source: Tutorials/FitPeaks/Fit Peaks.htm @ 1720

Last change on this file since 1720 was 1720, checked in by toby, 8 years ago

update fit peak example & missing files
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385        mso-pagination:widow-orphan;
386        mso-outline-level:1;
387        font-size:24.0pt;
388        font-family:"Times New Roman","serif";
389        mso-fareast-font-family:"Times New Roman";
390        mso-fareast-theme-font:minor-fareast;
391        font-weight:bold;}
392h2
393        {mso-style-noshow:yes;
394        mso-style-priority:9;
395        mso-style-qformat:yes;
396        mso-style-link:"Heading 2 Char";
397        mso-margin-top-alt:auto;
398        margin-right:0in;
399        mso-margin-bottom-alt:auto;
400        margin-left:0in;
401        mso-pagination:widow-orphan;
402        mso-outline-level:2;
403        font-size:18.0pt;
404        font-family:"Times New Roman","serif";
405        mso-fareast-font-family:"Times New Roman";
406        mso-fareast-theme-font:minor-fareast;
407        font-weight:bold;}
408h3
409        {mso-style-noshow:yes;
410        mso-style-priority:9;
411        mso-style-qformat:yes;
412        mso-style-link:"Heading 3 Char";
413        mso-margin-top-alt:auto;
414        margin-right:0in;
415        mso-margin-bottom-alt:auto;
416        margin-left:0in;
417        mso-pagination:widow-orphan;
418        mso-outline-level:3;
419        font-size:13.5pt;
420        font-family:"Times New Roman","serif";
421        mso-fareast-font-family:"Times New Roman";
422        mso-fareast-theme-font:minor-fareast;
423        font-weight:bold;}
424h4
425        {mso-style-noshow:yes;
426        mso-style-priority:9;
427        mso-style-qformat:yes;
428        mso-style-link:"Heading 4 Char";
429        mso-style-next:Normal;
430        margin-top:10.0pt;
431        margin-right:0in;
432        margin-bottom:0in;
433        margin-left:0in;
434        margin-bottom:.0001pt;
435        mso-pagination:widow-orphan lines-together;
436        page-break-after:avoid;
437        mso-outline-level:4;
438        font-size:13.0pt;
439        font-family:"Cambria","serif";
440        mso-ascii-font-family:Cambria;
441        mso-ascii-theme-font:major-latin;
442        mso-fareast-font-family:"Times New Roman";
443        mso-fareast-theme-font:major-fareast;
444        mso-hansi-font-family:Cambria;
445        mso-hansi-theme-font:major-latin;
446        mso-bidi-font-family:"Times New Roman";
447        mso-bidi-theme-font:major-bidi;
448        color:#4F81BD;
449        mso-themecolor:accent1;
450        font-weight:bold;
451        font-style:italic;}
452h5
453        {mso-style-noshow:yes;
454        mso-style-priority:9;
455        mso-style-qformat:yes;
456        mso-style-link:"Heading 5 Char";
457        mso-margin-top-alt:auto;
458        margin-right:0in;
459        mso-margin-bottom-alt:auto;
460        margin-left:0in;
461        mso-pagination:widow-orphan;
462        mso-outline-level:5;
463        font-size:12.0pt;
464        font-family:"Times New Roman","serif";
465        mso-fareast-font-family:"Times New Roman";
466        mso-fareast-theme-font:minor-fareast;
467        color:#4F4FFF;
468        font-weight:bold;}
469p.MsoTitle, li.MsoTitle, div.MsoTitle
470        {mso-style-noshow:yes;
471        mso-style-priority:10;
472        mso-style-unhide:no;
473        mso-style-qformat:yes;
474        mso-style-link:"Title Char";
475        mso-style-next:Normal;
476        margin-top:0in;
477        margin-right:0in;
478        margin-bottom:15.0pt;
479        margin-left:0in;
480        mso-add-space:auto;
481        mso-pagination:widow-orphan;
482        border:none;
483        mso-border-bottom-alt:solid #4F81BD 1.0pt;
484        mso-border-bottom-themecolor:accent1;
485        padding:0in;
486        mso-padding-alt:0in 0in 4.0pt 0in;
487        font-size:26.0pt;
488        font-family:"Cambria","serif";
489        mso-ascii-font-family:Cambria;
490        mso-ascii-theme-font:major-latin;
491        mso-fareast-font-family:"Times New Roman";
492        mso-fareast-theme-font:major-fareast;
493        mso-hansi-font-family:Cambria;
494        mso-hansi-theme-font:major-latin;
495        mso-bidi-font-family:"Times New Roman";
496        mso-bidi-theme-font:major-bidi;
497        color:#17365D;
498        mso-themecolor:text2;
499        mso-themeshade:191;
500        letter-spacing:.25pt;
501        mso-font-kerning:14.0pt;}
502p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
503        {mso-style-noshow:yes;
504        mso-style-priority:10;
505        mso-style-unhide:no;
506        mso-style-qformat:yes;
507        mso-style-link:"Title Char";
508        mso-style-next:Normal;
509        mso-style-type:export-only;
510        margin:0in;
511        margin-bottom:.0001pt;
512        mso-add-space:auto;
513        mso-pagination:widow-orphan;
514        border:none;
515        mso-border-bottom-alt:solid #4F81BD 1.0pt;
516        mso-border-bottom-themecolor:accent1;
517        padding:0in;
518        mso-padding-alt:0in 0in 4.0pt 0in;
519        font-size:26.0pt;
520        font-family:"Cambria","serif";
521        mso-ascii-font-family:Cambria;
522        mso-ascii-theme-font:major-latin;
523        mso-fareast-font-family:"Times New Roman";
524        mso-fareast-theme-font:major-fareast;
525        mso-hansi-font-family:Cambria;
526        mso-hansi-theme-font:major-latin;
527        mso-bidi-font-family:"Times New Roman";
528        mso-bidi-theme-font:major-bidi;
529        color:#17365D;
530        mso-themecolor:text2;
531        mso-themeshade:191;
532        letter-spacing:.25pt;
533        mso-font-kerning:14.0pt;}
534p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
535        {mso-style-noshow:yes;
536        mso-style-priority:10;
537        mso-style-unhide:no;
538        mso-style-qformat:yes;
539        mso-style-link:"Title Char";
540        mso-style-next:Normal;
541        mso-style-type:export-only;
542        margin:0in;
543        margin-bottom:.0001pt;
544        mso-add-space:auto;
545        mso-pagination:widow-orphan;
546        border:none;
547        mso-border-bottom-alt:solid #4F81BD 1.0pt;
548        mso-border-bottom-themecolor:accent1;
549        padding:0in;
550        mso-padding-alt:0in 0in 4.0pt 0in;
551        font-size:26.0pt;
552        font-family:"Cambria","serif";
553        mso-ascii-font-family:Cambria;
554        mso-ascii-theme-font:major-latin;
555        mso-fareast-font-family:"Times New Roman";
556        mso-fareast-theme-font:major-fareast;
557        mso-hansi-font-family:Cambria;
558        mso-hansi-theme-font:major-latin;
559        mso-bidi-font-family:"Times New Roman";
560        mso-bidi-theme-font:major-bidi;
561        color:#17365D;
562        mso-themecolor:text2;
563        mso-themeshade:191;
564        letter-spacing:.25pt;
565        mso-font-kerning:14.0pt;}
566p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
567        {mso-style-noshow:yes;
568        mso-style-priority:10;
569        mso-style-unhide:no;
570        mso-style-qformat:yes;
571        mso-style-link:"Title Char";
572        mso-style-next:Normal;
573        mso-style-type:export-only;
574        margin-top:0in;
575        margin-right:0in;
576        margin-bottom:15.0pt;
577        margin-left:0in;
578        mso-add-space:auto;
579        mso-pagination:widow-orphan;
580        border:none;
581        mso-border-bottom-alt:solid #4F81BD 1.0pt;
582        mso-border-bottom-themecolor:accent1;
583        padding:0in;
584        mso-padding-alt:0in 0in 4.0pt 0in;
585        font-size:26.0pt;
586        font-family:"Cambria","serif";
587        mso-ascii-font-family:Cambria;
588        mso-ascii-theme-font:major-latin;
589        mso-fareast-font-family:"Times New Roman";
590        mso-fareast-theme-font:major-fareast;
591        mso-hansi-font-family:Cambria;
592        mso-hansi-theme-font:major-latin;
593        mso-bidi-font-family:"Times New Roman";
594        mso-bidi-theme-font:major-bidi;
595        color:#17365D;
596        mso-themecolor:text2;
597        mso-themeshade:191;
598        letter-spacing:.25pt;
599        mso-font-kerning:14.0pt;}
600a:link, span.MsoHyperlink
601        {mso-style-noshow:yes;
602        mso-style-priority:99;
603        color:blue;
604        text-decoration:underline;
605        text-underline:single;}
606a:visited, span.MsoHyperlinkFollowed
607        {mso-style-noshow:yes;
608        mso-style-priority:99;
609        color:purple;
610        text-decoration:underline;
611        text-underline:single;}
612p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
613        {mso-style-noshow:yes;
614        mso-style-priority:99;
615        mso-style-link:"Document Map Char";
616        margin:0in;
617        margin-bottom:.0001pt;
618        mso-pagination:widow-orphan;
619        font-size:8.0pt;
620        font-family:"Tahoma","sans-serif";
621        mso-fareast-font-family:"Times New Roman";
622        mso-fareast-theme-font:minor-fareast;}
623p
624        {mso-style-noshow:yes;
625        mso-style-priority:99;
626        mso-margin-top-alt:auto;
627        margin-right:0in;
628        mso-margin-bottom-alt:auto;
629        margin-left:0in;
630        mso-pagination:widow-orphan;
631        font-size:12.0pt;
632        font-family:"Times New Roman","serif";
633        mso-fareast-font-family:"Times New Roman";
634        mso-fareast-theme-font:minor-fareast;}
635pre
636        {mso-style-noshow:yes;
637        mso-style-priority:99;
638        mso-style-link:"HTML Preformatted Char";
639        margin:0in;
640        margin-bottom:.0001pt;
641        mso-pagination:widow-orphan;
642        tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
643        font-size:10.0pt;
644        font-family:"Courier New";
645        mso-fareast-font-family:"Times New Roman";}
646p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
647        {mso-style-noshow:yes;
648        mso-style-priority:99;
649        mso-style-link:"Balloon Text Char";
650        margin:0in;
651        margin-bottom:.0001pt;
652        mso-pagination:widow-orphan;
653        font-size:8.0pt;
654        font-family:"Tahoma","sans-serif";
655        mso-fareast-font-family:"Times New Roman";
656        mso-fareast-theme-font:minor-fareast;}
657span.MsoPlaceholderText
658        {mso-style-noshow:yes;
659        mso-style-priority:99;
660        mso-style-unhide:no;
661        color:gray;}
662p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
663        {mso-style-noshow:yes;
664        mso-style-priority:1;
665        mso-style-unhide:no;
666        mso-style-qformat:yes;
667        mso-style-parent:"";
668        margin:0in;
669        margin-bottom:.0001pt;
670        mso-pagination:widow-orphan;
671        font-size:12.0pt;
672        font-family:"Times New Roman","serif";
673        mso-fareast-font-family:"Times New Roman";
674        mso-fareast-theme-font:minor-fareast;}
675p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
676        {mso-style-noshow:yes;
677        mso-style-priority:34;
678        mso-style-unhide:no;
679        mso-style-qformat:yes;
680        margin-top:0in;
681        margin-right:0in;
682        margin-bottom:0in;
683        margin-left:.5in;
684        margin-bottom:.0001pt;
685        mso-add-space:auto;
686        mso-pagination:widow-orphan;
687        font-size:12.0pt;
688        font-family:"Times New Roman","serif";
689        mso-fareast-font-family:"Times New Roman";
690        mso-fareast-theme-font:minor-fareast;}
691p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
692        {mso-style-noshow:yes;
693        mso-style-priority:34;
694        mso-style-unhide:no;
695        mso-style-qformat:yes;
696        mso-style-type:export-only;
697        margin-top:0in;
698        margin-right:0in;
699        margin-bottom:0in;
700        margin-left:.5in;
701        margin-bottom:.0001pt;
702        mso-add-space:auto;
703        mso-pagination:widow-orphan;
704        font-size:12.0pt;
705        font-family:"Times New Roman","serif";
706        mso-fareast-font-family:"Times New Roman";
707        mso-fareast-theme-font:minor-fareast;}
708p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
709        {mso-style-noshow:yes;
710        mso-style-priority:34;
711        mso-style-unhide:no;
712        mso-style-qformat:yes;
713        mso-style-type:export-only;
714        margin-top:0in;
715        margin-right:0in;
716        margin-bottom:0in;
717        margin-left:.5in;
718        margin-bottom:.0001pt;
719        mso-add-space:auto;
720        mso-pagination:widow-orphan;
721        font-size:12.0pt;
722        font-family:"Times New Roman","serif";
723        mso-fareast-font-family:"Times New Roman";
724        mso-fareast-theme-font:minor-fareast;}
725p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
726        {mso-style-noshow:yes;
727        mso-style-priority:34;
728        mso-style-unhide:no;
729        mso-style-qformat:yes;
730        mso-style-type:export-only;
731        margin-top:0in;
732        margin-right:0in;
733        margin-bottom:0in;
734        margin-left:.5in;
735        margin-bottom:.0001pt;
736        mso-add-space:auto;
737        mso-pagination:widow-orphan;
738        font-size:12.0pt;
739        font-family:"Times New Roman","serif";
740        mso-fareast-font-family:"Times New Roman";
741        mso-fareast-theme-font:minor-fareast;}
742span.MsoIntenseReference
743        {mso-style-priority:32;
744        mso-style-unhide:no;
745        mso-style-qformat:yes;
746        font-variant:small-caps;
747        color:#C0504D;
748        mso-themecolor:accent2;
749        letter-spacing:.25pt;
750        font-weight:bold;
751        text-decoration:underline;
752        text-underline:single;}
753span.Heading1Char
754        {mso-style-name:"Heading 1 Char";
755        mso-style-priority:9;
756        mso-style-unhide:no;
757        mso-style-locked:yes;
758        mso-style-link:"Heading 1";
759        mso-ansi-font-size:24.0pt;
760        mso-bidi-font-size:24.0pt;
761        font-family:"Times New Roman","serif";
762        mso-ascii-font-family:"Times New Roman";
763        mso-fareast-font-family:"Times New Roman";
764        mso-fareast-theme-font:minor-fareast;
765        mso-hansi-font-family:"Times New Roman";
766        mso-bidi-font-family:"Times New Roman";
767        mso-font-kerning:18.0pt;
768        font-weight:bold;}
769span.Heading2Char
770        {mso-style-name:"Heading 2 Char";
771        mso-style-noshow:yes;
772        mso-style-priority:9;
773        mso-style-unhide:no;
774        mso-style-locked:yes;
775        mso-style-link:"Heading 2";
776        mso-ansi-font-size:18.0pt;
777        mso-bidi-font-size:18.0pt;
778        font-family:"Times New Roman","serif";
779        mso-ascii-font-family:"Times New Roman";
780        mso-fareast-font-family:"Times New Roman";
781        mso-fareast-theme-font:minor-fareast;
782        mso-hansi-font-family:"Times New Roman";
783        mso-bidi-font-family:"Times New Roman";
784        font-weight:bold;}
785span.Heading3Char
786        {mso-style-name:"Heading 3 Char";
787        mso-style-noshow:yes;
788        mso-style-priority:9;
789        mso-style-unhide:no;
790        mso-style-locked:yes;
791        mso-style-link:"Heading 3";
792        mso-ansi-font-size:13.5pt;
793        mso-bidi-font-size:13.5pt;
794        font-family:"Times New Roman","serif";
795        mso-ascii-font-family:"Times New Roman";
796        mso-fareast-font-family:"Times New Roman";
797        mso-fareast-theme-font:minor-fareast;
798        mso-hansi-font-family:"Times New Roman";
799        mso-bidi-font-family:"Times New Roman";
800        font-weight:bold;}
801span.Heading4Char
802        {mso-style-name:"Heading 4 Char";
803        mso-style-noshow:yes;
804        mso-style-priority:9;
805        mso-style-unhide:no;
806        mso-style-locked:yes;
807        mso-style-link:"Heading 4";
808        mso-ansi-font-size:13.0pt;
809        mso-bidi-font-size:13.0pt;
810        font-family:"Cambria","serif";
811        mso-ascii-font-family:Cambria;
812        mso-ascii-theme-font:major-latin;
813        mso-fareast-font-family:"Times New Roman";
814        mso-fareast-theme-font:major-fareast;
815        mso-hansi-font-family:Cambria;
816        mso-hansi-theme-font:major-latin;
817        mso-bidi-font-family:"Times New Roman";
818        mso-bidi-theme-font:major-bidi;
819        color:#4F81BD;
820        mso-themecolor:accent1;
821        font-weight:bold;
822        font-style:italic;}
823span.Heading5Char
824        {mso-style-name:"Heading 5 Char";
825        mso-style-noshow:yes;
826        mso-style-priority:9;
827        mso-style-unhide:no;
828        mso-style-locked:yes;
829        mso-style-link:"Heading 5";
830        mso-ansi-font-size:12.0pt;
831        mso-bidi-font-size:12.0pt;
832        font-family:"Times New Roman","serif";
833        mso-ascii-font-family:"Times New Roman";
834        mso-fareast-font-family:"Times New Roman";
835        mso-fareast-theme-font:minor-fareast;
836        mso-hansi-font-family:"Times New Roman";
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1122
1123<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1124
1125<div class=WordSection1>
1126
1127<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1128
1129<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1130cell that matches a set of diffraction peaks -- a process known as
1131auto-indexing. First peaks must be located and optimized and then indexing can
1132be done.</p>
1133
1134<p class=MsoNormal>If you have not done so already, <a
1135href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
1136
1137<h2>Step 1: read in the data file</h2>
1138
1139<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1140style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1141style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1142the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1143mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1144Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
1145data file</span></b> menu item to read the data file into the current GSAS-II project.
1146This read option is set to read any of the powder data formats defined for GSAS
1147(angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu
1148items will read the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1149style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1150mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1151minor-latin'>cif</span></b></span> format or the <span class=SpellE><b
1152style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1153mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1154Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format (angles
1155in degrees) used by <span class=SpellE>Topas</span>, etc.
1156If you used the
1157<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1158mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1159Calibri;mso-bidi-theme-font:minor-latin'>Help/Download tutorial
1160</span></b> menu entry to open this page and downloaded the exercise
1161files (recommended), then the Import/... entry will bring you to the location where
1162the files have been downloaded. (It is also possible to download them manually
1163from
1164<A href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">
1165https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>. In
1166this case you will need to navigate to the download location
1167manually.)<BR>
1168For this tutorial you should see the data files in the file browser, but if
1169extensions on data files are not the expected ones, you may need to
1170change the file type to
1171<b style='mso-bidi-font-weight:normal'>All files (*.*)</style></b> to find the desired
1172file.</p>
1173
1174<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1175style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1176style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1177the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1179Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.fxye</span></b><span
1180style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1181mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1182minor-latin'> data</span> file in the first dialog and press <b
1183style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1184mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1185Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
1186Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1187style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1188mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1189minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
1190style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1191mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1192minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1193style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1194mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1195Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
1196proceed.</p>
1197
1198<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1199style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1200style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1201file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1202mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1203Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.prm</span></b> instrument
1204parameter file is automatically selected; it was produced by 11BM-B instrument
1205processing software when the corresponding <span class=SpellE><b
1206style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1207mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1208Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was
1209created from the 12 detector raw data. If absent or the name doesn’t match the
1210data file name, a file dialog will appear for you to select the correct
1211instrument parameter file.</p>
1212
1213<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1214style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1215mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1216minor-latin'>GSAS-II data tree</span></b> window will have several entries </p>
1217
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1234  <v:f eqn="sum @10 21600 0"/>
1235 </v:formulas>
1236 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1237 <o:lock v:ext="edit" aspectratio="t"/>
1238</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75"
1239 style='width:300pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
1240 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
1241</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
1242src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1243
1244<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1245powder pattern</p>
1246
1247<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1248 id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1249 height:450pt;visibility:visible;mso-wrap-style:square'>
1250 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
1251</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1252src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1253
1254<h2>Step 2: Select Limits </h2>
1255
1256<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1257more data than we need, so it is helpful to cut down the range. Click on the <b
1258style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1259mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1260Calibri;mso-bidi-theme-font:minor-latin'>Limits</span></b> item in the <b
1261style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1263Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. The
1264small window is repainted. Use the <b style='mso-bidi-font-weight:normal'><span
1265style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1266mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1267minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b
1268style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1269mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1270Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span
1271class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1272"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1273minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1274to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1275mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1276Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
1277normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1278minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1279mso-bidi-theme-font:minor-latin'>27.5</span></b>. Notice on the plot that the
1280limit lines have moved to these positions; the green lower limit is just below
1281the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks.
1282You may also drag the limit lines to the desired location or place them by a
1283left mouse click on a data point for the lower limit or a right click on a data
1284point for the upper limit.</p>
1285
1286<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1287 id="_x0000_i1050" type="#_x0000_t75" style='width:226.5pt;height:123.75pt;
1288 visibility:visible;mso-wrap-style:square'>
1289 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1290</v:shape><![endif]--><![if !vml]><img border=0 width=302 height=165
1291src="Fit%20Peaks_files/image003.png" v:shapes="_x0000_i1050"><![endif]></span></p>
1292
1293<h2>Step 3: Determine Peak Positions</h2>
1294
1295<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1296auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1297style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1299on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1300mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1301Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> item in the <b
1302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1304Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. This
1305creates an empty window of peak positions (the <b style='mso-bidi-font-weight:
1306normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1307minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1308mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this point
1309it is wise to zoom in on the data that will be used for indexing. </p>
1310
1311<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1312auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1313style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1314style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1315on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1316 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:21.75pt;
1317 height:18.75pt;visibility:visible;mso-wrap-style:square'>
1318 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1319  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1320</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
1321src="Fit%20Peaks_files/image029.jpg" v:shapes="Picture_x0020_4"><![endif]></span>,
1322then press the left mouse in one corner of the region to be used; holding the
1323mouse button down, drag over the region to the opposite corner; a box will be
1324drawn over the region to be zoomed. </p>
1325
1326<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1327auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1328style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1329style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1330style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
1331style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
1332 o:spid="_x0000_i1048" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
1333 visibility:visible;mso-wrap-style:square'>
1334 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1335  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1336</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
1337src="Fit%20Peaks_files/image030.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
1338style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
1339
1340<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1341auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1342style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1343style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1344<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1345mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1346in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1347mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
1348window select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1349"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1350minor-latin'>Auto search</span></b>. The plot window will immediately show that
1351all peaks were picked with a blue vertical line on each one</p>
1352
1353<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1354auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_27"
1355 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;
1356 visibility:visible;mso-wrap-style:square'>
1357 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
1358</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1359src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
1360
1361<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1362auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1363normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1364minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1365mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of
1366increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1367
1368<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1369auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29"
1370 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
1371 visibility:visible;mso-wrap-style:square'>
1372 <v:imagedata src="Fit%20Peaks_files/image031.png" o:title=""/>
1373</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1374src="Fit%20Peaks_files/image031.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1375
1376<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1377will be 20+ peaks in this example. You should examine both the list and the
1378plot to be sure the auto search did not pick a peak twice (quite rarely) or
1379skip a peak or shoulder. You can add a peak to the list by pressing the left
1380mouse button with the pointer on a data point at the peak top or shoulder; be
1381sure the zoom/shift buttons are off. You may drag a peak position as needed. A
1382position may be deleted with a right click with the mouse on the blue line. You
1383can also delete a peak by selecting the row in the table; it will be
1384highlighted in blue. Then press the <b style='mso-bidi-font-weight:normal'><span
1385style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1386mso-hansi-theme-font:minor-latin'>Delete</span></b> key; it will be removed
1387from the table and the plot. The list will always show the peaks sorted by
1388position. When done you should have 20 unique peak positions.</p>
1389
1390<h2>Step 4: Refine Peak Positions</h2>
1391
1392<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1393refinement and then adding parameters to complete the fitting,</p>
1394
1395<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1396style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1397style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1398the peak intensities and the background. These parameters have their refinement
1399flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1400normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1401minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1402mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span>
1403</span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family:
1404"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1405minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak
1406List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use
1407the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1408mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1409Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item
1410in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1411mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1412Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window;
1413that it to be used for <span class=SpellE>Rietveld</span>/Pawley refinements.
1414You will be asked to save the current project before the fit will proceed;
1415change directory if desired and provide a suitable name (we assume <b
1416style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1417mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1418Calibri;mso-bidi-theme-font:minor-latin'>LaB6</span></b>). A window will show
1419the progress of the refinement and will close when the least-squares fit <span
1420class=GramE>is</span> complete (usually very fast). The plot is updated with
1421the fit, the peak list window is updated with the new peak values and a summary
1422of the refinement is shown on the console window as well.</p>
1423
1424<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1425 id="Picture_x0020_8" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1426 height:450pt;visibility:visible;mso-wrap-style:square'>
1427 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1428</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1429src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1430
1431<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1432 id="Picture_x0020_24" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:401.25pt;
1433 height:262.5pt;visibility:visible;mso-wrap-style:square'>
1434 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
1435</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1436src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1437
1438<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1439style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1440style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1441add refinement of the peak positions. This can be done by clicking on all the
1442refinement flags for the individual peaks or it is possible to set them all at
1443the same time using this recipe: </p>
1444
1445<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1446auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1447style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1448style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1449class=GramE>single-click</span> on any value in the table to select it, for
1450example the first peak position. A black box appears around the value. </p>
1451
1452<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1453text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1454style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1455style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1456class=GramE>single-click</span> on the <b style='mso-bidi-font-weight:normal'><span
1457style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1458mso-hansi-theme-font:minor-latin'>refine</span></b> label above the peak
1459position check-boxes. The entire column of checkboxes is highlighted in blue.
1460Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1461mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1462Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
1463refinement flags (<b style='mso-bidi-font-weight:normal'><span
1464style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1465mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1466minor-latin'>n</span></b> would turn them off).</p>
1467
1468<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1469the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1470mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1471Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
1472menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1473"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1474minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak
1475List</span></b> window.</p>
1476
1477<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1478refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1479performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1480width) and/or gamma (<span class=SpellE>Lorentzian</span> width) for individual
1481peaks. &nbsp;To do this, click the refinement flags for sigma and/or gamma in
1482the Peak List window. &nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the
1483LS&nbsp;refinement of&nbsp;peak widths can be&nbsp;constrained to&nbsp;follow
1484an instrumental broadening equation as described below.&nbsp;Note - one cannot
1485refine ALL peak widths using both individual&nbsp;sigma &amp; gamma&nbsp;values
1486AND&nbsp;instrumental broadening terms at the same time.<b style='mso-bidi-font-weight:
1487normal'>&nbsp;</b><o:p></o:p></span></p>
1488
1489<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1490"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1491to an instrumental broadening equation, first<b> s</b></span>elect the <b
1492style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1494Calibri;mso-bidi-theme-font:minor-latin'>Instrumental Parameters</span></b>
1495item in the data tree. This opens a window for peak profile terms<b> </b><span
1496style='mso-bidi-font-weight:bold'>and also creates a new plot
1497window&nbsp;showing the instrument profile resolution curve.</span></p>
1498
1499<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1500 id="Picture_x0020_30" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:419.25pt;
1501 height:183.75pt;visibility:visible;mso-wrap-style:square'>
1502 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1503</v:shape><![endif]--><![if !vml]><img border=0 width=559 height=245
1504src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1505
1506<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1507corresponding to the values of the Gaussian U, V, W, <span class=SpellE>Lorentzian</span>
1508X &amp; Y coefficients; ‘+’ marks show the individual values based on the sig
1509&amp; gam values for the peaks in Peak List. Select the refine flag checkbox
1510for Gaussian <b style='mso-bidi-font-weight:normal'><span style='font-family:
1511"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1512minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>,
1513<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1514mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1515Calibri;mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
1516normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1517minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1518mso-bidi-theme-font:minor-latin'>W</span></b>, and <span class=SpellE>Lorentzian</span>
1519<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1520mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1521Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
1522normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1523minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1524mso-bidi-theme-font:minor-latin'>Y</span></b>. </p>
1525
1526<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1527style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1528style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1529repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1530style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1531mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1532minor-latin'>Peak List</span></b> item in the data tree and then refine using
1533the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1534mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1535Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
1536menu item. At this point a good fit should be seen by zooming in on individual
1537peaks. For example see </p>
1538
1539<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1540 id="Picture_x0020_11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1541 height:450pt;visibility:visible;mso-wrap-style:square'>
1542 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
1543</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1544src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1545
1546<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to the
1547right of the peak top. This is a consequence of the peak asymmetry arising from
1548axial divergence in the <span class=SpellE>diffractometer</span>. The <span
1549class=SpellE>Rwp</span> is ~6% as shown on the console window. Again the <b
1550style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1551mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1552Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all
1553updated with new values and those in <b style='mso-bidi-font-weight:normal'><span
1554style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1555mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1556minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1557
1558<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1559
1560<p class=MsoNormal>A separate list of peaks is kept for use in <span
1561class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1562normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1563minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1564mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data
1565tree. In the initially empty window created by this action, use menu item <b
1566style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1567mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1568Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load/Reload</span></b>
1569to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1570style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1571mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1572minor-latin'>Peak List</span></b>.</p>
1573
1574<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1575 id="Picture_x0020_26" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:367.5pt;
1576 height:225pt;visibility:visible;mso-wrap-style:square'>
1577 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1578</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
1579src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1580
1581<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1582may choose to not use a fitted peak (e.g. if suspected it is from a
1583contaminant).</p>
1584
1585<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
1586
1587<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1588style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1589mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1590minor-latin'>Unit Cells List</span></b> data item. This brings up a window for
1591indexing and cell refinement options</p>
1592
1593<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1594 id="Picture_x0020_13" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:527.25pt;
1595 height:204pt;visibility:visible;mso-wrap-style:square'>
1596 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
1597</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
1598src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1599
1600<p class=MsoNormal>For the most rapid search (since we know the right answer),
1601select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1602mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1603Calibri;mso-bidi-theme-font:minor-latin'>Cubic-P</span></b> and launch the
1604search using menu item <b style='mso-bidi-font-weight:normal'><span
1605style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1606mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1607minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and
1608the console shows a running list of possible cells as they are found; the
1609sorted by M20 list of possible matching cells is shown in the <b
1610style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1611mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1612Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
1613
1614<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1615 id="Picture_x0020_28" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:527.25pt;
1616 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1617 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1618</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1619src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1620
1621<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
1622
1623<p class=MsoNormal>Review the list of cells associated with the <b
1624style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1625mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1626Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> data item.
1627Note that as one selects a unit cell, the generated reflections for that cell
1628are shown in the plot with dashed red lines. Sliding the cursor over these
1629lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
1630for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å
1631generates very many lines with no corresponding peaks (NB: this solution might
1632not always show up!)</p>
1633
1634<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1635 id="Picture_x0020_38" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1636 height:450pt;visibility:visible;mso-wrap-style:square'>
1637 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1638</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1639src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_38"><![endif]></span><span
1640style='mso-spacerun:yes'> </span></p>
1641
1642<p class=MsoNormal><span class=GramE>while</span> the (M20~600) cell with
1643a=2.93932 Å generates not enough lines to match all the peaks</p>
1644
1645<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1646 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1647 height:450pt;visibility:visible;mso-wrap-style:square'>
1648 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
1649</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1650src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
1651
1652<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
1653
1654<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1655indexes all peaks with almost a perfect fit to the peak positions (compare dashed
1656red lines to solid blue ones). Import the cell information using the <b
1657style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1658mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1659Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b>
1660menu option. Then optimize the cell by refining the lattice parameters and the
1661two-theta zero: click on the refine checkbox next to the <b style='mso-bidi-font-weight:
1662normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1663minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1664mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then the <b
1665style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1666mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1667Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
1668menu option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
1669parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
1670certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
1671style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1672mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1673Calibri;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
1674positions </span></b>button to update the plot including the refined <b
1675style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1676mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1677Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
1678hardly anything happens!). <span style='mso-spacerun:yes'> </span></p>
1679
1680<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1681 id="Picture_x0020_17" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;
1682 height:334.5pt;visibility:visible;mso-wrap-style:square'>
1683 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1684</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
1685src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1686
1687<p class=MsoNormal>Notice that a new entry heads the list in the <b
1688style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1689mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1690Calibri;mso-bidi-theme-font:minor-latin'>Indexing Result</span></b> section of
1691the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1692mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1693Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine</span></b>
1694window with an improved M20(~3600) and a new value for <b style='mso-bidi-font-weight:
1695normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1696minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1697mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown. NB: the <b
1698style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1699mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
1700class=SpellE>hkl</span> positions</span></b> button has an additional use; you
1701can enter the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1702style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1703mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b style='mso-bidi-font-weight:
1704normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1705minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>, <b
1706style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1707mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b>
1708&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1709mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
1710for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
1711style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1712mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
1713will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
1714style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1715mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
1716useful to identify e.g. a second phase in your pattern.</p>
1717
1718<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
1719normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1720minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1721mso-bidi-theme-font:minor-latin'>Cell Index/Refine/New phase</span></b> menu
1722option allows one to create a phase with these lattice parameters in the data
1723tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1724"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1725minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
1726style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
1727creates the tree item <b style='mso-bidi-font-weight:normal'><span
1728style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1729mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1730minor-latin'>Phases</span></b> (if it wasn’t already present). This new phase
1731can be used in future analysis (e.g. <span class=SpellE>Rietveld</span> or
1732Pawley refinement).</p>
1733
1734<p class=MsoNormal>To continue with the second part of this exercise, select
1735the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
1736"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1737minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/New
1738project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1739style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1740mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1741minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
1742the current project saved; if <span class=GramE><b style='mso-bidi-font-weight:
1743normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1744minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1745mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the peak
1746fitting/indexing &amp; cell refinement results will be saved to the <b
1747style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1748mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1749Calibri;mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
1750style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1751mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1752Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will
1753remain as it was when created at Step 4 above.</p>
1754
1755<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
1756class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
1757style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
1758
1759<p class=MsoNormal>In this exercise we will fit peaks and index them for the
1760new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
1761(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
1762data were also collected on 11BM-B at APS. The unit cell is monoclinic so it is
1763a more substantial test of the indexing capability of GSAS-II.</p>
1764
1765<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1766
1767<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1768style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1769mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1770minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a
1771corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1772style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1773mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1774minor-latin'>prm</span></b></span> file. Load them in &amp; the plot is</p>
1775
1776<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1777 id="Picture_x0020_18" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
1778 height:450pt;visibility:visible;mso-wrap-style:square'>
1779 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1780</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1781src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
1782
1783<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
1784lower part of the pattern.</p>
1785
1786<h2>Step 2 Set limits</h2>
1787
1788<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
1789style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1790mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1791minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:normal'><span
1792style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1793mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1794minor-latin'>9</span></b>.</p>
1795
1796<h2>Step 3 Pick peaks</h2>
1797
1798<p class=MsoNormal>Pick all peaks you can see between the limits (including the
1799small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
1800"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1801minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
1802peaks by left-clicking on a data point near the top of the peak. Peak positions
1803can be moved by dragging the peak line and peaks can be deleted by
1804right-clicking on them. This only works when the zoom and reposition modes
1805(below) are not selected. Also note some peaks have shoulders most notably at
18065.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
1807deg. I skipped – it might be from a second phase? We’ll see later).</p>
1808
1809<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1810 id="Picture_x0020_19" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
1811 height:450pt;visibility:visible;mso-wrap-style:square'>
1812 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
1813</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1814src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_19"><![endif]></span><br
1815clear=all style='mso-special-character:line-break'>
1816</p>
1817
1818<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
1819
1820<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example above,
1821refine the peaks and the profile shape parameters in <b style='mso-bidi-font-weight:
1822normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1823minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1824mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You will be
1825asked for a project file name at the first refinement (I used ‘<span
1826class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1827"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1828minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
1829style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1830mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1831Calibri;mso-bidi-theme-font:minor-latin'>’</span></b>). In the end my
1832refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do
1833show some discrepancy as the sample is more complex than the simple <b
1834style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1835mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1836Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1837normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1838minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1839mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
1840normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1841minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1842mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
1843normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1844minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1845mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
1846normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1847minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1848mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
1849no peaks drift away during refinement (one weak one at ~6.67 is particularly
1850troublesome). However, this is good enough to proceed.</p>
1851
1852<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1853
1854<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
1855style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1856mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1857minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
1858normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1859minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1860mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
1861
1862<h2><span class=GramE>Step 6.</span> Index the cell</h2>
1863
1864<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic.
1865In a real world case we wouldn’t know this and we would have to try each <span
1866class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
1867time to go through all the bad cases.</p>
1868
1869<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1870style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1871mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1872minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
1873normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1874minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1875mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
1876<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1877mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1878Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
1879Progress will be much slower and suitable results will be slow in coming so be
1880patient. Watch the console window; the right answer will have an obviously
1881large M20 (~380) and a volume of ~594Å<sup>3</sup> (10<sup>th</sup> column of
1882console display). Once this is seen (it may take more than one try to get this)
1883you can stop the indexing search by pressing <b style='mso-bidi-font-weight:
1884normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1885minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1886mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window.
1887Notice the ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
1888"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1889minor-latin'>keep</span></b>’ column; this allows you to keep some solutions
1890from one indexing run to the next. It may take more than one press to fully
1891stop it. My result was </p>
1892
1893<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1894 id="Picture_x0020_20" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
1895 height:450pt;visibility:visible;mso-wrap-style:square'>
1896 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1897</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1898src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_20"><![endif]><!--[if gte vml 1]><v:shape
1899 id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;
1900 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1901 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
1902</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1903src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1904
1905<p class=MsoNormal>Notice other equally good M20 results with different
1906volumes; other solutions may be obtained as you keep trying the indexing. Be
1907sure to use <b style='mso-bidi-font-weight:normal'><span style='font-family:
1908"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1909minor-latin'>Keep</span></b> to keep good ones as you try new indexing runs.
1910The best solution is the one with the smaller volume and &#946; &gt; 90 deg.
1911The plot shows every peak indexed including a weak peak not selected for the
1912peak fitting, although the weak peak at 2<span style='font-family:Symbol;
1913mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1914symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
1915wasn’t indexed. I presume that is a contaminant. Copy the best cell and try to
1916refine it along with the <b style='mso-bidi-font-weight:normal'><span
1917style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1918mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I obtained an
1919improved M20 ~444 and slightly different lattice parameters. Try different
1920space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
1921style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1922mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
1923each time to see which lines vanish. By sliding the cursor over the index lines
1924without any visible peak you can see that the missing ones are 010, 100, 001,
1925110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
1926accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
1927space group P2<sub>1</sub>/n. Armed with this information you can <b
1928style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1929mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1930Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
1931indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
1932style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1933mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1934minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
1935normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1936minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
1937the GSAS-II data tree.</p>
1938
1939<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1940 id="Picture_x0020_36" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:542.25pt;
1941 height:356.25pt;visibility:visible;mso-wrap-style:square'>
1942 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1943</v:shape><![endif]--><![if !vml]><img border=0 width=723 height=475
1944src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_36"><![endif]></span><span
1945style='mso-spacerun:yes'> </span></p>
1946
1947<p class=MsoNormal>Notice that the lattice parameters and space group have been
1948set for you. If you set the space group here a dialog box will appear.</p>
1949
1950<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1951 id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:333.75pt;
1952 height:209.25pt;visibility:visible;mso-wrap-style:square'>
1953 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
1954</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
1955src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1956
1957<p class=MsoNormal>This concludes this exercise; <span class=GramE><b
1958style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1959mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1960Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project file
1961as it is needed for the <b style='mso-bidi-font-weight:normal'><span
1962style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1963mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1964minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
1965exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
1966style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1967mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1968minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
1969
1970<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
1971in GSAS-II </h1>
1972
1973<p class=MsoNormal>In this exercise we will fit peaks and index them for
1974sucrose in preparation for a charge flipping exercise. If continuing from the
1975previous indexing example do <b style='mso-bidi-font-weight:normal'><span
1976style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1977mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
1978GSAS-II data tree menu; you will be asked if you wish to save the old project.
1979The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
1980is a more substantial test of the indexing capability of GSAS-II.</p>
1981
1982<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1983
1984<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1985style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1986mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1987minor-latin'>\Exercises\sucrose\11bmb_8716.fxye</span></b>; it has a
1988corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1989style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1990mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1991minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under
1992acetone. <span class=GramE>The other <span class=SpellE><b style='mso-bidi-font-weight:
1993normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1994minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in
1995this directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
1996"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1997minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X powdered sugar used
1998“as is” out of the box.</span> Load the <b style='mso-bidi-font-weight:normal'><span
1999style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2000mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the plot is</p>
2001
2002<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2003 id="Picture_x0020_31" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
2004 height:450pt;visibility:visible;mso-wrap-style:square'>
2005 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
2006</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2007src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
2008
2009<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2010lower part of the pattern; I’ve also chosen to plot the square root of the
2011intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2012"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2013minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2014
2015<h2>Step 2 Set limits</h2>
2016
2017<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2018style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2019mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2020minor-latin'>2</span></b> and <b style='mso-bidi-font-weight:normal'><span
2021style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2022mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2023minor-latin'>8</span></b>.</p>
2024
2025<h2>Step 3 Pick peaks</h2>
2026
2027<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2028small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2029"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2030minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2031peaks by left-clicking on a data point near the top of the peak. Peak positions
2032can be moved by dragging the peak line and peaks can be deleted by
2033right-clicking on them. This only works when the zoom and reposition modes
2034(below) are not selected. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2035that should be added to the list. I skipped a couple of very weak peaks; the total
2036list has &gt;28 peaks.</p>
2037
2038<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2039 id="Picture_x0020_32" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
2040 height:450pt;visibility:visible;mso-wrap-style:square'>
2041 <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/>
2042</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2043src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_32"><![endif]></span><br
2044clear=all style='mso-special-character:line-break'>
2045</p>
2046
2047<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
2048
2049<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2050kryptonite examples above, refine the peaks and the profile shape parameters in
2051<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2052mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2053Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
2054will be asked for a project file name at the first refinement (I used ‘<b
2055style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2056mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2057Calibri;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>). In the end my
2058refinement converged at <span class=SpellE>Rwp</span>=7.15% and some peaks do
2059show some discrepancy as the sample is more complex than the simple <b
2060style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2061mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2062Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2063normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2064minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2065mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
2066normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2067minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2068mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
2069normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2070minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2071mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
2072normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2073minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2074mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
2075no peaks drift away during refinement. However, this is good enough to proceed.</p>
2076
2077<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
2078
2079<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2080style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2081mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2082minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
2083normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2084minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2085mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
2086
2087<h2><span class=GramE>Step 6.</span> Index the cell</h2>
2088
2089<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2090In a real world case we wouldn’t know this and we would have to try each <span
2091class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2092time to go through all the bad cases.</p>
2093
2094<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2095style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2096mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2097minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
2098normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2099minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2100mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
2101<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2102mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2103Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
2104Progress will be much slower than for LaB<sub>6</sub> but oddly much faster
2105than for kryptonite and suitable results may appear almost immediately. Watch
2106the console window; the right answer will have an obviously large M20 (~900)
2107and a volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display).
2108Once this is seen (it may take more than one try to get this) you can stop the
2109indexing search by pressing <b style='mso-bidi-font-weight:normal'><span
2110style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2111mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2112minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2113style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2114some solutions from one indexing run to the next. It may take more than one
2115press to fully stop it. My result was </p>
2116
2117<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2118 id="Picture_x0020_33" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:527.25pt;
2119 height:376.5pt;visibility:visible;mso-wrap-style:square'>
2120 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
2121</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
2122src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_33"><![endif]><!--[if gte vml 1]><v:shape
2123 id="Picture_x0020_34" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2124 height:450pt;visibility:visible;mso-wrap-style:square'>
2125 <v:imagedata src="Fit%20Peaks_files/image027.png" o:title=""/>
2126</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2127src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
2128
2129<p class=MsoNormal>Notice there may be other equally good M20 results with
2130different volumes; still other solutions may be obtained as you keep trying the
2131indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2132style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2133mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2134new indexing runs. The best solution is the one with the smaller volume and
2135&#946; &gt; 90 deg. The plot shows every peak indexed including the weak peaks
2136not selected for the peak fitting. Copy the best cell and try to refine it
2137along with the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2138"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2139minor-latin'>Zero offset</span></b>. I obtained an improved M20 ~1257 and
2140slightly different lattice parameters. Try different space groups, pressing the
2141<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
2143class=SpellE>hkl</span> positions</span></b> each time to see which lines
2144vanish. The correct space group is P2<sub>1</sub>. Armed with this information
2145you can <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2146mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2147Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
2148indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
2149style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2150mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2151minor-latin'>sucrose</span></b>) and select <b style='mso-bidi-font-weight:
2152normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2153minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> from
2154the GSAS-II data tree.</p>
2155
2156<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2157 id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:542.25pt;
2158 height:351pt;visibility:visible;mso-wrap-style:square'>
2159 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2160</v:shape><![endif]--><![if !vml]><img border=0 width=723 height=468
2161src="Fit%20Peaks_files/image028.png" v:shapes="Picture_x0020_35"><![endif]></span><span
2162style='mso-spacerun:yes'> </span></p>
2163
2164<p class=MsoNormal>Notice that the lattice parameters and space group have been
2165set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2166style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2167mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2168minor-latin'>Save</span></b> the project file as it is needed for the sucrose <b
2169style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2171Calibri;mso-bidi-theme-font:minor-latin'><a
2172href="Charge%20Flipping%20-%20sucrose.htm">Charge Flipping</a></span></b>
2173exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
2174style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2175mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2176minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
2177
2178<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2179
2180</div>
2181
2182</body>
2183
2184</html>
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