Changeset 2390 for Tutorials/SeqRefine


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

Legend:

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Added
Removed

  • 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>
    … …  
    4747<!--[if gte mso 9]><xml>
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    … …  
    923922        color:#4F81BD;
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     924p.msonormal0, li.msonormal0, div.msonormal0
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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
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    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  
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  • Tutorials/SeqRefine/SequentialTutorial_files/item0111.xml

    r1752 r2390  
    1 <b:Sources SelectedStyle="/APA.XSL" StyleName="APA" xmlns:b="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" xmlns="http://schemas.openxmlformats.org/officeDocument/2006/bibliography"></b:Sources>
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  • Tutorials/SeqRefine/SequentialTutorial_files/props112.xml

    r1752 r2390  
    11<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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