source: Tutorials/FitPeaks/Fit Peaks.htm @ 3569

Last change on this file since 3569 was 3569, checked in by toby, 3 years ago

fix some tutorial typos

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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><B>A video version of this tutorial is available at
1460<A href="https://anl.box.com/v/FitPeaks" target="_blank">
1461https://anl.box.com/v/FitPeaks</A></B></P>
1462 
1463<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1464cell that matches a set of diffraction peaks -- a process known as
1465auto-indexing. First peaks must be located and optimized and then indexing can
1466be done.</p>
1467
1468<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1469
1470<h2>Step 1: Read in the data file</h2>
1471
1472<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1473style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1474style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1475the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1476mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1477minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1478to read the data file into the current GSAS-II project. This read option is set
1479to read any of the powder data formats defined for GSAS (angles in <span
1480class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
1481the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1482style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1483mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1484format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1485style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1486mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1487format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1488style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1489directory to <b style='mso-bidi-font-weight:normal'>
1490data file</span></b> menu item to read the data file into the current GSAS-II project.
1491Because you used <span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1492minor-latin'>the </span><b style='mso-bidi-font-weight:normal'><span
1493style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1494mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1495minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family:
1496Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and
1497downloaded the exercise files (recommended), then the </span><span
1498class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1499"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1500Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>FitPeaks</span></b></span><b
1501style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1502mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1503minor-latin;mso-hansi-theme-font:minor-latin'>/data/...</span></b><span
1504style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1505entry will bring you to the location where the files have been downloaded. (It
1506is also possible to download them manually from <a
1507href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/</a>.
1508In this case you will need to navigate to the download location manually.)<br>
1509For this tutorial you should see the data file in the file browser, but if
1510extensions on data files are not the expected ones, you may need to change the
1511file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find
1512the desired file.</span></p>
1513
1514<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1515style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1516style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1517the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1518mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1519minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri",sans-serif;
1520mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1521minor-latin'> data</span> file in the first dialog and press <b
1522style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1523mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1524minor-latin'>Open</span></b>. There will be a Dialog box asking <b
1525style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1526mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1527minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
1528normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1529minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
1530button to proceed.</p>
1531
1532<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1533style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1534style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1535file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1536mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1537minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
1538automatically selected; it was produced by 11BM-B instrument processing
1539software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
1540normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1541minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1542file was created from the 12 detector raw data. If absent or the name doesn’t
1543match the data file name, a file dialog will appear for you to select the
1544correct instrument parameter file.</p>
1545
1546<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1547style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1548mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1549tree</span></b> window will have several entries </p>
1550
1551<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1552 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1553 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
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1559  <v:f eqn="prod @2 1 2"/>
1560  <v:f eqn="prod @3 21600 pixelWidth"/>
1561  <v:f eqn="prod @3 21600 pixelHeight"/>
1562  <v:f eqn="sum @0 0 1"/>
1563  <v:f eqn="prod @6 1 2"/>
1564  <v:f eqn="prod @7 21600 pixelWidth"/>
1565  <v:f eqn="sum @8 21600 0"/>
1566  <v:f eqn="prod @7 21600 pixelHeight"/>
1567  <v:f eqn="sum @10 21600 0"/>
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1572 style='width:468pt;height:300.75pt;visibility:visible;mso-wrap-style:square'>
1573 <v:imagedata src="Fit%20Peaks_files/image001.png" o:title=""/>
1574</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=401
1575src="Fit%20Peaks_files/image002.png" v:shapes="Picture_x0020_27"><![endif]></span></p>
1576
1577<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1578powder pattern</p>
1579
1580<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1581 id="Picture_x0020_28" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:397.5pt;
1582 height:340.5pt;visibility:visible;mso-wrap-style:square'>
1583 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1584</v:shape><![endif]--><![if !vml]><img border=0 width=530 height=454
1585src="Fit%20Peaks_files/image004.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1586
1587<h2>Step 2: Select Limits </h2>
1588
1589<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1590more data than we need, so it is helpful to cut down the range. Click on the <b
1591style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1592mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1593minor-latin'>Limits</span></b> item in the <b
1594style='mso-bidi-font-weight:normal'>
1595<span style='font-family:
1596"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>
1597GSAS-II
1598data tree</span></b>. Use the <b style='mso-bidi-font-weight:normal'><span
1599style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1600mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>New:</span></b>
1601row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
1602normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1603minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
1604and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1605style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1606mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1607to <b style='mso-bidi-font-weight:normal'><span
1608style='font-family:"Calibri",sans-serif;mso-hansi-theme-font:minor-latin;
1609mso-bidi-theme-font:minor-latin'>4</span></b> and <b style='mso-bidi-font-weight:
1610normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1611minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1612Notice on the plot that the limit lines have moved to these positions; the
1613green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1614is in a wide gap between peaks. You may also drag the limit lines to the
1615desired location or place them by a left mouse click on a data point for the
1616lower limit or a right click on a data point for the upper limit.</p>
1617
1618<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1619 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:446.25pt;
1620 height:224.25pt;visibility:visible;mso-wrap-style:square'>
1621 <v:imagedata src="Fit%20Peaks_files/image005.png" o:title=""/>
1622</v:shape><![endif]--><![if !vml]><img border=0 width=595 height=299
1623src="Fit%20Peaks_files/image005.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1624
1625<h2>Step 3: Determine Peak Positions</h2>
1626
1627<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1628auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1629style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1630style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1631on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1632mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1633minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1634normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1635minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1636data tree</span></b>. This creates an empty window of peak positions (the <b
1637style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1638mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1639minor-latin'>Limits</span></b> window is erased). At this point it is wise to
1640zoom in on the data that will be used for indexing. </p>
1641
1642<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1643auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1644style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1645style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1646on the Zoom button (5<sup>th</sup> one from the left on the plot toolbar), then
1647press the left mouse in one corner of the region to be used; holding the mouse
1648button down, drag over the region to the opposite corner; a box will be drawn
1649over the region to be zoomed and the plot will be redrawn with the new limits.
1650The toolbar has a number of buttons to the right of the help button (‘?’) that
1651can be used to incrementally change the view.</p>
1652
1653<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1654auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1655style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1656style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1657style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom button
1658again to turn off the zoom mode. </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'>4.<span
1663style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1664<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1665mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1666in the menu select <b style='mso-bidi-font-weight:normal'><span
1667style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1668mso-hansi-theme-font:minor-latin'>Auto search</span></b>. The plot window will
1669immediately show that all peaks were picked with a blue vertical line on each
1670one</p>
1671
1672<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1673auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_31"
1674 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:395.25pt;height:339pt;
1675 visibility:visible;mso-wrap-style:square'>
1676 <v:imagedata src="Fit%20Peaks_files/image006.png" o:title=""/>
1677</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1678src="Fit%20Peaks_files/image007.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
1679
1680<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1681auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1682normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1683minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1684List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1685
1686<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1687auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
1688 o:spid="_x0000_i1045" type="#_x0000_t75" style='width:426pt;height:198.75pt;
1689 visibility:visible;mso-wrap-style:square'>
1690 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1691</v:shape><![endif]--><![if !vml]><img border=0 width=568 height=265
1692src="Fit%20Peaks_files/image009.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
1693
1694<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1695will be 20 peaks in this example. You should examine both the list and the plot
1696to be sure the auto search did not pick a peak twice (rarely) or skip a peak or
1697shoulder. You can add a peak to the list by pressing the left mouse button with
1698the pointer on a data point at the peak top or shoulder; be sure the zoom/shift
1699buttons are off. You may drag a peak position as needed. A position may be
1700deleted with a right click with the mouse on the blue line. You can also delete
1701a peak by selecting the row in the table; it will be highlighted in blue. Then
1702press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1703mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b>
1704key; it will be removed from the table and the plot. The list will always show
1705the peaks sorted by position. When done you should have 20 unique peak
1706positions.</p>
1707
1708<h2>Step 4: Refine Peak Positions</h2>
1709
1710<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1711refinement and then adding parameters to complete the fitting,</p>
1712
1713<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1714style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1715style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1716the peak intensities and the background. These parameters have their refinement
1717flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1718normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1719minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1720Fitting/<span class=SpellE>Peakfit</span></span></b>. Do <b style='mso-bidi-font-weight:
1721normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1722style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1723mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1724menu item; that it to be used for Rietveld/Pawley refinements. You will be
1725asked to save the current project before the fit will proceed; change directory
1726if desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1727normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1728minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1729A window will show the progress of the refinement and will close when the
1730least-squares fit is complete (usually very fast). The plot is updated with the
1731fit, the peak list window is updated with the new peak values and a summary of
1732the refinement is shown on the console window as well.</p>
1733
1734<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1735 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:407.25pt;
1736 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1737 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1738</v:shape><![endif]--><![if !vml]><img border=0 width=543 height=466
1739src="Fit%20Peaks_files/image011.png" v:shapes="Picture_x0020_33"><![endif]></span></p>
1740
1741<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1742 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:420pt;
1743 height:195.75pt;visibility:visible;mso-wrap-style:square'>
1744 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1745</v:shape><![endif]--><![if !vml]><img border=0 width=560 height=261
1746src="Fit%20Peaks_files/image013.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1747
1748<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1749style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1750style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1751add refinement of the peak positions. This can be done by clicking on all the
1752refinement flags for the individual peaks or it is possible to set them all at
1753the same time using this recipe: </p>
1754
1755<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1756auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1757style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1758style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1759on any value in the table to select it, for example the first peak position. A
1760black box appears around the value. </p>
1761
1762<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1763text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1764style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1765style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1766on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1767mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1768label above the peak position check-boxes. The entire column of checkboxes is
1769highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
1770style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1771mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y</span></b>
1772key to turn on all refinement flags (<b style='mso-bidi-font-weight:normal'><span
1773style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1774mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>n</span></b>
1775would turn them off).</p>
1776
1777<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1778the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1779mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1780minor-latin'>Peak Fitting/<span class=SpellE>Peakfit</span></span></b> menu
1781item.</p>
1782
1783<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1784refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1785performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1786width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
1787click the refinement flags for sigma and/or gamma in the Peak List window.
1788&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1789widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening equation
1790as described below.&nbsp;Note - one cannot refine ALL peak widths using both
1791individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental broadening
1792terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1793
1794<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1795"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1796to an instrumental broadening equation, first<b> s</b></span>elect the <b
1797style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1798mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1799minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
1800opens a window for peak profile terms<b> </b><span style='mso-bidi-font-weight:
1801bold'>and also creates a new plot window&nbsp;showing the instrument profile
1802resolution curve.</span></p>
1803
1804<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1805 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:415.5pt;
1806 height:298.5pt;visibility:visible;mso-wrap-style:square'>
1807 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1808</v:shape><![endif]--><![if !vml]><img border=0 width=554 height=398
1809src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_35"><![endif]></span></p>
1810
1811<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1812corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1813coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1814values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1815<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1816mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1817minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
1818style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1819mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
1820<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1821mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1822minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
1823style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1824mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
1825<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1826mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1827minor-latin'>Y</span></b>. </p>
1828
1829<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1830style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1831style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1832repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1833style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1834mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1835item in the data tree and then refine using the <b style='mso-bidi-font-weight:
1836normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1837minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1838Fitting/<span class=SpellE>Peakfit</span></span></b> menu item. At this point a
1839good fit should be seen by zooming in on individual peaks. For example see </p>
1840
1841<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1842 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:408pt;
1843 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1844 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1845</v:shape><![endif]--><![if !vml]><img border=0 width=544 height=466
1846src="Fit%20Peaks_files/image016.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1847
1848<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
1849the right of the peak top. This is a consequence of the peak asymmetry arising
1850from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
1851is ~7% as shown on the console window. Again the <b style='mso-bidi-font-weight:
1852normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1853minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1854List</span></b> entries are all updated with new values and those in <b
1855style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1856mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1857minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1858
1859<h2>Step 5. Prepare Indexing Peak List</h2>
1860
1861<p class=MsoNormal>A separate list of peaks is kept for use in <span
1862class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1863normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1864minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1865Peak List</span></b> item in the data tree. In the initially empty window
1866created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1867style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1868mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1869to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1870style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1871mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>.</p>
1872
1873<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1874 id="Picture_x0020_37" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:431.25pt;
1875 height:309.75pt;visibility:visible;mso-wrap-style:square'>
1876 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1877</v:shape><![endif]--><![if !vml]><img border=0 width=575 height=413
1878src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
1879
1880<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1881may choose to not use a fitted peak (e.g. if suspected it is from a
1882contaminant).</p>
1883
1884<h2>Step 6. Run <span class=SpellE>Autoindexing</span></h2>
1885
1886<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1887style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1888mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1889List</span></b> data item. This brings up a window for indexing and cell
1890refinement options</p>
1891
1892<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1893 id="Picture_x0020_38" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1894 height:157.5pt;visibility:visible;mso-wrap-style:square'>
1895 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1896</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=210
1897src="Fit%20Peaks_files/image019.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
1898
1899<p class=MsoNormal>For the most rapid search (since we know the right answer),
1900select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1901mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1902minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1903style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1904mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1905minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and the
1906console shows a running list of possible cells as they are found; the sorted by
1907M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1908normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1909minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1910Cells List</span></b> window</p>
1911
1912<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1913 id="Picture_x0020_13" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1914 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1915 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1916</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1917src="Fit%20Peaks_files/image021.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1918
1919<h2>Step 7. Review Cell Choices</h2>
1920
1921<p class=MsoNormal>Review the list of cells associated with the <b
1922style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1923mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1924minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1925unit cell, the generated reflections for that cell are shown in the plot with
1926dashed red lines. Sliding the cursor over these lines shows a small popup
1927window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1928first cell in the list (M20~2970) with a=5.87864 Å generates very many lines
1929with no corresponding peaks (NB: this solution might not always show up!)</p>
1930
1931<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1932 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:447pt;
1933 height:383.25pt;visibility:visible;mso-wrap-style:square'>
1934 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1935</v:shape><![endif]--><![if !vml]><img border=0 width=596 height=511
1936src="Fit%20Peaks_files/image023.png" v:shapes="Picture_x0020_40"><![endif]></span><span
1937style='mso-spacerun:yes'> </span></p>
1938
1939<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
1940enough lines to match all the peaks</p>
1941
1942<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1943 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:428.25pt;
1944 height:366.75pt;visibility:visible;mso-wrap-style:square'>
1945 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1946</v:shape><![endif]--><![if !vml]><img border=0 width=571 height=489
1947src="Fit%20Peaks_files/image025.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1948
1949<h2>Step 8. Select/Refine Cell</h2>
1950
1951<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1952indexes all peaks with almost a perfect fit to the peak positions (compare
1953dashed red lines to solid blue ones). Import the cell information using the <b
1954style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1955mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1956minor-latin'>Cell Index/Refine/Copy Cell</span></b> menu option. Then optimize
1957the cell by refining the lattice parameters and the two-theta zero: click on
1958the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1959mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
1960checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1961style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1962mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1963value and then the <b style='mso-bidi-font-weight:normal'><span
1964style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1965mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1966Index/Refine/Refine Cell</span></b> menu option. The M20 improves to ~3600 and <span
1967class=GramE>the a</span> cell parameter value shifts from 4.15683 to 4.15691
1968when zero is refined. (NB: The certificate value for NIST SRM 660a is 4.15692
1969Å). Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1970"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1971minor-latin;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
1972positions </span></b>button to update the plot including the refined <b
1973style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1974mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1975minor-latin'>Zero offset</span></b> (in this case hardly anything
1976happens!).<span style='mso-spacerun:yes'>  </span></p>
1977
1978<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1979 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1980 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1981 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
1982</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1983src="Fit%20Peaks_files/image027.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1984
1985<p class=MsoNormal>Notice that a new entry heads the list in the <b
1986style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1987mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1988minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
1989normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1990minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1991Cells List</span></b> window with an improved <span class=GramE>M20(</span>~3600)
1992and a new value for <b style='mso-bidi-font-weight:normal'><span
1993style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1994mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1995is shown. NB: the <b style='mso-bidi-font-weight:normal'><span
1996style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1997mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
1998button has an additional use; you can enter the <span class=SpellE><b
1999style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2000mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b
2001style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2002mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>,
2003<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2004mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b>
2005&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2006mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
2007for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
2008style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2009mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2010will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
2011style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2012mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
2013useful to identify e.g. a second phase in your pattern.</p>
2014
2015<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
2016normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2017minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
2018Index/Refine/Make new phase</span></b> menu option allows one to create a phase
2019with these lattice parameters in the data tree under <b style='mso-bidi-font-weight:
2020normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2021minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
2022style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
2023creates the tree item <b style='mso-bidi-font-weight:normal'><span
2024style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2025mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
2026(if it wasn’t already present). This new phase can be used in future analysis
2027(e.g. Rietveld or Pawley refinement).</p>
2028
2029<p class=MsoNormal>To continue with the second part of this exercise, select
2030the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
2031"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2032minor-latin;mso-bidi-theme-font:minor-latin'>File/New project</span></b> in the
2033<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2034mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2035minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
2036the current project saved; if <b style='mso-bidi-font-weight:normal'><span
2037style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2038mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
2039then all the peak fitting/indexing &amp; cell refinement results will be saved
2040to the <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'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
2043style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2044mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
2045then the file will remain as it was when created at Step 4 above.</p>
2046
2047<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
2048class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
2049style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
2050
2051<p class=MsoNormal>In this exercise we will fit peaks and index them for the
2052mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
2053href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
2054also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
2055substantial test of the indexing capability of GSAS-II. The required data files
2056should have been downloaded when you downloaded this tutorial. Otherwise you
2057will need to get them manually from <span style='mso-fareast-font-family:Calibri;
2058mso-fareast-theme-font:minor-latin'><a
2059href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/</a>.
2060Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span
2061style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2062mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2063minor-latin'>11bmb_6231.fxye</span></b><span style='mso-fareast-font-family:
2064Calibri;mso-fareast-theme-font:minor-latin'> and </span><b style='mso-bidi-font-weight:
2065normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2066minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2067mso-hansi-theme-font:minor-latin'>11bmb_6231.prm</span></b></p>
2068
2069<h2>Step 1. Read in the data. </h2>
2070
2071<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2072normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2073minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2074style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2075mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2076minor-latin'>\data\11bmb_6231.fxye</span></b>; it has a corresponding <span
2077class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2078"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2079minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file. Load
2080them in &amp; the plot is</p>
2081
2082<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2083 id="Picture_x0020_43" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:405pt;
2084 height:347.25pt;visibility:visible;mso-wrap-style:square'>
2085 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2086</v:shape><![endif]--><![if !vml]><img border=0 width=540 height=463
2087src="Fit%20Peaks_files/image029.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2088
2089<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2090lower part of the pattern.</p>
2091
2092<h2>Step 2 Set limits</h2>
2093
2094<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2095style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2096mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
2097and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2098mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2099minor-latin'>9</span></b>. This will give a suitable number of lines for
2100indexing.</p>
2101
2102<h2>Step 3 Pick peaks</h2>
2103
2104<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2105small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2106"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2107minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2108peaks by left-clicking on a data point near the top of the peak. Peak positions
2109can be moved by dragging the peak line and peaks can be deleted by
2110right-clicking on them. This only works when the zoom and reposition modes
2111(below) are not selected. Also note some peaks have shoulders most notably at
21125.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
2113deg. I skipped – it might be from a second phase? We’ll see later).</p>
2114
2115<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2116 id="Picture_x0020_39" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:436.5pt;
2117 height:374.25pt;visibility:visible;mso-wrap-style:square'>
2118 <v:imagedata src="Fit%20Peaks_files/image030.png" o:title=""/>
2119</v:shape><![endif]--><![if !vml]><img border=0 width=582 height=499
2120src="Fit%20Peaks_files/image031.png" v:shapes="Picture_x0020_39"><![endif]></span><br
2121clear=all style='mso-special-character:line-break'>
2122</p>
2123
2124<h2>Step 4. Refine peaks</h2>
2125
2126<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
2127above, refine the peaks and the profile shape parameters in <b
2128style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2129mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2130minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2131file name at the first refinement (I used ‘<span class=SpellE><b
2132style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2133mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2134minor-latin'>jadarite</span></b></span><b style='mso-bidi-font-weight:normal'><span
2135style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2136mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>’</span></b>).
2137In the end my refinement converged at <span class=SpellE>Rwp</span>=11.41% and
2138some peaks do show some discrepancy as the sample is more complex than the
2139simple <b style='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'>U</span></b>, <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'>V</span></b>,
2144<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2145mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2146minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2147style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2148mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2149<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2150mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2151minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away
2152during refinement (one weak one at ~6.67 is particularly troublesome). However,
2153this is good enough to proceed.</p>
2154
2155<h2>Step 5. Prepare Indexing Peak List</h2>
2156
2157<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2158style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2159mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2160in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2161mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2162minor-latin'>Index Peak List</span></b> window.</p>
2163
2164<h2>Step 6. Index the cell</h2>
2165
2166<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic. In
2167a real world case we wouldn’t know this and we would have to try each <span
2168class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2169time to go through all the bad cases.</p>
2170
2171<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2172style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2173mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2174and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2175mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2176minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2179minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2180and suitable results will be slow in coming so be patient. Watch the console
2181window; the right answer will have an obviously large M20 (~380) and a volume
2182of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
2183seen (it may take more than one try to get this) you can stop the indexing
2184search by pressing <b style='mso-bidi-font-weight:normal'><span
2185style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2186mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
2187on the progress bar window. Notice the ‘<b style='mso-bidi-font-weight:normal'><span
2188style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2189mso-hansi-theme-font:minor-latin'>keep</span></b>’ column; this allows you to
2190keep some solutions from one indexing run to the next. It may take more than
2191one press to fully stop it. My result was </p>
2192
2193<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2194 id="Picture_x0020_19" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:359.25pt;
2195 height:297pt;visibility:visible;mso-wrap-style:square'>
2196 <v:imagedata src="Fit%20Peaks_files/image032.png" o:title=""/>
2197</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=396
2198src="Fit%20Peaks_files/image033.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2199
2200<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2201 id="Picture_x0020_20" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
2202 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2203 <v:imagedata src="Fit%20Peaks_files/image034.png" o:title=""/>
2204</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2205src="Fit%20Peaks_files/image035.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
2206
2207<p class=MsoNormal>Notice there may be other equally good M20 results with
2208different volumes; other solutions may be obtained as you keep trying the
2209indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2210style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2211mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2212new indexing runs. The best solution is the one with the smaller volume and
2213&#946; &gt; 90 deg. The plot shows every peak indexed including a weak peak not
2214selected for the peak fitting, although the weak peak at 2<span
2215style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
2216style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
2217has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
2218best cell and try to refine it along with the <b style='mso-bidi-font-weight:
2219normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2220minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
2221obtained an improved M20 ~444 and slightly different lattice parameters. Try
2222different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2223style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2224mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2225each time to see which lines vanish. By sliding the cursor over the index lines
2226without any visible peak you can see that the missing ones are 010, 100, 001,
2227110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
2228accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
2229space group P2<sub>1</sub>/n. Armed with this information you can <b
2230style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2231mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2232minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
2233style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2234mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2235minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
2236normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2237minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
2238the GSAS-II data tree.</p>
2239
2240<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2241 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
2242 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2243 <v:imagedata src="Fit%20Peaks_files/image036.png" o:title=""/>
2244</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2245src="Fit%20Peaks_files/image037.png" v:shapes="Picture_x0020_46"><![endif]></span><span
2246style='mso-spacerun:yes'> </span></p>
2247
2248<p class=MsoNormal>Notice that the lattice parameters and space group have been
2249set for you. </p>
2250
2251<p class=MsoNormal>This concludes this exercise; do <span class=GramE><b
2252style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2253mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2254minor-latin'>Save</span></b></span> <b style='mso-bidi-font-weight:normal'><span
2255style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2256mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>project</span></b>
2257as it is needed for the <b style='mso-bidi-font-weight:normal'><span
2258style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2259mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2260Flipping</span></b> <b style='mso-bidi-font-weight:normal'><span
2261style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2262mso-hansi-theme-font:minor-latin'>in GSAS</span></b> exercise. The features of
2263the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2264mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2265minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
2266
2267<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
2268in GSAS-II </h1>
2269
2270<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
2271in preparation for a charge flipping exercise. If continuing from the previous
2272indexing example do <b style='mso-bidi-font-weight:normal'><span
2273style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2274mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
2275GSAS-II data tree menu; you will be asked if you wish to save the old project.
2276The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
2277is another more substantial test of the indexing capability of GSAS-II. The
2278required data files should have been downloaded when you downloaded this
2279tutorial. Otherwise you will need to get them manually from <span
2280style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><a
2281href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/data/</a>.
2282Be sure to get </span><b style='mso-bidi-font-weight:normal'><span
2283style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2284mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2285minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif;
2286font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11bmb</span>_8716.fxye</span></b><span
2287style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and
2288the corresponding .<span class=SpellE>prm</span> files.</span></p>
2289
2290<h2>Step 1. Read in the data. </h2>
2291
2292<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2293normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2294minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2295style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2296mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2297minor-latin'>\data\11bmb_8716.fxye</span></b>; it has a corresponding <span
2298class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2299"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2300minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file and is
2301for Domino® sugar ground under acetone. The other <span class=SpellE><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'>fxye</span></b></span>
2304file in this directory <b style='mso-bidi-font-weight:normal'><span
2305style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2306mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X
2307powdered sugar used “as is” out of the box. Load the <b style='mso-bidi-font-weight:
2308normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2309minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the
2310plot is</p>
2311
2312<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2313 id="Picture_x0020_44" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:452.25pt;
2314 height:387.75pt;visibility:visible;mso-wrap-style:square'>
2315 <v:imagedata src="Fit%20Peaks_files/image038.png" o:title=""/>
2316</v:shape><![endif]--><![if !vml]><img border=0 width=603 height=517
2317src="Fit%20Peaks_files/image039.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2318
2319<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2320lower part of the pattern; I’ve also chosen to plot the square root of the
2321intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2322"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2323minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2324
2325<h2>Step 2 Set limits</h2>
2326
2327<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2328style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2329mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>2</span></b>
2330and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2331mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2332minor-latin'>8</span></b>. Again, this gives a reasonable number of peaks for
2333indexing.</p>
2334
2335<h2>Step 3 Pick peaks</h2>
2336
2337<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2338small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2339"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2340minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2341peaks by left-clicking on a data point near the top of the peak. Peak positions
2342can be moved by dragging the peak line and peaks can be deleted by
2343right-clicking on them. This only works when the zoom and reposition modes
2344(below) are not selected. An easy to shift the view is to use the ‘&lt;’ and
2345‘&gt;’ buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2346that should be added to the list. I skipped a couple of very weak peaks; the
2347total list has &gt;28 peaks.</p>
2348
2349<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2350 id="Picture_x0020_45" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:465.75pt;
2351 height:399pt;visibility:visible;mso-wrap-style:square'>
2352 <v:imagedata src="Fit%20Peaks_files/image040.png" o:title=""/>
2353</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=532
2354src="Fit%20Peaks_files/image041.png" v:shapes="Picture_x0020_45"><![endif]></span><br
2355clear=all style='mso-special-character:line-break'>
2356</p>
2357
2358<h2>Step 4. Refine peaks</h2>
2359
2360<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2361kryptonite examples above, refine the peaks and the profile shape parameters in
2362<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2363mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2364minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2365file name at the first refinement (I used ‘<b style='mso-bidi-font-weight:normal'><span
2366style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2367mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose’</span></b>).
2368In the end my refinement converged at <span class=SpellE>Rwp</span>=6.69% and
2369some peaks do show some discrepancy as the sample is more complex than the
2370simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2371mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2372minor-latin'>U</span></b>, <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'>V</span></b>,
2375<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2376mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2377minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2378style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2379mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2380<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2381mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2382minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away during
2383refinement. However, this is good enough to proceed.</p>
2384
2385<h2>Step 5. Prepare Indexing Peak List</h2>
2386
2387<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2388style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2389mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2390in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2391mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2392minor-latin'>Index Peak List</span></b> window.</p>
2393
2394<h2>Step 6. Index the cell</h2>
2395
2396<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2397In a real world case we wouldn’t know this and we would have to try each <span
2398class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2399time to go through all the bad cases.</p>
2400
2401<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2402style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2403mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2404and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2406minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2407style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2408mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2409minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2410than for LaB<sub>6</sub> but oddly much faster than for kryptonite and suitable
2411results may appear almost immediately. Watch the console window; the right
2412answer will have an obviously large M20 (~900) and a volume of ~704Å<sup>3</sup>
2413(10<sup>th</sup> column of console display). Once this is seen (it may take
2414more than one try to get this) you can stop the indexing search by pressing <b
2415style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2416mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2417minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2418style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2419some solutions from one indexing run to the next. It may take more than one
2420press to fully stop it. My result was </p>
2421
2422<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2423 id="Picture_x0020_24" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2424 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2425 <v:imagedata src="Fit%20Peaks_files/image042.png" o:title=""/>
2426</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2427src="Fit%20Peaks_files/image043.png" v:shapes="Picture_x0020_24"><![endif]><!--[if gte vml 1]><v:shape
2428 id="Picture_x0020_47" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:434.25pt;
2429 height:372pt;visibility:visible;mso-wrap-style:square'>
2430 <v:imagedata src="Fit%20Peaks_files/image044.png" o:title=""/>
2431</v:shape><![endif]--><![if !vml]><img border=0 width=579 height=496
2432src="Fit%20Peaks_files/image045.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2433
2434<p class=MsoNormal>Notice there may be other equally good M20 results with
2435different volumes; still other solutions may be obtained as you keep trying the
2436indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2437style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2438mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2439new indexing runs. The best solution is the one with the smaller volume and
2440&#946; &gt; 90 <span class=SpellE>deg</span> and c&gt;a (I got both solutions!).
2441The plot shows every peak indexed including the weak peaks not selected for the
2442peak fitting. Copy the best cell and try to refine it along with the <b
2443style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2444mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
2445I obtained an improved M20 ~1300 and slightly different lattice parameters. Try
2446different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2447style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2448mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2449each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
2450Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
2451style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2452mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
2453phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
2454normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2455minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose</span></b>)
2456and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2457"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2458minor-latin'>Phases/sucrose</span></b> from the GSAS-II data tree.</p>
2459
2460<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2461 id="Picture_x0020_48" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2462 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2463 <v:imagedata src="Fit%20Peaks_files/image046.png" o:title=""/>
2464</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2465src="Fit%20Peaks_files/image047.png" v:shapes="Picture_x0020_48"><![endif]></span><span
2466style='mso-spacerun:yes'> </span></p>
2467
2468<p class=MsoNormal>Notice that the lattice parameters and space group have been
2469set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2470style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2471mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b>
2472the project file as it is needed for the sucrose <b style='mso-bidi-font-weight:
2473normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2474minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2475Flipping</span></b> exercise. The features of the <b style='mso-bidi-font-weight:
2476normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2477minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase
2478Data</span></b> window will be presented in other exercises.</p>
2479
2480<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2481
2482</div>
2483
2484</body>
2485
2486</html>
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