source: Tutorials/FitPeaks/Fit Peaks.htm

Last change on this file was 4457, checked in by toby, 3 years ago

add data link to tutorials
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415  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
416  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
417  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
418  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
419  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
420  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
421  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
422  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
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424   Name="List Paragraph"/>
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427   Name="Intense Quote"/>
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430  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
431  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
432  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
433  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
434  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
435  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
436  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
437  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
438  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
439  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
440  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
441  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
442  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
443  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
444  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
445  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
446  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
447  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
448  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
449  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
450  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
451  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
452  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
453  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
454  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
455  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
456  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
457  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
458  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
459  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
460  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
461  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
462  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
463  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
464  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
465  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
466  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
467  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
468  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
469  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
470  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
471  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
472  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
473  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
474  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
475  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
476  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
477  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
478  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
479  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
480  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
481  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
482  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
483  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
484  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
485  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
486  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
487  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
488  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
489  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
490  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
491  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
492  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
493  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
494  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
495  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
496  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
497  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
498  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
499  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
500  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
501  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
502  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
503  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
504  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
505  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
506  <w:LsdException Locked="false" Priority="19" QFormat="true"
507   Name="Subtle Emphasis"/>
508  <w:LsdException Locked="false" Priority="21" QFormat="true"
509   Name="Intense Emphasis"/>
510  <w:LsdException Locked="false" Priority="31" QFormat="true"
511   Name="Subtle Reference"/>
512  <w:LsdException Locked="false" Priority="32" QFormat="true"
513   Name="Intense Reference"/>
514  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
515  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
516   UnhideWhenUsed="true" Name="Bibliography"/>
517  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
518   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
519  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
520  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
521  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
522  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
523  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
524  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
525  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
526  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
527  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
528  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
529  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
530  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
531  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
532  <w:LsdException Locked="false" Priority="46"
533   Name="Grid Table 1 Light Accent 1"/>
534  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
535  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
536  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
537  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
538  <w:LsdException Locked="false" Priority="51"
539   Name="Grid Table 6 Colorful Accent 1"/>
540  <w:LsdException Locked="false" Priority="52"
541   Name="Grid Table 7 Colorful Accent 1"/>
542  <w:LsdException Locked="false" Priority="46"
543   Name="Grid Table 1 Light Accent 2"/>
544  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
545  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
546  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
547  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
548  <w:LsdException Locked="false" Priority="51"
549   Name="Grid Table 6 Colorful Accent 2"/>
550  <w:LsdException Locked="false" Priority="52"
551   Name="Grid Table 7 Colorful Accent 2"/>
552  <w:LsdException Locked="false" Priority="46"
553   Name="Grid Table 1 Light Accent 3"/>
554  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
555  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
556  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
557  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
558  <w:LsdException Locked="false" Priority="51"
559   Name="Grid Table 6 Colorful Accent 3"/>
560  <w:LsdException Locked="false" Priority="52"
561   Name="Grid Table 7 Colorful Accent 3"/>
562  <w:LsdException Locked="false" Priority="46"
563   Name="Grid Table 1 Light Accent 4"/>
564  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
565  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
566  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
567  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
568  <w:LsdException Locked="false" Priority="51"
569   Name="Grid Table 6 Colorful Accent 4"/>
570  <w:LsdException Locked="false" Priority="52"
571   Name="Grid Table 7 Colorful Accent 4"/>
572  <w:LsdException Locked="false" Priority="46"
573   Name="Grid Table 1 Light Accent 5"/>
574  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
575  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
576  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
577  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
578  <w:LsdException Locked="false" Priority="51"
579   Name="Grid Table 6 Colorful Accent 5"/>
580  <w:LsdException Locked="false" Priority="52"
581   Name="Grid Table 7 Colorful Accent 5"/>
582  <w:LsdException Locked="false" Priority="46"
583   Name="Grid Table 1 Light Accent 6"/>
584  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
585  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
586  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
587  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
588  <w:LsdException Locked="false" Priority="51"
589   Name="Grid Table 6 Colorful Accent 6"/>
590  <w:LsdException Locked="false" Priority="52"
591   Name="Grid Table 7 Colorful Accent 6"/>
592  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
593  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
594  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
595  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
596  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
597  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
598  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
599  <w:LsdException Locked="false" Priority="46"
600   Name="List Table 1 Light Accent 1"/>
601  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
602  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
603  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
604  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
605  <w:LsdException Locked="false" Priority="51"
606   Name="List Table 6 Colorful Accent 1"/>
607  <w:LsdException Locked="false" Priority="52"
608   Name="List Table 7 Colorful Accent 1"/>
609  <w:LsdException Locked="false" Priority="46"
610   Name="List Table 1 Light Accent 2"/>
611  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
612  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
613  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
614  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
615  <w:LsdException Locked="false" Priority="51"
616   Name="List Table 6 Colorful Accent 2"/>
617  <w:LsdException Locked="false" Priority="52"
618   Name="List Table 7 Colorful Accent 2"/>
619  <w:LsdException Locked="false" Priority="46"
620   Name="List Table 1 Light Accent 3"/>
621  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
622  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
623  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
624  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
625  <w:LsdException Locked="false" Priority="51"
626   Name="List Table 6 Colorful Accent 3"/>
627  <w:LsdException Locked="false" Priority="52"
628   Name="List Table 7 Colorful Accent 3"/>
629  <w:LsdException Locked="false" Priority="46"
630   Name="List Table 1 Light Accent 4"/>
631  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
632  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
633  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
634  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
635  <w:LsdException Locked="false" Priority="51"
636   Name="List Table 6 Colorful Accent 4"/>
637  <w:LsdException Locked="false" Priority="52"
638   Name="List Table 7 Colorful Accent 4"/>
639  <w:LsdException Locked="false" Priority="46"
640   Name="List Table 1 Light Accent 5"/>
641  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
642  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
643  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
644  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
645  <w:LsdException Locked="false" Priority="51"
646   Name="List Table 6 Colorful Accent 5"/>
647  <w:LsdException Locked="false" Priority="52"
648   Name="List Table 7 Colorful Accent 5"/>
649  <w:LsdException Locked="false" Priority="46"
650   Name="List Table 1 Light Accent 6"/>
651  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
652  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
653  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
654  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
655  <w:LsdException Locked="false" Priority="51"
656   Name="List Table 6 Colorful Accent 6"/>
657  <w:LsdException Locked="false" Priority="52"
658   Name="List Table 7 Colorful Accent 6"/>
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786        mso-style-unhide:no;
787        mso-style-qformat:yes;
788        mso-style-link:"Title Char";
789        mso-style-next:Normal;
790        margin-top:0in;
791        margin-right:0in;
792        margin-bottom:15.0pt;
793        margin-left:0in;
794        mso-add-space:auto;
795        mso-pagination:widow-orphan;
796        border:none;
797        mso-border-bottom-alt:solid #4F81BD 1.0pt;
798        mso-border-bottom-themecolor:accent1;
799        padding:0in;
800        mso-padding-alt:0in 0in 4.0pt 0in;
801        font-size:26.0pt;
802        font-family:"Cambria",serif;
803        mso-ascii-font-family:Cambria;
804        mso-ascii-theme-font:major-latin;
805        mso-fareast-font-family:"Times New Roman";
806        mso-fareast-theme-font:major-fareast;
807        mso-hansi-font-family:Cambria;
808        mso-hansi-theme-font:major-latin;
809        mso-bidi-font-family:"Times New Roman";
810        mso-bidi-theme-font:major-bidi;
811        color:#17365D;
812        mso-themecolor:text2;
813        mso-themeshade:191;
814        letter-spacing:.25pt;
815        mso-font-kerning:14.0pt;}
816p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
817        {mso-style-noshow:yes;
818        mso-style-priority:10;
819        mso-style-unhide:no;
820        mso-style-qformat:yes;
821        mso-style-link:"Title Char";
822        mso-style-next:Normal;
823        mso-style-type:export-only;
824        margin:0in;
825        margin-bottom:.0001pt;
826        mso-add-space:auto;
827        mso-pagination:widow-orphan;
828        border:none;
829        mso-border-bottom-alt:solid #4F81BD 1.0pt;
830        mso-border-bottom-themecolor:accent1;
831        padding:0in;
832        mso-padding-alt:0in 0in 4.0pt 0in;
833        font-size:26.0pt;
834        font-family:"Cambria",serif;
835        mso-ascii-font-family:Cambria;
836        mso-ascii-theme-font:major-latin;
837        mso-fareast-font-family:"Times New Roman";
838        mso-fareast-theme-font:major-fareast;
839        mso-hansi-font-family:Cambria;
840        mso-hansi-theme-font:major-latin;
841        mso-bidi-font-family:"Times New Roman";
842        mso-bidi-theme-font:major-bidi;
843        color:#17365D;
844        mso-themecolor:text2;
845        mso-themeshade:191;
846        letter-spacing:.25pt;
847        mso-font-kerning:14.0pt;}
848p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
849        {mso-style-noshow:yes;
850        mso-style-priority:10;
851        mso-style-unhide:no;
852        mso-style-qformat:yes;
853        mso-style-link:"Title Char";
854        mso-style-next:Normal;
855        mso-style-type:export-only;
856        margin:0in;
857        margin-bottom:.0001pt;
858        mso-add-space:auto;
859        mso-pagination:widow-orphan;
860        border:none;
861        mso-border-bottom-alt:solid #4F81BD 1.0pt;
862        mso-border-bottom-themecolor:accent1;
863        padding:0in;
864        mso-padding-alt:0in 0in 4.0pt 0in;
865        font-size:26.0pt;
866        font-family:"Cambria",serif;
867        mso-ascii-font-family:Cambria;
868        mso-ascii-theme-font:major-latin;
869        mso-fareast-font-family:"Times New Roman";
870        mso-fareast-theme-font:major-fareast;
871        mso-hansi-font-family:Cambria;
872        mso-hansi-theme-font:major-latin;
873        mso-bidi-font-family:"Times New Roman";
874        mso-bidi-theme-font:major-bidi;
875        color:#17365D;
876        mso-themecolor:text2;
877        mso-themeshade:191;
878        letter-spacing:.25pt;
879        mso-font-kerning:14.0pt;}
880p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
881        {mso-style-noshow:yes;
882        mso-style-priority:10;
883        mso-style-unhide:no;
884        mso-style-qformat:yes;
885        mso-style-link:"Title Char";
886        mso-style-next:Normal;
887        mso-style-type:export-only;
888        margin-top:0in;
889        margin-right:0in;
890        margin-bottom:15.0pt;
891        margin-left:0in;
892        mso-add-space:auto;
893        mso-pagination:widow-orphan;
894        border:none;
895        mso-border-bottom-alt:solid #4F81BD 1.0pt;
896        mso-border-bottom-themecolor:accent1;
897        padding:0in;
898        mso-padding-alt:0in 0in 4.0pt 0in;
899        font-size:26.0pt;
900        font-family:"Cambria",serif;
901        mso-ascii-font-family:Cambria;
902        mso-ascii-theme-font:major-latin;
903        mso-fareast-font-family:"Times New Roman";
904        mso-fareast-theme-font:major-fareast;
905        mso-hansi-font-family:Cambria;
906        mso-hansi-theme-font:major-latin;
907        mso-bidi-font-family:"Times New Roman";
908        mso-bidi-theme-font:major-bidi;
909        color:#17365D;
910        mso-themecolor:text2;
911        mso-themeshade:191;
912        letter-spacing:.25pt;
913        mso-font-kerning:14.0pt;}
914a:link, span.MsoHyperlink
915        {mso-style-noshow:yes;
916        mso-style-priority:99;
917        color:blue;
918        text-decoration:underline;
919        text-underline:single;}
920a:visited, span.MsoHyperlinkFollowed
921        {mso-style-noshow:yes;
922        mso-style-priority:99;
923        color:purple;
924        text-decoration:underline;
925        text-underline:single;}
926p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
927        {mso-style-noshow:yes;
928        mso-style-priority:99;
929        mso-style-link:"Document Map Char";
930        margin:0in;
931        margin-bottom:.0001pt;
932        mso-pagination:widow-orphan;
933        font-size:8.0pt;
934        font-family:"Tahoma",sans-serif;
935        mso-fareast-font-family:"Times New Roman";
936        mso-fareast-theme-font:minor-fareast;}
937p
938        {mso-style-noshow:yes;
939        mso-style-priority:99;
940        mso-margin-top-alt:auto;
941        margin-right:0in;
942        mso-margin-bottom-alt:auto;
943        margin-left:0in;
944        mso-pagination:widow-orphan;
945        font-size:12.0pt;
946        font-family:"Times New Roman",serif;
947        mso-fareast-font-family:"Times New Roman";
948        mso-fareast-theme-font:minor-fareast;}
949pre
950        {mso-style-noshow:yes;
951        mso-style-priority:99;
952        mso-style-link:"HTML Preformatted Char";
953        margin:0in;
954        margin-bottom:.0001pt;
955        mso-pagination:widow-orphan;
956        tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
957        font-size:10.0pt;
958        font-family:"Courier New";
959        mso-fareast-font-family:"Times New Roman";}
960p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
961        {mso-style-noshow:yes;
962        mso-style-priority:99;
963        mso-style-link:"Balloon Text Char";
964        margin:0in;
965        margin-bottom:.0001pt;
966        mso-pagination:widow-orphan;
967        font-size:8.0pt;
968        font-family:"Tahoma",sans-serif;
969        mso-fareast-font-family:"Times New Roman";
970        mso-fareast-theme-font:minor-fareast;}
971span.MsoPlaceholderText
972        {mso-style-noshow:yes;
973        mso-style-priority:99;
974        mso-style-unhide:no;
975        color:gray;}
976p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
977        {mso-style-noshow:yes;
978        mso-style-priority:1;
979        mso-style-unhide:no;
980        mso-style-qformat:yes;
981        mso-style-parent:"";
982        margin:0in;
983        margin-bottom:.0001pt;
984        mso-pagination:widow-orphan;
985        font-size:12.0pt;
986        font-family:"Times New Roman",serif;
987        mso-fareast-font-family:"Times New Roman";
988        mso-fareast-theme-font:minor-fareast;}
989p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
990        {mso-style-noshow:yes;
991        mso-style-priority:34;
992        mso-style-unhide:no;
993        mso-style-qformat:yes;
994        margin-top:0in;
995        margin-right:0in;
996        margin-bottom:0in;
997        margin-left:.5in;
998        margin-bottom:.0001pt;
999        mso-add-space:auto;
1000        mso-pagination:widow-orphan;
1001        font-size:12.0pt;
1002        font-family:"Times New Roman",serif;
1003        mso-fareast-font-family:"Times New Roman";
1004        mso-fareast-theme-font:minor-fareast;}
1005p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
1006        {mso-style-noshow:yes;
1007        mso-style-priority:34;
1008        mso-style-unhide:no;
1009        mso-style-qformat:yes;
1010        mso-style-type:export-only;
1011        margin-top:0in;
1012        margin-right:0in;
1013        margin-bottom:0in;
1014        margin-left:.5in;
1015        margin-bottom:.0001pt;
1016        mso-add-space:auto;
1017        mso-pagination:widow-orphan;
1018        font-size:12.0pt;
1019        font-family:"Times New Roman",serif;
1020        mso-fareast-font-family:"Times New Roman";
1021        mso-fareast-theme-font:minor-fareast;}
1022p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
1023        {mso-style-noshow:yes;
1024        mso-style-priority:34;
1025        mso-style-unhide:no;
1026        mso-style-qformat:yes;
1027        mso-style-type:export-only;
1028        margin-top:0in;
1029        margin-right:0in;
1030        margin-bottom:0in;
1031        margin-left:.5in;
1032        margin-bottom:.0001pt;
1033        mso-add-space:auto;
1034        mso-pagination:widow-orphan;
1035        font-size:12.0pt;
1036        font-family:"Times New Roman",serif;
1037        mso-fareast-font-family:"Times New Roman";
1038        mso-fareast-theme-font:minor-fareast;}
1039p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
1040        {mso-style-noshow:yes;
1041        mso-style-priority:34;
1042        mso-style-unhide:no;
1043        mso-style-qformat:yes;
1044        mso-style-type:export-only;
1045        margin-top:0in;
1046        margin-right:0in;
1047        margin-bottom:0in;
1048        margin-left:.5in;
1049        margin-bottom:.0001pt;
1050        mso-add-space:auto;
1051        mso-pagination:widow-orphan;
1052        font-size:12.0pt;
1053        font-family:"Times New Roman",serif;
1054        mso-fareast-font-family:"Times New Roman";
1055        mso-fareast-theme-font:minor-fareast;}
1056span.MsoIntenseReference
1057        {mso-style-priority:32;
1058        mso-style-unhide:no;
1059        mso-style-qformat:yes;
1060        font-variant:small-caps;
1061        color:#C0504D;
1062        mso-themecolor:accent2;
1063        letter-spacing:.25pt;
1064        font-weight:bold;
1065        text-decoration:underline;
1066        text-underline:single;}
1067span.Heading1Char
1068        {mso-style-name:"Heading 1 Char";
1069        mso-style-priority:9;
1070        mso-style-unhide:no;
1071        mso-style-locked:yes;
1072        mso-style-link:"Heading 1";
1073        mso-ansi-font-size:24.0pt;
1074        mso-bidi-font-size:24.0pt;
1075        font-family:"Times New Roman",serif;
1076        mso-ascii-font-family:"Times New Roman";
1077        mso-fareast-font-family:"Times New Roman";
1078        mso-fareast-theme-font:minor-fareast;
1079        mso-hansi-font-family:"Times New Roman";
1080        mso-bidi-font-family:"Times New Roman";
1081        mso-font-kerning:18.0pt;
1082        font-weight:bold;}
1083span.Heading2Char
1084        {mso-style-name:"Heading 2 Char";
1085        mso-style-noshow:yes;
1086        mso-style-priority:9;
1087        mso-style-unhide:no;
1088        mso-style-locked:yes;
1089        mso-style-link:"Heading 2";
1090        mso-ansi-font-size:18.0pt;
1091        mso-bidi-font-size:18.0pt;
1092        font-family:"Times New Roman",serif;
1093        mso-ascii-font-family:"Times New Roman";
1094        mso-fareast-font-family:"Times New Roman";
1095        mso-fareast-theme-font:minor-fareast;
1096        mso-hansi-font-family:"Times New Roman";
1097        mso-bidi-font-family:"Times New Roman";
1098        font-weight:bold;}
1099span.Heading3Char
1100        {mso-style-name:"Heading 3 Char";
1101        mso-style-noshow:yes;
1102        mso-style-priority:9;
1103        mso-style-unhide:no;
1104        mso-style-locked:yes;
1105        mso-style-link:"Heading 3";
1106        mso-ansi-font-size:13.5pt;
1107        mso-bidi-font-size:13.5pt;
1108        font-family:"Times New Roman",serif;
1109        mso-ascii-font-family:"Times New Roman";
1110        mso-fareast-font-family:"Times New Roman";
1111        mso-fareast-theme-font:minor-fareast;
1112        mso-hansi-font-family:"Times New Roman";
1113        mso-bidi-font-family:"Times New Roman";
1114        font-weight:bold;}
1115span.Heading4Char
1116        {mso-style-name:"Heading 4 Char";
1117        mso-style-noshow:yes;
1118        mso-style-priority:9;
1119        mso-style-unhide:no;
1120        mso-style-locked:yes;
1121        mso-style-link:"Heading 4";
1122        mso-ansi-font-size:13.0pt;
1123        mso-bidi-font-size:13.0pt;
1124        font-family:"Cambria",serif;
1125        mso-ascii-font-family:Cambria;
1126        mso-ascii-theme-font:major-latin;
1127        mso-fareast-font-family:"Times New Roman";
1128        mso-fareast-theme-font:major-fareast;
1129        mso-hansi-font-family:Cambria;
1130        mso-hansi-theme-font:major-latin;
1131        mso-bidi-font-family:"Times New Roman";
1132        mso-bidi-theme-font:major-bidi;
1133        color:#4F81BD;
1134        mso-themecolor:accent1;
1135        font-weight:bold;
1136        font-style:italic;}
1137span.Heading5Char
1138        {mso-style-name:"Heading 5 Char";
1139        mso-style-noshow:yes;
1140        mso-style-priority:9;
1141        mso-style-unhide:no;
1142        mso-style-locked:yes;
1143        mso-style-link:"Heading 5";
1144        mso-ansi-font-size:12.0pt;
1145        mso-bidi-font-size:12.0pt;
1146        font-family:"Times New Roman",serif;
1147        mso-ascii-font-family:"Times New Roman";
1148        mso-fareast-font-family:"Times New Roman";
1149        mso-fareast-theme-font:minor-fareast;
1150        mso-hansi-font-family:"Times New Roman";
1151        mso-bidi-font-family:"Times New Roman";
1152        color:#4F4FFF;
1153        font-weight:bold;}
1154span.HTMLPreformattedChar
1155        {mso-style-name:"HTML Preformatted Char";
1156        mso-style-noshow:yes;
1157        mso-style-priority:99;
1158        mso-style-unhide:no;
1159        mso-style-locked:yes;
1160        mso-style-link:"HTML Preformatted";
1161        font-family:"Courier New";
1162        mso-ascii-font-family:"Courier New";
1163        mso-fareast-font-family:"Times New Roman";
1164        mso-hansi-font-family:"Courier New";
1165        mso-bidi-font-family:"Courier New";}
1166p.msonormal0, li.msonormal0, div.msonormal0
1167        {mso-style-name:msonormal;
1168        mso-style-noshow:yes;
1169        mso-style-priority:99;
1170        mso-style-unhide:no;
1171        mso-margin-top-alt:auto;
1172        margin-right:0in;
1173        mso-margin-bottom-alt:auto;
1174        margin-left:0in;
1175        mso-pagination:widow-orphan;
1176        font-size:12.0pt;
1177        font-family:"Times New Roman",serif;
1178        mso-fareast-font-family:"Times New Roman";
1179        mso-fareast-theme-font:minor-fareast;}
1180span.TitleChar
1181        {mso-style-name:"Title Char";
1182        mso-style-priority:10;
1183        mso-style-unhide:no;
1184        mso-style-locked:yes;
1185        mso-style-link:Title;
1186        mso-ansi-font-size:26.0pt;
1187        mso-bidi-font-size:26.0pt;
1188        font-family:"Cambria",serif;
1189        mso-ascii-font-family:Cambria;
1190        mso-ascii-theme-font:major-latin;
1191        mso-fareast-font-family:"Times New Roman";
1192        mso-fareast-theme-font:major-fareast;
1193        mso-hansi-font-family:Cambria;
1194        mso-hansi-theme-font:major-latin;
1195        mso-bidi-font-family:"Times New Roman";
1196        mso-bidi-theme-font:major-bidi;
1197        color:#17365D;
1198        mso-themecolor:text2;
1199        mso-themeshade:191;
1200        letter-spacing:.25pt;
1201        mso-font-kerning:14.0pt;}
1202span.DocumentMapChar
1203        {mso-style-name:"Document Map Char";
1204        mso-style-noshow:yes;
1205        mso-style-priority:99;
1206        mso-style-unhide:no;
1207        mso-style-locked:yes;
1208        mso-style-link:"Document Map";
1209        mso-ansi-font-size:8.0pt;
1210        mso-bidi-font-size:8.0pt;
1211        font-family:"Tahoma",sans-serif;
1212        mso-ascii-font-family:Tahoma;
1213        mso-fareast-font-family:"Times New Roman";
1214        mso-fareast-theme-font:minor-fareast;
1215        mso-hansi-font-family:Tahoma;
1216        mso-bidi-font-family:Tahoma;}
1217span.BalloonTextChar
1218        {mso-style-name:"Balloon Text Char";
1219        mso-style-noshow:yes;
1220        mso-style-priority:99;
1221        mso-style-unhide:no;
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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><BL>
1460  <LI><B>A video version of this tutorial is available at
1461<A href="https://anl.box.com/v/FitPeaks----" target="_blank">
1462https://anl.box.com/v/FitPeaks----</A></B>
1463  <LI>Exercise files are found <A href="./data/" target="_blank">here</a>
1464</BL></P><P></P>
1465
1466 
1467<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1468cell that matches a set of diffraction peaks -- a process known as
1469auto-indexing. First peaks must be located and optimized and then indexing can
1470be done.</p>
1471
1472<h1>1<sup>st</sup> Example: Fit Peaks/<span class=SpellE>Autoindexing</span>
1473  in GSAS-II </h1>
1474 
1475<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1476
1477<h2>Step 1: Read in the data file</h2>
1478
1479<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1480style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1481style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1482the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1483mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1484minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1485to read the data file into the current GSAS-II project. This read option is set
1486to read any of the powder data formats defined for GSAS (angles in <span
1487class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
1488the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1489style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1490mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1491format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1492style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1493mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1494format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1495style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1496directory to <b style='mso-bidi-font-weight:normal'>
1497data file</span></b> menu item to read the data file into the current GSAS-II project.
1498Because you used <span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1499minor-latin'>the </span><b style='mso-bidi-font-weight:normal'><span
1500style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1501mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1502minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family:
1503Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and
1504downloaded the exercise files (recommended), then the </span><span
1505class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1506"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1507Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>FitPeaks</span></b></span><b
1508style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1509mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1510minor-latin;mso-hansi-theme-font:minor-latin'>/data/...</span></b><span
1511style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1512entry will bring you to the location where the files have been downloaded. (It
1513is also possible to download them manually from <a
1514href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/</a>.
1515In this case you will need to navigate to the download location manually.)<br>
1516For this tutorial you should see the data file in the file browser, but if
1517extensions on data files are not the expected ones, you may need to change the
1518file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find
1519the desired file.</span></p>
1520
1521<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1522style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1523style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1524the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1526minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri",sans-serif;
1527mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1528minor-latin'> data</span> file in the first dialog and press <b
1529style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1530mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1531minor-latin'>Open</span></b>. There will be a Dialog box asking <b
1532style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1533mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1534minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
1535normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1536minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
1537button to proceed.</p>
1538
1539<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1540style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1541style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1542file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1543mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1544minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
1545automatically selected; it was produced by 11BM-B instrument processing
1546software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
1547normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1548minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1549file was created from the 12 detector raw data. If absent or the name doesn’t
1550match the data file name, a file dialog will appear for you to select the
1551correct instrument parameter file.</p>
1552
1553<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1554style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1555mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1556tree</span></b> window will have several entries </p>
1557
1558<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1559 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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1566  <v:f eqn="prod @2 1 2"/>
1567  <v:f eqn="prod @3 21600 pixelWidth"/>
1568  <v:f eqn="prod @3 21600 pixelHeight"/>
1569  <v:f eqn="sum @0 0 1"/>
1570  <v:f eqn="prod @6 1 2"/>
1571  <v:f eqn="prod @7 21600 pixelWidth"/>
1572  <v:f eqn="sum @8 21600 0"/>
1573  <v:f eqn="prod @7 21600 pixelHeight"/>
1574  <v:f eqn="sum @10 21600 0"/>
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1579 style='width:468pt;height:300.75pt;visibility:visible;mso-wrap-style:square'>
1580 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
1581</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=401
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1583
1584<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1585powder pattern</p>
1586
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1590 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1591</v:shape><![endif]--><![if !vml]><img border=0 width=530 height=454
1592src="Fit%20Peaks_files/image004.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1593
1594<h2>Step 2: Select Limits </h2>
1595
1596<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1597more data than we need, so it is helpful to cut down the range. Click on the <b
1598style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1599mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1600minor-latin'>Limits</span></b> item in the <b
1601style='mso-bidi-font-weight:normal'>
1602<span style='font-family:
1603"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>
1604GSAS-II
1605data tree</span></b>. Use the <b style='mso-bidi-font-weight:normal'><span
1606style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1607mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>New:</span></b>
1608row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
1609normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1610minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
1611and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1612style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1613mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1614to <b style='mso-bidi-font-weight:normal'><span
1615style='font-family:"Calibri",sans-serif;mso-hansi-theme-font:minor-latin;
1616mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
1617normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1618minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1619Notice on the plot that the limit lines have moved to these positions; the
1620green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1621is in a wide gap between peaks. You may also drag the limit lines to the
1622desired location or place them by a left mouse click on a data point for the
1623lower limit or a right click on a data point for the upper limit.</p>
1624
1625<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1626 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:446.25pt;
1627 height:224.25pt;visibility:visible;mso-wrap-style:square'>
1628 <v:imagedata src="Fit%20Peaks_files/image005.png" o:title=""/>
1629</v:shape><![endif]--><![if !vml]><img border=0 width=595 height=299
1630src="Fit%20Peaks_files/image005.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1631
1632<h2>Step 3: Determine Peak Positions</h2>
1633
1634<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1635auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1636style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1637style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1638on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1639mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1640minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1641normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1642minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1643data tree</span></b>. This creates an empty window of peak positions (the <b
1644style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1645mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1646minor-latin'>Limits</span></b> window is erased). At this point it is wise to
1647zoom in on the data that will be used for indexing. </p>
1648
1649<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1650auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1651style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1652style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1653on the Zoom button (5<sup>th</sup> one from the left on the plot toolbar), then
1654press the left mouse in one corner of the region to be used; holding the mouse
1655button down, drag over the region to the opposite corner; a box will be drawn
1656over the region to be zoomed and the plot will be redrawn with the new limits.
1657The toolbar has a number of buttons to the right of the help button (‘?’) that
1658can be used to incrementally change the view.</p>
1659
1660<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1661auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1662style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1663style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1664style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom button
1665again to turn off the zoom mode. </p>
1666
1667<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1668auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1669style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1670style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1671<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1672mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1673in the menu select <b style='mso-bidi-font-weight:normal'><span
1674style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1675mso-hansi-theme-font:minor-latin'>Auto search</span></b>. The plot window will
1676immediately show that all peaks were picked with a blue vertical line on each
1677one</p>
1678
1679<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1680auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_31"
1681 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:395.25pt;height:339pt;
1682 visibility:visible;mso-wrap-style:square'>
1683 <v:imagedata src="Fit%20Peaks_files/image006.png" o:title=""/>
1684</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1685src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
1686
1687<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1688auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1689normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1690minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1691List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1692
1693<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1694auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
1695 o:spid="_x0000_i1045" type="#_x0000_t75" style='width:426pt;height:198.75pt;
1696 visibility:visible;mso-wrap-style:square'>
1697 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1698</v:shape><![endif]--><![if !vml]><img border=0 width=568 height=265
1699src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
1700
1701<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1702will be 20 peaks in this example. You should examine both the list and the plot
1703to be sure the auto search did not pick a peak twice (rarely) or skip a peak or
1704shoulder. You can add a peak to the list by pressing the left mouse button with
1705the pointer on a data point at the peak top or shoulder; be sure the zoom/shift
1706buttons are off. You may drag a peak position as needed. A position may be
1707deleted with a right click with the mouse on the blue line. You can also delete
1708a peak by selecting the row in the table; it will be highlighted in blue. Then
1709press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1710mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b>
1711key; it will be removed from the table and the plot. The list will always show
1712the peaks sorted by position. When done you should have 20 unique peak
1713positions.</p>
1714
1715<h2>Step 4: Refine Peak Positions</h2>
1716
1717<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1718refinement and then adding parameters to complete the fitting,</p>
1719
1720<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1721style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1722style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1723the peak intensities and the background. These parameters have their refinement
1724flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1725normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1726minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1727Fitting/<span class=SpellE>Peakfit</span></span></b>. Do <b style='mso-bidi-font-weight:
1728normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1729style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1730mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1731menu item; that should used for Rietveld/Pawley refinements. You will be
1732asked to save the current project before the fit will proceed; change directory
1733if desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1734normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1735minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1736A window will show the progress of the refinement and will close when the
1737least-squares fit is complete (usually very fast). The plot is updated with the
1738fit, the peak list window is updated with the new peak values and a summary of
1739the refinement is shown on the console window as well.</p>
1740
1741<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1742 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:407.25pt;
1743 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1744 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1745</v:shape><![endif]--><![if !vml]><img border=0 width=543 height=466
1746src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_33"><![endif]></span></p>
1747
1748<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1749 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:420pt;
1750 height:195.75pt;visibility:visible;mso-wrap-style:square'>
1751 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1752</v:shape><![endif]--><![if !vml]><img border=0 width=560 height=261
1753src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1754
1755<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1756style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1757style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1758add refinement of the peak positions. This can be done by clicking on all the
1759refinement flags for the individual peaks or it is possible to set them all at
1760the same time using this recipe: </p>
1761
1762<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1763auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1764style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1765style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1766on any value in the table to select it, for example the first peak position. A
1767black box appears around the value. </p>
1768
1769<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1770text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1771style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1772style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1773on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1774mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1775label above the peak position check-boxes. The entire column of checkboxes is
1776highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
1777style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1778mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y</span></b>
1779key to turn on all refinement flags (<b style='mso-bidi-font-weight:normal'><span
1780style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1781mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>n</span></b>
1782would turn them off).</p>
1783
1784<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1785the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1786mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1787minor-latin'>Peak Fitting/<span class=SpellE>Peakfit</span></span></b> menu
1788item.</p>
1789
1790<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1791refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1792performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1793width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
1794click the refinement flags for sigma and/or gamma in the Peak List window.
1795&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1796widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening equation
1797as described below.&nbsp;Note - one cannot refine ALL peak widths using both
1798individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental broadening
1799terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1800
1801<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1802"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1803to an instrumental broadening equation, first<b> s</b></span>elect the <b
1804style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1805mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1806minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
1807opens a window for peak profile terms<b> </b><span style='mso-bidi-font-weight:
1808bold'>and also creates a new plot window&nbsp;showing the instrument profile
1809resolution curve.</span></p>
1810
1811<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1812 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:415.5pt;
1813 height:298.5pt;visibility:visible;mso-wrap-style:square'>
1814 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1815</v:shape><![endif]--><![if !vml]><img border=0 width=554 height=398
1816src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_35"><![endif]></span></p>
1817
1818<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1819corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1820coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1821values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1822<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1823mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1824minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
1825style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1826mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
1827<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1828mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1829minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
1830style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1831mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
1832<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1833mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1834minor-latin'>Y</span></b>. </p>
1835
1836<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1837style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1838style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1839repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1840style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1841mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1842item in the data tree and then refine using the <b style='mso-bidi-font-weight:
1843normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1844minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1845Fitting/<span class=SpellE>Peakfit</span></span></b> menu item. At this point a
1846good fit should be seen by zooming in on individual peaks. For example see </p>
1847
1848<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1849 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:408pt;
1850 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1851 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1852</v:shape><![endif]--><![if !vml]><img border=0 width=544 height=466
1853src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1854
1855<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
1856the right of the peak top. This is a consequence of the peak asymmetry arising
1857from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
1858is ~7% as shown on the console window. Again the <b style='mso-bidi-font-weight:
1859normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1860minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1861List</span></b> entries are all updated with new values and those in <b
1862style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1863mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1864minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1865
1866<h2>Step 5. Prepare Indexing Peak List</h2>
1867
1868<p class=MsoNormal>A separate list of peaks is kept for use in <span
1869class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1870normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1871minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1872Peak List</span></b> item in the data tree. In the initially empty window
1873created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1874style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1875mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1876to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1877style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1878mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>.</p>
1879
1880<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1881 id="Picture_x0020_37" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:431.25pt;
1882 height:309.75pt;visibility:visible;mso-wrap-style:square'>
1883 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1884</v:shape><![endif]--><![if !vml]><img border=0 width=575 height=413
1885src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
1886
1887<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1888may choose to not use a fitted peak (e.g. if suspected it is from a
1889contaminant).</p>
1890
1891<h2>Step 6. Run <span class=SpellE>Autoindexing</span></h2>
1892
1893<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1894style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1895mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1896List</span></b> data item. This brings up a window for indexing and cell
1897refinement options</p>
1898
1899<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1900 id="Picture_x0020_38" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1901 height:157.5pt;visibility:visible;mso-wrap-style:square'>
1902 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1903</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=210
1904src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
1905
1906<p class=MsoNormal>For the most rapid search (since we know the right answer),
1907select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1908mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1909minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1910style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1911mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1912minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and the
1913console shows a running list of possible cells as they are found; the sorted by
1914M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1915normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1916minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1917Cells List</span></b> window</p>
1918
1919<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1920 id="Picture_x0020_13" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1921 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1922 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1923</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1924src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1925
1926<h2>Step 7. Review Cell Choices</h2>
1927
1928<p class=MsoNormal>Review the list of cells associated with the <b
1929style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1930mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1931minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1932unit cell, the generated reflections for that cell are shown in the plot with
1933dashed red lines. Sliding the cursor over these lines shows a small popup
1934window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1935first cell in the list (M20~2970) with a=5.87864 Å generates very many lines
1936with no corresponding peaks (NB: this solution might not always show up!)</p>
1937
1938<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1939 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:447pt;
1940 height:383.25pt;visibility:visible;mso-wrap-style:square'>
1941 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1942</v:shape><![endif]--><![if !vml]><img border=0 width=596 height=511
1943src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_40"><![endif]></span><span
1944style='mso-spacerun:yes'> </span></p>
1945
1946<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
1947enough lines to match all the peaks</p>
1948
1949<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1950 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:428.25pt;
1951 height:366.75pt;visibility:visible;mso-wrap-style:square'>
1952 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1953</v:shape><![endif]--><![if !vml]><img border=0 width=571 height=489
1954src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1955
1956<h2>Step 8. Select/Refine Cell</h2>
1957
1958<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1959indexes all peaks with almost a perfect fit to the peak positions (compare
1960dashed red lines to solid blue ones). Import the cell information using the <b
1961style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1962mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1963minor-latin'>Cell Index/Refine/Copy Cell</span></b> menu option. Then optimize
1964the cell by refining the lattice parameters and the two-theta zero: click on
1965the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1966mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
1967checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1968style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1969mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1970value and then the <b style='mso-bidi-font-weight:normal'><span
1971style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1972mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1973Index/Refine/Refine Cell</span></b> menu option. The M20 improves to
1974~3600 as the <I>a</I> cell parameter value shifts from 4.15683 to 4.15691
1975because the zero is now refined. (NB: The certificate value for NIST SRM 660a is 4.15692
1976Å). Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1977"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1978minor-latin;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
1979positions </span></b>button to update the plot including the refined <b
1980style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1981mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1982minor-latin'>Zero offset</span></b> (in this case hardly anything
1983happens!).<span style='mso-spacerun:yes'>  </span></p>
1984
1985<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1986 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1987 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1988 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
1989</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1990src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1991
1992<p class=MsoNormal>Notice that a new entry heads the list in the <b
1993style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1994mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1995minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
1996normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1997minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1998Cells List</span></b> window with an improved <span class=GramE>M20(</span>~3600)
1999and a new value for <b style='mso-bidi-font-weight:normal'><span
2000style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2001mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
2002is shown. NB: the <b style='mso-bidi-font-weight:normal'><span
2003style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2004mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2005button has an additional use; you can enter the <span class=SpellE><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'>Bravais</span></b></span><b
2008style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2009mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>,
2010<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'>Space group</span></b>
2012&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2013mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
2014for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
2015style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2016mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2017will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
2018style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2019mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
2020useful to identify e.g. a second phase in your pattern.</p>
2021
2022<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
2023normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2024minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
2025Index/Refine/Make new phase</span></b> menu option allows one to create a phase
2026with these lattice parameters in the data tree under <b style='mso-bidi-font-weight:
2027normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2028minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
2029style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
2030creates the tree item <b style='mso-bidi-font-weight:normal'><span
2031style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2032mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
2033(if it wasn’t already present). This new phase can be used in future analysis
2034(e.g. Rietveld or Pawley refinement).</p>
2035
2036<p class=MsoNormal>To continue with the second part of this exercise, select
2037the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
2038"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2039minor-latin;mso-bidi-theme-font:minor-latin'>File/New project</span></b> in the
2040<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2041mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2042minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
2043the current project saved; if <b style='mso-bidi-font-weight:normal'><span
2044style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2045mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
2046then all the peak fitting/indexing &amp; cell refinement results will be saved
2047to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2048mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2049minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
2050style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2051mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
2052then the file will remain as it was when created at Step 4 above.</p>
2053
2054<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Example: Fit Peaks/</a><span
2055class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
2056style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
2057
2058<p class=MsoNormal>In this exercise we will fit peaks and index them for the
2059mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
2060href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
2061also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
2062substantial test of the indexing capability of GSAS-II. The required data files
2063should have been downloaded when you downloaded this tutorial. Otherwise you
2064will need to get them manually from <span style='mso-fareast-font-family:Calibri;
2065mso-fareast-theme-font:minor-latin'><a
2066href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/</a>.
2067Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span
2068style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2069mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2070minor-latin'>11bmb_6231.fxye</span></b><span style='mso-fareast-font-family:
2071Calibri;mso-fareast-theme-font:minor-latin'> and </span><b style='mso-bidi-font-weight:
2072normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2073minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2074mso-hansi-theme-font:minor-latin'>11bmb_6231.prm</span></b></p>
2075
2076<h2>Step 1. Read in the data. </h2>
2077
2078<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2079normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2080minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2081style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2082mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2083minor-latin'>\data\11bmb_6231.fxye</span></b>; it has a corresponding <span
2084class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2085"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2086minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file. Load
2087them in &amp; the plot is</p>
2088
2089<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2090 id="Picture_x0020_43" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:405pt;
2091 height:347.25pt;visibility:visible;mso-wrap-style:square'>
2092 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2093</v:shape><![endif]--><![if !vml]><img border=0 width=540 height=463
2094src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2095
2096<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2097lower part of the pattern.</p>
2098
2099<h2>Step 2 Set limits</h2>
2100
2101<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2102style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2103mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
2104and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2105mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2106minor-latin'>9</span></b>. This will give a suitable number of lines for
2107indexing.</p>
2108
2109<h2>Step 3 Pick peaks</h2>
2110
2111<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2112small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2113"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2114minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2115peaks by left-clicking on a data point near the top of the peak. Peak positions
2116can be moved by dragging the peak line and peaks can be deleted by
2117right-clicking on them. This only works when the zoom and reposition modes
2118(below) are not selected. Also note some peaks have shoulders most notably at
21195.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
2120deg. I skipped – it might be from a second phase? We’ll see later).</p>
2121
2122<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2123 id="Picture_x0020_39" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:436.5pt;
2124 height:374.25pt;visibility:visible;mso-wrap-style:square'>
2125 <v:imagedata src="Fit%20Peaks_files/image030.png" o:title=""/>
2126</v:shape><![endif]--><![if !vml]><img border=0 width=582 height=499
2127src="Fit%20Peaks_files/image031.png" v:shapes="Picture_x0020_39"><![endif]></span><br
2128clear=all style='mso-special-character:line-break'>
2129</p>
2130
2131<h2>Step 4. Refine peaks</h2>
2132
2133<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
2134above, refine the peaks and the profile shape parameters in <b
2135style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2136mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2137minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2138file name at the first refinement (I used ‘<span class=SpellE><b
2139style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2140mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2141minor-latin'>jadarite</span></b></span><b style='mso-bidi-font-weight:normal'><span
2142style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2143mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>’</span></b>).
2144In the end my refinement converged at <span class=SpellE>Rwp</span>=11.41% and
2145some peaks do show some discrepancy as the sample is more complex than the
2146simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2147mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2148minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2149style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2150mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2151<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2152mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2153minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2154style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2155mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2156<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2157mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2158minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away
2159during refinement (one weak one at ~6.67 is particularly troublesome). However,
2160this is good enough to proceed.</p>
2161
2162<h2>Step 5. Prepare Indexing Peak List</h2>
2163
2164<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2165style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2166mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2167in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2168mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2169minor-latin'>Index Peak List</span></b> window.</p>
2170
2171<h2>Step 6. Index the cell</h2>
2172
2173<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic. In
2174a real world case we wouldn’t know this and we would have to try each <span
2175class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2176time to go through all the bad cases.</p>
2177
2178<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2179style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2180mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2181and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2183minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2184style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2185mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2186minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2187and suitable results will be slow in coming so be patient. Watch the console
2188window; the right answer will have an obviously large M20 (~380) and a volume
2189of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
2190seen (it may take more than one try to get this) you can stop the indexing
2191search by pressing <b style='mso-bidi-font-weight:normal'><span
2192style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2193mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
2194on the progress bar window. Notice the ‘<b style='mso-bidi-font-weight:normal'><span
2195style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2196mso-hansi-theme-font:minor-latin'>keep</span></b>’ column; this allows you to
2197keep some solutions from one indexing run to the next. It may take more than
2198one press to fully stop it. My result was </p>
2199
2200<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2201 id="Picture_x0020_19" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:359.25pt;
2202 height:297pt;visibility:visible;mso-wrap-style:square'>
2203 <v:imagedata src="Fit%20Peaks_files/image032.png" o:title=""/>
2204</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=396
2205src="Fit%20Peaks_files/image033.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2206
2207<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2208 id="Picture_x0020_20" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
2209 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2210 <v:imagedata src="Fit%20Peaks_files/image034.png" o:title=""/>
2211</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2212src="Fit%20Peaks_files/image035.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
2213
2214<p class=MsoNormal>Notice there may be other equally good M20 results with
2215different volumes; other solutions may be obtained as you keep trying the
2216indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2217style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2218mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2219new indexing runs. The best solution is the one with the smaller volume and
2220&#946; &gt; 90 deg. The plot shows every peak indexed including a weak peak not
2221selected for the peak fitting, although the weak peak at 2<span
2222style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
2223style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
2224has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
2225best cell and try to refine it along with the <b style='mso-bidi-font-weight:
2226normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2227minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
2228obtained an improved M20 ~444 and slightly different lattice parameters. Try
2229different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2230style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2231mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2232each time to see which lines vanish. By sliding the cursor over the index lines
2233without any visible peak you can see that the missing ones are 010, 100, 001,
2234110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
2235accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
2236space group P2<sub>1</sub>/n. Armed with this information you can <b
2237style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2238mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2239minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
2240style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2241mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2242minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
2243normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2244minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
2245the GSAS-II data tree.</p>
2246
2247<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2248 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
2249 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2250 <v:imagedata src="Fit%20Peaks_files/image036.png" o:title=""/>
2251</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2252src="Fit%20Peaks_files/image037.png" v:shapes="Picture_x0020_46"><![endif]></span><span
2253style='mso-spacerun:yes'> </span></p>
2254
2255<p class=MsoNormal>Notice that the lattice parameters and space group have been
2256set for you. </p>
2257
2258<p class=MsoNormal>This concludes this exercise; do <span class=GramE><b
2259style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2260mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2261minor-latin'>Save</span></b></span> <b style='mso-bidi-font-weight:normal'><span
2262style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2263mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>project</span></b>
2264as it is needed for the <b style='mso-bidi-font-weight:normal'><span
2265style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2266mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2267Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span
2268style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2269mso-hansi-theme-font:minor-latin'>in GSAS</span></b> exercise. The features of
2270the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2271mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2272minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
2273
2274<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Example: Fit Peaks/<span class=SpellE>Autoindexing</span>
2275in GSAS-II </h1>
2276
2277<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
2278in preparation for a charge flipping exercise. If continuing from the previous
2279indexing example do <b style='mso-bidi-font-weight:normal'><span
2280style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2281mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
2282GSAS-II data tree menu; you will be asked if you wish to save the old project.
2283The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
2284is another more substantial test of the indexing capability of GSAS-II. The
2285required data files should have been downloaded when you downloaded this
2286tutorial. Otherwise you will need to get them manually from <span
2287style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><a
2288href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/</a>.
2289Be sure to get </span><b style='mso-bidi-font-weight:normal'><span
2290style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2291mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2292minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif;
2293font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11bmb</span>_8716.fxye</span></b><span
2294style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and
2295the corresponding .<span class=SpellE>prm</span> files.</span></p>
2296
2297<h2>Step 1. Read in the data. </h2>
2298
2299<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2300normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2301minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2304minor-latin'>\data\11bmb_8716.fxye</span></b>; it has a corresponding <span
2305class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2306"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2307minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file and is
2308for Domino® sugar ground under acetone. The other <span class=SpellE><b
2309style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2310mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span>
2311file in this directory <b style='mso-bidi-font-weight:normal'><span
2312style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2313mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X
2314powdered sugar used “as is” out of the box. Load the <b style='mso-bidi-font-weight:
2315normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2316minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the
2317plot is</p>
2318
2319<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2320 id="Picture_x0020_44" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:452.25pt;
2321 height:387.75pt;visibility:visible;mso-wrap-style:square'>
2322 <v:imagedata src="Fit%20Peaks_files/image038.png" o:title=""/>
2323</v:shape><![endif]--><![if !vml]><img border=0 width=603 height=517
2324src="Fit%20Peaks_files/image039.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2325
2326<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2327lower part of the pattern; I’ve also chosen to plot the square root of the
2328intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2329"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2330minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2331
2332<h2>Step 2 Set limits</h2>
2333
2334<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2335style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2336mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>2</span></b>
2337and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2338mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2339minor-latin'>8</span></b>. Again, this gives a reasonable number of peaks for
2340indexing.</p>
2341
2342<h2>Step 3 Pick peaks</h2>
2343
2344<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2345small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2346"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2347minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2348peaks by left-clicking on a data point near the top of the peak. Peak positions
2349can be moved by dragging the peak line and peaks can be deleted by
2350right-clicking on them. This only works when the zoom and reposition modes
2351(below) are not selected. An easy to shift the view is to use the ‘&lt;’ and
2352‘&gt;’ buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2353that should be added to the list. I skipped a couple of very weak peaks; the
2354total list has &gt;28 peaks.</p>
2355
2356<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2357 id="Picture_x0020_45" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:465.75pt;
2358 height:399pt;visibility:visible;mso-wrap-style:square'>
2359 <v:imagedata src="Fit%20Peaks_files/image040.png" o:title=""/>
2360</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=532
2361src="Fit%20Peaks_files/image041.png" v:shapes="Picture_x0020_45"><![endif]></span><br
2362clear=all style='mso-special-character:line-break'>
2363</p>
2364
2365<h2>Step 4. Refine peaks</h2>
2366
2367<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2368kryptonite examples above, refine the peaks and the profile shape parameters in
2369<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2370mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2371minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2372file name at the first refinement (I used ‘<b style='mso-bidi-font-weight:normal'><span
2373style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2374mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>).
2375In the end my refinement converged at <span class=SpellE>Rwp</span>=6.69% and
2376some peaks do show some discrepancy as the sample is more complex than the
2377simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2378mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2379minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2380style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2381mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2382<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2383mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2384minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2385style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2386mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2387<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2388mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2389minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away during
2390refinement. However, this is good enough to proceed.</p>
2391
2392<h2>Step 5. Prepare Indexing Peak List</h2>
2393
2394<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2395style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2396mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2397in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2398mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2399minor-latin'>Index Peak List</span></b> window.</p>
2400
2401<h2>Step 6. Index the cell</h2>
2402
2403<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2404In a real world case we wouldn’t know this and we would have to try each <span
2405class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2406time to go through all the bad cases.</p>
2407
2408<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2409style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2410mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2411and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2412mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2413minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2414style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2415mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2416minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2417than for LaB<sub>6</sub> but oddly much faster than for kryptonite and suitable
2418results may appear almost immediately. Watch the console window; the right
2419answer will have an obviously large M20 (~900) and a volume of ~704Å<sup>3</sup>
2420(10<sup>th</sup> column of console display). Once this is seen (it may take
2421more than one try to get this) you can stop the indexing search by pressing <b
2422style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2423mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2424minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2425style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2426some solutions from one indexing run to the next. It may take more than one
2427press to fully stop it. My result was </p>
2428
2429<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2430 id="Picture_x0020_24" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2431 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2432 <v:imagedata src="Fit%20Peaks_files/image042.png" o:title=""/>
2433</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2434src="Fit%20Peaks_files/image043.png" v:shapes="Picture_x0020_24"><![endif]><!--[if gte vml 1]><v:shape
2435 id="Picture_x0020_47" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:434.25pt;
2436 height:372pt;visibility:visible;mso-wrap-style:square'>
2437 <v:imagedata src="Fit%20Peaks_files/image044.png" o:title=""/>
2438</v:shape><![endif]--><![if !vml]><img border=0 width=579 height=496
2439src="Fit%20Peaks_files/image045.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2440
2441<p class=MsoNormal>Notice there may be other equally good M20 results with
2442different volumes; still other solutions may be obtained as you keep trying the
2443indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2444style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2445mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2446new indexing runs. The best solution is the one with the smaller volume and
2447&#946; &gt; 90 <span class=SpellE>deg</span> and c&gt;a (I got both solutions!).
2448The plot shows every peak indexed including the weak peaks not selected for the
2449peak fitting. Copy the best cell and try to refine it along with the <b
2450style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2451mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
2452I obtained an improved M20 ~1300 and slightly different lattice parameters. Try
2453different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2454style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2455mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2456each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
2457Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
2458style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2459mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
2460phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
2461normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2462minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose</span></b>)
2463and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2464"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2465minor-latin'>Phases/sucrose</span></b> from the GSAS-II data tree.</p>
2466
2467<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2468 id="Picture_x0020_48" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2469 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2470 <v:imagedata src="Fit%20Peaks_files/image046.png" o:title=""/>
2471</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2472src="Fit%20Peaks_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span><span
2473style='mso-spacerun:yes'> </span></p>
2474
2475<p class=MsoNormal>Notice that the lattice parameters and space group have been
2476set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2477style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2478mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b>
2479the project file as it is needed for the sucrose <b style='mso-bidi-font-weight:
2480normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2481minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2482Flipping</span></b> exercise. The features of the <b style='mso-bidi-font-weight:
2483normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2484minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase
2485Data</span></b> window will be presented in other exercises.</p>
2486
2487<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2488
2489</div>
2490
2491</body>
2492
2493</html>
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