source: Tutorials/FitPeaks/Fit Peaks.htm @ 3553

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finish web tutorials for now

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415  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
416  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
417  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
418  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
419  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
420  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
421  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
422  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
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424   Name="List Paragraph"/>
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427   Name="Intense Quote"/>
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430  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
431  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
432  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
433  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
434  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
435  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
436  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
437  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
438  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
439  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
440  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
441  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
442  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
443  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
444  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
445  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
446  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
447  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
448  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
449  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
450  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
451  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
452  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
453  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
454  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
455  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
456  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
457  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
458  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
459  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
460  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
461  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
462  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
463  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
464  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
465  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
466  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
467  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
468  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
469  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
470  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
471  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
472  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
473  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
474  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
475  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
476  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
477  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
478  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
479  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
480  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
481  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
482  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
483  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
484  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
485  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
486  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
487  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
488  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
489  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
490  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
491  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
492  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
493  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
494  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
495  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
496  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
497  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
498  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
499  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
500  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
501  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
502  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
503  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
504  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
505  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
506  <w:LsdException Locked="false" Priority="19" QFormat="true"
507   Name="Subtle Emphasis"/>
508  <w:LsdException Locked="false" Priority="21" QFormat="true"
509   Name="Intense Emphasis"/>
510  <w:LsdException Locked="false" Priority="31" QFormat="true"
511   Name="Subtle Reference"/>
512  <w:LsdException Locked="false" Priority="32" QFormat="true"
513   Name="Intense Reference"/>
514  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
515  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
516   UnhideWhenUsed="true" Name="Bibliography"/>
517  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
518   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
519  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
520  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
521  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
522  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
523  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
524  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
525  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
526  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
527  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
528  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
529  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
530  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
531  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
532  <w:LsdException Locked="false" Priority="46"
533   Name="Grid Table 1 Light Accent 1"/>
534  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
535  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
536  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
537  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
538  <w:LsdException Locked="false" Priority="51"
539   Name="Grid Table 6 Colorful Accent 1"/>
540  <w:LsdException Locked="false" Priority="52"
541   Name="Grid Table 7 Colorful Accent 1"/>
542  <w:LsdException Locked="false" Priority="46"
543   Name="Grid Table 1 Light Accent 2"/>
544  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
545  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
546  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
547  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
548  <w:LsdException Locked="false" Priority="51"
549   Name="Grid Table 6 Colorful Accent 2"/>
550  <w:LsdException Locked="false" Priority="52"
551   Name="Grid Table 7 Colorful Accent 2"/>
552  <w:LsdException Locked="false" Priority="46"
553   Name="Grid Table 1 Light Accent 3"/>
554  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
555  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
556  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
557  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
558  <w:LsdException Locked="false" Priority="51"
559   Name="Grid Table 6 Colorful Accent 3"/>
560  <w:LsdException Locked="false" Priority="52"
561   Name="Grid Table 7 Colorful Accent 3"/>
562  <w:LsdException Locked="false" Priority="46"
563   Name="Grid Table 1 Light Accent 4"/>
564  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
565  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
566  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
567  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
568  <w:LsdException Locked="false" Priority="51"
569   Name="Grid Table 6 Colorful Accent 4"/>
570  <w:LsdException Locked="false" Priority="52"
571   Name="Grid Table 7 Colorful Accent 4"/>
572  <w:LsdException Locked="false" Priority="46"
573   Name="Grid Table 1 Light Accent 5"/>
574  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
575  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
576  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
577  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
578  <w:LsdException Locked="false" Priority="51"
579   Name="Grid Table 6 Colorful Accent 5"/>
580  <w:LsdException Locked="false" Priority="52"
581   Name="Grid Table 7 Colorful Accent 5"/>
582  <w:LsdException Locked="false" Priority="46"
583   Name="Grid Table 1 Light Accent 6"/>
584  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
585  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
586  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
587  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
588  <w:LsdException Locked="false" Priority="51"
589   Name="Grid Table 6 Colorful Accent 6"/>
590  <w:LsdException Locked="false" Priority="52"
591   Name="Grid Table 7 Colorful Accent 6"/>
592  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
593  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
594  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
595  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
596  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
597  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
598  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
599  <w:LsdException Locked="false" Priority="46"
600   Name="List Table 1 Light Accent 1"/>
601  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
602  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
603  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
604  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
605  <w:LsdException Locked="false" Priority="51"
606   Name="List Table 6 Colorful Accent 1"/>
607  <w:LsdException Locked="false" Priority="52"
608   Name="List Table 7 Colorful Accent 1"/>
609  <w:LsdException Locked="false" Priority="46"
610   Name="List Table 1 Light Accent 2"/>
611  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
612  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
613  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
614  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
615  <w:LsdException Locked="false" Priority="51"
616   Name="List Table 6 Colorful Accent 2"/>
617  <w:LsdException Locked="false" Priority="52"
618   Name="List Table 7 Colorful Accent 2"/>
619  <w:LsdException Locked="false" Priority="46"
620   Name="List Table 1 Light Accent 3"/>
621  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
622  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
623  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
624  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
625  <w:LsdException Locked="false" Priority="51"
626   Name="List Table 6 Colorful Accent 3"/>
627  <w:LsdException Locked="false" Priority="52"
628   Name="List Table 7 Colorful Accent 3"/>
629  <w:LsdException Locked="false" Priority="46"
630   Name="List Table 1 Light Accent 4"/>
631  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
632  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
633  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
634  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
635  <w:LsdException Locked="false" Priority="51"
636   Name="List Table 6 Colorful Accent 4"/>
637  <w:LsdException Locked="false" Priority="52"
638   Name="List Table 7 Colorful Accent 4"/>
639  <w:LsdException Locked="false" Priority="46"
640   Name="List Table 1 Light Accent 5"/>
641  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
642  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
643  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
644  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
645  <w:LsdException Locked="false" Priority="51"
646   Name="List Table 6 Colorful Accent 5"/>
647  <w:LsdException Locked="false" Priority="52"
648   Name="List Table 7 Colorful Accent 5"/>
649  <w:LsdException Locked="false" Priority="46"
650   Name="List Table 1 Light Accent 6"/>
651  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
652  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
653  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
654  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
655  <w:LsdException Locked="false" Priority="51"
656   Name="List Table 6 Colorful Accent 6"/>
657  <w:LsdException Locked="false" Priority="52"
658   Name="List Table 7 Colorful Accent 6"/>
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786        mso-style-unhide:no;
787        mso-style-qformat:yes;
788        mso-style-link:"Title Char";
789        mso-style-next:Normal;
790        margin-top:0in;
791        margin-right:0in;
792        margin-bottom:15.0pt;
793        margin-left:0in;
794        mso-add-space:auto;
795        mso-pagination:widow-orphan;
796        border:none;
797        mso-border-bottom-alt:solid #4F81BD 1.0pt;
798        mso-border-bottom-themecolor:accent1;
799        padding:0in;
800        mso-padding-alt:0in 0in 4.0pt 0in;
801        font-size:26.0pt;
802        font-family:"Cambria",serif;
803        mso-ascii-font-family:Cambria;
804        mso-ascii-theme-font:major-latin;
805        mso-fareast-font-family:"Times New Roman";
806        mso-fareast-theme-font:major-fareast;
807        mso-hansi-font-family:Cambria;
808        mso-hansi-theme-font:major-latin;
809        mso-bidi-font-family:"Times New Roman";
810        mso-bidi-theme-font:major-bidi;
811        color:#17365D;
812        mso-themecolor:text2;
813        mso-themeshade:191;
814        letter-spacing:.25pt;
815        mso-font-kerning:14.0pt;}
816p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
817        {mso-style-noshow:yes;
818        mso-style-priority:10;
819        mso-style-unhide:no;
820        mso-style-qformat:yes;
821        mso-style-link:"Title Char";
822        mso-style-next:Normal;
823        mso-style-type:export-only;
824        margin:0in;
825        margin-bottom:.0001pt;
826        mso-add-space:auto;
827        mso-pagination:widow-orphan;
828        border:none;
829        mso-border-bottom-alt:solid #4F81BD 1.0pt;
830        mso-border-bottom-themecolor:accent1;
831        padding:0in;
832        mso-padding-alt:0in 0in 4.0pt 0in;
833        font-size:26.0pt;
834        font-family:"Cambria",serif;
835        mso-ascii-font-family:Cambria;
836        mso-ascii-theme-font:major-latin;
837        mso-fareast-font-family:"Times New Roman";
838        mso-fareast-theme-font:major-fareast;
839        mso-hansi-font-family:Cambria;
840        mso-hansi-theme-font:major-latin;
841        mso-bidi-font-family:"Times New Roman";
842        mso-bidi-theme-font:major-bidi;
843        color:#17365D;
844        mso-themecolor:text2;
845        mso-themeshade:191;
846        letter-spacing:.25pt;
847        mso-font-kerning:14.0pt;}
848p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
849        {mso-style-noshow:yes;
850        mso-style-priority:10;
851        mso-style-unhide:no;
852        mso-style-qformat:yes;
853        mso-style-link:"Title Char";
854        mso-style-next:Normal;
855        mso-style-type:export-only;
856        margin:0in;
857        margin-bottom:.0001pt;
858        mso-add-space:auto;
859        mso-pagination:widow-orphan;
860        border:none;
861        mso-border-bottom-alt:solid #4F81BD 1.0pt;
862        mso-border-bottom-themecolor:accent1;
863        padding:0in;
864        mso-padding-alt:0in 0in 4.0pt 0in;
865        font-size:26.0pt;
866        font-family:"Cambria",serif;
867        mso-ascii-font-family:Cambria;
868        mso-ascii-theme-font:major-latin;
869        mso-fareast-font-family:"Times New Roman";
870        mso-fareast-theme-font:major-fareast;
871        mso-hansi-font-family:Cambria;
872        mso-hansi-theme-font:major-latin;
873        mso-bidi-font-family:"Times New Roman";
874        mso-bidi-theme-font:major-bidi;
875        color:#17365D;
876        mso-themecolor:text2;
877        mso-themeshade:191;
878        letter-spacing:.25pt;
879        mso-font-kerning:14.0pt;}
880p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
881        {mso-style-noshow:yes;
882        mso-style-priority:10;
883        mso-style-unhide:no;
884        mso-style-qformat:yes;
885        mso-style-link:"Title Char";
886        mso-style-next:Normal;
887        mso-style-type:export-only;
888        margin-top:0in;
889        margin-right:0in;
890        margin-bottom:15.0pt;
891        margin-left:0in;
892        mso-add-space:auto;
893        mso-pagination:widow-orphan;
894        border:none;
895        mso-border-bottom-alt:solid #4F81BD 1.0pt;
896        mso-border-bottom-themecolor:accent1;
897        padding:0in;
898        mso-padding-alt:0in 0in 4.0pt 0in;
899        font-size:26.0pt;
900        font-family:"Cambria",serif;
901        mso-ascii-font-family:Cambria;
902        mso-ascii-theme-font:major-latin;
903        mso-fareast-font-family:"Times New Roman";
904        mso-fareast-theme-font:major-fareast;
905        mso-hansi-font-family:Cambria;
906        mso-hansi-theme-font:major-latin;
907        mso-bidi-font-family:"Times New Roman";
908        mso-bidi-theme-font:major-bidi;
909        color:#17365D;
910        mso-themecolor:text2;
911        mso-themeshade:191;
912        letter-spacing:.25pt;
913        mso-font-kerning:14.0pt;}
914a:link, span.MsoHyperlink
915        {mso-style-noshow:yes;
916        mso-style-priority:99;
917        color:blue;
918        text-decoration:underline;
919        text-underline:single;}
920a:visited, span.MsoHyperlinkFollowed
921        {mso-style-noshow:yes;
922        mso-style-priority:99;
923        color:purple;
924        text-decoration:underline;
925        text-underline:single;}
926p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
927        {mso-style-noshow:yes;
928        mso-style-priority:99;
929        mso-style-link:"Document Map Char";
930        margin:0in;
931        margin-bottom:.0001pt;
932        mso-pagination:widow-orphan;
933        font-size:8.0pt;
934        font-family:"Tahoma",sans-serif;
935        mso-fareast-font-family:"Times New Roman";
936        mso-fareast-theme-font:minor-fareast;}
937p
938        {mso-style-noshow:yes;
939        mso-style-priority:99;
940        mso-margin-top-alt:auto;
941        margin-right:0in;
942        mso-margin-bottom-alt:auto;
943        margin-left:0in;
944        mso-pagination:widow-orphan;
945        font-size:12.0pt;
946        font-family:"Times New Roman",serif;
947        mso-fareast-font-family:"Times New Roman";
948        mso-fareast-theme-font:minor-fareast;}
949pre
950        {mso-style-noshow:yes;
951        mso-style-priority:99;
952        mso-style-link:"HTML Preformatted Char";
953        margin:0in;
954        margin-bottom:.0001pt;
955        mso-pagination:widow-orphan;
956        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;
957        font-size:10.0pt;
958        font-family:"Courier New";
959        mso-fareast-font-family:"Times New Roman";}
960p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
961        {mso-style-noshow:yes;
962        mso-style-priority:99;
963        mso-style-link:"Balloon Text Char";
964        margin:0in;
965        margin-bottom:.0001pt;
966        mso-pagination:widow-orphan;
967        font-size:8.0pt;
968        font-family:"Tahoma",sans-serif;
969        mso-fareast-font-family:"Times New Roman";
970        mso-fareast-theme-font:minor-fareast;}
971span.MsoPlaceholderText
972        {mso-style-noshow:yes;
973        mso-style-priority:99;
974        mso-style-unhide:no;
975        color:gray;}
976p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
977        {mso-style-noshow:yes;
978        mso-style-priority:1;
979        mso-style-unhide:no;
980        mso-style-qformat:yes;
981        mso-style-parent:"";
982        margin:0in;
983        margin-bottom:.0001pt;
984        mso-pagination:widow-orphan;
985        font-size:12.0pt;
986        font-family:"Times New Roman",serif;
987        mso-fareast-font-family:"Times New Roman";
988        mso-fareast-theme-font:minor-fareast;}
989p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
990        {mso-style-noshow:yes;
991        mso-style-priority:34;
992        mso-style-unhide:no;
993        mso-style-qformat:yes;
994        margin-top:0in;
995        margin-right:0in;
996        margin-bottom:0in;
997        margin-left:.5in;
998        margin-bottom:.0001pt;
999        mso-add-space:auto;
1000        mso-pagination:widow-orphan;
1001        font-size:12.0pt;
1002        font-family:"Times New Roman",serif;
1003        mso-fareast-font-family:"Times New Roman";
1004        mso-fareast-theme-font:minor-fareast;}
1005p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
1006        {mso-style-noshow:yes;
1007        mso-style-priority:34;
1008        mso-style-unhide:no;
1009        mso-style-qformat:yes;
1010        mso-style-type:export-only;
1011        margin-top:0in;
1012        margin-right:0in;
1013        margin-bottom:0in;
1014        margin-left:.5in;
1015        margin-bottom:.0001pt;
1016        mso-add-space:auto;
1017        mso-pagination:widow-orphan;
1018        font-size:12.0pt;
1019        font-family:"Times New Roman",serif;
1020        mso-fareast-font-family:"Times New Roman";
1021        mso-fareast-theme-font:minor-fareast;}
1022p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
1023        {mso-style-noshow:yes;
1024        mso-style-priority:34;
1025        mso-style-unhide:no;
1026        mso-style-qformat:yes;
1027        mso-style-type:export-only;
1028        margin-top:0in;
1029        margin-right:0in;
1030        margin-bottom:0in;
1031        margin-left:.5in;
1032        margin-bottom:.0001pt;
1033        mso-add-space:auto;
1034        mso-pagination:widow-orphan;
1035        font-size:12.0pt;
1036        font-family:"Times New Roman",serif;
1037        mso-fareast-font-family:"Times New Roman";
1038        mso-fareast-theme-font:minor-fareast;}
1039p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
1040        {mso-style-noshow:yes;
1041        mso-style-priority:34;
1042        mso-style-unhide:no;
1043        mso-style-qformat:yes;
1044        mso-style-type:export-only;
1045        margin-top:0in;
1046        margin-right:0in;
1047        margin-bottom:0in;
1048        margin-left:.5in;
1049        margin-bottom:.0001pt;
1050        mso-add-space:auto;
1051        mso-pagination:widow-orphan;
1052        font-size:12.0pt;
1053        font-family:"Times New Roman",serif;
1054        mso-fareast-font-family:"Times New Roman";
1055        mso-fareast-theme-font:minor-fareast;}
1056span.MsoIntenseReference
1057        {mso-style-priority:32;
1058        mso-style-unhide:no;
1059        mso-style-qformat:yes;
1060        font-variant:small-caps;
1061        color:#C0504D;
1062        mso-themecolor:accent2;
1063        letter-spacing:.25pt;
1064        font-weight:bold;
1065        text-decoration:underline;
1066        text-underline:single;}
1067span.Heading1Char
1068        {mso-style-name:"Heading 1 Char";
1069        mso-style-priority:9;
1070        mso-style-unhide:no;
1071        mso-style-locked:yes;
1072        mso-style-link:"Heading 1";
1073        mso-ansi-font-size:24.0pt;
1074        mso-bidi-font-size:24.0pt;
1075        font-family:"Times New Roman",serif;
1076        mso-ascii-font-family:"Times New Roman";
1077        mso-fareast-font-family:"Times New Roman";
1078        mso-fareast-theme-font:minor-fareast;
1079        mso-hansi-font-family:"Times New Roman";
1080        mso-bidi-font-family:"Times New Roman";
1081        mso-font-kerning:18.0pt;
1082        font-weight:bold;}
1083span.Heading2Char
1084        {mso-style-name:"Heading 2 Char";
1085        mso-style-noshow:yes;
1086        mso-style-priority:9;
1087        mso-style-unhide:no;
1088        mso-style-locked:yes;
1089        mso-style-link:"Heading 2";
1090        mso-ansi-font-size:18.0pt;
1091        mso-bidi-font-size:18.0pt;
1092        font-family:"Times New Roman",serif;
1093        mso-ascii-font-family:"Times New Roman";
1094        mso-fareast-font-family:"Times New Roman";
1095        mso-fareast-theme-font:minor-fareast;
1096        mso-hansi-font-family:"Times New Roman";
1097        mso-bidi-font-family:"Times New Roman";
1098        font-weight:bold;}
1099span.Heading3Char
1100        {mso-style-name:"Heading 3 Char";
1101        mso-style-noshow:yes;
1102        mso-style-priority:9;
1103        mso-style-unhide:no;
1104        mso-style-locked:yes;
1105        mso-style-link:"Heading 3";
1106        mso-ansi-font-size:13.5pt;
1107        mso-bidi-font-size:13.5pt;
1108        font-family:"Times New Roman",serif;
1109        mso-ascii-font-family:"Times New Roman";
1110        mso-fareast-font-family:"Times New Roman";
1111        mso-fareast-theme-font:minor-fareast;
1112        mso-hansi-font-family:"Times New Roman";
1113        mso-bidi-font-family:"Times New Roman";
1114        font-weight:bold;}
1115span.Heading4Char
1116        {mso-style-name:"Heading 4 Char";
1117        mso-style-noshow:yes;
1118        mso-style-priority:9;
1119        mso-style-unhide:no;
1120        mso-style-locked:yes;
1121        mso-style-link:"Heading 4";
1122        mso-ansi-font-size:13.0pt;
1123        mso-bidi-font-size:13.0pt;
1124        font-family:"Cambria",serif;
1125        mso-ascii-font-family:Cambria;
1126        mso-ascii-theme-font:major-latin;
1127        mso-fareast-font-family:"Times New Roman";
1128        mso-fareast-theme-font:major-fareast;
1129        mso-hansi-font-family:Cambria;
1130        mso-hansi-theme-font:major-latin;
1131        mso-bidi-font-family:"Times New Roman";
1132        mso-bidi-theme-font:major-bidi;
1133        color:#4F81BD;
1134        mso-themecolor:accent1;
1135        font-weight:bold;
1136        font-style:italic;}
1137span.Heading5Char
1138        {mso-style-name:"Heading 5 Char";
1139        mso-style-noshow:yes;
1140        mso-style-priority:9;
1141        mso-style-unhide:no;
1142        mso-style-locked:yes;
1143        mso-style-link:"Heading 5";
1144        mso-ansi-font-size:12.0pt;
1145        mso-bidi-font-size:12.0pt;
1146        font-family:"Times New Roman",serif;
1147        mso-ascii-font-family:"Times New Roman";
1148        mso-fareast-font-family:"Times New Roman";
1149        mso-fareast-theme-font:minor-fareast;
1150        mso-hansi-font-family:"Times New Roman";
1151        mso-bidi-font-family:"Times New Roman";
1152        color:#4F4FFF;
1153        font-weight:bold;}
1154span.HTMLPreformattedChar
1155        {mso-style-name:"HTML Preformatted Char";
1156        mso-style-noshow:yes;
1157        mso-style-priority:99;
1158        mso-style-unhide:no;
1159        mso-style-locked:yes;
1160        mso-style-link:"HTML Preformatted";
1161        font-family:"Courier New";
1162        mso-ascii-font-family:"Courier New";
1163        mso-fareast-font-family:"Times New Roman";
1164        mso-hansi-font-family:"Courier New";
1165        mso-bidi-font-family:"Courier New";}
1166p.msonormal0, li.msonormal0, div.msonormal0
1167        {mso-style-name:msonormal;
1168        mso-style-noshow:yes;
1169        mso-style-priority:99;
1170        mso-style-unhide:no;
1171        mso-margin-top-alt:auto;
1172        margin-right:0in;
1173        mso-margin-bottom-alt:auto;
1174        margin-left:0in;
1175        mso-pagination:widow-orphan;
1176        font-size:12.0pt;
1177        font-family:"Times New Roman",serif;
1178        mso-fareast-font-family:"Times New Roman";
1179        mso-fareast-theme-font:minor-fareast;}
1180span.TitleChar
1181        {mso-style-name:"Title Char";
1182        mso-style-priority:10;
1183        mso-style-unhide:no;
1184        mso-style-locked:yes;
1185        mso-style-link:Title;
1186        mso-ansi-font-size:26.0pt;
1187        mso-bidi-font-size:26.0pt;
1188        font-family:"Cambria",serif;
1189        mso-ascii-font-family:Cambria;
1190        mso-ascii-theme-font:major-latin;
1191        mso-fareast-font-family:"Times New Roman";
1192        mso-fareast-theme-font:major-fareast;
1193        mso-hansi-font-family:Cambria;
1194        mso-hansi-theme-font:major-latin;
1195        mso-bidi-font-family:"Times New Roman";
1196        mso-bidi-theme-font:major-bidi;
1197        color:#17365D;
1198        mso-themecolor:text2;
1199        mso-themeshade:191;
1200        letter-spacing:.25pt;
1201        mso-font-kerning:14.0pt;}
1202span.DocumentMapChar
1203        {mso-style-name:"Document Map Char";
1204        mso-style-noshow:yes;
1205        mso-style-priority:99;
1206        mso-style-unhide:no;
1207        mso-style-locked:yes;
1208        mso-style-link:"Document Map";
1209        mso-ansi-font-size:8.0pt;
1210        mso-bidi-font-size:8.0pt;
1211        font-family:"Tahoma",sans-serif;
1212        mso-ascii-font-family:Tahoma;
1213        mso-fareast-font-family:"Times New Roman";
1214        mso-fareast-theme-font:minor-fareast;
1215        mso-hansi-font-family:Tahoma;
1216        mso-bidi-font-family:Tahoma;}
1217span.BalloonTextChar
1218        {mso-style-name:"Balloon Text Char";
1219        mso-style-noshow:yes;
1220        mso-style-priority:99;
1221        mso-style-unhide:no;
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1451</head>
1452
1453<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1454
1455<div class=WordSection1>
1456
1457<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1458
1459<P><B>A video version of this tutorial is available at
1460<A href="https://anl.box.com/v/FitPeaks" target="_blank">
1461https://anl.box.com/v/FitPeaks</A></B></P>
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-theme-font:
1477minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1478to read the data file into the current GSAS-II project. This read option is set
1479to read any of the powder data formats defined for GSAS (angles in <span
1480class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
1481the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1482style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1483mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1484format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1485style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1486mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1487format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1488style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1489directory to <b style='mso-bidi-font-weight:normal'><span style='=======
1490data file</span></b> menu item to read the data file into the current GSAS-II project.
1491This read option is set to read any of the powder data formats defined for GSAS
1492(angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu
1493items will read the <span class=SpellE><b style='
1494'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1495mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></span></b>
1496format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1497style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1498mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1499format (angles in degrees) used by <span class=SpellE>Topas</span>, etc. to see
1500them. Because you used <span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1501minor-latin'>the </span><b style='mso-bidi-font-weight:normal'><span
1502style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1503mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1504minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family:
1505Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and
1506downloaded the exercise files (recommended), then the </span><span
1507class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1508"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1509Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>FitPeaks</span></b></span><b
1510style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1511mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1512minor-latin;mso-hansi-theme-font:minor-latin'>/data/...</span></b><span
1513style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1514entry will bring you to the location where the files have been downloaded. (It
1515is also possible to download them manually from <a
1516href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
1517In this case you will need to navigate to the download location manually.)<br>
1518For this tutorial you should see the data file in the file browser, but if
1519extensions on data files are not the expected ones, you may need to change the
1520file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find
1521the desired file.</span></p>
1522
1523<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1524style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1525style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1526the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1527mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1528minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri",sans-serif;
1529mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1530minor-latin'> data</span> file in the first dialog and press <b
1531style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1532mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1533minor-latin'>Open</span></b>. There will be a Dialog box asking <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-theme-font:
1536minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
1537normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1538minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
1539button to proceed.</p>
1540
1541<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1542style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1543style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1544file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1545mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1546minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
1547automatically selected; it was produced by 11BM-B instrument processing
1548software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
1549normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1550minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1551file was created from the 12 detector raw data. If absent or the name doesn’t
1552match the data file name, a file dialog will appear for you to select the
1553correct instrument parameter file.</p>
1554
1555<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1556style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1557mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1558tree</span></b> window will have several entries </p>
1559
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1585
1586<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1587powder pattern</p>
1588
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1592 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1593</v:shape><![endif]--><![if !vml]><img border=0 width=530 height=454
1594src="Fit%20Peaks_files/image004.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1595
1596<h2>Step 2: Select Limits </h2>
1597
1598<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1599more data than we need, so it is helpful to cut down the range. Click on the <b
1600style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1601mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1602minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
1603style='<<<<<<< .mine
1604mso-hansi-theme-font:minor-latin'><span style='font-family:
1605"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1606data tree</span></span></b>. Use the <b style='mso-bidi-font-weight:normal'><span
1607style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1608mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>New:</span></b>
1609row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
1610normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1611minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
1612and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1613style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1614mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1615to <b style='mso-bidi-font-weight:normal'><span style='<<<<<<< .mine
1616mso-ascii-theme-font:minor-latin'><span
1617style='font-family:"Calibri",sans-serif;mso-hansi-theme-font:minor-latin;
1618mso-bidi-theme-font:minor-latin'>4</span></span></b> and <b style='mso-bidi-font-weight:
1619normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1620minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1621Notice on the plot that the limit lines have moved to these positions; the
1622green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1623is in a wide gap between peaks. You may also drag the limit lines to the
1624desired location or place them by a left mouse click on a data point for the
1625lower limit or a right click on a data point for the upper limit.</p>
1626
1627<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1628 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:446.25pt;
1629 height:224.25pt;visibility:visible;mso-wrap-style:square'>
1630 <v:imagedata src="Fit%20Peaks_files/image005.png" o:title=""/>
1631</v:shape><![endif]--><![if !vml]><img border=0 width=595 height=299
1632src="Fit%20Peaks_files/image005.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1633
1634<h2>Step 3: Determine Peak Positions</h2>
1635
1636<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1637auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1638style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1639style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1640on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1641mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1642minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1643normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1644minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1645data tree</span></b>. This creates an empty window of peak positions (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-theme-font:
1648minor-latin'>Limits</span></b> window is erased). At this point it is wise to
1649zoom in on the data that will be used for indexing. </p>
1650
1651<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1652auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1653style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1654style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1655on the Zoom button (5<sup>th</sup> one from the left on the plot toolbar), then
1656press the left mouse in one corner of the region to be used; holding the mouse
1657button down, drag over the region to the opposite corner; a box will be drawn
1658over the region to be zoomed and the plot will be redrawn with the new limits.
1659The toolbar has a number of buttons to the right of the help button (‘?’) that
1660can be used to incrementally change the view.</p>
1661
1662<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1663auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1664style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1665style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1666style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom button
1667again to turn off the zoom mode. </p>
1668
1669<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1670auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1671style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1672style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1673<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1674mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1675in the menu select <b style='mso-bidi-font-weight:normal'><span
1676style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1677mso-hansi-theme-font:minor-latin'>Auto search</span></b>. The plot window will
1678immediately show that all peaks were picked with a blue vertical line on each
1679one</p>
1680
1681<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1682auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_31"
1683 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:395.25pt;height:339pt;
1684 visibility:visible;mso-wrap-style:square'>
1685 <v:imagedata src="Fit%20Peaks_files/image006.png" o:title=""/>
1686</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1687src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
1688
1689<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1690auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1691normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1692minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1693List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1694
1695<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1696auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
1697 o:spid="_x0000_i1045" type="#_x0000_t75" style='width:426pt;height:198.75pt;
1698 visibility:visible;mso-wrap-style:square'>
1699 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1700</v:shape><![endif]--><![if !vml]><img border=0 width=568 height=265
1701src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
1702
1703<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1704will be 20 peaks in this example. You should examine both the list and the plot
1705to be sure the auto search did not pick a peak twice (rarely) or skip a peak or
1706shoulder. You can add a peak to the list by pressing the left mouse button with
1707the pointer on a data point at the peak top or shoulder; be sure the zoom/shift
1708buttons are off. You may drag a peak position as needed. A position may be
1709deleted with a right click with the mouse on the blue line. You can also delete
1710a peak by selecting the row in the table; it will be highlighted in blue. Then
1711press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1712mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b>
1713key; it will be removed from the table and the plot. The list will always show
1714the peaks sorted by position. When done you should have 20 unique peak
1715positions.</p>
1716
1717<h2>Step 4: Refine Peak Positions</h2>
1718
1719<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1720refinement and then adding parameters to complete the fitting,</p>
1721
1722<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1723style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1724style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1725the peak intensities and the background. These parameters have their refinement
1726flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1727normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1728minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1729Fitting/<span class=SpellE>Peakfit</span></span></b>. Do <b style='mso-bidi-font-weight:
1730normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1731style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1732mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1733menu item; that it to be used for Rietveld/Pawley refinements. You will be
1734asked to save the current project before the fit will proceed; change directory
1735if desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1736normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1737minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1738A window will show the progress of the refinement and will close when the
1739least-squares fit is complete (usually very fast). The plot is updated with the
1740fit, the peak list window is updated with the new peak values and a summary of
1741the refinement is shown on the console window as well.</p>
1742
1743<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1744 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:407.25pt;
1745 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1746 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1747</v:shape><![endif]--><![if !vml]><img border=0 width=543 height=466
1748src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_33"><![endif]></span></p>
1749
1750<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1751 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:420pt;
1752 height:195.75pt;visibility:visible;mso-wrap-style:square'>
1753 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1754</v:shape><![endif]--><![if !vml]><img border=0 width=560 height=261
1755src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1756
1757<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1758style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1759style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1760add refinement of the peak positions. This can be done by clicking on all the
1761refinement flags for the individual peaks or it is possible to set them all at
1762the same time using this recipe: </p>
1763
1764<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1765auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1766style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1767style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1768on any value in the table to select it, for example the first peak position. A
1769black box appears around the value. </p>
1770
1771<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1772text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1773style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1774style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1775on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1776mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1777label above the peak position check-boxes. The entire column of checkboxes is
1778highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
1779style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1780mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y</span></b>
1781key to turn on all refinement flags (<b style='mso-bidi-font-weight:normal'><span
1782style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1783mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>n</span></b>
1784would turn them off).</p>
1785
1786<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1787the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1788mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1789minor-latin'>Peak Fitting/<span class=SpellE>Peakfit</span></span></b> menu
1790item.</p>
1791
1792<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1793refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1794performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1795width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
1796click the refinement flags for sigma and/or gamma in the Peak List window.
1797&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1798widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening equation
1799as described below.&nbsp;Note - one cannot refine ALL peak widths using both
1800individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental broadening
1801terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1802
1803<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1804"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1805to an instrumental broadening equation, first<b> s</b></span>elect the <b
1806style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1807mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1808minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
1809opens a window for peak profile terms<b> </b><span style='mso-bidi-font-weight:
1810bold'>and also creates a new plot window&nbsp;showing the instrument profile
1811resolution curve.</span></p>
1812
1813<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1814 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:415.5pt;
1815 height:298.5pt;visibility:visible;mso-wrap-style:square'>
1816 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1817</v:shape><![endif]--><![if !vml]><img border=0 width=554 height=398
1818src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_35"><![endif]></span></p>
1819
1820<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1821corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1822coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1823values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1824<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1825mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1826minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
1827style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1828mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
1829<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1830mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1831minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
1832style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1833mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
1834<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1835mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1836minor-latin'>Y</span></b>. </p>
1837
1838<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1839style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1840style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1841repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1842style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1843mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1844item in the data tree and then refine using the <b style='mso-bidi-font-weight:
1845normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1846minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1847Fitting/<span class=SpellE>Peakfit</span></span></b> menu item. At this point a
1848good fit should be seen by zooming in on individual peaks. For example see </p>
1849
1850<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1851 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:408pt;
1852 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1853 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1854</v:shape><![endif]--><![if !vml]><img border=0 width=544 height=466
1855src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1856
1857<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
1858the right of the peak top. This is a consequence of the peak asymmetry arising
1859from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
1860is ~7% as shown on the console window. Again the <b style='mso-bidi-font-weight:
1861normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1862minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1863List</span></b> entries are all updated with new values and those in <b
1864style='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-theme-font:
1866minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1867
1868<h2>Step 5. Prepare Indexing Peak List</h2>
1869
1870<p class=MsoNormal>A separate list of peaks is kept for use in <span
1871class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1872normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1873minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1874Peak List</span></b> item in the data tree. In the initially empty window
1875created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1876style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1877mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1878to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1879style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1880mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>.</p>
1881
1882<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1883 id="Picture_x0020_37" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:431.25pt;
1884 height:309.75pt;visibility:visible;mso-wrap-style:square'>
1885 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1886</v:shape><![endif]--><![if !vml]><img border=0 width=575 height=413
1887src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
1888
1889<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1890may choose to not use a fitted peak (e.g. if suspected it is from a
1891contaminant).</p>
1892
1893<h2>Step 6. Run <span class=SpellE>Autoindexing</span></h2>
1894
1895<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1896style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1897mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1898List</span></b> data item. This brings up a window for indexing and cell
1899refinement options</p>
1900
1901<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1902 id="Picture_x0020_38" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1903 height:157.5pt;visibility:visible;mso-wrap-style:square'>
1904 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1905</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=210
1906src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
1907
1908<p class=MsoNormal>For the most rapid search (since we know the right answer),
1909select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1910mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1911minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1912style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1913mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1914minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and the
1915console shows a running list of possible cells as they are found; the sorted by
1916M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1917normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1918minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1919Cells List</span></b> window</p>
1920
1921<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1922 id="Picture_x0020_13" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1923 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1924 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1925</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1926src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1927
1928<h2>Step 7. Review Cell Choices</h2>
1929
1930<p class=MsoNormal>Review the list of cells associated with the <b
1931style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1932mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1933minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1934unit cell, the generated reflections for that cell are shown in the plot with
1935dashed red lines. Sliding the cursor over these lines shows a small popup
1936window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1937first cell in the list (M20~2970) with a=5.87864 Å generates very many lines
1938with no corresponding peaks (NB: this solution might not always show up!)</p>
1939
1940<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1941 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:447pt;
1942 height:383.25pt;visibility:visible;mso-wrap-style:square'>
1943 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1944</v:shape><![endif]--><![if !vml]><img border=0 width=596 height=511
1945src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_40"><![endif]></span><span
1946style='mso-spacerun:yes'> </span></p>
1947
1948<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
1949enough lines to match all the peaks</p>
1950
1951<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1952 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:428.25pt;
1953 height:366.75pt;visibility:visible;mso-wrap-style:square'>
1954 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1955</v:shape><![endif]--><![if !vml]><img border=0 width=571 height=489
1956src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1957
1958<h2>Step 8. Select/Refine Cell</h2>
1959
1960<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1961indexes all peaks with almost a perfect fit to the peak positions (compare
1962dashed red lines to solid blue ones). Import the cell information using the <b
1963style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1964mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1965minor-latin'>Cell Index/Refine/Copy Cell</span></b> menu option. Then optimize
1966the cell by refining the lattice parameters and the two-theta zero: click on
1967the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1968mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
1969checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1970style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1971mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1972value and then the <b style='mso-bidi-font-weight:normal'><span
1973style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1974mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1975Index/Refine/Refine Cell</span></b> menu option. The M20 improves to ~3600 and <span
1976class=GramE>the a</span> cell parameter value shifts from 4.15683 to 4.15691
1977when zero is refined. (NB: The certificate value for NIST SRM 660a is 4.15692
1978Å). Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1979"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1980minor-latin;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
1981positions </span></b>button to update the plot including the refined <b
1982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1984minor-latin'>Zero offset</span></b> (in this case hardly anything
1985happens!).<span style='mso-spacerun:yes'>  </span></p>
1986
1987<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1988 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1989 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1990 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
1991</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1992src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1993
1994<p class=MsoNormal>Notice that a new entry heads the list in 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-theme-font:
1997minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
1998normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1999minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
2000Cells List</span></b> window with an improved <span class=GramE>M20(</span>~3600)
2001and a new value for <b style='mso-bidi-font-weight:normal'><span
2002style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2003mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
2004is shown. NB: the <b style='mso-bidi-font-weight:normal'><span
2005style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2006mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2007button has an additional use; you can enter the <span class=SpellE><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'>Bravais</span></b></span><b
2010style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2011mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>,
2012<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2013mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b>
2014&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2015mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
2016for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
2017style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2018mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2019will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
2020style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2021mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
2022useful to identify e.g. a second phase in your pattern.</p>
2023
2024<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
2025normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2026minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
2027Index/Refine/Make new phase</span></b> menu option allows one to create a phase
2028with these lattice parameters in the data tree under <b style='mso-bidi-font-weight:
2029normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2030minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
2031style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
2032creates the tree item <b style='mso-bidi-font-weight:normal'><span
2033style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2034mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
2035(if it wasn’t already present). This new phase can be used in future analysis
2036(e.g. Rietveld or Pawley refinement).</p>
2037
2038<p class=MsoNormal>To continue with the second part of this exercise, select
2039the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
2040"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2041minor-latin;mso-bidi-theme-font:minor-latin'>File/New project</span></b> in the
2042<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2043mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2044minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
2045the current project saved; if <b style='mso-bidi-font-weight:normal'><span
2046style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2047mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
2048then all the peak fitting/indexing &amp; cell refinement results will be saved
2049to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2050mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2051minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
2052style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2053mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
2054then the file will remain as it was when created at Step 4 above.</p>
2055
2056<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
2057class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
2058style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
2059
2060<p class=MsoNormal>In this exercise we will fit peaks and index them for the
2061mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
2062href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
2063also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
2064substantial test of the indexing capability of GSAS-II. The required data files
2065should have been downloaded when you downloaded this tutorial. Otherwise you
2066will need to get them manually from <span style='mso-fareast-font-family:Calibri;
2067mso-fareast-theme-font:minor-latin'><a
2068href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2069Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span
2070style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2071mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2072minor-latin'>11bmb_6231.fxye</span></b><span style='mso-fareast-font-family:
2073Calibri;mso-fareast-theme-font:minor-latin'> and </span><b style='mso-bidi-font-weight:
2074normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2075minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2076mso-hansi-theme-font:minor-latin'>11bmb_6231.prm</span></b></p>
2077
2078<h2>Step 1. Read in the data. </h2>
2079
2080<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2081normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2082minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2083style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2084mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2085minor-latin'>\data\11bmb_6231.fxye</span></b>; it has a corresponding <span
2086class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2087"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2088minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file. Load
2089them in &amp; the plot is</p>
2090
2091<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2092 id="Picture_x0020_43" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:405pt;
2093 height:347.25pt;visibility:visible;mso-wrap-style:square'>
2094 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2095</v:shape><![endif]--><![if !vml]><img border=0 width=540 height=463
2096src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2097
2098<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2099lower part of the pattern.</p>
2100
2101<h2>Step 2 Set limits</h2>
2102
2103<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2104style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2105mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
2106and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2107mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2108minor-latin'>9</span></b>. This will give a suitable number of lines for
2109indexing.</p>
2110
2111<h2>Step 3 Pick peaks</h2>
2112
2113<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2114small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2115"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2116minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2117peaks by left-clicking on a data point near the top of the peak. Peak positions
2118can be moved by dragging the peak line and peaks can be deleted by
2119right-clicking on them. This only works when the zoom and reposition modes
2120(below) are not selected. Also note some peaks have shoulders most notably at
21215.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
2122deg. I skipped – it might be from a second phase? We’ll see later).</p>
2123
2124<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2125 id="Picture_x0020_39" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:436.5pt;
2126 height:374.25pt;visibility:visible;mso-wrap-style:square'>
2127 <v:imagedata src="Fit%20Peaks_files/image030.png" o:title=""/>
2128</v:shape><![endif]--><![if !vml]><img border=0 width=582 height=499
2129src="Fit%20Peaks_files/image031.png" v:shapes="Picture_x0020_39"><![endif]></span><br
2130clear=all style='mso-special-character:line-break'>
2131</p>
2132
2133<h2>Step 4. Refine peaks</h2>
2134
2135<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
2136above, refine the peaks and the profile shape parameters in <b
2137style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2138mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2139minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2140file name at the first refinement (I used ‘<span class=SpellE><b
2141style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2142mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2143minor-latin'>jadarite</span></b></span><b style='mso-bidi-font-weight:normal'><span
2144style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2145mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>’</span></b>).
2146In the end my refinement converged at <span class=SpellE>Rwp</span>=11.41% and
2147some peaks do show some discrepancy as the sample is more complex than the
2148simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2149mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2150minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2151style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2152mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2153<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2154mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2155minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2156style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2157mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2158<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2159mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2160minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away
2161during refinement (one weak one at ~6.67 is particularly troublesome). However,
2162this is good enough to proceed.</p>
2163
2164<h2>Step 5. Prepare Indexing Peak List</h2>
2165
2166<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2167style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2168mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2169in the <b style='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-theme-font:
2171minor-latin'>Index Peak List</span></b> window.</p>
2172
2173<h2>Step 6. Index the cell</h2>
2174
2175<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic. In
2176a real world case we wouldn’t know this and we would have to try each <span
2177class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2178time to go through all the bad cases.</p>
2179
2180<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2181style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2182mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2183and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2184mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2185minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2186style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2187mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2188minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2189and suitable results will be slow in coming so be patient. Watch the console
2190window; the right answer will have an obviously large M20 (~380) and a volume
2191of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
2192seen (it may take more than one try to get this) you can stop the indexing
2193search by pressing <b style='mso-bidi-font-weight:normal'><span
2194style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2195mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
2196on the progress bar window. Notice the ‘<b style='mso-bidi-font-weight:normal'><span
2197style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2198mso-hansi-theme-font:minor-latin'>keep</span></b>’ column; this allows you to
2199keep some solutions from one indexing run to the next. It may take more than
2200one press to fully stop it. My result was </p>
2201
2202<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2203 id="Picture_x0020_19" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:359.25pt;
2204 height:297pt;visibility:visible;mso-wrap-style:square'>
2205 <v:imagedata src="Fit%20Peaks_files/image032.png" o:title=""/>
2206</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=396
2207src="Fit%20Peaks_files/image033.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2208
2209<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2210 id="Picture_x0020_20" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
2211 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2212 <v:imagedata src="Fit%20Peaks_files/image034.png" o:title=""/>
2213</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2214src="Fit%20Peaks_files/image035.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
2215
2216<p class=MsoNormal>Notice there may be other equally good M20 results with
2217different volumes; other solutions may be obtained as you keep trying the
2218indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2219style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2220mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2221new indexing runs. The best solution is the one with the smaller volume and
2222&#946; &gt; 90 deg. The plot shows every peak indexed including a weak peak not
2223selected for the peak fitting, although the weak peak at 2<span
2224style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
2225style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
2226has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
2227best cell and try to refine it along with the <b style='mso-bidi-font-weight:
2228normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2229minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
2230obtained an improved M20 ~444 and slightly different lattice parameters. Try
2231different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2232style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2233mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2234each time to see which lines vanish. By sliding the cursor over the index lines
2235without any visible peak you can see that the missing ones are 010, 100, 001,
2236110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
2237accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
2238space group P2<sub>1</sub>/n. Armed with this information you can <b
2239style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2240mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2241minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
2242style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2243mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2244minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
2245normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2246minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
2247the GSAS-II data tree.</p>
2248
2249<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2250 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
2251 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2252 <v:imagedata src="Fit%20Peaks_files/image036.png" o:title=""/>
2253</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2254src="Fit%20Peaks_files/image037.png" v:shapes="Picture_x0020_46"><![endif]></span><span
2255style='mso-spacerun:yes'> </span></p>
2256
2257<p class=MsoNormal>Notice that the lattice parameters and space group have been
2258set for you. </p>
2259
2260<p class=MsoNormal>This concludes this exercise; do <span class=GramE><b
2261style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2263minor-latin'>Save</span></b></span> <b style='mso-bidi-font-weight:normal'><span
2264style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2265mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>project</span></b>
2266as it is needed for the <b style='mso-bidi-font-weight:normal'><span
2267style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2268mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2269Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span
2270style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2271mso-hansi-theme-font:minor-latin'>in GSAS</span></b> exercise. The features of
2272the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2273mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2274minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
2275
2276<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
2277in GSAS-II </h1>
2278
2279<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
2280in preparation for a charge flipping exercise. If continuing from the previous
2281indexing example do <b style='mso-bidi-font-weight:normal'><span
2282style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2283mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
2284GSAS-II data tree menu; you will be asked if you wish to save the old project.
2285The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
2286is another more substantial test of the indexing capability of GSAS-II. The
2287required data files should have been downloaded when you downloaded this
2288tutorial. Otherwise you will need to get them manually from <span
2289style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><a
2290href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2291Be sure to get </span><b style='mso-bidi-font-weight:normal'><span
2292style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2293mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2294minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif;
2295font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11bmb</span>_8716.fxye</span></b><span
2296style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and
2297the corresponding .<span class=SpellE>prm</span> files.</span></p>
2298
2299<h2>Step 1. Read in the data. </h2>
2300
2301<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2302normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2303minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2304style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2305mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2306minor-latin'>\data\11bmb_8716.fxye</span></b>; it has a corresponding <span
2307class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2308"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2309minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file and is
2310for Domino® sugar ground under acetone. The other <span class=SpellE><b
2311style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2312mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span>
2313file in this directory <b style='mso-bidi-font-weight:normal'><span
2314style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2315mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X
2316powdered sugar used “as is” out of the box. Load the <b style='mso-bidi-font-weight:
2317normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2318minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the
2319plot is</p>
2320
2321<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2322 id="Picture_x0020_44" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:452.25pt;
2323 height:387.75pt;visibility:visible;mso-wrap-style:square'>
2324 <v:imagedata src="Fit%20Peaks_files/image038.png" o:title=""/>
2325</v:shape><![endif]--><![if !vml]><img border=0 width=603 height=517
2326src="Fit%20Peaks_files/image039.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2327
2328<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2329lower part of the pattern; I’ve also chosen to plot the square root of the
2330intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2331"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2332minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2333
2334<h2>Step 2 Set limits</h2>
2335
2336<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2337style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2338mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>2</span></b>
2339and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2340mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2341minor-latin'>8</span></b>. Again, this gives a reasonable number of peaks for
2342indexing.</p>
2343
2344<h2>Step 3 Pick peaks</h2>
2345
2346<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2347small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2348"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2349minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2350peaks by left-clicking on a data point near the top of the peak. Peak positions
2351can be moved by dragging the peak line and peaks can be deleted by
2352right-clicking on them. This only works when the zoom and reposition modes
2353(below) are not selected. An easy to shift the view is to use the ‘&lt;’ and
2354‘&gt;’ buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2355that should be added to the list. I skipped a couple of very weak peaks; the
2356total list has &gt;28 peaks.</p>
2357
2358<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2359 id="Picture_x0020_45" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:465.75pt;
2360 height:399pt;visibility:visible;mso-wrap-style:square'>
2361 <v:imagedata src="Fit%20Peaks_files/image040.png" o:title=""/>
2362</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=532
2363src="Fit%20Peaks_files/image041.png" v:shapes="Picture_x0020_45"><![endif]></span><br
2364clear=all style='mso-special-character:line-break'>
2365</p>
2366
2367<h2>Step 4. Refine peaks</h2>
2368
2369<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2370kryptonite examples above, refine the peaks and the profile shape parameters in
2371<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2372mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2373minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2374file name at the first refinement (I used ‘<b style='mso-bidi-font-weight:normal'><span
2375style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2376mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>).
2377In the end my refinement converged at <span class=SpellE>Rwp</span>=6.69% and
2378some peaks do show some discrepancy as the sample is more complex than the
2379simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2380mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2381minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2382style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2383mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2384<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2385mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2386minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2387style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2388mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2389<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2390mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2391minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away during
2392refinement. However, this is good enough to proceed.</p>
2393
2394<h2>Step 5. Prepare Indexing Peak List</h2>
2395
2396<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2397style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2398mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2399in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2400mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2401minor-latin'>Index Peak List</span></b> window.</p>
2402
2403<h2>Step 6. Index the cell</h2>
2404
2405<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2406In a real world case we wouldn’t know this and we would have to try each <span
2407class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2408time to go through all the bad cases.</p>
2409
2410<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2411style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2412mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2413and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2414mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2415minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2416style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2417mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2418minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2419than for LaB<sub>6</sub> but oddly much faster than for kryptonite and suitable
2420results may appear almost immediately. Watch the console window; the right
2421answer will have an obviously large M20 (~900) and a volume of ~704Å<sup>3</sup>
2422(10<sup>th</sup> column of console display). Once this is seen (it may take
2423more than one try to get this) you can stop the indexing search by pressing <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-theme-font:
2426minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2427style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2428some solutions from one indexing run to the next. It may take more than one
2429press to fully stop it. My result was </p>
2430
2431<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2432 id="Picture_x0020_24" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2433 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2434 <v:imagedata src="Fit%20Peaks_files/image042.png" o:title=""/>
2435</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2436src="Fit%20Peaks_files/image043.png" v:shapes="Picture_x0020_24"><![endif]><!--[if gte vml 1]><v:shape
2437 id="Picture_x0020_47" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:434.25pt;
2438 height:372pt;visibility:visible;mso-wrap-style:square'>
2439 <v:imagedata src="Fit%20Peaks_files/image044.png" o:title=""/>
2440</v:shape><![endif]--><![if !vml]><img border=0 width=579 height=496
2441src="Fit%20Peaks_files/image045.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2442
2443<p class=MsoNormal>Notice there may be other equally good M20 results with
2444different volumes; still other solutions may be obtained as you keep trying the
2445indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2446style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2447mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2448new indexing runs. The best solution is the one with the smaller volume and
2449&#946; &gt; 90 <span class=SpellE>deg</span> and c&gt;a (I got both solutions!).
2450The plot shows every peak indexed including the weak peaks not selected for the
2451peak fitting. Copy the best cell and try to refine it along with the <b
2452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
2454I obtained an improved M20 ~1300 and slightly different lattice parameters. Try
2455different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2456style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2457mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2458each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
2459Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
2460style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2461mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
2462phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
2463normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2464minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose</span></b>)
2465and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2466"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2467minor-latin'>Phases/sucrose</span></b> from the GSAS-II data tree.</p>
2468
2469<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2470 id="Picture_x0020_48" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2471 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2472 <v:imagedata src="Fit%20Peaks_files/image046.png" o:title=""/>
2473</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2474src="Fit%20Peaks_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span><span
2475style='mso-spacerun:yes'> </span></p>
2476
2477<p class=MsoNormal>Notice that the lattice parameters and space group have been
2478set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2479style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2480mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b>
2481the project file as it is needed for the sucrose <b style='mso-bidi-font-weight:
2482normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2483minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2484Flipping</span></b> exercise. The features of the <b style='mso-bidi-font-weight:
2485normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2486minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase
2487Data</span></b> window will be presented in other exercises.</p>
2488
2489<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2490
2491</div>
2492
2493</body>
2494
2495</html>
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