source: Tutorials/FitPeaks/Fit Peaks.htm @ 2983

Last change on this file since 2983 was 2983, checked in by vondreele, 4 years ago

fix

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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;
1222        mso-style-locked:yes;
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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 class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1460cell that matches a set of diffraction peaks -- a process known as
1461auto-indexing. First peaks must be located and optimized and then indexing can
1462be done.</p>
1463
1464<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1465
1466<h2>Step 1: Read in the data file</h2>
1467
1468<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1469style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1470style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1471the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1472mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1473minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1474to read the data file into the current GSAS-II project. This read option is set
1475to read any of the powder data formats defined for GSAS (angles in <span
1476class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
1477the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1478style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1479mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1480format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1481style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1482mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1483format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1484style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1485directory to <b style='mso-bidi-font-weight:normal'><span style='=======
1486data file</span></b> menu item to read the data file into the current GSAS-II project.
1487This read option is set to read any of the powder data formats defined for GSAS
1488(angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu
1489items will read the <span class=SpellE><b style='
1490'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1491mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></span></b>
1492format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1493style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1494mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1495format (angles in degrees) used by <span class=SpellE>Topas</span>, etc. to see
1496them. Because you used <span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1497minor-latin'>the </span><b style='mso-bidi-font-weight:normal'><span
1498style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1499mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1500minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family:
1501Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and
1502downloaded the exercise files (recommended), then the </span><span
1503class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1504"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1505Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>FitPeaks</span></b></span><b
1506style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1507mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1508minor-latin;mso-hansi-theme-font:minor-latin'>/data/...</span></b><span
1509style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1510entry will bring you to the location where the files have been downloaded. (It
1511is also possible to download them manually from <a
1512href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
1513In this case you will need to navigate to the download location manually.)<br>
1514For this tutorial you should see the data file in the file browser, but if
1515extensions on data files are not the expected ones, you may need to change the
1516file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find
1517the desired file.</span></p>
1518
1519<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1520style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1521style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1522the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1523mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1524minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri",sans-serif;
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1526minor-latin'> data</span> file in the first dialog and press <b
1527style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1528mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1529minor-latin'>Open</span></b>. There will be a Dialog box asking <b
1530style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1531mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1532minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
1533normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1534minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
1535button to proceed.</p>
1536
1537<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1538style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1539style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1540file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1541mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1542minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
1543automatically selected; it was produced by 11BM-B instrument processing
1544software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
1545normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1546minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1547file was created from the 12 detector raw data. If absent or the name doesn’t
1548match the data file name, a file dialog will appear for you to select the
1549correct instrument parameter file.</p>
1550
1551<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1552style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1553mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1554tree</span></b> window will have several entries </p>
1555
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1557 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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1566  <v:f eqn="prod @3 21600 pixelHeight"/>
1567  <v:f eqn="sum @0 0 1"/>
1568  <v:f eqn="prod @6 1 2"/>
1569  <v:f eqn="prod @7 21600 pixelWidth"/>
1570  <v:f eqn="sum @8 21600 0"/>
1571  <v:f eqn="prod @7 21600 pixelHeight"/>
1572  <v:f eqn="sum @10 21600 0"/>
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1579</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=401
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1581
1582<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1583powder pattern</p>
1584
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1590src="Fit%20Peaks_files/image004.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1591
1592<h2>Step 2: Select Limits </h2>
1593
1594<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1595more data than we need, so it is helpful to cut down the range. Click on the <b
1596style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1597mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1598minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
1599style='<<<<<<< .mine
1600mso-hansi-theme-font:minor-latin'><span style='font-family:
1601"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1602data tree</span></span></b>. Use the <b style='mso-bidi-font-weight:normal'><span
1603style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1604mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>New:</span></b>
1605row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
1606normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1607minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
1608and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1609style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1610mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1611to <b style='mso-bidi-font-weight:normal'><span style='<<<<<<< .mine
1612mso-ascii-theme-font:minor-latin'><span
1613style='font-family:"Calibri",sans-serif;mso-hansi-theme-font:minor-latin;
1614mso-bidi-theme-font:minor-latin'>4</span></span></b> and <b style='mso-bidi-font-weight:
1615normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1616minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1617Notice on the plot that the limit lines have moved to these positions; the
1618green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1619is in a wide gap between peaks. You may also drag the limit lines to the
1620desired location or place them by a left mouse click on a data point for the
1621lower limit or a right click on a data point for the upper limit.</p>
1622
1623<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1624 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:446.25pt;
1625 height:224.25pt;visibility:visible;mso-wrap-style:square'>
1626 <v:imagedata src="Fit%20Peaks_files/image005.png" o:title=""/>
1627</v:shape><![endif]--><![if !vml]><img border=0 width=595 height=299
1628src="Fit%20Peaks_files/image005.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1629
1630<h2>Step 3: Determine Peak Positions</h2>
1631
1632<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1633auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1634style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1635style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1636on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1637mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1638minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1639normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1640minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1641data tree</span></b>. This creates an empty window of peak positions (the <b
1642style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1643mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1644minor-latin'>Limits</span></b> window is erased). At this point it is wise to
1645zoom in on the data that will be used for indexing. </p>
1646
1647<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1648auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1649style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1650style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1651on the Zoom button (5<sup>th</sup> one from the left on the plot toolbar), then
1652press the left mouse in one corner of the region to be used; holding the mouse
1653button down, drag over the region to the opposite corner; a box will be drawn
1654over the region to be zoomed and the plot will be redrawn with the new limits.
1655The toolbar has a number of buttons to the right of the help button (‘?’) that
1656can be used to incrementally change the view.</p>
1657
1658<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1659auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1660style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1661style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1662style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom button
1663again to turn off the zoom mode. </p>
1664
1665<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1666auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1667style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1668style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1669<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1670mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1671in the menu select <b style='mso-bidi-font-weight:normal'><span
1672style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1673mso-hansi-theme-font:minor-latin'>Auto search</span></b>. The plot window will
1674immediately show that all peaks were picked with a blue vertical line on each
1675one</p>
1676
1677<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1678auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_31"
1679 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:395.25pt;height:339pt;
1680 visibility:visible;mso-wrap-style:square'>
1681 <v:imagedata src="Fit%20Peaks_files/image006.png" o:title=""/>
1682</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1683src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
1684
1685<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1686auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1687normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1688minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1689List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1690
1691<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1692auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
1693 o:spid="_x0000_i1045" type="#_x0000_t75" style='width:426pt;height:198.75pt;
1694 visibility:visible;mso-wrap-style:square'>
1695 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1696</v:shape><![endif]--><![if !vml]><img border=0 width=568 height=265
1697src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
1698
1699<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1700will be 20 peaks in this example. You should examine both the list and the plot
1701to be sure the auto search did not pick a peak twice (rarely) or skip a peak or
1702shoulder. You can add a peak to the list by pressing the left mouse button with
1703the pointer on a data point at the peak top or shoulder; be sure the zoom/shift
1704buttons are off. You may drag a peak position as needed. A position may be
1705deleted with a right click with the mouse on the blue line. You can also delete
1706a peak by selecting the row in the table; it will be highlighted in blue. Then
1707press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1708mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b>
1709key; it will be removed from the table and the plot. The list will always show
1710the peaks sorted by position. When done you should have 20 unique peak
1711positions.</p>
1712
1713<h2>Step 4: Refine Peak Positions</h2>
1714
1715<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1716refinement and then adding parameters to complete the fitting,</p>
1717
1718<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1719style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1720style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1721the peak intensities and the background. These parameters have their refinement
1722flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1723normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1724minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1725Fitting/<span class=SpellE>Peakfit</span></span></b>. Do <b style='mso-bidi-font-weight:
1726normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1727style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1728mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1729menu item; that it to be used for Rietveld/Pawley refinements. You will be
1730asked to save the current project before the fit will proceed; change directory
1731if desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1732normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1733minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1734A window will show the progress of the refinement and will close when the
1735least-squares fit is complete (usually very fast). The plot is updated with the
1736fit, the peak list window is updated with the new peak values and a summary of
1737the refinement is shown on the console window as well.</p>
1738
1739<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1740 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:407.25pt;
1741 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1742 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1743</v:shape><![endif]--><![if !vml]><img border=0 width=543 height=466
1744src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_33"><![endif]></span></p>
1745
1746<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1747 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:420pt;
1748 height:195.75pt;visibility:visible;mso-wrap-style:square'>
1749 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1750</v:shape><![endif]--><![if !vml]><img border=0 width=560 height=261
1751src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1752
1753<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1754style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1755style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1756add refinement of the peak positions. This can be done by clicking on all the
1757refinement flags for the individual peaks or it is possible to set them all at
1758the same time using this recipe: </p>
1759
1760<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1761auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1762style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1763style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1764on any value in the table to select it, for example the first peak position. A
1765black box appears around the value. </p>
1766
1767<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1768text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1769style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1770style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1771on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1772mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1773label above the peak position check-boxes. The entire column of checkboxes is
1774highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
1775style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1776mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y</span></b>
1777key to turn on all refinement flags (<b style='mso-bidi-font-weight:normal'><span
1778style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1779mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>n</span></b>
1780would turn them off).</p>
1781
1782<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1783the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1784mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1785minor-latin'>Peak Fitting/<span class=SpellE>Peakfit</span></span></b> menu
1786item.</p>
1787
1788<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1789refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1790performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1791width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
1792click the refinement flags for sigma and/or gamma in the Peak List window.
1793&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1794widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening equation
1795as described below.&nbsp;Note - one cannot refine ALL peak widths using both
1796individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental broadening
1797terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1798
1799<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1800"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1801to an instrumental broadening equation, first<b> s</b></span>elect the <b
1802style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1803mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1804minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
1805opens a window for peak profile terms<b> </b><span style='mso-bidi-font-weight:
1806bold'>and also creates a new plot window&nbsp;showing the instrument profile
1807resolution curve.</span></p>
1808
1809<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1810 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:415.5pt;
1811 height:298.5pt;visibility:visible;mso-wrap-style:square'>
1812 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1813</v:shape><![endif]--><![if !vml]><img border=0 width=554 height=398
1814src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_35"><![endif]></span></p>
1815
1816<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1817corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1818coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1819values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1820<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1821mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1822minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
1823style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1824mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
1825<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1826mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1827minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
1828style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1829mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
1830<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1831mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1832minor-latin'>Y</span></b>. </p>
1833
1834<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1835style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1836style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1837repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1838style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1839mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1840item in the data tree and then refine using the <b style='mso-bidi-font-weight:
1841normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1842minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1843Fitting/<span class=SpellE>Peakfit</span></span></b> menu item. At this point a
1844good fit should be seen by zooming in on individual peaks. For example see </p>
1845
1846<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1847 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:408pt;
1848 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1849 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1850</v:shape><![endif]--><![if !vml]><img border=0 width=544 height=466
1851src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1852
1853<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
1854the right of the peak top. This is a consequence of the peak asymmetry arising
1855from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
1856is ~7% as shown on the console window. Again the <b style='mso-bidi-font-weight:
1857normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1858minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1859List</span></b> entries are all updated with new values and those in <b
1860style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1861mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1862minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1863
1864<h2>Step 5. Prepare Indexing Peak List</h2>
1865
1866<p class=MsoNormal>A separate list of peaks is kept for use in <span
1867class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1868normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1869minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1870Peak List</span></b> item in the data tree. In the initially empty window
1871created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1872style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1873mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1874to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1875style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1876mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>.</p>
1877
1878<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1879 id="Picture_x0020_37" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:431.25pt;
1880 height:309.75pt;visibility:visible;mso-wrap-style:square'>
1881 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1882</v:shape><![endif]--><![if !vml]><img border=0 width=575 height=413
1883src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
1884
1885<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1886may choose to not use a fitted peak (e.g. if suspected it is from a
1887contaminant).</p>
1888
1889<h2>Step 6. Run <span class=SpellE>Autoindexing</span></h2>
1890
1891<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1892style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1893mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1894List</span></b> data item. This brings up a window for indexing and cell
1895refinement options</p>
1896
1897<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1898 id="Picture_x0020_38" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1899 height:157.5pt;visibility:visible;mso-wrap-style:square'>
1900 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1901</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=210
1902src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
1903
1904<p class=MsoNormal>For the most rapid search (since we know the right answer),
1905select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1906mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1907minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1908style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1909mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1910minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and the
1911console shows a running list of possible cells as they are found; the sorted by
1912M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1913normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1914minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1915Cells List</span></b> window</p>
1916
1917<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1918 id="Picture_x0020_13" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1919 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1920 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1921</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1922src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1923
1924<h2>Step 7. Review Cell Choices</h2>
1925
1926<p class=MsoNormal>Review the list of cells associated with the <b
1927style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1928mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1929minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1930unit cell, the generated reflections for that cell are shown in the plot with
1931dashed red lines. Sliding the cursor over these lines shows a small popup
1932window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1933first cell in the list (M20~2970) with a=5.87864 Å generates very many lines
1934with no corresponding peaks (NB: this solution might not always show up!)</p>
1935
1936<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1937 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:447pt;
1938 height:383.25pt;visibility:visible;mso-wrap-style:square'>
1939 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1940</v:shape><![endif]--><![if !vml]><img border=0 width=596 height=511
1941src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_40"><![endif]></span><span
1942style='mso-spacerun:yes'> </span></p>
1943
1944<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
1945enough lines to match all the peaks</p>
1946
1947<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1948 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:428.25pt;
1949 height:366.75pt;visibility:visible;mso-wrap-style:square'>
1950 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1951</v:shape><![endif]--><![if !vml]><img border=0 width=571 height=489
1952src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1953
1954<h2>Step 8. Select/Refine Cell</h2>
1955
1956<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1957indexes all peaks with almost a perfect fit to the peak positions (compare
1958dashed red lines to solid blue ones). Import the cell information using the <b
1959style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1960mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1961minor-latin'>Cell Index/Refine/Copy Cell</span></b> menu option. Then optimize
1962the cell by refining the lattice parameters and the two-theta zero: click on
1963the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1964mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
1965checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1966style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1967mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1968value and then the <b style='mso-bidi-font-weight:normal'><span
1969style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1970mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1971Index/Refine/Refine Cell</span></b> menu option. The M20 improves to ~3600 and <span
1972class=GramE>the a</span> cell parameter value shifts from 4.15683 to 4.15691
1973when zero is refined. (NB: The certificate value for NIST SRM 660a is 4.15692
1974Å). Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1975"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1976minor-latin;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
1977positions </span></b>button to update the plot including the refined <b
1978style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1979mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1980minor-latin'>Zero offset</span></b> (in this case hardly anything
1981happens!).<span style='mso-spacerun:yes'>  </span></p>
1982
1983<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1984 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1985 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1986 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
1987</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1988src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1989
1990<p class=MsoNormal>Notice that a new entry heads the list in the <b
1991style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1992mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1993minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
1994normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1995minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1996Cells List</span></b> window with an improved <span class=GramE>M20(</span>~3600)
1997and a new value for <b style='mso-bidi-font-weight:normal'><span
1998style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1999mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
2000is shown. NB: the <b style='mso-bidi-font-weight:normal'><span
2001style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2002mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2003button has an additional use; you can enter the <span class=SpellE><b
2004style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2005mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b
2006style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2007mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>,
2008<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2009mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b>
2010&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2011mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
2012for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
2013style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2014mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2015will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
2016style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2017mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
2018useful to identify e.g. a second phase in your pattern.</p>
2019
2020<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
2021normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2022minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
2023Index/Refine/Make new phase</span></b> menu option allows one to create a phase
2024with these lattice parameters in the data tree under <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'>Phases</span></b>.<span
2027style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
2028creates the tree item <b style='mso-bidi-font-weight:normal'><span
2029style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2030mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
2031(if it wasn’t already present). This new phase can be used in future analysis
2032(e.g. Rietveld or Pawley refinement).</p>
2033
2034<p class=MsoNormal>To continue with the second part of this exercise, select
2035the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
2036"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2037minor-latin;mso-bidi-theme-font:minor-latin'>File/New project</span></b> in the
2038<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2039mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2040minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
2041the current project saved; if <b style='mso-bidi-font-weight:normal'><span
2042style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2043mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
2044then all the peak fitting/indexing &amp; cell refinement results will be saved
2045to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2046mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2047minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
2048style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2049mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
2050then the file will remain as it was when created at Step 4 above.</p>
2051
2052<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
2053class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
2054style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
2055
2056<p class=MsoNormal>In this exercise we will fit peaks and index them for the
2057mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
2058href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
2059also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
2060substantial test of the indexing capability of GSAS-II. The required data files
2061should have been downloaded when you downloaded this tutorial. Otherwise you
2062will need to get them manually from <span style='mso-fareast-font-family:Calibri;
2063mso-fareast-theme-font:minor-latin'><a
2064href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2065Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span
2066style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2067mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2068minor-latin'>11bmb_6231.fxye</span></b><span style='mso-fareast-font-family:
2069Calibri;mso-fareast-theme-font:minor-latin'> and </span><b style='mso-bidi-font-weight:
2070normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2071minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2072mso-hansi-theme-font:minor-latin'>11bmb_6231.prm</span></b></p>
2073
2074<h2>Step 1. Read in the data. </h2>
2075
2076<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2077normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2078minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2079style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2080mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2081minor-latin'>\data\11bmb_6231.fxye</span></b>; it has a corresponding <span
2082class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2083"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2084minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file. Load
2085them in &amp; the plot is</p>
2086
2087<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2088 id="Picture_x0020_43" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:405pt;
2089 height:347.25pt;visibility:visible;mso-wrap-style:square'>
2090 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2091</v:shape><![endif]--><![if !vml]><img border=0 width=540 height=463
2092src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2093
2094<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2095lower part of the pattern.</p>
2096
2097<h2>Step 2 Set limits</h2>
2098
2099<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2100style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2101mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
2102and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2103mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2104minor-latin'>9</span></b>. This will give a suitable number of lines for
2105indexing.</p>
2106
2107<h2>Step 3 Pick peaks</h2>
2108
2109<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2110small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2111"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2112minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2113peaks by left-clicking on a data point near the top of the peak. Peak positions
2114can be moved by dragging the peak line and peaks can be deleted by
2115right-clicking on them. This only works when the zoom and reposition modes
2116(below) are not selected. Also note some peaks have shoulders most notably at
21175.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
2118deg. I skipped – it might be from a second phase? We’ll see later).</p>
2119
2120<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2121 id="Picture_x0020_39" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:436.5pt;
2122 height:374.25pt;visibility:visible;mso-wrap-style:square'>
2123 <v:imagedata src="Fit%20Peaks_files/image030.png" o:title=""/>
2124</v:shape><![endif]--><![if !vml]><img border=0 width=582 height=499
2125src="Fit%20Peaks_files/image031.png" v:shapes="Picture_x0020_39"><![endif]></span><br
2126clear=all style='mso-special-character:line-break'>
2127</p>
2128
2129<h2>Step 4. Refine peaks</h2>
2130
2131<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
2132above, refine the peaks and the profile shape parameters in <b
2133style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2134mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2135minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2136file name at the first refinement (I used ‘<span class=SpellE><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'>jadarite</span></b></span><b style='mso-bidi-font-weight:normal'><span
2140style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2141mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>’</span></b>).
2142In the end my refinement converged at <span class=SpellE>Rwp</span>=11.41% and
2143some peaks do show some discrepancy as the sample is more complex than the
2144simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2145mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2146minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2147style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2148mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2149<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2150mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2151minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2152style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2153mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2154<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2155mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2156minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away
2157during refinement (one weak one at ~6.67 is particularly troublesome). However,
2158this is good enough to proceed.</p>
2159
2160<h2>Step 5. Prepare Indexing Peak List</h2>
2161
2162<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2163style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2164mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2165in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2166mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2167minor-latin'>Index Peak List</span></b> window.</p>
2168
2169<h2>Step 6. Index the cell</h2>
2170
2171<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic. In
2172a real world case we wouldn’t know this and we would have to try each <span
2173class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2174time to go through all the bad cases.</p>
2175
2176<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2177style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2178mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2179and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2180mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2181minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2182style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2183mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2184minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2185and suitable results will be slow in coming so be patient. Watch the console
2186window; the right answer will have an obviously large M20 (~380) and a volume
2187of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
2188seen (it may take more than one try to get this) you can stop the indexing
2189search by pressing <b style='mso-bidi-font-weight:normal'><span
2190style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2191mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
2192on the progress bar window. Notice the ‘<b style='mso-bidi-font-weight:normal'><span
2193style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2194mso-hansi-theme-font:minor-latin'>keep</span></b>’ column; this allows you to
2195keep some solutions from one indexing run to the next. It may take more than
2196one press to fully stop it. My result was </p>
2197
2198<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2199 id="Picture_x0020_19" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:359.25pt;
2200 height:297pt;visibility:visible;mso-wrap-style:square'>
2201 <v:imagedata src="Fit%20Peaks_files/image032.png" o:title=""/>
2202</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=396
2203src="Fit%20Peaks_files/image033.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2204
2205<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2206 id="Picture_x0020_20" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
2207 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2208 <v:imagedata src="Fit%20Peaks_files/image034.png" o:title=""/>
2209</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2210src="Fit%20Peaks_files/image035.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
2211
2212<p class=MsoNormal>Notice there may be other equally good M20 results with
2213different volumes; other solutions may be obtained as you keep trying the
2214indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2215style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2216mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2217new indexing runs. The best solution is the one with the smaller volume and
2218&#946; &gt; 90 deg. The plot shows every peak indexed including a weak peak not
2219selected for the peak fitting, although the weak peak at 2<span
2220style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
2221style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
2222has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
2223best cell and try to refine it along with the <b style='mso-bidi-font-weight:
2224normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2225minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
2226obtained an improved M20 ~444 and slightly different lattice parameters. Try
2227different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2228style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2229mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2230each time to see which lines vanish. By sliding the cursor over the index lines
2231without any visible peak you can see that the missing ones are 010, 100, 001,
2232110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
2233accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
2234space group P2<sub>1</sub>/n. Armed with this information you can <b
2235style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2236mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2237minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
2238style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2239mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2240minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
2241normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2242minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
2243the GSAS-II data tree.</p>
2244
2245<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2246 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
2247 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2248 <v:imagedata src="Fit%20Peaks_files/image036.png" o:title=""/>
2249</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2250src="Fit%20Peaks_files/image037.png" v:shapes="Picture_x0020_46"><![endif]></span><span
2251style='mso-spacerun:yes'> </span></p>
2252
2253<p class=MsoNormal>Notice that the lattice parameters and space group have been
2254set for you. </p>
2255
2256<p class=MsoNormal>This concludes this exercise; do <span class=GramE><b
2257style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2258mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2259minor-latin'>Save</span></b></span> <b style='mso-bidi-font-weight:normal'><span
2260style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2261mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>project</span></b>
2262as it is needed for the <b style='mso-bidi-font-weight:normal'><span
2263style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2264mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2265Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span
2266style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2267mso-hansi-theme-font:minor-latin'>in GSAS</span></b> exercise. The features of
2268the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2269mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2270minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
2271
2272<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
2273in GSAS-II </h1>
2274
2275<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
2276in preparation for a charge flipping exercise. If continuing from the previous
2277indexing example do <b style='mso-bidi-font-weight:normal'><span
2278style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2279mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
2280GSAS-II data tree menu; you will be asked if you wish to save the old project.
2281The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
2282is another more substantial test of the indexing capability of GSAS-II. The
2283required data files should have been downloaded when you downloaded this
2284tutorial. Otherwise you will need to get them manually from <span
2285style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><a
2286href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2287Be sure to get </span><b style='mso-bidi-font-weight:normal'><span
2288style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2289mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2290minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif;
2291font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11bmb</span>_8716.fxye</span></b><span
2292style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and
2293the corresponding .<span class=SpellE>prm</span> files.</span></p>
2294
2295<h2>Step 1. Read in the data. </h2>
2296
2297<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2298normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2299minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2300style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2301mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2302minor-latin'>\data\11bmb_8716.fxye</span></b>; it has a corresponding <span
2303class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2304"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2305minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file and is
2306for Domino® sugar ground under acetone. The other <span class=SpellE><b
2307style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2308mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span>
2309file in this directory <b style='mso-bidi-font-weight:normal'><span
2310style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2311mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X
2312powdered sugar used “as is” out of the box. Load the <b style='mso-bidi-font-weight:
2313normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2314minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the
2315plot is</p>
2316
2317<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2318 id="Picture_x0020_44" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:452.25pt;
2319 height:387.75pt;visibility:visible;mso-wrap-style:square'>
2320 <v:imagedata src="Fit%20Peaks_files/image038.png" o:title=""/>
2321</v:shape><![endif]--><![if !vml]><img border=0 width=603 height=517
2322src="Fit%20Peaks_files/image039.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2323
2324<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2325lower part of the pattern; I’ve also chosen to plot the square root of the
2326intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2327"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2328minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2329
2330<h2>Step 2 Set limits</h2>
2331
2332<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2333style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2334mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>2</span></b>
2335and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2336mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2337minor-latin'>8</span></b>. Again, this gives a reasonable number of peaks for
2338indexing.</p>
2339
2340<h2>Step 3 Pick peaks</h2>
2341
2342<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2343small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2344"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2345minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2346peaks by left-clicking on a data point near the top of the peak. Peak positions
2347can be moved by dragging the peak line and peaks can be deleted by
2348right-clicking on them. This only works when the zoom and reposition modes
2349(below) are not selected. An easy to shift the view is to use the ‘&lt;’ and
2350‘&gt;’ buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2351that should be added to the list. I skipped a couple of very weak peaks; the
2352total list has &gt;28 peaks.</p>
2353
2354<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2355 id="Picture_x0020_45" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:465.75pt;
2356 height:399pt;visibility:visible;mso-wrap-style:square'>
2357 <v:imagedata src="Fit%20Peaks_files/image040.png" o:title=""/>
2358</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=532
2359src="Fit%20Peaks_files/image041.png" v:shapes="Picture_x0020_45"><![endif]></span><br
2360clear=all style='mso-special-character:line-break'>
2361</p>
2362
2363<h2>Step 4. Refine peaks</h2>
2364
2365<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2366kryptonite examples above, refine the peaks and the profile shape parameters in
2367<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2368mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2369minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2370file name at the first refinement (I used ‘<b style='mso-bidi-font-weight:normal'><span
2371style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2372mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>).
2373In the end my refinement converged at <span class=SpellE>Rwp</span>=6.69% and
2374some peaks do show some discrepancy as the sample is more complex than the
2375simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2376mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2377minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2378style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2379mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2380<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2381mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2382minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2383style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2384mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2385<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2386mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2387minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away during
2388refinement. However, this is good enough to proceed.</p>
2389
2390<h2>Step 5. Prepare Indexing Peak List</h2>
2391
2392<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2393style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2394mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2395in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2396mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2397minor-latin'>Index Peak List</span></b> window.</p>
2398
2399<h2>Step 6. Index the cell</h2>
2400
2401<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2402In a real world case we wouldn’t know this and we would have to try each <span
2403class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2404time to go through all the bad cases.</p>
2405
2406<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2407style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2408mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2409and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2410mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2411minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2412style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2413mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2414minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2415than for LaB<sub>6</sub> but oddly much faster than for kryptonite and suitable
2416results may appear almost immediately. Watch the console window; the right
2417answer will have an obviously large M20 (~900) and a volume of ~704Å<sup>3</sup>
2418(10<sup>th</sup> column of console display). Once this is seen (it may take
2419more than one try to get this) you can stop the indexing search by pressing <b
2420style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2421mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2422minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2423style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2424some solutions from one indexing run to the next. It may take more than one
2425press to fully stop it. My result was </p>
2426
2427<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2428 id="Picture_x0020_24" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2429 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2430 <v:imagedata src="Fit%20Peaks_files/image042.png" o:title=""/>
2431</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2432src="Fit%20Peaks_files/image043.png" v:shapes="Picture_x0020_24"><![endif]><!--[if gte vml 1]><v:shape
2433 id="Picture_x0020_47" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:434.25pt;
2434 height:372pt;visibility:visible;mso-wrap-style:square'>
2435 <v:imagedata src="Fit%20Peaks_files/image044.png" o:title=""/>
2436</v:shape><![endif]--><![if !vml]><img border=0 width=579 height=496
2437src="Fit%20Peaks_files/image045.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2438
2439<p class=MsoNormal>Notice there may be other equally good M20 results with
2440different volumes; still other solutions may be obtained as you keep trying the
2441indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2442style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2443mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2444new indexing runs. The best solution is the one with the smaller volume and
2445&#946; &gt; 90 <span class=SpellE>deg</span> and c&gt;a (I got both solutions!).
2446The plot shows every peak indexed including the weak peaks not selected for the
2447peak fitting. Copy the best cell and try to refine it along with the <b
2448style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2449mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
2450I obtained an improved M20 ~1300 and slightly different lattice parameters. Try
2451different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2452style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2453mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2454each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
2455Armed with this information you can <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;mso-bidi-theme-font:minor-latin'>Make new
2458phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
2459normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2460minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose</span></b>)
2461and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2462"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2463minor-latin'>Phases/sucrose</span></b> from the GSAS-II data tree.</p>
2464
2465<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2466 id="Picture_x0020_48" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2467 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2468 <v:imagedata src="Fit%20Peaks_files/image046.png" o:title=""/>
2469</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2470src="Fit%20Peaks_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span><span
2471style='mso-spacerun:yes'> </span></p>
2472
2473<p class=MsoNormal>Notice that the lattice parameters and space group have been
2474set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2475style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2476mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b>
2477the project file as it is needed for the sucrose <b style='mso-bidi-font-weight:
2478normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2479minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2480Flipping</span></b> exercise. The features of the <b style='mso-bidi-font-weight:
2481normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2482minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase
2483Data</span></b> window will be presented in other exercises.</p>
2484
2485<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2486
2487</div>
2488
2489</body>
2490
2491</html>
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