source: Tutorials/FitPeaks/Fit Peaks.htm @ 1705

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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.<span
1156style='mso-spacerun:yes'>  </span>Change the file directory to <b
1157style='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'>Exercises/LaB6</span></b><span
1160style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1161mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1162minor-latin'> to find the file; you may need to change the file type to <b
1163style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
1164file.</span></p>
1165
1166<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1167style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1168style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1169the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1171Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.fxye</span></b><span
1172style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1173mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1174minor-latin'> data</span> file in the first dialog and press <b
1175style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1176mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1177Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
1178Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1179style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1180mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1181minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
1182style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1183mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1184minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1185style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1186mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1187Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
1188proceed.</p>
1189
1190<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1191style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1192style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1193file <b style='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'>11bmb_3844.prm</span></b> instrument
1196parameter file is automatically selected; it was produced by 11BM-B instrument
1197processing software when the corresponding <span class=SpellE><b
1198style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1199mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1200Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was
1201created from the 12 detector raw data. If absent or the name doesn’t match the
1202data file name, a file dialog will appear for you to select the correct
1203instrument parameter file.</p>
1204
1205<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1206style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1207mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1208minor-latin'>GSAS-II data tree</span></b> window will have several entries </p>
1209
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1229 <o:lock v:ext="edit" aspectratio="t"/>
1230</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75"
1231 style='width:300pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
1232 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
1233</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
1234src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1235
1236<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1237powder pattern</p>
1238
1239<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1240 id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1241 height:450pt;visibility:visible;mso-wrap-style:square'>
1242 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
1243</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1244src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1245
1246<h2>Step 2: Select Limits </h2>
1247
1248<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1249more data than we need, so it is helpful to cut down the range. Click on the <b
1250style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1251mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1252Calibri;mso-bidi-theme-font:minor-latin'>Limits</span></b> item in the <b
1253style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1254mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1255Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. The
1256small window is repainted. Use the <b style='mso-bidi-font-weight:normal'><span
1257style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1258mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1259minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b
1260style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1261mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1262Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span
1263class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1264"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1265minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1266to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1267mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1268Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
1269normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1270minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1271mso-bidi-theme-font:minor-latin'>27.5</span></b>. Notice on the plot that the
1272limit lines have moved to these positions; the green lower limit is just below
1273the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks.
1274You may also drag the limit lines to the desired location or place them by a
1275left mouse click on a data point for the lower limit or a right click on a data
1276point for the upper limit.</p>
1277
1278<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1279 id="_x0000_i1050" type="#_x0000_t75" style='width:226.5pt;height:123.75pt;
1280 visibility:visible;mso-wrap-style:square'>
1281 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1282</v:shape><![endif]--><![if !vml]><img border=0 width=302 height=165
1283src="Fit%20Peaks_files/image003.png" v:shapes="_x0000_i1050"><![endif]></span></p>
1284
1285<h2>Step 3: Determine Peak Positions</h2>
1286
1287<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1288auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1289style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1290style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1291on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1292mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1293Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> item in the <b
1294style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1295mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1296Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. This
1297creates an empty window of peak positions (the <b style='mso-bidi-font-weight:
1298normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1299minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1300mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this point
1301it is wise to zoom in on the data that will be used for indexing. </p>
1302
1303<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1304auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1305style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1306style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1307on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1308 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:21.75pt;
1309 height:18.75pt;visibility:visible;mso-wrap-style:square'>
1310 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1311  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1312</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
1313src="Fit%20Peaks_files/image029.jpg" v:shapes="Picture_x0020_4"><![endif]></span>,
1314then press the left mouse in one corner of the region to be used; holding the
1315mouse button down, drag over the region to the opposite corner; a box will be
1316drawn over the region to be zoomed. </p>
1317
1318<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1319auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1320style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1321style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1322style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
1323style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
1324 o:spid="_x0000_i1048" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
1325 visibility:visible;mso-wrap-style:square'>
1326 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1327  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1328</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
1329src="Fit%20Peaks_files/image030.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
1330style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
1331
1332<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1333auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1334style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1335style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1336<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1337mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1338in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
1340window select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1341"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1342minor-latin'>Auto search</span></b>. The plot window will immediately show that
1343all peaks were picked with a blue vertical line on each one</p>
1344
1345<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1346auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_27"
1347 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;
1348 visibility:visible;mso-wrap-style:square'>
1349 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
1350</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1351src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
1352
1353<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1354auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1355normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1356minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1357mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of
1358increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1359
1360<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1361auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29"
1362 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
1363 visibility:visible;mso-wrap-style:square'>
1364 <v:imagedata src="Fit%20Peaks_files/image031.png" o:title=""/>
1365</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1366src="Fit%20Peaks_files/image031.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1367
1368<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1369will be 20+ peaks in this example. You should examine both the list and the
1370plot to be sure the auto search did not pick a peak twice (quite rarely) or
1371skip a peak or shoulder. You can add a peak to the list by pressing the left
1372mouse button with the pointer on a data point at the peak top or shoulder; be
1373sure the zoom/shift buttons are off. You may drag a peak position as needed. A
1374position may be deleted with a right click with the mouse on the blue line. You
1375can also delete a peak by selecting the row in the table; it will be
1376highlighted in blue. Then press the <b style='mso-bidi-font-weight:normal'><span
1377style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1378mso-hansi-theme-font:minor-latin'>Delete</span></b> key; it will be removed
1379from the table and the plot. The list will always show the peaks sorted by
1380position. When done you should have 20 unique peak positions.</p>
1381
1382<h2>Step 4: Refine Peak Positions</h2>
1383
1384<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1385refinement and then adding parameters to complete the fitting,</p>
1386
1387<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1388style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1389style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1390the peak intensities and the background. These parameters have their refinement
1391flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1392normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1393minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1394mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span>
1395</span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family:
1396"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1397minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak
1398List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use
1399the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1400mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1401Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item
1402in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1403mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1404Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window;
1405that it to be used for <span class=SpellE>Rietveld</span>/Pawley refinements.
1406You will be asked to save the current project before the fit will proceed;
1407change directory if desired and provide a suitable name (we assume <b
1408style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1409mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1410Calibri;mso-bidi-theme-font:minor-latin'>LaB6</span></b>). A window will show
1411the progress of the refinement and will close when the least-squares fit <span
1412class=GramE>is</span> complete (usually very fast). The plot is updated with
1413the fit, the peak list window is updated with the new peak values and a summary
1414of the refinement is shown on the console window as well.</p>
1415
1416<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1417 id="Picture_x0020_8" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1418 height:450pt;visibility:visible;mso-wrap-style:square'>
1419 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1420</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1421src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1422
1423<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1424 id="Picture_x0020_24" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:401.25pt;
1425 height:262.5pt;visibility:visible;mso-wrap-style:square'>
1426 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
1427</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1428src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1429
1430<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1431style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1432style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1433add refinement of the peak positions. This can be done by clicking on all the
1434refinement flags for the individual peaks or it is possible to set them all at
1435the same time using this recipe: </p>
1436
1437<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1438auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1439style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1440style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1441class=GramE>single-click</span> on any value in the table to select it, for
1442example the first peak position. A black box appears around the value. </p>
1443
1444<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1445text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1446style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1447style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1448class=GramE>single-click</span> on the <b style='mso-bidi-font-weight:normal'><span
1449style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1450mso-hansi-theme-font:minor-latin'>refine</span></b> label above the peak
1451position check-boxes. The entire column of checkboxes is highlighted in blue.
1452Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1454Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
1455refinement flags (<b style='mso-bidi-font-weight:normal'><span
1456style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1457mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1458minor-latin'>n</span></b> would turn them off).</p>
1459
1460<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1461the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1462mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1463Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
1464menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1465"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1466minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak
1467List</span></b> window.</p>
1468
1469<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1470refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1471performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1472width) and/or gamma (<span class=SpellE>Lorentzian</span> width) for individual
1473peaks. &nbsp;To do this, click the refinement flags for sigma and/or gamma in
1474the Peak List window. &nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the
1475LS&nbsp;refinement of&nbsp;peak widths can be&nbsp;constrained to&nbsp;follow
1476an instrumental broadening equation as described below.&nbsp;Note - one cannot
1477refine ALL peak widths using both individual&nbsp;sigma &amp; gamma&nbsp;values
1478AND&nbsp;instrumental broadening terms at the same time.<b style='mso-bidi-font-weight:
1479normal'>&nbsp;</b><o:p></o:p></span></p>
1480
1481<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1482"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1483to an instrumental broadening equation, first<b> s</b></span>elect the <b
1484style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1485mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1486Calibri;mso-bidi-theme-font:minor-latin'>Instrumental Parameters</span></b>
1487item in the data tree. This opens a window for peak profile terms<b> </b><span
1488style='mso-bidi-font-weight:bold'>and also creates a new plot
1489window&nbsp;showing the instrument profile resolution curve.</span></p>
1490
1491<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1492 id="Picture_x0020_30" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:419.25pt;
1493 height:183.75pt;visibility:visible;mso-wrap-style:square'>
1494 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1495</v:shape><![endif]--><![if !vml]><img border=0 width=559 height=245
1496src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1497
1498<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1499corresponding to the values of the Gaussian U, V, W, <span class=SpellE>Lorentzian</span>
1500X &amp; Y coefficients; ‘+’ marks show the individual values based on the sig
1501&amp; gam values for the peaks in Peak List. Select the refine flag checkbox
1502for Gaussian <b style='mso-bidi-font-weight:normal'><span style='font-family:
1503"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1504minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>,
1505<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1506mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1507Calibri;mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
1508normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1509minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1510mso-bidi-theme-font:minor-latin'>W</span></b>, and <span class=SpellE>Lorentzian</span>
1511<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1512mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1513Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
1514normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1515minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1516mso-bidi-theme-font:minor-latin'>Y</span></b>. </p>
1517
1518<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1519style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1520style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1521repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1522style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1523mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1524minor-latin'>Peak List</span></b> item in the data tree and then refine using
1525the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1526mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1527Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
1528menu item. At this point a good fit should be seen by zooming in on individual
1529peaks. For example see </p>
1530
1531<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1532 id="Picture_x0020_11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1533 height:450pt;visibility:visible;mso-wrap-style:square'>
1534 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
1535</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1536src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1537
1538<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to the
1539right of the peak top. This is a consequence of the peak asymmetry arising from
1540axial divergence in the <span class=SpellE>diffractometer</span>. The <span
1541class=SpellE>Rwp</span> is ~6% as shown on the console window. Again the <b
1542style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1543mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1544Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all
1545updated with new values and those in <b style='mso-bidi-font-weight:normal'><span
1546style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1547mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1548minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1549
1550<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1551
1552<p class=MsoNormal>A separate list of peaks is kept for use in <span
1553class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1554normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1555minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1556mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data
1557tree. In the initially empty window created by this action, use menu item <b
1558style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1559mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1560Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load/Reload</span></b>
1561to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1562style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1563mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1564minor-latin'>Peak List</span></b>.</p>
1565
1566<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1567 id="Picture_x0020_26" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:367.5pt;
1568 height:225pt;visibility:visible;mso-wrap-style:square'>
1569 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1570</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
1571src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1572
1573<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1574may choose to not use a fitted peak (e.g. if suspected it is from a
1575contaminant).</p>
1576
1577<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
1578
1579<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1580style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1581mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1582minor-latin'>Unit Cells List</span></b> data item. This brings up a window for
1583indexing and cell refinement options</p>
1584
1585<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1586 id="Picture_x0020_13" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:527.25pt;
1587 height:204pt;visibility:visible;mso-wrap-style:square'>
1588 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
1589</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
1590src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1591
1592<p class=MsoNormal>For the most rapid search (since we know the right answer),
1593select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1594mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1595Calibri;mso-bidi-theme-font:minor-latin'>Cubic-P</span></b> and launch the
1596search using menu item <b style='mso-bidi-font-weight:normal'><span
1597style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1598mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1599minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and
1600the console shows a running list of possible cells as they are found; the
1601sorted by M20 list of possible matching cells is shown in the <b
1602style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1603mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1604Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
1605
1606<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1607 id="Picture_x0020_28" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:527.25pt;
1608 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1609 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1610</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1611src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1612
1613<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
1614
1615<p class=MsoNormal>Review the list of cells associated with the <b
1616style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1617mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1618Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> data item.
1619Note that as one selects a unit cell, the generated reflections for that cell
1620are shown in the plot with dashed red lines. Sliding the cursor over these
1621lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
1622for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å
1623generates very many lines with no corresponding peaks (NB: this solution might
1624not always show up!)</p>
1625
1626<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1627 id="Picture_x0020_38" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1628 height:450pt;visibility:visible;mso-wrap-style:square'>
1629 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1630</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1631src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_38"><![endif]></span><span
1632style='mso-spacerun:yes'> </span></p>
1633
1634<p class=MsoNormal><span class=GramE>while</span> the (M20~600) cell with
1635a=2.93932 Å generates not enough lines to match all the peaks</p>
1636
1637<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1638 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1639 height:450pt;visibility:visible;mso-wrap-style:square'>
1640 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
1641</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1642src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
1643
1644<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
1645
1646<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1647indexes all peaks with almost a perfect fit to the peak positions (compare dashed
1648red lines to solid blue ones). Import the cell information using the <b
1649style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1651Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b>
1652menu option. Then optimize the cell by refining the lattice parameters and the
1653two-theta zero: click on the refine checkbox next to the <b style='mso-bidi-font-weight:
1654normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1655minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1656mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then 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/Refine Cell</span></b>
1660menu option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
1661parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
1662certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
1663style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1664mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1665Calibri;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
1666positions </span></b>button to update the plot including the refined <b
1667style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1668mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1669Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
1670hardly anything happens!). <span style='mso-spacerun:yes'> </span></p>
1671
1672<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1673 id="Picture_x0020_17" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;
1674 height:334.5pt;visibility:visible;mso-wrap-style:square'>
1675 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1676</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
1677src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1678
1679<p class=MsoNormal>Notice that a new entry heads the list in the <b
1680style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1681mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1682Calibri;mso-bidi-theme-font:minor-latin'>Indexing Result</span></b> section of
1683the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1684mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1685Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine</span></b>
1686window with an improved M20(~3600) and a new value for <b style='mso-bidi-font-weight:
1687normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1688minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1689mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown. NB: the <b
1690style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1691mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
1692class=SpellE>hkl</span> positions</span></b> button has an additional use; you
1693can enter the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1694style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1695mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b style='mso-bidi-font-weight:
1696normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1697minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>, <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'>Space group</span></b>
1700&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1701mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
1702for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
1703style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1704mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
1705will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
1706style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1707mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
1708useful to identify e.g. a second phase in your pattern.</p>
1709
1710<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
1711normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1712minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1713mso-bidi-theme-font:minor-latin'>Cell Index/Refine/New phase</span></b> menu
1714option allows one to create a phase with these lattice parameters in the data
1715tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
1716"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1717minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
1718style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
1719creates the tree item <b style='mso-bidi-font-weight:normal'><span
1720style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1721mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1722minor-latin'>Phases</span></b> (if it wasn’t already present). This new phase
1723can be used in future analysis (e.g. <span class=SpellE>Rietveld</span> or
1724Pawley refinement).</p>
1725
1726<p class=MsoNormal>To continue with the second part of this exercise, select
1727the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
1728"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1729minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/New
1730project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1731style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1732mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1733minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
1734the current project saved; if <span class=GramE><b style='mso-bidi-font-weight:
1735normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1736minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1737mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the peak
1738fitting/indexing &amp; cell refinement results will be saved to the <b
1739style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1740mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1741Calibri;mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
1742style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1743mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1744Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will
1745remain as it was when created at Step 4 above.</p>
1746
1747<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
1748class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
1749style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
1750
1751<p class=MsoNormal>In this exercise we will fit peaks and index them for the
1752new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
1753(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
1754data were also collected on 11BM-B at APS. The unit cell is monoclinic so it is
1755a more substantial test of the indexing capability of GSAS-II.</p>
1756
1757<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1758
1759<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1760style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1761mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1762minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a
1763corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1764style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1765mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1766minor-latin'>prm</span></b></span> file. Load them in &amp; the plot is</p>
1767
1768<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1769 id="Picture_x0020_18" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
1770 height:450pt;visibility:visible;mso-wrap-style:square'>
1771 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1772</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1773src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
1774
1775<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
1776lower part of the pattern.</p>
1777
1778<h2>Step 2 Set limits</h2>
1779
1780<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
1781style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1782mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1783minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:normal'><span
1784style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1785mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1786minor-latin'>9</span></b>.</p>
1787
1788<h2>Step 3 Pick peaks</h2>
1789
1790<p class=MsoNormal>Pick all peaks you can see between the limits (including the
1791small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
1792"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1793minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
1794peaks by left-clicking on a data point near the top of the peak. Peak positions
1795can be moved by dragging the peak line and peaks can be deleted by
1796right-clicking on them. This only works when the zoom and reposition modes
1797(below) are not selected. Also note some peaks have shoulders most notably at
17985.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
1799deg. I skipped – it might be from a second phase? We’ll see later).</p>
1800
1801<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1802 id="Picture_x0020_19" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
1803 height:450pt;visibility:visible;mso-wrap-style:square'>
1804 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
1805</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1806src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_19"><![endif]></span><br
1807clear=all style='mso-special-character:line-break'>
1808</p>
1809
1810<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
1811
1812<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example above,
1813refine the peaks and the profile shape parameters in <b style='mso-bidi-font-weight:
1814normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1815minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1816mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You will be
1817asked for a project file name at the first refinement (I used ‘<span
1818class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1819"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1820minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
1821style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1822mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1823Calibri;mso-bidi-theme-font:minor-latin'>’</span></b>). In the end my
1824refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do
1825show some discrepancy as the sample is more complex than the simple <b
1826style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1827mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1828Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1829normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1830minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1831mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
1832normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1833minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1834mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
1835normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1836minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1837mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
1838normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1839minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1840mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
1841no peaks drift away during refinement (one weak one at ~6.67 is particularly
1842troublesome). However, this is good enough to proceed.</p>
1843
1844<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1845
1846<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
1847style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1848mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1849minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
1850normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1851minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1852mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
1853
1854<h2><span class=GramE>Step 6.</span> Index the cell</h2>
1855
1856<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic.
1857In a real world case we wouldn’t know this and we would have to try each <span
1858class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
1859time to go through all the bad cases.</p>
1860
1861<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1862style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1863mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1864minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
1865normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1866minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1867mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
1868<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1869mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1870Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
1871Progress will be much slower and suitable results will be slow in coming so be
1872patient. Watch the console window; the right answer will have an obviously
1873large M20 (~380) and a volume of ~594Å<sup>3</sup> (10<sup>th</sup> column of
1874console display). Once this is seen (it may take more than one try to get this)
1875you can stop the indexing search by pressing <b style='mso-bidi-font-weight:
1876normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1877minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1878mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window.
1879Notice the ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
1880"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1881minor-latin'>keep</span></b>’ column; this allows you to keep some solutions
1882from one indexing run to the next. It may take more than one press to fully
1883stop it. My result was </p>
1884
1885<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1886 id="Picture_x0020_20" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
1887 height:450pt;visibility:visible;mso-wrap-style:square'>
1888 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1889</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1890src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_20"><![endif]><!--[if gte vml 1]><v:shape
1891 id="Picture_x0020_21" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;
1892 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1893 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
1894</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1895src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1896
1897<p class=MsoNormal>Notice other equally good M20 results with different
1898volumes; other solutions may be obtained as you keep trying the indexing. Be
1899sure to use <b style='mso-bidi-font-weight:normal'><span style='font-family:
1900"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1901minor-latin'>Keep</span></b> to keep good ones as you try new indexing runs.
1902The best solution is the one with the smaller volume and &#946; &gt; 90 deg.
1903The plot shows every peak indexed including a weak peak not selected for the
1904peak fitting, although the weak peak at 2<span style='font-family:Symbol;
1905mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1906symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
1907wasn’t indexed. I presume that is a contaminant. Copy the best cell and try to
1908refine it along with the <b style='mso-bidi-font-weight:normal'><span
1909style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1910mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I obtained an
1911improved M20 ~444 and slightly different lattice parameters. Try different
1912space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
1913style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1914mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
1915each time to see which lines vanish. By sliding the cursor over the index lines
1916without any visible peak you can see that the missing ones are 010, 100, 001,
1917110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
1918accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
1919space group P2<sub>1</sub>/n. Armed with this information you can <b
1920style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1921mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1922Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
1923indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
1924style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1925mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1926minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
1927normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1928minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
1929the GSAS-II data tree.</p>
1930
1931<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1932 id="Picture_x0020_36" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:542.25pt;
1933 height:356.25pt;visibility:visible;mso-wrap-style:square'>
1934 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1935</v:shape><![endif]--><![if !vml]><img border=0 width=723 height=475
1936src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_36"><![endif]></span><span
1937style='mso-spacerun:yes'> </span></p>
1938
1939<p class=MsoNormal>Notice that the lattice parameters and space group have been
1940set for you. If you set the space group here a dialog box will appear.</p>
1941
1942<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1943 id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:333.75pt;
1944 height:209.25pt;visibility:visible;mso-wrap-style:square'>
1945 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
1946</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
1947src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1948
1949<p class=MsoNormal>This concludes this exercise; <span class=GramE><b
1950style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1951mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1952Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project file
1953as it is needed for the <b style='mso-bidi-font-weight:normal'><span
1954style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1955mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1956minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
1957exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
1958style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1959mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1960minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
1961
1962<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
1963in GSAS-II </h1>
1964
1965<p class=MsoNormal>In this exercise we will fit peaks and index them for
1966sucrose in preparation for a charge flipping exercise. If continuing from the
1967previous indexing example do <b style='mso-bidi-font-weight:normal'><span
1968style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1969mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
1970GSAS-II data tree menu; you will be asked if you wish to save the old project.
1971The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
1972is a more substantial test of the indexing capability of GSAS-II.</p>
1973
1974<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1975
1976<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1977style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1978mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1979minor-latin'>\Exercises\sucrose\11bmb_8716.fxye</span></b>; it has a
1980corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1981style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1982mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1983minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under
1984acetone. <span class=GramE>The other <span class=SpellE><b style='mso-bidi-font-weight:
1985normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1986minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in
1987this directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
1988"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1989minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X powdered sugar used
1990“as is” out of the box.</span> Load the <b style='mso-bidi-font-weight:normal'><span
1991style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1992mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the plot is</p>
1993
1994<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1995 id="Picture_x0020_31" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1996 height:450pt;visibility:visible;mso-wrap-style:square'>
1997 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1998</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1999src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
2000
2001<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2002lower part of the pattern; I’ve also chosen to plot the square root of the
2003intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2004"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2005minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2006
2007<h2>Step 2 Set limits</h2>
2008
2009<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2010style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2011mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2012minor-latin'>2</span></b> and <b style='mso-bidi-font-weight:normal'><span
2013style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2014mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2015minor-latin'>8</span></b>.</p>
2016
2017<h2>Step 3 Pick peaks</h2>
2018
2019<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2020small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2021"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2022minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2023peaks by left-clicking on a data point near the top of the peak. Peak positions
2024can be moved by dragging the peak line and peaks can be deleted by
2025right-clicking on them. This only works when the zoom and reposition modes
2026(below) are not selected. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2027that should be added to the list. I skipped a couple of very weak peaks; the total
2028list has &gt;28 peaks.</p>
2029
2030<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2031 id="Picture_x0020_32" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
2032 height:450pt;visibility:visible;mso-wrap-style:square'>
2033 <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/>
2034</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2035src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_32"><![endif]></span><br
2036clear=all style='mso-special-character:line-break'>
2037</p>
2038
2039<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
2040
2041<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2042kryptonite examples above, refine the peaks and the profile shape parameters in
2043<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2044mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2045Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
2046will be asked for a project file name at the first refinement (I used ‘<b
2047style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2048mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2049Calibri;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>). In the end my
2050refinement converged at <span class=SpellE>Rwp</span>=7.15% and some peaks do
2051show some discrepancy as the sample is more complex than the simple <b
2052style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2053mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2054Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2055normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2056minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2057mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
2058normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2059minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2060mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
2061normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2062minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2063mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
2064normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2065minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2066mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
2067no peaks drift away during refinement. However, this is good enough to proceed.</p>
2068
2069<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
2070
2071<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2072style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2073mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2074minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
2075normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2076minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2077mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
2078
2079<h2><span class=GramE>Step 6.</span> Index the cell</h2>
2080
2081<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2082In a real world case we wouldn’t know this and we would have to try each <span
2083class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2084time to go through all the bad cases.</p>
2085
2086<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2087style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2088mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2089minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
2090normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2091minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2092mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
2093<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2094mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2095Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
2096Progress will be much slower than for LaB<sub>6</sub> but oddly much faster
2097than for kryptonite and suitable results may appear almost immediately. Watch
2098the console window; the right answer will have an obviously large M20 (~900)
2099and a volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display).
2100Once this is seen (it may take more than one try to get this) you can stop the
2101indexing search by pressing <b style='mso-bidi-font-weight:normal'><span
2102style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2103mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2104minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2105style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2106some solutions from one indexing run to the next. It may take more than one
2107press to fully stop it. My result was </p>
2108
2109<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2110 id="Picture_x0020_33" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:527.25pt;
2111 height:376.5pt;visibility:visible;mso-wrap-style:square'>
2112 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
2113</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
2114src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_33"><![endif]><!--[if gte vml 1]><v:shape
2115 id="Picture_x0020_34" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2116 height:450pt;visibility:visible;mso-wrap-style:square'>
2117 <v:imagedata src="Fit%20Peaks_files/image027.png" o:title=""/>
2118</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2119src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
2120
2121<p class=MsoNormal>Notice there may be other equally good M20 results with
2122different volumes; still other solutions may be obtained as you keep trying the
2123indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2124style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2125mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2126new indexing runs. The best solution is the one with the smaller volume and
2127&#946; &gt; 90 deg. The plot shows every peak indexed including the weak peaks
2128not selected for the peak fitting. Copy the best cell and try to refine it
2129along with the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2130"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2131minor-latin'>Zero offset</span></b>. I obtained an improved M20 ~1257 and
2132slightly different lattice parameters. Try different space groups, pressing the
2133<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2134mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show <span
2135class=SpellE>hkl</span> positions</span></b> each time to see which lines
2136vanish. The correct space group is P2<sub>1</sub>. Armed with this information
2137you can <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2138mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2139Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
2140indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
2141style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2142mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2143minor-latin'>sucrose</span></b>) and select <b style='mso-bidi-font-weight:
2144normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2145minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b> from
2146the GSAS-II data tree.</p>
2147
2148<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2149 id="Picture_x0020_35" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:542.25pt;
2150 height:351pt;visibility:visible;mso-wrap-style:square'>
2151 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2152</v:shape><![endif]--><![if !vml]><img border=0 width=723 height=468
2153src="Fit%20Peaks_files/image028.png" v:shapes="Picture_x0020_35"><![endif]></span><span
2154style='mso-spacerun:yes'> </span></p>
2155
2156<p class=MsoNormal>Notice that the lattice parameters and space group have been
2157set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2158style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2159mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2160minor-latin'>Save</span></b> the project file as it is needed for the sucrose <b
2161style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2162mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2163Calibri;mso-bidi-theme-font:minor-latin'><a
2164href="Charge%20Flipping%20-%20sucrose.htm">Charge Flipping</a></span></b>
2165exercise. The features of the <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'>Phase Data</span></b> window will be presented in other exercises.</p>
2169
2170<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2171
2172</div>
2173
2174</body>
2175
2176</html>
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