source: tutorials/tutorial4/FapatitleExample.htm @ 1202

Last change on this file since 1202 was 1202, checked in by toby, 10 years ago

fix error in html version

  • Property svn:mime-type set to text/html
File size: 50.6 KB
Line 
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2xmlns:o="urn:schemas-microsoft-com:office:office"
3xmlns:w="urn:schemas-microsoft-com:office:word"
4xmlns:m="http://schemas.microsoft.com/office/2004/12/omml"
5xmlns:mv="http://macVmlSchemaUri" xmlns="http://www.w3.org/TR/REC-html40">
6
7<head>
8<meta name=Title content="">
9<meta name=Keywords content="">
10<meta http-equiv=Content-Type content="text/html; charset=macintosh">
11<meta name=ProgId content=Word.Document>
12<meta name=Generator content="Microsoft Word 14">
13<meta name=Originator content="Microsoft Word 14">
14<link rel=File-List href="FapatitleExample_files/filelist.xml">
15<link rel=Edit-Time-Data href="FapatitleExample_files/editdata.mso">
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24 <o:DocumentProperties>
25  <o:Author>B Toby</o:Author>
26  <o:LastAuthor>B Toby</o:LastAuthor>
27  <o:Revision>5</o:Revision>
28  <o:TotalTime>100</o:TotalTime>
29  <o:LastPrinted>2012-06-22T19:54:00Z</o:LastPrinted>
30  <o:Created>2012-06-22T20:12:00Z</o:Created>
31  <o:LastSaved>2012-06-22T23:31:00Z</o:LastSaved>
32  <o:Pages>15</o:Pages>
33  <o:Words>1002</o:Words>
34  <o:Characters>5714</o:Characters>
35  <o:Company>Argonne National Laboratory</o:Company>
36  <o:Lines>47</o:Lines>
37  <o:Paragraphs>13</o:Paragraphs>
38  <o:CharactersWithSpaces>6703</o:CharactersWithSpaces>
39  <o:Version>14.0</o:Version>
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486</head>
487
488<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
489
490<div class=WordSection1>
491
492<p class=MsoNormal>Se<span style='mso-fareast-font-family:"Times New Roman"'>e <a
493href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/browser/tutorials/tutorial4"><span
494class=icon><span style='color:blue'>https://subversion.xor.aps.anl.gov/trac/EXPGUI/browser/tutorials/tutorial4</span></span></a>
495for files. Download and expand the FAP.zip file or download the four files that
496are contained (FAP.GSA, <span class=SpellE>FAP.cif</span>, FapatitleExample.pdf,
497INST_XRY.PRM) one at <span class=SpellE>at</span> time. To download, click on
498the file and then use &quot;Download in other formats:&quot; Original Format to
499start the download (at bottom of page) to do this.</span></p>
500
501<p class=MsoNormal><o:p>&nbsp;</o:p></p>
502
503<p class=MsoNormal>Start EXPGUI</p>
504
505<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
506 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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508 <v:stroke joinstyle="miter"/>
509 <v:formulas>
510  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
511  <v:f eqn="sum @0 1 0"/>
512  <v:f eqn="sum 0 0 @1"/>
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514  <v:f eqn="prod @3 21600 pixelWidth"/>
515  <v:f eqn="prod @3 21600 pixelHeight"/>
516  <v:f eqn="sum @0 0 1"/>
517  <v:f eqn="prod @6 1 2"/>
518  <v:f eqn="prod @7 21600 pixelWidth"/>
519  <v:f eqn="sum @8 21600 0"/>
520  <v:f eqn="prod @7 21600 pixelHeight"/>
521  <v:f eqn="sum @10 21600 0"/>
522 </v:formulas>
523 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
524 <o:lock v:ext="edit" aspectratio="t"/>
525</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1060" type="#_x0000_t75"
526 style='width:404pt;height:291pt;visibility:visible;mso-wrap-style:square'>
527 <v:imagedata src="FapatitleExample_files/image001.png" o:title=""/>
528</v:shape><![endif]--><![if !vml]><img border=0 width=406 height=293
529src="FapatitleExample_files/image002.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
530
531<p class=MsoNormal>Enter a name for the experiment file (your choice).<span
532style="mso-spacerun:yes">&nbsp; </span>Press Read. Since this is a file we want
533to create we get a warning box:</p>
534
535<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
536 id="Picture_x0020_2" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:404pt;
537 height:122pt;visibility:visible;mso-wrap-style:square'>
538 <v:imagedata src="FapatitleExample_files/image003.png" o:title=""/>
539</v:shape><![endif]--><![if !vml]><img border=0 width=406 height=124
540src="FapatitleExample_files/image004.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
541
542<p class=MsoNormal>Press Create and enter an arbitrary title (for your own
543use):</p>
544
545<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
546 id="Picture_x0020_3" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:402pt;
547 height:106pt;visibility:visible;mso-wrap-style:square'>
548 <v:imagedata src="FapatitleExample_files/image005.png" o:title=""/>
549</v:shape><![endif]--><![if !vml]><img border=0 width=404 height=108
550src="FapatitleExample_files/image006.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
551
552<p class=MsoNormal>Press Continue. EXPGUI then opens and brings you to the
553phase panel (this is a hint). Note that almost all other tabs are disabled
554(also a hint).</p>
555
556<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
557 id="Picture_x0020_4" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:445pt;
558 height:306pt;visibility:visible;mso-wrap-style:square'>
559 <v:imagedata src="FapatitleExample_files/image007.png" o:title=""/>
560</v:shape><![endif]--><![if !vml]><img border=0 width=447 height=308
561src="FapatitleExample_files/image008.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
562
563<p class=MsoNormal>Press Add Phase to enter the structural information. Note
564that we are going to read a cell and atoms in one step, but this can be done in
565different steps. This information can be read from a file or be typed into
566windows. </p>
567
568<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
569 id="Picture_x0020_5" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:523pt;
570 height:155pt;visibility:visible;mso-wrap-style:square'>
571 <v:imagedata src="FapatitleExample_files/image009.png" o:title=""/>
572</v:shape><![endif]--><![if !vml]><img border=0 width=525 height=157
573src="FapatitleExample_files/image010.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
574
575<p class=MsoNormal>Here we read from a CIF file by changing <span class=SpellE>PowderCell</span>
576to CIF. This brings up a window where we can select the CIF file (note this
577window will appear different depending on the operating system):</p>
578
579<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
580 id="Picture_x0020_6" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:474pt;
581 height:240pt;visibility:visible;mso-wrap-style:square'>
582 <v:imagedata src="FapatitleExample_files/image011.png" o:title=""/>
583</v:shape><![endif]--><![if !vml]><img border=0 width=476 height=242
584src="FapatitleExample_files/image012.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
585
586<p class=MsoNormal>Press Open. Lattice/space group information is loaded into
587the window for us:</p>
588
589<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
590 id="Picture_x0020_7" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:493pt;
591 height:139pt;visibility:visible;mso-wrap-style:square'>
592 <v:imagedata src="FapatitleExample_files/image013.png" o:title=""/>
593</v:shape><![endif]--><![if !vml]><img border=0 width=495 height=141
594src="FapatitleExample_files/image014.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
595
596<p class=MsoNormal>Look this information <span class=GramE>over,</span> it is
597not always correct &#8211; particularly the space group (at least one space is
598needed here between the P and the 6, for example). Here all is OK so, press
599Continue. EXPGUI shows the generated symmetry operations:</p>
600
601<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
602 id="Picture_x0020_8" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:394pt;
603 height:278pt;visibility:visible;mso-wrap-style:square'>
604 <v:imagedata src="FapatitleExample_files/image015.png" o:title=""/>
605</v:shape><![endif]--><![if !vml]><img border=0 width=396 height=280
606src="FapatitleExample_files/image016.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
607
608<p class=MsoNormal>It is a good idea to check these against the International
609Tables Volume A. These are what <span class=GramE>was</span> wanted, so we
610press Continue. Next we see the atoms:</p>
611
612<p class=MsoNormal><span style="mso-spacerun:yes">&nbsp;</span><span
613style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
614 id="Picture_x0020_9" o:spid="_x0000_i1052" type="#_x0000_t75" style='width:374pt;
615 height:225pt;visibility:visible;mso-wrap-style:square'>
616 <v:imagedata src="FapatitleExample_files/image017.png" o:title=""/>
617</v:shape><![endif]--><![if !vml]><img border=0 width=376 height=227
618src="FapatitleExample_files/image018.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
619
620<p class=MsoNormal>Note that these <span class=SpellE>Uiso</span> values are very
621large! This CIF must have them wrong. We can change them now, but we will deal
622with this later. Otherwise the input is OK, so press Add Atoms to continue. Now
623the Phase panel has been filled out with our first (and in this case, only)
624phase. Note we can now access the Powder panel. So lets do that. Now we will
625add data (a histogram in GSAS jargon).</p>
626
627<p class=MsoNormal><span style="mso-spacerun:yes">&nbsp;</span><span
628style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
629 id="Picture_x0020_10" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:419pt;
630 height:289pt;visibility:visible;mso-wrap-style:square'>
631 <v:imagedata src="FapatitleExample_files/image019.png" o:title=""/>
632</v:shape><![endif]--><![if !vml]><img border=0 width=421 height=291
633src="FapatitleExample_files/image020.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
634
635<p class=MsoNormal>Press Add New Histogram (at bottom). Here we will enter the
636data file name by pressing the upper Select File button</p>
637
638<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
639 id="Picture_x0020_11" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:464pt;
640 height:273pt;visibility:visible;mso-wrap-style:square'>
641 <v:imagedata src="FapatitleExample_files/image021.png" o:title=""/>
642</v:shape><![endif]--><![if !vml]><img border=0 width=466 height=275
643src="FapatitleExample_files/image022.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
644
645<p class=MsoNormal>Select the FAP.GSA data file:</p>
646
647<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
648 id="Picture_x0020_12" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:435pt;
649 height:238pt;visibility:visible;mso-wrap-style:square'>
650 <v:imagedata src="FapatitleExample_files/image023.png" o:title=""/>
651</v:shape><![endif]--><![if !vml]><img border=0 width=437 height=240
652src="FapatitleExample_files/image024.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
653
654<p class=MsoNormal>Then press Open. We now need an instrument parameter file to
655specify the data type, provide default peak widths etc. We will use a
656GSAS-distributed file for this. Press the lower Select file button and select
657file INST_XRY.PRM</p>
658
659<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
660 id="Picture_x0020_13" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:425pt;
661 height:257pt;visibility:visible;mso-wrap-style:square'>
662 <v:imagedata src="FapatitleExample_files/image025.png" o:title=""/>
663</v:shape><![endif]--><![if !vml]><img border=0 width=427 height=259
664src="FapatitleExample_files/image026.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
665
666<p class=MsoNormal><span class=GramE>The press Open.</span> You may get a warning
667that you can ignore (just press OK):</p>
668
669<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
670 id="Picture_x0020_14" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:441pt;
671 height:149pt;visibility:visible;mso-wrap-style:square'>
672 <v:imagedata src="FapatitleExample_files/image027.png" o:title=""/>
673</v:shape><![endif]--><![if !vml]><img border=0 width=443 height=151
674src="FapatitleExample_files/image028.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
675
676<p class=MsoNormal>The powder histogram information is now ready to be added to
677the experiment, but before we do that we might want to change the data limit to
678use less data. One can use RAWPLOT to look at the data, but here lets use all
679the data (to 130 degrees). </p>
680
681<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
682 id="Picture_x0020_15" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:435pt;
683 height:264pt;visibility:visible;mso-wrap-style:square'>
684 <v:imagedata src="FapatitleExample_files/image029.png" o:title=""/>
685</v:shape><![endif]--><![if !vml]><img border=0 width=437 height=266
686src="FapatitleExample_files/image030.png" v:shapes="Picture_x0020_15"><![endif]></span></p>
687
688<p class=MsoNormal>Press Add to add the data.<span
689style="mso-spacerun:yes">&nbsp; </span>We see this in the Histogram panel:</p>
690
691<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
692 id="Picture_x0020_16" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:610pt;
693 height:427pt;visibility:visible;mso-wrap-style:square'>
694 <v:imagedata src="FapatitleExample_files/image031.png" o:title=""/>
695</v:shape><![endif]--><![if !vml]><img border=0 width=612 height=429
696src="FapatitleExample_files/image032.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
697
698<p class=MsoNormal><o:p>&nbsp;</o:p></p>
699
700<p class=MsoNormal>Before we do any refinement, we should see what the pattern
701looks like. On the controls panel set the number of cycles to zero:</p>
702
703<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
704 id="Picture_x0020_17" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:623pt;
705 height:434pt;visibility:visible;mso-wrap-style:square'>
706 <v:imagedata src="FapatitleExample_files/image033.png" o:title=""/>
707</v:shape><![endif]--><![if !vml]><img border=0 width=625 height=436
708src="FapatitleExample_files/image034.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
709
710<p class=MsoNormal>To start running press the <span class=SpellE>powpref</span>
711button</p>
712
713<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
714 id="Picture_x0020_18" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:483pt;
715 height:335pt;visibility:visible;mso-wrap-style:square'>
716 <v:imagedata src="FapatitleExample_files/image035.png" o:title=""/>
717</v:shape><![endif]--><![if !vml]><img border=0 width=485 height=337
718src="FapatitleExample_files/image036.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
719
720<p class=MsoNormal><span class=GramE>Press Enter in the window to continue.</span>
721The <span class=GramE>EXP file has been changed by the POWPREF program</span>,
722so we press Load New </p>
723
724<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1216" type="#_x0000_t75"
725 style='width:364pt;height:203pt'>
726 <v:imagedata src="FapatitleExample_files/image037.png" o:title=""/>
727</v:shape><![endif]--><![if !vml]><img border=0 width=366 height=205
728src="FapatitleExample_files/image038.png" v:shapes="_x0000_i1216"><![endif]></p>
729
730<p class=MsoNormal>Then press the <span class=SpellE>genles</span> button to
731start that program. With 0 cycles, it will compute the powder intensities, but
732not refine any parameters. </p>
733
734<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1067" type="#_x0000_t75"
735 style='width:540pt;height:377pt'>
736 <v:imagedata src="FapatitleExample_files/image039.png" o:title=""/>
737</v:shape><![endif]--><![if !vml]><img border=0 width=542 height=379
738src="FapatitleExample_files/image040.png" v:shapes="_x0000_i1067"><![endif]></p>
739
740<p class=MsoNormal>As before press Enter and then Load New in the next window.
741Now press the <span class=SpellE>liveplot</span> button to see a plot. We see
742the plotted data, but no computed intensity. </p>
743
744<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1073" type="#_x0000_t75"
745 style='width:469pt;height:471pt'>
746 <v:imagedata src="FapatitleExample_files/image041.png" o:title=""/>
747</v:shape><![endif]--><![if !vml]><img border=0 width=471 height=473
748src="FapatitleExample_files/image042.png" v:shapes="_x0000_i1073"><![endif]></p>
749
750<p class=MsoNormal>If we zoom in enough (drag a box with the left mouse button
751to zoom in; click with the right to zoom out), we see that there are computed
752intensities but they are computed with perhaps 50 counts, while the raw data
753have 20,000 counts.</p>
754
755<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1076" type="#_x0000_t75"
756 style='width:535pt;height:537pt'>
757 <v:imagedata src="FapatitleExample_files/image043.png" o:title=""/>
758</v:shape><![endif]--><![if !vml]><img border=0 width=537 height=539
759src="FapatitleExample_files/image044.png" v:shapes="_x0000_i1076"><![endif]></p>
760
761<p class=MsoNormal>While we could refine the scale factor, lets instead
762multiply the scale factor by 20,000/50 (400) using the scaling panel:</p>
763
764<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1079" type="#_x0000_t75"
765 style='width:535pt;height:405pt'>
766 <v:imagedata src="FapatitleExample_files/image045.png" o:title=""/>
767</v:shape><![endif]--><![if !vml]><img border=0 width=537 height=407
768src="FapatitleExample_files/image046.png" v:shapes="_x0000_i1079"><![endif]></p>
769
770<p class=MsoNormal>Then press <span class=SpellE>Genles</span>, press Enter and
771Load New as before. <span class=SpellE>Liveplot</span> updates to show us the
772new plot automatically:</p>
773
774<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1083" type="#_x0000_t75"
775 style='width:496pt;height:500pt'>
776 <v:imagedata src="FapatitleExample_files/image047.png" o:title=""/>
777</v:shape><![endif]--><![if !vml]><img border=0 width=498 height=502
778src="FapatitleExample_files/image048.png" v:shapes="_x0000_i1083"><![endif]></p>
779
780<p class=MsoNormal>Or when we zoom out:</p>
781
782<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1086" type="#_x0000_t75"
783 style='width:527pt;height:529pt'>
784 <v:imagedata src="FapatitleExample_files/image049.png" o:title=""/>
785</v:shape><![endif]--><![if !vml]><img border=0 width=529 height=531
786src="FapatitleExample_files/image050.png" v:shapes="_x0000_i1086"><![endif]></p>
787
788<p class=MsoNormal>Note that peaks are more or less lining up. The intensity
789falls off way too fast (this is due to the <span class=SpellE>Uiso</span>
790values being too high. Lets change them. On the phase panel drag the mouse over
791all atoms:</p>
792
793<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1095" type="#_x0000_t75"
794 style='width:585pt;height:444pt'>
795 <v:imagedata src="FapatitleExample_files/image051.png" o:title=""/>
796</v:shape><![endif]--><![if !vml]><img border=0 width=587 height=446
797src="FapatitleExample_files/image052.png" v:shapes="_x0000_i1095"><![endif]></p>
798
799<p class=MsoNormal>Press Modify Atoms. Change the <span class=SpellE>Uiso</span>
800value in the new window to 0.01</p>
801
802<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1103" type="#_x0000_t75"
803 style='width:399pt;height:593pt'>
804 <v:imagedata src="FapatitleExample_files/image053.png" o:title=""/>
805</v:shape><![endif]--><![if !vml]><img border=0 width=401 height=595
806src="FapatitleExample_files/image054.png" v:shapes="_x0000_i1103"><![endif]></p>
807
808<p class=MsoNormal>Press Set U and then <span class=GramE>Close</span>. Note
809the <span class=SpellE>Uiso</span> values are now changed on the phase panel:</p>
810
811<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1111" type="#_x0000_t75"
812 style='width:600pt;height:453pt'>
813 <v:imagedata src="FapatitleExample_files/image055.png" o:title=""/>
814</v:shape><![endif]--><![if !vml]><img border=0 width=602 height=455
815src="FapatitleExample_files/image056.png" v:shapes="_x0000_i1111"><![endif]></p>
816
817<p class=MsoNormal><span class=SpellE>Recompute</span> with <span class=SpellE>Genles</span>,
818as before. <span class=SpellE>Liveplot</span> now shows much better
819intensities, though now our scale factor is probably too big. </p>
820
821<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1113" type="#_x0000_t75"
822 style='width:434pt;height:435pt'>
823 <v:imagedata src="FapatitleExample_files/image057.png" o:title=""/>
824</v:shape><![endif]--><![if !vml]><img border=0 width=436 height=437
825src="FapatitleExample_files/image058.png" v:shapes="_x0000_i1113"><![endif]></p>
826
827<p class=MsoNormal><o:p>&nbsp;</o:p></p>
828
829<p class=MsoNormal>Lets start refining the model to better fit the data. Change
830the number of cycles to 3</p>
831
832<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1117" type="#_x0000_t75"
833 style='width:464pt;height:351pt'>
834 <v:imagedata src="FapatitleExample_files/image059.png" o:title=""/>
835</v:shape><![endif]--><![if !vml]><img border=0 width=466 height=353
836src="FapatitleExample_files/image060.png" v:shapes="_x0000_i1117"><![endif]></p>
837
838<p class=MsoNormal>Use the refine cell option on the phase panel</p>
839
840<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1127" type="#_x0000_t75"
841 style='width:517pt;height:391pt'>
842 <v:imagedata src="FapatitleExample_files/image061.png" o:title=""/>
843</v:shape><![endif]--><![if !vml]><img border=0 width=519 height=393
844src="FapatitleExample_files/image062.png" v:shapes="_x0000_i1127"><![endif]></p>
845
846<p class=MsoNormal>Change the background to type 1 with six parameters. Select
847the Powder Panel, use Edit Background. One the edit cell window select function
848type 1, and number of terms 6. </p>
849
850<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1130" type="#_x0000_t75"
851 style='width:507pt;height:175pt'>
852 <v:imagedata src="FapatitleExample_files/image063.png" o:title=""/>
853</v:shape><![endif]--><![if !vml]><img border=0 width=509 height=177
854src="FapatitleExample_files/image064.png" v:shapes="_x0000_i1130"><![endif]></p>
855
856<p class=MsoNormal><span class=GramE>The press Continue.</span> Confirm that
857Refine background is checked. </p>
858
859<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1133" type="#_x0000_t75"
860 style='width:535pt;height:405pt'>
861 <v:imagedata src="FapatitleExample_files/image065.png" o:title=""/>
862</v:shape><![endif]--><![if !vml]><img border=0 width=537 height=407
863src="FapatitleExample_files/image066.png" v:shapes="_x0000_i1133"><![endif]></p>
864
865<p class=MsoNormal>Now lets refine by pressing the <span class=SpellE>genles</span>
866button.</p>
867
868<p class=MsoNormal>The GENLES output shows the <b style='mso-bidi-font-weight:
869normal'><span style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
870style='mso-bidi-font-size:12.0pt'>2</span></sup> dropping from 6813 to 74<sup><span
871style='mso-bidi-font-size:12.0pt'><o:p></o:p></span></sup></p>
872
873<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1138" type="#_x0000_t75"
874 style='width:502pt;height:349pt'>
875 <v:imagedata src="FapatitleExample_files/image067.png" o:title=""/>
876</v:shape><![endif]--><![if !vml]><img border=0 width=504 height=351
877src="FapatitleExample_files/image068.png" v:shapes="_x0000_i1138"><![endif]><!--[if gte vml 1]><v:shape
878 id="_x0000_i1141" type="#_x0000_t75" style='width:513pt;height:357pt'>
879 <v:imagedata src="FapatitleExample_files/image069.png" o:title=""/>
880</v:shape><![endif]--><![if !vml]><img border=0 width=515 height=359
881src="FapatitleExample_files/image070.png" v:shapes="_x0000_i1141"><![endif]></p>
882
883<p class=MsoNormal><span class=SpellE>Liveplot</span> will also show the fit
884looks better. </p>
885
886<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1149" type="#_x0000_t75"
887 style='width:591pt;height:593pt'>
888 <v:imagedata src="FapatitleExample_files/image071.png" o:title=""/>
889</v:shape><![endif]--><![if !vml]><img border=0 width=593 height=595
890src="FapatitleExample_files/image072.png" v:shapes="_x0000_i1149"><![endif]></p>
891
892<p class=MsoNormal>Run <span class=SpellE>powpref</span> and <span
893class=SpellE>genles</span> again (because the cell dimensions changed a fair
894amount). <b style='mso-bidi-font-weight:normal'><span style='font-family:"Lucida Grande";
895color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:12.0pt'>2</span></sup>
896drops to 61.</p>
897
898<p class=MsoNormal><o:p>&nbsp;</o:p></p>
899
900<p class=MsoNormal>Zooming in on the pattern in <span class=SpellE>liveplot</span>
901shows the match to the intensities <span class=GramE>are</span> not bad. The
902peak shape is a bit narrow, but not bad. </p>
903
904<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1156" type="#_x0000_t75"
905 style='width:463pt;height:464pt'>
906 <v:imagedata src="FapatitleExample_files/image073.png" o:title=""/>
907</v:shape><![endif]--><![if !vml]><img border=0 width=465 height=466
908src="FapatitleExample_files/image074.png" v:shapes="_x0000_i1156"><![endif]></p>
909
910<p class=MsoNormal>Select to refine the atom positions (as allowed by symmetry)
911and <span class=SpellE>Uiso</span> values by selecting all atoms and click on X
912and F below the atoms:</p>
913
914<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1159" type="#_x0000_t75"
915 style='width:547pt;height:414pt'>
916 <v:imagedata src="FapatitleExample_files/image075.png" o:title=""/>
917</v:shape><![endif]--><![if !vml]><img border=0 width=549 height=416
918src="FapatitleExample_files/image076.png" v:shapes="_x0000_i1159"><![endif]></p>
919
920<p class=MsoNormal>Press <span class=SpellE>genles</span> to refine. The
921agreement improves a bit. If this structure were a bit more complex, we might
922have initially grouped some <span class=SpellE>Uiso</span> values or only vary
923some of the heavy atoms. </p>
924
925<p class=MsoNormal><o:p>&nbsp;</o:p></p>
926
927<p class=MsoNormal>Now lets improve the peak shapes. The initial profile is not
928fitting the tails of the pattern well (see the <span class=SpellE>liveplot</span>
929example above), so letÕs refine the two <span class=SpellE>Lorentian</span>
930terms LX and LY &#8211; but one at a time. <!--[if gte vml 1]><v:shape id="_x0000_i1162"
931 type="#_x0000_t75" style='width:581pt;height:202pt'>
932 <v:imagedata src="FapatitleExample_files/image077.png" o:title=""/>
933</v:shape><![endif]--><![if !vml]><img border=0 width=583 height=204
934src="FapatitleExample_files/image078.png" v:shapes="_x0000_i1162"><![endif]></p>
935
936<p class=MsoNormal>Click on LX and then <span class=SpellE>genles</span>. <b
937style='mso-bidi-font-weight:normal'><span style='font-family:"Lucida Grande";
938color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:12.0pt'>2</span></sup>
939drops to 29.</p>
940
941<p class=MsoNormal>Try the same with LY turning LX off</p>
942
943<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1163" type="#_x0000_t75"
944 style='width:464pt;height:212pt'>
945 <v:imagedata src="FapatitleExample_files/image079.png" o:title=""/>
946</v:shape><![endif]--><![if !vml]><img border=0 width=466 height=214
947src="FapatitleExample_files/image080.png" v:shapes="_x0000_i1163"><![endif]></p>
948
949<p class=MsoNormal>Run <span class=SpellE>genles</span>, <b style='mso-bidi-font-weight:
950normal'><span style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
951style='mso-bidi-font-size:12.0pt'>2</span></sup> barely drops, so we do not
952need this. We could reject the change by pressing Continue with Old. Lets try
953the Gaussian U<span class=GramE>,V,W</span> terms without LX or LY:</p>
954
955<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1168" type="#_x0000_t75"
956 style='width:483pt;height:175pt'>
957 <v:imagedata src="FapatitleExample_files/image081.png" o:title=""/>
958</v:shape><![endif]--><![if !vml]><img border=0 width=485 height=177
959src="FapatitleExample_files/image082.png" v:shapes="_x0000_i1168"><![endif]></p>
960
961<p class=MsoNormal>Run <span class=SpellE>genles</span>, <b style='mso-bidi-font-weight:
962normal'><span style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
963style='mso-bidi-font-size:12.0pt'>2</span></sup> barely drops just a bit, to
96426. Now we can try LX with those terms</p>
965
966<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1173" type="#_x0000_t75"
967 style='width:473pt;height:172pt'>
968 <v:imagedata src="FapatitleExample_files/image083.png" o:title=""/>
969</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=174
970src="FapatitleExample_files/image084.png" v:shapes="_x0000_i1173"><![endif]></p>
971
972<p class=MsoNormal><span class=GramE>since</span> the peak shape has been
973changed a fair amount, lets run <span class=SpellE>powpref</span> and then <span
974class=SpellE>genles</span>. <b style='mso-bidi-font-weight:normal'><span
975style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
976style='mso-bidi-font-size:12.0pt'>2</span></sup> drops quite a bit, to 17. It
977is a good idea to run <span class=SpellE>powpref</span> and <span class=SpellE>genles</span>
978again, but not much changes. </p>
979
980<p class=MsoNormal><o:p>&nbsp;</o:p></p>
981
982<p class=MsoNormal>Since this is Bragg-Brentano (lab) data, lets correct for
983sample shift and transparency (since the sample is not that absorbing).<span
984style="mso-spacerun:yes">&nbsp; </span>Turn on <span class=SpellE>shft</span>
985and <span class=SpellE>trns</span>:</p>
986
987<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1253" type="#_x0000_t75"
988 style='width:464pt;height:214pt'>
989 <v:imagedata src="FapatitleExample_files/image085.png" o:title=""/>
990</v:shape><![endif]--><![if !vml]><img border=0 width=466 height=216
991src="FapatitleExample_files/image086.png" v:shapes="_x0000_i1253"><![endif]></p>
992
993<p class=MsoNormal><span class=GramE>lets</span> run <span class=SpellE>genles</span>.
994<b style='mso-bidi-font-weight:normal'><span style='font-family:"Lucida Grande";
995color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:12.0pt'>2</span></sup>
996drops quite a bit, to 5. Again since peaks have moved, lets run <span
997class=SpellE>powpref</span> and then <span class=SpellE>genles</span> again. <span
998class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
999"Lucida Grande";color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:
100012.0pt'>2</span></sup> even more, to 3.2.</span> Doing that again causes no
1001improvement. </p>
1002
1003<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1004
1005<p class=MsoNormal>There are probably a few more things we should try in this
1006fit, but it is mostly complete. </p>
1007
1008</div>
1009
1010</body>
1011
1012</html>
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