Changeset 2390 for Tutorials/SeqRefine
- Timestamp:
- Jul 28, 2016 2:18:10 PM (7 years ago)
- Location:
- Tutorials/SeqRefine
- Files:
-
- 9 edited
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Tutorials/SeqRefine/SequentialTutorial.htm
r2363 r2390 23 23 <o:Author>B Toby</o:Author> 24 24 <o:LastAuthor>Von Dreele</o:LastAuthor> 25 <o:Revision> 2</o:Revision>26 <o:TotalTime>39 6</o:TotalTime>25 <o:Revision>3</o:Revision> 26 <o:TotalTime>397</o:TotalTime> 27 27 <o:Created>2015-03-21T14:51:00Z</o:Created> 28 <o:LastSaved>201 5-03-21T14:51:00Z</o:LastSaved>28 <o:LastSaved>2016-07-28T18:50:00Z</o:LastSaved> 29 29 <o:Pages>1</o:Pages> 30 <o:Words>376 9</o:Words>31 <o:Characters>2148 4</o:Characters>30 <o:Words>3768</o:Words> 31 <o:Characters>21480</o:Characters> 32 32 <o:Company>Argonne National Laboratory</o:Company> 33 33 <o:Lines>179</o:Lines> 34 34 <o:Paragraphs>50</o:Paragraphs> 35 <o:CharactersWithSpaces>25 203</o:CharactersWithSpaces>36 <o:Version>1 5.00</o:Version>35 <o:CharactersWithSpaces>25198</o:CharactersWithSpaces> 36 <o:Version>16.00</o:Version> 37 37 </o:DocumentProperties> 38 38 <o:OfficeDocumentSettings> … … 47 47 <!--[if gte mso 9]><xml> 48 48 <w:WordDocument> 49 <w:Zoom>116</w:Zoom>50 49 <w:TrackMoves>false</w:TrackMoves> 51 50 <w:TrackFormatting/> … … 923 922 color:#4F81BD; 924 923 font-weight:bold;} 924 p.msonormal0, li.msonormal0, div.msonormal0 925 {mso-style-name:msonormal; 926 mso-style-noshow:yes; 927 mso-style-priority:99; 928 mso-style-unhide:no; 929 mso-margin-top-alt:auto; 930 margin-right:0in; 931 mso-margin-bottom-alt:auto; 932 margin-left:0in; 933 mso-pagination:widow-orphan; 934 font-size:12.0pt; 935 font-family:"Times New Roman",serif; 936 mso-fareast-font-family:"Times New Roman"; 937 mso-fareast-theme-font:minor-fareast;} 925 938 span.BalloonTextChar 926 939 {mso-style-name:"Balloon Text Char"; … … 1458 1471 <w:wrap type="square" anchorx="margin" anchory="margin"/> 1459 1472 </v:shape><![endif]--><![if !vml]><img width=271 height=93 1460 src="SequentialTutorial_files/image00 2.jpg" align=right hspace=12 v:shapes="Picture_x0020_1"><![endif]>Use1473 src="SequentialTutorial_files/image008.jpg" align=right hspace=12 v:shapes="Picture_x0020_1"><![endif]>Use 1461 1474 the <b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; 1462 1475 mso-hansi-theme-font:major-latin'>Import/Phase/from CIF file menu item</span></b> … … 1479 1492 bold'>file</span> (change the file directory to <b style='mso-bidi-font-weight: 1480 1493 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1481 major-latin;mso-hansi-theme-font:major-latin'> exercises/SeqRefine</span></b>).1494 major-latin;mso-hansi-theme-font:major-latin'>SeqRefine/data</span></b>). 1482 1495 Another dialog window will be created showing all the files in the zip archive. 1483 1496 To simplify the view to only show the phase files, type <b style='mso-bidi-font-weight: … … 1531 1544 <w:wrap type="square" anchorx="margin" anchory="margin"/> 1532 1545 </v:shape><![endif]--><![if !vml]><img width=284 height=119 1533 src="SequentialTutorial_files/image0 04.jpg" align=right hspace=12 v:shapes="Picture_x0020_21"><![endif]><span1546 src="SequentialTutorial_files/image032.jpg" align=right hspace=12 v:shapes="Picture_x0020_21"><![endif]><span 1534 1547 style='mso-spacerun:yes'> </span>Read in the ~7 K dataset (<b style='mso-bidi-font-weight: 1535 1548 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: … … 1569 1582 <tr> 1570 1583 <td></td> 1571 <td><img width=216 height=210 src="SequentialTutorial_files/image0 06.png"1584 <td><img width=216 height=210 src="SequentialTutorial_files/image042.png" 1572 1585 v:shapes="Picture_x0020_3"></td> 1573 1586 </tr> … … 1586 1599 <v:imagedata src="SequentialTutorial_files/image007.png" o:title=""/> 1587 1600 </v:shape><![endif]--><![if !vml]><img width=317 height=167 1588 src="SequentialTutorial_files/image0 08.png" v:shapes="Picture_x0020_1"><![endif]></span></p>1601 src="SequentialTutorial_files/image051.png" v:shapes="Picture_x0020_1"><![endif]></span></p> 1589 1602 1590 1603 <p class=MsoListParagraphCxSpMiddle>Note that the instrument parameter file … … 1610 1623 <v:imagedata src="SequentialTutorial_files/image009.png" o:title=""/> 1611 1624 </v:shape><![endif]--><![if !vml]><img width=235 height=195 1612 src="SequentialTutorial_files/image0 10.png" v:shapes="Picture_x0020_2"><![endif]></span></p>1625 src="SequentialTutorial_files/image055.png" v:shapes="Picture_x0020_2"><![endif]></span></p> 1613 1626 1614 1627 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 1629 1642 <w:wrap type="square" anchorx="margin" anchory="margin"/> 1630 1643 </v:shape><![endif]--><![if !vml]><img width=334 height=170 1631 src="SequentialTutorial_files/image0 12.png" align=right hspace=12 v:shapes="Picture_x0020_4"><![endif]>We1644 src="SequentialTutorial_files/image057.png" align=right hspace=12 v:shapes="Picture_x0020_4"><![endif]>We 1632 1645 want to fit the lattice parameters, background, and a phase fraction 1633 1646 initially.<span style='mso-spacerun:yes'> </span>To illustrate how constraints … … 1653 1666 <v:imagedata src="SequentialTutorial_files/image013.png" o:title=""/> 1654 1667 </v:shape><![endif]--><![if !vml]><img width=104 height=72 1655 src="SequentialTutorial_files/image0 14.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span1668 src="SequentialTutorial_files/image099.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span 1656 1669 style='mso-spacerun:yes'> </span></p> 1657 1670 … … 1675 1688 <v:imagedata src="SequentialTutorial_files/image015.png" o:title=""/> 1676 1689 </v:shape><![endif]--><![if !vml]><img width=437 height=172 1677 src="SequentialTutorial_files/image 016.png" v:shapes="Picture_x0020_8"><![endif]></span><span1690 src="SequentialTutorial_files/image101.png" v:shapes="Picture_x0020_8"><![endif]></span><span 1678 1691 style='mso-spacerun:yes'> </span></p> 1679 1692 … … 1695 1708 <v:imagedata src="SequentialTutorial_files/image017.png" o:title=""/> 1696 1709 </v:shape><![endif]--><![if !vml]><img width=451 height=173 1697 src="SequentialTutorial_files/image 018.png" v:shapes="Picture_x0020_10"><![endif]></span><span1710 src="SequentialTutorial_files/image106.png" v:shapes="Picture_x0020_10"><![endif]></span><span 1698 1711 style='font-family:"Cambria",serif'><o:p></o:p></span></p> 1699 1712 … … 1710 1723 <v:imagedata src="SequentialTutorial_files/image019.png" o:title=""/> 1711 1724 </v:shape><![endif]--><![if !vml]><img width=339 height=172 1712 src="SequentialTutorial_files/image 020.png" v:shapes="Picture_x0020_11"><![endif]></span></p>1725 src="SequentialTutorial_files/image107.png" v:shapes="Picture_x0020_11"><![endif]></span></p> 1713 1726 1714 1727 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 1733 1746 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1734 1747 mso-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 this1736 phase, so <span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span1748 entry to open the tree item). We also want to refine the phase fraction for 1749 this phase, so <span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span 1737 1750 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; 1738 1751 mso-hansi-theme-font:major-latin'>Data</span> </b><span style='mso-bidi-font-weight: … … 1751 1764 <v:imagedata src="SequentialTutorial_files/image021.png" o:title=""/> 1752 1765 </v:shape><![endif]--><![if !vml]><img width=347 height=132 1753 src="SequentialTutorial_files/image 022.jpg" v:shapes="Picture_x0020_7"><![endif]></span></p>1766 src="SequentialTutorial_files/image108.jpg" v:shapes="Picture_x0020_7"><![endif]></span></p> 1754 1767 1755 1768 <p class=MsoListParagraphCxSpMiddle>Repeat this with the second phase (<b … … 1793 1806 <w:wrap type="square" anchorx="margin" anchory="margin"/> 1794 1807 </v:shape><![endif]--><![if !vml]><img width=346 height=123 1795 src="SequentialTutorial_files/image 024.png" align=right hspace=12 v:shapes="Picture_x0020_14"><![endif]>Also1808 src="SequentialTutorial_files/image109.png" align=right hspace=12 v:shapes="Picture_x0020_14"><![endif]>Also 1796 1809 <span style='mso-bidi-font-weight:bold'>select<b> </b>the<b> </b></span><b><span 1797 1810 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; … … 1842 1855 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; 1843 1856 mso-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 will1845 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;1857 normal'><i style='mso-bidi-font-style:normal'><u>Important</u></i></b>: you 1858 will 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; 1847 1860 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>4.5</span></b>) 1848 1861 and then click on some other box in the window so that the change registers. </p> … … 1865 1878 <w:wrap type="square" anchorx="margin" anchory="margin"/> 1866 1879 </v:shape><![endif]--><![if !vml]><img width=205 height=315 1867 src="SequentialTutorial_files/image 026.png" align=right hspace=12 v:shapes="Picture_x0020_15"><![endif]>Optional:1880 src="SequentialTutorial_files/image110.png" align=right hspace=12 v:shapes="Picture_x0020_15"><![endif]>Optional: 1868 1881 confirm that the initial parameters have been selected correctly for refinement 1869 1882 using <span style='mso-bidi-font-weight:bold'>the<b> </b></span><b><span … … 1929 1942 <w:wrap type="square" anchorx="margin" anchory="margin"/> 1930 1943 </v:shape><![endif]--><![if !vml]><img width=375 height=174 1931 src="SequentialTutorial_files/image 028.png" align=right hspace=12 v:shapes="Picture_x0020_13"><![endif]><span1944 src="SequentialTutorial_files/image111.png" align=right hspace=12 v:shapes="Picture_x0020_13"><![endif]><span 1932 1945 style='mso-fareast-language:EN-US;mso-no-proof:yes'>Selecting</span><b> </b><span 1933 1946 style='mso-bidi-font-weight:bold'>the<b> </b></span><b><span style='font-family: … … 1935 1948 major-latin'>PWDR OH_00.fxye Bank 1</span> </b><span style='mso-bidi-font-weight: 1936 1949 bold'>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 canalter the view to show the square root of the intensity (use the <b1950 regions of the pattern provides insight on how the fit could be improved. You can 1951 alter the view to show the square root of the intensity (use the <b 1939 1952 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1940 1953 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>S</span></b> … … 1989 2002 <w:wrap type="square" anchorx="margin" anchory="margin"/> 1990 2003 </v:shape><![endif]--><![if !vml]><img width=350 height=338 1991 src="SequentialTutorial_files/image 030.png" align=right hspace=12 v:shapes="Picture_x0020_16"><![endif]>While2004 src="SequentialTutorial_files/image112.png" align=right hspace=12 v:shapes="Picture_x0020_16"><![endif]>While 1992 2005 in other projects I might postpone this until later, we can also start on 1993 2006 improving the peak fit. We will do this by varying the sample broadening for … … 2075 2088 <v:imagedata src="SequentialTutorial_files/image031.png" o:title=""/> 2076 2089 </v:shape><![endif]--><![if !vml]><img width=453 height=340 2077 src="SequentialTutorial_files/image 032.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>2090 src="SequentialTutorial_files/image113.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p> 2078 2091 2079 2092 <h1>Step 2: Prepare for sequential fit. </h1> … … 2127 2140 <v:imagedata src="SequentialTutorial_files/image033.png" o:title=""/> 2128 2141 </v:shape><![endif]--><![if !vml]><img width=539 height=115 2129 src="SequentialTutorial_files/image 034.png" v:shapes="Picture_x0020_9"><![endif]></span></p>2142 src="SequentialTutorial_files/image114.png" v:shapes="Picture_x0020_9"><![endif]></span></p> 2130 2143 2131 2144 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2157 2170 <v:imagedata src="SequentialTutorial_files/image035.png" o:title=""/> 2158 2171 </v:shape><![endif]--><![if !vml]><img width=353 height=339 2159 src="SequentialTutorial_files/image 036.png" v:shapes="Picture_x0020_72"><![endif]></span></p>2172 src="SequentialTutorial_files/image115.png" v:shapes="Picture_x0020_72"><![endif]></span></p> 2160 2173 2161 2174 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2204 2217 cropbottom="5827f" cropleft="4311f" cropright="4217f"/> 2205 2218 </v:shape><![endif]--><![if !vml]><img width=352 height=337 2206 src="SequentialTutorial_files/image 038.png" v:shapes="Picture_x0020_71"><![endif]></span></p>2219 src="SequentialTutorial_files/image116.png" v:shapes="Picture_x0020_71"><![endif]></span></p> 2207 2220 2208 2221 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2234 2247 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2235 2248 </v:shape><![endif]--><![if !vml]><img width=237 height=312 2236 src="SequentialTutorial_files/image 040.png" align=right hspace=12 v:shapes="Picture_x0020_33"><![endif]><span2249 src="SequentialTutorial_files/image117.png" align=right hspace=12 v:shapes="Picture_x0020_33"><![endif]><span 2237 2250 style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape 2238 2251 id="Picture_x0020_13" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:290.25pt; … … 2241 2254 cropbottom="9111f" cropleft="3592f" cropright="4103f"/> 2242 2255 </v:shape><![endif]--><![if !vml]><img width=387 height=179 2243 src="SequentialTutorial_files/image 042.png" v:shapes="Picture_x0020_13"><![endif]></span></p>2256 src="SequentialTutorial_files/image118.png" v:shapes="Picture_x0020_13"><![endif]></span></p> 2244 2257 2245 2258 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2293 2306 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2294 2307 </v:shape><![endif]--><![if !vml]><img width=214 height=209 2295 src="SequentialTutorial_files/image 044.png" align=right hspace=12 v:shapes="Picture_x0020_17"><![endif]>The2308 src="SequentialTutorial_files/image119.png" align=right hspace=12 v:shapes="Picture_x0020_17"><![endif]>The 2296 2309 remaining datasets are read <span style='mso-bidi-font-weight:bold'>using<b> </b></span><b><span 2297 2310 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; … … 2326 2339 cropbottom="7136f" cropleft="3738f" cropright="3737f"/> 2327 2340 </v:shape><![endif]--><![if !vml]><img width=398 height=271 2328 src="SequentialTutorial_files/image 046.png" v:shapes="Picture_x0020_19"><![endif]></span></p>2341 src="SequentialTutorial_files/image120.png" v:shapes="Picture_x0020_19"><![endif]></span></p> 2329 2342 2330 2343 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2356 2369 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2357 2370 </v:shape><![endif]--><![if !vml]><img width=209 height=112 2358 src="SequentialTutorial_files/image 048.png" align=right hspace=12 v:shapes="Picture_x0020_18"><![endif]>Optional:2371 src="SequentialTutorial_files/image121.png" align=right hspace=12 v:shapes="Picture_x0020_18"><![endif]>Optional: 2359 2372 Note that the default graphics mode is to display the last dataset read 2360 2373 in.<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;2374 ensemble 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; 2363 2376 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>PWDR 2364 2377 OH_00.fxye Bank 1</span></b>), click on the frame of the plot window and press … … 2431 2444 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2432 2445 </v:shape><![endif]--><![if !vml]><img width=93 height=44 2433 src="SequentialTutorial_files/image 051.jpg" align=right hspace=12 v:shapes="Picture_x0020_19"><![endif]>Copy2446 src="SequentialTutorial_files/image122.jpg" align=right hspace=12 v:shapes="Picture_x0020_19"><![endif]>Copy 2434 2447 the histogram parameters from the first histogram to the new ones: <span 2435 2448 style='mso-bidi-font-weight:bold'>Select the original </span><b><span … … 2455 2468 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2456 2469 </v:shape><![endif]--><![if !vml]><img width=217 height=212 2457 src="SequentialTutorial_files/image 053.png" align=right hspace=12 v:shapes="Picture_x0020_20"><![endif]>This2470 src="SequentialTutorial_files/image123.png" align=right hspace=12 v:shapes="Picture_x0020_20"><![endif]>This 2458 2471 causes a dialog box where the sections to be copied are selected. We need to 2459 2472 duplicate the <b style='mso-bidi-font-weight:normal'><span style='font-family: … … 2496 2509 cropbottom="8776f" cropleft="6460f" cropright="6263f"/> 2497 2510 </v:shape><![endif]--><![if !vml]><img width=215 height=212 2498 src="SequentialTutorial_files/image 055.png" v:shapes="Picture_x0020_20"><![endif]></span></p>2511 src="SequentialTutorial_files/image124.png" v:shapes="Picture_x0020_20"><![endif]></span></p> 2499 2512 2500 2513 <p class=MsoListParagraphCxSpLast>That the copy has been performed can be … … 2526 2539 <v:imagedata src="SequentialTutorial_files/image056.png" o:title=""/> 2527 2540 </v:shape><![endif]--><![if !vml]><img width=363 height=416 2528 src="SequentialTutorial_files/image 057.png" v:shapes="Picture_x0020_16"><![endif]></span><span2541 src="SequentialTutorial_files/image125.png" v:shapes="Picture_x0020_16"><![endif]></span><span 2529 2542 style='mso-spacerun:yes'> </span></p> 2530 2543 … … 2551 2564 cropbottom="9070f" cropleft="5898f" cropright="3179f"/> 2552 2565 </v:shape><![endif]--><![if !vml]><img width=229 height=211 2553 src="SequentialTutorial_files/image 059.png" v:shapes="Picture_x0020_23"><![endif]><!--[if gte vml 1]><v:shape2566 src="SequentialTutorial_files/image126.png" v:shapes="Picture_x0020_23"><![endif]><!--[if gte vml 1]><v:shape 2554 2567 id="Picture_x0020_22" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:156.75pt; 2555 2568 height:156.75pt;visibility:visible;mso-wrap-style:square'> … … 2557 2570 cropbottom="9050f" cropleft="6461f" cropright="7653f"/> 2558 2571 </v:shape><![endif]--><![if !vml]><img width=209 height=209 2559 src="SequentialTutorial_files/image 061.png" v:shapes="Picture_x0020_22"><![endif]></span></p>2572 src="SequentialTutorial_files/image127.png" v:shapes="Picture_x0020_22"><![endif]></span></p> 2560 2573 2561 2574 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2609 2622 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2610 2623 </v:shape><![endif]--><![if !vml]><img width=217 height=209 2611 src="SequentialTutorial_files/image 063.png" align=right hspace=12 v:shapes="Picture_x0020_24"><![endif]>First,2624 src="SequentialTutorial_files/image128.png" align=right hspace=12 v:shapes="Picture_x0020_24"><![endif]>First, 2612 2625 <span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span 2613 2626 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; … … 2624 2637 <v:imagedata src="SequentialTutorial_files/image064.png" o:title=""/> 2625 2638 </v:shape><![endif]--><![if !vml]><img width=356 height=113 2626 src="SequentialTutorial_files/image 065.png" v:shapes="Picture_x0020_25"><![endif]></span></p>2627 2628 <p class=MsoListParagraphCxSpMiddle>This opens a window where all histograms 2629 canbe selected (it would be equally valid to skip the first histogram, since that2639 src="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 2642 be selected (it would be equally valid to skip the first histogram, since that 2630 2643 has already been fully fit). <span style='mso-bidi-font-weight:bold'>Press<b> </b></span><b><span 2631 2644 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; … … 2654 2667 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2655 2668 </v:shape><![endif]--><![if !vml]><img width=360 height=128 2656 src="SequentialTutorial_files/image 067.png" align=right hspace=12 v:shapes="Picture_x0020_34"><![endif]><span2669 src="SequentialTutorial_files/image130.png" align=right hspace=12 v:shapes="Picture_x0020_34"><![endif]><span 2657 2670 style='mso-bidi-font-weight:bold'>Check the<b> </b></span><b><span 2658 2671 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; … … 2702 2715 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2703 2716 </v:shape><![endif]--><![if !vml]><img width=106 height=69 2704 src="SequentialTutorial_files/image 069.jpg" align=right hspace=12 v:shapes="Picture_x0020_28"><![endif]>Start2717 src="SequentialTutorial_files/image131.jpg" align=right hspace=12 v:shapes="Picture_x0020_28"><![endif]>Start 2705 2718 the sequential refinement with <b><span style='font-family:"Calibri",sans-serif; 2706 2719 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Calculate/Sequential … … 2796 2809 <tr> 2797 2810 <td></td> 2798 <td><img width=572 height=10 9 src="SequentialTutorial_files/image070.png"2811 <td><img width=572 height=108 src="SequentialTutorial_files/image132.png" 2799 2812 alt="Text Box: **** ERROR - variable list for this histogram does not match previous current histogram PWDR OH_04.fxye Bank 1 has 6 variables Variables in previous but not in current: 1::D22, 1::D33, 1::D11, Previous refinement has 7 variables Variables in current but not in previous: 1::Scale, 1::Mustrain;i, " 2800 2813 v:shapes="Text_x0020_Box_x0020_3"></td> … … 2840 2853 <tr> 2841 2854 <td></td> 2842 <td><img width=321 height=103 src="SequentialTutorial_files/image 072.png"2855 <td><img width=321 height=103 src="SequentialTutorial_files/image133.png" 2843 2856 v:shapes="Picture_x0020_29"></td> 2844 2857 </tr> … … 2864 2877 <v:imagedata src="SequentialTutorial_files/image073.png" o:title=""/> 2865 2878 </v:shape><![endif]--><![if !vml]><img width=700 height=350 2866 src="SequentialTutorial_files/image 074.png" v:shapes="Picture_x0020_54"><![endif]></span></p>2867 2868 <p class=MsoListParagraphCxSpMiddle><o:p> </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 Δχ<sup>2</sup> value in the third column shows 2875 thepercent improvement in χ<sup>2</sup> seen in the last cycle of refinement.2879 src="SequentialTutorial_files/image134.png" v:shapes="Picture_x0020_54"><![endif]></span></p> 2880 2881 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> 2882 2883 <p class=MsoListParagraphCxSpMiddle>The second column shows the weighted profile 2884 R-factor, from each fit. This shows a steady increase with temperature, as 2885 might be expected if there were a systematic change in some sample parameters, 2886 such as strain or background or even atomic coordinates (which have not yet 2887 been fit). The Δχ<sup>2</sup> value in the third column shows the 2888 percent improvement in χ<sup>2</sup> seen in the last cycle of refinement. 2876 2889 (If this changes from 4.1 to 4.0, then the value will be 100*(4.1-4.0)/4.0, or 2877 2890 2.5). Since the convergence criterion in the controls is 0.0001 (or 0.01%) we … … 2907 2920 <v:imagedata src="SequentialTutorial_files/image075.png" o:title=""/> 2908 2921 </v:shape><![endif]--><![if !vml]><img width=466 height=400 2909 src="SequentialTutorial_files/image 076.jpg" v:shapes="Picture_x0020_42"><![endif]></span></p>2922 src="SequentialTutorial_files/image135.jpg" v:shapes="Picture_x0020_42"><![endif]></span></p> 2910 2923 2911 2924 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2925 2938 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2926 2939 </v:shape><![endif]--><![if !vml]><img width=213 height=207 2927 src="SequentialTutorial_files/image 078.png" align=right hspace=12 v:shapes="Picture_x0020_43"><![endif]>Pressing2940 src="SequentialTutorial_files/image136.png" align=right hspace=12 v:shapes="Picture_x0020_43"><![endif]>Pressing 2928 2941 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 2929 2942 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>K</span></b> … … 2931 2944 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; 2932 2945 mso-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>2946 bold'> key</span> brings up a menu where the x-axis can be selected as 2947 temperature. If the plot fails to update, click on another column and then 2948 return to the original column. </p> 2936 2949 2937 2950 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2943 2956 <v:imagedata src="SequentialTutorial_files/image079.png" o:title=""/> 2944 2957 </v:shape><![endif]--><![if !vml]><img width=389 height=296 2945 src="SequentialTutorial_files/image 080.jpg" v:shapes="Picture_x0020_45"><![endif]></span></p>2958 src="SequentialTutorial_files/image137.jpg" v:shapes="Picture_x0020_45"><![endif]></span></p> 2946 2959 2947 2960 <p class=MsoListParagraphCxSpLast><o:p> </o:p></p> … … 2981 2994 cropbottom="9604f" cropleft="4103f" cropright="3837f"/> 2982 2995 </v:shape><![endif]--><![if !vml]><img width=384 height=176 2983 src="SequentialTutorial_files/image 082.png" v:shapes="Picture_x0020_47"><![endif]><o:p></o:p></span></p>2996 src="SequentialTutorial_files/image138.png" v:shapes="Picture_x0020_47"><![endif]><o:p></o:p></span></p> 2984 2997 2985 2998 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 2998 3011 <w:wrap type="square" anchorx="margin" anchory="margin"/> 2999 3012 </v:shape><![endif]--><![if !vml]><img width=75 height=47 3000 src="SequentialTutorial_files/image 084.jpg" align=left hspace=12 v:shapes="Picture_x0020_48"><![endif]><span3013 src="SequentialTutorial_files/image139.jpg" align=left hspace=12 v:shapes="Picture_x0020_48"><![endif]><span 3001 3014 style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape 3002 3015 id="Picture_x0020_49" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:158.25pt; … … 3004 3017 <v:imagedata src="SequentialTutorial_files/image085.png" o:title=""/> 3005 3018 </v:shape><![endif]--><![if !vml]><img width=211 height=203 3006 src="SequentialTutorial_files/image 086.jpg" v:shapes="Picture_x0020_49"><![endif]></span></p>3019 src="SequentialTutorial_files/image140.jpg" v:shapes="Picture_x0020_49"><![endif]></span></p> 3007 3020 3008 3021 <p class=MsoNormal><o:p> </o:p></p> … … 3027 3040 croptop="2496f" cropbottom="6549f" cropleft="5811f" cropright="6065f"/> 3028 3041 </v:shape><![endif]--><![if !vml]><img width=237 height=311 3029 src="SequentialTutorial_files/image 088.png"3042 src="SequentialTutorial_files/image141.png" 3030 3043 alt="Description: BHT3 HD:private:tmp:s1.png" v:shapes="Picture_x0020_84"><![endif]></span></p> 3031 3044 … … 3040 3053 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin; 3041 3054 mso-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 the3044 s ingle sample broadening term and the remaining lattice parameter</span> via3045 the <bstyle='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;3055 style='mso-bidi-font-weight:bold'>button</span>. (Important: not the Copy button!) 3056 For the <span style='mso-bidi-font-weight:bold'>CuO phase, add the single 3057 sample broadening term and the remaining lattice parameter</span> via the <b 3058 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 3046 3059 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>D13</span></b> 3047 3060 term.<span style='mso-spacerun:yes'> </span>Again, <span style='mso-bidi-font-weight: … … 3060 3073 <v:imagedata src="SequentialTutorial_files/image089.png" o:title=""/> 3061 3074 </v:shape><![endif]--><![if !vml]><img width=332 height=241 3062 src="SequentialTutorial_files/image 090.jpg" v:shapes="Picture_x0020_52"><![endif]></span></p>3075 src="SequentialTutorial_files/image142.jpg" v:shapes="Picture_x0020_52"><![endif]></span></p> 3063 3076 3064 3077 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 3070 3083 <v:imagedata src="SequentialTutorial_files/image091.png" o:title=""/> 3071 3084 </v:shape><![endif]--><![if !vml]><img width=332 height=249 3072 src="SequentialTutorial_files/image 092.jpg" v:shapes="Picture_x0020_53"><![endif]></span></p>3085 src="SequentialTutorial_files/image143.jpg" v:shapes="Picture_x0020_53"><![endif]></span></p> 3073 3086 3074 3087 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 3176 3189 <tr> 3177 3190 <td></td> 3178 <td><img width=572 height=10 8 src="SequentialTutorial_files/image093.png"3191 <td><img width=572 height=109 src="SequentialTutorial_files/image144.png" 3179 3192 alt="Text Box: **** ERROR - variable list for this histogram does not match previous current histogram PWDR OH_04.fxye Bank 1 has 24 variables Variables in previous but not in current: ::constr0, Previous refinement has 23 variables Variables in current but not in previous: 1::Scale, 0::Scale, " 3180 3193 v:shapes="Text_x0020_Box_x0020_87"></td> … … 3192 3205 mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>1:0:Scale</span></b>) 3193 3206 pertains 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 affects3195 the first histogram, giving rise to the error above. We could set up a3207 of the variables in it are included in the refinement, so this constraint only 3208 affects the first histogram, giving rise to the error above. We could set up a 3196 3209 constraint for each histogram that has been added, but this would be rather 3197 3210 tedious to set up. The alternate is to set up a constraint where a wildcard (<span … … 3224 3237 cropbottom="8174f" cropleft="3258f" cropright="2910f"/> 3225 3238 </v:shape><![endif]--><![if !vml]><img width=479 height=207 3226 src="SequentialTutorial_files/image 095.png" v:shapes="Picture_x0020_26"><![endif]></span></p>3239 src="SequentialTutorial_files/image145.png" v:shapes="Picture_x0020_26"><![endif]></span></p> 3227 3240 3228 3241 <p class=MsoListParagraphCxSpMiddle>There will only be one possible matching … … 3238 3251 cropbottom="11943f" cropleft="3390f" cropright="3551f"/> 3239 3252 </v:shape><![endif]--><![if !vml]><img width=415 height=139 3240 src="SequentialTutorial_files/image 097.png" v:shapes="Picture_x0020_27"><![endif]></span></p>3253 src="SequentialTutorial_files/image146.png" v:shapes="Picture_x0020_27"><![endif]></span></p> 3241 3254 3242 3255 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 3252 3265 cropbottom="13784f" cropleft="4299f" cropright="4371f"/> 3253 3266 </v:shape><![endif]--><![if !vml]><img width=333 height=111 3254 src="SequentialTutorial_files/image 099.png" v:shapes="Picture_x0020_28"><![endif]></span></p>3267 src="SequentialTutorial_files/image147.png" v:shapes="Picture_x0020_28"><![endif]></span></p> 3255 3268 3256 3269 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 3270 3283 cropbottom="14017f" cropleft="4425f" cropright="4157f"/> 3271 3284 </v:shape><![endif]--><![if !vml]><img width=337 height=112 3272 src="SequentialTutorial_files/image1 01.png" v:shapes="Picture_x0020_29"><![endif]></span></p>3285 src="SequentialTutorial_files/image148.png" v:shapes="Picture_x0020_29"><![endif]></span></p> 3273 3286 3274 3287 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> … … 3333 3346 <v:imagedata src="SequentialTutorial_files/image102.png" o:title=""/> 3334 3347 </v:shape><![endif]--><![if !vml]><img width=223 height=208 3335 src="SequentialTutorial_files/image1 03.png" v:shapes="Picture_x0020_31"><![endif]></span></p>3348 src="SequentialTutorial_files/image149.png" v:shapes="Picture_x0020_31"><![endif]></span></p> 3336 3349 3337 3350 <p class=MsoListParagraphCxSpMiddle>Note the change in the atom table.</p> … … 3343 3356 <v:imagedata src="SequentialTutorial_files/image104.png" o:title=""/> 3344 3357 </v:shape><![endif]--><![if !vml]><img width=471 height=203 3345 src="SequentialTutorial_files/image1 05.png" v:shapes="Picture_x0020_32"><![endif]></span></p>3358 src="SequentialTutorial_files/image150.png" v:shapes="Picture_x0020_32"><![endif]></span></p> 3346 3359 3347 3360 <p class=MsoListParagraphCxSpMiddle>Note that since these parameters are shared -
Tutorials/SeqRefine/SequentialTutorial_files/filelist.xml
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Tutorials/SeqRefine/SequentialTutorial_files/item0111.xml
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Tutorials/SeqRefine/SequentialTutorial_files/props112.xml
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