source: trunk/help/Fit Peaks.htm @ 729

Last change on this file since 729 was 729, checked in by vondreele, 10 years ago

minor fixes to mapPeaks plotting
begin to add charge flipping tutorial

  • Property svn:keywords set to Author
  • Property svn:mime-type set to text/html
File size: 91.0 KB
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384        margin-left:0in;
385        mso-pagination:widow-orphan;
386        mso-outline-level:1;
387        font-size:24.0pt;
388        font-family:"Times New Roman","serif";
389        mso-fareast-font-family:"Times New Roman";
390        mso-fareast-theme-font:minor-fareast;
391        font-weight:bold;}
392h2
393        {mso-style-noshow:yes;
394        mso-style-priority:9;
395        mso-style-qformat:yes;
396        mso-style-link:"Heading 2 Char";
397        mso-margin-top-alt:auto;
398        margin-right:0in;
399        mso-margin-bottom-alt:auto;
400        margin-left:0in;
401        mso-pagination:widow-orphan;
402        mso-outline-level:2;
403        font-size:18.0pt;
404        font-family:"Times New Roman","serif";
405        mso-fareast-font-family:"Times New Roman";
406        mso-fareast-theme-font:minor-fareast;
407        font-weight:bold;}
408h3
409        {mso-style-noshow:yes;
410        mso-style-priority:9;
411        mso-style-qformat:yes;
412        mso-style-link:"Heading 3 Char";
413        mso-margin-top-alt:auto;
414        margin-right:0in;
415        mso-margin-bottom-alt:auto;
416        margin-left:0in;
417        mso-pagination:widow-orphan;
418        mso-outline-level:3;
419        font-size:13.5pt;
420        font-family:"Times New Roman","serif";
421        mso-fareast-font-family:"Times New Roman";
422        mso-fareast-theme-font:minor-fareast;
423        font-weight:bold;}
424h4
425        {mso-style-noshow:yes;
426        mso-style-priority:9;
427        mso-style-qformat:yes;
428        mso-style-link:"Heading 4 Char";
429        mso-style-next:Normal;
430        margin-top:10.0pt;
431        margin-right:0in;
432        margin-bottom:0in;
433        margin-left:0in;
434        margin-bottom:.0001pt;
435        mso-pagination:widow-orphan lines-together;
436        page-break-after:avoid;
437        mso-outline-level:4;
438        font-size:13.0pt;
439        font-family:"Cambria","serif";
440        mso-ascii-font-family:Cambria;
441        mso-ascii-theme-font:major-latin;
442        mso-fareast-font-family:"Times New Roman";
443        mso-fareast-theme-font:major-fareast;
444        mso-hansi-font-family:Cambria;
445        mso-hansi-theme-font:major-latin;
446        mso-bidi-font-family:"Times New Roman";
447        mso-bidi-theme-font:major-bidi;
448        color:#4F81BD;
449        mso-themecolor:accent1;
450        font-weight:bold;
451        font-style:italic;}
452h5
453        {mso-style-noshow:yes;
454        mso-style-priority:9;
455        mso-style-qformat:yes;
456        mso-style-link:"Heading 5 Char";
457        mso-margin-top-alt:auto;
458        margin-right:0in;
459        mso-margin-bottom-alt:auto;
460        margin-left:0in;
461        mso-pagination:widow-orphan;
462        mso-outline-level:5;
463        font-size:12.0pt;
464        font-family:"Times New Roman","serif";
465        mso-fareast-font-family:"Times New Roman";
466        mso-fareast-theme-font:minor-fareast;
467        color:#4F4FFF;
468        font-weight:bold;}
469p.MsoTitle, li.MsoTitle, div.MsoTitle
470        {mso-style-noshow:yes;
471        mso-style-priority:10;
472        mso-style-unhide:no;
473        mso-style-qformat:yes;
474        mso-style-link:"Title Char";
475        mso-style-next:Normal;
476        margin-top:0in;
477        margin-right:0in;
478        margin-bottom:15.0pt;
479        margin-left:0in;
480        mso-add-space:auto;
481        mso-pagination:widow-orphan;
482        border:none;
483        mso-border-bottom-alt:solid #4F81BD 1.0pt;
484        mso-border-bottom-themecolor:accent1;
485        padding:0in;
486        mso-padding-alt:0in 0in 4.0pt 0in;
487        font-size:26.0pt;
488        font-family:"Cambria","serif";
489        mso-ascii-font-family:Cambria;
490        mso-ascii-theme-font:major-latin;
491        mso-fareast-font-family:"Times New Roman";
492        mso-fareast-theme-font:major-fareast;
493        mso-hansi-font-family:Cambria;
494        mso-hansi-theme-font:major-latin;
495        mso-bidi-font-family:"Times New Roman";
496        mso-bidi-theme-font:major-bidi;
497        color:#17365D;
498        mso-themecolor:text2;
499        mso-themeshade:191;
500        letter-spacing:.25pt;
501        mso-font-kerning:14.0pt;}
502p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
503        {mso-style-noshow:yes;
504        mso-style-priority:10;
505        mso-style-unhide:no;
506        mso-style-qformat:yes;
507        mso-style-link:"Title Char";
508        mso-style-next:Normal;
509        mso-style-type:export-only;
510        margin:0in;
511        margin-bottom:.0001pt;
512        mso-add-space:auto;
513        mso-pagination:widow-orphan;
514        border:none;
515        mso-border-bottom-alt:solid #4F81BD 1.0pt;
516        mso-border-bottom-themecolor:accent1;
517        padding:0in;
518        mso-padding-alt:0in 0in 4.0pt 0in;
519        font-size:26.0pt;
520        font-family:"Cambria","serif";
521        mso-ascii-font-family:Cambria;
522        mso-ascii-theme-font:major-latin;
523        mso-fareast-font-family:"Times New Roman";
524        mso-fareast-theme-font:major-fareast;
525        mso-hansi-font-family:Cambria;
526        mso-hansi-theme-font:major-latin;
527        mso-bidi-font-family:"Times New Roman";
528        mso-bidi-theme-font:major-bidi;
529        color:#17365D;
530        mso-themecolor:text2;
531        mso-themeshade:191;
532        letter-spacing:.25pt;
533        mso-font-kerning:14.0pt;}
534p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
535        {mso-style-noshow:yes;
536        mso-style-priority:10;
537        mso-style-unhide:no;
538        mso-style-qformat:yes;
539        mso-style-link:"Title Char";
540        mso-style-next:Normal;
541        mso-style-type:export-only;
542        margin:0in;
543        margin-bottom:.0001pt;
544        mso-add-space:auto;
545        mso-pagination:widow-orphan;
546        border:none;
547        mso-border-bottom-alt:solid #4F81BD 1.0pt;
548        mso-border-bottom-themecolor:accent1;
549        padding:0in;
550        mso-padding-alt:0in 0in 4.0pt 0in;
551        font-size:26.0pt;
552        font-family:"Cambria","serif";
553        mso-ascii-font-family:Cambria;
554        mso-ascii-theme-font:major-latin;
555        mso-fareast-font-family:"Times New Roman";
556        mso-fareast-theme-font:major-fareast;
557        mso-hansi-font-family:Cambria;
558        mso-hansi-theme-font:major-latin;
559        mso-bidi-font-family:"Times New Roman";
560        mso-bidi-theme-font:major-bidi;
561        color:#17365D;
562        mso-themecolor:text2;
563        mso-themeshade:191;
564        letter-spacing:.25pt;
565        mso-font-kerning:14.0pt;}
566p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
567        {mso-style-noshow:yes;
568        mso-style-priority:10;
569        mso-style-unhide:no;
570        mso-style-qformat:yes;
571        mso-style-link:"Title Char";
572        mso-style-next:Normal;
573        mso-style-type:export-only;
574        margin-top:0in;
575        margin-right:0in;
576        margin-bottom:15.0pt;
577        margin-left:0in;
578        mso-add-space:auto;
579        mso-pagination:widow-orphan;
580        border:none;
581        mso-border-bottom-alt:solid #4F81BD 1.0pt;
582        mso-border-bottom-themecolor:accent1;
583        padding:0in;
584        mso-padding-alt:0in 0in 4.0pt 0in;
585        font-size:26.0pt;
586        font-family:"Cambria","serif";
587        mso-ascii-font-family:Cambria;
588        mso-ascii-theme-font:major-latin;
589        mso-fareast-font-family:"Times New Roman";
590        mso-fareast-theme-font:major-fareast;
591        mso-hansi-font-family:Cambria;
592        mso-hansi-theme-font:major-latin;
593        mso-bidi-font-family:"Times New Roman";
594        mso-bidi-theme-font:major-bidi;
595        color:#17365D;
596        mso-themecolor:text2;
597        mso-themeshade:191;
598        letter-spacing:.25pt;
599        mso-font-kerning:14.0pt;}
600a:link, span.MsoHyperlink
601        {mso-style-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";
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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'>Import/Powder Data/from GSAS file</span></b> menu item to read the
1146data file into the current GSAS-II project. This read option is set to read any
1147of the powder data formats (except neutron TOF time map files) defined for GSAS
1148(angles in <span class=SpellE>centidegrees</span>). Other submenu items will
1149read the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1150style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1151mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1152format or 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'>xye</span></b></span>
1155format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1156style='mso-spacerun:yes'>  </span>Change the file directory to <b
1157style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1158mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1159minor-latin'>Exercises/LaB6</span></b><span style='font-family:"Calibri","sans-serif";
1160mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1161minor-latin'> to find the file; you may need to change the file type to <b
1162style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired
1163file.</span></p>
1164
1165<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1166style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1167style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1168the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1169mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1170minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri","sans-serif";
1171mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1172minor-latin'> data</span> file in the first dialog and press <b
1173style='mso-bidi-font-weight:normal'><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'>Open</span></b>. There will be a Dialog box asking <span
1176class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1177"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1178minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
1179style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1180mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1181minor-latin'> this the file you want?</span></b> Press <span class=GramE><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'>Yes</span></b></span> button to proceed.</p>
1185
1186<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1187style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1188style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1189file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1190mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1191minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
1192automatically selected; it was produced by 11BM-B instrument processing
1193software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
1194normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1195minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1196file was created from the 12 detector raw data. If absent or the name doesn’t
1197match the data file name, a file dialog will appear for you to select the
1198correct instrument parameter file.</p>
1199
1200<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1201style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1202mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1203tree</span></b> window will have several entries </p>
1204
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1230
1231<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1232powder pattern</p>
1233
1234<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1235 id="Picture_x0020_2" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1236 height:450pt;visibility:visible;mso-wrap-style:square'>
1237 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
1238</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1239src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1240
1241<h2>Step 2: Select Limits </h2>
1242
1243<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1244more data than we need, so it is helpful to cut down the range. Click on the <b
1245style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1246mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1247minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
1248style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1249mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1250tree</span></b>. The small window is repainted. Use the <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'>changed</span></b>
1253row of entry boxes to set <span class=SpellE><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'>Tmin</span></b></span>
1256and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1257style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1258mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1259to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1260mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1261minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:normal'><span
1262style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1263mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1264Notice on the plot that the limit lines have moved to these positions; the
1265green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1266is in a wide gap between peaks. You may also drag the limit lines to the
1267desired location or place them by a left mouse click on a data point for the
1268lower limit or a right click on a data point for the upper limit.</p>
1269
1270<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1271 id="Picture_x0020_3" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:225pt;
1272 height:120pt;visibility:visible;mso-wrap-style:square'>
1273 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1274</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=160
1275src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1276
1277<h2>Step 3: Determine Peak Positions</h2>
1278
1279<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1280auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1281style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1282style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1283on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1284mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1285minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1286normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1287minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1288data tree</span></b>. This creates an empty window of peak positions (the <b
1289style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1290mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1291minor-latin'>Limits</span></b> window is erased). At this point it is wise <span
1292class=GramE>to<span style='mso-spacerun:yes'>  </span>zoom</span> in on the
1293data that will be used for indexing. </p>
1294
1295<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1296auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1297style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1299on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1300 id="Picture_x0020_4" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:21.75pt;
1301 height:18.75pt;visibility:visible;mso-wrap-style:square'>
1302 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1303  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1304</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
1305src="Fit%20Peaks_files/image005.jpg" v:shapes="Picture_x0020_4"><![endif]></span>,
1306then press the left mouse in one corner of the region to be used; holding the
1307mouse button down, drag over the region to the opposite corner; a box will be
1308drawn over the region to be zoomed. </p>
1309
1310<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1311auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1312style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1313style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1314style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
1315style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
1316 o:spid="_x0000_i1042" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
1317 visibility:visible;mso-wrap-style:square'>
1318 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1319  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1320</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
1321src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
1322style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
1323
1324<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1325auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1326style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1327style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Using
1328the left mouse button, click on a data point near the top of each peak to be
1329added to the peak list. It is usually best to start at the upper end of the
1330pattern as the next peak to pick isn’t obscured by the tool tip. As this is
1331done, a vertical blue line is drawn in the plot window<span
1332style='mso-spacerun:yes'>  </span>for each peak selected</p>
1333
1334<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1335auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6"
1336 o:spid="_x0000_i1041" type="#_x0000_t75" style='width:525pt;height:450pt;
1337 visibility:visible;mso-wrap-style:square'>
1338 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
1339</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1340src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_6"><![endif]></span></p>
1341
1342<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1343auto'><span class=GramE>and</span> peaks are added to the <b style='mso-bidi-font-weight:
1344normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1345minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1346List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1347
1348<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1349auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
1350 o:spid="_x0000_i1040" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
1351 visibility:visible;mso-wrap-style:square'>
1352 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1353</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1354src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1355
1356<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1357auto'>Note that if peaks are not being added, you probably have not exited zoom
1358mode.</p>
1359
1360<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>Add
1361approximately 20-25 peaks total to the peak list (there will be 20 in this
1362example). Be sure to add the lowest angle peaks that are visible in the plot.
1363You may drag a peak position as needed; be sure the zoom/shift buttons are off.
1364A position may be deleted with a right click with the mouse on the blue line.</p>
1365
1366<h2>Step 4: Refine Peak Positions</h2>
1367
1368<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1369refinement and then adding <span class=GramE>a parameters</span> to complete
1370the fitting,</p>
1371
1372<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1373style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1374style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1375the peak intensities and the background. These parameters have their refinement
1376flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1377normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1378minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1379Fitting/LSQ <span class=SpellE>PeakFit</span> </span></b>on the<b
1380style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1381mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1382minor-latin'> Peak List </span></b>window. Do <b style='mso-bidi-font-weight:
1383normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1384style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1385mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1386menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1387"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1388minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>
1389window; that it to be used for Rietveld/Pawley refinements. You will be asked
1390to save the current project before the fit will proceed; change directory if
1391desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1392normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1393minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1394A window will show the progress of the refinement and will close when the
1395least-squares fit <span class=GramE>is</span> complete (usually very fast). The
1396plot is updated with the fit, the peak list window is updated with the new peak
1397values and a summary of the refinement is shown on the console window as well.</p>
1398
1399<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1400 id="Picture_x0020_8" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:525pt;
1401 height:450pt;visibility:visible;mso-wrap-style:square'>
1402 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
1403</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1404src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_8"><![endif]></span></p>
1405
1406<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1407 id="Picture_x0020_9" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:401.25pt;
1408 height:262.5pt;visibility:visible;mso-wrap-style:square'>
1409 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1410</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1411src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_9"><![endif]></span></p>
1412
1413<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1414style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1415style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1416add refinement of the peak positions. This can be done by clicking on all the
1417refinement flags for the individual peaks or it is possible to set them all at
1418the same time using this recipe: </p>
1419
1420<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1421auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1422style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1423style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1424class=GramE>single-click</span> on any value in the table to select it, for
1425example the first peak position. A black box appears around the value. </p>
1426
1427<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1428text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1429style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1430style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1431class=GramE>single-click</span> on the refine label above the peak position
1432check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
1433style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1434mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1435minor-latin'>y</span></b> key to turn on all refinement flags (<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'>n</span></b> would turn them off).</p>
1439
1440<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1441the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1442mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1443minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu
1444item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1445"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1446minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b> window.</p>
1447
1448<p class=MsoNormal style='margin-left:.5in'><span
1449style='mso-spacerun:yes'> </span>Now, select peak widths for refinement. <span
1450style='mso-fareast-font-family:"Times New Roman"'>This can be performed in 2
1451different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian width) and/or
1452gamma (Lorentzian width) for individual peaks. &nbsp;To do this, click the
1453refinement flags for sigma and/or gamma in the Peak List window.
1454&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1455widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening
1456equation as described below.&nbsp;Note - one cannot refine ALL peak widths
1457using both individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental
1458broadening terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1459
1460<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1461"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1462to an instrumental broadening equation, first<b> s</b></span>elect the <b
1463style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1464mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1465minor-latin'>Instrumental Parameters</span></b> item in the data tree. <span
1466class=GramE>This opens a window for peak profile terms<b> </b><span
1467style='mso-bidi-font-weight:bold'>and also create</span></span><span
1468style='mso-bidi-font-weight:bold'> a new plot window&nbsp;showing the
1469instrument profile resolution curve.</span></p>
1470
1471<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1472 id="Picture_x0020_10" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:422.25pt;
1473 height:154.5pt;visibility:visible;mso-wrap-style:square'>
1474 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
1475</v:shape><![endif]--><![if !vml]><img border=0 width=563 height=206
1476src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
1477
1478<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1479corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1480coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1481values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1482<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1483mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1484minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
1485style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1486mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
1487<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1489minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
1490style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1491mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
1492<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1493mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1494minor-latin'>Y</span></b>. </p>
1495
1496<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1497style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1498style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1499repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1500style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1501mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1502item in the data tree and then refine using 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'>Peak
1505Fitting/LSQ <span class=SpellE>PeakFit</span></span></b> menu item. At this
1506point a good fit should be seen by zooming in on individual peaks. (For example
1507see </p>
1508
1509<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1510 id="Picture_x0020_11" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1511 height:450pt;visibility:visible;mso-wrap-style:square'>
1512 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1513</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1514src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1515
1516<p class=MsoListParagraphCxSpLast>The <span class=SpellE>Rwp</span> is ~6% as
1517shown on the console window. Again the <b style='mso-bidi-font-weight:normal'><span
1518style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1519mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1520entries are all updated with new values and those in <b style='mso-bidi-font-weight:
1521normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1522minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
1523Parameters</span></b> are also updated.</p>
1524
1525<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1526
1527<p class=MsoNormal>A separate list of peaks is kept for use in <span
1528class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1529normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1530minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1531Peak List</span></b> item in the data tree. In the initially empty window
1532created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1533style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1534mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index Peaks
1535Operations/Load</span></b> to copy the fitted peaks from the <b
1536style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1537mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1538minor-latin'>Peak List</span></b>.</p>
1539
1540<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1541 id="Picture_x0020_12" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:367.5pt;
1542 height:225pt;visibility:visible;mso-wrap-style:square'>
1543 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
1544</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
1545src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_12"><![endif]></span></p>
1546
1547<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1548may choose to not use a fitted peak (e.g. if suspected it is from a
1549contaminant).</p>
1550
1551<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
1552
1553<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1554style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1555mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1556List</span></b> data item. This brings up a window for indexing and cell refinement
1557options</p>
1558
1559<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1560 id="Picture_x0020_13" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:527.25pt;
1561 height:204pt;visibility:visible;mso-wrap-style:square'>
1562 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1563</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
1564src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1565
1566<p class=MsoNormal>For the most rapid search (since we know the right answer),
1567select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1568mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1569minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1570style='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'>Cell Index/Index Cell</span></b>. The search then runs and the console
1573shows a running list of possible cells as they are found; the sorted by M20
1574list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1575normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1576minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1577Cells List</span></b> window</p>
1578
1579<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1580 id="Picture_x0020_14" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:527.25pt;
1581 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1582 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1583</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1584src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_14"><![endif]></span></p>
1585
1586<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
1587
1588<p class=MsoNormal>Review the list of cells associated with the <b
1589style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1590mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1591minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1592unit cell, the generated reflections for that cell are shown in the plot with
1593dashed red lines. Sliding the cursor over these lines shows a small popup
1594window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1595first cell in the list (M20~3000) with a=5.87864 Å generates very many lines
1596with no corresponding peaks (NB: this solution might not always show up!)</p>
1597
1598<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1599 id="Picture_x0020_15" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1600 height:450pt;visibility:visible;mso-wrap-style:square'>
1601 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
1602</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1603src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_15"><![endif]></span><span
1604style='mso-spacerun:yes'> </span></p>
1605
1606<p class=MsoNormal><span class=GramE>while</span> the (M20~600) cell with
1607a=2.93932 Å generates not enough lines to match all the peaks</p>
1608
1609<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1610 id="Picture_x0020_16" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
1611 height:450pt;visibility:visible;mso-wrap-style:square'>
1612 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1613</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1614src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_16"><![endif]></span></p>
1615
1616<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
1617
1618<p class=MsoNormal>Select the cell with M20 ~ 2900 with a = 4.1568 Å. This
1619indexes all peaks with almost a perfect fit to the peak positions (compare
1620dashed red lines to solid blue ones). Import the cell information using the <b
1621style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1622mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1623minor-latin'>Cell Index/Copy Cell</span></b> menu option. Then optimize the
1624cell by refining the lattice parameters and the two-theta zero: click on the
1625refine checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1626style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1627mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1628value and then 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'>Cell
1631Index/Refine Cell</span></b> menu option. <span class=GramE>The a</span> cell
1632parameter value shifts from 4.15679 to 4.15684 when zero is refined. Press the <b
1633style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1634mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1635minor-latin'>Show refined <span class=SpellE>hkl</span> positions + Zero offset</span></b>
1636button to update the plot including the refined <b style='mso-bidi-font-weight:
1637normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1638minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero
1639offset</span></b> (in this case hardly anything happens!) </p>
1640
1641<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1642 id="Picture_x0020_17" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:527.25pt;
1643 height:334.5pt;visibility:visible;mso-wrap-style:square'>
1644 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1645</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
1646src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_17"><![endif]></span></p>
1647
1648<p class=MsoNormal>Notice that a new entry heads the list in the <b
1649style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1651minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
1652normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1653minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1654Index/Refine</span></b> window with an improved M20(=3614.66) and a new value
1655for <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1656mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1657minor-latin'>Zero offset</span></b> is shown.</p>
1658
1659<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
1660normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1661minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1662Index/New phase</span></b> menu option allows one to create a phase with these
1663lattice parameters in the data tree under <b style='mso-bidi-font-weight:normal'><span
1664style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1665mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
1666style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
1667creates the tree item <b style='mso-bidi-font-weight:normal'><span
1668style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1669mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
1670(if it wasn’t already present). This new phase can be used in future analysis
1671(e.g. Rietveld or Pawley refinement).</p>
1672
1673<p class=MsoNormal>To continue with the second part of this exercise, <span
1674class=GramE>do the menu item</span> <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'>File/Close
1677project</span></b> in the <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'>GSAS-II data
1680tree </span></b>window. You will be asked if you want it saved; if <span
1681class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1682"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1683minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> then all the
1684peak fitting/indexing &amp; cell refinement results will be saved to the <b
1685style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1686mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1687minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
1688style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1689mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
1690then the file will remain as it was when created at Step 4 above.</p>
1691
1692<h1>2<sup>nd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1693
1694<p class=MsoNormal>In this exercise we will fit peaks and index them for the
1695new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
1696(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
1697data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a
1698more substantial test of the indexing capability of GSAS-II.</p>
1699
1700<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1701
1702<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1703style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1704mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>\Exercises\<span
1705class=SpellE>krptonite</span>\11bmb_6231.fxye</span></b>; it has a
1706corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1707style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1708mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span>
1709file. Load them in &amp; the plot is</p>
1710
1711<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1712 id="Picture_x0020_18" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1713 height:450pt;visibility:visible;mso-wrap-style:square'>
1714 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
1715</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1716src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_18"><![endif]></span></p>
1717
1718<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
1719lower part of the pattern.</p>
1720
1721<h2>Step 2 Set limits</h2>
1722
1723<p class=MsoNormal>Set the limits as <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'>3</span></b>
1726and <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'>10</span></b>.</p>
1729
1730<h2>Step 3 Pick peaks</h2>
1731
1732<p class=MsoNormal>Pick all peaks you can see between the limits (including the
1733small ones). Note some peaks have shoulders most notably at 5.07, 6.04,
17347.81deg. I found 28 peaks (there were a few very weak ones I skipped – they
1735might be from a second phase? We’ll see later).</p>
1736
1737<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_19" o:spid="_x0000_s1026"
1738 type="#_x0000_t75" style='position:absolute;margin-left:0;margin-top:0;
1739 width:525pt;height:450pt;z-index:251658240;visibility:visible;
1740 mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
1741 mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1742 mso-wrap-distance-bottom:0;mso-position-horizontal:left;
1743 mso-position-horizontal-relative:text;mso-position-vertical:top;
1744 mso-position-vertical-relative:text;mso-width-percent:0;mso-height-percent:0;
1745 mso-width-relative:page;mso-height-relative:page'>
1746 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1747 <w:wrap type="square"/>
1748</v:shape><![endif]--><![if !vml]><img width=700 height=600
1749src="Fit%20Peaks_files/image020.png" align=left hspace=12 v:shapes="Picture_x0020_19"><![endif]><br
1750clear=all style='mso-special-character:line-break'>
1751</p>
1752
1753<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
1754
1755<p class=MsoNormal>Following the steps above, refine the peaks and the profile
1756shape parameters in <b style='mso-bidi-font-weight:normal'><span
1757style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1758mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Instrument
1759Parameters</span></b>. You will be asked for a project file name at the first
1760refinement (I used ‘<span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1761style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1762mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
1763style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1764mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1765minor-latin'>’</span></b>). In the end my refinement converged at <span
1766class=SpellE>Rwp</span>=13.18% and some peaks do show some discrepancy as the
1767sample is more complex than the simple <b style='mso-bidi-font-weight:normal'><span
1768style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1769mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>U</span></b>,
1770<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1771mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1772minor-latin'>V</span></b>, <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'>W</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'>X</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'>Y</span></b>
1780model can accommodate. However, this is good enough to proceed.</p>
1781
1782<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1783
1784<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
1785style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1786mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1787in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1788mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1789minor-latin'>Index Peak List</span></b> window.</p>
1790
1791<h2><span class=GramE>Step 6.</span> Index the cell</h2>
1792
1793<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
1794In a real world case we wouldn’t know this and we would have to try each <span
1795class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
1796time to go through all the bad cases.</p>
1797
1798<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1799style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1800mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
1801and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1802mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1803minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
1804style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1805mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1806minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
1807and suitable results will be slow in coming so be patient. Watch the console
1808window; the right answer will have an obviously large M20 (~630) and a volume
1809of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
1810seen (it may take more than one try to get this) you can stop the indexing
1811search by pressing <b style='mso-bidi-font-weight:normal'><span
1812style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1813mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
1814on the progress bar window. It may take more than one press to fully stop it.
1815My result was </p>
1816
1817<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1818 id="Picture_x0020_20" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:527.25pt;
1819 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1820 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
1821</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1822src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
1823
1824<p class=MsoNormal>Notice an equally good M20 result with twice the volume. The
1825plot shows every peak indexed including a couple of weak peaks not selected for
1826the peak fitting.</p>
1827
1828<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1829 id="Picture_x0020_21" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
1830 height:450pt;visibility:visible;mso-wrap-style:square'>
1831 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1832</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1833src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_21"><![endif]></span></p>
1834
1835<p class=MsoNormal>Although the weak peak at 2<span style='font-family:Symbol;
1836mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1837symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3 has a shoulder that
1838wasn’t indexed. I presume that is a contaminant. By sliding the cursor over the
1839index lines without any visible peak you can see that the missing ones are
1840(010, 100, 001, 110, 030, 111, 20-1, 10-2, 041, 050, 21-2, 23-1, 22-2, 141,
1841201,102, 15-1, 112, &amp; 24-1). Many of these are accidental but the 0k0; k&#8800;2n
1842and h0l; h+l&#8800;2n ones characterize the space group P2<sub>1</sub>/n. Armed
1843with this information you can <b style='mso-bidi-font-weight:normal'><span
1844style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1845mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
1846phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
1847normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1848minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>kryptonite’</span></b>)
1849and set the space group in the <b style='mso-bidi-font-weight:normal'><span
1850style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1851mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data
1852for kryptonite</span></b> window.</p>
1853
1854<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1855 id="Picture_x0020_22" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:597.75pt;
1856 height:214.5pt;visibility:visible;mso-wrap-style:square'>
1857 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
1858</v:shape><![endif]--><![if !vml]><img border=0 width=797 height=286
1859src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_22"><![endif]></span></p>
1860
1861<p class=MsoNormal>Setting the space group will show a window with some
1862information. Press <b style='mso-bidi-font-weight:normal'><span
1863style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1864mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
1865to close it.</p>
1866
1867<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1868 id="Picture_x0020_23" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:333.75pt;
1869 height:209.25pt;visibility:visible;mso-wrap-style:square'>
1870 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1871</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
1872src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1873
1874<p class=MsoNormal>This concludes this exercise; <span class=GramE><b
1875style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1876mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1877minor-latin'>Save</span></b></span> the project file as it is needed for the <b
1878style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1879mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1880minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
1881exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
1882style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1883mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase Data</span></b>
1884window will be presented in other exercises.</p>
1885
1886</div>
1887
1888</body>
1889
1890</html>
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