source: Tutorials/FitPeaks/Fit Peaks.htm @ 2653

Last change on this file since 2653 was 2653, checked in by toby, 6 years ago

fix Update bug; Enhancements for Peak List: widen selected peak line; remove peak highlight on cell selection; add double-click on labels; change Tutorial limits fig.
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413  <w:LsdException Locked="false" Priority="72" Name="Colorful List"/>
414  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
415  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
416  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
417  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
418  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
419  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
420  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
421  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
422  <w:LsdException Locked="false" Priority="34" QFormat="true"
423   Name="List Paragraph"/>
424  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
425  <w:LsdException Locked="false" Priority="30" QFormat="true"
426   Name="Intense Quote"/>
427  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
428  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
429  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
430  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
431  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
432  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
433  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
434  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
435  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
436  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
437  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
438  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
439  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
440  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
441  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
442  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
443  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
444  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
445  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
446  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
447  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
448  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
449  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
450  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
451  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
452  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
453  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
454  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
455  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
456  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
457  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
458  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
459  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
460  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
461  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
462  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
463  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
464  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
465  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
466  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
467  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
468  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
469  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
470  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
471  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
472  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
473  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
474  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
475  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
476  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
477  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
478  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
479  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
480  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
481  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
482  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
483  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
484  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
485  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
486  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
487  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
488  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
489  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
490  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
491  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
492  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
493  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
494  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
495  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
496  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
497  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
498  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
499  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
500  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
501  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
502  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
503  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
504  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
505  <w:LsdException Locked="false" Priority="19" QFormat="true"
506   Name="Subtle Emphasis"/>
507  <w:LsdException Locked="false" Priority="21" QFormat="true"
508   Name="Intense Emphasis"/>
509  <w:LsdException Locked="false" Priority="31" QFormat="true"
510   Name="Subtle Reference"/>
511  <w:LsdException Locked="false" Priority="32" QFormat="true"
512   Name="Intense Reference"/>
513  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
514  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
515   UnhideWhenUsed="true" Name="Bibliography"/>
516  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
517   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
518  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
519  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
520  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
521  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
522  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
523  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
524  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
525  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
526  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
527  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
528  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
529  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
530  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
531  <w:LsdException Locked="false" Priority="46"
532   Name="Grid Table 1 Light Accent 1"/>
533  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
534  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
535  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
536  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
537  <w:LsdException Locked="false" Priority="51"
538   Name="Grid Table 6 Colorful Accent 1"/>
539  <w:LsdException Locked="false" Priority="52"
540   Name="Grid Table 7 Colorful Accent 1"/>
541  <w:LsdException Locked="false" Priority="46"
542   Name="Grid Table 1 Light Accent 2"/>
543  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
544  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
545  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
546  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
547  <w:LsdException Locked="false" Priority="51"
548   Name="Grid Table 6 Colorful Accent 2"/>
549  <w:LsdException Locked="false" Priority="52"
550   Name="Grid Table 7 Colorful Accent 2"/>
551  <w:LsdException Locked="false" Priority="46"
552   Name="Grid Table 1 Light Accent 3"/>
553  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
554  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
555  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
556  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
557  <w:LsdException Locked="false" Priority="51"
558   Name="Grid Table 6 Colorful Accent 3"/>
559  <w:LsdException Locked="false" Priority="52"
560   Name="Grid Table 7 Colorful Accent 3"/>
561  <w:LsdException Locked="false" Priority="46"
562   Name="Grid Table 1 Light Accent 4"/>
563  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
564  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
565  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
566  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
567  <w:LsdException Locked="false" Priority="51"
568   Name="Grid Table 6 Colorful Accent 4"/>
569  <w:LsdException Locked="false" Priority="52"
570   Name="Grid Table 7 Colorful Accent 4"/>
571  <w:LsdException Locked="false" Priority="46"
572   Name="Grid Table 1 Light Accent 5"/>
573  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
574  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
575  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
576  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
577  <w:LsdException Locked="false" Priority="51"
578   Name="Grid Table 6 Colorful Accent 5"/>
579  <w:LsdException Locked="false" Priority="52"
580   Name="Grid Table 7 Colorful Accent 5"/>
581  <w:LsdException Locked="false" Priority="46"
582   Name="Grid Table 1 Light Accent 6"/>
583  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
584  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
585  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
586  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
587  <w:LsdException Locked="false" Priority="51"
588   Name="Grid Table 6 Colorful Accent 6"/>
589  <w:LsdException Locked="false" Priority="52"
590   Name="Grid Table 7 Colorful Accent 6"/>
591  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
592  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
593  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
594  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
595  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
596  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
597  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
598  <w:LsdException Locked="false" Priority="46"
599   Name="List Table 1 Light Accent 1"/>
600  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
601  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
602  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
603  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
604  <w:LsdException Locked="false" Priority="51"
605   Name="List Table 6 Colorful Accent 1"/>
606  <w:LsdException Locked="false" Priority="52"
607   Name="List Table 7 Colorful Accent 1"/>
608  <w:LsdException Locked="false" Priority="46"
609   Name="List Table 1 Light Accent 2"/>
610  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
611  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
612  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
613  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
614  <w:LsdException Locked="false" Priority="51"
615   Name="List Table 6 Colorful Accent 2"/>
616  <w:LsdException Locked="false" Priority="52"
617   Name="List Table 7 Colorful Accent 2"/>
618  <w:LsdException Locked="false" Priority="46"
619   Name="List Table 1 Light Accent 3"/>
620  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
621  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
622  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
623  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
624  <w:LsdException Locked="false" Priority="51"
625   Name="List Table 6 Colorful Accent 3"/>
626  <w:LsdException Locked="false" Priority="52"
627   Name="List Table 7 Colorful Accent 3"/>
628  <w:LsdException Locked="false" Priority="46"
629   Name="List Table 1 Light Accent 4"/>
630  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
631  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
632  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
633  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
634  <w:LsdException Locked="false" Priority="51"
635   Name="List Table 6 Colorful Accent 4"/>
636  <w:LsdException Locked="false" Priority="52"
637   Name="List Table 7 Colorful Accent 4"/>
638  <w:LsdException Locked="false" Priority="46"
639   Name="List Table 1 Light Accent 5"/>
640  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
641  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
642  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
643  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
644  <w:LsdException Locked="false" Priority="51"
645   Name="List Table 6 Colorful Accent 5"/>
646  <w:LsdException Locked="false" Priority="52"
647   Name="List Table 7 Colorful Accent 5"/>
648  <w:LsdException Locked="false" Priority="46"
649   Name="List Table 1 Light Accent 6"/>
650  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
651  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
652  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
653  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
654  <w:LsdException Locked="false" Priority="51"
655   Name="List Table 6 Colorful Accent 6"/>
656  <w:LsdException Locked="false" Priority="52"
657   Name="List Table 7 Colorful Accent 6"/>
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783        font-size:12.0pt;
784        font-family:"Times New Roman",serif;
785        mso-fareast-font-family:"Times New Roman";
786        mso-fareast-theme-font:minor-fareast;
787        color:#4F4FFF;
788        font-weight:bold;}
789p.MsoTitle, li.MsoTitle, div.MsoTitle
790        {mso-style-noshow:yes;
791        mso-style-priority:10;
792        mso-style-unhide:no;
793        mso-style-qformat:yes;
794        mso-style-link:"Title Char";
795        mso-style-next:Normal;
796        margin-top:0in;
797        margin-right:0in;
798        margin-bottom:15.0pt;
799        margin-left:0in;
800        mso-add-space:auto;
801        mso-pagination:widow-orphan;
802        border:none;
803        mso-border-bottom-alt:solid #4F81BD 1.0pt;
804        mso-border-bottom-themecolor:accent1;
805        padding:0in;
806        mso-padding-alt:0in 0in 4.0pt 0in;
807        font-size:26.0pt;
808        font-family:"Cambria",serif;
809        mso-ascii-font-family:Cambria;
810        mso-ascii-theme-font:major-latin;
811        mso-fareast-font-family:"Times New Roman";
812        mso-fareast-theme-font:major-fareast;
813        mso-hansi-font-family:Cambria;
814        mso-hansi-theme-font:major-latin;
815        mso-bidi-font-family:"Times New Roman";
816        mso-bidi-theme-font:major-bidi;
817        color:#17365D;
818        mso-themecolor:text2;
819        mso-themeshade:191;
820        letter-spacing:.25pt;
821        mso-font-kerning:14.0pt;}
822p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
823        {mso-style-noshow:yes;
824        mso-style-priority:10;
825        mso-style-unhide:no;
826        mso-style-qformat:yes;
827        mso-style-link:"Title Char";
828        mso-style-next:Normal;
829        mso-style-type:export-only;
830        margin:0in;
831        margin-bottom:.0001pt;
832        mso-add-space:auto;
833        mso-pagination:widow-orphan;
834        border:none;
835        mso-border-bottom-alt:solid #4F81BD 1.0pt;
836        mso-border-bottom-themecolor:accent1;
837        padding:0in;
838        mso-padding-alt:0in 0in 4.0pt 0in;
839        font-size:26.0pt;
840        font-family:"Cambria",serif;
841        mso-ascii-font-family:Cambria;
842        mso-ascii-theme-font:major-latin;
843        mso-fareast-font-family:"Times New Roman";
844        mso-fareast-theme-font:major-fareast;
845        mso-hansi-font-family:Cambria;
846        mso-hansi-theme-font:major-latin;
847        mso-bidi-font-family:"Times New Roman";
848        mso-bidi-theme-font:major-bidi;
849        color:#17365D;
850        mso-themecolor:text2;
851        mso-themeshade:191;
852        letter-spacing:.25pt;
853        mso-font-kerning:14.0pt;}
854p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
855        {mso-style-noshow:yes;
856        mso-style-priority:10;
857        mso-style-unhide:no;
858        mso-style-qformat:yes;
859        mso-style-link:"Title Char";
860        mso-style-next:Normal;
861        mso-style-type:export-only;
862        margin:0in;
863        margin-bottom:.0001pt;
864        mso-add-space:auto;
865        mso-pagination:widow-orphan;
866        border:none;
867        mso-border-bottom-alt:solid #4F81BD 1.0pt;
868        mso-border-bottom-themecolor:accent1;
869        padding:0in;
870        mso-padding-alt:0in 0in 4.0pt 0in;
871        font-size:26.0pt;
872        font-family:"Cambria",serif;
873        mso-ascii-font-family:Cambria;
874        mso-ascii-theme-font:major-latin;
875        mso-fareast-font-family:"Times New Roman";
876        mso-fareast-theme-font:major-fareast;
877        mso-hansi-font-family:Cambria;
878        mso-hansi-theme-font:major-latin;
879        mso-bidi-font-family:"Times New Roman";
880        mso-bidi-theme-font:major-bidi;
881        color:#17365D;
882        mso-themecolor:text2;
883        mso-themeshade:191;
884        letter-spacing:.25pt;
885        mso-font-kerning:14.0pt;}
886p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
887        {mso-style-noshow:yes;
888        mso-style-priority:10;
889        mso-style-unhide:no;
890        mso-style-qformat:yes;
891        mso-style-link:"Title Char";
892        mso-style-next:Normal;
893        mso-style-type:export-only;
894        margin-top:0in;
895        margin-right:0in;
896        margin-bottom:15.0pt;
897        margin-left:0in;
898        mso-add-space:auto;
899        mso-pagination:widow-orphan;
900        border:none;
901        mso-border-bottom-alt:solid #4F81BD 1.0pt;
902        mso-border-bottom-themecolor:accent1;
903        padding:0in;
904        mso-padding-alt:0in 0in 4.0pt 0in;
905        font-size:26.0pt;
906        font-family:"Cambria",serif;
907        mso-ascii-font-family:Cambria;
908        mso-ascii-theme-font:major-latin;
909        mso-fareast-font-family:"Times New Roman";
910        mso-fareast-theme-font:major-fareast;
911        mso-hansi-font-family:Cambria;
912        mso-hansi-theme-font:major-latin;
913        mso-bidi-font-family:"Times New Roman";
914        mso-bidi-theme-font:major-bidi;
915        color:#17365D;
916        mso-themecolor:text2;
917        mso-themeshade:191;
918        letter-spacing:.25pt;
919        mso-font-kerning:14.0pt;}
920a:link, span.MsoHyperlink
921        {mso-style-noshow:yes;
922        mso-style-priority:99;
923        color:blue;
924        text-decoration:underline;
925        text-underline:single;}
926a:visited, span.MsoHyperlinkFollowed
927        {mso-style-noshow:yes;
928        mso-style-priority:99;
929        color:purple;
930        text-decoration:underline;
931        text-underline:single;}
932p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
933        {mso-style-noshow:yes;
934        mso-style-priority:99;
935        mso-style-link:"Document Map Char";
936        margin:0in;
937        margin-bottom:.0001pt;
938        mso-pagination:widow-orphan;
939        font-size:8.0pt;
940        font-family:"Tahoma",sans-serif;
941        mso-fareast-font-family:"Times New Roman";
942        mso-fareast-theme-font:minor-fareast;}
943p
944        {mso-style-noshow:yes;
945        mso-style-priority:99;
946        mso-margin-top-alt:auto;
947        margin-right:0in;
948        mso-margin-bottom-alt:auto;
949        margin-left:0in;
950        mso-pagination:widow-orphan;
951        font-size:12.0pt;
952        font-family:"Times New Roman",serif;
953        mso-fareast-font-family:"Times New Roman";
954        mso-fareast-theme-font:minor-fareast;}
955pre
956        {mso-style-noshow:yes;
957        mso-style-priority:99;
958        mso-style-link:"HTML Preformatted Char";
959        margin:0in;
960        margin-bottom:.0001pt;
961        mso-pagination:widow-orphan;
962        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;
963        font-size:10.0pt;
964        font-family:"Courier New";
965        mso-fareast-font-family:"Times New Roman";}
966p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
967        {mso-style-noshow:yes;
968        mso-style-priority:99;
969        mso-style-link:"Balloon Text Char";
970        margin:0in;
971        margin-bottom:.0001pt;
972        mso-pagination:widow-orphan;
973        font-size:8.0pt;
974        font-family:"Tahoma",sans-serif;
975        mso-fareast-font-family:"Times New Roman";
976        mso-fareast-theme-font:minor-fareast;}
977span.MsoPlaceholderText
978        {mso-style-noshow:yes;
979        mso-style-priority:99;
980        mso-style-unhide:no;
981        color:gray;}
982p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
983        {mso-style-noshow:yes;
984        mso-style-priority:1;
985        mso-style-unhide:no;
986        mso-style-qformat:yes;
987        mso-style-parent:"";
988        margin:0in;
989        margin-bottom:.0001pt;
990        mso-pagination:widow-orphan;
991        font-size:12.0pt;
992        font-family:"Times New Roman",serif;
993        mso-fareast-font-family:"Times New Roman";
994        mso-fareast-theme-font:minor-fareast;}
995p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
996        {mso-style-noshow:yes;
997        mso-style-priority:34;
998        mso-style-unhide:no;
999        mso-style-qformat:yes;
1000        margin-top:0in;
1001        margin-right:0in;
1002        margin-bottom:0in;
1003        margin-left:.5in;
1004        margin-bottom:.0001pt;
1005        mso-add-space:auto;
1006        mso-pagination:widow-orphan;
1007        font-size:12.0pt;
1008        font-family:"Times New Roman",serif;
1009        mso-fareast-font-family:"Times New Roman";
1010        mso-fareast-theme-font:minor-fareast;}
1011p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
1012        {mso-style-noshow:yes;
1013        mso-style-priority:34;
1014        mso-style-unhide:no;
1015        mso-style-qformat:yes;
1016        mso-style-type:export-only;
1017        margin-top:0in;
1018        margin-right:0in;
1019        margin-bottom:0in;
1020        margin-left:.5in;
1021        margin-bottom:.0001pt;
1022        mso-add-space:auto;
1023        mso-pagination:widow-orphan;
1024        font-size:12.0pt;
1025        font-family:"Times New Roman",serif;
1026        mso-fareast-font-family:"Times New Roman";
1027        mso-fareast-theme-font:minor-fareast;}
1028p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
1029        {mso-style-noshow:yes;
1030        mso-style-priority:34;
1031        mso-style-unhide:no;
1032        mso-style-qformat:yes;
1033        mso-style-type:export-only;
1034        margin-top:0in;
1035        margin-right:0in;
1036        margin-bottom:0in;
1037        margin-left:.5in;
1038        margin-bottom:.0001pt;
1039        mso-add-space:auto;
1040        mso-pagination:widow-orphan;
1041        font-size:12.0pt;
1042        font-family:"Times New Roman",serif;
1043        mso-fareast-font-family:"Times New Roman";
1044        mso-fareast-theme-font:minor-fareast;}
1045p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
1046        {mso-style-noshow:yes;
1047        mso-style-priority:34;
1048        mso-style-unhide:no;
1049        mso-style-qformat:yes;
1050        mso-style-type:export-only;
1051        margin-top:0in;
1052        margin-right:0in;
1053        margin-bottom:0in;
1054        margin-left:.5in;
1055        margin-bottom:.0001pt;
1056        mso-add-space:auto;
1057        mso-pagination:widow-orphan;
1058        font-size:12.0pt;
1059        font-family:"Times New Roman",serif;
1060        mso-fareast-font-family:"Times New Roman";
1061        mso-fareast-theme-font:minor-fareast;}
1062span.MsoIntenseReference
1063        {mso-style-priority:32;
1064        mso-style-unhide:no;
1065        mso-style-qformat:yes;
1066        font-variant:small-caps;
1067        color:#C0504D;
1068        mso-themecolor:accent2;
1069        letter-spacing:.25pt;
1070        font-weight:bold;
1071        text-decoration:underline;
1072        text-underline:single;}
1073span.Heading1Char
1074        {mso-style-name:"Heading 1 Char";
1075        mso-style-priority:9;
1076        mso-style-unhide:no;
1077        mso-style-locked:yes;
1078        mso-style-link:"Heading 1";
1079        mso-ansi-font-size:24.0pt;
1080        mso-bidi-font-size:24.0pt;
1081        font-family:"Times New Roman",serif;
1082        mso-ascii-font-family:"Times New Roman";
1083        mso-fareast-font-family:"Times New Roman";
1084        mso-fareast-theme-font:minor-fareast;
1085        mso-hansi-font-family:"Times New Roman";
1086        mso-bidi-font-family:"Times New Roman";
1087        mso-font-kerning:18.0pt;
1088        font-weight:bold;}
1089span.Heading2Char
1090        {mso-style-name:"Heading 2 Char";
1091        mso-style-noshow:yes;
1092        mso-style-priority:9;
1093        mso-style-unhide:no;
1094        mso-style-locked:yes;
1095        mso-style-link:"Heading 2";
1096        mso-ansi-font-size:18.0pt;
1097        mso-bidi-font-size:18.0pt;
1098        font-family:"Times New Roman",serif;
1099        mso-ascii-font-family:"Times New Roman";
1100        mso-fareast-font-family:"Times New Roman";
1101        mso-fareast-theme-font:minor-fareast;
1102        mso-hansi-font-family:"Times New Roman";
1103        mso-bidi-font-family:"Times New Roman";
1104        font-weight:bold;}
1105span.Heading3Char
1106        {mso-style-name:"Heading 3 Char";
1107        mso-style-noshow:yes;
1108        mso-style-priority:9;
1109        mso-style-unhide:no;
1110        mso-style-locked:yes;
1111        mso-style-link:"Heading 3";
1112        mso-ansi-font-size:13.5pt;
1113        mso-bidi-font-size:13.5pt;
1114        font-family:"Times New Roman",serif;
1115        mso-ascii-font-family:"Times New Roman";
1116        mso-fareast-font-family:"Times New Roman";
1117        mso-fareast-theme-font:minor-fareast;
1118        mso-hansi-font-family:"Times New Roman";
1119        mso-bidi-font-family:"Times New Roman";
1120        font-weight:bold;}
1121span.Heading4Char
1122        {mso-style-name:"Heading 4 Char";
1123        mso-style-noshow:yes;
1124        mso-style-priority:9;
1125        mso-style-unhide:no;
1126        mso-style-locked:yes;
1127        mso-style-link:"Heading 4";
1128        mso-ansi-font-size:13.0pt;
1129        mso-bidi-font-size:13.0pt;
1130        font-family:"Cambria",serif;
1131        mso-ascii-font-family:Cambria;
1132        mso-ascii-theme-font:major-latin;
1133        mso-fareast-font-family:"Times New Roman";
1134        mso-fareast-theme-font:major-fareast;
1135        mso-hansi-font-family:Cambria;
1136        mso-hansi-theme-font:major-latin;
1137        mso-bidi-font-family:"Times New Roman";
1138        mso-bidi-theme-font:major-bidi;
1139        color:#4F81BD;
1140        mso-themecolor:accent1;
1141        font-weight:bold;
1142        font-style:italic;}
1143span.Heading5Char
1144        {mso-style-name:"Heading 5 Char";
1145        mso-style-noshow:yes;
1146        mso-style-priority:9;
1147        mso-style-unhide:no;
1148        mso-style-locked:yes;
1149        mso-style-link:"Heading 5";
1150        mso-ansi-font-size:12.0pt;
1151        mso-bidi-font-size:12.0pt;
1152        font-family:"Times New Roman",serif;
1153        mso-ascii-font-family:"Times New Roman";
1154        mso-fareast-font-family:"Times New Roman";
1155        mso-fareast-theme-font:minor-fareast;
1156        mso-hansi-font-family:"Times New Roman";
1157        mso-bidi-font-family:"Times New Roman";
1158        color:#4F4FFF;
1159        font-weight:bold;}
1160span.HTMLPreformattedChar
1161        {mso-style-name:"HTML Preformatted Char";
1162        mso-style-noshow:yes;
1163        mso-style-priority:99;
1164        mso-style-unhide:no;
1165        mso-style-locked:yes;
1166        mso-style-link:"HTML Preformatted";
1167        font-family:"Courier New";
1168        mso-ascii-font-family:"Courier New";
1169        mso-fareast-font-family:"Times New Roman";
1170        mso-hansi-font-family:"Courier New";
1171        mso-bidi-font-family:"Courier New";}
1172p.msonormal0, li.msonormal0, div.msonormal0
1173        {mso-style-name:msonormal;
1174        mso-style-noshow:yes;
1175        mso-style-priority:99;
1176        mso-style-unhide:no;
1177        mso-margin-top-alt:auto;
1178        margin-right:0in;
1179        mso-margin-bottom-alt:auto;
1180        margin-left:0in;
1181        mso-pagination:widow-orphan;
1182        font-size:12.0pt;
1183        font-family:"Times New Roman",serif;
1184        mso-fareast-font-family:"Times New Roman";
1185        mso-fareast-theme-font:minor-fareast;}
1186span.TitleChar
1187        {mso-style-name:"Title Char";
1188        mso-style-priority:10;
1189        mso-style-unhide:no;
1190        mso-style-locked:yes;
1191        mso-style-link:Title;
1192        mso-ansi-font-size:26.0pt;
1193        mso-bidi-font-size:26.0pt;
1194        font-family:"Cambria",serif;
1195        mso-ascii-font-family:Cambria;
1196        mso-ascii-theme-font:major-latin;
1197        mso-fareast-font-family:"Times New Roman";
1198        mso-fareast-theme-font:major-fareast;
1199        mso-hansi-font-family:Cambria;
1200        mso-hansi-theme-font:major-latin;
1201        mso-bidi-font-family:"Times New Roman";
1202        mso-bidi-theme-font:major-bidi;
1203        color:#17365D;
1204        mso-themecolor:text2;
1205        mso-themeshade:191;
1206        letter-spacing:.25pt;
1207        mso-font-kerning:14.0pt;}
1208span.DocumentMapChar
1209        {mso-style-name:"Document Map Char";
1210        mso-style-noshow:yes;
1211        mso-style-priority:99;
1212        mso-style-unhide:no;
1213        mso-style-locked:yes;
1214        mso-style-link:"Document Map";
1215        mso-ansi-font-size:8.0pt;
1216        mso-bidi-font-size:8.0pt;
1217        font-family:"Tahoma",sans-serif;
1218        mso-ascii-font-family:Tahoma;
1219        mso-fareast-font-family:"Times New Roman";
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1456
1457<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1458
1459<div class=WordSection1>
1460
1461<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1462
1463<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1464cell that matches a set of diffraction peaks -- a process known as
1465auto-indexing. First peaks must be located and optimized and then indexing can
1466be done.</p>
1467
1468<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1469
1470<h2>Step 1: Read in the data file</h2>
1471
1472<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1473style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1474style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1475the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1476mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1477Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
1478data file</span></b> menu item to read the data file into the current GSAS-II
1479project. This read option is set to read any of the powder data formats defined
1480for GSAS (angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other
1481submenu items will read the <span class=SpellE><b style='mso-bidi-font-weight:
1482normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1483minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1484mso-bidi-theme-font:minor-latin'>cif</span></b></span> format or the <span
1485class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1486"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1487minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1488format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1489style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1490directory to <b style='mso-bidi-font-weight:normal'><span style='=======
1491data file</span></b> menu item to read the data file into the current GSAS-II project.
1492This read option is set to read any of the powder data formats defined for GSAS
1493(angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu
1494items will read the <span class=SpellE><b style='
1495'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1496mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1497minor-latin'>cif</span></span></b> format or the <span class=SpellE><b
1498style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1499mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1500Calibri;mso-bidi-theme-font:minor-latin'>xye</span></b></span> format (angles
1501in degrees) used by <span class=SpellE>Topas</span>, etc. to see them. Because
1502you used <span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1503minor-latin'>the </span><b style='mso-bidi-font-weight:normal'><span
1504style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1505mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1506minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family:
1507Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and
1508downloaded the exercise files (recommended), then the </span><span
1509class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1510"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1511Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>FitPeaks</span></b></span><b
1512style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1513mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1514minor-latin;mso-hansi-theme-font:minor-latin'>/data/...</span></b><span
1515style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1516entry will bring you to the location where the files have been downloaded. (It
1517is also possible to download them manually from <a
1518href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
1519In this case you will need to navigate to the download location manually.)<br>
1520For this tutorial you should see the data file in the file browser, but if
1521extensions on data files are not the expected ones, you may need to change the
1522file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find
1523the desired file.</span></p>
1524
1525<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1526style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1527style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1528the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1529mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1530Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.fxye</span></b><span
1531style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1532mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1533minor-latin'> data</span> file in the first dialog and press <b
1534style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1535mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1536Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
1537Dialog box asking <b style='mso-bidi-font-weight:normal'><span
1538style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1539mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1540minor-latin'>Is this the file you want?</span></b> Press <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'>Yes</span></b> button to proceed.</p>
1544
1545<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1546style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1547style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1548file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1549mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1550Calibri;mso-bidi-theme-font:minor-latin'>11bmb_3844.prm</span></b> instrument
1551parameter file is automatically selected; it was produced by 11BM-B instrument
1552processing software when the corresponding <span class=SpellE><b
1553style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1554mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1555Calibri;mso-bidi-theme-font:minor-latin'>fxye</span></b></span> file was
1556created from the 12 detector raw data. If absent or the name doesn’t match the
1557data file name, a file dialog will appear for you to select the correct
1558instrument parameter file.</p>
1559
1560<p class=MsoNormal>At this point 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'>GSAS-II data tree</span></b> window will have several entries </p>
1564
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1587 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
1588</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=250
1589src="Fit%20Peaks_files/image001.png" v:shapes="Picture_x0020_1"><![endif]></span></p>
1590
1591<p class=MsoNormal>and the plot window will show the powder pattern</p>
1592
1593<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1594 id="Picture_x0020_2" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:525pt;
1595 height:450pt;visibility:visible;mso-wrap-style:square'>
1596 <v:imagedata src="Fit%20Peaks_files/image002.png" o:title=""/>
1597</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1598src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_2"><![endif]></span></p>
1599
1600<h2>Step 2: Select Limits </h2>
1601
1602<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1603more data than we need, so it is helpful to cut down the range. Click on the <b
1604style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1605mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1606Calibri;mso-bidi-theme-font:minor-latin'>Limits</span></b> item in the <b
1607style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1608mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1609Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. The
1610small window is repainted. Use the <b style='mso-bidi-font-weight:normal'><span
1611style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1612mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1613minor-latin'>new</span></b> column of entry boxes to set <span class=SpellE><b
1614style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1615mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1616Calibri;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span> and <span
1617class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1618"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1619minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1620to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1621mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1622Calibri;mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
1623normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1624minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1625mso-bidi-theme-font:minor-latin'>27.5</span></b>. Notice on the plot that the
1626limit lines have moved to these positions; the green lower limit is just below
1627the 1<sup>st</sup> peak and the red upper limit is in a wide gap between peaks.
1628You may also drag the limit lines to the desired location. Limits may
1629also be set by a left
1630mouse click on a data point for the lower limit or a right click on a data
1631point for the upper limit.</p>
1632
1633<p class=MsoNormal><span style='mso-no-proof:yes'>
1634<img border=0 width=296 height=121
1635src="Fit%20Peaks_files/image003.png" v:shapes="Picture_x0020_3"></span></p>
1636
1637<h2>Step 3: Determine Peak Positions</h2>
1638
1639<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1640auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1641style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1642style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1643on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1645Calibri;mso-bidi-theme-font:minor-latin'>Peak List</span></b> item in the <b
1646style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1647mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1648Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b>. This
1649creates an empty window of peak positions (the <b style='mso-bidi-font-weight:
1650normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1651minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1652mso-bidi-theme-font:minor-latin'>Limits</span></b> window is erased). At this
1653point it is wise to zoom in on the data that will be used for indexing. </p>
1654
1655<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1656auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1657style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1658style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1659on the Zoom button (5<sup>th</sup> one from the left on the plot toolbar), then
1660press the left mouse in one corner of the region to be used; holding the mouse
1661button down, drag over the region to the opposite corner; a box will be drawn
1662over the region to be zoomed and the plot will be redrawn with the new limits.
1663The toolbar has a number of buttons to the right of the help button (‘?’) that
1664can be used to incrementally change the view.</p>
1665
1666<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1667auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1668style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1669style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1670style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom button
1671again to turn off the zoom mode. </p>
1672
1673<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1674auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1675style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1676style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1677<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1678mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1679in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1680mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
1681window select <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'>Auto search</span></b>. The plot window will immediately show that
1684all peaks were picked with a blue vertical line on each one</p>
1685
1686<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1687auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_4"
1688 o:spid="_x0000_i1047" type="#_x0000_t75" style='width:525pt;height:450pt;
1689 visibility:visible;mso-wrap-style:square'>
1690 <v:imagedata src="Fit%20Peaks_files/image004.png" o:title=""/>
1691</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1692src="Fit%20Peaks_files/image004.png" v:shapes="Picture_x0020_4"><![endif]></span></p>
1693
1694<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1695auto'>and peaks are shown in the <b style='mso-bidi-font-weight:normal'><span
1696style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1697mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1698minor-latin'>Peak List</span></b> window in order of increasing 2<span
1699style='font-family:Symbol'>Q</span>.</p>
1700
1701<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1702auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29"
1703 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:401.25pt;height:262.5pt;
1704 visibility:visible;mso-wrap-style:square'>
1705 <v:imagedata src="Fit%20Peaks_files/image005.png" o:title=""/>
1706</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1707src="Fit%20Peaks_files/image005.png" v:shapes="Picture_x0020_29"><![endif]></span></p>
1708
1709<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1710will be 20 peaks in this example. You should examine both the list and the plot
1711to be sure the auto search did not pick a peak twice (rarely) or skip a peak or
1712shoulder. You can add a peak to the list by pressing the left mouse button with
1713the pointer on a data point at the peak top or shoulder; be sure the zoom/shift
1714buttons are off. You may drag a peak position as needed. A position may be
1715deleted with a right click with the mouse on the blue line. You can also delete
1716a peak by selecting the row in the table; it will be highlighted in blue. Then
1717press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1718mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b>
1719key; it will be removed from the table and the plot. The list will always show
1720the peaks sorted by position. When done you should have 20 unique peak
1721positions.</p>
1722
1723<h2>Step 4: Refine Peak Positions</h2>
1724
1725<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1726refinement and then adding parameters to complete the fitting,</p>
1727
1728<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1729style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1730style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1731the peak intensities and the background. These parameters have their refinement
1732flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1733normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1734minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1735mso-bidi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span>
1736</span></b>on the<b style='mso-bidi-font-weight:normal'><span style='font-family:
1737"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1738minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'> Peak
1739List </span></b>window. Do <b style='mso-bidi-font-weight:normal'>NOT</b> use
1740the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1741mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1742Calibri;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b> menu item
1743in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1744mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1745Calibri;mso-bidi-theme-font:minor-latin'>GSAS-II data tree</span></b> window;
1746that it to be used for Rietveld/Pawley refinements. You will be asked to save
1747the current project before the fit will proceed; change directory if desired
1748and provide a suitable name (we assume <b style='mso-bidi-font-weight:normal'><span
1749style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1750mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1751minor-latin'>LaB6</span></b>). A window will show the progress of the
1752refinement and will close when the least-squares fit is complete (usually very
1753fast). The plot is updated with the fit, the peak list window is updated with
1754the new peak values and a summary of the refinement is shown on the console
1755window as well.</p>
1756
1757<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1758 id="Picture_x0020_31" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:525pt;
1759 height:450pt;visibility:visible;mso-wrap-style:square'>
1760 <v:imagedata src="Fit%20Peaks_files/image006.png" o:title=""/>
1761</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1762src="Fit%20Peaks_files/image006.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
1763
1764<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1765 id="Picture_x0020_24" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:401.25pt;
1766 height:262.5pt;visibility:visible;mso-wrap-style:square'>
1767 <v:imagedata src="Fit%20Peaks_files/image007.png" o:title=""/>
1768</v:shape><![endif]--><![if !vml]><img border=0 width=535 height=350
1769src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_24"><![endif]></span></p>
1770
1771<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1772style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1773style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1774add refinement of the peak positions. This can be done by clicking on all the
1775refinement flags for the individual peaks or it is possible to set them all at
1776the same time using this recipe: </p>
1777
1778<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1779auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1780style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1781style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1782on any value in the table to select it, for example the first peak position. A
1783black box appears around the value. </p>
1784
1785<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1786text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1787style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1788style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1789on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1790mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1791label above the peak position check-boxes. The entire column of checkboxes is
1792highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
1793style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1794mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1795minor-latin'>y</span></b> key to turn on all refinement flags (<b
1796style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1797mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1798Calibri;mso-bidi-theme-font:minor-latin'>n</span></b> would turn them off).</p>
1799
1800<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1801the <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-font-family:
1803Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span></span></b>
1804menu item in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1805"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1806minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Peak
1807List</span></b> window.</p>
1808
1809<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1810refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1811performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1812width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
1813click the refinement flags for sigma and/or gamma in the Peak List window.
1814&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1815widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening
1816equation as described below.&nbsp;Note - one cannot refine ALL peak widths
1817using both individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental
1818broadening terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1819
1820<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1821"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1822to an instrumental broadening equation, first<b> s</b></span>elect the <b
1823style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1824mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1825Calibri;mso-bidi-theme-font:minor-latin'>Instrumental Parameters</span></b>
1826item in the data tree. This opens a window for peak profile terms<b> </b><span
1827style='mso-bidi-font-weight:bold'>and also creates a new plot
1828window&nbsp;showing the instrument profile resolution curve.</span></p>
1829
1830<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1831 id="Picture_x0020_30" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:419.25pt;
1832 height:183.75pt;visibility:visible;mso-wrap-style:square'>
1833 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1834</v:shape><![endif]--><![if !vml]><img border=0 width=559 height=245
1835src="Fit%20Peaks_files/image008.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1836
1837<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1838corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1839coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1840values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1841<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1842mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1843Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1844normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1845minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1846mso-bidi-theme-font:minor-latin'>V</span></b>, <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-font-family:Calibri;
1849mso-bidi-theme-font:minor-latin'>W</span></b>, and Lorentzian <b
1850style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1851mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1852Calibri;mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
1853normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1854minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1855mso-bidi-theme-font:minor-latin'>Y</span></b>. </p>
1856
1857<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1858style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1859style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1860repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1861style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1862mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1863minor-latin'>Peak List</span></b> item in the data tree and then refine using
1864the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1865mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1866Calibri;mso-bidi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span></span></b>
1867menu item. At this point a good fit should be seen by zooming in on individual
1868peaks. For example see </p>
1869
1870<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1871 id="Picture_x0020_32" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1872 height:450pt;visibility:visible;mso-wrap-style:square'>
1873 <v:imagedata src="Fit%20Peaks_files/image009.png" o:title=""/>
1874</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1875src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
1876
1877<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
1878the right of the peak top. This is a consequence of the peak asymmetry arising
1879from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
1880is ~6% as shown on the console window. Again the <b style='mso-bidi-font-weight:
1881normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1882minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1883mso-bidi-theme-font:minor-latin'>Peak List</span></b> entries are all updated
1884with new values and those in <b style='mso-bidi-font-weight:normal'><span
1885style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1886mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1887minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1888
1889<h2>Step 5. Prepare Indexing Peak List</h2>
1890
1891<p class=MsoNormal>A separate list of peaks is kept for use in <span
1892class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1893normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1894minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1895mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> item in the data
1896tree. In the initially empty window created by this action, use menu item <b
1897style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1898mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1899Calibri;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b> to
1900copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1901style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1902mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1903minor-latin'>Peak List</span></b>.</p>
1904
1905<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1906 id="Picture_x0020_26" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:367.5pt;
1907 height:225pt;visibility:visible;mso-wrap-style:square'>
1908 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1909</v:shape><![endif]--><![if !vml]><img border=0 width=490 height=300
1910src="Fit%20Peaks_files/image010.png" v:shapes="Picture_x0020_26"><![endif]></span></p>
1911
1912<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1913may choose to not use a fitted peak (e.g. if suspected it is from a
1914contaminant).</p>
1915
1916<h2>Step 6. Run <span class=SpellE>Autoindexing</span></h2>
1917
1918<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1919style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1920mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1921minor-latin'>Unit Cells List</span></b> data item. This brings up a window for
1922indexing and cell refinement options</p>
1923
1924<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1925 id="Picture_x0020_33" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:546pt;
1926 height:204pt;visibility:visible;mso-wrap-style:square'>
1927 <v:imagedata src="Fit%20Peaks_files/image011.png" o:title=""/>
1928</v:shape><![endif]--><![if !vml]><img border=0 width=728 height=272
1929src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_33"><![endif]></span></p>
1930
1931<p class=MsoNormal>For the most rapid search (since we know the right answer),
1932select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1933mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1934Calibri;mso-bidi-theme-font:minor-latin'>Cubic-P</span></b> and launch the
1935search using menu item <b style='mso-bidi-font-weight:normal'><span
1936style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1937mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1938minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and
1939the console shows a running list of possible cells as they are found; the
1940sorted by M20 list of possible matching cells is shown in the <b
1941style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1943Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window</p>
1944
1945<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1946 id="Picture_x0020_34" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:546pt;
1947 height:324pt;visibility:visible;mso-wrap-style:square'>
1948 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1949</v:shape><![endif]--><![if !vml]><img border=0 width=728 height=432
1950src="Fit%20Peaks_files/image012.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1951
1952<h2>Step 7. Review Cell Choices</h2>
1953
1954<p class=MsoNormal>Review the list of cells associated with the <b
1955style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1956mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1957Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> data item.
1958Note that as one selects a unit cell, the generated reflections for that cell
1959are shown in the plot with dashed red lines. Sliding the cursor over these
1960lines shows a small popup window with the indexed <span class=SpellE>hkl</span>
1961for them. Note how the first cell in the list (M20~2970) with a=5.87864 Å
1962generates very many lines with no corresponding peaks (NB: this solution might
1963not always show up!)</p>
1964
1965<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1966 id="Picture_x0020_35" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:525pt;
1967 height:450pt;visibility:visible;mso-wrap-style:square'>
1968 <v:imagedata src="Fit%20Peaks_files/image013.png" o:title=""/>
1969</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1970src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_35"><![endif]></span><span
1971style='mso-spacerun:yes'> </span></p>
1972
1973<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
1974enough lines to match all the peaks</p>
1975
1976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1977 id="Picture_x0020_36" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1978 height:450pt;visibility:visible;mso-wrap-style:square'>
1979 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1980</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1981src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1982
1983<h2>Step 8. Select/Refine Cell</h2>
1984
1985<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1986indexes all peaks with almost a perfect fit to the peak positions (compare
1987dashed red lines to solid blue ones). Import the cell information using the <b
1988style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1989mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1990Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Copy Cell</span></b>
1991menu option. Then optimize the cell by refining the lattice parameters and the
1992two-theta zero: click on the <b style='mso-bidi-font-weight:normal'><span
1993style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1994mso-hansi-theme-font:minor-latin'>Refine?</span></b> checkbox next to the <b
1995style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1996mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1997Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> value and then
1998the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1999mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2000Calibri;mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
2001menu option. The M20 improves to ~3600 and <span class=GramE>the a</span> cell
2002parameter value shifts from 4.15683 to 4.15691 when zero is refined. (NB: The
2003certificate value for NIST SRM 660a is 4.15692 Å). Press the <b
2004style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2006Calibri;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
2007positions </span></b>button to update the plot including the refined <b
2008style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2009mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2010Calibri;mso-bidi-theme-font:minor-latin'>Zero offset</span></b> (in this case
2011hardly anything happens!).<span style='mso-spacerun:yes'>  </span></p>
2012
2013<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2014 id="Picture_x0020_37" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:546pt;
2015 height:309.75pt;visibility:visible;mso-wrap-style:square'>
2016 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
2017</v:shape><![endif]--><![if !vml]><img border=0 width=728 height=413
2018src="Fit%20Peaks_files/image015.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
2019
2020<p class=MsoNormal>Notice that a new entry heads the list in the <b
2021style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2022mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2023Calibri;mso-bidi-theme-font:minor-latin'>Indexing Result</span></b> section of
2024the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2025mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2026Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window with
2027an improved M20(~3600) and a new value for <b style='mso-bidi-font-weight:normal'><span
2028style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2029mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2030minor-latin'>Zero offset</span></b> is shown. NB: the <b style='mso-bidi-font-weight:
2031normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2032minor-latin;mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
2033positions</span></b> button has an additional use; you can enter the <span
2034class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2035"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2036minor-latin'>Bravais</span></b></span><b style='mso-bidi-font-weight:normal'><span
2037style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2038mso-hansi-theme-font:minor-latin'> lattice</span></b>, <b style='mso-bidi-font-weight:
2039normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2040minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b> &amp; <b
2041style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2042mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
2043for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
2044style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2045mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2046will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
2047style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2048mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
2049useful to identify e.g. a second phase in your pattern.</p>
2050
2051<p class=MsoNormal>(Optional) Finally, use of the <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/Make new phase</span></b>
2055menu option allows one to create a phase with these lattice parameters in the
2056data tree under <b style='mso-bidi-font-weight:normal'><span style='font-family:
2057"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2058minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
2059style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
2060creates the tree item <b style='mso-bidi-font-weight:normal'><span
2061style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2062mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2063minor-latin'>Phases</span></b> (if it wasn’t already present). This new phase
2064can be used in future analysis (e.g. Rietveld or Pawley refinement).</p>
2065
2066<p class=MsoNormal>To continue with the second part of this exercise, select
2067the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
2068"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2069minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>File/New
2070project</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2071style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2072mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2073minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
2074the current project saved; if <b style='mso-bidi-font-weight:normal'><span
2075style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2076mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2077minor-latin'>Yes</span></b> then all the peak fitting/indexing &amp; cell
2078refinement results will be saved to the <b style='mso-bidi-font-weight:normal'><span
2079style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2080mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2081minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
2082style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2083mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2084minor-latin'>No</span></b> then the file will remain as it was when created at
2085Step 4 above.</p>
2086
2087<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
2088class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
2089style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
2090
2091<p class=MsoNormal>In this exercise we will fit peaks and index them for the
2092new mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
2093href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
2094also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
2095substantial test of the indexing capability of GSAS-II. The required data files
2096should have been downloaded when you downloaded this tutorial. Otherwise you
2097will need to get them manually from <span style='mso-fareast-font-family:Calibri;
2098mso-fareast-theme-font:minor-latin'><a
2099href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2100Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span
2101style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2102mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2103minor-latin'>11bmb_6231.fxye</span></b><span style='mso-fareast-font-family:
2104Calibri;mso-fareast-theme-font:minor-latin'> and </span><b style='mso-bidi-font-weight:
2105normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2106minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2107mso-hansi-theme-font:minor-latin'>11bmb_6231.prm</span></b></p>
2108
2109<h2>Step 1. Read in the data. </h2>
2110
2111<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2112normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2113minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2114mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b style='mso-bidi-font-weight:
2115normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2116minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2117mso-bidi-theme-font:minor-latin'>\data\11bmb_6231.fxye</span></b>; it has a
2118corresponding <span class=SpellE><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'>prm</span></b></span> file. Load them in &amp; the plot is</p>
2122
2123<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2124 id="Picture_x0020_38" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:525pt;
2125 height:450pt;visibility:visible;mso-wrap-style:square'>
2126 <v:imagedata src="Fit%20Peaks_files/image016.png" o:title=""/>
2127</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2128src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
2129
2130<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2131lower part of the pattern.</p>
2132
2133<h2>Step 2 Set limits</h2>
2134
2135<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2136style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2137mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2138minor-latin'>3</span></b> and <b style='mso-bidi-font-weight:normal'><span
2139style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2140mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2141minor-latin'>9</span></b>.</p>
2142
2143<h2>Step 3 Pick peaks</h2>
2144
2145<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2146small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2147"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2148minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2149peaks by left-clicking on a data point near the top of the peak. Peak positions
2150can be moved by dragging the peak line and peaks can be deleted by
2151right-clicking on them. This only works when the zoom and reposition modes
2152(below) are not selected. Also note some peaks have shoulders most notably at
21535.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
2154deg. I skipped – it might be from a second phase? We’ll see later).</p>
2155
2156<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2157 id="Picture_x0020_39" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
2158 height:450pt;visibility:visible;mso-wrap-style:square'>
2159 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
2160</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2161src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_39"><![endif]></span><br
2162clear=all style='mso-special-character:line-break'>
2163</p>
2164
2165<h2>Step 4. Refine peaks</h2>
2166
2167<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
2168above, refine the peaks and the profile shape parameters in <b
2169style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2171Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
2172will be asked for a project file name at the first refinement (I used ‘<span
2173class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2174"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2175minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>jadarite</span></b></span><b
2176style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2177mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2178Calibri;mso-bidi-theme-font:minor-latin'>’</span></b>). In the end my
2179refinement converged at <span class=SpellE>Rwp</span>=11.41% and some peaks do
2180show some discrepancy as the sample is more complex than the simple <b
2181style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2183Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2184normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2185minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2186mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
2187normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2188minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2189mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
2190normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2191minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2192mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
2193normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2194minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2195mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
2196no peaks drift away during refinement (one weak one at ~6.67 is particularly
2197troublesome). However, this is good enough to proceed.</p>
2198
2199<h2>Step 5. Prepare Indexing Peak List</h2>
2200
2201<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2202style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2203mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2204minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
2205normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2206minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2207mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
2208
2209<h2>Step 6. Index the cell</h2>
2210
2211<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic.
2212In a real world case we wouldn’t know this and we would have to try each <span
2213class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2214time to go through all the bad cases.</p>
2215
2216<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2217style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2218mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2219minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
2220normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2221minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2222mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
2223<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2224mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2225Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
2226Progress will be much slower and suitable results will be slow in coming so be
2227patient. Watch the console window; the right answer will have an obviously
2228large M20 (~380) and a volume of ~594Å<sup>3</sup> (10<sup>th</sup> column of
2229console display). Once this is seen (it may take more than one try to get this)
2230you can stop the indexing search by pressing <b style='mso-bidi-font-weight:
2231normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2232minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2233mso-bidi-theme-font:minor-latin'>Cancel</span></b> on the progress bar window.
2234Notice the ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2235"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2236minor-latin'>keep</span></b>’ column; this allows you to keep some solutions
2237from one indexing run to the next. It may take more than one press to fully
2238stop it. My result was </p>
2239
2240<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2241 id="Picture_x0020_40" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525pt;
2242 height:450pt;visibility:visible;mso-wrap-style:square'>
2243 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
2244</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2245src="Fit%20Peaks_files/image018.png" v:shapes="Picture_x0020_40"><![endif]><!--[if gte vml 1]><v:shape
2246 id="Picture_x0020_41" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:546pt;
2247 height:348.75pt;visibility:visible;mso-wrap-style:square'>
2248 <v:imagedata src="Fit%20Peaks_files/image019.png" o:title=""/>
2249</v:shape><![endif]--><![if !vml]><img border=0 width=728 height=465
2250src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
2251
2252<p class=MsoNormal>Notice there may be other equally good M20 results with
2253different volumes; other solutions may be obtained as you keep trying the
2254indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2255style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2256mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try new
2257indexing runs. The best solution is the one with the smaller volume and &#946;
2258&gt; 90 deg. The plot shows every peak indexed including a weak peak not
2259selected for the peak fitting, although the weak peak at 2<span
2260style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
2261style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
2262has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
2263best cell and try to refine it along with the <b style='mso-bidi-font-weight:
2264normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2265minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
2266obtained an improved M20 ~444 and slightly different lattice parameters. Try
2267different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2268style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2269mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2270each time to see which lines vanish. By sliding the cursor over the index lines
2271without any visible peak you can see that the missing ones are 010, 100, 001,
2272110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
2273accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
2274space group P2<sub>1</sub>/n. Armed with this information you can <b
2275style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2276mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2277Calibri;mso-bidi-theme-font:minor-latin'>Make new phase</span></b> for the
2278indexed cell (I called it ‘<b style='mso-bidi-font-weight:normal'><span
2279style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2280mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2281minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
2282normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2283minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
2284the GSAS-II data tree.</p>
2285
2286<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2287 id="Picture_x0020_42" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:542.25pt;
2288 height:375pt;visibility:visible;mso-wrap-style:square'>
2289 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
2290</v:shape><![endif]--><![if !vml]><img border=0 width=723 height=500
2291src="Fit%20Peaks_files/image020.png" v:shapes="Picture_x0020_42"><![endif]></span><span
2292style='mso-spacerun:yes'> </span></p>
2293
2294<p class=MsoNormal>Notice that the lattice parameters and space group have been
2295set for you. If you set the space group here a dialog box will appear.</p>
2296
2297<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2298 id="Picture_x0020_43" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:228.75pt;
2299 height:168pt;visibility:visible;mso-wrap-style:square'>
2300 <v:imagedata src="Fit%20Peaks_files/image021.png" o:title=""/>
2301</v:shape><![endif]--><![if !vml]><img border=0 width=305 height=224
2302src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2303
2304<p class=MsoNormal>This concludes this exercise; <b style='mso-bidi-font-weight:
2305normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2306minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2307mso-bidi-theme-font:minor-latin'>Save</span></b> the project file as it is
2308needed for the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2309"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2310minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin'>Charge
2311Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span
2312style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2313mso-hansi-theme-font:minor-latin'>in GSAS</span></b> exercise. The features of
2314the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2315mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2316Calibri;mso-bidi-theme-font:minor-latin'>Phase Data</span></b> window will be
2317presented in other exercises.</p>
2318
2319<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
2320in GSAS-II </h1>
2321
2322<p class=MsoNormal>In this exercise we will fit peaks and index them for
2323sucrose in preparation for a charge flipping exercise. If continuing from the
2324previous indexing example do <b style='mso-bidi-font-weight:normal'><span
2325style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2326mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
2327GSAS-II data tree menu; you will be asked if you wish to save the old project.
2328The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
2329is another more substantial test of the indexing capability of GSAS-II. The
2330required data files should have been downloaded when you downloaded this
2331tutorial. Otherwise you will need to get them manually from <span
2332style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><a
2333href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2334Be sure to get </span><b style='mso-bidi-font-weight:normal'><span
2335style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2336mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2337minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif;
2338font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11</span>bmb_8716.fxye</span></b><span
2339style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and
2340the corresponding .<span class=SpellE>prm</span> files.</span></p>
2341
2342<h2>Step 1. Read in the data. </h2>
2343
2344<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2345normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2346minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2347mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b style='mso-bidi-font-weight:
2348normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2349minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2350mso-bidi-theme-font:minor-latin'>\data\11bmb_8716.fxye</span></b>; it has a
2351corresponding <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2352style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2353mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2354minor-latin'>prm</span></b></span> file and is for Domino® sugar ground under
2355acetone. The other <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2356style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2357mso-hansi-theme-font:minor-latin'>fxye</span></b></span> file in this directory
2358<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2359mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b>
2360is for Domino® 10X powdered sugar used “as is” out of the box. Load the <b
2361style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2362mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b>
2363file in &amp; the plot is</p>
2364
2365<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2366 id="Picture_x0020_44" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
2367 height:450pt;visibility:visible;mso-wrap-style:square'>
2368 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
2369</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2370src="Fit%20Peaks_files/image022.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2371
2372<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2373lower part of the pattern; I’ve also chosen to plot the square root of the
2374intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2375"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2376minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2377
2378<h2>Step 2 Set limits</h2>
2379
2380<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2381style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2382mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2383minor-latin'>2</span></b> and <b style='mso-bidi-font-weight:normal'><span
2384style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2385mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2386minor-latin'>8</span></b>.</p>
2387
2388<h2>Step 3 Pick peaks</h2>
2389
2390<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2391small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2392"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2393minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2394peaks by left-clicking on a data point near the top of the peak. Peak positions
2395can be moved by dragging the peak line and peaks can be deleted by
2396right-clicking on them. This only works when the zoom and reposition modes
2397(below) are not selected. An easy to shift the view is to use the ‘&lt;’ and
2398‘&gt;’ buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2399that should be added to the list. I skipped a couple of very weak peaks; the
2400total list has &gt;28 peaks.</p>
2401
2402<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2403 id="Picture_x0020_45" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:525pt;
2404 height:450pt;visibility:visible;mso-wrap-style:square'>
2405 <v:imagedata src="Fit%20Peaks_files/image023.png" o:title=""/>
2406</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2407src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_45"><![endif]></span><br
2408clear=all style='mso-special-character:line-break'>
2409</p>
2410
2411<h2>Step 4. Refine peaks</h2>
2412
2413<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2414kryptonite examples above, refine the peaks and the profile shape parameters in
2415<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2416mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2417Calibri;mso-bidi-theme-font:minor-latin'>Instrument Parameters</span></b>. You
2418will be asked for a project file name at the first refinement (I used ‘<b
2419style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2420mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2421Calibri;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>). In the end my
2422refinement converged at <span class=SpellE>Rwp</span>=6.69% and some peaks do
2423show some discrepancy as the sample is more complex than the simple <b
2424style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2425mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2426Calibri;mso-bidi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
2427normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2428minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2429mso-bidi-theme-font:minor-latin'>V</span></b>, <b style='mso-bidi-font-weight:
2430normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2431minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2432mso-bidi-theme-font:minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:
2433normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2434minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2435mso-bidi-theme-font:minor-latin'>X</span></b>, <b style='mso-bidi-font-weight:
2436normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2437minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2438mso-bidi-theme-font:minor-latin'>Y</span></b> model can accommodate. Make sure
2439no peaks drift away during refinement. However, this is good enough to proceed.</p>
2440
2441<h2>Step 5. Prepare Indexing Peak List</h2>
2442
2443<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2444style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2445mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2446minor-latin'>Operations/Load/Reload</span></b> in the <b style='mso-bidi-font-weight:
2447normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2448minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2449mso-bidi-theme-font:minor-latin'>Index Peak List</span></b> window.</p>
2450
2451<h2>Step 6. Index the cell</h2>
2452
2453<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2454In a real world case we wouldn’t know this and we would have to try each <span
2455class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2456time to go through all the bad cases.</p>
2457
2458<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2459style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2460mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2461minor-latin'>Monoclinic-P</span></b> and do <b style='mso-bidi-font-weight:
2462normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2463minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
2464mso-bidi-theme-font:minor-latin'>Cell Index/Refine/Index cell</span></b> in the
2465<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2466mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2467Calibri;mso-bidi-theme-font:minor-latin'>Unit Cells List</span></b> window.
2468Progress will be much slower than for LaB<sub>6</sub> but oddly much faster
2469than for kryptonite and suitable results may appear almost immediately. Watch
2470the console window; the right answer will have an obviously large M20 (~900)
2471and a volume of ~704Å<sup>3</sup> (10<sup>th</sup> column of console display).
2472Once this is seen (it may take more than one try to get this) you can stop the
2473indexing search by pressing <b style='mso-bidi-font-weight:normal'><span
2474style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2475mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2476minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2477style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2478some solutions from one indexing run to the next. It may take more than one
2479press to fully stop it. My result was </p>
2480
2481<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2482 id="Picture_x0020_46" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:546pt;
2483 height:5in;visibility:visible;mso-wrap-style:square'>
2484 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
2485</v:shape><![endif]--><![if !vml]><img border=0 width=728 height=480
2486src="Fit%20Peaks_files/image024.png" v:shapes="Picture_x0020_46"><![endif]><!--[if gte vml 1]><v:shape
2487 id="Picture_x0020_47" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2488 height:450pt;visibility:visible;mso-wrap-style:square'>
2489 <v:imagedata src="Fit%20Peaks_files/image025.png" o:title=""/>
2490</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2491src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2492
2493<p class=MsoNormal>Notice there may be other equally good M20 results with
2494different volumes; still other solutions may be obtained as you keep trying the
2495indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2496style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2497mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2498new indexing runs. The best solution is the one with the smaller volume and
2499&#946; &gt; 90 deg. The plot shows every peak indexed including the weak peaks
2500not selected for the peak fitting. Copy the best cell and try to refine it along
2501with the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2502mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
2503I obtained an improved M20 ~1300 and slightly different lattice parameters. Try
2504different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2505style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2506mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2507each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
2508Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
2509style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2510mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2511minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
2512style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2513mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2514Calibri;mso-bidi-theme-font:minor-latin'>sucrose</span></b>) and select <b
2515style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2516mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/sucrose</span></b>
2517from the GSAS-II data tree.</p>
2518
2519<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2520 id="Picture_x0020_48" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:542.25pt;
2521 height:375pt;visibility:visible;mso-wrap-style:square'>
2522 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
2523</v:shape><![endif]--><![if !vml]><img border=0 width=723 height=500
2524src="Fit%20Peaks_files/image026.png" v:shapes="Picture_x0020_48"><![endif]></span><span
2525style='mso-spacerun:yes'> </span></p>
2526
2527<p class=MsoNormal>Notice that the lattice parameters and space group have been
2528set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2529style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2530mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2531minor-latin'>Save</span></b> the project file as it is needed for the sucrose <b
2532style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2533mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
2534Calibri;mso-bidi-theme-font:minor-latin'>Charge Flipping</span></b> exercise.
2535The features of the <b style='mso-bidi-font-weight:normal'><span
2536style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2537mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
2538minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
2539
2540<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2541
2542</div>
2543
2544</body>
2545
2546</html>
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