source: tutorials/tutorial4/FapatitleExample.htm @ 1200

Last change on this file since 1200 was 1200, checked in by toby, 9 years ago

add html version

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9<meta name=Keywords content="">
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13<meta name=Originator content="Microsoft Word 14">
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25  <o:Author>B Toby</o:Author>
26  <o:LastAuthor>B Toby</o:LastAuthor>
27  <o:Revision>2</o:Revision>
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35  <o:Company>Argonne National Laboratory</o:Company>
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469
470<body lang=EN-US style='tab-interval:.5in'>
471
472<div class=WordSection1>
473
474<p class=MsoNormal>Start EXPGUI</p>
475
476<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
477 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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497 style='width:239pt;height:172pt;visibility:visible;mso-wrap-style:square'>
498 <v:imagedata src="FapatitleExample_files/image001.png" o:title=""/>
499</v:shape><![endif]--><![if !vml]><img width=241 height=174
500src="FapatitleExample_files/image002.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
501
502<p class=MsoNormal>Enter a name for the experiment file (your choice).<span
503style="mso-spacerun:yes">&nbsp; </span>Press Read. Since this is a file we want
504to create we get a warning box:</p>
505
506<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
507 id="Picture_x0020_2" o:spid="_x0000_i1059" type="#_x0000_t75" style='width:265pt;
508 height:80pt;visibility:visible;mso-wrap-style:square'>
509 <v:imagedata src="FapatitleExample_files/image003.png" o:title=""/>
510</v:shape><![endif]--><![if !vml]><img width=267 height=82
511src="FapatitleExample_files/image004.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
512
513<p class=MsoNormal>Press Create and enter an arbitrary title (for your own
514use):</p>
515
516<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
517 id="Picture_x0020_3" o:spid="_x0000_i1058" type="#_x0000_t75" style='width:231pt;
518 height:61pt;visibility:visible;mso-wrap-style:square'>
519 <v:imagedata src="FapatitleExample_files/image005.png" o:title=""/>
520</v:shape><![endif]--><![if !vml]><img width=233 height=63
521src="FapatitleExample_files/image006.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
522
523<p class=MsoNormal>Press Continue. EXPGUI then opens and brings you to the
524phase panel (this is a hint). Note that almost all other tabs are disabled
525(also a hint).</p>
526
527<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
528 id="Picture_x0020_4" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:301pt;
529 height:207pt;visibility:visible;mso-wrap-style:square'>
530 <v:imagedata src="FapatitleExample_files/image007.png" o:title=""/>
531</v:shape><![endif]--><![if !vml]><img width=303 height=209
532src="FapatitleExample_files/image008.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
533
534<p class=MsoNormal>Press Add Phase to enter the structural information. Note
535that we are going to read a cell and atoms in one step, but this can be done in
536different steps. This information can be read from a file or be typed into
537windows. </p>
538
539<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
540 id="Picture_x0020_5" o:spid="_x0000_i1056" type="#_x0000_t75" style='width:6in;
541 height:128pt;visibility:visible;mso-wrap-style:square'>
542 <v:imagedata src="FapatitleExample_files/image009.png" o:title=""/>
543</v:shape><![endif]--><![if !vml]><img width=434 height=130
544src="FapatitleExample_files/image010.png" v:shapes="Picture_x0020_5"><![endif]></span></p>
545
546<p class=MsoNormal>Here we read from a CIF file by changing <span class=SpellE>PowderCell</span>
547to CIF. This brings up a window where we can select the CIF file (note this
548window will appear different depending on the operating system):</p>
549
550<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
551 id="Picture_x0020_6" o:spid="_x0000_i1055" type="#_x0000_t75" style='width:283pt;
552 height:143pt;visibility:visible;mso-wrap-style:square'>
553 <v:imagedata src="FapatitleExample_files/image011.png" o:title=""/>
554</v:shape><![endif]--><![if !vml]><img width=285 height=145
555src="FapatitleExample_files/image012.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
556
557<p class=MsoNormal>Press Open. Lattice/space group information is loaded into
558the window for us:</p>
559
560<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
561 id="Picture_x0020_7" o:spid="_x0000_i1054" type="#_x0000_t75" style='width:355pt;
562 height:100pt;visibility:visible;mso-wrap-style:square'>
563 <v:imagedata src="FapatitleExample_files/image013.png" o:title=""/>
564</v:shape><![endif]--><![if !vml]><img width=357 height=102
565src="FapatitleExample_files/image014.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
566
567<p class=MsoNormal>Look this information <span class=GramE>over,</span> it is
568not always correct &#8211; particularly the space group (at least one space is
569needed here between the P and the 6, for example). Here all is OK so, press
570Continue. EXPGUI shows the generated symmetry operations:</p>
571
572<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
573 id="Picture_x0020_8" o:spid="_x0000_i1053" type="#_x0000_t75" style='width:234pt;
574 height:165pt;visibility:visible;mso-wrap-style:square'>
575 <v:imagedata src="FapatitleExample_files/image015.png" o:title=""/>
576</v:shape><![endif]--><![if !vml]><img width=236 height=167
577src="FapatitleExample_files/image016.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
578
579<p class=MsoNormal>It is a good idea to check these against the International
580Tables Volume A. These are what <span class=GramE>was</span> wanted, so we
581press Continue. Next we see the atoms: <span style='mso-fareast-language:EN-US;
582mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9" o:spid="_x0000_i1052"
583 type="#_x0000_t75" style='width:252pt;height:152pt;visibility:visible;
584 mso-wrap-style:square'>
585 <v:imagedata src="FapatitleExample_files/image017.png" o:title=""/>
586</v:shape><![endif]--><![if !vml]><img width=254 height=154
587src="FapatitleExample_files/image018.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
588
589<p class=MsoNormal>Note that these <span class=SpellE>Uiso</span> values are very
590large! This CIF must have them wrong. We can change them now, but we will deal
591with this later. Otherwise the input is OK, so press Add Atoms to continue. Now
592the Phase panel has been filled out with our first (and in this case, only)
593phase. Note we can now access the Powder panel. So lets do that. Now we will
594add data (a histogram in GSAS jargon).</p>
595
596<p class=MsoNormal><span style="mso-spacerun:yes">&nbsp;</span><span
597style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
598 id="Picture_x0020_10" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:265pt;
599 height:183pt;visibility:visible;mso-wrap-style:square'>
600 <v:imagedata src="FapatitleExample_files/image019.png" o:title=""/>
601</v:shape><![endif]--><![if !vml]><img width=267 height=185
602src="FapatitleExample_files/image020.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
603
604<p class=MsoNormal>Press Add New Histogram (at bottom). Here we will enter the
605data file name by pressing the upper Select File button</p>
606
607<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
608 id="Picture_x0020_11" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:265pt;
609 height:156pt;visibility:visible;mso-wrap-style:square'>
610 <v:imagedata src="FapatitleExample_files/image021.png" o:title=""/>
611</v:shape><![endif]--><![if !vml]><img width=267 height=158
612src="FapatitleExample_files/image022.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
613
614<p class=MsoNormal>Select the FAP.GSA data file:</p>
615
616<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
617 id="Picture_x0020_12" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:229pt;
618 height:125pt;visibility:visible;mso-wrap-style:square'>
619 <v:imagedata src="FapatitleExample_files/image023.png" o:title=""/>
620</v:shape><![endif]--><![if !vml]><img width=231 height=127
621src="FapatitleExample_files/image024.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
622
623<p class=MsoNormal>Then press Open. We now need an instrument parameter file to
624specify the data type, provide default peak widths etc. We will use a
625GSAS-distributed file for this. Press the lower Select file button and select
626file INST_XRY.PRM</p>
627
628<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
629 id="Picture_x0020_13" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:220pt;
630 height:133pt;visibility:visible;mso-wrap-style:square'>
631 <v:imagedata src="FapatitleExample_files/image025.png" o:title=""/>
632</v:shape><![endif]--><![if !vml]><img width=222 height=135
633src="FapatitleExample_files/image026.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
634
635<p class=MsoNormal><span class=GramE>The press Open.</span> You may get a warning
636that you can ignore (just press OK):</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_14" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:311pt;
640 height:105pt;visibility:visible;mso-wrap-style:square'>
641 <v:imagedata src="FapatitleExample_files/image027.png" o:title=""/>
642</v:shape><![endif]--><![if !vml]><img width=313 height=107
643src="FapatitleExample_files/image028.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
644
645<p class=MsoNormal>The powder histogram information is now ready to be added to
646the experiment, but before we do that we might want to change the data limit to
647use less data. One can use RAWPLOT to look at the data, but here lets use all
648the data (to 130 degrees). </p>
649
650<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
651 id="Picture_x0020_15" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:209pt;
652 height:127pt;visibility:visible;mso-wrap-style:square'>
653 <v:imagedata src="FapatitleExample_files/image029.png" o:title=""/>
654</v:shape><![endif]--><![if !vml]><img width=211 height=129
655src="FapatitleExample_files/image030.png" v:shapes="Picture_x0020_15"><![endif]></span></p>
656
657<p class=MsoNormal>Press Add to add the data.<span
658style="mso-spacerun:yes">&nbsp; </span>We see this in the Histogram panel:</p>
659
660<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
661 id="Picture_x0020_16" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:289pt;
662 height:202pt;visibility:visible;mso-wrap-style:square'>
663 <v:imagedata src="FapatitleExample_files/image031.png" o:title=""/>
664</v:shape><![endif]--><![if !vml]><img width=291 height=204
665src="FapatitleExample_files/image032.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
666
667<p class=MsoNormal><o:p>&nbsp;</o:p></p>
668
669<p class=MsoNormal>Before we do any refinement, we should see what the pattern
670looks like. On the controls panel set the number of cycles to zero:</p>
671
672<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
673 id="Picture_x0020_17" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:6in;
674 height:301pt;visibility:visible;mso-wrap-style:square'>
675 <v:imagedata src="FapatitleExample_files/image033.png" o:title=""/>
676</v:shape><![endif]--><![if !vml]><img width=434 height=303
677src="FapatitleExample_files/image034.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
678
679<p class=MsoNormal>To start running press the <span class=SpellE>powpref</span>
680button</p>
681
682<p class=MsoNormal><span style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
683 id="Picture_x0020_18" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:238pt;
684 height:165pt;visibility:visible;mso-wrap-style:square'>
685 <v:imagedata src="FapatitleExample_files/image035.png" o:title=""/>
686</v:shape><![endif]--><![if !vml]><img width=240 height=167
687src="FapatitleExample_files/image036.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
688
689<p class=MsoNormal><span class=GramE>Press Enter in the window to continue.</span>
690The <span class=GramE>EXP file has been changed by the POWPREF program</span>,
691so we press Load New </p>
692
693<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1061" type="#_x0000_t75"
694 style='width:211pt;height:118pt'>
695 <v:imagedata src="FapatitleExample_files/image037.png" o:title=""/>
696</v:shape><![endif]--><![if !vml]><img width=213 height=120
697src="FapatitleExample_files/image038.png" v:shapes="_x0000_i1061"><![endif]></p>
698
699<p class=MsoNormal>Then press the <span class=SpellE>genles</span> button to
700start that program. With 0 cycles, it will compute the powder intensities, but
701not refine any parameters. </p>
702
703<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1067" type="#_x0000_t75"
704 style='width:265pt;height:185pt'>
705 <v:imagedata src="FapatitleExample_files/image039.png" o:title=""/>
706</v:shape><![endif]--><![if !vml]><img width=267 height=187
707src="FapatitleExample_files/image040.png" v:shapes="_x0000_i1067"><![endif]></p>
708
709<p class=MsoNormal>As before press Enter and then Load New in the next window.
710Now press the <span class=SpellE>liveplot</span> button to see a plot. We see
711the plotted data, but no computed intensity. </p>
712
713<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1073" type="#_x0000_t75"
714 style='width:251pt;height:252pt'>
715 <v:imagedata src="FapatitleExample_files/image041.png" o:title=""/>
716</v:shape><![endif]--><![if !vml]><img width=253 height=254
717src="FapatitleExample_files/image042.png" v:shapes="_x0000_i1073"><![endif]></p>
718
719<p class=MsoNormal>If we zoom in enough (drag a box with the left mouse button
720to zoom in; click with the right to zoom out), we see that there are computed
721intensities but they are computed with perhaps 50 counts, while the raw data
722have 20,000 counts.</p>
723
724<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1076" type="#_x0000_t75"
725 style='width:258pt;height:259pt'>
726 <v:imagedata src="FapatitleExample_files/image043.png" o:title=""/>
727</v:shape><![endif]--><![if !vml]><img width=260 height=261
728src="FapatitleExample_files/image044.png" v:shapes="_x0000_i1076"><![endif]></p>
729
730<p class=MsoNormal>While we could refine the scale factor, lets instead
731multiply the scale factor by 20,000/50 (400) using the scaling panel:</p>
732
733<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1079" type="#_x0000_t75"
734 style='width:337pt;height:255pt'>
735 <v:imagedata src="FapatitleExample_files/image045.png" o:title=""/>
736</v:shape><![endif]--><![if !vml]><img width=339 height=257
737src="FapatitleExample_files/image046.png" v:shapes="_x0000_i1079"><![endif]></p>
738
739<p class=MsoNormal>Then press <span class=SpellE>Genles</span>, press Enter and
740Load New as before. <span class=SpellE>Liveplot</span> updates to show us the
741new plot automatically:</p>
742
743<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1083" type="#_x0000_t75"
744 style='width:265pt;height:267pt'>
745 <v:imagedata src="FapatitleExample_files/image047.png" o:title=""/>
746</v:shape><![endif]--><![if !vml]><img width=267 height=269
747src="FapatitleExample_files/image048.png" v:shapes="_x0000_i1083"><![endif]></p>
748
749<p class=MsoNormal>Or when we zoom out:</p>
750
751<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1086" type="#_x0000_t75"
752 style='width:305pt;height:306pt'>
753 <v:imagedata src="FapatitleExample_files/image049.png" o:title=""/>
754</v:shape><![endif]--><![if !vml]><img width=307 height=308
755src="FapatitleExample_files/image050.png" v:shapes="_x0000_i1086"><![endif]></p>
756
757<p class=MsoNormal>Note that peaks are more or less lining up. The intensity
758falls off way too fast (this is due to the <span class=SpellE>Uiso</span>
759values being too high. Lets change them. On the phase panel drag the mouse over
760all atoms:</p>
761
762<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1095" type="#_x0000_t75"
763 style='width:266pt;height:202pt'>
764 <v:imagedata src="FapatitleExample_files/image051.png" o:title=""/>
765</v:shape><![endif]--><![if !vml]><img width=268 height=204
766src="FapatitleExample_files/image052.png" v:shapes="_x0000_i1095"><![endif]></p>
767
768<p class=MsoNormal>Press Modify Atoms. Change the <span class=SpellE>Uiso</span>
769value in the new window to 0.01</p>
770
771<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1103" type="#_x0000_t75"
772 style='width:218pt;height:324pt'>
773 <v:imagedata src="FapatitleExample_files/image053.png" o:title=""/>
774</v:shape><![endif]--><![if !vml]><img width=220 height=326
775src="FapatitleExample_files/image054.png" v:shapes="_x0000_i1103"><![endif]></p>
776
777<p class=MsoNormal>Press Set U and then <span class=GramE>Close</span>. Note
778the <span class=SpellE>Uiso</span> values are now changed on the phase panel:</p>
779
780<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1111" type="#_x0000_t75"
781 style='width:383pt;height:289pt'>
782 <v:imagedata src="FapatitleExample_files/image055.png" o:title=""/>
783</v:shape><![endif]--><![if !vml]><img width=385 height=291
784src="FapatitleExample_files/image056.png" v:shapes="_x0000_i1111"><![endif]></p>
785
786<p class=MsoNormal><span class=SpellE>Recompute</span> with <span class=SpellE>Genles</span>,
787as before. <span class=SpellE>Liveplot</span> now shows much better
788intensities, though now our scale factor is probably too big. </p>
789
790<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1113" type="#_x0000_t75"
791 style='width:237pt;height:238pt'>
792 <v:imagedata src="FapatitleExample_files/image057.png" o:title=""/>
793</v:shape><![endif]--><![if !vml]><img width=239 height=240
794src="FapatitleExample_files/image058.png" v:shapes="_x0000_i1113"><![endif]></p>
795
796<p class=MsoNormal><o:p>&nbsp;</o:p></p>
797
798<p class=MsoNormal>Lets start refining the model to better fit the data. Change
799the number of cycles to 3</p>
800
801<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1117" type="#_x0000_t75"
802 style='width:283pt;height:214pt'>
803 <v:imagedata src="FapatitleExample_files/image059.png" o:title=""/>
804</v:shape><![endif]--><![if !vml]><img width=285 height=216
805src="FapatitleExample_files/image060.png" v:shapes="_x0000_i1117"><![endif]></p>
806
807<p class=MsoNormal>Use the refine cell option on the phase panel</p>
808
809<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1127" type="#_x0000_t75"
810 style='width:283pt;height:214pt'>
811 <v:imagedata src="FapatitleExample_files/image061.png" o:title=""/>
812</v:shape><![endif]--><![if !vml]><img width=285 height=216
813src="FapatitleExample_files/image062.png" v:shapes="_x0000_i1127"><![endif]></p>
814
815<p class=MsoNormal>Change the background to type 1 with six parameters. <span
816class=GramE>Select the Powder Panel</span>, <span class=GramE>use Edit Cell</span>.
817One the edit cell window <span class=GramE>select</span> function type 1, and
818number of terms 6. </p>
819
820<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1130" type="#_x0000_t75"
821 style='width:229pt;height:79pt'>
822 <v:imagedata src="FapatitleExample_files/image063.png" o:title=""/>
823</v:shape><![endif]--><![if !vml]><img width=231 height=81
824src="FapatitleExample_files/image064.png" v:shapes="_x0000_i1130"><![endif]></p>
825
826<p class=MsoNormal><span class=GramE>The press Continue.</span> Confirm that
827Refine background is checked. </p>
828
829<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1133" type="#_x0000_t75"
830 style='width:337pt;height:255pt'>
831 <v:imagedata src="FapatitleExample_files/image065.png" o:title=""/>
832</v:shape><![endif]--><![if !vml]><img width=339 height=257
833src="FapatitleExample_files/image066.png" v:shapes="_x0000_i1133"><![endif]></p>
834
835<p class=MsoNormal>Now lets refine by pressing the <span class=SpellE>genles</span>
836button.</p>
837
838<p class=MsoNormal>The GENLES output shows the <b style='mso-bidi-font-weight:
839normal'><span style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
840style='mso-bidi-font-size:12.0pt'>2</span></sup> dropping from 6813 to 74<sup><span
841style='mso-bidi-font-size:12.0pt'><o:p></o:p></span></sup></p>
842
843<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1138" type="#_x0000_t75"
844 style='width:342pt;height:238pt'>
845 <v:imagedata src="FapatitleExample_files/image067.png" o:title=""/>
846</v:shape><![endif]--><![if !vml]><img width=344 height=240
847src="FapatitleExample_files/image068.png" v:shapes="_x0000_i1138"><![endif]><!--[if gte vml 1]><v:shape
848 id="_x0000_i1141" type="#_x0000_t75" style='width:346pt;height:241pt'>
849 <v:imagedata src="FapatitleExample_files/image069.png" o:title=""/>
850</v:shape><![endif]--><![if !vml]><img width=348 height=243
851src="FapatitleExample_files/image070.png" v:shapes="_x0000_i1141"><![endif]></p>
852
853<p class=MsoNormal><span class=SpellE>Liveplot</span> will also show the fit
854looks better. </p>
855
856<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1149" type="#_x0000_t75"
857 style='width:261pt;height:262pt'>
858 <v:imagedata src="FapatitleExample_files/image071.png" o:title=""/>
859</v:shape><![endif]--><![if !vml]><img width=263 height=264
860src="FapatitleExample_files/image072.png" v:shapes="_x0000_i1149"><![endif]></p>
861
862<p class=MsoNormal>Run <span class=SpellE>powpref</span> and <span
863class=SpellE>genles</span> again (because the cell dimensions changed a fair
864amount). <b style='mso-bidi-font-weight:normal'><span style='font-family:"Lucida Grande";
865color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:12.0pt'>2</span></sup>
866drops to 61.</p>
867
868<p class=MsoNormal><o:p>&nbsp;</o:p></p>
869
870<p class=MsoNormal>Zooming in on the pattern in <span class=SpellE>liveplot</span>
871shows the match to the intensities <span class=GramE>are</span> not bad. The
872peak shape is a bit narrow, but not bad. </p>
873
874<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1156" type="#_x0000_t75"
875 style='width:286pt;height:287pt'>
876 <v:imagedata src="FapatitleExample_files/image073.png" o:title=""/>
877</v:shape><![endif]--><![if !vml]><img width=288 height=289
878src="FapatitleExample_files/image074.png" v:shapes="_x0000_i1156"><![endif]></p>
879
880<p class=MsoNormal>Select to refine the atom positions (as allowed by symmetry)
881and <span class=SpellE>Uiso</span> values by selecting all atoms and click on X
882and F below the atoms:</p>
883
884<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1159" type="#_x0000_t75"
885 style='width:383pt;height:290pt'>
886 <v:imagedata src="FapatitleExample_files/image075.png" o:title=""/>
887</v:shape><![endif]--><![if !vml]><img width=385 height=292
888src="FapatitleExample_files/image076.png" v:shapes="_x0000_i1159"><![endif]></p>
889
890<p class=MsoNormal>Press <span class=SpellE>genles</span> to refine. The
891agreement improves a bit. If this structure were a bit more complex, we might
892have initially grouped some <span class=SpellE>Uiso</span> values or only vary
893some of the heavy atoms. </p>
894
895<p class=MsoNormal><o:p>&nbsp;</o:p></p>
896
897<p class=MsoNormal>Now lets improve the peak shapes. The initial profile is not
898fitting the tails of the pattern well (see the <span class=SpellE>liveplot</span>
899example above), so letÕs refine the two <span class=SpellE>Lorentian</span>
900terms LX and LY &#8211; but one at a time. <!--[if gte vml 1]><v:shape id="_x0000_i1162"
901 type="#_x0000_t75" style='width:383pt;height:133pt'>
902 <v:imagedata src="FapatitleExample_files/image077.png" o:title=""/>
903</v:shape><![endif]--><![if !vml]><img width=385 height=135
904src="FapatitleExample_files/image078.png" v:shapes="_x0000_i1162"><![endif]></p>
905
906<p class=MsoNormal>Click on LX and then <span class=SpellE>genles</span>. <b
907style='mso-bidi-font-weight:normal'><span style='font-family:"Lucida Grande";
908color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:12.0pt'>2</span></sup>
909drops to 29.</p>
910
911<p class=MsoNormal>Try the same with LY turning LX off</p>
912
913<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1163" type="#_x0000_t75"
914 style='width:346pt;height:158pt'>
915 <v:imagedata src="FapatitleExample_files/image079.png" o:title=""/>
916</v:shape><![endif]--><![if !vml]><img width=348 height=160
917src="FapatitleExample_files/image080.png" v:shapes="_x0000_i1163"><![endif]></p>
918
919<p class=MsoNormal>Run <span class=SpellE>genles</span>, <b style='mso-bidi-font-weight:
920normal'><span style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
921style='mso-bidi-font-size:12.0pt'>2</span></sup> barely drops, so we do not
922need this. We could reject the change by pressing Continue with Old. Lets try
923the Gaussian U<span class=GramE>,V,W</span> terms without LX or LY:</p>
924
925<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1168" type="#_x0000_t75"
926 style='width:337pt;height:122pt'>
927 <v:imagedata src="FapatitleExample_files/image081.png" o:title=""/>
928</v:shape><![endif]--><![if !vml]><img width=339 height=124
929src="FapatitleExample_files/image082.png" v:shapes="_x0000_i1168"><![endif]></p>
930
931<p class=MsoNormal>Run <span class=SpellE>genles</span>, <b style='mso-bidi-font-weight:
932normal'><span style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
933style='mso-bidi-font-size:12.0pt'>2</span></sup> barely drops just a bit, to
93426. Now we can try LX with those terms</p>
935
936<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1173" type="#_x0000_t75"
937 style='width:338pt;height:123pt'>
938 <v:imagedata src="FapatitleExample_files/image083.png" o:title=""/>
939</v:shape><![endif]--><![if !vml]><img width=340 height=125
940src="FapatitleExample_files/image084.png" v:shapes="_x0000_i1173"><![endif]></p>
941
942<p class=MsoNormal><span class=GramE>since</span> the peak shape has been
943changed a fair amount, lets run <span class=SpellE>powpref</span> and then <span
944class=SpellE>genles</span>. <b style='mso-bidi-font-weight:normal'><span
945style='font-family:"Lucida Grande";color:black'>&#967;</span></b><sup><span
946style='mso-bidi-font-size:12.0pt'>2</span></sup> drops quite a bit, to 17. It
947is a good idea to run <span class=SpellE>powpref</span> and <span class=SpellE>genles</span>
948again, but not much changes. </p>
949
950<p class=MsoNormal><o:p>&nbsp;</o:p></p>
951
952<p class=MsoNormal>Since this is Bragg-Brentano (lab) data, lets correct for
953sample shift and transparency (since the sample is not that absorbing).<span
954style="mso-spacerun:yes">&nbsp; </span>Turn on <span class=SpellE>shft</span>
955and <span class=SpellE>trns</span>:</p>
956
957<p class=MsoNormal><!--[if gte vml 1]><v:shape id="_x0000_i1176" type="#_x0000_t75"
958 style='width:301pt;height:139pt'>
959 <v:imagedata src="FapatitleExample_files/image085.png" o:title=""/>
960</v:shape><![endif]--><![if !vml]><img width=303 height=141
961src="FapatitleExample_files/image086.png" v:shapes="_x0000_i1176"><![endif]></p>
962
963<p class=MsoNormal><span class=GramE>lets</span> run <span class=SpellE>genles</span>.
964<b style='mso-bidi-font-weight:normal'><span style='font-family:"Lucida Grande";
965color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:12.0pt'>2</span></sup>
966drops quite a bit, to 5. Again since peaks have moved, lets run <span
967class=SpellE>powpref</span> and then <span class=SpellE>genles</span> again. <span
968class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
969"Lucida Grande";color:black'>&#967;</span></b><sup><span style='mso-bidi-font-size:
97012.0pt'>2</span></sup> even more, to 3.2.</span> Doing that again causes no
971improvement. </p>
972
973<p class=MsoNormal><o:p>&nbsp;</o:p></p>
974
975<p class=MsoNormal>There are probably a few more things we should try in this
976fit, but it is mostly complete. </p>
977
978</div>
979
980</body>
981
982</html>
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