source: trunk/help/Fit Peaks.htm @ 780

Last change on this file since 780 was 780, checked in by vondreele, 10 years ago

fix sph. harm. error - bad acosd in CrsAng?
small detail in G2struct - value of 4*pi.
Start on charge flip tutorial

  • Property svn:keywords set to Author
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File size: 91.3 KB
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382        mso-style-link:"Heading 1 Char";
383        mso-margin-top-alt:auto;
384        margin-right:0in;
385        mso-margin-bottom-alt:auto;
386        margin-left:0in;
387        mso-pagination:widow-orphan;
388        mso-outline-level:1;
389        font-size:24.0pt;
390        font-family:"Times New Roman","serif";
391        mso-fareast-font-family:"Times New Roman";
392        mso-fareast-theme-font:minor-fareast;
393        font-weight:bold;}
394h2
395        {mso-style-noshow:yes;
396        mso-style-priority:9;
397        mso-style-qformat:yes;
398        mso-style-link:"Heading 2 Char";
399        mso-margin-top-alt:auto;
400        margin-right:0in;
401        mso-margin-bottom-alt:auto;
402        margin-left:0in;
403        mso-pagination:widow-orphan;
404        mso-outline-level:2;
405        font-size:18.0pt;
406        font-family:"Times New Roman","serif";
407        mso-fareast-font-family:"Times New Roman";
408        mso-fareast-theme-font:minor-fareast;
409        font-weight:bold;}
410h3
411        {mso-style-noshow:yes;
412        mso-style-priority:9;
413        mso-style-qformat:yes;
414        mso-style-link:"Heading 3 Char";
415        mso-margin-top-alt:auto;
416        margin-right:0in;
417        mso-margin-bottom-alt:auto;
418        margin-left:0in;
419        mso-pagination:widow-orphan;
420        mso-outline-level:3;
421        font-size:13.5pt;
422        font-family:"Times New Roman","serif";
423        mso-fareast-font-family:"Times New Roman";
424        mso-fareast-theme-font:minor-fareast;
425        font-weight:bold;}
426h4
427        {mso-style-noshow:yes;
428        mso-style-priority:9;
429        mso-style-qformat:yes;
430        mso-style-link:"Heading 4 Char";
431        mso-style-next:Normal;
432        margin-top:10.0pt;
433        margin-right:0in;
434        margin-bottom:0in;
435        margin-left:0in;
436        margin-bottom:.0001pt;
437        mso-pagination:widow-orphan lines-together;
438        page-break-after:avoid;
439        mso-outline-level:4;
440        font-size:13.0pt;
441        font-family:"Cambria","serif";
442        mso-ascii-font-family:Cambria;
443        mso-ascii-theme-font:major-latin;
444        mso-fareast-font-family:"Times New Roman";
445        mso-fareast-theme-font:major-fareast;
446        mso-hansi-font-family:Cambria;
447        mso-hansi-theme-font:major-latin;
448        mso-bidi-font-family:"Times New Roman";
449        mso-bidi-theme-font:major-bidi;
450        color:#4F81BD;
451        mso-themecolor:accent1;
452        font-weight:bold;
453        font-style:italic;}
454h5
455        {mso-style-noshow:yes;
456        mso-style-priority:9;
457        mso-style-qformat:yes;
458        mso-style-link:"Heading 5 Char";
459        mso-margin-top-alt:auto;
460        margin-right:0in;
461        mso-margin-bottom-alt:auto;
462        margin-left:0in;
463        mso-pagination:widow-orphan;
464        mso-outline-level:5;
465        font-size:12.0pt;
466        font-family:"Times New Roman","serif";
467        mso-fareast-font-family:"Times New Roman";
468        mso-fareast-theme-font:minor-fareast;
469        color:#4F4FFF;
470        font-weight:bold;}
471p.MsoTitle, li.MsoTitle, div.MsoTitle
472        {mso-style-noshow:yes;
473        mso-style-priority:10;
474        mso-style-unhide:no;
475        mso-style-qformat:yes;
476        mso-style-link:"Title Char";
477        mso-style-next:Normal;
478        margin-top:0in;
479        margin-right:0in;
480        margin-bottom:15.0pt;
481        margin-left:0in;
482        mso-add-space:auto;
483        mso-pagination:widow-orphan;
484        border:none;
485        mso-border-bottom-alt:solid #4F81BD 1.0pt;
486        mso-border-bottom-themecolor:accent1;
487        padding:0in;
488        mso-padding-alt:0in 0in 4.0pt 0in;
489        font-size:26.0pt;
490        font-family:"Cambria","serif";
491        mso-ascii-font-family:Cambria;
492        mso-ascii-theme-font:major-latin;
493        mso-fareast-font-family:"Times New Roman";
494        mso-fareast-theme-font:major-fareast;
495        mso-hansi-font-family:Cambria;
496        mso-hansi-theme-font:major-latin;
497        mso-bidi-font-family:"Times New Roman";
498        mso-bidi-theme-font:major-bidi;
499        color:#17365D;
500        mso-themecolor:text2;
501        mso-themeshade:191;
502        letter-spacing:.25pt;
503        mso-font-kerning:14.0pt;}
504p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
505        {mso-style-noshow:yes;
506        mso-style-priority:10;
507        mso-style-unhide:no;
508        mso-style-qformat:yes;
509        mso-style-link:"Title Char";
510        mso-style-next:Normal;
511        mso-style-type:export-only;
512        margin:0in;
513        margin-bottom:.0001pt;
514        mso-add-space:auto;
515        mso-pagination:widow-orphan;
516        border:none;
517        mso-border-bottom-alt:solid #4F81BD 1.0pt;
518        mso-border-bottom-themecolor:accent1;
519        padding:0in;
520        mso-padding-alt:0in 0in 4.0pt 0in;
521        font-size:26.0pt;
522        font-family:"Cambria","serif";
523        mso-ascii-font-family:Cambria;
524        mso-ascii-theme-font:major-latin;
525        mso-fareast-font-family:"Times New Roman";
526        mso-fareast-theme-font:major-fareast;
527        mso-hansi-font-family:Cambria;
528        mso-hansi-theme-font:major-latin;
529        mso-bidi-font-family:"Times New Roman";
530        mso-bidi-theme-font:major-bidi;
531        color:#17365D;
532        mso-themecolor:text2;
533        mso-themeshade:191;
534        letter-spacing:.25pt;
535        mso-font-kerning:14.0pt;}
536p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
537        {mso-style-noshow:yes;
538        mso-style-priority:10;
539        mso-style-unhide:no;
540        mso-style-qformat:yes;
541        mso-style-link:"Title Char";
542        mso-style-next:Normal;
543        mso-style-type:export-only;
544        margin:0in;
545        margin-bottom:.0001pt;
546        mso-add-space:auto;
547        mso-pagination:widow-orphan;
548        border:none;
549        mso-border-bottom-alt:solid #4F81BD 1.0pt;
550        mso-border-bottom-themecolor:accent1;
551        padding:0in;
552        mso-padding-alt:0in 0in 4.0pt 0in;
553        font-size:26.0pt;
554        font-family:"Cambria","serif";
555        mso-ascii-font-family:Cambria;
556        mso-ascii-theme-font:major-latin;
557        mso-fareast-font-family:"Times New Roman";
558        mso-fareast-theme-font:major-fareast;
559        mso-hansi-font-family:Cambria;
560        mso-hansi-theme-font:major-latin;
561        mso-bidi-font-family:"Times New Roman";
562        mso-bidi-theme-font:major-bidi;
563        color:#17365D;
564        mso-themecolor:text2;
565        mso-themeshade:191;
566        letter-spacing:.25pt;
567        mso-font-kerning:14.0pt;}
568p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
569        {mso-style-noshow:yes;
570        mso-style-priority:10;
571        mso-style-unhide:no;
572        mso-style-qformat:yes;
573        mso-style-link:"Title Char";
574        mso-style-next:Normal;
575        mso-style-type:export-only;
576        margin-top:0in;
577        margin-right:0in;
578        margin-bottom:15.0pt;
579        margin-left:0in;
580        mso-add-space:auto;
581        mso-pagination:widow-orphan;
582        border:none;
583        mso-border-bottom-alt:solid #4F81BD 1.0pt;
584        mso-border-bottom-themecolor:accent1;
585        padding:0in;
586        mso-padding-alt:0in 0in 4.0pt 0in;
587        font-size:26.0pt;
588        font-family:"Cambria","serif";
589        mso-ascii-font-family:Cambria;
590        mso-ascii-theme-font:major-latin;
591        mso-fareast-font-family:"Times New Roman";
592        mso-fareast-theme-font:major-fareast;
593        mso-hansi-font-family:Cambria;
594        mso-hansi-theme-font:major-latin;
595        mso-bidi-font-family:"Times New Roman";
596        mso-bidi-theme-font:major-bidi;
597        color:#17365D;
598        mso-themecolor:text2;
599        mso-themeshade:191;
600        letter-spacing:.25pt;
601        mso-font-kerning:14.0pt;}
602a:link, span.MsoHyperlink
603        {mso-style-noshow:yes;
604        mso-style-priority:99;
605        color:blue;
606        text-decoration:underline;
607        text-underline:single;}
608a:visited, span.MsoHyperlinkFollowed
609        {mso-style-noshow:yes;
610        mso-style-priority:99;
611        color:purple;
612        text-decoration:underline;
613        text-underline:single;}
614p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
615        {mso-style-noshow:yes;
616        mso-style-priority:99;
617        mso-style-link:"Document Map Char";
618        margin:0in;
619        margin-bottom:.0001pt;
620        mso-pagination:widow-orphan;
621        font-size:8.0pt;
622        font-family:"Tahoma","sans-serif";
623        mso-fareast-font-family:"Times New Roman";
624        mso-fareast-theme-font:minor-fareast;}
625p
626        {mso-style-noshow:yes;
627        mso-style-priority:99;
628        mso-margin-top-alt:auto;
629        margin-right:0in;
630        mso-margin-bottom-alt:auto;
631        margin-left:0in;
632        mso-pagination:widow-orphan;
633        font-size:12.0pt;
634        font-family:"Times New Roman","serif";
635        mso-fareast-font-family:"Times New Roman";
636        mso-fareast-theme-font:minor-fareast;}
637pre
638        {mso-style-noshow:yes;
639        mso-style-priority:99;
640        mso-style-link:"HTML Preformatted Char";
641        margin:0in;
642        margin-bottom:.0001pt;
643        mso-pagination:widow-orphan;
644        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;
645        font-size:10.0pt;
646        font-family:"Courier New";
647        mso-fareast-font-family:"Times New Roman";}
648p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
649        {mso-style-noshow:yes;
650        mso-style-priority:99;
651        mso-style-link:"Balloon Text Char";
652        margin:0in;
653        margin-bottom:.0001pt;
654        mso-pagination:widow-orphan;
655        font-size:8.0pt;
656        font-family:"Tahoma","sans-serif";
657        mso-fareast-font-family:"Times New Roman";
658        mso-fareast-theme-font:minor-fareast;}
659span.MsoPlaceholderText
660        {mso-style-noshow:yes;
661        mso-style-priority:99;
662        mso-style-unhide:no;
663        color:gray;}
664p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
665        {mso-style-noshow:yes;
666        mso-style-priority:1;
667        mso-style-unhide:no;
668        mso-style-qformat:yes;
669        mso-style-parent:"";
670        margin:0in;
671        margin-bottom:.0001pt;
672        mso-pagination:widow-orphan;
673        font-size:12.0pt;
674        font-family:"Times New Roman","serif";
675        mso-fareast-font-family:"Times New Roman";
676        mso-fareast-theme-font:minor-fareast;}
677p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
678        {mso-style-noshow:yes;
679        mso-style-priority:34;
680        mso-style-unhide:no;
681        mso-style-qformat:yes;
682        margin-top:0in;
683        margin-right:0in;
684        margin-bottom:0in;
685        margin-left:.5in;
686        margin-bottom:.0001pt;
687        mso-add-space:auto;
688        mso-pagination:widow-orphan;
689        font-size:12.0pt;
690        font-family:"Times New Roman","serif";
691        mso-fareast-font-family:"Times New Roman";
692        mso-fareast-theme-font:minor-fareast;}
693p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
694        {mso-style-noshow:yes;
695        mso-style-priority:34;
696        mso-style-unhide:no;
697        mso-style-qformat:yes;
698        mso-style-type:export-only;
699        margin-top:0in;
700        margin-right:0in;
701        margin-bottom:0in;
702        margin-left:.5in;
703        margin-bottom:.0001pt;
704        mso-add-space:auto;
705        mso-pagination:widow-orphan;
706        font-size:12.0pt;
707        font-family:"Times New Roman","serif";
708        mso-fareast-font-family:"Times New Roman";
709        mso-fareast-theme-font:minor-fareast;}
710p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
711        {mso-style-noshow:yes;
712        mso-style-priority:34;
713        mso-style-unhide:no;
714        mso-style-qformat:yes;
715        mso-style-type:export-only;
716        margin-top:0in;
717        margin-right:0in;
718        margin-bottom:0in;
719        margin-left:.5in;
720        margin-bottom:.0001pt;
721        mso-add-space:auto;
722        mso-pagination:widow-orphan;
723        font-size:12.0pt;
724        font-family:"Times New Roman","serif";
725        mso-fareast-font-family:"Times New Roman";
726        mso-fareast-theme-font:minor-fareast;}
727p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
728        {mso-style-noshow:yes;
729        mso-style-priority:34;
730        mso-style-unhide:no;
731        mso-style-qformat:yes;
732        mso-style-type:export-only;
733        margin-top:0in;
734        margin-right:0in;
735        margin-bottom:0in;
736        margin-left:.5in;
737        margin-bottom:.0001pt;
738        mso-add-space:auto;
739        mso-pagination:widow-orphan;
740        font-size:12.0pt;
741        font-family:"Times New Roman","serif";
742        mso-fareast-font-family:"Times New Roman";
743        mso-fareast-theme-font:minor-fareast;}
744span.MsoIntenseReference
745        {mso-style-priority:32;
746        mso-style-unhide:no;
747        mso-style-qformat:yes;
748        font-variant:small-caps;
749        color:#C0504D;
750        mso-themecolor:accent2;
751        letter-spacing:.25pt;
752        font-weight:bold;
753        text-decoration:underline;
754        text-underline:single;}
755span.Heading1Char
756        {mso-style-name:"Heading 1 Char";
757        mso-style-priority:9;
758        mso-style-unhide:no;
759        mso-style-locked:yes;
760        mso-style-link:"Heading 1";
761        mso-ansi-font-size:24.0pt;
762        mso-bidi-font-size:24.0pt;
763        font-family:"Times New Roman","serif";
764        mso-ascii-font-family:"Times New Roman";
765        mso-fareast-font-family:"Times New Roman";
766        mso-fareast-theme-font:minor-fareast;
767        mso-hansi-font-family:"Times New Roman";
768        mso-bidi-font-family:"Times New Roman";
769        mso-font-kerning:18.0pt;
770        font-weight:bold;}
771span.Heading2Char
772        {mso-style-name:"Heading 2 Char";
773        mso-style-noshow:yes;
774        mso-style-priority:9;
775        mso-style-unhide:no;
776        mso-style-locked:yes;
777        mso-style-link:"Heading 2";
778        mso-ansi-font-size:18.0pt;
779        mso-bidi-font-size:18.0pt;
780        font-family:"Times New Roman","serif";
781        mso-ascii-font-family:"Times New Roman";
782        mso-fareast-font-family:"Times New Roman";
783        mso-fareast-theme-font:minor-fareast;
784        mso-hansi-font-family:"Times New Roman";
785        mso-bidi-font-family:"Times New Roman";
786        font-weight:bold;}
787span.Heading3Char
788        {mso-style-name:"Heading 3 Char";
789        mso-style-noshow:yes;
790        mso-style-priority:9;
791        mso-style-unhide:no;
792        mso-style-locked:yes;
793        mso-style-link:"Heading 3";
794        mso-ansi-font-size:13.5pt;
795        mso-bidi-font-size:13.5pt;
796        font-family:"Times New Roman","serif";
797        mso-ascii-font-family:"Times New Roman";
798        mso-fareast-font-family:"Times New Roman";
799        mso-fareast-theme-font:minor-fareast;
800        mso-hansi-font-family:"Times New Roman";
801        mso-bidi-font-family:"Times New Roman";
802        font-weight:bold;}
803span.Heading4Char
804        {mso-style-name:"Heading 4 Char";
805        mso-style-noshow:yes;
806        mso-style-priority:9;
807        mso-style-unhide:no;
808        mso-style-locked:yes;
809        mso-style-link:"Heading 4";
810        mso-ansi-font-size:13.0pt;
811        mso-bidi-font-size:13.0pt;
812        font-family:"Cambria","serif";
813        mso-ascii-font-family:Cambria;
814        mso-ascii-theme-font:major-latin;
815        mso-fareast-font-family:"Times New Roman";
816        mso-fareast-theme-font:major-fareast;
817        mso-hansi-font-family:Cambria;
818        mso-hansi-theme-font:major-latin;
819        mso-bidi-font-family:"Times New Roman";
820        mso-bidi-theme-font:major-bidi;
821        color:#4F81BD;
822        mso-themecolor:accent1;
823        font-weight:bold;
824        font-style:italic;}
825span.Heading5Char
826        {mso-style-name:"Heading 5 Char";
827        mso-style-noshow:yes;
828        mso-style-priority:9;
829        mso-style-unhide:no;
830        mso-style-locked:yes;
831        mso-style-link:"Heading 5";
832        mso-ansi-font-size:12.0pt;
833        mso-bidi-font-size:12.0pt;
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1127<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1128
1129<div class=WordSection1>
1130
1131<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1132
1133<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1134cell that matches a set of diffraction peaks -- a process known as
1135auto-indexing. First peaks must be located and optimized and then indexing can
1136be done.</p>
1137
1138<p class=MsoNormal>If you have not done so already, <a
1139href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
1140
1141<h2>Step 1: read in the data file</h2>
1142
1143<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1144style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1145style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1146the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1147mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1148minor-latin'>Import/Powder Data/from GSAS file</span></b> menu item to read the
1149data file into the current GSAS-II project. This read option is set to read any
1150of the powder data formats (except neutron TOF time map files) defined for GSAS
1151(angles in <span class=SpellE>centidegrees</span>). Other submenu items will
1152read the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1153style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1154mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1155format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><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'>xye</span></b></span>
1158format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1159style='mso-spacerun:yes'>  </span>Change the file directory to <b
1160style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1161mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1162minor-latin'>Exercises/LaB6</span></b><span style='font-family:"Calibri","sans-serif";
1163mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1164minor-latin'> to find the file; you may need to change the file type to <b
1165style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
1166file.</span></p>
1167
1168<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1169style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1170style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1171the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1172mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1173minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri","sans-serif";
1174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1175minor-latin'> data</span> file in the first dialog and press <b
1176style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1177mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1178minor-latin'>Open</span></b>. There will be a Dialog box asking <span
1179class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1180"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1181minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
1182style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1183mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;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-theme-font:
1187minor-latin'>Yes</span></b></span> button to proceed.</p>
1188
1189<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1190style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1191style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1192file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1193mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1194minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
1195automatically selected; it was produced by 11BM-B instrument processing
1196software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
1197normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1198minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1199file was created from the 12 detector raw data. If absent or the name doesn’t
1200match the data file name, a file dialog will appear for you to select the
1201correct instrument parameter file.</p>
1202
1203<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1204style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1205mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1206tree</span></b> window will have several entries </p>
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1229 style='width:225pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
1230 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
1231</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1232src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1233
1234<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1235powder pattern</p>
1236
1237<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1238 id="Picture_x0020_2" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1239 height:450pt;visibility:visible;mso-wrap-style:square'>
1240 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
1241</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1242src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1243
1244<h2>Step 2: Select Limits </h2>
1245
1246<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1247more data than we need, so it is helpful to cut down the range. Click on the <b
1248style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1249mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1250minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
1251style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1252mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1253tree</span></b>. The small window is repainted. Use the <b style='mso-bidi-font-weight:
1254normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1255minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>changed</span></b>
1256row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
1257normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1258minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
1259and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1260style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1261mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1262to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1263mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1264minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:normal'><span
1265style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1266mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1267Notice on the plot that the limit lines have moved to these positions; the
1268green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1269is in a wide gap between peaks. You may also drag the limit lines to the
1270desired location or place them by a left mouse click on a data point for the
1271lower limit or a right click on a data point for the upper limit.</p>
1272
1273<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1274 id="Picture_x0020_3" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:225pt;
1275 height:120pt;visibility:visible;mso-wrap-style:square'>
1276 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1277</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=160
1278src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1279
1280<h2>Step 3: Determine Peak Positions</h2>
1281
1282<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1283auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1284style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1285style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1286on the <b style='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'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1289normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1290minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1291data tree</span></b>. This creates an empty window of peak positions (the <b
1292style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1293mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1294minor-latin'>Limits</span></b> window is erased). At this point it is wise <span
1295class=GramE>to<span style='mso-spacerun:yes'>  </span>zoom</span> in on the
1296data that will be used for indexing. </p>
1297
1298<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1299auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1300style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1301style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1302on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1303 id="Picture_x0020_4" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:21.75pt;
1304 height:18.75pt;visibility:visible;mso-wrap-style:square'>
1305 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1306  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1307</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
1308src="Fit%20Peaks_files/image005.jpg" v:shapes="Picture_x0020_4"><![endif]></span>,
1309then press the left mouse in one corner of the region to be used; holding the
1310mouse button down, drag over the region to the opposite corner; a box will be
1311drawn over the region to be zoomed. </p>
1312
1313<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1314auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1315style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1316style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1317style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
1318style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
1319 o:spid="_x0000_i1042" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
1320 visibility:visible;mso-wrap-style:square'>
1321 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1322  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1323</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
1324src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
1325style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
1326
1327<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1328auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1329style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1330style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Using
1331the left mouse button, click on a data point near the top of each peak to be
1332added to the peak list. It is usually best to start at the upper end of the
1333pattern as the next peak to pick isn’t obscured by the tool tip. As this is
1334done, a vertical blue line is drawn in the plot window<span
1335style='mso-spacerun:yes'>  </span>for each peak selected</p>
1336
1337<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1338auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
1339 o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;height:450pt;
1340 visibility:visible;mso-wrap-style:square'>
1341 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
1342</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1343src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1344
1345<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1346auto'><span class=GramE>and</span> peaks are added to the <b style='mso-bidi-font-weight:
1347normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1348minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1349List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1350
1351<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1352auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
1353 o:spid="_x0000_i1040" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
1354 visibility:visible;mso-wrap-style:square'>
1355 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1356</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1357src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1358
1359<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1360auto'>Note that if peaks are not being added, you probably have not exited zoom
1361mode.</p>
1362
1363<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>Add
1364approximately 20-25 peaks total to the peak list (there will be 20 in this
1365example). Be sure to add the lowest angle peaks that are visible in the plot.
1366You may drag a peak position as needed; be sure the zoom/shift buttons are off.
1367A position may be deleted with a right click with the mouse on the blue line.</p>
1368
1369<h2>Step 4: Refine Peak Positions</h2>
1370
1371<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1372refinement and then adding <span class=GramE>a parameters</span> to complete
1373the fitting,</p>
1374
1375<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1376style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1377style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1378the peak intensities and the background. These parameters have their refinement
1379flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1380normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1381minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1382Fitting/LSQ <span class=SpellE>PeakFit</span> </span></b>on the<b
1383style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1384mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1385minor-latin'> Peak List </span></b>window. Do <b style='mso-bidi-font-weight:
1386normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1387style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1388mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1389menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1390"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1391minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
1392window; that it to be used for Rietveld/Pawley refinements. You will be asked
1393to save the current project before the fit will proceed; change directory if
1394desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1395normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1396minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1397A window will show the progress of the refinement and will close when the
1398least-squares fit <span class=GramE>is</span> complete (usually very fast). The
1399plot is updated with the fit, the peak list window is updated with the new peak
1400values and a summary of the refinement is shown on the console window as well.</p>
1401
1402<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1403 id="Picture_x0020_8" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1404 height:450pt;visibility:visible;mso-wrap-style:square'>
1405 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
1406</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1407src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1408
1409<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1410 id="Picture_x0020_9" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:401.25pt;
1411 height:262.5pt;visibility:visible;mso-wrap-style:square'>
1412 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1413</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1414src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1415
1416<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1417style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1418style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1419add refinement of the peak positions. This can be done by clicking on all the refinement
1420flags for the individual peaks or it is possible to set them all at the same
1421time using this recipe: </p>
1422
1423<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1424auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1425style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1426style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1427class=GramE>single-click</span> on any value in the table to select it, for
1428example the first peak position. A black box appears around the value. </p>
1429
1430<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1431text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1432style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1433style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1434class=GramE>single-click</span> on the refine label above the peak position
1435check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
1436style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1437mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1438minor-latin'>y</span></b> key to turn on all refinement flags (<b
1439style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1440mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1441minor-latin'>n</span></b> would turn them off).</p>
1442
1443<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1444the <b style='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 Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu
1447item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1448"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1449minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b> window.</p>
1450
1451<p class=MsoNormal style='margin-left:.5in'><span
1452style='mso-spacerun:yes'> </span>Now, select peak widths for refinement. <span
1453style='mso-fareast-font-family:"Times New Roman"'>This can be performed in 2
1454different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian width) and/or
1455gamma (Lorentzian width) for individual peaks. &nbsp;To do this, click the
1456refinement flags for sigma and/or gamma in the Peak List window.
1457&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1458widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening
1459equation as described below.&nbsp;Note - one cannot refine ALL peak widths
1460using both individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental
1461broadening terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1462
1463<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1464"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1465to an instrumental broadening equation, first<b> s</b></span>elect the <b
1466style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1467mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1468minor-latin'>Instrumental Parameters</span></b> item in the data tree. <span
1469class=GramE>This opens a window for peak profile terms<b> </b><span
1470style='mso-bidi-font-weight:bold'>and also create</span></span><span
1471style='mso-bidi-font-weight:bold'> a new plot window&nbsp;showing the
1472instrument profile resolution curve.</span></p>
1473
1474<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1475 id="Picture_x0020_10" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:422.25pt;
1476 height:154.5pt;visibility:visible;mso-wrap-style:square'>
1477 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
1478</v:shape><![endif]--><![if !vml]><img border=0 width=563 height=206
1479src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
1480
1481<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1482corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y coefficients;
1483‘+’ marks show the individual values based on the sig &amp; gam values for the
1484peaks in Peak List. Select the refine flag checkbox for Gaussian <b
1485style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1487minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
1488style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1489mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
1490<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1491mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1492minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
1493style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1494mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
1495<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1496mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1497minor-latin'>Y</span></b>. </p>
1498
1499<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1500style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1501style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1502repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1503style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1504mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1505item in the data tree and then refine using the <b style='mso-bidi-font-weight:
1506normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1507minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1508Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item. At this
1509point a good fit should be seen by zooming in on individual peaks. (For example
1510see </p>
1511
1512<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1513 id="Picture_x0020_11" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1514 height:450pt;visibility:visible;mso-wrap-style:square'>
1515 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1516</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1517src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1518
1519<p class=MsoListParagraphCxSpLast>The <span class=SpellE>Rwp</span> is ~6% as shown
1520on the console window. Again the <b style='mso-bidi-font-weight:normal'><span
1521style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1522mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1523entries are all updated with new values and those in <b style='mso-bidi-font-weight:
1524normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1525minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
1526Parameters</span></b> are also updated.</p>
1527
1528<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1529
1530<p class=MsoNormal>A separate list of peaks is kept for use in <span
1531class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1532normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1533minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1534Peak List</span></b> item in the data tree. In the initially empty window
1535created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1536style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1537mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index Peaks
1538Operations/Load</span></b> to copy the fitted peaks from the <b
1539style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1540mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1541minor-latin'>Peak List</span></b>.</p>
1542
1543<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1544 id="Picture_x0020_12" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:367.5pt;
1545 height:225pt;visibility:visible;mso-wrap-style:square'>
1546 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
1547</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
1548src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
1549
1550<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1551may choose to not use a fitted peak (e.g. if suspected it is from a
1552contaminant).</p>
1553
1554<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
1555
1556<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1557style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1558mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1559List</span></b> data item. This brings up a window for indexing and cell refinement
1560options</p>
1561
1562<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1563 id="Picture_x0020_13" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:527.25pt;
1564 height:204pt;visibility:visible;mso-wrap-style:square'>
1565 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1566</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
1567src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1568
1569<p class=MsoNormal>For the most rapid search (since we know the right answer),
1570select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1571mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1572minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1573style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1574mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1575minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the console
1576shows a running list of possible cells as they are found; the sorted by M20
1577list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1578normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1579minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1580Cells List</span></b> window</p>
1581
1582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1583 id="Picture_x0020_14" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:527.25pt;
1584 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1585 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1586</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1587src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
1588
1589<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
1590
1591<p class=MsoNormal>Review the list of cells associated with the <b
1592style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1593mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1594minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1595unit cell, the generated reflections for that cell are shown in the plot with
1596dashed red lines. Sliding the cursor over these lines shows a small popup
1597window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1598first cell in the list (M20~3000) with a=5.87864 Å generates very many lines
1599with no corresponding peaks (NB: this solution might not always show up!)</p>
1600
1601<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1602 id="Picture_x0020_15" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1603 height:450pt;visibility:visible;mso-wrap-style:square'>
1604 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
1605</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1606src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_15"><![endif]></span><span
1607style='mso-spacerun:yes'> </span></p>
1608
1609<p class=MsoNormal><span class=GramE>while</span> the (M20~600) cell with
1610a=2.93932 Å generates not enough lines to match all the peaks</p>
1611
1612<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1613 id="Picture_x0020_16" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
1614 height:450pt;visibility:visible;mso-wrap-style:square'>
1615 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1616</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1617src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
1618
1619<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
1620
1621<p class=MsoNormal>Select the cell with M20 ~ 2900 with a = 4.1568 Å. This
1622indexes all peaks with almost a perfect fit to the peak positions (compare
1623dashed red lines to solid blue ones). Import the cell information using the <b
1624style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1625mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1626minor-latin'>Cell Index/Copy Cell</span></b> menu option. Then optimize the
1627cell by refining the lattice parameters and the two-theta zero: click on the
1628refine checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1629style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1630mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1631value and then the <b style='mso-bidi-font-weight:normal'><span
1632style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1633mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1634Index/Refine Cell</span></b> menu option. <span class=GramE>The a</span> cell
1635parameter value shifts from 4.15679 to 4.15684 when zero is refined. Press the <b
1636style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1637mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1638minor-latin'>Show refined <span class=SpellE>hkl</span> positions + Zero offset</span></b>
1639button to update the plot including the refined <b style='mso-bidi-font-weight:
1640normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1641minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero
1642offset</span></b> (in this case hardly anything happens!) </p>
1643
1644<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1645 id="Picture_x0020_17" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:527.25pt;
1646 height:334.5pt;visibility:visible;mso-wrap-style:square'>
1647 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1648</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
1649src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1650
1651<p class=MsoNormal>Notice that a new entry heads the list in the <b
1652style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1653mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1654minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
1655normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1656minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1657Index/Refine</span></b> window with an improved M20(=3614.66) and a new value
1658for <b style='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'>Zero offset</span></b> is shown.</p>
1661
1662<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
1663normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1664minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1665Index/New phase</span></b> menu option allows one to create a phase with these
1666lattice parameters in the data tree under <b style='mso-bidi-font-weight:normal'><span
1667style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1668mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
1669style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
1670creates the tree item <b style='mso-bidi-font-weight:normal'><span
1671style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1672mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
1673(if it wasn’t already present). This new phase can be used in future analysis
1674(e.g. Rietveld or Pawley refinement).</p>
1675
1676<p class=MsoNormal>To continue with the second part of this exercise, <span
1677class=GramE>do the menu item</span> <b style='mso-bidi-font-weight:normal'><span
1678style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1679mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Close
1680project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1681style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1682mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1683tree </span></b>window. You will be asked if you want it saved; if <span
1684class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1685"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1686minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the
1687peak fitting/indexing &amp; cell refinement results will be saved to the <b
1688style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1689mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1690minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
1691style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1692mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
1693then the file will remain as it was when created at Step 4 above.</p>
1694
1695<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
1696class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
1697style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
1698
1699<p class=MsoNormal>In this exercise we will fit peaks and index them for the
1700new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
1701(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
1702data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a
1703more substantial test of the indexing capability of GSAS-II.</p>
1704
1705<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1706
1707<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1708style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1709mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>\Exercises\<span
1710class=SpellE>krptonite</span>\11bmb_6231.fxye</span></b>; it has a
1711corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1712style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1713mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span>
1714file. Load them in &amp; the plot is</p>
1715
1716<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1717 id="Picture_x0020_18" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1718 height:450pt;visibility:visible;mso-wrap-style:square'>
1719 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
1720</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1721src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
1722
1723<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
1724lower part of the pattern.</p>
1725
1726<h2>Step 2 Set limits</h2>
1727
1728<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
1729style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1730mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
1731and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1732mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1733minor-latin'>10</span></b>.</p>
1734
1735<h2>Step 3 Pick peaks</h2>
1736
1737<p class=MsoNormal>Pick all peaks you can see between the limits (including the
1738small ones). Note some peaks have shoulders most notably at 5.07, 6.04,
17397.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
1740might be from a second phase? We’ll see later).</p>
1741
1742<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_19" o:spid="_x0000_s1026"
1743 type="#_x0000_t75" style='position:absolute;margin-left:0;margin-top:0;
1744 width:525pt;height:450pt;z-index:251658240;visibility:visible;
1745 mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
1746 mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1747 mso-wrap-distance-bottom:0;mso-position-horizontal:left;
1748 mso-position-horizontal-relative:text;mso-position-vertical:top;
1749 mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
1750 mso-width-relative:page;mso-height-relative:page'>
1751 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1752 <w:wrap type="square"/>
1753</v:shape><![endif]--><![if !vml]><img width=700 height=600
1754src="Fit%20Peaks_files/image020.png" align=left hspace=12 v:shapes="Picture_x0020_19"><![endif]><br
1755clear=all style='mso-special-character:line-break'>
1756</p>
1757
1758<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
1759
1760<p class=MsoNormal>Following the steps above, refine the peaks and the profile
1761shape parameters in <b style='mso-bidi-font-weight:normal'><span
1762style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1763mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
1764Parameters</span></b>. You will be asked for a project file name at the first
1765refinement (I used ‘<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1766style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1767mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
1768style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1769mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1770minor-latin'>’</span></b>). In the end my refinement converged at <span
1771class=SpellE>Rwp</span>=13.18% and some peaks do show some discrepancy as the
1772sample is more complex than the simple <b style='mso-bidi-font-weight:normal'><span
1773style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1774mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>U</span></b>,
1775<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1776mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1777minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:normal'><span
1778style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1779mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>W</span></b>,
1780<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1781mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1782minor-latin'>X</span></b>, <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'>Y</span></b>
1785model can accommodate. However, this is good enough to proceed.</p>
1786
1787<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1788
1789<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
1790style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1791mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1792in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1793mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1794minor-latin'>Index Peak List</span></b> window.</p>
1795
1796<h2><span class=GramE>Step 6.</span> Index the cell</h2>
1797
1798<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
1799In a real world case we wouldn’t know this and we would have to try each <span
1800class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
1801time to go through all the bad cases.</p>
1802
1803<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1804style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1805mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
1806and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1807mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1808minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
1809style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1810mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1811minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
1812and suitable results will be slow in coming so be patient. Watch the console
1813window; the right answer will have an obviously large M20 (~630) and a volume
1814of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
1815seen (it may take more than one try to get this) you can stop the indexing
1816search by pressing <b style='mso-bidi-font-weight:normal'><span
1817style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1818mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
1819on the progress bar window. It may take more than one press to fully stop it.
1820My result was </p>
1821
1822<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1823 id="Picture_x0020_20" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
1824 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1825 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
1826</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1827src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
1828
1829<p class=MsoNormal>Notice an equally good M20 result with twice the volume. The
1830plot shows every peak indexed including a couple of weak peaks not selected for
1831the peak fitting.</p>
1832
1833<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1834 id="Picture_x0020_21" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
1835 height:450pt;visibility:visible;mso-wrap-style:square'>
1836 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1837</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1838src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1839
1840<p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol;
1841mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1842symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
1843wasn’t indexed. I presume that is a contaminant. By sliding the cursor over the
1844index lines without any visible peak you can see that the missing ones are
1845(010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2, 23-1, 22-2, 141,
1846201,102, 15-1, 112, &amp; 24-1). Many of these are accidental but the 0k0; k&#8800;2n
1847and h0l; h+l&#8800;2n ones characterize the space group P2<sub>1</sub>/n. Armed
1848with this information you can <b style='mso-bidi-font-weight:normal'><span
1849style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1850mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
1851phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
1852normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1853minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>kryptonite’</span></b>)
1854and set the space group in the <b style='mso-bidi-font-weight:normal'><span
1855style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1856mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data
1857for kryptonite</span></b> window.</p>
1858
1859<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1860 id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:597.75pt;
1861 height:214.5pt;visibility:visible;mso-wrap-style:square'>
1862 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
1863</v:shape><![endif]--><![if !vml]><img border=0 width=797 height=286
1864src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1865
1866<p class=MsoNormal>Setting the space group will show a window with some
1867information. Press <b style='mso-bidi-font-weight:normal'><span
1868style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1869mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
1870to close it.</p>
1871
1872<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1873 id="Picture_x0020_23" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:333.75pt;
1874 height:209.25pt;visibility:visible;mso-wrap-style:square'>
1875 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1876</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
1877src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1878
1879<p class=MsoNormal>This concludes this exercise; <span class=GramE><b
1880style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1881mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1882minor-latin'>Save</span></b></span> the project file as it is needed for the <b
1883style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1884mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1885minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
1886exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
1887style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1888mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data</span></b>
1889window will be presented in other exercises.</p>
1890
1891</div>
1892
1893</body>
1894
1895</html>
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