style='mso-spacerun:yes'>   </span>6)<span style='mso-spacerun:yes'> 
     3291</span>2.3434(24)<span style='mso-spacerun:yes'>  </span>102.85(8)<span
     3292style='mso-spacerun:yes'>    </span>85.36(8)<span style='mso-spacerun:yes'>  
     3293</span>135.15(12)<o:p></o:p></span></p>
     3294
     3295<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
     3296style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
     3297</span>[ 0 1 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3298style='mso-spacerun:yes'>  </span>-3)<span style='mso-spacerun:yes'> 
     3299</span>2.3434(24)<span style='mso-spacerun:yes'>  </span>102.85(8)<span
     3300style='mso-spacerun:yes'>    </span>85.36(8)<span style='mso-spacerun:yes'>   
     3301</span>77.50(6)<span style='mso-spacerun:yes'>   </span>141.17(14)<o:p></o:p></span></p>
     3302
     3303<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
     3304style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
     3305</span>[ 0 1 1]<span style='mso-spacerun:yes'>  </span>+(<span
     3306style='mso-spacerun:yes'>  </span>-4)<span style='mso-spacerun:yes'> 
     3307</span>2.5128(30)<span style='mso-spacerun:yes'>   </span>81.10(7)<span
     3308style='mso-spacerun:yes'>   </span>74.63(11)<span style='mso-spacerun:yes'>  
     3309</span>58.76(12)<span style='mso-spacerun:yes'>    </span>77.50(6)<span
    33333310style='mso-spacerun:yes'>   </span>135.15(12)<o:p></o:p></span></p>
    3334 
    3335 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3336 style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3337 </span><span class=GramE>[ 0</span> 1 0]<span style='mso-spacerun:yes'> 
    3338 </span>+(<span style='mso-spacerun:yes'>  </span>-3)<span
    3339 style='mso-spacerun:yes'>  </span>2.3434(24)<span style='mso-spacerun:yes'> 
    3340 </span>102.85(8)<span style='mso-spacerun:yes'>    </span>85.36(8)<span
    3341 style='mso-spacerun:yes'>    </span>77.50(6)<span style='mso-spacerun:yes'>  
    3342 </span>141.17(14)<o:p></o:p></span></p>
    3343 
    3344 <p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    3345 style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3346 </span><span class=GramE>[ 0</span> 1 1]<span style='mso-spacerun:yes'> 
    3347 </span>+(<span style='mso-spacerun:yes'>  </span>-4)<span
    3348 style='mso-spacerun:yes'>  </span>2.5128(30)<span style='mso-spacerun:yes'>  
    3349 </span>81.10(7)<span style='mso-spacerun:yes'>   </span>74.63(11)<span
    3350 style='mso-spacerun:yes'>   </span>58.76(12)<span style='mso-spacerun:yes'>   
    3351 </span>77.50(6)<span style='mso-spacerun:yes'>   </span>135.15(12)<o:p></o:p></span></p>
    33523311
    33533312<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><o:p>&nbsp;</o:p></span></p>
    … …  
    33633322<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33643323style='mso-spacerun:yes'>  </span>To<span style='mso-spacerun:yes'>      
    3365 </span>cell <span class=GramE>+(</span>sym. op.)<span
    3366 style='mso-spacerun:yes'>      </span>dist.<span
     3324</span>cell +(sym. op.)<span style='mso-spacerun:yes'>      </span>dist.<span
    33673325style='mso-spacerun:yes'>       </span>O5<span
    33683326style='mso-spacerun:yes'>          </span>O6<span
    … …  
    33713329<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33723330style='mso-spacerun:yes'>  </span>O5<span style='mso-spacerun:yes'>     
    3373 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3374 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3375 style='mso-spacerun:yes'>   </span>1.548(4)<o:p></o:p></span></p>
     3331</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3332style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'>  
     3333</span>1.548(4)<o:p></o:p></span></p>
    33763334
    33773335<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33783336style='mso-spacerun:yes'>  </span>O6<span style='mso-spacerun:yes'>     
    3379 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3380 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3381 style='mso-spacerun:yes'>   </span>1.569(4)<span style='mso-spacerun:yes'>  
    3382 </span>110.37(23)<o:p></o:p></span></p>
     3337</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3338style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'>  
     3339</span>1.569(4)<span style='mso-spacerun:yes'>   </span>110.37(23)<o:p></o:p></span></p>
    33833340
    33843341<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33853342style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3386 </span><span class=GramE>[ 0</span> 0 0]<span style='mso-spacerun:yes'> 
    3387 </span>+(<span style='mso-spacerun:yes'>   </span>1)<span
    3388 style='mso-spacerun:yes'>  </span>1.5167(27)<span style='mso-spacerun:yes'> 
    3389 </span>110.07(15)<span style='mso-spacerun:yes'>  </span>108.77(15)<o:p></o:p></span></p>
     3343</span>[ 0 0 0]<span style='mso-spacerun:yes'>  </span>+(<span
     3344style='mso-spacerun:yes'>   </span>1)<span style='mso-spacerun:yes'> 
     3345</span>1.5167(27)<span style='mso-spacerun:yes'>  </span>110.07(15)<span
     3346style='mso-spacerun:yes'>  </span>108.77(15)<o:p></o:p></span></p>
    33903347
    33913348<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Courier New"'><span
    33923349style='mso-spacerun:yes'>  </span>O7<span style='mso-spacerun:yes'>     
    3393 </span><span class=GramE>[ 0</span> 0 1]<span style='mso-spacerun:yes'> 
    3394 </span>+(<span style='mso-spacerun:yes'>  </span>-4)<span
    3395 style='mso-spacerun:yes'>  </span>1.5167(27)<span style='mso-spacerun:yes'> 
    3396 </span>110.07(15)<span style='mso-spacerun:yes'>  </span>108.77(15)<span
    3397 style='mso-spacerun:yes'>  </span>108.74(23)<o:p></o:p></span></p>
     3350</span>[ 0 0 1]<span style='mso-spacerun:yes'>  </span>+(<span
     3351style='mso-spacerun:yes'>  </span>-4)<span style='mso-spacerun:yes'> 
     3352</span>1.5167(27)<span style='mso-spacerun:yes'>  </span>110.07(15)<span
     3353style='mso-spacerun:yes'>  </span>108.77(15)<span style='mso-spacerun:yes'> 
     3354</span>108.74(23)<o:p></o:p></span></p>
    33983355
    33993356<p class=MsoNormal>which is probably more reasonable.</p>
    34003357
    3401 <p class=MsoNormal>This concludes this tutorial for Rietveld refinement of <span
    3402 class=SpellE>fluroapatite</span>.</p>
     3358<p class=MsoNormal>This concludes this tutorial for Rietveld refinement of
     3359fluroapatite.</p>
    34033360
    34043361<p class=MsoNormal style='margin-left:.25in'><o:p>&nbsp;</o:p></p>

  • Tutorials/LabData/Laboratory X_files/filelist.xml

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  • 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>
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    … …  
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    645644 /* Font Definitions */
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    11131119        mso-bidi-font-size:10.0pt;
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    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
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    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

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

    r1718 r2390  
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  • Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS.htm

    r2294 r2390  
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    36   <o:CharactersWithSpaces>22211</o:CharactersWithSpaces>
     36  <o:CharactersWithSpaces>22226</o:CharactersWithSpaces>
    3737  <o:Version>16.00</o:Version>
    3838 </o:DocumentProperties>
    … …  
    811811
    812812<p class=MsoNormal>In these exercises you will use GSAS-II to refine the
    813 structure of a few single crystal structures where there is merohedral twinning.
    814 There is a general discussion of twinning in International Tables for
     813structure of a few single crystal structures where there is merohedral
     814twinning. There is a general discussion of twinning in International Tables for
    815815Crystallography (2006), Vol. C, Chapter 1.3, pp 10-14. Merohedral twinning
    816816occurs when the twin operation (2, m or <span style='position:relative;
    … …  
    892892
    893893<p class=MsoNormal>This example was taken from Luo, et al., Dalton Trans.
    894 4491(2006). The structure is given in the file <b><span style='font-family:
    895 "Calibri",sans-serif'>/exercises/<span class=SpellE>MerohedralTwins</span>/1b.cif</span></b>
    896 and the data are in <b><span style='font-family:"Calibri",sans-serif'>/exercises/<span
    897 class=SpellE>MerohedralTwins</span>/1b.fcf</span></b>. This example is <span
    898 class=SpellE>noncentrosymmetric</span> and the data was collected with
     8944491(2006). The structure is given in the file <span class=SpellE><b><span
     895style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span
     896style='font-family:"Calibri",sans-serif'>/data/1b.cif</span></b> and the data
     897are in <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>MerohedralTwins</span></b></span><b><span
     898style='font-family:"Calibri",sans-serif'>/data/1b.fcf</span></b>. This example
     899is <span class=SpellE>noncentrosymmetric</span> and the data was collected with
    899900radiation (<span class=SpellE>MoK</span>&#945;) that gives significant resonant
    900901scattering from the Ga atoms. </p>
    … …  
    918919and you will see the General page for this phase</p>
    919920
    920 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=650 height=500
     921<p class=MsoNormal><span style='mso-no-proof:yes'><img width=403 height=310
    921922id="_x0000_i1056"
    922923src="Merohedral%20twin%20refinement%20in%20GSAS_files/image007.png"></span></p>
    … …  
    924925<p class=MsoNormal>Next do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
    925926Factor/from CIF file</span></b> (that is the format of a “<span class=SpellE>fcf</span>”
    926 file); a file selection dialog box will appear with the previously selected directory
    927 chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>;
     927file); a file selection dialog box will appear with the previously selected
     928directory chosen. Select <b><span style='font-family:"Calibri",sans-serif'>1b.fcf</span></b>;
    928929a popup window will appear</p>
    929930
    … …  
    992993parameter</span></b> for refinement and do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
    993994from the main GSAS-II data tree menu. The structure will quickly refine to give
    994 <span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable
    995 improvement on Scale factor alone. The Flack parameter is now 0.452, meaning
    996 that both hands somehow exist in the structure. This can happen if the crystal
    997 is <span class=SpellE>merohedrally</span> inversion twinned.</p>
     995<span class=SpellE>R<sub>w</sub></span>=2.087% which is a considerable improvement
     996on Scale factor alone. The Flack parameter is now 0.452, meaning that both
     997hands somehow exist in the structure. This can happen if the crystal is <span
     998class=SpellE>merohedrally</span> inversion twinned.</p>
    998999
    9991000<p class=MsoNormal>To introduce this twin, press the <b><span style='font-family:
    … …  
    10271028[NC<sub>7</sub>H<sub>8</sub>]<sup>+</sup><o:p></o:p></span></h2>
    10281029
    1029 <p class=MsoNormal>In this case the data collection Laue statistics (very
    1030 nearly <span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m)
     1030<p class=MsoNormal>In this case the data collection Laue statistics (very nearly
     1031<span style='position:relative;top:3pt'><span style='mso-no-proof:yes'>-3</span>m)
    10311032and systematic extinctions indicated that the space group was either one of the
    10321033<span class=SpellE>enantiomorphic</span> pair P3<sub>1</sub>21 or P3<sub>2</sub>21
    … …  
    10731074  o:title=""/>
    10741075</v:shape><![endif]--><![if !vml]><img width=495 height=235
    1075 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
     1076src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
    10761077
    10771078<p class=MsoNormal>There are two significant warnings concerning <span
    … …  
    11781179width=9 height=19 id="_x0000_i1039"
    11791180src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1
    1180 Laue data symmetries that there is twinning so don’t bother trying to make it better
    1181 by refining the structure. To determine the possible twin law we refer to Table
    1182 1.3.4.2 of the International Tables for Crystallography Vol C. and see that
    1183 indeed Laue <span style='position:relative;top:3pt'><span style='mso-no-proof:
    1184 yes'><img width=9 height=19 id="_x0000_i1038"
     1181Laue data symmetries that there is twinning so don’t bother trying to make it
     1182better by refining the structure. To determine the possible twin law we refer
     1183to Table 1.3.4.2 of the International Tables for Crystallography Vol C. and see
     1184that indeed Laue <span style='position:relative;top:3pt'><span
     1185style='mso-no-proof:yes'><img width=9 height=19 id="_x0000_i1038"
    11851186src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.png"></span>m1
    11861187as P3<sub>2</sub>21 can be simulated by twinned Laue <span style='position:
    … …  
    12831284
    12841285<p class=MsoNormal>Before beginning the refinement, it usually the practice to
    1285 eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub>
    1286 &lt; 2<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span
     1286eliminate the poorly measured reflections where F<sup>2</sup><sub>obs</sub> &lt;
     12872<span style='font-family:Symbol'>s</span>(F<sup>2</sup>). Select the <b><span
    12871288style='font-family:"Calibri",sans-serif'>Controls</span></b> entry from the
    12881289GSAS-II data tree.</p>
    … …  
    13161317that indeed Laue 6/mmm as P6<sub>1</sub>22 can be simulated by twinned Laue 6/m
    13171318crystals in P6<sub>1</sub>; the possible operator is shown in Table 1.3.4.1
    1318 (reproduced above) as either a mirror or a 2-fold. The detailed symbolism in
    1319 the table (‘m.., ..2/.2.’) indicates (perhaps obscurely) the operator
    1320 specifics; they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr
     1319(reproduced above) as either a mirror or a 2-fold. The detailed symbolism in the
     1320table (‘m.., ..2/.2.’) indicates (perhaps obscurely) the operator specifics;
     1321they are m as <span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><m:acc><m:accPr><m:chr
    13211322    m:val="&#773;"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family:
    13221323   "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic;
    … …  
    13331334EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    13341335 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'>
    1335  <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image003.png"
     1336 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image004.png"
    13361337  o:title="" chromakey="white"/>
    13371338</v:shape><![endif]--><![if !vml]><img width=26 height=19
    1338 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;or
     1339src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;or
    133913402 as <!--[if gte msEquation 12]><m:oMath><i style='mso-bidi-font-style:normal'><span
    13401341 style='font-family:"Cambria Math",serif'><span style='position:relative;
    … …  
    13491350EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    13501351 type="#_x0000_t75" style='width:19.5pt;height:14.25pt'>
    1351  <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image005.png"
     1352 <v:imagedata src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.png"
    13521353  o:title="" chromakey="white"/>
    13531354</v:shape><![endif]--><![if !vml]><img width=26 height=19
    1354 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image006.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
     1355src="Merohedral%20twin%20refinement%20in%20GSAS_files/image019.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]><span
    13551356style='font-family:"Cambria Math",serif'>; we will use the 2-fold, m and
    13561357inversion operators to fully test for presence of the 4 possible twin laws.
    … …  
    13811382  o:title=""/>
    13821383</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1383 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
    1384 
    1385 <p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is
    1386 nonphysical and the 1<sup>st</sup> twin fraction is small. It is likely that
    1387 the true space group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
     1384src="Merohedral%20twin%20refinement%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
     1385
     1386<p class=MsoNormal>The negative one for the 3<sup>rd</sup> twin fraction is nonphysical
     1387and the 1<sup>st</sup> twin fraction is small. It is likely that the true space
     1388group is P6<sub>5</sub> and Type 2 <span class=SpellE>merohedrally</span>
    13881389twinned (twin fractions 2 &amp; 4). We can improve it by refining the atom
    13891390positions and thermal parameters, but first we need to replace the hydrogen
    … …  
    13991400  o:title=""/>
    14001401</v:shape><![endif]--><![if !vml]><img width=700 height=300
    1401 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
     1402src="Merohedral%20twin%20refinement%20in%20GSAS_files/image021.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
    14021403
    14031404<p class=MsoNormal>If you scroll down the page, you’ll see H-atoms with default
    … …  
    14341435  o:title=""/>
    14351436</v:shape><![endif]--><![if !vml]><img width=400 height=485
    1436 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
    1437 
    1438 <p class=MsoNormal>It specifies the expected geometry around each C-atom for H-atom
    1439 placement. As expected we want 3 H-atoms on the terminal CH<sub>3</sub> groups
    1440 on the <span class=SpellE>Cp</span>* ring and one for each C-atom for the NC<sub>5</sub>H<sub>5</sub>
    1441 molecule. Press <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1442 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1443 minor-latin'>Ok</span></b>; you will see the H-atoms added in turn to the
    1444 structure and they will be inserted immediately after their respective C-atom.
    1445 Their positions and thermal parameters are tied to the C-atoms so that after
    1446 refinement of the structure they can be shifted to the <span class=SpellE>stereochemically</span>
    1447 best positions. For the refinement, double click the <b style='mso-bidi-font-weight:
     1437src="Merohedral%20twin%20refinement%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
     1438
     1439<p class=MsoNormal>It specifies the expected geometry around each C-atom for
     1440H-atom placement. As expected we want 3 H-atoms on the terminal CH<sub>3</sub>
     1441groups on the <span class=SpellE>Cp</span>* ring and one for each C-atom for
     1442the NC<sub>5</sub>H<sub>5</sub> molecule. Press <b style='mso-bidi-font-weight:
    14481443normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1449 minor-latin;mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading
    1450 and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
    1451 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1452 minor-latin'>X</span></b> and <b style='mso-bidi-font-weight:normal'><span
     1444minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; you will see the
     1445H-atoms added in turn to the structure and they will be inserted immediately
     1446after their respective C-atom. Their positions and thermal parameters are tied
     1447to the C-atoms so that after refinement of the structure they can be shifted to
     1448the <span class=SpellE>stereochemically</span> best positions. For the
     1449refinement, double click the <b style='mso-bidi-font-weight:normal'><span
    14531450style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1454 mso-hansi-theme-font:minor-latin'>U</span></b> from the popup; press <b
     1451mso-hansi-theme-font:minor-latin'>Refine</span></b> column heading and select <b
    14551452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1456 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
    1457 The Atom table will be redrawn with XU in every entry under Refine. Now do <b
    1458 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1459 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>
    1460 from the main GSASII data tree window; the <span class=SpellE>Rw</span> will
    1461 drop to ~1.92%. If you look at the <b style='mso-bidi-font-weight:normal'><span
     1453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
     1454and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1455mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
     1456from the popup; press <b style='mso-bidi-font-weight:normal'><span
     1457style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1458mso-hansi-theme-font:minor-latin'>OK</span></b>. The Atom table will be redrawn
     1459with XU in every entry under Refine. Now do <b style='mso-bidi-font-weight:
     1460normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1461minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
     1462the main GSASII data tree window; the <span class=SpellE>Rw</span> will drop to
     1463~1.92%. If you look at the <b style='mso-bidi-font-weight:normal'><span
    14621464style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14631465mso-hansi-theme-font:minor-latin'>Data</span></b> tab the Twin element
    … …  
    14701472  o:title=""/>
    14711473</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1472 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
     1474src="Merohedral%20twin%20refinement%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
    14731475style='mso-spacerun:yes'> </span></p>
    14741476
    … …  
    15061508  o:title=""/>
    15071509</v:shape><![endif]--><![if !vml]><img width=360 height=351
    1508 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
     1510src="Merohedral%20twin%20refinement%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
    15091511
    15101512<p class=MsoNormal>Check the <b style='mso-bidi-font-weight:normal'><span
    15111513style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1512 mso-hansi-theme-font:minor-latin'>Choose inversion</span></b> box and (important)
    1513 set <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1514 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Choose unit
    1515 cell</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1516 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1517 mso-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put the inverted
    1518 structure back inside the unit cell. Press <b style='mso-bidi-font-weight:normal'><span
    1519 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1520 mso-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot will both
    1521 be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span
     1514mso-hansi-theme-font:minor-latin'>Choose inversion</span></b> box and
     1515(important) set <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1516"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1517minor-latin'>Choose unit cell</span></b> to <b style='mso-bidi-font-weight:
     1518normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1519minor-latin;mso-hansi-theme-font:minor-latin'>1 1 1</span></b>; this will put
     1520the inverted structure back inside the unit cell. Press <b style='mso-bidi-font-weight:
     1521normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1522minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; the table and plot
     1523will both be redrawn. Now do <b style='mso-bidi-font-weight:normal'><span
    15221524style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    15231525mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the <span
    … …  
    15331535  o:title=""/>
    15341536</v:shape><![endif]--><![if !vml]><img width=449 height=500
    1535 src="Merohedral%20twin%20refinement%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
     1537src="Merohedral%20twin%20refinement%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_46"><![endif]></span></p>
    15361538
    15371539<p class=MsoNormal>Now the identity Twin Law is ~2/3 and the 2-fold Twin Law is
    15381540the other ~1/3 while the other two are ~zero. You can delete them and repeat
    1539 the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the
    1540 merohedral twin exercises. You can save this project if desired.</p>
     1541the refinement; <span class=SpellE>Rw</span> ~1.7%. This completed the merohedral
     1542twin exercises. You can save this project if desired.</p>
    15411543
    15421544<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    15431545
    1544 </span></span></span></span></span></span></span></span></span></span></span></div>
    1545 
     1546</span></div>
     1547
     1548</span></span></span></span></span></span></span></span></span></span>
    15461549</body>
    15471550

  • Tutorials/MerohedralTwins/Merohedral twin refinement in GSAS_files/filelist.xml

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    22  <o:File HRef="image018.gif"/>
     22 <o:File HRef="image026.gif"/>
    2323 <o:File HRef="filelist.xml"/>
    2424</xml>

  • Tutorials/SAimages/Small Angle Image Processing.htm

    r1741 r2390  
    2424  <o:Author>Von Dreele</o:Author>
    2525  <o:LastAuthor>Von Dreele</o:LastAuthor>
    26   <o:Revision>13</o:Revision>
     26  <o:Revision>14</o:Revision>
    2727  <o:TotalTime>2504</o:TotalTime>
    2828  <o:Created>2014-05-13T20:30:00Z</o:Created>
    29   <o:LastSaved>2015-03-18T20:33:00Z</o:LastSaved>
     29  <o:LastSaved>2016-07-28T18:47:00Z</o:LastSaved>
    3030  <o:Pages>1</o:Pages>
    31   <o:Words>1982</o:Words>
    32   <o:Characters>11299</o:Characters>
     31  <o:Words>1981</o:Words>
     32  <o:Characters>11295</o:Characters>
    3333  <o:Company>Argonne National Laboratory</o:Company>
    3434  <o:Lines>94</o:Lines>
    3535  <o:Paragraphs>26</o:Paragraphs>
    36   <o:CharactersWithSpaces>13255</o:CharactersWithSpaces>
    37   <o:Version>15.00</o:Version>
     36  <o:CharactersWithSpaces>13250</o:CharactersWithSpaces>
     37  <o:Version>16.00</o:Version>
    3838 </o:DocumentProperties>
    3939 <o:OfficeDocumentSettings>
    … …  
    661661        {font-family:"Cambria Math";
    662662        panose-1:2 4 5 3 5 4 6 3 2 4;
    663         mso-font-charset:0;
     663        mso-font-charset:1;
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    667667@font-face
    668668        {font-family:Calibri;
    … …  
    10361036        mso-hansi-font-family:"Courier New";
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     1038p.msonormal0, li.msonormal0, div.msonormal0
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     1043        mso-margin-top-alt:auto;
     1044        margin-right:0in;
     1045        mso-margin-bottom-alt:auto;
     1046        margin-left:0in;
     1047        mso-pagination:widow-orphan;
     1048        font-size:12.0pt;
     1049        font-family:"Times New Roman",serif;
     1050        mso-fareast-font-family:"Times New Roman";
     1051        mso-fareast-theme-font:minor-fareast;}
    10381052span.DocumentMapChar
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    … …  
    11871201mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data/Read
    11881202Image data
    1189 </span></b> and a file selection dialog box will appear. Go to <b
    1190 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1191 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>exercises/<span
    1192 class=SpellE>SAimages</span></span></b> and select <b style='mso-bidi-font-weight:
    1193 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1194 minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>
     1203</span></b> and a file selection dialog box will appear. Go to <span
     1204class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1205"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1206minor-latin'>SAimages</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1207style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1208mso-hansi-theme-font:minor-latin'>/data</span></b> and select <b
     1209style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1210mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>AgBehenate_003.tif</span></b>
    11951211with either a mouse button double click or <b style='mso-bidi-font-weight:normal'><span
    11961212style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    … …  
    13371353 <o:lock v:ext="edit" shapetype="f"/>
    13381354</v:shape><![endif]--><![if !vml]><span style='mso-ignore:vglayout;position:
    1339 absolute;z-index:251659264;margin-left:234px;margin-top:274px;width:73px;
     1355absolute;z-index:251659264;margin-left:234px;margin-top:273px;width:73px;
    13401356height:38px'><img width=73 height=38
    1341 src="Small%20Angle%20Image%20Processing_files/image004.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
     1357src="Small%20Angle%20Image%20Processing_files/image040.png" v:shapes="Straight_x0020_Arrow_x0020_Connector_x0020_21"></span><![endif]><span
    13421358style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
    13431359 o:spid="_x0000_i1059" type="#_x0000_t75" style='width:525pt;height:450pt;
    … …  
    13951411rings. I suggest you change <b style='mso-bidi-font-weight:normal'><span
    13961412style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1397 mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE><span
    1398 class=GramE>Ib</span></span></span></b> to <b style='mso-bidi-font-weight:normal'><span
    1399 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1400 mso-hansi-theme-font:minor-latin'>0.5</span></b> and <b style='mso-bidi-font-weight:
    1401 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1402 minor-latin;mso-hansi-theme-font:minor-latin'>Min <span class=SpellE>calib</span>
    1403 d-spacing</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1404 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1405 mso-hansi-theme-font:minor-latin'>10.0</span></b>. Do <b style='mso-bidi-font-weight:
    1406 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1407 minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Recalibrate</span></b>;
     1413mso-hansi-theme-font:minor-latin'>Min ring I/<span class=SpellE>Ib</span></span></b>
     1414to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1415mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.5</span></b>
     1416and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1417mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Min <span
     1418class=SpellE>calib</span> d-spacing</span></b> to <b style='mso-bidi-font-weight:
     1419normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1420minor-latin;mso-hansi-theme-font:minor-latin'>10.0</span></b>. Do <b
     1421style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1422mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Recalibrate</span></b>;
    14081423more points will be used and they will be limited to the 5 visible rings in the
    14091424pattern.</p>
    … …  
    14751490
    14761491<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1477  id="_x0000_i1054" type="#_x0000_t75" style='width:300pt;height:310.5pt;
    1478  visibility:visible;mso-wrap-style:square'>
     1492 id="Picture_x0020_9" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:300pt;
     1493 height:310.5pt;visibility:visible;mso-wrap-style:square'>
    14791494 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image010.png"
    14801495  o:title=""/>
    14811496</v:shape><![endif]--><![if !vml]><img width=400 height=414
    1482 src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="_x0000_i1054"><![endif]></span></p>
     1497src="Small%20Angle%20Image%20Processing_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
    14831498
    14841499<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    15001515
    15011516<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1502  id="_x0000_i1053" type="#_x0000_t75" style='width:472.5pt;height:388.5pt;
    1503  visibility:visible;mso-wrap-style:square'>
     1517 id="Picture_x0020_10" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:472.5pt;
     1518 height:388.5pt;visibility:visible;mso-wrap-style:square'>
    15041519 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image011.png"
    15051520  o:title=""/>
    15061521</v:shape><![endif]--><![if !vml]><img width=630 height=518
    1507 src="Small%20Angle%20Image%20Processing_files/image011.png" v:shapes="_x0000_i1053"><![endif]></span></p>
     1522src="Small%20Angle%20Image%20Processing_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
    15081523
    15091524<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    15241539
    15251540<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1526  id="_x0000_i1052" type="#_x0000_t75" style='width:472.5pt;height:388.5pt;
    1527  visibility:visible;mso-wrap-style:square'>
     1541 id="Picture_x0020_11" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:472.5pt;
     1542 height:388.5pt;visibility:visible;mso-wrap-style:square'>
    15281543 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image012.png"
    15291544  o:title=""/>
    15301545</v:shape><![endif]--><![if !vml]><img width=630 height=518
    1531 src="Small%20Angle%20Image%20Processing_files/image012.png" v:shapes="_x0000_i1052"><![endif]></span></p>
    1532 
    1533 <p class=MsoNormal><o:p>&nbsp;</o:p></p>
    1534 
    1535 <p class=MsoNormal><span class=GramE>and</span> the image will be that of
    1536 glassy carbon. Changing the <b style='mso-bidi-font-weight:normal'><span
    1537 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1538 mso-hansi-theme-font:minor-latin'>Max intensity</span></b> slider on the <b
    1539 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1540 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Image
    1541 Controls</span></b> window will show that the image from the <span
    1542 class=SpellE>MarCCD</span> is circular and slightly offset from the beam
     1546src="Small%20Angle%20Image%20Processing_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
     1547
     1548<p class=MsoNormal><o:p>&nbsp;</o:p></p>
     1549
     1550<p class=MsoNormal>and the image will be that of glassy carbon. Changing the <b
     1551style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1552mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Max intensity</span></b>
     1553slider on the <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1554"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1555minor-latin'>Image Controls</span></b> window will show that the image from the
     1556<span class=SpellE>MarCCD</span> is circular and slightly offset from the beam
    15431557center. A beam stop shadow is evident as well as an arc-like fault in the image
    15441558(toward the upper left corner of the image). We will sort those out later.</p>
    … …  
    15731587normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    15741588minor-latin;mso-hansi-theme-font:minor-latin'>Show integration limits?</span></b>
    1575 <span class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
    1576 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1577 mso-hansi-theme-font:minor-latin'>Do full integration?</span></b> A pair of
    1578 circles with a connecting diagonal line will appear on the plot. Set the <b
    1579 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1580 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Inner/Outer
    1581 q</span></b> values to <b style='mso-bidi-font-weight:normal'><span
    1582 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1583 mso-hansi-theme-font:minor-latin'>0.05</span></b> and <b style='mso-bidi-font-weight:
    1584 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1585 minor-latin;mso-hansi-theme-font:minor-latin'>0.9</span></b>, respectively, and
    1586 set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1587 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Start
    1588 azimuth</span></b> to <b style='mso-bidi-font-weight:normal'><span
    1589 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1590 mso-hansi-theme-font:minor-latin'>0</span></b>. Set the <b style='mso-bidi-font-weight:
    1591 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1592 minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta bins</span></b> to <b
    1593 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1594 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>250</span></b>,
    1595 which is more appropriate for small angle scattering, and set the <b
    1596 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1597 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bin style:
    1598 Constant step bins in</span></b> to <span class=GramE><b style='mso-bidi-font-weight:
    1599 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1600 minor-latin;mso-hansi-theme-font:minor-latin'>log(</span></b></span><b
    1601 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1602 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>q)</span></b>.
     1589and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1590mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do full
     1591integration?</span></b> A pair of circles with a connecting diagonal line will
     1592appear on the plot. Set the <b style='mso-bidi-font-weight:normal'><span
     1593style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1594mso-hansi-theme-font:minor-latin'>Inner/Outer q</span></b> values to <b
     1595style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1596mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.05</span></b>
     1597and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1598mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.9</span></b>,
     1599respectively, and set the <b style='mso-bidi-font-weight:normal'><span
     1600style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1601mso-hansi-theme-font:minor-latin'>Start azimuth</span></b> to <b
     1602style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1603mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0</span></b>.
     1604Set the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1605mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. 2-theta
     1606bins</span></b> to <b style='mso-bidi-font-weight:normal'><span
     1607style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1608mso-hansi-theme-font:minor-latin'>250</span></b>, which is more appropriate for
     1609small angle scattering, and set the <b style='mso-bidi-font-weight:normal'><span
     1610style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1611mso-hansi-theme-font:minor-latin'>Bin style: Constant step bins in</span></b>
     1612to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1613mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>log(q)</span></b>.
    16031614You should also check the <b style='mso-bidi-font-weight:normal'><span
    16041615style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1605 mso-hansi-theme-font:minor-latin'>Apply sample absorption?</span></b> <span
    1606 class=GramE>and</span> <b style='mso-bidi-font-weight:normal'><span
    1607 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1608 mso-hansi-theme-font:minor-latin'>Apply polarization?</span></b> <span
    1609 class=GramE>boxes</span>; enter the measured <b style='mso-bidi-font-weight:
     1616mso-hansi-theme-font:minor-latin'>Apply sample absorption?</span></b> and <b
     1617style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1618mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Apply
     1619polarization?</span></b> boxes; enter the measured <b style='mso-bidi-font-weight:
    16101620normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16111621minor-latin;mso-hansi-theme-font:minor-latin'>transmission</span></b> (<b
    … …  
    17831793
    17841794<p class=MsoNormal>To add the mask 1: be sure the focus is on the image and the
    1785 zoom buttons are off, 2: type <span class=GramE><b style='mso-bidi-font-weight:
    1786 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1787 minor-latin;mso-hansi-theme-font:minor-latin'>a</span></b> to</span> activate
    1788 the arc mask entry 3: press the left mouse button (<b style='mso-bidi-font-weight:
    1789 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1790 minor-latin;mso-hansi-theme-font:minor-latin'>LB</span></b>) with the cursor
    1791 centered on the bad arc. The <b style='mso-bidi-font-weight:normal'><span
    1792 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1793 mso-hansi-theme-font:minor-latin'>Masks</span></b> window will show a new entry
    1794 </p>
     1795zoom buttons are off, 2: type <b style='mso-bidi-font-weight:normal'><span
     1796style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1797mso-hansi-theme-font:minor-latin'>a</span></b> to activate the arc mask entry
     17983: press the left mouse button (<b style='mso-bidi-font-weight:normal'><span
     1799style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1800mso-hansi-theme-font:minor-latin'>LB</span></b>) with the cursor centered on
     1801the bad arc. The <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1802"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1803minor-latin'>Masks</span></b> window will show a new entry </p>
    17951804
    17961805<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    18051814<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    18061815
    1807 <p class=MsoNormal><span class=GramE>and</span> an arc mask will be drawn on
    1808 the plot.</p>
     1816<p class=MsoNormal>and an arc mask will be drawn on the plot.</p>
    18091817
    18101818<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    18391847
    18401848<p class=MsoNormal>Next let’s deal with the beam stop. I’m going to use both a
    1841 polygon and a spot to cover it. Move the zoom area to be around the center, make
    1842 sure the zoom buttons are off, enter ‘<b style='mso-bidi-font-weight:normal'><span
     1849polygon and a spot to cover it. Move the zoom area to be around the center,
     1850make sure the zoom buttons are off, enter ‘<b style='mso-bidi-font-weight:normal'><span
    18431851style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    18441852mso-hansi-theme-font:minor-latin'>s</span></b>’ on the plot and press mouse <b
    … …  
    19161924closely dragging it with mouse <b style='mso-bidi-font-weight:normal'><span
    19171925style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1918 mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be added
    1919 by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
     1926mso-hansi-theme-font:minor-latin'>LB</span></b> pressed; a new vertex can be
     1927added by dragging an existing vertex with the mouse <b style='mso-bidi-font-weight:
    19201928normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    19211929minor-latin;mso-hansi-theme-font:minor-latin'>RB</span></b> pressed. If you
    … …  
    19271935mask</span></b>; a <b style='mso-bidi-font-weight:normal'><span
    19281936style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1929 mso-hansi-theme-font:minor-latin'>Copy mask information</span></b> dialog box will
    1930 appear. Select the <b style='mso-bidi-font-weight:normal'><span
     1937mso-hansi-theme-font:minor-latin'>Copy mask information</span></b> dialog box
     1938will appear. Select the <b style='mso-bidi-font-weight:normal'><span
    19311939style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19321940mso-hansi-theme-font:minor-latin'>Sa1-4</span></b> items and press <b
    … …  
    19411949
    19421950<p class=MsoNormal>We are now ready to integrate the glassy carbon and the four
    1943 <span class=GramE>Sa</span> images. Select any <b style='mso-bidi-font-weight:
    1944 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1945 minor-latin;mso-hansi-theme-font:minor-latin'>Image Controls</span></b> and
    1946 then do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1951Sa images. Select any <b style='mso-bidi-font-weight:normal'><span
     1952style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1953mso-hansi-theme-font:minor-latin'>Image Controls</span></b> and then do <b
     1954style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19471955mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Integrate
    19481956all</span></b>. A selection dialog will appear; select only the <b
    … …  
    19541962style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    19551963mso-hansi-theme-font:minor-latin'>Ok</span></b>. The image integration will
    1956 proceed; a progress bar shows as each one is done. Five SASD data items will appear
    1957 on the GSAS-II data tree; the last one (<b style='mso-bidi-font-weight:normal'><span
    1958 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1959 mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span class=SpellE>Azm</span>=45.00</span></b>)
    1960 will be expanded and plotted (you may have to select the <b style='mso-bidi-font-weight:
    1961 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1962 minor-latin;mso-hansi-theme-font:minor-latin'>Powder Patterns</span></b> tab to
    1963 see it).</p>
    1964 
    1965 <p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1966  id="_x0000_i1037" type="#_x0000_t75" style='width:525pt;height:450pt;
    1967  visibility:visible;mso-wrap-style:square'>
     1964proceed; a progress bar shows as each one is done. Five SASD data items will
     1965appear on the GSAS-II data tree; the last one (<b style='mso-bidi-font-weight:
     1966normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1967minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa4_40s_061.tif <span
     1968class=SpellE>Azm</span>=45.00</span></b>) will be expanded and plotted (you may
     1969have to select the <b style='mso-bidi-font-weight:normal'><span
     1970style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1971mso-hansi-theme-font:minor-latin'>Powder Patterns</span></b> tab to see it).</p>
     1972
     1973<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1974 id="Picture_x0020_26" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
     1975 height:450pt;visibility:visible;mso-wrap-style:square'>
    19681976 <v:imagedata src="Small%20Angle%20Image%20Processing_files/image027.png"
    19691977  o:title=""/>
    19701978</v:shape><![endif]--><![if !vml]><img width=700 height=600
    1971 src="Small%20Angle%20Image%20Processing_files/image027.png" v:shapes="_x0000_i1037"><![endif]></span></p>
     1979src="Small%20Angle%20Image%20Processing_files/image027.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
    19721980
    19731981<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    19932001the image data; do <b style='mso-bidi-font-weight:normal'><span
    19942002style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1995 mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from <span
    1996 class=GramE>q(</span>A-1) step X-ray QIE data file</span></b> and select <b
    1997 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1998 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>GC
    1999 calibrated data.txt</span></b> from the file selection dialog. You will need to
    2000 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2001 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>any <span
    2002 class=GramE>file(</span>*.*)</span></b> to see it. A <b style='mso-bidi-font-weight:
    2003 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    2004 minor-latin;mso-hansi-theme-font:minor-latin'>Is this the file you want</span></b>
    2005 dialog will appear – respond <b style='mso-bidi-font-weight:normal'><span
    2006 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    2007 mso-hansi-theme-font:minor-latin'>Yes</span></b> to read the file; it will be
    2008 plotted.</p>
     2003mso-hansi-theme-font:minor-latin'>Import/Small Angle Data/ from q(A-1) step
     2004X-ray QIE data file</span></b> and select <b style='mso-bidi-font-weight:normal'><span
     2005style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     2006mso-hansi-theme-font:minor-latin'>GC calibrated data.txt</span></b> from the
     2007file selection dialog. You will need to select <b style='mso-bidi-font-weight:
     2008normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2009minor-latin;mso-hansi-theme-font:minor-latin'>any <span class=GramE>file(</span>*.*)</span></b>
     2010to see it. A <b style='mso-bidi-font-weight:normal'><span style='font-family:
     2011"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     2012minor-latin'>Is this the file you want</span></b> dialog will appear – respond <b
     2013style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2014mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b>
     2015to read the file; it will be plotted.</p>
    20092016
    20102017<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    20882095mso-hansi-theme-font:minor-latin'>GC calibrated data</span></b> and the <b
    20892096style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2090 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
    2091 scale factor</span></b> will be changed to the new scaling factor (<b
     2097mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale
     2098factor</span></b> will be changed to the new scaling factor (<b
    20922099style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    20932100mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0.0008536</span></b>).
    … …  
    21642171
    21652172<p class=MsoNormal>I’ve changed the zoom to show all the data. We are not quite
    2166 done; the scales for the Sa1-Sa4 data sets have to be further reduced by a
    2167 factor of 8 to account for the longer exposure time. Select <b
    2168 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2169 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SASD
    2170 Sa1_40s_067.tif</span></b> from the GSAS-II data tree, expand it and choose <b
    2171 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    2172 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
    2173 Parameters</span></b></p>
     2173done; the scales for the Sa1-Sa4 data sets have to be further reduced by a factor
     2174of 8 to account for the longer exposure time. Select <b style='mso-bidi-font-weight:
     2175normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2176minor-latin;mso-hansi-theme-font:minor-latin'>SASD Sa1_40s_067.tif</span></b>
     2177from the GSAS-II data tree, expand it and choose <b style='mso-bidi-font-weight:
     2178normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     2179minor-latin;mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b></p>
    21742180
    21752181<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    22082214style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    22092215mso-hansi-theme-font:minor-latin'>Command/Copy selected</span></b> as before to
    2210 copy this new scale factor to the other <span class=GramE>Sa</span> data sets.
    2211 The plot will again be redrawn</p>
     2216copy this new scale factor to the other Sa data sets. The plot will again be
     2217redrawn</p>
    22122218
    22132219<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape

  • Tutorials/SAimages/Small Angle Image Processing_files/filelist.xml

    r1741 r2390  
    66 <o:File HRef="image002.png"/>
    77 <o:File HRef="image003.png"/>
    8  <o:File HRef="image004.png"/>
     8 <o:File HRef="image040.png"/>
    99 <o:File HRef="image005.png"/>
    1010 <o:File HRef="image006.png"/>

  • Tutorials/SAseqref/Sequential Refinement of Small Angle Scattering Data.htm

    r1742 r2390  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>18</o:Revision>
     27  <o:Revision>19</o:Revision>
    2828  <o:TotalTime>2550</o:TotalTime>
    2929  <o:Created>2014-05-03T14:24:00Z</o:Created>
    30   <o:LastSaved>2015-03-19T16:41:00Z</o:LastSaved>
     30  <o:LastSaved>2016-07-28T18:48:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    32   <o:Words>1532</o:Words>
    33   <o:Characters>8734</o:Characters>
     32  <o:Words>1531</o:Words>
     33  <o:Characters>8730</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>72</o:Lines>
    3636  <o:Paragraphs>20</o:Paragraphs>
    37   <o:CharactersWithSpaces>10246</o:CharactersWithSpaces>
    38   <o:Version>15.00</o:Version>
     37  <o:CharactersWithSpaces>10241</o:CharactersWithSpaces>
     38  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
    4040 <o:OfficeDocumentSettings>
    … …  
    660660 /* Font Definitions */
    661661 @font-face
    662         {font-family:"Cambria Math";
    663         panose-1:2 4 5 3 5 4 6 3 2 4;
    664         mso-font-charset:0;
    665         mso-generic-font-family:roman;
    666         mso-font-pitch:variable;
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    … …  
    10371030        mso-hansi-font-family:"Courier New";
    10381031        mso-bidi-font-family:"Courier New";}
     1032p.msonormal0, li.msonormal0, div.msonormal0
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     1034        mso-style-noshow:yes;
     1035        mso-style-priority:99;
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     1037        mso-margin-top-alt:auto;
     1038        margin-right:0in;
     1039        mso-margin-bottom-alt:auto;
     1040        margin-left:0in;
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     1043        font-family:"Times New Roman",serif;
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    10391046span.DocumentMapChar
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    … …  
    12281235in intensity; there may be a header with metadata information in the front of
    12291236this file.<span style='mso-spacerun:yes'>  </span>It will read multiple files
    1230 from a single directory. Change the file directory to <b style='mso-bidi-font-weight:
    1231 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1232 minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
    1233 mso-bidi-theme-font:minor-latin'>exercises/<span class=SpellE>SAseqref</span></span></b><span
     1237from a single directory. Change the file directory to <span class=SpellE><b
     1238style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1239mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1240Calibri;mso-bidi-theme-font:minor-latin'>SAseqref</span></b></span><b
     1241style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1242mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
     1243Calibri;mso-bidi-theme-font:minor-latin'>/data</span></b><span
    12341244style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12351245mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    … …  
    13101320
    13111321<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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     1322 id="_x0000_i1055" type="#_x0000_t75" style='width:225pt;height:195pt;
     1323 visibility:visible;mso-wrap-style:square'>
    13141324 <v:imagedata src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image002.png"
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    13161326</v:shape><![endif]--><![if !vml]><img width=300 height=260
    13171327src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image002.png"
    1318 v:shapes="Picture_x0020_26"><![endif]></span><span
     1328v:shapes="_x0000_i1055"><![endif]></span><span
    13191329style='mso-spacerun:yes'> </span></p>
    13201330
    … …  
    14131423
    14141424<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1415  id="Picture_x0020_29" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:435pt;
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     1425 id="_x0000_i1051" type="#_x0000_t75" style='width:435pt;height:270pt;
     1426 visibility:visible;mso-wrap-style:square'>
    14171427 <v:imagedata src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image006.png"
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    14191429</v:shape><![endif]--><![if !vml]><img width=580 height=360
    14201430src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image006.png"
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     1431v:shapes="_x0000_i1051"><![endif]></span><span
    14221432style='mso-spacerun:yes'> </span></p>
    14231433
    … …  
    16041614
    16051615<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1606  id="_x0000_i1044" type="#_x0000_t75" style='width:525pt;height:450pt;
    1607  visibility:visible;mso-wrap-style:square'>
     1616 id="Picture_x0020_13" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
     1617 height:450pt;visibility:visible;mso-wrap-style:square'>
    16081618 <v:imagedata src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image013.png"
    16091619  o:title=""/>
    16101620</v:shape><![endif]--><![if !vml]><img width=700 height=600
    16111621src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image013.png"
    1612 v:shapes="_x0000_i1044"><![endif]></span></p>
     1622v:shapes="Picture_x0020_13"><![endif]></span></p>
    16131623
    16141624<p class=MsoNormal><span style='mso-no-proof:yes'><o:p>&nbsp;</o:p></span></p>
    … …  
    16291639<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16301640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Structure
    1631 factor</span></b> to <span class=GramE><b style='mso-bidi-font-weight:normal'><span
    1632 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1633 mso-hansi-theme-font:minor-latin'>Hard</span></b></span><b style='mso-bidi-font-weight:
    1634 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1635 minor-latin;mso-hansi-theme-font:minor-latin'> sphere</span></b> and set the <b
     1641factor</span></b> to <b style='mso-bidi-font-weight:normal'><span
     1642style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1643mso-hansi-theme-font:minor-latin'>Hard sphere</span></b> and set the <b
    16361644style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    16371645mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SF <span
    … …  
    16421650
    16431651<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1644  id="_x0000_i1043" type="#_x0000_t75" style='width:384.75pt;height:358.5pt;
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     1652 id="Picture_x0020_14" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:384.75pt;
     1653 height:358.5pt;visibility:visible;mso-wrap-style:square'>
    16461654 <v:imagedata src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image014.png"
    16471655  o:title=""/>
    16481656</v:shape><![endif]--><![if !vml]><img width=513 height=478
    16491657src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image014.png"
    1650 v:shapes="_x0000_i1043"><![endif]></span></p>
     1658v:shapes="Picture_x0020_14"><![endif]></span></p>
    16511659
    16521660<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    16991707<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    17001708
    1701 <p class=MsoNormal><span class=GramE>to</span> give a pretty nice initial fit.</p>
     1709<p class=MsoNormal>to give a pretty nice initial fit.</p>
    17021710
    17031711<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    17141722<p class=MsoNormal>We can be brave and set all six <b style='mso-bidi-font-weight:
    17151723normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1716 minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b> <span
    1717 class=GramE>boxes</span> (NB: the one for <b style='mso-bidi-font-weight:normal'><span
    1718 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1719 mso-hansi-theme-font:minor-latin'>Matrix Volume fraction</span></b> currently
    1720 does not operate – ignore it). Then do <b style='mso-bidi-font-weight:normal'><span
    1721 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1722 mso-hansi-theme-font:minor-latin'>Models/Fit</span></b>; the least squares very
    1723 quickly minimizes to give</p>
     1724minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b> boxes (NB: the
     1725one for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1726mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Matrix
     1727Volume fraction</span></b> currently does not operate – ignore it). Then do <b
     1728style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1729mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Models/Fit</span></b>;
     1730the least squares very quickly minimizes to give</p>
    17241731
    17251732<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    17851792<p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span
    17861793style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1787 mso-hansi-theme-font:minor-latin'>Set <span class=GramE>All</span></span></b>,
    1788 all boxes will be checked showing selection of the data sets. Then press <b
    1789 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1790 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>;
    1791 a new dialog box will appear</p>
     1794mso-hansi-theme-font:minor-latin'>Set All</span></b>, all boxes will be checked
     1795showing selection of the data sets. Then press <b style='mso-bidi-font-weight:
     1796normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1797minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>; a new dialog box
     1798will appear</p>
    17921799
    17931800<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    18361843
    18371844<p class=MsoNormal>Note the comment in the plot status bar: double click on the
    1838 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1839 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0<span
    1840 class=GramE>;Volume</span></span></b> and a new plot will appear.</p>
     1845<span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1846style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1847mso-hansi-theme-font:minor-latin'>0;Volume</span></b></span> and a new plot
     1848will appear.</p>
    18411849
    18421850<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    18641872mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>fraction</span></b>
    18651873and the plot will be redrawn (it may require selection of another column &amp;
    1866 then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1867 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0<span
    1868 class=GramE>;Volume</span></span></b> to make it appear).</p>
     1874then <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1875style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1876mso-hansi-theme-font:minor-latin'>0;Volume</span></b></span> to make it
     1877appear).</p>
    18691878
    18701879<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    18801889
    18811890<p class=MsoNormal>It is gratifying how this relation between Volume and the
    1882 composition is linear. You can now determine the slope &amp; intercept (or fit
    1883 to some other function!) directly with GSAS-II; do <b style='mso-bidi-font-weight:
     1891composition is linear. You can now determine the slope &amp; intercept (or fit to
     1892some other function!) directly with GSAS-II; do <b style='mso-bidi-font-weight:
    18841893normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    18851894minor-latin;mso-hansi-theme-font:minor-latin'>Parametric Fit/Add function</span></b>
    … …  
    18891898
    18901899<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1891  id="_x0000_i1031" type="#_x0000_t75" style='width:465pt;height:225pt;
    1892  visibility:visible;mso-wrap-style:square'>
     1900 id="Picture_x0020_26" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:465pt;
     1901 height:225pt;visibility:visible;mso-wrap-style:square'>
    18931902 <v:imagedata src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image026.png"
    18941903  o:title=""/>
    18951904</v:shape><![endif]--><![if !vml]><img width=620 height=300
    18961905src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image026.png"
    1897 v:shapes="_x0000_i1031"><![endif]></span></p>
     1906v:shapes="Picture_x0020_26"><![endif]></span></p>
    18981907
    18991908<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    19051914style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19061915mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sequential
    1907 results</span></b> table. Select <b style='mso-bidi-font-weight:normal'><span
    1908 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1909 mso-hansi-theme-font:minor-latin'>0<span class=GramE>;Volume</span></span></b>
    1910 and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1916results</span></b> table. Select <span class=GramE><b style='mso-bidi-font-weight:
     1917normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1918minor-latin;mso-hansi-theme-font:minor-latin'>0;Volume</span></b></span> and
     1919the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19111920mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Expression
    19121921Editor</span></b> will reappear.</p>
    … …  
    19231932<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    19241933
    1925 <p class=MsoNormal>Next enter the function you wish to use in fitting <b
    1926 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1927 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>0<span
    1928 class=GramE>:Volume</span></span></b>; enter <b style='mso-bidi-font-weight:
     1934<p class=MsoNormal>Next enter the function you wish to use in fitting <span
     1935class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1936"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1937minor-latin'>0:Volume</span></b></span>; enter <b style='mso-bidi-font-weight:
    19291938normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    19301939minor-latin;mso-hansi-theme-font:minor-latin'>m*<span class=SpellE>x+b</span></span></b>
    … …  
    19551964mso-hansi-theme-font:minor-latin'>b</span></b> &amp; <b style='mso-bidi-font-weight:
    19561965normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1957 minor-latin;mso-hansi-theme-font:minor-latin'>m</span></b> select <span
    1958 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
    1959 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
    1960 minor-latin'>Free</span></b></span>; these will be the parameters for your fit.
    1961 For <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1962 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>x</span></b>
    1963 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1966minor-latin;mso-hansi-theme-font:minor-latin'>m</span></b> select <b
     1967style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1968mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Free</span></b>;
     1969these will be the parameters for your fit. For <b style='mso-bidi-font-weight:
     1970normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1971minor-latin;mso-hansi-theme-font:minor-latin'>x</span></b> select <b
     1972style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19641973mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Global</span></b>;
    19651974a new dialog box will appear giving you two choices.</p>
    19661975
    19671976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1968  id="_x0000_i1028" type="#_x0000_t75" style='width:468.75pt;height:187.5pt;
    1969  visibility:visible;mso-wrap-style:square'>
     1977 id="Picture_x0020_29" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468.75pt;
     1978 height:187.5pt;visibility:visible;mso-wrap-style:square'>
    19701979 <v:imagedata src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image029.png"
    19711980  o:title=""/>
    19721981</v:shape><![endif]--><![if !vml]><img width=625 height=250
    19731982src="Sequential%20Refinement%20of%20Small%20Angle%20Scattering%20Data_files/image029.png"
    1974 v:shapes="_x0000_i1028"><![endif]></span></p>
     1983v:shapes="Picture_x0020_29"><![endif]></span></p>
    19751984
    19761985<p class=MsoNormal><o:p>&nbsp;</o:p></p>

  • Tutorials/SAsize/Small Angle Size Distribution.htm

    r1739 r2390  
    2525  <o:Author>Von Dreele</o:Author>
    2626  <o:LastAuthor>Von Dreele</o:LastAuthor>
    27   <o:Revision>13</o:Revision>
    28   <o:TotalTime>1916</o:TotalTime>
     27  <o:Revision>14</o:Revision>
     28  <o:TotalTime>1917</o:TotalTime>
    2929  <o:Created>2014-03-20T16:54:00Z</o:Created>
    30   <o:LastSaved>2015-03-18T17:22:00Z</o:LastSaved>
     30  <o:LastSaved>2016-07-28T18:49:00Z</o:LastSaved>
    3131  <o:Pages>1</o:Pages>
    3232  <o:Words>1272</o:Words>
    33   <o:Characters>7256</o:Characters>
     33  <o:Characters>7251</o:Characters>
    3434  <o:Company>Argonne National Laboratory</o:Company>
    3535  <o:Lines>60</o:Lines>
    3636  <o:Paragraphs>17</o:Paragraphs>
    37   <o:CharactersWithSpaces>8511</o:CharactersWithSpaces>
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     37  <o:CharactersWithSpaces>8506</o:CharactersWithSpaces>
     38  <o:Version>16.00</o:Version>
    3939 </o:DocumentProperties>
    4040 <o:OfficeDocumentSettings>
    … …  
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    … …  
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     1046        mso-margin-bottom-alt:auto;
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     1050        font-family:"Times New Roman",serif;
     1051        mso-fareast-font-family:"Times New Roman";
     1052        mso-fareast-theme-font:minor-fareast;}
    10391053span.DocumentMapChar
    10401054        {mso-style-name:"Document Map Char";
    … …  
    10701084        {mso-style-name:"";
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    1072 span.GramE
    1073         {mso-style-name:"";
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    10751086.MsoChpDefault
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    … …  
    12071218<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'>In
    12081219this tutorial you will determine the size distribution of particles in an
    1209 alumina polishing powder using data from a constant wavelength synchrotron
    1210 X-ray USAXS instrument. You will use both Maximum Entropy (<span class=SpellE>MaxEnt</span>)
     1220alumina polishing powder using data from a constant wavelength synchrotron X-ray
     1221USAXS instrument. You will use both Maximum Entropy (<span class=SpellE>MaxEnt</span>)
    12111222and Total Non-Negative Least Squares (TNNLS) methods assuming spherical
    12121223particles. The data were collected from <span style='mso-fareast-font-family:
    … …  
    12281239the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12291240mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1230 Calibri;mso-bidi-theme-font:minor-latin'>Import/Small Angle Data/from q (A-1) step
    1231 X-ray QIE data file</span></b> menu item to read the data file into GSAS-II.
    1232 This read option is set to read three column small angle scattering data (SASD)
    1233 as Q in Å<sup>-1</sup>, intensity and estimated standard deviation in
    1234 intensity; there may be a header with metadata information in the front of this
    1235 file.<span style='mso-spacerun:yes'>  </span>Change the file directory to <b
     1241Calibri;mso-bidi-theme-font:minor-latin'>Import/Small Angle Data/from q (A-1)
     1242step X-ray QIE data file</span></b> menu item to read the data file into
     1243GSAS-II. This read option is set to read three column small angle scattering
     1244data (SASD) as Q in Å<sup>-1</sup>, intensity and estimated standard deviation
     1245in intensity; there may be a header with metadata information in the front of
     1246this file.<span style='mso-spacerun:yes'>  </span>Change the file directory to <span
     1247class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1248"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1249minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>SAsize</span></b></span><b
    12361250style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    12371251mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1238 Calibri;mso-bidi-theme-font:minor-latin'>exercises/<span class=SpellE>SAsize</span></span></b><span
     1252Calibri;mso-bidi-theme-font:minor-latin'>/data</span></b><span
    12391253style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12401254mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    … …  
    12561270mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    12571271Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
    1258 Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
     1272Dialog box asking <b style='mso-bidi-font-weight:normal'><span
    12591273style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    12601274mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1261 minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
    1262 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1263 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
    1264 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
    1265 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1266 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
    1267 Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
    1268 proceed.</p>
     1275minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
     1276normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1277minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
     1278mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
    12691279
    12701280<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
    … …  
    13301340
    13311341<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    1332  id="_x0000_i1037" type="#_x0000_t75" style='width:225pt;height:195pt;
    1333  visibility:visible;mso-wrap-style:square'>
     1342 id="Picture_x0020_2" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:225pt;
     1343 height:195pt;visibility:visible;mso-wrap-style:square'>
    13341344 <v:imagedata src="Small%20Angle%20Size%20Distribution_files/image002.png"
    13351345  o:title=""/>
    13361346</v:shape><![endif]--><![if !vml]><img width=300 height=260
    1337 src="Small%20Angle%20Size%20Distribution_files/image002.png" v:shapes="_x0000_i1037"><![endif]></span><span
     1347src="Small%20Angle%20Size%20Distribution_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span><span
    13381348style='mso-spacerun:yes'> </span></p>
    13391349
    13401350<h2>Step 3 Select the scattering substances for your sample</h2>
    13411351
    1342 <p class=MsoNormal><span style='mso-no-proof:yes'>Two scsttering substances need
    1343 to be defined for your sample to give the anticipated scattering contrast; in
    1344 this case one is alumina and the other is “vacuum” (really air). Parameters for
    1345 a number of substances are defined in the file </span><b style='mso-bidi-font-weight:
     1352<p class=MsoNormal><span style='mso-no-proof:yes'>Two scsttering substances
     1353need to be defined for your sample to give the anticipated scattering contrast;
     1354in this case one is alumina and the other is “vacuum” (really air). Parameters
     1355for a number of substances are defined in the file </span><b style='mso-bidi-font-weight:
    13461356normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    13471357minor-latin;mso-hansi-theme-font:minor-latin;mso-no-proof:yes'>Substances.py</span></b><span
    … …  
    14271437minor-latin;mso-hansi-theme-font:minor-latin'>vacuum</span></b>). The window
    14281438will show at the bottom the computed contrast between alumina and vacuum
    1429 without and with consideration of resonant scattering effects; the latter is
    1430 used in subsequent calculations.</p>
     1439without and with consideration of resonant scattering effects; the latter is used
     1440in subsequent calculations.</p>
    14311441
    14321442<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    14741484
    14751485<p class=MsoNormal>Many selections are made by default for this analysis;
    1476 however it is important that an appropriate value is selected for the
    1477 background. From the high Q end of the data plot</p>
     1486however it is important that an appropriate value is selected for the background.
     1487From the high Q end of the data plot</p>
    14781488
    14791489<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    14921502style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    14931503mso-hansi-theme-font:minor-latin'>0.12</span></b>; enter that into the
    1494 appropriate place in the data window. The plot will be redrawn showing a horizontal
    1495 red line for the background. All the other parameters seem reasonable for a 1<sup>st</sup>
    1496 attempt at a <span class=SpellE>MaxEnt</span> solution. Do <b style='mso-bidi-font-weight:
    1497 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1498 minor-latin;mso-hansi-theme-font:minor-latin'>Models/Fit</span></b>; the
    1499 console window will show that the calculation did not converge and the <b
    1500 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1501 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Size
    1502 Distribution</span></b> plot has a “choppy” appearance.</p>
     1504appropriate place in the data window. The plot will be redrawn showing a
     1505horizontal red line for the background. All the other parameters seem
     1506reasonable for a 1<sup>st</sup> attempt at a <span class=SpellE>MaxEnt</span>
     1507solution. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
     1508"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1509minor-latin'>Models/Fit</span></b>; the console window will show that the
     1510calculation did not converge and the <b style='mso-bidi-font-weight:normal'><span
     1511style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1512mso-hansi-theme-font:minor-latin'>Size Distribution</span></b> plot has a
     1513“choppy” appearance.</p>
    15031514
    15041515<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    16191630style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    16201631mso-hansi-theme-font:minor-latin'>2.0</span></b>; the IPG fit con<span
    1621 style='mso-no-proof:yes'>verges in &lt;20 cycles and gives a smoother size
    1622 distribution.<o:p></o:p></span></p>
     1632style='mso-no-proof:yes'>verges in &lt;20 cycles and gives a smoother size distribution.<o:p></o:p></span></p>
    16231633
    16241634<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    16531663normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    16541664minor-latin;mso-hansi-theme-font:minor-latin'>0-4</span></b>, that changes the
    1655 data weighting to <span class=SpellE><span class=GramE>Q<sup>p</sup></span></span>.
    1656 This can change the convergence of the IPG method and yield improved results if
    1657 one is unsuccessful with the default settings. I got a nice fit with a <b
    1658 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1659 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Q power
    1660 weight</span></b> of <b style='mso-bidi-font-weight:normal'><span
     1665data weighting to <span class=SpellE>Q<sup>p</sup></span>. This can change the
     1666convergence of the IPG method and yield improved results if one is unsuccessful
     1667with the default settings. I got a nice fit with a <b style='mso-bidi-font-weight:
     1668normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1669minor-latin;mso-hansi-theme-font:minor-latin'>Q power weight</span></b> of <b
     1670style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1671mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3</span></b>
     1672and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1673mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Error
     1674multiplier</span></b> of <b style='mso-bidi-font-weight:normal'><span
    16611675style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1662 mso-hansi-theme-font:minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:
    1663 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1664 minor-latin;mso-hansi-theme-font:minor-latin'>Error multiplier</span></b> of <b
    1665 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1666 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>2.0</span></b>.</p>
    1667 
    1668 <p class=MsoNormal>You should save this GSAS-II project as it will be used in the
    1669 tutorial for fitting small angle scattering data; I used <span class=SpellE><b
    1670 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    1671 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>alumina.gpx</span></b></span>.</p>
     1676mso-hansi-theme-font:minor-latin'>2.0</span></b>.</p>
     1677
     1678<p class=MsoNormal>You should save this GSAS-II project as it will be used in
     1679the tutorial for fitting small angle scattering data; I used <span
     1680class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
     1681"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
     1682minor-latin'>alumina.gpx</span></b></span>.</p>
    16721683
    16731684</div>

  • Tutorials/SeqRefine/SequentialTutorial.htm

    r2363 r2390  
    2323  <o:Author>B Toby</o:Author>
    2424  <o:LastAuthor>Von Dreele</o:LastAuthor>
    25   <o:Revision>2</o:Revision>
    26   <o:TotalTime>396</o:TotalTime>
     25  <o:Revision>3</o:Revision>
     26  <o:TotalTime>397</o:TotalTime>
    2727  <o:Created>2015-03-21T14:51:00Z</o:Created>
    28   <o:LastSaved>2015-03-21T14:51:00Z</o:LastSaved>
     28  <o:LastSaved>2016-07-28T18:50:00Z</o:LastSaved>
    2929  <o:Pages>1</o:Pages>
    30   <o:Words>3769</o:Words>
    31   <o:Characters>21484</o:Characters>
     30  <o:Words>3768</o:Words>
     31  <o:Characters>21480</o:Characters>
    3232  <o:Company>Argonne National Laboratory</o:Company>
    3333  <o:Lines>179</o:Lines>
    3434  <o:Paragraphs>50</o:Paragraphs>
    35   <o:CharactersWithSpaces>25203</o:CharactersWithSpaces>
    36   <o:Version>15.00</o:Version>
     35  <o:CharactersWithSpaces>25198</o:CharactersWithSpaces>
     36  <o:Version>16.00</o:Version>
    3737 </o:DocumentProperties>
    3838 <o:OfficeDocumentSettings>
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    14581471 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    14591472</v:shape><![endif]--><![if !vml]><img width=271 height=93
    1460 src="SequentialTutorial_files/image002.jpg" align=right hspace=12 v:shapes="Picture_x0020_1"><![endif]>Use
     1473src="SequentialTutorial_files/image008.jpg" align=right hspace=12 v:shapes="Picture_x0020_1"><![endif]>Use
    14611474the <b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    14621475mso-hansi-theme-font:major-latin'>Import/Phase/from CIF file menu item</span></b>
    … …  
    14791492bold'>file</span> (change the file directory to <b style='mso-bidi-font-weight:
    14801493normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    1481 major-latin;mso-hansi-theme-font:major-latin'>exercises/SeqRefine</span></b>).
     1494major-latin;mso-hansi-theme-font:major-latin'>SeqRefine/data</span></b>).
    14821495Another dialog window will be created showing all the files in the zip archive.
    14831496To simplify the view to only show the phase files, type “<b style='mso-bidi-font-weight:
    … …  
    15311544 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    15321545</v:shape><![endif]--><![if !vml]><img width=284 height=119
    1533 src="SequentialTutorial_files/image004.jpg" align=right hspace=12 v:shapes="Picture_x0020_21"><![endif]><span
     1546src="SequentialTutorial_files/image032.jpg" align=right hspace=12 v:shapes="Picture_x0020_21"><![endif]><span
    15341547style='mso-spacerun:yes'> </span>Read in the ~7 K dataset (<b style='mso-bidi-font-weight:
    15351548normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
    … …  
    15691582  <tr>
    15701583   <td></td>
    1571    <td><img width=216 height=210 src="SequentialTutorial_files/image006.png"
     1584   <td><img width=216 height=210 src="SequentialTutorial_files/image042.png"
    15721585   v:shapes="Picture_x0020_3"></td>
    15731586  </tr>
    … …  
    15861599 <v:imagedata src="SequentialTutorial_files/image007.png" o:title=""/>
    15871600</v:shape><![endif]--><![if !vml]><img width=317 height=167
    1588 src="SequentialTutorial_files/image008.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
     1601src="SequentialTutorial_files/image051.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
    15891602
    15901603<p class=MsoListParagraphCxSpMiddle>Note that the instrument parameter file
    … …  
    16101623 <v:imagedata src="SequentialTutorial_files/image009.png" o:title=""/>
    16111624</v:shape><![endif]--><![if !vml]><img width=235 height=195
    1612 src="SequentialTutorial_files/image010.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
     1625src="SequentialTutorial_files/image055.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
    16131626
    16141627<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    16291642 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    16301643</v:shape><![endif]--><![if !vml]><img width=334 height=170
    1631 src="SequentialTutorial_files/image012.png" align=right hspace=12 v:shapes="Picture_x0020_4"><![endif]>We
     1644src="SequentialTutorial_files/image057.png" align=right hspace=12 v:shapes="Picture_x0020_4"><![endif]>We
    16321645want to fit the lattice parameters, background, and a phase fraction
    16331646initially.<span style='mso-spacerun:yes'>  </span>To illustrate how constraints
    … …  
    16531666 <v:imagedata src="SequentialTutorial_files/image013.png" o:title=""/>
    16541667</v:shape><![endif]--><![if !vml]><img width=104 height=72
    1655 src="SequentialTutorial_files/image014.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
     1668src="SequentialTutorial_files/image099.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
    16561669style='mso-spacerun:yes'> </span></p>
    16571670
    … …  
    16751688 <v:imagedata src="SequentialTutorial_files/image015.png" o:title=""/>
    16761689</v:shape><![endif]--><![if !vml]><img width=437 height=172
    1677 src="SequentialTutorial_files/image016.png" v:shapes="Picture_x0020_8"><![endif]></span><span
     1690src="SequentialTutorial_files/image101.png" v:shapes="Picture_x0020_8"><![endif]></span><span
    16781691style='mso-spacerun:yes'> </span></p>
    16791692
    … …  
    16951708 <v:imagedata src="SequentialTutorial_files/image017.png" o:title=""/>
    16961709</v:shape><![endif]--><![if !vml]><img width=451 height=173
    1697 src="SequentialTutorial_files/image018.png" v:shapes="Picture_x0020_10"><![endif]></span><span
     1710src="SequentialTutorial_files/image106.png" v:shapes="Picture_x0020_10"><![endif]></span><span
    16981711style='font-family:"Cambria",serif'><o:p></o:p></span></p>
    16991712
    … …  
    17101723 <v:imagedata src="SequentialTutorial_files/image019.png" o:title=""/>
    17111724</v:shape><![endif]--><![if !vml]><img width=339 height=172
    1712 src="SequentialTutorial_files/image020.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
     1725src="SequentialTutorial_files/image107.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
    17131726
    17141727<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    17331746the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    17341747mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Phase</span></b>
    1735 entry to “open” the tree item). We also want to refine the phase fraction for this
    1736 phase, so <span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span
     1748entry to “open” the tree item). We also want to refine the phase fraction for
     1749this phase, so <span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span
    17371750style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    17381751mso-hansi-theme-font:major-latin'>Data</span> </b><span style='mso-bidi-font-weight:
    … …  
    17511764 <v:imagedata src="SequentialTutorial_files/image021.png" o:title=""/>
    17521765</v:shape><![endif]--><![if !vml]><img width=347 height=132
    1753 src="SequentialTutorial_files/image022.jpg" v:shapes="Picture_x0020_7"><![endif]></span></p>
     1766src="SequentialTutorial_files/image108.jpg" v:shapes="Picture_x0020_7"><![endif]></span></p>
    17541767
    17551768<p class=MsoListParagraphCxSpMiddle>Repeat this with the second phase (<b
    … …  
    17931806 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    17941807</v:shape><![endif]--><![if !vml]><img width=346 height=123
    1795 src="SequentialTutorial_files/image024.png" align=right hspace=12 v:shapes="Picture_x0020_14"><![endif]>Also
     1808src="SequentialTutorial_files/image109.png" align=right hspace=12 v:shapes="Picture_x0020_14"><![endif]>Also
    17961809<span style='mso-bidi-font-weight:bold'>select<b> </b>the<b> </b></span><b><span
    17971810style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    … …  
    18421855style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    18431856mso-hansi-theme-font:major-latin'>4.5</span>.</b> <b style='mso-bidi-font-weight:
    1844 normal'><i style='mso-bidi-font-style:normal'><u>Important</u></i></b>: you will
    1845 have to select the data box (it will turn blue) and then enter the number (<b
    1846 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1857normal'><i style='mso-bidi-font-style:normal'><u>Important</u></i></b>: you
     1858will have to select the data box (it will turn blue) and then enter the number
     1859(<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    18471860mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>4.5</span></b>)
    18481861and then click on some other box in the window so that the change registers. </p>
    … …  
    18651878 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    18661879</v:shape><![endif]--><![if !vml]><img width=205 height=315
    1867 src="SequentialTutorial_files/image026.png" align=right hspace=12 v:shapes="Picture_x0020_15"><![endif]>Optional:
     1880src="SequentialTutorial_files/image110.png" align=right hspace=12 v:shapes="Picture_x0020_15"><![endif]>Optional:
    18681881confirm that the initial parameters have been selected correctly for refinement
    18691882using <span style='mso-bidi-font-weight:bold'>the<b> </b></span><b><span
    … …  
    19291942 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    19301943</v:shape><![endif]--><![if !vml]><img width=375 height=174
    1931 src="SequentialTutorial_files/image028.png" align=right hspace=12 v:shapes="Picture_x0020_13"><![endif]><span
     1944src="SequentialTutorial_files/image111.png" align=right hspace=12 v:shapes="Picture_x0020_13"><![endif]><span
    19321945style='mso-fareast-language:EN-US;mso-no-proof:yes'>Selecting</span><b> </b><span
    19331946style='mso-bidi-font-weight:bold'>the<b> </b></span><b><span style='font-family:
    … …  
    19351948major-latin'>PWDR OH_00.fxye Bank 1</span> </b><span style='mso-bidi-font-weight:
    19361949bold'>entry</span> shows the “Rietveld plot” and zooming in on different
    1937 regions of the pattern provides insight on how the fit could be improved. You
    1938 can alter the view to show the square root of the intensity (use the ‘<b
     1950regions of the pattern provides insight on how the fit could be improved. You can
     1951alter the view to show the square root of the intensity (use the ‘<b
    19391952style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    19401953mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>S</span></b>’
    … …  
    19892002 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    19902003</v:shape><![endif]--><![if !vml]><img width=350 height=338
    1991 src="SequentialTutorial_files/image030.png" align=right hspace=12 v:shapes="Picture_x0020_16"><![endif]>While
     2004src="SequentialTutorial_files/image112.png" align=right hspace=12 v:shapes="Picture_x0020_16"><![endif]>While
    19922005in other projects I might postpone this until later, we can also start on
    19932006improving the peak fit. We will do this by varying the sample broadening for
    … …  
    20752088 <v:imagedata src="SequentialTutorial_files/image031.png" o:title=""/>
    20762089</v:shape><![endif]--><![if !vml]><img width=453 height=340
    2077 src="SequentialTutorial_files/image032.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
     2090src="SequentialTutorial_files/image113.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
    20782091
    20792092<h1>Step 2: Prepare for sequential fit. </h1>
    … …  
    21272140 <v:imagedata src="SequentialTutorial_files/image033.png" o:title=""/>
    21282141</v:shape><![endif]--><![if !vml]><img width=539 height=115
    2129 src="SequentialTutorial_files/image034.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
     2142src="SequentialTutorial_files/image114.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
    21302143
    21312144<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    21572170 <v:imagedata src="SequentialTutorial_files/image035.png" o:title=""/>
    21582171</v:shape><![endif]--><![if !vml]><img width=353 height=339
    2159 src="SequentialTutorial_files/image036.png" v:shapes="Picture_x0020_72"><![endif]></span></p>
     2172src="SequentialTutorial_files/image115.png" v:shapes="Picture_x0020_72"><![endif]></span></p>
    21602173
    21612174<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    22042217  cropbottom="5827f" cropleft="4311f" cropright="4217f"/>
    22052218</v:shape><![endif]--><![if !vml]><img width=352 height=337
    2206 src="SequentialTutorial_files/image038.png" v:shapes="Picture_x0020_71"><![endif]></span></p>
     2219src="SequentialTutorial_files/image116.png" v:shapes="Picture_x0020_71"><![endif]></span></p>
    22072220
    22082221<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    22342247 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    22352248</v:shape><![endif]--><![if !vml]><img width=237 height=312
    2236 src="SequentialTutorial_files/image040.png" align=right hspace=12 v:shapes="Picture_x0020_33"><![endif]><span
     2249src="SequentialTutorial_files/image117.png" align=right hspace=12 v:shapes="Picture_x0020_33"><![endif]><span
    22372250style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    22382251 id="Picture_x0020_13" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:290.25pt;
    … …  
    22412254  cropbottom="9111f" cropleft="3592f" cropright="4103f"/>
    22422255</v:shape><![endif]--><![if !vml]><img width=387 height=179
    2243 src="SequentialTutorial_files/image042.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
     2256src="SequentialTutorial_files/image118.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
    22442257
    22452258<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    22932306 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    22942307</v:shape><![endif]--><![if !vml]><img width=214 height=209
    2295 src="SequentialTutorial_files/image044.png" align=right hspace=12 v:shapes="Picture_x0020_17"><![endif]>The
     2308src="SequentialTutorial_files/image119.png" align=right hspace=12 v:shapes="Picture_x0020_17"><![endif]>The
    22962309remaining datasets are read <span style='mso-bidi-font-weight:bold'>using<b> </b></span><b><span
    22972310style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    … …  
    23262339  cropbottom="7136f" cropleft="3738f" cropright="3737f"/>
    23272340</v:shape><![endif]--><![if !vml]><img width=398 height=271
    2328 src="SequentialTutorial_files/image046.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
     2341src="SequentialTutorial_files/image120.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
    23292342
    23302343<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    23562369 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    23572370</v:shape><![endif]--><![if !vml]><img width=209 height=112
    2358 src="SequentialTutorial_files/image048.png" align=right hspace=12 v:shapes="Picture_x0020_18"><![endif]>Optional:
     2371src="SequentialTutorial_files/image121.png" align=right hspace=12 v:shapes="Picture_x0020_18"><![endif]>Optional:
    23592372Note that the default graphics mode is to display the last dataset read
    23602373in.<span style='mso-spacerun:yes'>  </span>If you want to see the entire
    2361 ensemble of data sets, click on the main entry for any of the datasets (for
    2362 example <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     2374ensemble of data sets, click on the main entry for any of the datasets (for example
     2375<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    23632376mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>PWDR
    23642377OH_00.fxye Bank 1</span></b>), click on the frame of the plot window and press
    … …  
    24312444 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    24322445</v:shape><![endif]--><![if !vml]><img width=93 height=44
    2433 src="SequentialTutorial_files/image051.jpg" align=right hspace=12 v:shapes="Picture_x0020_19"><![endif]>Copy
     2446src="SequentialTutorial_files/image122.jpg" align=right hspace=12 v:shapes="Picture_x0020_19"><![endif]>Copy
    24342447the histogram parameters from the first histogram to the new ones: <span
    24352448style='mso-bidi-font-weight:bold'>Select the original </span><b><span
    … …  
    24552468 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    24562469</v:shape><![endif]--><![if !vml]><img width=217 height=212
    2457 src="SequentialTutorial_files/image053.png" align=right hspace=12 v:shapes="Picture_x0020_20"><![endif]>This
     2470src="SequentialTutorial_files/image123.png" align=right hspace=12 v:shapes="Picture_x0020_20"><![endif]>This
    24582471causes a dialog box where the sections to be copied are selected. We need to
    24592472duplicate the <b style='mso-bidi-font-weight:normal'><span style='font-family:
    … …  
    24962509  cropbottom="8776f" cropleft="6460f" cropright="6263f"/>
    24972510</v:shape><![endif]--><![if !vml]><img width=215 height=212
    2498 src="SequentialTutorial_files/image055.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
     2511src="SequentialTutorial_files/image124.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
    24992512
    25002513<p class=MsoListParagraphCxSpLast>That the copy has been performed can be
    … …  
    25262539 <v:imagedata src="SequentialTutorial_files/image056.png" o:title=""/>
    25272540</v:shape><![endif]--><![if !vml]><img width=363 height=416
    2528 src="SequentialTutorial_files/image057.png" v:shapes="Picture_x0020_16"><![endif]></span><span
     2541src="SequentialTutorial_files/image125.png" v:shapes="Picture_x0020_16"><![endif]></span><span
    25292542style='mso-spacerun:yes'> </span></p>
    25302543
    … …  
    25512564  cropbottom="9070f" cropleft="5898f" cropright="3179f"/>
    25522565</v:shape><![endif]--><![if !vml]><img width=229 height=211
    2553 src="SequentialTutorial_files/image059.png" v:shapes="Picture_x0020_23"><![endif]><!--[if gte vml 1]><v:shape
     2566src="SequentialTutorial_files/image126.png" v:shapes="Picture_x0020_23"><![endif]><!--[if gte vml 1]><v:shape
    25542567 id="Picture_x0020_22" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:156.75pt;
    25552568 height:156.75pt;visibility:visible;mso-wrap-style:square'>
    … …  
    25572570  cropbottom="9050f" cropleft="6461f" cropright="7653f"/>
    25582571</v:shape><![endif]--><![if !vml]><img width=209 height=209
    2559 src="SequentialTutorial_files/image061.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
     2572src="SequentialTutorial_files/image127.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
    25602573
    25612574<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    26092622 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    26102623</v:shape><![endif]--><![if !vml]><img width=217 height=209
    2611 src="SequentialTutorial_files/image063.png" align=right hspace=12 v:shapes="Picture_x0020_24"><![endif]>First,
     2624src="SequentialTutorial_files/image128.png" align=right hspace=12 v:shapes="Picture_x0020_24"><![endif]>First,
    26122625<span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span
    26132626style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    … …  
    26242637 <v:imagedata src="SequentialTutorial_files/image064.png" o:title=""/>
    26252638</v:shape><![endif]--><![if !vml]><img width=356 height=113
    2626 src="SequentialTutorial_files/image065.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
    2627 
    2628 <p class=MsoListParagraphCxSpMiddle>This opens a window where all histograms
    2629 can be selected (it would be equally valid to skip the first histogram, since that
     2639src="SequentialTutorial_files/image129.png" v:shapes="Picture_x0020_25"><![endif]></span></p>
     2640
     2641<p class=MsoListParagraphCxSpMiddle>This opens a window where all histograms can
     2642be selected (it would be equally valid to skip the first histogram, since that
    26302643has already been fully fit). <span style='mso-bidi-font-weight:bold'>Press<b> </b></span><b><span
    26312644style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    … …  
    26542667 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    26552668</v:shape><![endif]--><![if !vml]><img width=360 height=128
    2656 src="SequentialTutorial_files/image067.png" align=right hspace=12 v:shapes="Picture_x0020_34"><![endif]><span
     2669src="SequentialTutorial_files/image130.png" align=right hspace=12 v:shapes="Picture_x0020_34"><![endif]><span
    26572670style='mso-bidi-font-weight:bold'>Check the<b> </b></span><b><span
    26582671style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    … …  
    27022715 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    27032716</v:shape><![endif]--><![if !vml]><img width=106 height=69
    2704 src="SequentialTutorial_files/image069.jpg" align=right hspace=12 v:shapes="Picture_x0020_28"><![endif]>Start
     2717src="SequentialTutorial_files/image131.jpg" align=right hspace=12 v:shapes="Picture_x0020_28"><![endif]>Start
    27052718the sequential refinement with <b><span style='font-family:"Calibri",sans-serif;
    27062719mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Calculate/Sequential
    … …  
    27962809  <tr>
    27972810   <td></td>
    2798    <td><img width=572 height=109 src="SequentialTutorial_files/image070.png"
     2811   <td><img width=572 height=108 src="SequentialTutorial_files/image132.png"
    27992812   alt="Text Box: **** ERROR - variable list for this histogram does not match previous&#13;&#10;&#13;&#10;current histogram PWDR OH_04.fxye Bank 1 has 6 variables&#13;&#10;Variables in previous but not in current: 1::D22, 1::D33, 1::D11, &#13;&#10;&#13;&#10;Previous refinement has 7 variables&#13;&#10;Variables in current but not in previous: 1::Scale, 1::Mustrain;i, &#13;&#10;&#13;&#10;"
    28002813   v:shapes="Text_x0020_Box_x0020_3"></td>
    … …  
    28402853  <tr>
    28412854   <td></td>
    2842    <td><img width=321 height=103 src="SequentialTutorial_files/image072.png"
     2855   <td><img width=321 height=103 src="SequentialTutorial_files/image133.png"
    28432856   v:shapes="Picture_x0020_29"></td>
    28442857  </tr>
    … …  
    28642877 <v:imagedata src="SequentialTutorial_files/image073.png" o:title=""/>
    28652878</v:shape><![endif]--><![if !vml]><img width=700 height=350
    2866 src="SequentialTutorial_files/image074.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
    2867 
    2868 <p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    2869 
    2870 <p class=MsoListParagraphCxSpMiddle>The second column shows the weighted
    2871 profile R-factor, from each fit. This shows a steady increase with temperature,
    2872 as might be expected if there were a systematic change in some sample
    2873 parameters, such as strain or background or even atomic coordinates (which have
    2874 not yet been fit). The &#916;&#967;<sup>2</sup> value in the third column shows
    2875 the percent improvement in &#967;<sup>2</sup> seen in the last cycle of refinement.
     2879src="SequentialTutorial_files/image134.png" v:shapes="Picture_x0020_54"><![endif]></span></p>
     2880
     2881<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
     2882
     2883<p class=MsoListParagraphCxSpMiddle>The second column shows the weighted profile
     2884R-factor, from each fit. This shows a steady increase with temperature, as
     2885might be expected if there were a systematic change in some sample parameters,
     2886such as strain or background or even atomic coordinates (which have not yet
     2887been fit). The &#916;&#967;<sup>2</sup> value in the third column shows the
     2888percent improvement in &#967;<sup>2</sup> seen in the last cycle of refinement.
    28762889(If this changes from 4.1 to 4.0, then the value will be 100*(4.1-4.0)/4.0, or
    287728902.5). Since the convergence criterion in the controls is 0.0001 (or 0.01%) we
    … …  
    29072920 <v:imagedata src="SequentialTutorial_files/image075.png" o:title=""/>
    29082921</v:shape><![endif]--><![if !vml]><img width=466 height=400
    2909 src="SequentialTutorial_files/image076.jpg" v:shapes="Picture_x0020_42"><![endif]></span></p>
     2922src="SequentialTutorial_files/image135.jpg" v:shapes="Picture_x0020_42"><![endif]></span></p>
    29102923
    29112924<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    29252938 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    29262939</v:shape><![endif]--><![if !vml]><img width=213 height=207
    2927 src="SequentialTutorial_files/image078.png" align=right hspace=12 v:shapes="Picture_x0020_43"><![endif]>Pressing
     2940src="SequentialTutorial_files/image136.png" align=right hspace=12 v:shapes="Picture_x0020_43"><![endif]>Pressing
    29282941the “<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    29292942mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>K</span></b>”
    … …  
    29312944style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    29322945mso-hansi-theme-font:major-latin'>s</span></b><span style='mso-bidi-font-weight:
    2933 bold'>” key</span> brings up a menu where the x-axis can be selected as temperature.
    2934 If the plot fails to update, click on another column and then return to the
    2935 original column. </p>
     2946bold'>” key</span> brings up a menu where the x-axis can be selected as
     2947temperature. If the plot fails to update, click on another column and then
     2948return to the original column. </p>
    29362949
    29372950<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    29432956 <v:imagedata src="SequentialTutorial_files/image079.png" o:title=""/>
    29442957</v:shape><![endif]--><![if !vml]><img width=389 height=296
    2945 src="SequentialTutorial_files/image080.jpg" v:shapes="Picture_x0020_45"><![endif]></span></p>
     2958src="SequentialTutorial_files/image137.jpg" v:shapes="Picture_x0020_45"><![endif]></span></p>
    29462959
    29472960<p class=MsoListParagraphCxSpLast><o:p>&nbsp;</o:p></p>
    … …  
    29812994  cropbottom="9604f" cropleft="4103f" cropright="3837f"/>
    29822995</v:shape><![endif]--><![if !vml]><img width=384 height=176
    2983 src="SequentialTutorial_files/image082.png" v:shapes="Picture_x0020_47"><![endif]><o:p></o:p></span></p>
     2996src="SequentialTutorial_files/image138.png" v:shapes="Picture_x0020_47"><![endif]><o:p></o:p></span></p>
    29842997
    29852998<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    29983011 <w:wrap type="square" anchorx="margin" anchory="margin"/>
    29993012</v:shape><![endif]--><![if !vml]><img width=75 height=47
    3000 src="SequentialTutorial_files/image084.jpg" align=left hspace=12 v:shapes="Picture_x0020_48"><![endif]><span
     3013src="SequentialTutorial_files/image139.jpg" align=left hspace=12 v:shapes="Picture_x0020_48"><![endif]><span
    30013014style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    30023015 id="Picture_x0020_49" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:158.25pt;
    … …  
    30043017 <v:imagedata src="SequentialTutorial_files/image085.png" o:title=""/>
    30053018</v:shape><![endif]--><![if !vml]><img width=211 height=203
    3006 src="SequentialTutorial_files/image086.jpg" v:shapes="Picture_x0020_49"><![endif]></span></p>
     3019src="SequentialTutorial_files/image140.jpg" v:shapes="Picture_x0020_49"><![endif]></span></p>
    30073020
    30083021<p class=MsoNormal><o:p>&nbsp;</o:p></p>
    … …  
    30273040  croptop="2496f" cropbottom="6549f" cropleft="5811f" cropright="6065f"/>
    30283041</v:shape><![endif]--><![if !vml]><img width=237 height=311
    3029 src="SequentialTutorial_files/image088.png"
     3042src="SequentialTutorial_files/image141.png"
    30303043alt="Description: BHT3 HD:private:tmp:s1.png" v:shapes="Picture_x0020_84"><![endif]></span></p>
    30313044
    … …  
    30403053style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
    30413054mso-hansi-theme-font:major-latin'>Copy flags?</span> </b><span
    3042 style='mso-bidi-font-weight:bold'>button</span>. (Important: not the Copy
    3043 button!) For the <span style='mso-bidi-font-weight:bold'>CuO phase, add the
    3044 single sample broadening term and the remaining lattice parameter</span> via
    3045 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     3055style='mso-bidi-font-weight:bold'>button</span>. (Important: not the Copy button!)
     3056For the <span style='mso-bidi-font-weight:bold'>CuO phase, add the single
     3057sample broadening term and the remaining lattice parameter</span> via the <b
     3058style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    30463059mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>D13</span></b>
    30473060term.<span style='mso-spacerun:yes'>  </span>Again, <span style='mso-bidi-font-weight:
    … …  
    30603073 <v:imagedata src="SequentialTutorial_files/image089.png" o:title=""/>
    30613074</v:shape><![endif]--><![if !vml]><img width=332 height=241
    3062 src="SequentialTutorial_files/image090.jpg" v:shapes="Picture_x0020_52"><![endif]></span></p>
     3075src="SequentialTutorial_files/image142.jpg" v:shapes="Picture_x0020_52"><![endif]></span></p>
    30633076
    30643077<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    30703083 <v:imagedata src="SequentialTutorial_files/image091.png" o:title=""/>
    30713084</v:shape><![endif]--><![if !vml]><img width=332 height=249
    3072 src="SequentialTutorial_files/image092.jpg" v:shapes="Picture_x0020_53"><![endif]></span></p>
     3085src="SequentialTutorial_files/image143.jpg" v:shapes="Picture_x0020_53"><![endif]></span></p>
    30733086
    30743087<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    31763189  <tr>
    31773190   <td></td>
    3178    <td><img width=572 height=108 src="SequentialTutorial_files/image093.png"
     3191   <td><img width=572 height=109 src="SequentialTutorial_files/image144.png"
    31793192   alt="Text Box: **** ERROR - variable list for this histogram does not match previous&#13;&#10;&#13;&#10;current histogram PWDR OH_04.fxye Bank 1 has 24 variables&#13;&#10;Variables in previous but not in current: ::constr0, &#13;&#10;&#13;&#10;Previous refinement has 23 variables&#13;&#10;Variables in current but not in previous: 1::Scale, 0::Scale, &#13;&#10;&#13;&#10;"
    31803193   v:shapes="Text_x0020_Box_x0020_87"></td>
    … …  
    31923205mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>1:0:Scale</span></b>)
    31933206pertains only to the first histogram. Note that a constraint is ignored if none
    3194 of the variables in it are included in the refinement, so this constraint only affects
    3195 the first histogram, giving rise to the error above. We could set up a
     3207of the variables in it are included in the refinement, so this constraint only
     3208affects the first histogram, giving rise to the error above. We could set up a
    31963209constraint for each histogram that has been added, but this would be rather
    31973210tedious to set up. The alternate is to set up a constraint where a wildcard (<span
    … …  
    32243237  cropbottom="8174f" cropleft="3258f" cropright="2910f"/>
    32253238</v:shape><![endif]--><![if !vml]><img width=479 height=207
    3226 src="SequentialTutorial_files/image095.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
     3239src="SequentialTutorial_files/image145.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
    32273240
    32283241<p class=MsoListParagraphCxSpMiddle>There will only be one possible matching
    … …  
    32383251  cropbottom="11943f" cropleft="3390f" cropright="3551f"/>
    32393252</v:shape><![endif]--><![if !vml]><img width=415 height=139
    3240 src="SequentialTutorial_files/image097.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
     3253src="SequentialTutorial_files/image146.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
    32413254
    32423255<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    32523265  cropbottom="13784f" cropleft="4299f" cropright="4371f"/>
    32533266</v:shape><![endif]--><![if !vml]><img width=333 height=111
    3254 src="SequentialTutorial_files/image099.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
     3267src="SequentialTutorial_files/image147.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
    32553268
    32563269<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    32703283  cropbottom="14017f" cropleft="4425f" cropright="4157f"/>
    32713284</v:shape><![endif]--><![if !vml]><img width=337 height=112
    3272 src="SequentialTutorial_files/image101.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
     3285src="SequentialTutorial_files/image148.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
    32733286
    32743287<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
    … …  
    33333346 <v:imagedata src="SequentialTutorial_files/image102.png" o:title=""/>
    33343347</v:shape><![endif]--><![if !vml]><img width=223 height=208
    3335 src="SequentialTutorial_files/image103.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
     3348src="SequentialTutorial_files/image149.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
    33363349
    33373350<p class=MsoListParagraphCxSpMiddle>Note the change in the atom table.</p>
    … …  
    33433356 <v:imagedata src="SequentialTutorial_files/image104.png" o:title=""/>
    33443357</v:shape><![endif]--><![if !vml]><img width=471 height=203
    3345 src="SequentialTutorial_files/image105.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
     3358src="SequentialTutorial_files/image150.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
    33463359
    33473360<p class=MsoListParagraphCxSpMiddle>Note that since these parameters are shared

  • Tutorials/SeqRefine/SequentialTutorial_files/filelist.xml

    r1752 r2390  
    66 <o:File HRef="colorschememapping.xml"/>
    77 <o:File HRef="image001.png"/>
    8  <o:File HRef="image002.jpg"/>
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