source: trunk/help/Fit Peaks.htm @ 864

Last change on this file since 864 was 864, checked in by vondreele, 10 years ago

fix to mustrain plot scaling - generalized was off by 100X
remove a stray print in GSASIIstruct.py
work on tutorials - add charge flipping

  • Property svn:keywords set to Author
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File size: 108.1 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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1123</head>
1124
1125<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1126
1127<div class=WordSection1>
1128
1129<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1130
1131<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1132cell that matches a set of diffraction peaks -- a process known as
1133auto-indexing. First peaks must be located and optimized and then indexing can
1134be done.</p>
1135
1136<p class=MsoNormal>If you have not done so already, <a
1137href="Starting%20GSAS.htm">start GSAS-II</a>.</p>
1138
1139<h2>Step 1: read in the data file</h2>
1140
1141<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1142style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1143style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1144the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1145mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1146Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS file</span></b>
1147menu item to read the data file into the current GSAS-II project. This read
1148option is set to read any of the powder data formats (except neutron TOF time
1149map files) defined for GSAS (angles in <span class=SpellE>centidegrees</span>).
1150Other submenu items will read the <span class=SpellE><b style='mso-bidi-font-weight:
1151normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1152minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1153mso-bidi-theme-font:minor-latin'>cif</span></b></span> format or the <span
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1155"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1156minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1157format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1158style='mso-spacerun:yes'>  </span>Change the file directory to <b
1159style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1160mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1161Calibri;mso-bidi-theme-font:minor-latin'>Exercises/LaB6</span></b><span
1162style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1163mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;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-font-family:
1173Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.fxye</span></b><span
1174style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1175mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1176minor-latin'> data</span> file in the first dialog and press <b
1177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1179Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
1180Dialog box asking <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1181style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1182mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1183minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
1184style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1185mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1186minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1187style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1188mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1189Calibri;mso-bidi-theme-font:minor-latin'>Yes</span></b></span> button to
1190proceed.</p>
1191
1192<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1193style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1194style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1195file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1196mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1197Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.prm</span></b> instrument
1198parameter file is automatically selected; it was produced by 11BM-B instrument
1199processing software when the corresponding <span class=SpellE><b
1200style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
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1202Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was
1203created from the 12 detector raw data. If absent or the name doesn’t match the
1204data file name, a file dialog will appear for you to select the correct
1205instrument parameter file.</p>
1206
1207<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1208style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1209mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1210minor-latin'>GSAS-II data tree</span></b> window will have several entries </p>
1211
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1227  <v:f eqn="prod @7 21600 pixelHeight"/>
1228  <v:f eqn="sum @10 21600 0"/>
1229 </v:formulas>
1230 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1231 <o:lock v:ext="edit" aspectratio="t"/>
1232</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1052" type="#_x0000_t75"
1233 style='width:225pt;height:187.5pt;visibility:visible;mso-wrap-style:square'>
1234 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
1235</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=250
1236src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1237
1238<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1239powder pattern</p>
1240
1241<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1242 id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1243 height:450pt;visibility:visible;mso-wrap-style:square'>
1244 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
1245</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1246src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1247
1248<h2>Step 2: Select Limits </h2>
1249
1250<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1251more data than we need, so it is helpful to cut down the range. Click on the <b
1252style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1253mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1254Calibri;mso-bidi-theme-font:minor-latin'>Limits</span></b> item in the <b
1255style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1256mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1257Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. The
1258small window is repainted. Use the <b style='mso-bidi-font-weight:normal'><span
1259style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1260mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1261minor-latin'>changed</span></b> row of entry boxes to set <span class=SpellE><b
1262style='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-font-family:
1264Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span
1265class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1266"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1267minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1268to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1269mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1270Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
1271normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1272minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1273mso-bidi-theme-font:minor-latin'>27.5</span></b>. Notice on the plot that the
1274limit lines have moved to these positions; the green lower limit is just below
1275the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks.
1276You may also drag the limit lines to the desired location or place them by a
1277left mouse click on a data point for the lower limit or a right click on a data
1278point for the upper limit.</p>
1279
1280<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1281 id="Picture_x0020_3" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:225pt;
1282 height:120pt;visibility:visible;mso-wrap-style:square'>
1283 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1284</v:shape><![endif]--><![if !vml]><img border=0 width=300 height=160
1285src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_3"><![endif]></span></p>
1286
1287<h2>Step 3: Determine Peak Positions</h2>
1288
1289<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1290auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1291style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1292style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1293on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1294mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1295Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> item in the <b
1296style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1298Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. This
1299creates an empty window of peak positions (the <b style='mso-bidi-font-weight:
1300normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1301minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1302mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this
1303point it is wise <span class=GramE>to<span style='mso-spacerun:yes'> 
1304</span>zoom</span> in on the data that will be used for indexing. </p>
1305
1306<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1307auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1308style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1309style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1310on the Zoom button, <span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1311 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:21.75pt;
1312 height:18.75pt;visibility:visible;mso-wrap-style:square'>
1313 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1314  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1315</v:shape><![endif]--><![if !vml]><img border=0 width=29 height=25
1316src="Fit%20Peaks_files/image005.jpg" v:shapes="Picture_x0020_4"><![endif]></span>,
1317then press the left mouse in one corner of the region to be used; holding the
1318mouse button down, drag over the region to the opposite corner; a box will be
1319drawn over the region to be zoomed. </p>
1320
1321<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1322auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1323style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1324style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1325style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom <span
1326style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5"
1327 o:spid="_x0000_i1048" type="#_x0000_t75" style='width:23.25pt;height:20.25pt;
1328 visibility:visible;mso-wrap-style:square'>
1329 <v:imagedata src="Fit%20Peaks_files/image004.jpg" o:title="" croptop="1f"
1330  cropbottom="-1f" cropleft="35827f" cropright="19224f"/>
1331</v:shape><![endif]--><![if !vml]><img border=0 width=31 height=27
1332src="Fit%20Peaks_files/image006.jpg" v:shapes="Picture_x0020_5"><![endif]></span><span
1333style='mso-spacerun:yes'> </span>button again to turn off the zoom mode. </p>
1334
1335<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1336auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1337style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1338style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1339<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1341in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1342mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
1343window select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1344"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1345minor-latin'>Auto search</span></b>. The plot window will immediately show that
1346all peaks were picked with a blue vertical line on each one</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_27"
1350 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;
1351 visibility:visible;mso-wrap-style:square'>
1352 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
1353</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1354src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
1355
1356<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1357auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1358normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1359minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1360mso-bidi-theme-font:minor-latin'>Peak List</span></b> window in order of
1361increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1362
1363<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1364auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_7"
1365 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
1366 visibility:visible;mso-wrap-style:square'>
1367 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1368</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1369src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_7"><![endif]></span></p>
1370
1371<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1372will be 23 peaks in this example. You should examine both the list and the plot
1373to be sure the auto search did not pick a peak twice (there may be three of
1374these!) or skip a peak or shoulder. You can add a peak to the list by pressing
1375the left mouse button with the pointer on a data point at the peak top or
1376shoulder. You may drag a peak position as needed; be sure the zoom/shift
1377buttons are off. A position may be deleted with a right click with the mouse on
1378the blue line. You can also delete a peak by selecting the row in the <span
1379class=GramE>table,</span> it will be highlighted in blue. Then press the Delete
1380key; it will be removed from the table and the plot. The list will always show
1381the peaks sorted by position. When done you should have 20 unique peak
1382positions.</p>
1383
1384<h2>Step 4: Refine Peak Positions</h2>
1385
1386<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1387refinement and then adding parameters to complete the fitting,</p>
1388
1389<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1390style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1391style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1392the peak intensities and the background. These parameters have their refinement
1393flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1394normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1395minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1396mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span>
1397</span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family:
1398"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1399minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak
1400List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use
1401the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1402mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1403Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item
1404in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1406Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window;
1407that it to be used for Rietveld/Pawley refinements. You will be asked to save
1408the current project before the fit will proceed; change directory if desired
1409and provide a suitable name (we assume <b style='mso-bidi-font-weight:normal'><span
1410style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1411mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1412minor-latin'>LaB6</span></b>). A window will show the progress of the
1413refinement and will close when the least-squares fit <span class=GramE>is</span>
1414complete (usually very fast). The plot is updated with the fit, the peak list
1415window is updated with the new peak values and a summary of the refinement is
1416shown on the console window as well.</p>
1417
1418<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1419 id="_x0000_i1045" type="#_x0000_t75" style='width:525pt;height:450pt;
1420 visibility:visible;mso-wrap-style:square'>
1421 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
1422</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1423src="Fit%20Peaks_files/image009.png" v:shapes="_x0000_i1045"><![endif]></span></p>
1424
1425<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1426 id="Picture_x0020_24" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:401.25pt;
1427 height:262.5pt;visibility:visible;mso-wrap-style:square'>
1428 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1429</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1430src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1431
1432<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1433style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1434style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1435add refinement of the peak positions. This can be done by clicking on all the
1436refinement flags for the individual peaks or it is possible to set them all at
1437the same time using this recipe: </p>
1438
1439<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1440auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1441style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1442style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1443class=GramE>single-click</span> on any value in the table to select it, for
1444example the first peak position. A black box appears around the value. </p>
1445
1446<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1447text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1448style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1449style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1450class=GramE>single-click</span> on the refine label above the peak position
1451check-boxes. The entire column of checkboxes is highlighted in blue. Press the <b
1452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1454Calibri;mso-bidi-theme-font:minor-latin'>y</span></b> key to turn on all
1455refinement flags (<b style='mso-bidi-font-weight:normal'><span
1456style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1457mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1458minor-latin'>n</span></b> would turn them off).</p>
1459
1460<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1461the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1462mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1463Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
1464menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1465"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1466minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak
1467List</span></b> window.</p>
1468
1469<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1470refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1471performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1472width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
1473click the refinement flags for sigma and/or gamma in the Peak List window.
1474&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1475widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening
1476equation as described below.&nbsp;Note - one cannot refine ALL peak widths
1477using both individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental
1478broadening terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1479
1480<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1481"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1482to an instrumental broadening equation, first<b> s</b></span>elect the <b
1483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1485Calibri;mso-bidi-theme-font:minor-latin'>Instrumental Parameters</span></b>
1486item in the data tree. This opens a window for peak profile terms<b> </b><span
1487style='mso-bidi-font-weight:bold'>and also creates a new plot
1488window&nbsp;showing the instrument profile resolution curve.</span></p>
1489
1490<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1491 id="Picture_x0020_10" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:422.25pt;
1492 height:154.5pt;visibility:visible;mso-wrap-style:square'>
1493 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
1494</v:shape><![endif]--><![if !vml]><img border=0 width=563 height=206
1495src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_10"><![endif]></span></p>
1496
1497<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1498corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1499coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1500values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1501<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1502mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1503Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1504normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1505minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1506mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
1507normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1508minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1509mso-bidi-theme-font:minor-latin'>W</span></b>, and Lorentzian <b
1510style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1511mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1512Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
1513normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1514minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1515mso-bidi-theme-font:minor-latin'>Y</span></b>. </p>
1516
1517<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1518style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1519style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1520repeat the refinement. First click on 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-font-family:Calibri;mso-bidi-theme-font:
1523minor-latin'>Peak List</span></b> item in the data tree and then refine using
1524the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1526Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/LSQ <span class=SpellE>PeakFit</span></span></b>
1527menu item. At this point a good fit should be seen by zooming in on individual
1528peaks. For example see </p>
1529
1530<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1531 id="Picture_x0020_11" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1532 height:450pt;visibility:visible;mso-wrap-style:square'>
1533 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1534</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1535src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_11"><![endif]></span></p>
1536
1537<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
1538the right of the peak top. This is a consequence of the peak asymmetry arising
1539from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
1540is ~6% as shown on the console window. Again the <b style='mso-bidi-font-weight:
1541normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1542minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1543mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all updated
1544with new values and those in <b style='mso-bidi-font-weight:normal'><span
1545style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1546mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1547minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1548
1549<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1550
1551<p class=MsoNormal>A separate list of peaks is kept for use in <span
1552class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1553normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1554minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1555mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data
1556tree. In the initially empty window created by this action, use menu item <b
1557style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1558mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1559Calibri;mso-bidi-theme-font:minor-latin'>Index Peaks Operations/Load</span></b>
1560to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1561style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1562mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1563minor-latin'>Peak List</span></b>.</p>
1564
1565<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1566 id="Picture_x0020_26" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:367.5pt;
1567 height:225pt;visibility:visible;mso-wrap-style:square'>
1568 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
1569</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
1570src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1571
1572<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1573may choose to not use a fitted peak (e.g. if suspected it is from a
1574contaminant).</p>
1575
1576<h2><span class=GramE>Step 6.</span> Run <span class=SpellE>Autoindexing</span></h2>
1577
1578<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1579style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1580mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1581minor-latin'>Unit Cells List</span></b> data item. This brings up a window for
1582indexing and cell refinement options</p>
1583
1584<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1585 id="Picture_x0020_13" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:527.25pt;
1586 height:204pt;visibility:visible;mso-wrap-style:square'>
1587 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1588</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=272
1589src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1590
1591<p class=MsoNormal>For the most rapid search (since we know the right answer),
1592select <b style='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-font-family:
1594Calibri;mso-bidi-theme-font:minor-latin'>Cubic-P</span></b> and launch the
1595search using menu item <b style='mso-bidi-font-weight:normal'><span
1596style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1597mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1598minor-latin'>Cell Index/Index Cell</span></b>. The search then runs and the
1599console shows a running list of possible cells as they are found; the sorted by
1600M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1601normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1602minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1603mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
1604
1605<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1606 id="Picture_x0020_28" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:527.25pt;
1607 height:376.5pt;visibility:visible;mso-wrap-style:square'>
1608 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1609</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1610src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1611
1612<h2><span class=GramE>Step 7.</span> Review Cell Choices</h2>
1613
1614<p class=MsoNormal>Review the list of cells associated with the <b
1615style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1616mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1617Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> data item.
1618Note that as one selects a unit cell, the generated reflections for that cell
1619are shown in the plot with dashed red lines. Sliding the cursor over these
1620lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
1621for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å
1622generates very many lines with no corresponding peaks (NB: this solution might
1623not always show up!)</p>
1624
1625<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1626 id="Picture_x0020_38" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1627 height:450pt;visibility:visible;mso-wrap-style:square'>
1628 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
1629</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1630src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_38"><![endif]></span><span
1631style='mso-spacerun:yes'> </span></p>
1632
1633<p class=MsoNormal><span class=GramE>while</span> the (M20~600) cell with
1634a=2.93932 Å generates not enough lines to match all the peaks</p>
1635
1636<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1637 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1638 height:450pt;visibility:visible;mso-wrap-style:square'>
1639 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1640</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1641src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_39"><![endif]></span></p>
1642
1643<h2><span class=GramE>Step 8.</span> Select/Refine Cell</h2>
1644
1645<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1646indexes all peaks with almost a perfect fit to the peak positions (compare
1647dashed red lines to solid blue ones). Import the cell information using the <b
1648style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1649mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1650Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Copy Cell</span></b> menu
1651option. Then optimize the cell by refining the lattice parameters and the
1652two-theta zero: click on the refine checkbox next to the <b style='mso-bidi-font-weight:
1653normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1654minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1655mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then the <b
1656style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1657mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1658Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine Cell</span></b> menu
1659option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
1660parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
1661certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
1662style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1663mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1664Calibri;mso-bidi-theme-font:minor-latin'>Show refined <span class=SpellE>hkl</span>
1665positions + Zero offset</span></b> button to update the plot including the
1666refined <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1668Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
1669hardly anything happens!) </p>
1670
1671<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1672 id="_x0000_i1036" type="#_x0000_t75" style='width:527.25pt;height:334.5pt;
1673 visibility:visible;mso-wrap-style:square'>
1674 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1675</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=446
1676src="Fit%20Peaks_files/image018.png" v:shapes="_x0000_i1036"><![endif]></span></p>
1677
1678<p class=MsoNormal>Notice that a new entry heads the list in the <b
1679style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1680mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1681Calibri;mso-bidi-theme-font:minor-latin'>Indexing Result</span></b> section of
1682the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1683mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1684Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine</span></b> window
1685with an improved M20(=3607.97) and a new value for <b style='mso-bidi-font-weight:
1686normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1687minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1688mso-bidi-theme-font:minor-latin'>Zero offset</span></b> is shown.</p>
1689
1690<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
1691normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1692minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1693mso-bidi-theme-font:minor-latin'>Cell Index/New phase</span></b> menu option
1694allows one to create a phase with these lattice parameters in the data tree
1695under <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1696mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1697Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
1698style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
1699creates the tree item <b style='mso-bidi-font-weight:normal'><span
1700style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1701mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1702minor-latin'>Phases</span></b> (if it wasn’t already present). This new phase
1703can be used in future analysis (e.g. Rietveld or Pawley refinement).</p>
1704
1705<p class=MsoNormal>To continue with the second part of this exercise, select
1706the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
1707"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1708minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/Close
1709project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1710style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1711mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1712minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
1713it saved; if <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1714style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1715mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1716minor-latin'>Yes</span></b></span> then all the peak fitting/indexing &amp;
1717cell refinement results will be saved to the <b style='mso-bidi-font-weight:
1718normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1719minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1720mso-bidi-theme-font:minor-latin'>LaB6.gpx</span></b> file. If <b
1721style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1722mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1723Calibri;mso-bidi-theme-font:minor-latin'>No</span></b> then the file will
1724remain as it was when created at Step 4 above.</p>
1725
1726<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
1727class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
1728style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
1729
1730<p class=MsoNormal>In this exercise we will fit peaks and index them for the
1731new mineral <a href="http://en.wikipedia.org/wiki/Jadarite"><span class=SpellE>jadarite</span></a>
1732(aka “<a href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The
1733data was also collected on 11BM-B at APS. The unit cell is monoclinic so is a more
1734substantial test of the indexing capability of GSAS-II.</p>
1735
1736<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1737
1738<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1739style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1740mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1741minor-latin'>\Exercises\kryptonite\11bmb_6231.fxye</span></b>; it has a
1742corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1743style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1744mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1745minor-latin'>prm</span></b></span> file. Load them in &amp; the plot is</p>
1746
1747<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1748 id="_x0000_i1035" type="#_x0000_t75" style='width:525pt;height:450pt;
1749 visibility:visible;mso-wrap-style:square'>
1750 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
1751</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1752src="Fit%20Peaks_files/image019.png" v:shapes="_x0000_i1035"><![endif]></span></p>
1753
1754<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
1755lower part of the pattern.</p>
1756
1757<h2>Step 2 Set limits</h2>
1758
1759<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
1760style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1761mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1762minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:normal'><span
1763style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1764mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1765minor-latin'>9</span></b>.</p>
1766
1767<h2>Step 3 Pick peaks</h2>
1768
1769<p class=MsoNormal>Pick all peaks you can see between the limits (including the
1770small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
1771"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1772minor-latin'>Auto search</span></b> to start and then fill in by hand. Note
1773some peaks have shoulders most notably at 5.07, 6.04, 7.81deg. I found 28 peaks
1774(there was one very weak shoulder at ~7.3 deg. I skipped – it might be from a
1775second phase? We’ll see later).</p>
1776
1777<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1778 id="Picture_x0020_33" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
1779 height:450pt;visibility:visible;mso-wrap-style:square'>
1780 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1781</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1782src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_33"><![endif]></span><br
1783clear=all style='mso-special-character:line-break'>
1784</p>
1785
1786<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
1787
1788<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
1789above, refine the peaks and the profile shape parameters in <b
1790style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1791mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1792Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
1793will be asked for a project file name at the first refinement (I used ‘<span
1794class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1795"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1796minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
1797style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1798mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1799Calibri;mso-bidi-theme-font:minor-latin'>’</span></b>). In the end my
1800refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do
1801show some discrepancy as the sample is more complex than the simple <b
1802style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1803mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1804Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1805normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1806minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1807mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
1808normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1809minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1810mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
1811normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1812minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1813mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
1814normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1815minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1816mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure no
1817peaks drift away during refinement (one weak one at ~6.67 is particularly
1818troublesome). However, this is good enough to proceed.</p>
1819
1820<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
1821
1822<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
1823style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1824mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1825minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
1826normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1827minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1828mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
1829
1830<h2><span class=GramE>Step 6.</span> Index the cell</h2>
1831
1832<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
1833In a real world case we wouldn’t know this and we would have to try each <span
1834class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
1835time to go through all the bad cases.</p>
1836
1837<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
1838style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1839mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1840minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
1841normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1842minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1843mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
1844<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1845mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1846Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
1847Progress will be much slower and suitable results will be slow in coming so be
1848patient. Watch the console window; the right answer will have an obviously
1849large M20 (~372) and a volume of ~594Å<sup>3</sup> (10<sup>th</sup> column of
1850console display). Once this is seen (it may take more than one try to get this)
1851you can stop the indexing search by pressing <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-font-family:Calibri;
1854mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window.
1855Notice the ‘<b style='mso-bidi-font-weight:normal'>keep’</b> column; this
1856allows you to keep some solutions from one indexing run to the next. It may
1857take more than one press to fully stop it. My result was </p>
1858
1859<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1860 id="Picture_x0020_21" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
1861 height:450pt;visibility:visible;mso-wrap-style:square'>
1862 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
1863</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1864src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_21"><![endif]><!--[if gte vml 1]><v:shape
1865 id="_x0000_i1032" type="#_x0000_t75" style='width:527.25pt;height:376.5pt;
1866 visibility:visible;mso-wrap-style:square'>
1867 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1868</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
1869src="Fit%20Peaks_files/image022.png" v:shapes="_x0000_i1032"><![endif]></span></p>
1870
1871<p class=MsoNormal>Notice other equally good M20 results with different
1872volumes; other solutions may be obtained as you keep trying the indexing. Be
1873sure to use <b style='mso-bidi-font-weight:normal'><span style='font-family:
1874"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1875minor-latin'>Keep</span></b> to keep good ones as you try new indexing runs.
1876The best solution is the one with the smaller volume. The plot shows every peak
1877indexed including a weak peak not selected for the peak fitting, although the
1878weak peak at 2<span style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:
1879Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
1880has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
1881best cell and try to refine it along with the <b style='mso-bidi-font-weight:
1882normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1883minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
1884obtained an improved M20 ~444 and slightly different lattice parameters. Try
1885different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
1886style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1887mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
1888each time to see which lines vanish. By sliding the cursor over the index lines
1889without any visible peak you can see that the missing ones are 010, 100, 001,
1890110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
1891accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
1892space group P2<sub>1</sub>/n. Armed with this information you can <b
1893style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1895Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
1896indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
1897style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1898mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1899minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
1900normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1901minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
1902the GSAS-II data tree.</p>
1903
1904<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1905 id="Picture_x0020_35" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:545.25pt;
1906 height:303.75pt;visibility:visible;mso-wrap-style:square'>
1907 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
1908</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
1909src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_35"><![endif]></span><span
1910style='mso-spacerun:yes'> </span></p>
1911
1912<p class=MsoNormal>Notice that the lattice parameters and space group have been
1913set for you. If you set the space group here a dialog box will appear.</p>
1914
1915<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1916 id="Picture_x0020_23" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:333.75pt;
1917 height:209.25pt;visibility:visible;mso-wrap-style:square'>
1918 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1919</v:shape><![endif]--><![if !vml]><img border=0 width=445 height=279
1920src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_23"><![endif]></span></p>
1921
1922<p class=MsoNormal>This concludes this exercise; <span class=GramE><b
1923style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1924mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1925Calibri;mso-bidi-theme-font:minor-latin'>Save</span></b></span> the project
1926file as it is needed for the <b style='mso-bidi-font-weight:normal'><span
1927style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1928mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1929minor-latin'><a href="Charge%20Flipping%20in%20GSAS.htm">Charge Flipping</a></span></b>
1930exercise. The features of the <b style='mso-bidi-font-weight:normal'><span
1931style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1932mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1933minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
1934
1935<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
1936in GSAS-II </h1>
1937
1938<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
1939in preparation for a charge flipping exercise. The data was also collected on
194011BM-B at APS. The unit cell is monoclinic so is a more substantial test of the
1941indexing capability of GSAS-II.</p>
1942
1943<h2><span class=GramE>Step 1.</span> Read in the data. </h2>
1944
1945<p class=MsoNormal>The file is <b style='mso-bidi-font-weight:normal'><span
1946style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1947mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1948minor-latin'>\Exercises\sucrose\11bmb_8716.fxye</span></b>; it has a
1949corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1950style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1951mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1952minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under
1953acetone. <span class=GramE>The other <span class=SpellE><b style='mso-bidi-font-weight:
1954normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1955minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in
1956this directory <b style='mso-bidi-font-weight:normal'><span style='font-family:
1957"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1958minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X powdered sugar used
1959“as is” out of the box.</span> Load the <b style='mso-bidi-font-weight:normal'><span
1960style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1961mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the plot is</p>
1962
1963<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1964 id="Picture_x0020_29" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
1965 height:450pt;visibility:visible;mso-wrap-style:square'>
1966 <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/>
1967</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1968src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1969
1970<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
1971lower part of the pattern.</p>
1972
1973<h2>Step 2 Set limits</h2>
1974
1975<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
1976style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1977mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1978minor-latin'>2</span></b> and <b style='mso-bidi-font-weight:normal'><span
1979style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1980mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1981minor-latin'>8</span></b>.</p>
1982
1983<h2>Step 3 Pick peaks</h2>
1984
1985<p class=MsoNormal>Pick all peaks you can see between the limits (including the
1986small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
1987"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1988minor-latin'>Auto search</span></b> to start and then fill in by hand. Note the
1989shoulder at ~6.3 <span class=SpellE>deg</span> that should be added to the
1990list. I skipped a couple of very weak peaks; the total list has 28 peaks.</p>
1991
1992<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1993 id="Picture_x0020_30" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
1994 height:450pt;visibility:visible;mso-wrap-style:square'>
1995 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
1996</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1997src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_30"><![endif]></span><br
1998clear=all style='mso-special-character:line-break'>
1999</p>
2000
2001<h2><span class=GramE>Step 4.</span> Refine peaks</h2>
2002
2003<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2004kryptonite examples above, refine the peaks and the profile shape parameters in
2005<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2006mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2007Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
2008will be asked for a project file name at the first refinement (I used ‘<b
2009style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2010mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2011Calibri;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>). In the end my
2012refinement converged at <span class=SpellE>Rwp</span>=7.15% and some peaks do
2013show some discrepancy as the sample is more complex than the simple <b
2014style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2015mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2016Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2017normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2018minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2019mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
2020normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2021minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2022mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
2023normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2024minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2025mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
2026normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2027minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2028mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
2029no peaks drift away during refinement. However, this is good enough to proceed.</p>
2030
2031<h2><span class=GramE>Step 5.</span> Prepare Indexing Peak List</h2>
2032
2033<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2034style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2035mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2036minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
2037normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2038minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2039mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
2040
2041<h2><span class=GramE>Step 6.</span> Index the cell</h2>
2042
2043<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2044In a real world case we wouldn’t know this and we would have to try each <span
2045class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2046time to go through all the bad cases.</p>
2047
2048<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2049style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2050mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2051minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
2052normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2053minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2054mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
2055<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2056mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2057Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window. Progress
2058will be much slower than for LaB<sub>6</sub> but oddly much faster than for
2059kryptonite and suitable results may appear almost immediately. Watch the
2060console window; the right answer will have an obviously large M20 (~900) and a
2061volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display). Once
2062this is seen (it may take more than one try to get this) you can stop the
2063indexing search by pressing <b style='mso-bidi-font-weight:normal'><span
2064style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2065mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2066minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2067style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2068some solutions from one indexing run to the next. It may take more than one
2069press to fully stop it. My result was </p>
2070
2071<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2072 id="Picture_x0020_31" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:525pt;
2073 height:450pt;visibility:visible;mso-wrap-style:square'>
2074 <v:imagedata src="Fit%20Peaks_files/image027.png" o:title=""/>
2075</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2076src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_31"><![endif]><!--[if gte vml 1]><v:shape
2077 id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:527.25pt;
2078 height:376.5pt;visibility:visible;mso-wrap-style:square'>
2079 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2080</v:shape><![endif]--><![if !vml]><img border=0 width=703 height=502
2081src="Fit%20Peaks_files/image028.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
2082
2083<p class=MsoNormal>Notice there may be other equally good M20 results with
2084different volumes; still other solutions may be obtained as you keep trying the
2085indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2086style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2087mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2088new indexing runs. The best solution is the one with the smaller volume and &#946;
2089&gt; 90 deg. The plot shows every peak indexed including the weak peaks not
2090selected for the peak fitting. Copy the best cell and try to refine it along
2091with the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2092mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
2093I obtained an improved M20 ~1257 and slightly different lattice parameters. Try
2094different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2095style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2096mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2097each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
2098Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
2099style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2100mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2101minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
2102style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2103mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2104Calibri;mso-bidi-theme-font:minor-latin'>sucrose</span></b>) and select <b
2105style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2106mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
2107from the GSAS-II data tree.</p>
2108
2109<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2110 id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:545.25pt;
2111 height:303.75pt;visibility:visible;mso-wrap-style:square'>
2112 <v:imagedata src="Fit%20Peaks_files/image029.png" o:title=""/>
2113</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
2114src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_34"><![endif]></span><span
2115style='mso-spacerun:yes'> </span></p>
2116
2117<p class=MsoNormal>Notice that the lattice parameters and space group have been
2118set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2119style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2120mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2121minor-latin'>Save</span></b> the project file as it is needed for the sucrose <b
2122style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2123mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2124Calibri;mso-bidi-theme-font:minor-latin'><a href="Charge%20Flipping%20-%20sucrose.htm">Charge
2125Flipping</a></span></b> exercise. The features of the <b style='mso-bidi-font-weight:
2126normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2127minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2128mso-bidi-theme-font:minor-latin'>Phase Data</span></b> window will be presented
2129in other exercises.</p>
2130
2131<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2132
2133</div>
2134
2135</body>
2136
2137</html>
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