source: trunk/help/Fit Peaks.htm @ 602

Last change on this file since 602 was 602, checked in by vondreele, 10 years ago
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  • Property svn:mime-type set to text/html
File size: 85.2 KB
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385        mso-outline-level:1;
386        font-size:24.0pt;
387        font-family:"Times New Roman","serif";
388        mso-fareast-font-family:"Times New Roman";
389        mso-fareast-theme-font:minor-fareast;
390        font-weight:bold;}
391h2
392        {mso-style-noshow:yes;
393        mso-style-priority:9;
394        mso-style-qformat:yes;
395        mso-style-link:"Heading 2 Char";
396        mso-margin-top-alt:auto;
397        margin-right:0in;
398        mso-margin-bottom-alt:auto;
399        margin-left:0in;
400        mso-pagination:widow-orphan;
401        mso-outline-level:2;
402        font-size:18.0pt;
403        font-family:"Times New Roman","serif";
404        mso-fareast-font-family:"Times New Roman";
405        mso-fareast-theme-font:minor-fareast;
406        font-weight:bold;}
407h3
408        {mso-style-noshow:yes;
409        mso-style-priority:9;
410        mso-style-qformat:yes;
411        mso-style-link:"Heading 3 Char";
412        mso-margin-top-alt:auto;
413        margin-right:0in;
414        mso-margin-bottom-alt:auto;
415        margin-left:0in;
416        mso-pagination:widow-orphan;
417        mso-outline-level:3;
418        font-size:13.5pt;
419        font-family:"Times New Roman","serif";
420        mso-fareast-font-family:"Times New Roman";
421        mso-fareast-theme-font:minor-fareast;
422        font-weight:bold;}
423h4
424        {mso-style-noshow:yes;
425        mso-style-priority:9;
426        mso-style-qformat:yes;
427        mso-style-link:"Heading 4 Char";
428        mso-style-next:Normal;
429        margin-top:10.0pt;
430        margin-right:0in;
431        margin-bottom:0in;
432        margin-left:0in;
433        margin-bottom:.0001pt;
434        mso-pagination:widow-orphan lines-together;
435        page-break-after:avoid;
436        mso-outline-level:4;
437        font-size:13.0pt;
438        font-family:"Cambria","serif";
439        mso-ascii-font-family:Cambria;
440        mso-ascii-theme-font:major-latin;
441        mso-fareast-font-family:"Times New Roman";
442        mso-fareast-theme-font:major-fareast;
443        mso-hansi-font-family:Cambria;
444        mso-hansi-theme-font:major-latin;
445        mso-bidi-font-family:"Times New Roman";
446        mso-bidi-theme-font:major-bidi;
447        color:#4F81BD;
448        mso-themecolor:accent1;
449        font-weight:bold;
450        font-style:italic;}
451h5
452        {mso-style-noshow:yes;
453        mso-style-priority:9;
454        mso-style-qformat:yes;
455        mso-style-link:"Heading 5 Char";
456        mso-margin-top-alt:auto;
457        margin-right:0in;
458        mso-margin-bottom-alt:auto;
459        margin-left:0in;
460        mso-pagination:widow-orphan;
461        mso-outline-level:5;
462        font-size:12.0pt;
463        font-family:"Times New Roman","serif";
464        mso-fareast-font-family:"Times New Roman";
465        mso-fareast-theme-font:minor-fareast;
466        color:#4F4FFF;
467        font-weight:bold;}
468p.MsoTitle, li.MsoTitle, div.MsoTitle
469        {mso-style-noshow:yes;
470        mso-style-priority:10;
471        mso-style-unhide:no;
472        mso-style-qformat:yes;
473        mso-style-link:"Title Char";
474        mso-style-next:Normal;
475        margin-top:0in;
476        margin-right:0in;
477        margin-bottom:15.0pt;
478        margin-left:0in;
479        mso-add-space:auto;
480        mso-pagination:widow-orphan;
481        border:none;
482        mso-border-bottom-alt:solid #4F81BD 1.0pt;
483        mso-border-bottom-themecolor:accent1;
484        padding:0in;
485        mso-padding-alt:0in 0in 4.0pt 0in;
486        font-size:26.0pt;
487        font-family:"Cambria","serif";
488        mso-ascii-font-family:Cambria;
489        mso-ascii-theme-font:major-latin;
490        mso-fareast-font-family:"Times New Roman";
491        mso-fareast-theme-font:major-fareast;
492        mso-hansi-font-family:Cambria;
493        mso-hansi-theme-font:major-latin;
494        mso-bidi-font-family:"Times New Roman";
495        mso-bidi-theme-font:major-bidi;
496        color:#17365D;
497        mso-themecolor:text2;
498        mso-themeshade:191;
499        letter-spacing:.25pt;
500        mso-font-kerning:14.0pt;}
501p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
502        {mso-style-noshow:yes;
503        mso-style-priority:10;
504        mso-style-unhide:no;
505        mso-style-qformat:yes;
506        mso-style-link:"Title Char";
507        mso-style-next:Normal;
508        mso-style-type:export-only;
509        margin:0in;
510        margin-bottom:.0001pt;
511        mso-add-space:auto;
512        mso-pagination:widow-orphan;
513        border:none;
514        mso-border-bottom-alt:solid #4F81BD 1.0pt;
515        mso-border-bottom-themecolor:accent1;
516        padding:0in;
517        mso-padding-alt:0in 0in 4.0pt 0in;
518        font-size:26.0pt;
519        font-family:"Cambria","serif";
520        mso-ascii-font-family:Cambria;
521        mso-ascii-theme-font:major-latin;
522        mso-fareast-font-family:"Times New Roman";
523        mso-fareast-theme-font:major-fareast;
524        mso-hansi-font-family:Cambria;
525        mso-hansi-theme-font:major-latin;
526        mso-bidi-font-family:"Times New Roman";
527        mso-bidi-theme-font:major-bidi;
528        color:#17365D;
529        mso-themecolor:text2;
530        mso-themeshade:191;
531        letter-spacing:.25pt;
532        mso-font-kerning:14.0pt;}
533p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
534        {mso-style-noshow:yes;
535        mso-style-priority:10;
536        mso-style-unhide:no;
537        mso-style-qformat:yes;
538        mso-style-link:"Title Char";
539        mso-style-next:Normal;
540        mso-style-type:export-only;
541        margin:0in;
542        margin-bottom:.0001pt;
543        mso-add-space:auto;
544        mso-pagination:widow-orphan;
545        border:none;
546        mso-border-bottom-alt:solid #4F81BD 1.0pt;
547        mso-border-bottom-themecolor:accent1;
548        padding:0in;
549        mso-padding-alt:0in 0in 4.0pt 0in;
550        font-size:26.0pt;
551        font-family:"Cambria","serif";
552        mso-ascii-font-family:Cambria;
553        mso-ascii-theme-font:major-latin;
554        mso-fareast-font-family:"Times New Roman";
555        mso-fareast-theme-font:major-fareast;
556        mso-hansi-font-family:Cambria;
557        mso-hansi-theme-font:major-latin;
558        mso-bidi-font-family:"Times New Roman";
559        mso-bidi-theme-font:major-bidi;
560        color:#17365D;
561        mso-themecolor:text2;
562        mso-themeshade:191;
563        letter-spacing:.25pt;
564        mso-font-kerning:14.0pt;}
565p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
566        {mso-style-noshow:yes;
567        mso-style-priority:10;
568        mso-style-unhide:no;
569        mso-style-qformat:yes;
570        mso-style-link:"Title Char";
571        mso-style-next:Normal;
572        mso-style-type:export-only;
573        margin-top:0in;
574        margin-right:0in;
575        margin-bottom:15.0pt;
576        margin-left:0in;
577        mso-add-space:auto;
578        mso-pagination:widow-orphan;
579        border:none;
580        mso-border-bottom-alt:solid #4F81BD 1.0pt;
581        mso-border-bottom-themecolor:accent1;
582        padding:0in;
583        mso-padding-alt:0in 0in 4.0pt 0in;
584        font-size:26.0pt;
585        font-family:"Cambria","serif";
586        mso-ascii-font-family:Cambria;
587        mso-ascii-theme-font:major-latin;
588        mso-fareast-font-family:"Times New Roman";
589        mso-fareast-theme-font:major-fareast;
590        mso-hansi-font-family:Cambria;
591        mso-hansi-theme-font:major-latin;
592        mso-bidi-font-family:"Times New Roman";
593        mso-bidi-theme-font:major-bidi;
594        color:#17365D;
595        mso-themecolor:text2;
596        mso-themeshade:191;
597        letter-spacing:.25pt;
598        mso-font-kerning:14.0pt;}
599a:link, span.MsoHyperlink
600        {mso-style-noshow:yes;
601        mso-style-priority:99;
602        color:blue;
603        text-decoration:underline;
604        text-underline:single;}
605a:visited, span.MsoHyperlinkFollowed
606        {mso-style-noshow:yes;
607        mso-style-priority:99;
608        color:purple;
609        text-decoration:underline;
610        text-underline:single;}
611p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
612        {mso-style-noshow:yes;
613        mso-style-priority:99;
614        mso-style-link:"Document Map Char";
615        margin:0in;
616        margin-bottom:.0001pt;
617        mso-pagination:widow-orphan;
618        font-size:8.0pt;
619        font-family:"Tahoma","sans-serif";
620        mso-fareast-font-family:"Times New Roman";
621        mso-fareast-theme-font:minor-fareast;}
622p
623        {mso-style-noshow:yes;
624        mso-style-priority:99;
625        mso-margin-top-alt:auto;
626        margin-right:0in;
627        mso-margin-bottom-alt:auto;
628        margin-left:0in;
629        mso-pagination:widow-orphan;
630        font-size:12.0pt;
631        font-family:"Times New Roman","serif";
632        mso-fareast-font-family:"Times New Roman";
633        mso-fareast-theme-font:minor-fareast;}
634pre
635        {mso-style-noshow:yes;
636        mso-style-priority:99;
637        mso-style-link:"HTML Preformatted Char";
638        margin:0in;
639        margin-bottom:.0001pt;
640        mso-pagination:widow-orphan;
641        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;
642        font-size:10.0pt;
643        font-family:"Courier New";
644        mso-fareast-font-family:"Times New Roman";}
645p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
646        {mso-style-noshow:yes;
647        mso-style-priority:99;
648        mso-style-link:"Balloon Text Char";
649        margin:0in;
650        margin-bottom:.0001pt;
651        mso-pagination:widow-orphan;
652        font-size:8.0pt;
653        font-family:"Tahoma","sans-serif";
654        mso-fareast-font-family:"Times New Roman";
655        mso-fareast-theme-font:minor-fareast;}
656span.MsoPlaceholderText
657        {mso-style-noshow:yes;
658        mso-style-priority:99;
659        mso-style-unhide:no;
660        color:gray;}
661p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
662        {mso-style-noshow:yes;
663        mso-style-priority:1;
664        mso-style-unhide:no;
665        mso-style-qformat:yes;
666        mso-style-parent:"";
667        margin:0in;
668        margin-bottom:.0001pt;
669        mso-pagination:widow-orphan;
670        font-size:12.0pt;
671        font-family:"Times New Roman","serif";
672        mso-fareast-font-family:"Times New Roman";
673        mso-fareast-theme-font:minor-fareast;}
674p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
675        {mso-style-noshow:yes;
676        mso-style-priority:34;
677        mso-style-unhide:no;
678        mso-style-qformat:yes;
679        margin-top:0in;
680        margin-right:0in;
681        margin-bottom:0in;
682        margin-left:.5in;
683        margin-bottom:.0001pt;
684        mso-add-space:auto;
685        mso-pagination:widow-orphan;
686        font-size:12.0pt;
687        font-family:"Times New Roman","serif";
688        mso-fareast-font-family:"Times New Roman";
689        mso-fareast-theme-font:minor-fareast;}
690p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
691        {mso-style-noshow:yes;
692        mso-style-priority:34;
693        mso-style-unhide:no;
694        mso-style-qformat:yes;
695        mso-style-type:export-only;
696        margin-top:0in;
697        margin-right:0in;
698        margin-bottom:0in;
699        margin-left:.5in;
700        margin-bottom:.0001pt;
701        mso-add-space:auto;
702        mso-pagination:widow-orphan;
703        font-size:12.0pt;
704        font-family:"Times New Roman","serif";
705        mso-fareast-font-family:"Times New Roman";
706        mso-fareast-theme-font:minor-fareast;}
707p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
708        {mso-style-noshow:yes;
709        mso-style-priority:34;
710        mso-style-unhide:no;
711        mso-style-qformat:yes;
712        mso-style-type:export-only;
713        margin-top:0in;
714        margin-right:0in;
715        margin-bottom:0in;
716        margin-left:.5in;
717        margin-bottom:.0001pt;
718        mso-add-space:auto;
719        mso-pagination:widow-orphan;
720        font-size:12.0pt;
721        font-family:"Times New Roman","serif";
722        mso-fareast-font-family:"Times New Roman";
723        mso-fareast-theme-font:minor-fareast;}
724p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
725        {mso-style-noshow:yes;
726        mso-style-priority:34;
727        mso-style-unhide:no;
728        mso-style-qformat:yes;
729        mso-style-type:export-only;
730        margin-top:0in;
731        margin-right:0in;
732        margin-bottom:0in;
733        margin-left:.5in;
734        margin-bottom:.0001pt;
735        mso-add-space:auto;
736        mso-pagination:widow-orphan;
737        font-size:12.0pt;
738        font-family:"Times New Roman","serif";
739        mso-fareast-font-family:"Times New Roman";
740        mso-fareast-theme-font:minor-fareast;}
741span.MsoIntenseReference
742        {mso-style-priority:32;
743        mso-style-unhide:no;
744        mso-style-qformat:yes;
745        font-variant:small-caps;
746        color:#C0504D;
747        mso-themecolor:accent2;
748        letter-spacing:.25pt;
749        font-weight:bold;
750        text-decoration:underline;
751        text-underline:single;}
752span.Heading1Char
753        {mso-style-name:"Heading 1 Char";
754        mso-style-priority:9;
755        mso-style-unhide:no;
756        mso-style-locked:yes;
757        mso-style-link:"Heading 1";
758        mso-ansi-font-size:24.0pt;
759        mso-bidi-font-size:24.0pt;
760        font-family:"Times New Roman","serif";
761        mso-ascii-font-family:"Times New Roman";
762        mso-fareast-font-family:"Times New Roman";
763        mso-fareast-theme-font:minor-fareast;
764        mso-hansi-font-family:"Times New Roman";
765        mso-bidi-font-family:"Times New Roman";
766        mso-font-kerning:18.0pt;
767        font-weight:bold;}
768span.Heading2Char
769        {mso-style-name:"Heading 2 Char";
770        mso-style-noshow:yes;
771        mso-style-priority:9;
772        mso-style-unhide:no;
773        mso-style-locked:yes;
774        mso-style-link:"Heading 2";
775        mso-ansi-font-size:18.0pt;
776        mso-bidi-font-size:18.0pt;
777        font-family:"Times New Roman","serif";
778        mso-ascii-font-family:"Times New Roman";
779        mso-fareast-font-family:"Times New Roman";
780        mso-fareast-theme-font:minor-fareast;
781        mso-hansi-font-family:"Times New Roman";
782        mso-bidi-font-family:"Times New Roman";
783        font-weight:bold;}
784span.Heading3Char
785        {mso-style-name:"Heading 3 Char";
786        mso-style-noshow:yes;
787        mso-style-priority:9;
788        mso-style-unhide:no;
789        mso-style-locked:yes;
790        mso-style-link:"Heading 3";
791        mso-ansi-font-size:13.5pt;
792        mso-bidi-font-size:13.5pt;
793        font-family:"Times New Roman","serif";
794        mso-ascii-font-family:"Times New Roman";
795        mso-fareast-font-family:"Times New Roman";
796        mso-fareast-theme-font:minor-fareast;
797        mso-hansi-font-family:"Times New Roman";
798        mso-bidi-font-family:"Times New Roman";
799        font-weight:bold;}
800span.Heading4Char
801        {mso-style-name:"Heading 4 Char";
802        mso-style-noshow:yes;
803        mso-style-priority:9;
804        mso-style-unhide:no;
805        mso-style-locked:yes;
806        mso-style-link:"Heading 4";
807        mso-ansi-font-size:13.0pt;
808        mso-bidi-font-size:13.0pt;
809        font-family:"Cambria","serif";
810        mso-ascii-font-family:Cambria;
811        mso-ascii-theme-font:major-latin;
812        mso-fareast-font-family:"Times New Roman";
813        mso-fareast-theme-font:major-fareast;
814        mso-hansi-font-family:Cambria;
815        mso-hansi-theme-font:major-latin;
816        mso-bidi-font-family:"Times New Roman";
817        mso-bidi-theme-font:major-bidi;
818        color:#4F81BD;
819        mso-themecolor:accent1;
820        font-weight:bold;
821        font-style:italic;}
822span.Heading5Char
823        {mso-style-name:"Heading 5 Char";
824        mso-style-noshow:yes;
825        mso-style-priority:9;
826        mso-style-unhide:no;
827        mso-style-locked:yes;
828        mso-style-link:"Heading 5";
829        mso-ansi-font-size:12.0pt;
830        mso-bidi-font-size:12.0pt;
831        font-family:"Times New Roman","serif";
832        mso-ascii-font-family:"Times New Roman";
833        mso-fareast-font-family:"Times New Roman";
834        mso-fareast-theme-font:minor-fareast;
835        mso-hansi-font-family:"Times New Roman";
836        mso-bidi-font-family:"Times New Roman";
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1123
1124<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1125
1126<div class=WordSection1>
1127
1128<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1129
1130<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1131cell that matches a set of diffraction peaks -- a process known as
1132auto-indexing. First peaks must be located and optimized and then indexing can
1133be done.</p>
1134
1135<p class=MsoNormal>If you have not done so already, <a
1136href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
1137
1138<h2>Step 1: read in the data file</h2>
1139
1140<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1141style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1142style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1143the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1144mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1145minor-latin'>Data/Read powder data</span></b> menu item to read the data file into
1146the current GSAS-II project. This read option is set to read any of the powder
1147data formats (except neutron TOF time map files) defined for GSAS (angles in <span
1148class=SpellE>centidegrees</span>). It will also read the <span class=SpellE><b
1149style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1150mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1151minor-latin'>xye</span></b></span> format (angles in degrees) used by <span
1152class=SpellE>Topas</span>, etc.<span style='mso-spacerun:yes'>  </span>Change
1153the file directory to <b style='mso-bidi-font-weight:normal'><span
1154style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1155mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Exercises/LaB6</span></b><span
1156style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1157mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> to find the
1158file; you may need to change the file type to <b style='mso-bidi-font-weight:
1159normal'>All files (*.*)</b> to find the desired file.</span></p>
1160
1161<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1162style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1163style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1164the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1165mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1166minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri","sans-serif";
1167mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1168minor-latin'> data</span> file in the first dialog and press <b
1169style='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-theme-font:
1171minor-latin'>Open</span></b>. There will be a Dialog box asking <span
1172class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1173"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1174minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><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-theme-font:
1177minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1178style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1179mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1180minor-latin'>Yes</span></b></span> button to proceed.</p>
1181
1182<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1183style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1184style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1185the <b style='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-theme-font:
1187minor-latin'>11bmb_3844.prm</span></b> instrument parameter file in the second
1188dialog and press <b style='mso-bidi-font-weight:normal'><span style='font-family:
1189"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1190minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>. The 11BM-B
1191instrument processing software automatically produced this file when the
1192corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1193style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1194mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1195file was created from the 12 detector raw data.</p>
1196
1197<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1198style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1199mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1200tree</span></b> window will have several entries </p>
1201
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1227
1228<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1229powder pattern</p>
1230
1231<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1232 id="Picture_x0020_2" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1233 height:450pt;visibility:visible;mso-wrap-style:square'>
1234 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
1235</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1236src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1237
1238<h2>Step 2: Select Limits </h2>
1239
1240<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1241more data than we need, so it is helpful to cut down the range. Click on the <b
1242style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1243mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1244minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
1245style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1246mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1247tree</span></b>. The small window is repainted. Use the <b style='mso-bidi-font-weight:
1248normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1249minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>changed</span></b>
1250row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
1251normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1252minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
1253and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1254style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1255mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1256to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1257mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1258minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:normal'><span
1259style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1260mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1261Notice on the plot that the limit lines have moved to these positions; the
1262green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1263is in a wide gap between peaks. You may also drag the limit lines to the
1264desired location or place them by a left mouse click on a data point for the
1265lower limit or a right click on a data point for the upper limit.</p>
1266
1267<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1268 id="Picture_x0020_4" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:225pt;
1269 height:120pt;visibility:visible;mso-wrap-style:square'>
1270 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1271</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=160
1272src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1273
1274<h2>Step 3: Determine Peak Positions</h2>
1275
1276<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1277auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1278style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1279style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1280on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1281mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1282minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1283normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1284minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1285data tree</span></b>. This creates an empty window of peak positions (the <b
1286style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1287mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1288minor-latin'>Limits</span></b> window is erased). At this point it is wise <span
1289class=GramE>to<span style='mso-spacerun:yes'>  </span>zoom</span> in on the
1290data that will be used for indexing. </p>
1291
1292<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1293auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1294style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1295style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1296on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1297 id="_x0000_i1044" type="#_x0000_t75" style='width:21.75pt;height:18.75pt;
1298 visibility:visible;mso-wrap-style:square'>
1299 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1300  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1301</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
1302src="Fit%20Peaks_files/image005.jpg" v:shapes="_x0000_i1044"><![endif]></span>,
1303then press the left mouse in one corner of the region to be used; holding the
1304mouse button down, drag over the region to the opposite corner; a box will be
1305drawn over the region to be zoomed. </p>
1306
1307<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1308auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1309style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1310style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1311style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
1312style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
1313 o:spid="_x0000_i1043" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
1314 visibility:visible;mso-wrap-style:square'>
1315 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1316  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1317</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
1318src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
1319style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
1320
1321<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1322auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1323style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1324style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Using
1325the left mouse button, click on a data point near the top of each peak to be
1326added to the peak list. It is usually best to start at the upper end of the
1327pattern as the next peak to pick isn’t obscured by the tool tip. As this is
1328done, a vertical blue line is drawn in the plot window<span
1329style='mso-spacerun:yes'>  </span>for each peak selected</p>
1330
1331<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1332auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
1333 o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;height:450pt;
1334 visibility:visible;mso-wrap-style:square'>
1335 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
1336</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1337src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1338
1339<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1340auto'><span class=GramE>and</span> peaks are added to the <b style='mso-bidi-font-weight:
1341normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1342minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1343List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</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_7"
1347 o:spid="_x0000_i1041" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
1348 visibility:visible;mso-wrap-style:square'>
1349 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1350</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1351src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1352
1353<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1354auto'>Note that if peaks are not being added, you probably have not exited zoom
1355mode.</p>
1356
1357<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>Add
1358approximately 20-25 peaks total to the peak list (there will be 20 in this
1359example). Be sure to add the lowest angle peaks that are visible in the plot.
1360You may drag a peak position as needed; be sure the zoom/shift buttons are off.
1361A position may be deleted with a right click with the mouse on the blue line.</p>
1362
1363<h2>Step 4: Refine Peak Positions</h2>
1364
1365<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1366refinement and then adding <span class=GramE>a parameters</span> to complete
1367the fitting,</p>
1368
1369<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1370style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1371style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1372the peak intensities and the background. These parameters have their refinement
1373flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1374normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1375minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1376Fitting/LSQ <span class=SpellE>PeakFit</span> </span></b>on the<b
1377style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1378mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1379minor-latin'> Peak List </span></b>window. Do <b style='mso-bidi-font-weight:
1380normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1381style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1382mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1383menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1384"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1385minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
1386window; that it to be used for Rietveld/Pawley refinements. You will be asked
1387to save the current project before the fit will proceed; change directory if
1388desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1389normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1390minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1391A window will show the progress of the refinement and will close when the
1392least-squares fit <span class=GramE>is</span> complete (usually very fast). The
1393plot is updated with the fit, the peak list window is updated with the new peak
1394values and a summary of the refinement is shown on the console window as well.</p>
1395
1396<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1397 id="Picture_x0020_8" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:525pt;
1398 height:450pt;visibility:visible;mso-wrap-style:square'>
1399 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
1400</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1401src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1402
1403<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1404 id="Picture_x0020_9" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:401.25pt;
1405 height:262.5pt;visibility:visible;mso-wrap-style:square'>
1406 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1407</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1408src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1409
1410<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1411style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1412style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1413add refinement of the peak positions. This can be done by clicking on all the refinement
1414flags for the individual peaks or it is possible to set them all at the same
1415time using this recipe: </p>
1416
1417<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1418auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1419style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1420style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1421class=GramE>single-click</span> on any value in the table to select it, for
1422example the first peak position. A black box appears around the value. If the
1423field if opened for editing (the box turns to blue), select a different item in
1424the table.</p>
1425
1426<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1427text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1428style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1429style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1430class=GramE>double-click</span> on the refine label above the peak position
1431check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
1432style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1433mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1434minor-latin'>y</span></b> key to turn on all refinement flags (<b
1435style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1436mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1437minor-latin'>n</span></b> would turn them off).</p>
1438
1439<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Next, repeat the
1440refinement using the <b style='mso-bidi-font-weight:normal'><span
1441style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1442mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1443Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item in the <b
1444style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1445mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1446minor-latin'>Peak List</span></b> window.</p>
1447
1448<p class=MsoNormal><span style='mso-spacerun:yes'> </span>Now, select peak
1449widths for refinement. This can be done by refining sigma (Gaussian width)
1450and/or gamma (Lorentzian width) for individual peaks, but here we can constrain
1451the peaks to follow an instrumental broadening equation. Select the <b
1452style='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-theme-font:
1454minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
1455opens a window for peak profile terms</p>
1456
1457<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1458 id="Picture_x0020_10" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:422.25pt;
1459 height:154.5pt;visibility:visible;mso-wrap-style:square'>
1460 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
1461</v:shape><![endif]--><![if !vml]><img border=0 width=563 height=206
1462src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
1463
1464<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1465corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1466coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1467values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1468U, V, W, and Lorentzian X, Y. </p>
1469
1470<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1471style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1472style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1473repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1474style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1475mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1476item in the data tree and then refine using the <b style='mso-bidi-font-weight:
1477normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1478minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1479Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item. At this
1480point a good fit should be seen by zooming in on individual peaks. (For example
1481see </p>
1482
1483<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1484 id="Picture_x0020_11" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1485 height:450pt;visibility:visible;mso-wrap-style:square'>
1486 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1487</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1488src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1489
1490<p class=MsoListParagraphCxSpLast>The <span class=SpellE>Rwp</span> is ~6% as
1491shown on the console window. Again the <b style='mso-bidi-font-weight:normal'><span
1492style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1493mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1494entries are all updated with new values and those in <b style='mso-bidi-font-weight:
1495normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1496minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
1497Parameters</span></b> are also updated.</p>
1498
1499<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1500
1501<p class=MsoNormal>A separate list of peaks is kept for use in <span
1502class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1503normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1504minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1505Peak List</span></b> item in the data tree. In the initially empty window
1506created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1507style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1508mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index Peaks
1509Operations/Load</span></b> to copy the fitted peaks from the <b
1510style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1511mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1512minor-latin'>Peak List</span></b>.</p>
1513
1514<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1515 id="Picture_x0020_12" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:367.5pt;
1516 height:225pt;visibility:visible;mso-wrap-style:square'>
1517 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
1518</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
1519src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
1520
1521<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1522may choose to not use a fitted peak (e.g. if suspected as from a contaminant).</p>
1523
1524<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
1525
1526<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1527style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1528mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1529List</span></b> data item. This brings up a window for indexing and cell
1530refinement options</p>
1531
1532<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1533 id="Picture_x0020_13" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:527.25pt;
1534 height:204pt;visibility:visible;mso-wrap-style:square'>
1535 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1536</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
1537src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1538
1539<p class=MsoNormal>For the most rapid search (since we know the right answer),
1540select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1541mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1542minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1543style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1544mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1545minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the
1546console shows a running list of possible cells as they are found; the sorted by
1547M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1548normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1549minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1550Cells List</span></b> window</p>
1551
1552<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1553 id="Picture_x0020_14" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:527.25pt;
1554 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1555 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1556</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1557src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
1558
1559<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
1560
1561<p class=MsoNormal>Review the list of cells associated with the <b
1562style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1563mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1564minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1565unit cell, the generated reflections for that cell are shown in the plot with
1566dashed red lines. Sliding the cursor over these lines shows a small popup
1567window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1568first cell in the list (M20=2961.34) with a=5.87864 Å generates very many lines
1569with no corresponding peaks</p>
1570
1571<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1572 id="Picture_x0020_15" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
1573 height:450pt;visibility:visible;mso-wrap-style:square'>
1574 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
1575</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1576src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_15"><![endif]></span><span
1577style='mso-spacerun:yes'> </span></p>
1578
1579<p class=MsoNormal><span class=GramE>while</span> the (M20=609.02) cell with
1580a=2.93932 Å generates not enough lines to match all the peaks</p>
1581
1582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1583 id="Picture_x0020_16" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1584 height:450pt;visibility:visible;mso-wrap-style:square'>
1585 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1586</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1587src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
1588
1589<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
1590
1591<p class=MsoNormal>Select the cell with M20 = 2961.34 with a = 4.1568 Å. This
1592indexes all peaks with almost a perfect fit to the peak positions (compare
1593dashed red lines to solid blue ones). Import the cell information using the <b
1594style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1595mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1596minor-latin'>Cell Index/Copy Cell</span></b> menu option. Then optimize the
1597cell by refining the lattice parameters and the two-theta zero: click on the
1598refine checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1599style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1600mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1601value and then the <b style='mso-bidi-font-weight:normal'><span
1602style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1603mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1604Index/Refine Cell</span></b> menu option. <span class=GramE>The a</span> cell
1605parameter value shifts from 4.15679 to 4.15684 when zero is refined. Press the <b
1606style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1607mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1608minor-latin'>Show refined <span class=SpellE>hkl</span> positions + Zero offset</span></b>
1609button to update the plot including the refined <b style='mso-bidi-font-weight:
1610normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1611minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero
1612offset</span></b> (in this case hardly anything happens!) </p>
1613
1614<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1615 id="Picture_x0020_17" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:527.25pt;
1616 height:334.5pt;visibility:visible;mso-wrap-style:square'>
1617 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1618</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
1619src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1620
1621<p class=MsoNormal>Notice that a new entry heads the list in the <b
1622style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1623mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1624minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
1625normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1626minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1627Index/Refine</span></b> window with an improved M20(=3614.66) and a new value
1628for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1629mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1630minor-latin'>Zero offset</span></b> is shown.</p>
1631
1632<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
1633normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1634minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1635Index/New phase</span></b> menu option allows one to create a phase with these
1636lattice parameters in the data tree under <b style='mso-bidi-font-weight:normal'><span
1637style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1638mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
1639style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
1640creates the tree item <b style='mso-bidi-font-weight:normal'><span
1641style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1642mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
1643(if it wasn’t already present). This new phase can be used in future analysis
1644(e.g. Rietveld or Pawley refinement).</p>
1645
1646<p class=MsoNormal>To continue with the second part of this exercise, <span
1647class=GramE>do the menu item</span> <b style='mso-bidi-font-weight:normal'><span
1648style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1649mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Close
1650project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1651style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1652mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1653tree </span></b>window. You will be asked if you want it saved; if <span
1654class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1655"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1656minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the
1657peak fitting/indexing &amp; cell refinement results will be saved to the <b
1658style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1659mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1660minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
1661style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1662mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
1663then the file will remain as it was when created at Step 4 above.</p>
1664
1665<h1>2<sup>nd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1666
1667<p class=MsoNormal>In this exercise we will fit peaks and index them for the
1668new mineral <span class=SpellE>jadarite</span> (aka “kryptonite”). The data was
1669also collected on 11BM-B at APS. The unit cell is monoclinic so is a more
1670substantial test of the indexing capability of GSAS-II.</p>
1671
1672<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1673
1674<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1675style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1676mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>\Exercises\<span
1677class=SpellE>krptonite</span>\11bmb_6231.fxye</span></b>; it has a
1678corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1679style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1680mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span>
1681file. Load them in &amp; the plot is</p>
1682
1683<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1684 id="Picture_x0020_18" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:525pt;
1685 height:450pt;visibility:visible;mso-wrap-style:square'>
1686 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
1687</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1688src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
1689
1690<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
1691lower part of the pattern.</p>
1692
1693<h2>Step 2 Set limits</h2>
1694
1695<p class=MsoNormal>Set the limits as 3 and 10.</p>
1696
1697<h2>Step 3 Pick peaks</h2>
1698
1699<p class=MsoNormal>Pick all peaks you can see between the limits (including the
1700small ones). Note some peaks have shoulders most notably at 5.07, 6.04,
17017.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
1702might be from a second phase? We’ll see later).</p>
1703
1704<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1705 id="Picture_x0020_19" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1706 height:450pt;visibility:visible;mso-wrap-style:square'>
1707 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1708</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1709src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
1710
1711<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
1712
1713<p class=MsoNormal>Following the steps above, refine the peaks and the profile
1714shape parameters in Instrument parameters. You will be asked for a project file
1715name at the first refinement (I used ‘<span class=SpellE>jadarite</span>’). In
1716the end my refinement converged at <span class=SpellE>Rwp</span>=13.18% and
1717some peaks do show some discrepancy as the sample is more complex than the
1718simple U, V, W, X, Y model can accommodate. However, this is good enough to
1719proceed.</p>
1720
1721<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1722
1723<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
1724style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1725mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1726in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1727mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1728minor-latin'>Index Peak List</span></b> window.</p>
1729
1730<h2><span class=GramE>Step 6.</span> Index the cell</h2>
1731
1732<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
1733In a real world case we wouldn’t know this and we would have to try each <span
1734class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
1735time to go through all the bad cases.</p>
1736
1737<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1738style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1739mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
1740and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1741mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1742minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
1743style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1744mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1745minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
1746and suitable results will be slow in coming so be patient. Watch the console
1747window; the right answer will have an obviously large M20 (~630) and a volume
1748of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
1749seen (it may take more than one try to get this) you can stop the indexing
1750search by pressing <b style='mso-bidi-font-weight:normal'><span
1751style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1752mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
1753on the progress bar window. It may take more than one press to fully stop it.
1754My result was </p>
1755
1756<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1757 id="Picture_x0020_20" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
1758 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1759 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
1760</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1761src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
1762
1763<p class=MsoNormal>Notice an equally good M20 result with twice the volume. The
1764plot shows every peak indexed including a couple of weak peaks not selected for
1765the peak fitting.</p>
1766
1767<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1768 id="Picture_x0020_21" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
1769 height:450pt;visibility:visible;mso-wrap-style:square'>
1770 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1771</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1772src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1773
1774<p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol;
1775mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1776symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
1777wasn’t indexed. I presume that is a contaminant. By sliding the cursor over the
1778index lines without any visible peak you can see that the missing ones are
1779(010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2, 23-1, 22-2, 141,
1780201,102, 15-1, 112, &amp; 24-1). Many of these are accidental but the 0k0; k&#8800;2n
1781and h0l; h+l&#8800;2n ones characterize the space group P2<sub>1</sub>/n. Armed
1782with this information you can <b style='mso-bidi-font-weight:normal'><span
1783style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1784mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
1785phase</span></b> for the indexed cell (I called it ‘kryptonite’) and set the
1786space group in the Phase Data for kryptonite window.</p>
1787
1788<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1789 id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:597.75pt;
1790 height:214.5pt;visibility:visible;mso-wrap-style:square'>
1791 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
1792</v:shape><![endif]--><![if !vml]><img border=0 width=797 height=286
1793src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1794
1795<p class=MsoNormal>Setting the space group will show a window with some
1796information. Press <b style='mso-bidi-font-weight:normal'><span
1797style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1798mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
1799to close it.</p>
1800
1801<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1802 id="Picture_x0020_23" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:333.75pt;
1803 height:209.25pt;visibility:visible;mso-wrap-style:square'>
1804 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1805</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
1806src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1807
1808<p class=MsoNormal>This concludes this exercise. The features of the Phase Data
1809window will be presented in other exercises.</p>
1810
1811</div>
1812
1813</body>
1814
1815</html>
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