source: Tutorials/FitPeaks/Fit Peaks.htm @ 2980

Last change on this file since 2980 was 2980, checked in by vondreele, 4 years ago

fix

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415  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
416  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
417  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
418  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
419  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
420  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
421  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
422  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
423  <w:LsdException Locked="false" Priority="34" QFormat="true"
424   Name="List Paragraph"/>
425  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
426  <w:LsdException Locked="false" Priority="30" QFormat="true"
427   Name="Intense Quote"/>
428  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
429  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
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"/>
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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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785        font-family:"Times New Roman",serif;
786        mso-fareast-font-family:"Times New Roman";
787        mso-fareast-theme-font:minor-fareast;
788        color:#4F4FFF;
789        font-weight:bold;}
790p.MsoTitle, li.MsoTitle, div.MsoTitle
791        {mso-style-noshow:yes;
792        mso-style-priority:10;
793        mso-style-unhide:no;
794        mso-style-qformat:yes;
795        mso-style-link:"Title Char";
796        mso-style-next:Normal;
797        margin-top:0in;
798        margin-right:0in;
799        margin-bottom:15.0pt;
800        margin-left:0in;
801        mso-add-space:auto;
802        mso-pagination:widow-orphan;
803        border:none;
804        mso-border-bottom-alt:solid #4F81BD 1.0pt;
805        mso-border-bottom-themecolor:accent1;
806        padding:0in;
807        mso-padding-alt:0in 0in 4.0pt 0in;
808        font-size:26.0pt;
809        font-family:"Cambria",serif;
810        mso-ascii-font-family:Cambria;
811        mso-ascii-theme-font:major-latin;
812        mso-fareast-font-family:"Times New Roman";
813        mso-fareast-theme-font:major-fareast;
814        mso-hansi-font-family:Cambria;
815        mso-hansi-theme-font:major-latin;
816        mso-bidi-font-family:"Times New Roman";
817        mso-bidi-theme-font:major-bidi;
818        color:#17365D;
819        mso-themecolor:text2;
820        mso-themeshade:191;
821        letter-spacing:.25pt;
822        mso-font-kerning:14.0pt;}
823p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
824        {mso-style-noshow:yes;
825        mso-style-priority:10;
826        mso-style-unhide:no;
827        mso-style-qformat:yes;
828        mso-style-link:"Title Char";
829        mso-style-next:Normal;
830        mso-style-type:export-only;
831        margin:0in;
832        margin-bottom:.0001pt;
833        mso-add-space:auto;
834        mso-pagination:widow-orphan;
835        border:none;
836        mso-border-bottom-alt:solid #4F81BD 1.0pt;
837        mso-border-bottom-themecolor:accent1;
838        padding:0in;
839        mso-padding-alt:0in 0in 4.0pt 0in;
840        font-size:26.0pt;
841        font-family:"Cambria",serif;
842        mso-ascii-font-family:Cambria;
843        mso-ascii-theme-font:major-latin;
844        mso-fareast-font-family:"Times New Roman";
845        mso-fareast-theme-font:major-fareast;
846        mso-hansi-font-family:Cambria;
847        mso-hansi-theme-font:major-latin;
848        mso-bidi-font-family:"Times New Roman";
849        mso-bidi-theme-font:major-bidi;
850        color:#17365D;
851        mso-themecolor:text2;
852        mso-themeshade:191;
853        letter-spacing:.25pt;
854        mso-font-kerning:14.0pt;}
855p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
856        {mso-style-noshow:yes;
857        mso-style-priority:10;
858        mso-style-unhide:no;
859        mso-style-qformat:yes;
860        mso-style-link:"Title Char";
861        mso-style-next:Normal;
862        mso-style-type:export-only;
863        margin:0in;
864        margin-bottom:.0001pt;
865        mso-add-space:auto;
866        mso-pagination:widow-orphan;
867        border:none;
868        mso-border-bottom-alt:solid #4F81BD 1.0pt;
869        mso-border-bottom-themecolor:accent1;
870        padding:0in;
871        mso-padding-alt:0in 0in 4.0pt 0in;
872        font-size:26.0pt;
873        font-family:"Cambria",serif;
874        mso-ascii-font-family:Cambria;
875        mso-ascii-theme-font:major-latin;
876        mso-fareast-font-family:"Times New Roman";
877        mso-fareast-theme-font:major-fareast;
878        mso-hansi-font-family:Cambria;
879        mso-hansi-theme-font:major-latin;
880        mso-bidi-font-family:"Times New Roman";
881        mso-bidi-theme-font:major-bidi;
882        color:#17365D;
883        mso-themecolor:text2;
884        mso-themeshade:191;
885        letter-spacing:.25pt;
886        mso-font-kerning:14.0pt;}
887p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
888        {mso-style-noshow:yes;
889        mso-style-priority:10;
890        mso-style-unhide:no;
891        mso-style-qformat:yes;
892        mso-style-link:"Title Char";
893        mso-style-next:Normal;
894        mso-style-type:export-only;
895        margin-top:0in;
896        margin-right:0in;
897        margin-bottom:15.0pt;
898        margin-left:0in;
899        mso-add-space:auto;
900        mso-pagination:widow-orphan;
901        border:none;
902        mso-border-bottom-alt:solid #4F81BD 1.0pt;
903        mso-border-bottom-themecolor:accent1;
904        padding:0in;
905        mso-padding-alt:0in 0in 4.0pt 0in;
906        font-size:26.0pt;
907        font-family:"Cambria",serif;
908        mso-ascii-font-family:Cambria;
909        mso-ascii-theme-font:major-latin;
910        mso-fareast-font-family:"Times New Roman";
911        mso-fareast-theme-font:major-fareast;
912        mso-hansi-font-family:Cambria;
913        mso-hansi-theme-font:major-latin;
914        mso-bidi-font-family:"Times New Roman";
915        mso-bidi-theme-font:major-bidi;
916        color:#17365D;
917        mso-themecolor:text2;
918        mso-themeshade:191;
919        letter-spacing:.25pt;
920        mso-font-kerning:14.0pt;}
921a:link, span.MsoHyperlink
922        {mso-style-noshow:yes;
923        mso-style-priority:99;
924        color:blue;
925        text-decoration:underline;
926        text-underline:single;}
927a:visited, span.MsoHyperlinkFollowed
928        {mso-style-noshow:yes;
929        mso-style-priority:99;
930        color:purple;
931        text-decoration:underline;
932        text-underline:single;}
933p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
934        {mso-style-noshow:yes;
935        mso-style-priority:99;
936        mso-style-link:"Document Map Char";
937        margin:0in;
938        margin-bottom:.0001pt;
939        mso-pagination:widow-orphan;
940        font-size:8.0pt;
941        font-family:"Tahoma",sans-serif;
942        mso-fareast-font-family:"Times New Roman";
943        mso-fareast-theme-font:minor-fareast;}
944p
945        {mso-style-noshow:yes;
946        mso-style-priority:99;
947        mso-margin-top-alt:auto;
948        margin-right:0in;
949        mso-margin-bottom-alt:auto;
950        margin-left:0in;
951        mso-pagination:widow-orphan;
952        font-size:12.0pt;
953        font-family:"Times New Roman",serif;
954        mso-fareast-font-family:"Times New Roman";
955        mso-fareast-theme-font:minor-fareast;}
956pre
957        {mso-style-noshow:yes;
958        mso-style-priority:99;
959        mso-style-link:"HTML Preformatted Char";
960        margin:0in;
961        margin-bottom:.0001pt;
962        mso-pagination:widow-orphan;
963        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;
964        font-size:10.0pt;
965        font-family:"Courier New";
966        mso-fareast-font-family:"Times New Roman";}
967p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
968        {mso-style-noshow:yes;
969        mso-style-priority:99;
970        mso-style-link:"Balloon Text Char";
971        margin:0in;
972        margin-bottom:.0001pt;
973        mso-pagination:widow-orphan;
974        font-size:8.0pt;
975        font-family:"Tahoma",sans-serif;
976        mso-fareast-font-family:"Times New Roman";
977        mso-fareast-theme-font:minor-fareast;}
978span.MsoPlaceholderText
979        {mso-style-noshow:yes;
980        mso-style-priority:99;
981        mso-style-unhide:no;
982        color:gray;}
983p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
984        {mso-style-noshow:yes;
985        mso-style-priority:1;
986        mso-style-unhide:no;
987        mso-style-qformat:yes;
988        mso-style-parent:"";
989        margin:0in;
990        margin-bottom:.0001pt;
991        mso-pagination:widow-orphan;
992        font-size:12.0pt;
993        font-family:"Times New Roman",serif;
994        mso-fareast-font-family:"Times New Roman";
995        mso-fareast-theme-font:minor-fareast;}
996p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
997        {mso-style-noshow:yes;
998        mso-style-priority:34;
999        mso-style-unhide:no;
1000        mso-style-qformat:yes;
1001        margin-top:0in;
1002        margin-right:0in;
1003        margin-bottom:0in;
1004        margin-left:.5in;
1005        margin-bottom:.0001pt;
1006        mso-add-space:auto;
1007        mso-pagination:widow-orphan;
1008        font-size:12.0pt;
1009        font-family:"Times New Roman",serif;
1010        mso-fareast-font-family:"Times New Roman";
1011        mso-fareast-theme-font:minor-fareast;}
1012p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
1013        {mso-style-noshow:yes;
1014        mso-style-priority:34;
1015        mso-style-unhide:no;
1016        mso-style-qformat:yes;
1017        mso-style-type:export-only;
1018        margin-top:0in;
1019        margin-right:0in;
1020        margin-bottom:0in;
1021        margin-left:.5in;
1022        margin-bottom:.0001pt;
1023        mso-add-space:auto;
1024        mso-pagination:widow-orphan;
1025        font-size:12.0pt;
1026        font-family:"Times New Roman",serif;
1027        mso-fareast-font-family:"Times New Roman";
1028        mso-fareast-theme-font:minor-fareast;}
1029p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
1030        {mso-style-noshow:yes;
1031        mso-style-priority:34;
1032        mso-style-unhide:no;
1033        mso-style-qformat:yes;
1034        mso-style-type:export-only;
1035        margin-top:0in;
1036        margin-right:0in;
1037        margin-bottom:0in;
1038        margin-left:.5in;
1039        margin-bottom:.0001pt;
1040        mso-add-space:auto;
1041        mso-pagination:widow-orphan;
1042        font-size:12.0pt;
1043        font-family:"Times New Roman",serif;
1044        mso-fareast-font-family:"Times New Roman";
1045        mso-fareast-theme-font:minor-fareast;}
1046p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
1047        {mso-style-noshow:yes;
1048        mso-style-priority:34;
1049        mso-style-unhide:no;
1050        mso-style-qformat:yes;
1051        mso-style-type:export-only;
1052        margin-top:0in;
1053        margin-right:0in;
1054        margin-bottom:0in;
1055        margin-left:.5in;
1056        margin-bottom:.0001pt;
1057        mso-add-space:auto;
1058        mso-pagination:widow-orphan;
1059        font-size:12.0pt;
1060        font-family:"Times New Roman",serif;
1061        mso-fareast-font-family:"Times New Roman";
1062        mso-fareast-theme-font:minor-fareast;}
1063span.MsoIntenseReference
1064        {mso-style-priority:32;
1065        mso-style-unhide:no;
1066        mso-style-qformat:yes;
1067        font-variant:small-caps;
1068        color:#C0504D;
1069        mso-themecolor:accent2;
1070        letter-spacing:.25pt;
1071        font-weight:bold;
1072        text-decoration:underline;
1073        text-underline:single;}
1074span.Heading1Char
1075        {mso-style-name:"Heading 1 Char";
1076        mso-style-priority:9;
1077        mso-style-unhide:no;
1078        mso-style-locked:yes;
1079        mso-style-link:"Heading 1";
1080        mso-ansi-font-size:24.0pt;
1081        mso-bidi-font-size:24.0pt;
1082        font-family:"Times New Roman",serif;
1083        mso-ascii-font-family:"Times New Roman";
1084        mso-fareast-font-family:"Times New Roman";
1085        mso-fareast-theme-font:minor-fareast;
1086        mso-hansi-font-family:"Times New Roman";
1087        mso-bidi-font-family:"Times New Roman";
1088        mso-font-kerning:18.0pt;
1089        font-weight:bold;}
1090span.Heading2Char
1091        {mso-style-name:"Heading 2 Char";
1092        mso-style-noshow:yes;
1093        mso-style-priority:9;
1094        mso-style-unhide:no;
1095        mso-style-locked:yes;
1096        mso-style-link:"Heading 2";
1097        mso-ansi-font-size:18.0pt;
1098        mso-bidi-font-size:18.0pt;
1099        font-family:"Times New Roman",serif;
1100        mso-ascii-font-family:"Times New Roman";
1101        mso-fareast-font-family:"Times New Roman";
1102        mso-fareast-theme-font:minor-fareast;
1103        mso-hansi-font-family:"Times New Roman";
1104        mso-bidi-font-family:"Times New Roman";
1105        font-weight:bold;}
1106span.Heading3Char
1107        {mso-style-name:"Heading 3 Char";
1108        mso-style-noshow:yes;
1109        mso-style-priority:9;
1110        mso-style-unhide:no;
1111        mso-style-locked:yes;
1112        mso-style-link:"Heading 3";
1113        mso-ansi-font-size:13.5pt;
1114        mso-bidi-font-size:13.5pt;
1115        font-family:"Times New Roman",serif;
1116        mso-ascii-font-family:"Times New Roman";
1117        mso-fareast-font-family:"Times New Roman";
1118        mso-fareast-theme-font:minor-fareast;
1119        mso-hansi-font-family:"Times New Roman";
1120        mso-bidi-font-family:"Times New Roman";
1121        font-weight:bold;}
1122span.Heading4Char
1123        {mso-style-name:"Heading 4 Char";
1124        mso-style-noshow:yes;
1125        mso-style-priority:9;
1126        mso-style-unhide:no;
1127        mso-style-locked:yes;
1128        mso-style-link:"Heading 4";
1129        mso-ansi-font-size:13.0pt;
1130        mso-bidi-font-size:13.0pt;
1131        font-family:"Cambria",serif;
1132        mso-ascii-font-family:Cambria;
1133        mso-ascii-theme-font:major-latin;
1134        mso-fareast-font-family:"Times New Roman";
1135        mso-fareast-theme-font:major-fareast;
1136        mso-hansi-font-family:Cambria;
1137        mso-hansi-theme-font:major-latin;
1138        mso-bidi-font-family:"Times New Roman";
1139        mso-bidi-theme-font:major-bidi;
1140        color:#4F81BD;
1141        mso-themecolor:accent1;
1142        font-weight:bold;
1143        font-style:italic;}
1144span.Heading5Char
1145        {mso-style-name:"Heading 5 Char";
1146        mso-style-noshow:yes;
1147        mso-style-priority:9;
1148        mso-style-unhide:no;
1149        mso-style-locked:yes;
1150        mso-style-link:"Heading 5";
1151        mso-ansi-font-size:12.0pt;
1152        mso-bidi-font-size:12.0pt;
1153        font-family:"Times New Roman",serif;
1154        mso-ascii-font-family:"Times New Roman";
1155        mso-fareast-font-family:"Times New Roman";
1156        mso-fareast-theme-font:minor-fareast;
1157        mso-hansi-font-family:"Times New Roman";
1158        mso-bidi-font-family:"Times New Roman";
1159        color:#4F4FFF;
1160        font-weight:bold;}
1161span.HTMLPreformattedChar
1162        {mso-style-name:"HTML Preformatted Char";
1163        mso-style-noshow:yes;
1164        mso-style-priority:99;
1165        mso-style-unhide:no;
1166        mso-style-locked:yes;
1167        mso-style-link:"HTML Preformatted";
1168        font-family:"Courier New";
1169        mso-ascii-font-family:"Courier New";
1170        mso-fareast-font-family:"Times New Roman";
1171        mso-hansi-font-family:"Courier New";
1172        mso-bidi-font-family:"Courier New";}
1173p.msonormal0, li.msonormal0, div.msonormal0
1174        {mso-style-name:msonormal;
1175        mso-style-noshow:yes;
1176        mso-style-priority:99;
1177        mso-style-unhide:no;
1178        mso-margin-top-alt:auto;
1179        margin-right:0in;
1180        mso-margin-bottom-alt:auto;
1181        margin-left:0in;
1182        mso-pagination:widow-orphan;
1183        font-size:12.0pt;
1184        font-family:"Times New Roman",serif;
1185        mso-fareast-font-family:"Times New Roman";
1186        mso-fareast-theme-font:minor-fareast;}
1187span.TitleChar
1188        {mso-style-name:"Title Char";
1189        mso-style-priority:10;
1190        mso-style-unhide:no;
1191        mso-style-locked:yes;
1192        mso-style-link:Title;
1193        mso-ansi-font-size:26.0pt;
1194        mso-bidi-font-size:26.0pt;
1195        font-family:"Cambria",serif;
1196        mso-ascii-font-family:Cambria;
1197        mso-ascii-theme-font:major-latin;
1198        mso-fareast-font-family:"Times New Roman";
1199        mso-fareast-theme-font:major-fareast;
1200        mso-hansi-font-family:Cambria;
1201        mso-hansi-theme-font:major-latin;
1202        mso-bidi-font-family:"Times New Roman";
1203        mso-bidi-theme-font:major-bidi;
1204        color:#17365D;
1205        mso-themecolor:text2;
1206        mso-themeshade:191;
1207        letter-spacing:.25pt;
1208        mso-font-kerning:14.0pt;}
1209span.DocumentMapChar
1210        {mso-style-name:"Document Map Char";
1211        mso-style-noshow:yes;
1212        mso-style-priority:99;
1213        mso-style-unhide:no;
1214        mso-style-locked:yes;
1215        mso-style-link:"Document Map";
1216        mso-ansi-font-size:8.0pt;
1217        mso-bidi-font-size:8.0pt;
1218        font-family:"Tahoma",sans-serif;
1219        mso-ascii-font-family:Tahoma;
1220        mso-fareast-font-family:"Times New Roman";
1221        mso-fareast-theme-font:minor-fareast;
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1458</head>
1459
1460<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1461
1462<div class=WordSection1>
1463
1464<h1>Fit Peaks/<span class=SpellE>Autoindexing</span> in GSAS-II </h1>
1465
1466<p class=MsoNormal>In this exercise you will use GSAS-II to search for a unit
1467cell that matches a set of diffraction peaks -- a process known as
1468auto-indexing. First peaks must be located and optimized and then indexing can
1469be done.</p>
1470
1471<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1472
1473<h2>Step 1: Read in the data file</h2>
1474
1475<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1476style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1477style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1478the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1479mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1480minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1481to read the data file into the current GSAS-II project. This read option is set
1482to read any of the powder data formats defined for GSAS (angles in <span
1483class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
1484the <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'>cif</span></b></span>
1487format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1488style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1489mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1490format (angles in degrees) used by <span class=SpellE>Topas</span>, etc.<span
1491style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1492directory to <b style='mso-bidi-font-weight:normal'><span style='=======
1493data file</span></b> menu item to read the data file into the current GSAS-II project.
1494This read option is set to read any of the powder data formats defined for GSAS
1495(angles in <span class=SpellE>centidegrees</span>, TOF in µsec). Other submenu
1496items will read the <span class=SpellE><b style='
1497'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1498mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></span></b>
1499format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1500style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1501mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1502format (angles in degrees) used by <span class=SpellE>Topas</span>, etc. to see
1503them. Because you used <span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1504minor-latin'>the </span><b style='mso-bidi-font-weight:normal'><span
1505style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1506mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1507minor-latin'>Help/Download tutorial</span></b><span style='mso-fareast-font-family:
1508Calibri;mso-fareast-theme-font:minor-latin'> menu entry to open this page and
1509downloaded the exercise files (recommended), then the </span><span
1510class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1511"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1512Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>FitPeaks</span></b></span><b
1513style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1514mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1515minor-latin;mso-hansi-theme-font:minor-latin'>/data/...</span></b><span
1516style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1517entry will bring you to the location where the files have been downloaded. (It
1518is also possible to download them manually from <a
1519href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
1520In this case you will need to navigate to the download location manually.)<br>
1521For this tutorial you should see the data file in the file browser, but if
1522extensions on data files are not the expected ones, you may need to change the
1523file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find
1524the desired file.</span></p>
1525
1526<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1527style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1528style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1529the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1530mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1531minor-latin'>11bmb_3844.fxye</span></b><span style='font-family:"Calibri",sans-serif;
1532mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1533minor-latin'> data</span> file in the first dialog and press <b
1534style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1535mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1536minor-latin'>Open</span></b>. There will be a Dialog box asking <b
1537style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1538mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1539minor-latin'>Is this the file you want?</span></b> Press <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'>Yes</span></b>
1542button to proceed.</p>
1543
1544<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1545style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1546style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>The
1547file <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1548mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1549minor-latin'>11bmb_3844.prm</span></b> instrument parameter file is
1550automatically selected; it was produced by 11BM-B instrument processing
1551software when the corresponding <span class=SpellE><b style='mso-bidi-font-weight:
1552normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1553minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fxye</span></b></span>
1554file was created from the 12 detector raw data. If absent or the name doesn’t
1555match the data file name, a file dialog will appear for you to select the
1556correct instrument parameter file.</p>
1557
1558<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1559style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1560mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II data
1561tree</span></b> window will have several entries </p>
1562
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1588
1589<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1590powder pattern</p>
1591
1592<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1593 id="Picture_x0020_28" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:397.5pt;
1594 height:340.5pt;visibility:visible;mso-wrap-style:square'>
1595 <v:imagedata src="Fit%20Peaks_files/image003.png" o:title=""/>
1596</v:shape><![endif]--><![if !vml]><img border=0 width=530 height=454
1597src="Fit%20Peaks_files/image049.png" v:shapes="Picture_x0020_28"><![endif]></span></p>
1598
1599<h2>Step 2: Select Limits </h2>
1600
1601<p class=MsoNormal><span style='mso-spacerun:yes'> </span>This pattern has much
1602more data than we need, so it is helpful to cut down the range. Click on the <b
1603style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1604mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1605minor-latin'>Limits</span></b> item in the <b style='mso-bidi-font-weight:normal'><span
1606style='<<<<<<< .mine
1607mso-hansi-theme-font:minor-latin'><span style='font-family:
1608"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1609data tree</span></span></b>. Use the <b style='mso-bidi-font-weight:normal'><span
1610style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1611mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>New:</span></b>
1612row of entry boxes to set <span class=SpellE><b style='mso-bidi-font-weight:
1613normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1614minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmin</span></b></span>
1615and <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1616style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1617mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Tmax</span></b></span>
1618to <b style='mso-bidi-font-weight:normal'><span style='<<<<<<< .mine
1619mso-ascii-theme-font:minor-latin'><span
1620style='font-family:"Calibri",sans-serif;mso-hansi-theme-font:minor-latin;
1621mso-bidi-theme-font:minor-latin'>4</span></span></b> and <b style='mso-bidi-font-weight:
1622normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1623minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>27.5</span></b>.
1624Notice on the plot that the limit lines have moved to these positions; the
1625green lower limit is just below the 1<sup>st</sup> peak and the red upper limit
1626is in a wide gap between peaks. You may also drag the limit lines to the
1627desired location or place them by a left mouse click on a data point for the
1628lower limit or a right click on a data point for the upper limit.</p>
1629
1630<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1631 id="Picture_x0020_30" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:446.25pt;
1632 height:224.25pt;visibility:visible;mso-wrap-style:square'>
1633 <v:imagedata src="Fit%20Peaks_files/image005.png" o:title=""/>
1634</v:shape><![endif]--><![if !vml]><img border=0 width=595 height=299
1635src="Fit%20Peaks_files/image005.png" v:shapes="Picture_x0020_30"><![endif]></span></p>
1636
1637<h2>Step 3: Determine Peak Positions</h2>
1638
1639<p class=MsoListParagraphCxSpFirst style='margin-left:39.0pt;mso-add-space:
1640auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1641style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1642style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1643on the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1645minor-latin'>Peak List</span></b> item in the <b style='mso-bidi-font-weight:
1646normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1647minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>GSAS-II
1648data tree</span></b>. This creates an empty window of peak positions (the <b
1649style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1651minor-latin'>Limits</span></b> window is erased). At this point it is wise to
1652zoom in on the data that will be used for indexing. </p>
1653
1654<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1655auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1656style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1657style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Click
1658on the Zoom button (5<sup>th</sup> one from the left on the plot toolbar), then
1659press the left mouse in one corner of the region to be used; holding the mouse
1660button down, drag over the region to the opposite corner; a box will be drawn
1661over the region to be zoomed and the plot will be redrawn with the new limits.
1662The toolbar has a number of buttons to the right of the help button (‘?’) that
1663can be used to incrementally change the view.</p>
1664
1665<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1666auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1667style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1668style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1669style='mso-bidi-font-weight:normal'>Important</b>: Click on the Zoom button
1670again to turn off the zoom mode. </p>
1671
1672<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1673auto;text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1674style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1675style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Under
1676<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1677mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting</span></b>
1678in the menu select <b style='mso-bidi-font-weight:normal'><span
1679style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1680mso-hansi-theme-font:minor-latin'>Auto search</span></b>. The plot window will
1681immediately show that all peaks were picked with a blue vertical line on each
1682one</p>
1683
1684<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1685auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_31"
1686 o:spid="_x0000_i1046" type="#_x0000_t75" style='width:395.25pt;height:339pt;
1687 visibility:visible;mso-wrap-style:square'>
1688 <v:imagedata src="Fit%20Peaks_files/image006.png" o:title=""/>
1689</v:shape><![endif]--><![if !vml]><img border=0 width=527 height=452
1690src="Fit%20Peaks_files/image050.png" v:shapes="Picture_x0020_31"><![endif]></span></p>
1691
1692<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1693auto'><span class=GramE>and</span> peaks are shown in the <b style='mso-bidi-font-weight:
1694normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1695minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1696List</span></b> window in order of increasing 2<span style='font-family:Symbol'>Q</span>.</p>
1697
1698<p class=MsoListParagraphCxSpMiddle style='margin-left:39.0pt;mso-add-space:
1699auto'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32"
1700 o:spid="_x0000_i1045" type="#_x0000_t75" style='width:426pt;height:198.75pt;
1701 visibility:visible;mso-wrap-style:square'>
1702 <v:imagedata src="Fit%20Peaks_files/image008.png" o:title=""/>
1703</v:shape><![endif]--><![if !vml]><img border=0 width=568 height=265
1704src="Fit%20Peaks_files/image051.png" v:shapes="Picture_x0020_32"><![endif]></span></p>
1705
1706<p class=MsoListParagraphCxSpLast style='margin-left:39.0pt;mso-add-space:auto'>There
1707will be 20 peaks in this example. You should examine both the list and the plot
1708to be sure the auto search did not pick a peak twice (rarely) or skip a peak or
1709shoulder. You can add a peak to the list by pressing the left mouse button with
1710the pointer on a data point at the peak top or shoulder; be sure the zoom/shift
1711buttons are off. You may drag a peak position as needed. A position may be
1712deleted with a right click with the mouse on the blue line. You can also delete
1713a peak by selecting the row in the table; it will be highlighted in blue. Then
1714press the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1715mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Delete</span></b>
1716key; it will be removed from the table and the plot. The list will always show
1717the peaks sorted by position. When done you should have 20 unique peak
1718positions.</p>
1719
1720<h2>Step 4: Refine Peak Positions</h2>
1721
1722<p class=MsoNormal>This refinement proceeds stepwise; first doing the default
1723refinement and then adding parameters to complete the fitting,</p>
1724
1725<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1726style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1727style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Refine
1728the peak intensities and the background. These parameters have their refinement
1729flags turned on by default. Use the menu item <b style='mso-bidi-font-weight:
1730normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1731minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1732Fitting/<span class=SpellE>Peakfit</span></span></b>. Do <b style='mso-bidi-font-weight:
1733normal'>NOT</b> use the <b style='mso-bidi-font-weight:normal'><span
1734style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1735mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b>
1736menu item; that it to be used for Rietveld/Pawley refinements. You will be
1737asked to save the current project before the fit will proceed; change directory
1738if desired and provide a suitable name (we assume <b style='mso-bidi-font-weight:
1739normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1740minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>LaB6</span></b>).
1741A window will show the progress of the refinement and will close when the
1742least-squares fit is complete (usually very fast). The plot is updated with the
1743fit, the peak list window is updated with the new peak values and a summary of
1744the refinement is shown on the console window as well.</p>
1745
1746<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1747 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:407.25pt;
1748 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1749 <v:imagedata src="Fit%20Peaks_files/image010.png" o:title=""/>
1750</v:shape><![endif]--><![if !vml]><img border=0 width=543 height=466
1751src="Fit%20Peaks_files/image052.png" v:shapes="Picture_x0020_33"><![endif]></span></p>
1752
1753<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1754 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:420pt;
1755 height:195.75pt;visibility:visible;mso-wrap-style:square'>
1756 <v:imagedata src="Fit%20Peaks_files/image012.png" o:title=""/>
1757</v:shape><![endif]--><![if !vml]><img border=0 width=560 height=261
1758src="Fit%20Peaks_files/image053.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1759
1760<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1761style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1762style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Now
1763add refinement of the peak positions. This can be done by clicking on all the
1764refinement flags for the individual peaks or it is possible to set them all at
1765the same time using this recipe: </p>
1766
1767<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1768auto;text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1769style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1770style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1771on any value in the table to select it, for example the first peak position. A
1772black box appears around the value. </p>
1773
1774<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1775text-indent:-.25in;mso-list:l2 level2 lfo6'><![if !supportLists]><span
1776style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1777style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>single-click
1778on the <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'>refine</span></b>
1780label above the peak position check-boxes. The entire column of checkboxes is
1781highlighted in blue. Press the <b style='mso-bidi-font-weight:normal'><span
1782style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1783mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>y</span></b>
1784key to turn on all refinement flags (<b style='mso-bidi-font-weight:normal'><span
1785style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1786mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>n</span></b>
1787would turn them off).</p>
1788
1789<p class=MsoNormal style='margin-left:.5in'>Next, repeat the refinement using
1790the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1791mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1792minor-latin'>Peak Fitting/<span class=SpellE>Peakfit</span></span></b> menu
1793item.</p>
1794
1795<p class=MsoNormal style='margin-left:.5in'>Now, select peak widths for
1796refinement. <span style='mso-fareast-font-family:"Times New Roman"'>This can be
1797performed in 2 different ways. &nbsp;Method&nbsp;1:&nbsp;refine sigma (Gaussian
1798width) and/or gamma (Lorentzian width) for individual peaks. &nbsp;To do this,
1799click the refinement flags for sigma and/or gamma in the Peak List window.
1800&nbsp;&nbsp;Method&nbsp;2: preferably,&nbsp;the LS&nbsp;refinement of&nbsp;peak
1801widths can be&nbsp;constrained to&nbsp;follow an instrumental broadening equation
1802as described below.&nbsp;Note - one cannot refine ALL peak widths using both
1803individual&nbsp;sigma &amp; gamma&nbsp;values AND&nbsp;instrumental broadening
1804terms at the same time.<b style='mso-bidi-font-weight:normal'>&nbsp;</b><o:p></o:p></span></p>
1805
1806<p class=MsoNormal style='margin-left:.5in'><span style='mso-fareast-font-family:
1807"Times New Roman";mso-bidi-font-weight:bold'>To constrain refined peak widths
1808to an instrumental broadening equation, first<b> s</b></span>elect the <b
1809style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1810mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1811minor-latin'>Instrumental Parameters</span></b> item in the data tree. This
1812opens a window for peak profile terms<b> </b><span style='mso-bidi-font-weight:
1813bold'>and also creates a new plot window&nbsp;showing the instrument profile
1814resolution curve.</span></p>
1815
1816<p class=MsoNormal style='margin-left:.5in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1817 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:415.5pt;
1818 height:298.5pt;visibility:visible;mso-wrap-style:square'>
1819 <v:imagedata src="Fit%20Peaks_files/image014.png" o:title=""/>
1820</v:shape><![endif]--><![if !vml]><img border=0 width=554 height=398
1821src="Fit%20Peaks_files/image014.png" v:shapes="Picture_x0020_35"><![endif]></span></p>
1822
1823<p class=MsoListParagraphCxSpFirst>The plot window shows the resolution curves
1824corresponding to the values of the Gaussian U, V, W, Lorentzian X &amp; Y
1825coefficients; ‘+’ marks show the individual values based on the sig &amp; gam
1826values for the peaks in Peak List. Select the refine flag checkbox for Gaussian
1827<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1828mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1829minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
1830style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1831mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
1832<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1833mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1834minor-latin'>W</span></b>, and Lorentzian <b style='mso-bidi-font-weight:normal'><span
1835style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1836mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
1837<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1838mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1839minor-latin'>Y</span></b>. </p>
1840
1841<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l2 level1 lfo6'><![if !supportLists]><span
1842style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1843style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Then,
1844repeat the refinement. First click on the <b style='mso-bidi-font-weight:normal'><span
1845style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1846mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>
1847item in the data tree and then refine using the <b style='mso-bidi-font-weight:
1848normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1849minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1850Fitting/<span class=SpellE>Peakfit</span></span></b> menu item. At this point a
1851good fit should be seen by zooming in on individual peaks. For example see </p>
1852
1853<p class=MsoListParagraphCxSpMiddle><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1854 id="Picture_x0020_36" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:408pt;
1855 height:349.5pt;visibility:visible;mso-wrap-style:square'>
1856 <v:imagedata src="Fit%20Peaks_files/image015.png" o:title=""/>
1857</v:shape><![endif]--><![if !vml]><img border=0 width=544 height=466
1858src="Fit%20Peaks_files/image054.png" v:shapes="Picture_x0020_36"><![endif]></span></p>
1859
1860<p class=MsoListParagraphCxSpLast>Notice that the peak position is slightly to
1861the right of the peak top. This is a consequence of the peak asymmetry arising
1862from axial divergence in the diffractometer. The <span class=SpellE>Rwp</span>
1863is ~7% as shown on the console window. Again the <b style='mso-bidi-font-weight:
1864normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1865minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak
1866List</span></b> entries are all updated with new values and those in <b
1867style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1868mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1869minor-latin'>Instrument Parameters</span></b> are also updated.</p>
1870
1871<h2>Step 5. Prepare Indexing Peak List</h2>
1872
1873<p class=MsoNormal>A separate list of peaks is kept for use in <span
1874class=SpellE>autoindexing</span>. It is found in the <b style='mso-bidi-font-weight:
1875normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1876minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Index
1877Peak List</span></b> item in the data tree. In the initially empty window
1878created by this action, use menu item <b style='mso-bidi-font-weight:normal'><span
1879style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1880mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1881to copy the fitted peaks from the <b style='mso-bidi-font-weight:normal'><span
1882style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1883mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Peak List</span></b>.</p>
1884
1885<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1886 id="Picture_x0020_37" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:431.25pt;
1887 height:309.75pt;visibility:visible;mso-wrap-style:square'>
1888 <v:imagedata src="Fit%20Peaks_files/image017.png" o:title=""/>
1889</v:shape><![endif]--><![if !vml]><img border=0 width=575 height=413
1890src="Fit%20Peaks_files/image017.png" v:shapes="Picture_x0020_37"><![endif]></span></p>
1891
1892<p class=MsoNormal>Note that by default all peaks are selected to be used. You
1893may choose to not use a fitted peak (e.g. if suspected it is from a
1894contaminant).</p>
1895
1896<h2>Step 6. Run <span class=SpellE>Autoindexing</span></h2>
1897
1898<p class=MsoNormal>Select the <b style='mso-bidi-font-weight:normal'><span
1899style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1900mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit Cells
1901List</span></b> data item. This brings up a window for indexing and cell
1902refinement options</p>
1903
1904<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1905 id="Picture_x0020_38" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;
1906 height:157.5pt;visibility:visible;mso-wrap-style:square'>
1907 <v:imagedata src="Fit%20Peaks_files/image018.png" o:title=""/>
1908</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=210
1909src="Fit%20Peaks_files/image055.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
1910
1911<p class=MsoNormal>For the most rapid search (since we know the right answer),
1912select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1913mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1914minor-latin'>Cubic-P</span></b> and launch the search using menu item <b
1915style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1916mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1917minor-latin'>Cell Index/Refine/Index Cell</span></b>. The search then runs and the
1918console shows a running list of possible cells as they are found; the sorted by
1919M20 list of possible matching cells is shown in the <b style='mso-bidi-font-weight:
1920normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1921minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
1922Cells List</span></b> window</p>
1923
1924<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1925 id="Picture_x0020_13" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1926 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1927 <v:imagedata src="Fit%20Peaks_files/image020.png" o:title=""/>
1928</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1929src="Fit%20Peaks_files/image056.png" v:shapes="Picture_x0020_13"><![endif]></span></p>
1930
1931<h2>Step 7. Review Cell Choices</h2>
1932
1933<p class=MsoNormal>Review the list of cells associated with the <b
1934style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1935mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1936minor-latin'>Unit Cells List</span></b> data item. Note that as one selects a
1937unit cell, the generated reflections for that cell are shown in the plot with
1938dashed red lines. Sliding the cursor over these lines shows a small popup
1939window with the indexed <span class=SpellE>hkl</span> for them. Note how the
1940first cell in the list (M20~2970) with a=5.87864 Å generates very many lines
1941with no corresponding peaks (NB: this solution might not always show up!)</p>
1942
1943<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1944 id="Picture_x0020_40" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:447pt;
1945 height:383.25pt;visibility:visible;mso-wrap-style:square'>
1946 <v:imagedata src="Fit%20Peaks_files/image022.png" o:title=""/>
1947</v:shape><![endif]--><![if !vml]><img border=0 width=596 height=511
1948src="Fit%20Peaks_files/image057.png" v:shapes="Picture_x0020_40"><![endif]></span><span
1949style='mso-spacerun:yes'> </span></p>
1950
1951<p class=MsoNormal>while the (M20~600) cell with a=2.93932 Å generates not
1952enough lines to match all the peaks</p>
1953
1954<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1955 id="Picture_x0020_41" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:428.25pt;
1956 height:366.75pt;visibility:visible;mso-wrap-style:square'>
1957 <v:imagedata src="Fit%20Peaks_files/image024.png" o:title=""/>
1958</v:shape><![endif]--><![if !vml]><img border=0 width=571 height=489
1959src="Fit%20Peaks_files/image058.png" v:shapes="Picture_x0020_41"><![endif]></span></p>
1960
1961<h2>Step 8. Select/Refine Cell</h2>
1962
1963<p class=MsoNormal>Select the cell with M20 ~ 2970 with a = 4.15683 Å. This
1964indexes all peaks with almost a perfect fit to the peak positions (compare
1965dashed red lines to solid blue ones). Import the cell information using the <b
1966style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1967mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1968minor-latin'>Cell Index/Refine/Copy Cell</span></b> menu option. Then optimize
1969the cell by refining the lattice parameters and the two-theta zero: click on
1970the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1971mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
1972checkbox next to the <b style='mso-bidi-font-weight:normal'><span
1973style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1974mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
1975value and then the <b style='mso-bidi-font-weight:normal'><span
1976style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1977mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
1978Index/Refine/Refine Cell</span></b> menu option. The M20 improves to ~3600 and <span
1979class=GramE>the a</span> cell parameter value shifts from 4.15683 to 4.15691
1980when zero is refined. (NB: The certificate value for NIST SRM 660a is 4.15692
1981Å). Press the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1982"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1983minor-latin;mso-bidi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span>
1984positions </span></b>button to update the plot including the refined <b
1985style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1986mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1987minor-latin'>Zero offset</span></b> (in this case hardly anything
1988happens!).<span style='mso-spacerun:yes'>  </span></p>
1989
1990<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1991 id="Picture_x0020_42" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1992 height:222.75pt;visibility:visible;mso-wrap-style:square'>
1993 <v:imagedata src="Fit%20Peaks_files/image026.png" o:title=""/>
1994</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=297
1995src="Fit%20Peaks_files/image059.png" v:shapes="Picture_x0020_42"><![endif]></span></p>
1996
1997<p class=MsoNormal>Notice that a new entry heads the list in the <b
1998style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1999mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2000minor-latin'>Indexing Result</span></b> section of the <b style='mso-bidi-font-weight:
2001normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2002minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Unit
2003Cells List</span></b> window with an improved <span class=GramE>M20(</span>~3600)
2004and a new value for <b style='mso-bidi-font-weight:normal'><span
2005style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2006mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Zero offset</span></b>
2007is shown. NB: the <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>
2010button has an additional use; you can enter the <span class=SpellE><b
2011style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2012mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bravais</span></b></span><b
2013style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2014mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> lattice</span></b>,
2015<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2016mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Space group</span></b>
2017&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2018mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Unit cell</span></b>
2019for any material. Then pressing <b style='mso-bidi-font-weight:normal'><span
2020style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2021mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2022will use that cell to index the lines in <b style='mso-bidi-font-weight:normal'><span
2023style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2024mso-hansi-theme-font:minor-latin'>Index Peak List</span></b>. This might be
2025useful to identify e.g. a second phase in your pattern.</p>
2026
2027<p class=MsoNormal>(Optional) Finally, use of the <b style='mso-bidi-font-weight:
2028normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2029minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cell
2030Index/Refine/Make new phase</span></b> menu option allows one to create a phase
2031with these lattice parameters in the data tree under <b style='mso-bidi-font-weight:
2032normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2033minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>.<span
2034style='mso-spacerun:yes'>  </span>A name for the new phase is requested. This
2035creates the tree item <b style='mso-bidi-font-weight:normal'><span
2036style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2037mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases</span></b>
2038(if it wasn’t already present). This new phase can be used in future analysis
2039(e.g. Rietveld or Pawley refinement).</p>
2040
2041<p class=MsoNormal>To continue with the second part of this exercise, select
2042the menu item <b style='mso-bidi-font-weight:normal'><span style='font-family:
2043"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2044minor-latin;mso-bidi-theme-font:minor-latin'>File/New project</span></b> in the
2045<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2046mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2047minor-latin'>GSAS-II data tree </span></b>window. You will be asked if you want
2048the current project saved; if <b style='mso-bidi-font-weight:normal'><span
2049style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2050mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
2051then all the peak fitting/indexing &amp; cell refinement results will be saved
2052to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2053mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2054minor-latin'>LaB6.gpx</span></b> file. If <b style='mso-bidi-font-weight:normal'><span
2055style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2056mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>No</span></b>
2057then the file will remain as it was when created at Step 4 above.</p>
2058
2059<h1><a name="kryptonite_peak_fit">2<sup>nd</sup> Fit Peaks/</a><span
2060class=SpellE><span style='mso-bookmark:kryptonite_peak_fit'>Autoindexing</span></span><span
2061style='mso-bookmark:kryptonite_peak_fit'> in GSAS-II</span> </h1>
2062
2063<p class=MsoNormal>In this exercise we will fit peaks and index them for the
2064mineral <a href="http://en.wikipedia.org/wiki/Jadarite">jadarite</a> (aka “<a
2065href="http://en.wikipedia.org/wiki/Kryptonite">kryptonite</a>”). The data were
2066also collected on 11BM-B at APS. The unit cell is monoclinic so it is a more
2067substantial test of the indexing capability of GSAS-II. The required data files
2068should have been downloaded when you downloaded this tutorial. Otherwise you
2069will need to get them manually from <span style='mso-fareast-font-family:Calibri;
2070mso-fareast-theme-font:minor-latin'><a
2071href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2072Be sure to get both </span><b style='mso-bidi-font-weight:normal'><span
2073style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2074mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2075minor-latin'>11bmb_6231.fxye</span></b><span style='mso-fareast-font-family:
2076Calibri;mso-fareast-theme-font:minor-latin'> and </span><b style='mso-bidi-font-weight:
2077normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2078minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2079mso-hansi-theme-font:minor-latin'>11bmb_6231.prm</span></b></p>
2080
2081<h2>Step 1. Read in the data. </h2>
2082
2083<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2084normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2085minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2086style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2087mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2088minor-latin'>\data\11bmb_6231.fxye</span></b>; it has a corresponding <span
2089class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2090"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2091minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file. Load
2092them in &amp; the plot is</p>
2093
2094<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2095 id="Picture_x0020_43" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:405pt;
2096 height:347.25pt;visibility:visible;mso-wrap-style:square'>
2097 <v:imagedata src="Fit%20Peaks_files/image028.png" o:title=""/>
2098</v:shape><![endif]--><![if !vml]><img border=0 width=540 height=463
2099src="Fit%20Peaks_files/image060.png" v:shapes="Picture_x0020_43"><![endif]></span></p>
2100
2101<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2102lower part of the pattern.</p>
2103
2104<h2>Step 2 Set limits</h2>
2105
2106<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2107style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2108mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>3</span></b>
2109and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2110mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2111minor-latin'>9</span></b>. This will give a suitable number of lines for
2112indexing.</p>
2113
2114<h2>Step 3 Pick peaks</h2>
2115
2116<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2117small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2118"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2119minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2120peaks by left-clicking on a data point near the top of the peak. Peak positions
2121can be moved by dragging the peak line and peaks can be deleted by
2122right-clicking on them. This only works when the zoom and reposition modes
2123(below) are not selected. Also note some peaks have shoulders most notably at
21245.07, 6.04, 7.81deg. I found 28 peaks (there was one very weak shoulder at ~7.3
2125deg. I skipped – it might be from a second phase? We’ll see later).</p>
2126
2127<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2128 id="Picture_x0020_39" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:436.5pt;
2129 height:374.25pt;visibility:visible;mso-wrap-style:square'>
2130 <v:imagedata src="Fit%20Peaks_files/image030.png" o:title=""/>
2131</v:shape><![endif]--><![if !vml]><img border=0 width=582 height=499
2132src="Fit%20Peaks_files/image061.png" v:shapes="Picture_x0020_39"><![endif]></span><br
2133clear=all style='mso-special-character:line-break'>
2134</p>
2135
2136<h2>Step 4. Refine peaks</h2>
2137
2138<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> example
2139above, refine the peaks and the profile shape parameters in <b
2140style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2141mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2142minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2143file name at the first refinement (I used ‘<span class=SpellE><b
2144style='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'>jadarite</span></b></span><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'>’</span></b>).
2149In the end my refinement converged at <span class=SpellE>Rwp</span>=11.41% and
2150some peaks do show some discrepancy as the sample is more complex than the
2151simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2152mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2153minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2154style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2155mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2156<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2157mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2158minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2159style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2160mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2161<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2162mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2163minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away
2164during refinement (one weak one at ~6.67 is particularly troublesome). However,
2165this is good enough to proceed.</p>
2166
2167<h2>Step 5. Prepare Indexing Peak List</h2>
2168
2169<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2170style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2171mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2172in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2173mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2174minor-latin'>Index Peak List</span></b> window.</p>
2175
2176<h2>Step 6. Index the cell</h2>
2177
2178<p class=MsoNormal>Let’s assume that we know the cell is primitive monoclinic. In
2179a real world case we wouldn’t know this and we would have to try each <span
2180class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2181time to go through all the bad cases.</p>
2182
2183<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2184style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2185mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2186and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2187mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2188minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2189style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2190mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2191minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2192and suitable results will be slow in coming so be patient. Watch the console
2193window; the right answer will have an obviously large M20 (~380) and a volume
2194of ~594Å<sup>3</sup> (10<sup>th</sup> column of console display). Once this is
2195seen (it may take more than one try to get this) you can stop the indexing
2196search by pressing <b style='mso-bidi-font-weight:normal'><span
2197style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2198mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b>
2199on the progress bar window. Notice the ‘<b style='mso-bidi-font-weight:normal'><span
2200style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2201mso-hansi-theme-font:minor-latin'>keep</span></b>’ column; this allows you to
2202keep some solutions from one indexing run to the next. It may take more than
2203one press to fully stop it. My result was </p>
2204
2205<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2206 id="Picture_x0020_19" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:359.25pt;
2207 height:297pt;visibility:visible;mso-wrap-style:square'>
2208 <v:imagedata src="Fit%20Peaks_files/image032.png" o:title=""/>
2209</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=396
2210src="Fit%20Peaks_files/image062.png" v:shapes="Picture_x0020_19"><![endif]></span></p>
2211
2212<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2213 id="Picture_x0020_20" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
2214 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2215 <v:imagedata src="Fit%20Peaks_files/image034.png" o:title=""/>
2216</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2217src="Fit%20Peaks_files/image063.png" v:shapes="Picture_x0020_20"><![endif]></span></p>
2218
2219<p class=MsoNormal>Notice there may be other equally good M20 results with
2220different volumes; other solutions may be obtained as you keep trying the
2221indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2222style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2223mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2224new indexing runs. The best solution is the one with the smaller volume and
2225&#946; &gt; 90 deg. The plot shows every peak indexed including a weak peak not
2226selected for the peak fitting, although the weak peak at 2<span
2227style='font-family:Symbol;mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
2228style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>~7.3
2229has a shoulder that wasn’t indexed. I presume that is a contaminant. Copy the
2230best cell and try to refine it along with the <b style='mso-bidi-font-weight:
2231normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2232minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>. I
2233obtained an improved M20 ~444 and slightly different lattice parameters. Try
2234different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2235style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2236mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2237each time to see which lines vanish. By sliding the cursor over the index lines
2238without any visible peak you can see that the missing ones are 010, 100, 001,
2239110, 030, 111, 20-1, 10-2, 041, 050, 21-2 &amp; 23-1. Many of these are
2240accidental but the 0k0; k&#8800;2n and h0l; h+l&#8800;2n ones characterize the
2241space group P2<sub>1</sub>/n. Armed with this information you can <b
2242style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2243mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2244minor-latin'>Make new phase</span></b> for the indexed cell (I called it ‘<b
2245style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2246mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2247minor-latin'>kryptonite’</span></b>) and select <b style='mso-bidi-font-weight:
2248normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2249minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> from
2250the GSAS-II data tree.</p>
2251
2252<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2253 id="Picture_x0020_46" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
2254 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2255 <v:imagedata src="Fit%20Peaks_files/image036.png" o:title=""/>
2256</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2257src="Fit%20Peaks_files/image064.png" v:shapes="Picture_x0020_46"><![endif]></span><span
2258style='mso-spacerun:yes'> </span></p>
2259
2260<p class=MsoNormal>Notice that the lattice parameters and space group have been
2261set for you. </p>
2262
2263<p class=MsoNormal>This concludes this exercise; do <span class=GramE><b
2264style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2265mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2266minor-latin'>Save</span></b></span> <b style='mso-bidi-font-weight:normal'><span
2267style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2268mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>project</span></b>
2269as it is needed for the <b style='mso-bidi-font-weight:normal'><span
2270style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2271mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2272Flipping</span></b> <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'>in GSAS</span></b> exercise. The features of
2275the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2276mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2277minor-latin'>Phase Data</span></b> window will be presented in other exercises.</p>
2278
2279<h1><a name="sucrose_peak_fit"></a>3<sup>rd</sup> Fit Peaks/<span class=SpellE>Autoindexing</span>
2280in GSAS-II </h1>
2281
2282<p class=MsoNormal>In this exercise we will fit peaks and index them for sucrose
2283in preparation for a charge flipping exercise. If continuing from the previous
2284indexing example do <b style='mso-bidi-font-weight:normal'><span
2285style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2286mso-hansi-theme-font:minor-latin'>File/New project</span></b> from the main
2287GSAS-II data tree menu; you will be asked if you wish to save the old project.
2288The data were also collected on 11BM-B at APS. The unit cell is monoclinic so
2289is another more substantial test of the indexing capability of GSAS-II. The
2290required data files should have been downloaded when you downloaded this
2291tutorial. Otherwise you will need to get them manually from <span
2292style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><a
2293href="https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/">https://subversion.xray.aps.anl.gov/pyGSAS/Exercises/FitPeaks/</a>.
2294Be sure to get </span><b style='mso-bidi-font-weight:normal'><span
2295style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2296mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
2297minor-latin'>11bmb_8714.fxye<span class=GramE>, <span style='font-family:"Times New Roman",serif;
2298font-weight:normal'><span style='mso-spacerun:yes'> </span></span>11bmb</span>_8716.fxye</span></b><span
2299style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> and
2300the corresponding .<span class=SpellE>prm</span> files.</span></p>
2301
2302<h2>Step 1. Read in the data. </h2>
2303
2304<p class=MsoNormal>The file is <span class=SpellE><b style='mso-bidi-font-weight:
2305normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2306minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>FitPeaks</span></b></span><b
2307style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2308mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2309minor-latin'>\data\11bmb_8716.fxye</span></b>; it has a corresponding <span
2310class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2311"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2312minor-latin;mso-bidi-theme-font:minor-latin'>prm</span></b></span> file and is
2313for Domino® sugar ground under acetone. The other <span class=SpellE><b
2314style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2315mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>fxye</span></b></span>
2316file in this directory <b style='mso-bidi-font-weight:normal'><span
2317style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2318mso-hansi-theme-font:minor-latin'>11bmb_8714.fxye</span></b> is for Domino® 10X
2319powdered sugar used “as is” out of the box. Load the <b style='mso-bidi-font-weight:
2320normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2321minor-latin;mso-hansi-theme-font:minor-latin'>8716</span></b> file in &amp; the
2322plot is</p>
2323
2324<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2325 id="Picture_x0020_44" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:452.25pt;
2326 height:387.75pt;visibility:visible;mso-wrap-style:square'>
2327 <v:imagedata src="Fit%20Peaks_files/image038.png" o:title=""/>
2328</v:shape><![endif]--><![if !vml]><img border=0 width=603 height=517
2329src="Fit%20Peaks_files/image065.png" v:shapes="Picture_x0020_44"><![endif]></span></p>
2330
2331<p class=MsoNormal>I’ve zoomed in &amp; shifted the plot some to highlight the
2332lower part of the pattern; I’ve also chosen to plot the square root of the
2333intensity (use ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:
2334"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2335minor-latin'>S</span></b>’ key) as this shows weak peaks better.</p>
2336
2337<h2>Step 2 Set limits</h2>
2338
2339<p class=MsoNormal>Set the limits as <b style='mso-bidi-font-weight:normal'><span
2340style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2341mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>2</span></b>
2342and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2343mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2344minor-latin'>8</span></b>. Again, this gives a reasonable number of peaks for
2345indexing.</p>
2346
2347<h2>Step 3 Pick peaks</h2>
2348
2349<p class=MsoNormal>Pick all peaks you can see between the limits (including the
2350small ones); use <b style='mso-bidi-font-weight:normal'><span style='font-family:
2351"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2352minor-latin'>Auto search</span></b> to start and then fill in by hand: Add
2353peaks by left-clicking on a data point near the top of the peak. Peak positions
2354can be moved by dragging the peak line and peaks can be deleted by
2355right-clicking on them. This only works when the zoom and reposition modes
2356(below) are not selected. An easy to shift the view is to use the ‘&lt;’ and
2357‘&gt;’ buttons. Also note the shoulder at ~6.3 <span class=SpellE>deg</span>
2358that should be added to the list. I skipped a couple of very weak peaks; the
2359total list has &gt;28 peaks.</p>
2360
2361<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2362 id="Picture_x0020_45" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:465.75pt;
2363 height:399pt;visibility:visible;mso-wrap-style:square'>
2364 <v:imagedata src="Fit%20Peaks_files/image040.png" o:title=""/>
2365</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=532
2366src="Fit%20Peaks_files/image066.png" v:shapes="Picture_x0020_45"><![endif]></span><br
2367clear=all style='mso-special-character:line-break'>
2368</p>
2369
2370<h2>Step 4. Refine peaks</h2>
2371
2372<p class=MsoNormal>Following the steps used in the LaB<sub>6</sub> and
2373kryptonite examples above, refine the peaks and the profile shape parameters in
2374<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2375mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2376minor-latin'>Instrument Parameters</span></b>. You will be asked for a project
2377file name at the first refinement (I used ‘<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'>sucrose’</span></b>).
2380In the end my refinement converged at <span class=SpellE>Rwp</span>=6.69% and
2381some peaks do show some discrepancy as the sample is more complex than the
2382simple <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2383mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2384minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:normal'><span
2385style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2386mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>V</span></b>,
2387<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2388mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2389minor-latin'>W</span></b>, <b style='mso-bidi-font-weight:normal'><span
2390style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2391mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X</span></b>,
2392<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2394minor-latin'>Y</span></b> model can accommodate. Make sure no peaks drift away during
2395refinement. However, this is good enough to proceed.</p>
2396
2397<h2>Step 5. Prepare Indexing Peak List</h2>
2398
2399<p class=MsoNormal>As before do <b style='mso-bidi-font-weight:normal'><span
2400style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2401mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
2402in the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2403mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2404minor-latin'>Index Peak List</span></b> window.</p>
2405
2406<h2>Step 6. Index the cell</h2>
2407
2408<p class=MsoNormal>Let’s assume that we know the cell in primitive monoclinic.
2409In a real world case we wouldn’t know this and we would have to try each <span
2410class=SpellE>Bravais</span> lattice. These can be done as a group, but it takes
2411time to go through all the bad cases.</p>
2412
2413<p class=MsoNormal>Select <b style='mso-bidi-font-weight:normal'><span
2414style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2415mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Monoclinic-P</span></b>
2416and do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2417mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2418minor-latin'>Cell Index/Refine/Index cell</span></b> in the <b
2419style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2420mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2421minor-latin'>Unit Cells List</span></b> window. Progress will be much slower
2422than for LaB<sub>6</sub> but oddly much faster than for kryptonite and suitable
2423results may appear almost immediately. Watch the console window; the right
2424answer will have an obviously large M20 (~900) and a volume of ~704Å<sup>3</sup>
2425(10<sup>th</sup> column of console display). Once this is seen (it may take
2426more than one try to get this) you can stop the indexing search by pressing <b
2427style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2428mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2429minor-latin'>Cancel</span></b> on the progress bar window. Notice the ‘<b
2430style='mso-bidi-font-weight:normal'>keep’</b> column; this allows you to keep
2431some solutions from one indexing run to the next. It may take more than one
2432press to fully stop it. My result was </p>
2433
2434<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2435 id="Picture_x0020_24" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2436 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2437 <v:imagedata src="Fit%20Peaks_files/image042.png" o:title=""/>
2438</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2439src="Fit%20Peaks_files/image067.png" v:shapes="Picture_x0020_24"><![endif]><!--[if gte vml 1]><v:shape
2440 id="Picture_x0020_47" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:434.25pt;
2441 height:372pt;visibility:visible;mso-wrap-style:square'>
2442 <v:imagedata src="Fit%20Peaks_files/image044.png" o:title=""/>
2443</v:shape><![endif]--><![if !vml]><img border=0 width=579 height=496
2444src="Fit%20Peaks_files/image068.png" v:shapes="Picture_x0020_47"><![endif]></span></p>
2445
2446<p class=MsoNormal>Notice there may be other equally good M20 results with
2447different volumes; still other solutions may be obtained as you keep trying the
2448indexing. Be sure to use <b style='mso-bidi-font-weight:normal'><span
2449style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2450mso-hansi-theme-font:minor-latin'>Keep</span></b> to keep good ones as you try
2451new indexing runs. The best solution is the one with the smaller volume and
2452&#946; &gt; 90 <span class=SpellE>deg</span> and c&gt;a (I got both solutions!).
2453The plot shows every peak indexed including the weak peaks not selected for the
2454peak fitting. Copy the best cell and try to refine it along with the <b
2455style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2456mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Zero offset</span></b>.
2457I obtained an improved M20 ~1300 and slightly different lattice parameters. Try
2458different space groups, pressing the <b style='mso-bidi-font-weight:normal'><span
2459style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2460mso-hansi-theme-font:minor-latin'>Show <span class=SpellE>hkl</span> positions</span></b>
2461each time to see which lines vanish. The correct space group is P2<sub>1</sub>.
2462Armed with this information you can <b style='mso-bidi-font-weight:normal'><span
2463style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2464mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Make new
2465phase</span></b> for the indexed cell (I called it ‘<b style='mso-bidi-font-weight:
2466normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2467minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>sucrose</span></b>)
2468and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2469"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2470minor-latin'>Phases/sucrose</span></b> from the GSAS-II data tree.</p>
2471
2472<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2473 id="Picture_x0020_48" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2474 height:227.25pt;visibility:visible;mso-wrap-style:square'>
2475 <v:imagedata src="Fit%20Peaks_files/image046.png" o:title=""/>
2476</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=303
2477src="Fit%20Peaks_files/image069.png" v:shapes="Picture_x0020_48"><![endif]></span><span
2478style='mso-spacerun:yes'> </span></p>
2479
2480<p class=MsoNormal>Notice that the lattice parameters and space group have been
2481set for you. This concludes this exercise; <b style='mso-bidi-font-weight:normal'><span
2482style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2483mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b>
2484the project file as it is needed for the sucrose <b style='mso-bidi-font-weight:
2485normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2486minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Charge
2487Flipping</span></b> exercise. The features of the <b style='mso-bidi-font-weight:
2488normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2489minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phase
2490Data</span></b> window will be presented in other exercises.</p>
2491
2492<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2493
2494</div>
2495
2496</body>
2497
2498</html>
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