source: Tutorials/SeqRefine/SequentialTutorial.htm

Last change on this file was 5151, checked in by toby, 17 months ago

improve seq. ref. constraint warning
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415  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
416  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
417  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
418  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
419  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
420  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
421  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
422  <w:LsdException Locked="false" Priority="34" QFormat="true"
423   Name="List Paragraph"/>
424  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
425  <w:LsdException Locked="false" Priority="30" QFormat="true"
426   Name="Intense Quote"/>
427  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
428  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
429  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
430  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
431  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
432  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
433  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
434  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
435  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
436  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
437  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
438  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
439  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
440  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
441  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
442  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
443  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
444  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
445  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
446  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
447  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
448  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
449  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
450  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
451  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
452  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
453  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
454  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
455  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
456  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
457  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
458  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
459  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
460  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
461  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
462  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
463  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
464  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
465  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
466  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
467  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
468  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
469  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
470  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
471  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
472  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
473  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
474  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
475  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
476  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
477  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
478  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
479  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
480  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
481  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
482  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
483  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
484  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
485  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
486  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
487  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
488  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
489  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
490  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
491  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
492  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
493  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
494  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
495  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
496  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
497  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
498  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
499  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
500  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
501  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
502  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
503  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
504  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
505  <w:LsdException Locked="false" Priority="19" QFormat="true"
506   Name="Subtle Emphasis"/>
507  <w:LsdException Locked="false" Priority="21" QFormat="true"
508   Name="Intense Emphasis"/>
509  <w:LsdException Locked="false" Priority="31" QFormat="true"
510   Name="Subtle Reference"/>
511  <w:LsdException Locked="false" Priority="32" QFormat="true"
512   Name="Intense Reference"/>
513  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
514  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
515   UnhideWhenUsed="true" Name="Bibliography"/>
516  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
517   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
518  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
519  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
520  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
521  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
522  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
523  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
524  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
525  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
526  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
527  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
528  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
529  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
530  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
531  <w:LsdException Locked="false" Priority="46"
532   Name="Grid Table 1 Light Accent 1"/>
533  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
534  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
535  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
536  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
537  <w:LsdException Locked="false" Priority="51"
538   Name="Grid Table 6 Colorful Accent 1"/>
539  <w:LsdException Locked="false" Priority="52"
540   Name="Grid Table 7 Colorful Accent 1"/>
541  <w:LsdException Locked="false" Priority="46"
542   Name="Grid Table 1 Light Accent 2"/>
543  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
544  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
545  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
546  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
547  <w:LsdException Locked="false" Priority="51"
548   Name="Grid Table 6 Colorful Accent 2"/>
549  <w:LsdException Locked="false" Priority="52"
550   Name="Grid Table 7 Colorful Accent 2"/>
551  <w:LsdException Locked="false" Priority="46"
552   Name="Grid Table 1 Light Accent 3"/>
553  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
554  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
555  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
556  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
557  <w:LsdException Locked="false" Priority="51"
558   Name="Grid Table 6 Colorful Accent 3"/>
559  <w:LsdException Locked="false" Priority="52"
560   Name="Grid Table 7 Colorful Accent 3"/>
561  <w:LsdException Locked="false" Priority="46"
562   Name="Grid Table 1 Light Accent 4"/>
563  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
564  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
565  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
566  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
567  <w:LsdException Locked="false" Priority="51"
568   Name="Grid Table 6 Colorful Accent 4"/>
569  <w:LsdException Locked="false" Priority="52"
570   Name="Grid Table 7 Colorful Accent 4"/>
571  <w:LsdException Locked="false" Priority="46"
572   Name="Grid Table 1 Light Accent 5"/>
573  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
574  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
575  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
576  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
577  <w:LsdException Locked="false" Priority="51"
578   Name="Grid Table 6 Colorful Accent 5"/>
579  <w:LsdException Locked="false" Priority="52"
580   Name="Grid Table 7 Colorful Accent 5"/>
581  <w:LsdException Locked="false" Priority="46"
582   Name="Grid Table 1 Light Accent 6"/>
583  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
584  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
585  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
586  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
587  <w:LsdException Locked="false" Priority="51"
588   Name="Grid Table 6 Colorful Accent 6"/>
589  <w:LsdException Locked="false" Priority="52"
590   Name="Grid Table 7 Colorful Accent 6"/>
591  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
592  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
593  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
594  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
595  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
596  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
597  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
598  <w:LsdException Locked="false" Priority="46"
599   Name="List Table 1 Light Accent 1"/>
600  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
601  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
602  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
603  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
604  <w:LsdException Locked="false" Priority="51"
605   Name="List Table 6 Colorful Accent 1"/>
606  <w:LsdException Locked="false" Priority="52"
607   Name="List Table 7 Colorful Accent 1"/>
608  <w:LsdException Locked="false" Priority="46"
609   Name="List Table 1 Light Accent 2"/>
610  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
611  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
612  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
613  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
614  <w:LsdException Locked="false" Priority="51"
615   Name="List Table 6 Colorful Accent 2"/>
616  <w:LsdException Locked="false" Priority="52"
617   Name="List Table 7 Colorful Accent 2"/>
618  <w:LsdException Locked="false" Priority="46"
619   Name="List Table 1 Light Accent 3"/>
620  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
621  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
622  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
623  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
624  <w:LsdException Locked="false" Priority="51"
625   Name="List Table 6 Colorful Accent 3"/>
626  <w:LsdException Locked="false" Priority="52"
627   Name="List Table 7 Colorful Accent 3"/>
628  <w:LsdException Locked="false" Priority="46"
629   Name="List Table 1 Light Accent 4"/>
630  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
631  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
632  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
633  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
634  <w:LsdException Locked="false" Priority="51"
635   Name="List Table 6 Colorful Accent 4"/>
636  <w:LsdException Locked="false" Priority="52"
637   Name="List Table 7 Colorful Accent 4"/>
638  <w:LsdException Locked="false" Priority="46"
639   Name="List Table 1 Light Accent 5"/>
640  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
641  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
642  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
643  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
644  <w:LsdException Locked="false" Priority="51"
645   Name="List Table 6 Colorful Accent 5"/>
646  <w:LsdException Locked="false" Priority="52"
647   Name="List Table 7 Colorful Accent 5"/>
648  <w:LsdException Locked="false" Priority="46"
649   Name="List Table 1 Light Accent 6"/>
650  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
651  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
652  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
653  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
654  <w:LsdException Locked="false" Priority="51"
655   Name="List Table 6 Colorful Accent 6"/>
656  <w:LsdException Locked="false" Priority="52"
657   Name="List Table 7 Colorful Accent 6"/>
658 </w:LatentStyles>
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779        mso-fareast-font-family:"MS Gothic";
780        color:#4F81BD;
781        mso-fareast-language:JA;
782        font-weight:bold;}
783a:link, span.MsoHyperlink
784        {mso-style-noshow:yes;
785        mso-style-priority:99;
786        color:blue;
787        mso-themecolor:hyperlink;
788        text-decoration:underline;
789        text-underline:single;}
790a:visited, span.MsoHyperlinkFollowed
791        {mso-style-noshow:yes;
792        mso-style-priority:99;
793        color:purple;
794        mso-themecolor:followedhyperlink;
795        text-decoration:underline;
796        text-underline:single;}
797p
798        {mso-style-noshow:yes;
799        mso-style-priority:99;
800        mso-margin-top-alt:auto;
801        margin-right:0in;
802        mso-margin-bottom-alt:auto;
803        margin-left:0in;
804        mso-pagination:widow-orphan;
805        font-size:12.0pt;
806        font-family:"Times New Roman",serif;
807        mso-fareast-font-family:"Times New Roman";
808        mso-fareast-theme-font:minor-fareast;}
809p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
810        {mso-style-noshow:yes;
811        mso-style-priority:99;
812        mso-style-link:"Balloon Text Char";
813        margin:0in;
814        margin-bottom:.0001pt;
815        mso-pagination:widow-orphan;
816        font-size:9.0pt;
817        font-family:"Lucida Grande";
818        mso-fareast-font-family:"MS Mincho";
819        mso-fareast-language:JA;}
820p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
821        {mso-style-noshow:yes;
822        mso-style-priority:34;
823        mso-style-unhide:no;
824        mso-style-qformat:yes;
825        margin-top:0in;
826        margin-right:0in;
827        margin-bottom:0in;
828        margin-left:.5in;
829        margin-bottom:.0001pt;
830        mso-add-space:auto;
831        mso-pagination:widow-orphan;
832        font-size:12.0pt;
833        mso-bidi-font-size:10.0pt;
834        font-family:"Times New Roman",serif;
835        mso-fareast-font-family:"MS Mincho";
836        mso-fareast-language:JA;}
837p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
838        {mso-style-noshow:yes;
839        mso-style-priority:34;
840        mso-style-unhide:no;
841        mso-style-qformat:yes;
842        mso-style-type:export-only;
843        margin-top:0in;
844        margin-right:0in;
845        margin-bottom:0in;
846        margin-left:.5in;
847        margin-bottom:.0001pt;
848        mso-add-space:auto;
849        mso-pagination:widow-orphan;
850        font-size:12.0pt;
851        mso-bidi-font-size:10.0pt;
852        font-family:"Times New Roman",serif;
853        mso-fareast-font-family:"MS Mincho";
854        mso-fareast-language:JA;}
855p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
856        {mso-style-noshow:yes;
857        mso-style-priority:34;
858        mso-style-unhide:no;
859        mso-style-qformat:yes;
860        mso-style-type:export-only;
861        margin-top:0in;
862        margin-right:0in;
863        margin-bottom:0in;
864        margin-left:.5in;
865        margin-bottom:.0001pt;
866        mso-add-space:auto;
867        mso-pagination:widow-orphan;
868        font-size:12.0pt;
869        mso-bidi-font-size:10.0pt;
870        font-family:"Times New Roman",serif;
871        mso-fareast-font-family:"MS Mincho";
872        mso-fareast-language:JA;}
873p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
874        {mso-style-noshow:yes;
875        mso-style-priority:34;
876        mso-style-unhide:no;
877        mso-style-qformat:yes;
878        mso-style-type:export-only;
879        margin-top:0in;
880        margin-right:0in;
881        margin-bottom:0in;
882        margin-left:.5in;
883        margin-bottom:.0001pt;
884        mso-add-space:auto;
885        mso-pagination:widow-orphan;
886        font-size:12.0pt;
887        mso-bidi-font-size:10.0pt;
888        font-family:"Times New Roman",serif;
889        mso-fareast-font-family:"MS Mincho";
890        mso-fareast-language:JA;}
891span.Heading1Char
892        {mso-style-name:"Heading 1 Char";
893        mso-style-priority:9;
894        mso-style-unhide:no;
895        mso-style-locked:yes;
896        mso-style-parent:"";
897        mso-style-link:"Heading 1";
898        mso-ansi-font-size:18.0pt;
899        mso-bidi-font-size:16.0pt;
900        font-family:"Times New Roman",serif;
901        mso-ascii-font-family:"Times New Roman";
902        mso-fareast-font-family:"MS Gothic";
903        mso-hansi-font-family:"Times New Roman";
904        mso-bidi-font-family:"Times New Roman";
905        mso-fareast-language:JA;
906        font-weight:bold;}
907span.Heading2Char
908        {mso-style-name:"Heading 2 Char";
909        mso-style-noshow:yes;
910        mso-style-priority:9;
911        mso-style-unhide:no;
912        mso-style-locked:yes;
913        mso-style-parent:"";
914        mso-style-link:"Heading 2";
915        mso-ansi-font-size:13.0pt;
916        mso-bidi-font-size:13.0pt;
917        font-family:"Calibri",sans-serif;
918        mso-ascii-font-family:Calibri;
919        mso-fareast-font-family:"MS Gothic";
920        mso-hansi-font-family:Calibri;
921        mso-bidi-font-family:"Times New Roman";
922        color:#4F81BD;
923        font-weight:bold;}
924p.msonormal0, li.msonormal0, div.msonormal0
925        {mso-style-name:msonormal;
926        mso-style-noshow:yes;
927        mso-style-priority:99;
928        mso-style-unhide:no;
929        mso-margin-top-alt:auto;
930        margin-right:0in;
931        mso-margin-bottom-alt:auto;
932        margin-left:0in;
933        mso-pagination:widow-orphan;
934        font-size:12.0pt;
935        font-family:"Times New Roman",serif;
936        mso-fareast-font-family:"Times New Roman";
937        mso-fareast-theme-font:minor-fareast;}
938span.BalloonTextChar
939        {mso-style-name:"Balloon Text Char";
940        mso-style-noshow:yes;
941        mso-style-priority:99;
942        mso-style-unhide:no;
943        mso-style-locked:yes;
944        mso-style-parent:"";
945        mso-style-link:"Balloon Text";
946        mso-ansi-font-size:9.0pt;
947        mso-bidi-font-size:9.0pt;
948        font-family:"Lucida Grande";
949        mso-ascii-font-family:"Lucida Grande";
950        mso-hansi-font-family:"Lucida Grande";
951        mso-bidi-font-family:"Lucida Grande";}
952.MsoChpDefault
953        {mso-style-type:export-only;
954        mso-default-props:yes;
955        font-size:10.0pt;
956        mso-ansi-font-size:10.0pt;
957        mso-bidi-font-size:10.0pt;
958        font-family:"Cambria",serif;
959        mso-ascii-font-family:Cambria;
960        mso-fareast-font-family:"MS Mincho";
961        mso-hansi-font-family:Cambria;}
962@page WordSection1
963        {size:8.5in 11.0in;
964        margin:1.0in 1.25in 1.0in 1.25in;
965        mso-header-margin:.5in;
966        mso-footer-margin:.5in;
967        mso-paper-source:0;}
968div.WordSection1
969        {page:WordSection1;}
970 /* List Definitions */
971 @list l0
972        {mso-list-id:177306416;
973        mso-list-type:hybrid;
974        mso-list-template-ids:113260986 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
975@list l0:level1
976        {mso-level-tab-stop:none;
977        mso-level-number-position:left;
978        text-indent:-.25in;}
979@list l0:level2
980        {mso-level-number-format:alpha-lower;
981        mso-level-tab-stop:none;
982        mso-level-number-position:left;
983        text-indent:-.25in;}
984@list l0:level3
985        {mso-level-number-format:roman-lower;
986        mso-level-tab-stop:none;
987        mso-level-number-position:right;
988        text-indent:-9.0pt;}
989@list l0:level4
990        {mso-level-tab-stop:none;
991        mso-level-number-position:left;
992        text-indent:-.25in;}
993@list l0:level5
994        {mso-level-number-format:alpha-lower;
995        mso-level-tab-stop:none;
996        mso-level-number-position:left;
997        text-indent:-.25in;}
998@list l0:level6
999        {mso-level-number-format:roman-lower;
1000        mso-level-tab-stop:none;
1001        mso-level-number-position:right;
1002        text-indent:-9.0pt;}
1003@list l0:level7
1004        {mso-level-tab-stop:none;
1005        mso-level-number-position:left;
1006        text-indent:-.25in;}
1007@list l0:level8
1008        {mso-level-number-format:alpha-lower;
1009        mso-level-tab-stop:none;
1010        mso-level-number-position:left;
1011        text-indent:-.25in;}
1012@list l0:level9
1013        {mso-level-number-format:roman-lower;
1014        mso-level-tab-stop:none;
1015        mso-level-number-position:right;
1016        text-indent:-9.0pt;}
1017@list l1
1018        {mso-list-id:257300979;
1019        mso-list-type:hybrid;
1020        mso-list-template-ids:-1964622610 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1021@list l1:level1
1022        {mso-level-tab-stop:none;
1023        mso-level-number-position:left;
1024        text-indent:-.25in;}
1025@list l1:level2
1026        {mso-level-number-format:alpha-lower;
1027        mso-level-tab-stop:none;
1028        mso-level-number-position:left;
1029        text-indent:-.25in;}
1030@list l1:level3
1031        {mso-level-number-format:roman-lower;
1032        mso-level-tab-stop:none;
1033        mso-level-number-position:right;
1034        text-indent:-9.0pt;}
1035@list l1:level4
1036        {mso-level-tab-stop:none;
1037        mso-level-number-position:left;
1038        text-indent:-.25in;}
1039@list l1:level5
1040        {mso-level-number-format:alpha-lower;
1041        mso-level-tab-stop:none;
1042        mso-level-number-position:left;
1043        text-indent:-.25in;}
1044@list l1:level6
1045        {mso-level-number-format:roman-lower;
1046        mso-level-tab-stop:none;
1047        mso-level-number-position:right;
1048        text-indent:-9.0pt;}
1049@list l1:level7
1050        {mso-level-tab-stop:none;
1051        mso-level-number-position:left;
1052        text-indent:-.25in;}
1053@list l1:level8
1054        {mso-level-number-format:alpha-lower;
1055        mso-level-tab-stop:none;
1056        mso-level-number-position:left;
1057        text-indent:-.25in;}
1058@list l1:level9
1059        {mso-level-number-format:roman-lower;
1060        mso-level-tab-stop:none;
1061        mso-level-number-position:right;
1062        text-indent:-9.0pt;}
1063@list l2
1064        {mso-list-id:321734847;
1065        mso-list-type:hybrid;
1066        mso-list-template-ids:113260986 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1067@list l2:level1
1068        {mso-level-tab-stop:none;
1069        mso-level-number-position:left;
1070        text-indent:-.25in;}
1071@list l2:level2
1072        {mso-level-number-format:alpha-lower;
1073        mso-level-tab-stop:none;
1074        mso-level-number-position:left;
1075        text-indent:-.25in;}
1076@list l2:level3
1077        {mso-level-number-format:roman-lower;
1078        mso-level-tab-stop:none;
1079        mso-level-number-position:right;
1080        text-indent:-9.0pt;}
1081@list l2:level4
1082        {mso-level-tab-stop:none;
1083        mso-level-number-position:left;
1084        text-indent:-.25in;}
1085@list l2:level5
1086        {mso-level-number-format:alpha-lower;
1087        mso-level-tab-stop:none;
1088        mso-level-number-position:left;
1089        text-indent:-.25in;}
1090@list l2:level6
1091        {mso-level-number-format:roman-lower;
1092        mso-level-tab-stop:none;
1093        mso-level-number-position:right;
1094        text-indent:-9.0pt;}
1095@list l2:level7
1096        {mso-level-tab-stop:none;
1097        mso-level-number-position:left;
1098        text-indent:-.25in;}
1099@list l2:level8
1100        {mso-level-number-format:alpha-lower;
1101        mso-level-tab-stop:none;
1102        mso-level-number-position:left;
1103        text-indent:-.25in;}
1104@list l2:level9
1105        {mso-level-number-format:roman-lower;
1106        mso-level-tab-stop:none;
1107        mso-level-number-position:right;
1108        text-indent:-9.0pt;}
1109@list l3
1110        {mso-list-id:375742000;
1111        mso-list-type:hybrid;
1112        mso-list-template-ids:113260986 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1113@list l3:level1
1114        {mso-level-tab-stop:none;
1115        mso-level-number-position:left;
1116        text-indent:-.25in;}
1117@list l3:level2
1118        {mso-level-number-format:alpha-lower;
1119        mso-level-tab-stop:none;
1120        mso-level-number-position:left;
1121        text-indent:-.25in;}
1122@list l3:level3
1123        {mso-level-number-format:roman-lower;
1124        mso-level-tab-stop:none;
1125        mso-level-number-position:right;
1126        text-indent:-9.0pt;}
1127@list l3:level4
1128        {mso-level-tab-stop:none;
1129        mso-level-number-position:left;
1130        text-indent:-.25in;}
1131@list l3:level5
1132        {mso-level-number-format:alpha-lower;
1133        mso-level-tab-stop:none;
1134        mso-level-number-position:left;
1135        text-indent:-.25in;}
1136@list l3:level6
1137        {mso-level-number-format:roman-lower;
1138        mso-level-tab-stop:none;
1139        mso-level-number-position:right;
1140        text-indent:-9.0pt;}
1141@list l3:level7
1142        {mso-level-tab-stop:none;
1143        mso-level-number-position:left;
1144        text-indent:-.25in;}
1145@list l3:level8
1146        {mso-level-number-format:alpha-lower;
1147        mso-level-tab-stop:none;
1148        mso-level-number-position:left;
1149        text-indent:-.25in;}
1150@list l3:level9
1151        {mso-level-number-format:roman-lower;
1152        mso-level-tab-stop:none;
1153        mso-level-number-position:right;
1154        text-indent:-9.0pt;}
1155@list l4
1156        {mso-list-id:931935216;
1157        mso-list-type:hybrid;
1158        mso-list-template-ids:-1849530802 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1159@list l4:level1
1160        {mso-level-tab-stop:none;
1161        mso-level-number-position:left;
1162        margin-left:.75in;
1163        text-indent:-.25in;}
1164@list l4:level2
1165        {mso-level-number-format:alpha-lower;
1166        mso-level-tab-stop:none;
1167        mso-level-number-position:left;
1168        margin-left:1.25in;
1169        text-indent:-.25in;}
1170@list l4:level3
1171        {mso-level-number-format:roman-lower;
1172        mso-level-tab-stop:none;
1173        mso-level-number-position:right;
1174        margin-left:1.75in;
1175        text-indent:-9.0pt;}
1176@list l4:level4
1177        {mso-level-tab-stop:none;
1178        mso-level-number-position:left;
1179        margin-left:2.25in;
1180        text-indent:-.25in;}
1181@list l4:level5
1182        {mso-level-number-format:alpha-lower;
1183        mso-level-tab-stop:none;
1184        mso-level-number-position:left;
1185        margin-left:2.75in;
1186        text-indent:-.25in;}
1187@list l4:level6
1188        {mso-level-number-format:roman-lower;
1189        mso-level-tab-stop:none;
1190        mso-level-number-position:right;
1191        margin-left:3.25in;
1192        text-indent:-9.0pt;}
1193@list l4:level7
1194        {mso-level-tab-stop:none;
1195        mso-level-number-position:left;
1196        margin-left:3.75in;
1197        text-indent:-.25in;}
1198@list l4:level8
1199        {mso-level-number-format:alpha-lower;
1200        mso-level-tab-stop:none;
1201        mso-level-number-position:left;
1202        margin-left:4.25in;
1203        text-indent:-.25in;}
1204@list l4:level9
1205        {mso-level-number-format:roman-lower;
1206        mso-level-tab-stop:none;
1207        mso-level-number-position:right;
1208        margin-left:4.75in;
1209        text-indent:-9.0pt;}
1210@list l5
1211        {mso-list-id:1447852064;
1212        mso-list-type:hybrid;
1213        mso-list-template-ids:113260986 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1214@list l5:level1
1215        {mso-level-tab-stop:none;
1216        mso-level-number-position:left;
1217        text-indent:-.25in;}
1218@list l5:level2
1219        {mso-level-number-format:alpha-lower;
1220        mso-level-tab-stop:none;
1221        mso-level-number-position:left;
1222        text-indent:-.25in;}
1223@list l5:level3
1224        {mso-level-number-format:roman-lower;
1225        mso-level-tab-stop:none;
1226        mso-level-number-position:right;
1227        text-indent:-9.0pt;}
1228@list l5:level4
1229        {mso-level-tab-stop:none;
1230        mso-level-number-position:left;
1231        text-indent:-.25in;}
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1371<![endif]-->
1372<meta name=Title content="">
1373<meta name=Keywords content="">
1374<!--[if gte mso 9]><xml>
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1381
1382<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1383
1384<div class=WordSection1>
1385
1386<h1><span style='font-size:24.0pt'>Sequential refinement of multiple datasets –
1387CuCr<sub>2</sub>O<sub>4</sub> from 7K to 300K<o:p></o:p></span></h1>
1388
1389<P><BL>
1390  <LI><B>A video version of this tutorial is available at
1391<A href="https://anl.box.com/v/SequentialTutorial" target="_blank">
1392https://anl.box.com/v/SequentialTutorial</A></B>
1393  <LI>Exercise files are found <A href="./data/" target="_blank">here</a>
1394</BL></P><P></P>
1395 
1396<p class=MsoNormal>Sequential refinement is a way to fit a series of
1397  datasets collected under similar conditions with a set of closely
1398  related models. Each dataset receives an independent
1399  fit. Thus it is possible to track how the models
1400  evolve over the course of the measurements. One or more phases may
1401  be used to fit all all the datasets or some phases may appear in
1402  just some of the measurements, should there be phase transitions.
1403<P></P>
1404  Sequential refinements can
1405be performed in three different ways: </p>
1406  <OL>
1407    <LI>where the resulting parameters after a fit for a
1408    histogram are used as the starting point for the next histogram.</LI>
1409    <LI>with differing starting parameters for each histogram</LI>
1410    <LI>with the same starting parameters for each histogram</LI>
1411</OL><P></P>
1412Most commonly the first mode is used initially, where the parameters
1413for each fir are copied as the starting point for the fit of next
1414dataset. After this initial refinement of all datasets is complete,
1415the refinement is continued where each dataset has its own
1416parameters.
1417
1418<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1419
1420<p class=MsoNormal>
1421In this example, we will fit a temperature series where both the unit
1422cell and atomic parameters evolve with temperature. Note that
1423it is also possible to fit a temperature series as a combined refinement and,
1424as will be seen, one can still deal with thermal expansion (using the
1425Hydrostatic/Elastic strain terms), but a combined refinement would
1426allow only a single set of (averaged) atomic parameters for
1427all temperatures. A sequential refinement allows each
1428data set to determine the atomic parameters and allows their variation
1429with temperature to be determined.
1430<P></P>
1431Data for this example will be downloaded with the tutorial, if you used
1432that option to see this page. Otherwise, download file
1433<A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqRefine/data/">
1434SeqTut.zip from here</A>.
1435This example assumes that one is already familiar with use
1436of GSAS-II for simple refinements. <span style='mso-bidi-font-size:12.0pt;
1437mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-US'>Note that
1438menu entries are listed in bold face below, such as </span><b style='mso-bidi-font-weight:
1439normal'><span style='mso-bidi-font-size:12.0pt;font-family:"Calibri",sans-serif;
1440mso-fareast-font-family:"Times New Roman";mso-fareast-language:EN-US'>Help/About
1441GSAS-II</span></b><span style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:
1442"Times New Roman";mso-fareast-language:EN-US'>, which lists first the name of
1443the menu (here </span><b style='mso-bidi-font-weight:normal'><span
1444style='mso-bidi-font-size:12.0pt;font-family:"Calibri",sans-serif;mso-fareast-font-family:
1445"Times New Roman";mso-fareast-language:EN-US'>Help</span></b><span
1446style='mso-bidi-font-size:12.0pt;mso-fareast-font-family:"Times New Roman";
1447mso-fareast-language:EN-US'>) and second the name of the entry in the menu
1448(here </span><b style='mso-bidi-font-weight:normal'><span style='mso-bidi-font-size:
144912.0pt;font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman";
1450mso-fareast-language:EN-US'>About GSAS-II</span></b><span style='mso-bidi-font-size:
145112.0pt;mso-fareast-font-family:"Times New
1452Roman";mso-fareast-language:EN-US'>).</span>
1453</p>
1454
1455<h1>Step I: Fit a single temperature. </h1>
1456<p></p>
1457
1458If you have not done so already, start GSAS-II. While it is possible
1459to start a sequential refinement reading in all phases and datasets
1460from the beginning, usually it is best to know something about how the
1461fit will be performed and this usually means performing one or more
1462fits to representative individual datasets as the conditions or phases
1463present change. One way to do this could be to read in all datasets but select
1464only a single individual dataset for that fit until we are ready to
1465fit the entire sequence. Here we will start by reading in only the
1466first dataset and fit that. Then we will add more datasets and perform
1467a sequential fit.
1468
1469<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1470
1471<H3>1. Read phase files <B>CuCr2O4.cif</B> and <B>CuO.cif</B> from file <b>SeqTut.zip</B>.</H3>
1472
1473<OL style='PADDING-LEFT:0.75in' type="A"><LI>
1474 Use
1475the <b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1476mso-hansi-theme-font:major-latin'>
1477Import/Phase/from CIF file menu item</span></b> to read the phase information.</p>
1478  <P></P>
1479In
1480the file browser dialog window that is created, <span style='mso-bidi-font-weight:
1481bold'>change the file type from<b> “</b></span><b><span style='font-family:
1482"Calibri",sans-serif;mso-ascii-theme-font:major-latin;mso-hansi-theme-font:
1483major-latin'>CIF file</span>” </b><span style='mso-bidi-font-weight:bold'>to<b>
1484“</b></span><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1485major-latin;mso-hansi-theme-font:major-latin'>zip archive</span>”</b> and <span
1486style='mso-bidi-font-weight:bold'>select<b> </b>the<b> </b></span><b><span
1487style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1488mso-hansi-theme-font:major-latin'>SeqTut.zip</span> </b><span style='mso-bidi-font-weight:
1489bold'>file</span> (change the file directory to <b style='mso-bidi-font-weight:
1490normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1491major-latin;mso-hansi-theme-font:major-latin'>SeqRefine/data</span></b>).
1492Another dialog window will be created showing all the files in the zip archive.
1493To simplify the view to only show the phase files, type “<b style='mso-bidi-font-weight:
1494normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1495major-latin;mso-hansi-theme-font:major-latin'>cif</span></b>” (or “<b
1496style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1497mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>CIF</span></b>”
1498– case is ignored) into the filter. <span style='mso-bidi-font-weight:bold'>Select
1499the<b> </b></span><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1500major-latin;mso-hansi-theme-font:major-latin'>CuCr2O4.cif</span> </b><span
1501style='mso-bidi-font-weight:bold'>and the<b> </b></span><b><span
1502style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1503mso-hansi-theme-font:major-latin'>CuO.cif</span> </b><span style='mso-bidi-font-weight:
1504bold'>input files. Press<b> </b></span><b><span style='font-family:"Calibri",sans-serif;
1505mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>OK</span></b>.
1506<P></p>
1507(If this exercise is being repeated, files CuCr2O4.cif or the
1508CuO.cif will already exist. If so, you will be asked to OK overwriting them.)
1509
1510<P></p>
1511<LI>You
1512will be asked sequentially for the name for each phase. The defaults (<b
1513style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1514mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>CuCr2O4</span></b>
1515and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1516mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>CuO</span></b>)
1517are fine, so <b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1518major-latin;mso-hansi-theme-font:major-latin'>OK</span> </b><span
1519style='mso-bidi-font-weight:bold'>can be pressed for each question</span>.<span
1520style='mso-spacerun:yes'>  </span></p>
1521
1522<P></P>
1523<LI>Note that for CuCr<sub>2</sub>O<sub>4</sub>, the space group (<I>Fddd</I>) can
1524be set with two origin choices. Select <B>Keep current coordinates</B>
1525since the coordinates are already set properly.
1526<P></P>
1527<I>Discussion:
1528When there is a choice, GSAS-II requires the use of Origin 2, which
1529places the origin at a center of symmetry, and this CIF has been set
1530that way
1531(the presence of a -x,-y,-z symmetry operation confirms that), but GSAS-II
1532notes the possible choice and offers to apply the shift to the
1533coordinates that would shift from Origin 1 to Origin 2.
1534As shown in the window where this
1535choice would be made, this shift were applied,
1536the unit cell contents would be
1537Cu<sub>16</sub>Cr<sub>8</sub>O<sub>32</sub> rather than the correct
1538CuCr<sub>2</sub>O<sub>4</sub> stoichiometry, so this also confirms the
1539origin setting is correct and no coordinate shift should be applied.
1540<B>Choice of origin is a common problem in crystallographic
1541computations and many CIFs do not define this setting clearly, so use care with this.</B> 
1542</I>
1543
1544<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1545</OL>
1546
1547<H3>2.
1548Read in file <B>OH_00.fxye</B> from file <b>SeqTut.zip</B> and <B>map
1549both phases</B> to this dataset.  </H3>
1550
1551<OL style='PADDING-LEFT:0.75in' type="A"><LI>
1552Read in the ~7 K dataset (<b style='mso-bidi-font-weight:
1553normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1554major-latin;mso-hansi-theme-font:major-latin'>OH_00.fxye</span></b>) using <b><span
1555style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1556mso-hansi-theme-font:major-latin'>Import/Powder Data/from GSAS powder data file</span></b>
1557to open a file browser. Again <span style='mso-bidi-font-weight:bold'>select<b>
1558“</b></span><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1559major-latin;mso-hansi-theme-font:major-latin'>zip archive</span>” </b><span
1560style='mso-bidi-font-weight:bold'>and the<b> </b></span><b><span
1561style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1562mso-hansi-theme-font:major-latin'>SeqTut.zip</span> </b><span style='mso-bidi-font-weight:
1563bold'>file<b>. </b>Select file<b> </b></span><b><span style='font-family:"Calibri",sans-serif;
1564mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>OH_00.fxye</span></b>
1565(use of the filter can again be helpful) and <span style='mso-bidi-font-weight:
1566bold'>press<b> </b></span><b><span style='font-family:"Calibri",sans-serif;
1567mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>OK</span></b>.
1568</p>
1569
1570<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
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1579  <v:f eqn="prod @2 1 2"/>
1580  <v:f eqn="prod @3 21600 pixelWidth"/>
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1582  <v:f eqn="sum @0 0 1"/>
1583  <v:f eqn="prod @6 1 2"/>
1584  <v:f eqn="prod @7 21600 pixelWidth"/>
1585  <v:f eqn="sum @8 21600 0"/>
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1587  <v:f eqn="sum @10 21600 0"/>
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1596
1597<P></P>
1598<LI>You will be shown the first few lines from
1599the file. Confirm that the selected file is correct by <span style='mso-bidi-font-weight:
1600bold'>pressing<b> </b></span><b><span style='font-family:"Calibri",sans-serif;
1601mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>OK</span>.</b>
1602</p>
1603
1604<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
1605mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_55" o:spid="_x0000_i1058"
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1610src="SequentialTutorial_files/image002.png" v:shapes="Picture_x0020_55"><![endif]></span></p>
1611<P></P>
1612<p class=MsoListParagraphCxSpMiddle>Note that the instrument parameter file
1613with the matching name (<b style='mso-bidi-font-weight:normal'><span
1614style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1615mso-hansi-theme-font:major-latin'>OH_00.prm</span></b>) is read automatically. </p>
1616
1617<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
1618
1619<A name="I.2.C">
1620<LI>Map
1621the phases to the data: After reading in the dataset, a window used to select
1622phases is shown.</p>
1623
1624<p class=MsoListParagraphCxSpMiddle><span style='mso-spacerun:yes'> </span><span
1625style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1626 id="Picture_x0020_56" o:spid="_x0000_i1057" type="#_x0000_t75" style='width:217.5pt;
1627 height:228.75pt;visibility:visible;mso-wrap-style:square'>
1628 <v:imagedata src="SequentialTutorial_files/image003.png" o:title=""/>
1629</v:shape><![endif]--><![if !vml]><img width=290 height=305
1630src="SequentialTutorial_files/image003.png" v:shapes="Picture_x0020_56"><![endif]></span></p>
1631
1632<P></P>
1633<p class=MsoListParagraphCxSpMiddle><span style='mso-bidi-font-weight:bold'>Select
1634both phases and press<b> </b></span><b><span style='font-family:"Calibri",sans-serif;
1635mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>OK</span>.</b><span
1636style='mso-spacerun:yes'>  </span></p>
1637</OL>
1638
1639<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
1640
1641<A name="I.3"></A>
1642<H3>3. Prepare for fit: define <B>phase fraction constraint</B></H3>
1643<P></P>
1644<p class=MsoListParagraphCxSpMiddle>
1645We
1646want to fit the lattice parameters, background, and a phase fraction
1647initially. To illustrate how constraints
1648are used, we will refine both phase fractions, but constrain their sum to be
1649one. <I>Discussion: a single powder diffraction pattern provides
1650enough information to determine an overall scale factor and the
1651relative amounts of each phase (with two phases: two observables), but
1652with the scale factor and two phase fractions being varied
1653independently, we have three arbitrary
1654parameters, which would result in a very unstable refinement where the
1655GSAS-II minimizer would likely remove a degree of freedom. By defining
1656a constraint that sets the sum of the two phase fractions, we reduce
1657this to an appropriate two parameter problem. The error of refining the scale
1658factor and all phase fractions is made often enough that GSAS-II will
1659warn about this and will offer to define this constraint.</I>
1660
1661<OL style='PADDING-LEFT:0.75in' type="A"><LI>
1662To set up the phase fraction constraint, <span style='mso-bidi-font-weight:bold'>click on
1663the<b> </b></span><b><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1664major-latin;mso-hansi-theme-font:major-latin'>Constraints</span> </b><span
1665style='mso-bidi-font-weight:bold'>item</span> in the data tree and
1666then in the <b>Select tab</b> menu use the <b>Histogram/Phase</b> <span
1667style='mso-bidi-font-weight:bold'>menu item</span>, and then <span
1668style='mso-bidi-font-weight:bold'>click on the<b> </b></span><b><span
1669style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1670mso-hansi-theme-font:major-latin'>Edit Constr./Add</span> </b><b><span
1671style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1672mso-hansi-theme-font:major-latin'>constraint equation</span></b><span
1673style='mso-bidi-font-weight:bold'> menu item<b>.</b></span></p>
1674
1675
1676  <LI>In the next window use a <b
1677style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1678mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Filter</span></b>
1679of <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1680mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>scale</span></b>
1681to make the list shorter and then <span style='mso-bidi-font-weight:bold'>select
1682the phase fraction for the first phase<b> </b></span><b><span style='font-family:
1683"Calibri",sans-serif;mso-ascii-theme-font:major-latin;mso-hansi-theme-font:
1684major-latin'>0:0:Scale</span></b> (the second one, <b style='mso-bidi-font-weight:
1685normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1686major-latin;mso-hansi-theme-font:major-latin'>1:0:Scale</span></b><span
1687style='font-family:Courier'>,</span> would work too) </p>
1688
1689<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
1690mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_57" o:spid="_x0000_i1056"
1691 type="#_x0000_t75" style='width:6in;height:188.25pt;visibility:visible;
1692 mso-wrap-style:square'>
1693 <v:imagedata src="SequentialTutorial_files/image004.png" o:title=""/>
1694</v:shape><![endif]--><![if !vml]><img width=576 height=251
1695src="SequentialTutorial_files/image062.png" v:shapes="Picture_x0020_57"><![endif]></span><span
1696style='mso-spacerun:yes'> </span></p>
1697
1698<P></P>
1699
1700<LI>After pressing "OK" a new window
1701appears; in that next window either
1702<span
1703style='mso-bidi-font-weight:bold'>select the other phase fraction<b> (</b></span><b><span
1704style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1705mso-hansi-theme-font:major-latin'>1:0:Scale</span></b><b><span
1706style='font-family:Courier'>)</span></b><span style='font-family:"Cambria",serif;
1707mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> or select
1708all phases (</span><b style='mso-bidi-font-weight:normal'><span
1709style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1710mso-hansi-theme-font:major-latin'>all:0:Scale</span></b><span style='font-family:
1711"Cambria",serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>). The same result is obtained since there is only one additional
1712phase.
1713
1714<P></P>
1715<p class=MsoListParagraphCxSpMiddle><span style='font-family:"Cambria",serif;
1716mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_58"
1717 o:spid="_x0000_i1055" type="#_x0000_t75" style='width:6in;height:174pt;
1718 visibility:visible;mso-wrap-style:square'>
1719 <v:imagedata src="SequentialTutorial_files/image006.png" o:title=""/>
1720</v:shape><![endif]--><![if !vml]><img width=576 height=232
1721src="SequentialTutorial_files/image006.png" v:shapes="Picture_x0020_58"><![endif]></span><span
1722style='font-family:"Cambria",serif'><o:p></o:p></span></p>
1723
1724<P></P>
1725<p class=MsoListParagraphCxSpMiddle>
1726<LI>Press OK and this creates the desired constraint, which
1727forces the sum of phase fractions to be 1. (This is not needed here,
1728but to change the sum and/or multipliers, press the constraint's <b style='mso-bidi-font-weight:normal'><span
1729style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1730mso-hansi-theme-font:major-latin'>Edit</span></b> button.) </p>
1731
1732<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
1733mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_59" o:spid="_x0000_i1054"
1734 type="#_x0000_t75" style='width:6in;height:171pt;visibility:visible;
1735 mso-wrap-style:square'>
1736 <v:imagedata src="SequentialTutorial_files/image007.png" o:title=""/>
1737</v:shape><![endif]--><![if !vml]><img width=576 height=228
1738src="SequentialTutorial_files/image063.png" v:shapes="Picture_x0020_59"><![endif]></span></p>
1739
1740<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
1741
1742</OL>
1743
1744<H3>4. Initial fit: optimize <B>lattice</B> parameters & <B>phase
1745fractions</B>;
1746<B>background</B> (with <B>6 terms</B>); <B>scale factor</B>.
1747</H3>
1748<P></P>
1749<p class=MsoListParagraphCxSpMiddle>
1750 Now we select the variables to refine for each phase and then the
1751histogram parameters. </p>
1752
1753<OL style='PADDING-LEFT:0.75in' type="A"><LI>
1754  Select
1755the first phase</span> (<b style='mso-bidi-font-weight:normal'><span
1756style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1757mso-hansi-theme-font:major-latin'>CuCr2O4</span></b>) <span style='mso-bidi-font-weight:
1758bold'>click on the </span><b><span style='font-family:"Calibri",sans-serif;
1759mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Refine unit
1760cell</span></b><span style='mso-bidi-font-weight:bold'> option</span> (on the <b
1761style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1762mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>General</span></b>
1763tab). (You might need to click on the triangle to the left of
1764the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1765mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Phase</span></b>
1766entry to “open” the tree item). We also want to refine the phase fraction for
1767this phase, so <span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span
1768style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1769mso-hansi-theme-font:major-latin'>Data</span> </b><span style='mso-bidi-font-weight:
1770bold'>tab </span>and <span style='mso-bidi-font-weight:bold'>click on the<b> </b></span><b><span
1771style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1772mso-hansi-theme-font:major-latin'>Phase fraction</span> </b><span
1773style='mso-bidi-font-weight:bold'>box</span> to cause that to be refined.<span
1774style='mso-spacerun:yes'>  </span></p>
1775
1776<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
1777mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_60" o:spid="_x0000_i1053"
1778 type="#_x0000_t75" style='width:6in;height:252.75pt;visibility:visible;
1779 mso-wrap-style:square'>
1780 <v:imagedata src="SequentialTutorial_files/image009.png" o:title=""/>
1781</v:shape><![endif]--><![if !vml]><img width=576 height=337
1782src="SequentialTutorial_files/image064.png" v:shapes="Picture_x0020_60"><![endif]></span></p>
1783
1784<p></P>
1785<LI>Repeat this with the second phase (<b
1786style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1787mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>CuO</span></b>),
1788by <span style='mso-bidi-font-weight:bold'>selecting it</span> in the data
1789tree. Then <span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span
1790style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1791mso-hansi-theme-font:major-latin'>General</span> </b><span style='mso-bidi-font-weight:
1792bold'>tab</span> and on <span style='mso-bidi-font-weight:bold'>the<b> </b></span><b><span
1793style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1794mso-hansi-theme-font:major-latin'>Refine unit cell</span></b> option. We also
1795want to refine the phase fraction for this phase, so <span style='mso-bidi-font-weight:
1796bold'>select the </span><b><span style='font-family:"Calibri",sans-serif;
1797mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Data</span> </b><span
1798style='mso-bidi-font-weight:bold'>tab </span>and <span style='mso-bidi-font-weight:
1799bold'>click on the<b> </b></span><b><span style='font-family:"Calibri",sans-serif;
1800mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Phase
1801fraction</span> </b><span style='mso-bidi-font-weight:bold'>box</span> to cause
1802that to be refined.
1803
1804<P></P>
1805<LI>To refine the background,<span style='mso-bidi-font-weight:
1806bold'>
1807select the </span><b><span style='font-family:"Calibri",sans-serif;
1808mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Background</span>
1809</b><span style='mso-bidi-font-weight:bold' entry</span>
1810entry under the <b
1811style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1812mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>
1813PWDR
1814OH_00.fxye Bank 1</span></b> histogram sub-entries in the GSAS-II data tree. Confirm that <b style='mso-bidi-font-weight:normal'><span
1815style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1816mso-hansi-theme-font:major-latin'>Background function</span></b> should already
1817be set as <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1818mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>chebyshev-1</span></b>
1819and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1820mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Refine</span></b>
1821flag should be checked. <span style='mso-bidi-font-weight:bold'>Change the<b> </b></span><b><span
1822style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1823mso-hansi-theme-font:major-latin'>No. coeff</span>. </b><span style='mso-bidi-font-weight:
1824bold'>to<b> </b></span><b><span style='font-family:"Calibri",sans-serif;
1825mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>6</span></b>
1826to introduce more background terms. </p>
1827
1828<P></P>
1829<LI>The overall histogram scale factor should already be set to be
1830refined by default, but you may want to confirm this by clicking on the <b
1831style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1832mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Sample
1833Parameters</span></b> data tree entry.
1834</OL>
1835
1836<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
1837
1838<H3>5.<span
1839style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1840</span></span></span><![endif]>
1841Reduce <B>Data Range</B> to 4.5 degrees</H3>
1842
1843<P></P>
1844
1845<p class=MsoListParagraphCxSpMiddle>Finally, note that the first broad
1846peak at ~1.5 degrees in these data is spurious.
1847This artifact is known to arise from scattering from the kapton window in the
1848cryostat used for sample cooling; this was confirmed by collecting data without
1849a sample. We could model this peak, but it is easier to simply cut off the data
1850below the first peak at ~5 degrees. To do this<b style='mso-bidi-font-weight:
1851normal'>, </b><span style='mso-bidi-font-weight:bold'>select the<b> </b></span><b><span
1852style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1853mso-hansi-theme-font:major-latin'>Limits</span> </b><span style='mso-bidi-font-weight:
1854bold'>entry</span> for <b style='mso-bidi-font-weight:normal'><span
1855style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1856mso-hansi-theme-font:major-latin'>PWDR OH_00.fxye Bank 1</span></b> and in the <b
1857style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1858mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>Tmin/New</span></b>
1859box (to lower left) <span style='mso-bidi-font-weight:bold'>change it to </span><b><span
1860style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
1861mso-hansi-theme-font:major-latin'>4.5</span>.<o:p></o:p></b></p>
1862
1863<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
1864
1865<H3>6. Perform initial fit</H3>
1866
1867<p class=MsoListParagraphCxSpMiddle>
1868Use the<b><span style='font-family:
1869"Calibri",sans-serif;mso-ascii-theme-font:major-latin;mso-hansi-theme-font:
1870major-latin'>
1871Calculate/Refine</span></b><span style='mso-bidi-font-weight:bold'>
1872main GSAS-II menu item</span> to initiate the refinement. Since the project has
1873not been saved, you will be asked to select a name (and optionally a directory)
1874for the GSAS-II project (.gpx) file.<span style='mso-spacerun:yes'>  </span>The
1875file name <b style='mso-bidi-font-weight:normal'><span style='font-family:"Cambria",serif;
1876mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>SeqTut.gpx</span></b>
1877is assumed here. The refinement progresses quickly to a Rw of ~17%. </p>
1878
1879<h1>Step II: Improve the single-temperature fit. </h1>
1880
1881<P></P>
1882There are several additional variables that should now be added, now
1883that we have reasonable starting unit cell parameters, etc. This
1884includes a sample displacement parameter, a better background treatment
1885and some sample broadening terms for the profile.
1886
1887<H3>1. Improve sample-dependent fitting.</H3>
1888
1889<OL style='PADDING-LEFT:0.75in' type="A">
1890<LI>Refine the <B>Sample X displacement</B> term</LI>
1891
1892<P></P><p class=MsoNormal>
1893Click on the <B>Sample
1894Parameters</B> data tree subitem for <B>PWDR OH_00.fxye Bank 1</B>.
1895Select the refine checkbox that is
1896labeled <B>Sample X disp. perp. to peak</B>. The value for this is the
1897displacement in microns (10<sup>-6</sup> m), provided the
1898diffractometer radius is entered correctly. Set the Goniometer radius to 1000.
1899</P>
1900
1901<P></P>
1902<p class=MsoListParagraphCxSpMiddle><I>Discussion: Diffractometers are never 
1903perfectly aligned, which means one should always an alignment
1904parameter. While in older programs, the alignment parameter was a zero
1905correction (except for Bragg-Brentano instruments), this does not
1906properly correct for mispositioning of the sample from the center of
1907the goniometer arc. GSAS-II offers a geometrical correction for that
1908being offset perpendicular to the
1909direction of the beam as the Sample X displacement (and for where data is
1910collected to angles above 120 degrees 2theta, it is also possible to fit a
1911second term, Sample Y displacement for displacement along the beam
1912direction.)
1913When using GSAS-II, refine the Sample X displacement parameter rather than
1914the 2theta-zero correction. (Refinement of both is not normally
1915possible).</I>
1916
1917
1918<P></P><p class=MsoNormal>
1919Note: With a well characterized
1920instrument, as is the case here for 11-BM at the APS, none of the
1921Instrument Parameters or other Sample Parameters (beyond
1922"Histogram scale factor" and "Sample X displ.") need to be fit.
1923
1924<P></P>
1925<LI>Add a background peak.</LI>
1926
1927<P></P><p class=MsoNormal> 
1928Add a background peak at <B>pos=5.25</B> degrees with <B>int=5.0</B>
1929and a <B>sig=2000</B>.
1930</P>
1931
1932<P></P><p class=MsoNormal>
1933The background is not very well fit even with a six term polynomial
1934due to a kapton scattering peak in the range of 4-6 degrees
19352theta. This can be seen by selecting the
1936<b>PWDR OH_00.fxye Bank 1</b> tree entry and viewing the “Rietveld
1937plot.”
1938Then to see more detail, either press "s" to see the plot in the
1939square-root of intensities, or zoom in so the vertical intensity scale
1940is 0-500 counts and the horizontal region covers the first ~5 degrees
1941in the pattern.
1942While the fit for this could be improved by adding many more
1943background terms, a simpler way to improve this fit is to add a broad
1944peak in the pattern via the background fitting. This only needs 2 or 3
1945additional parameters.
1946
1947<P></P><p class=MsoNormal> 
1948After selecting the <b>Background</b> sub-item in the
1949<B>PWDR OH_00.fxye Bank 1</b> histogram, change the <b>Peaks in
1950Background</b> setting from "0" to "1". Then change
1951the peak position (<b>pos</b>) value to the approximate peak
1952center (<b>5.25</b> degrees) but that value should not be varied until
1953the background is fairly well fit. Since the background generated by the
1954Chebyschev polynomial and the background peak are highly correlated,
1955we need to get the width and intensity into the right vicinity. Note
1956that as the values in the peaks list are changed, the background curve
1957(in red) is recomputed. In that way the effect of the change in values
1958can be seen. A <B>sig</B> value of 2000 gives a Gaussian FWHM for this peak of
1959~2 degrees. Changing the <B>int</B> value from 1 to 5 makes the peak
1960much easier to see and also helps start the initial fit. Set both
1961<B>sig</B> and <B>int</B> to be <B>refined</B>.
1962
1963<P></P><p class=MsoNormal> 
1964<i><u>Important</u></i></b>: note that after clicking on a checkbox, one must
1965click elsewhere in the window so that the input is recorded.</p>
1966
1967<P></P>
1968<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
1969mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_62" o:spid="_x0000_i1052"
1970 type="#_x0000_t75" style='width:6in;height:223.5pt;visibility:visible;
1971 mso-wrap-style:square'>
1972 <v:imagedata src="SequentialTutorial_files/image013.png" o:title=""/>
1973</v:shape><![endif]--><![if !vml]><img width=576 height=298
1974src="SequentialTutorial_files/image065.png" v:shapes="Picture_x0020_62"><![endif]></span></p>
1975
1976<P></P><p class=MsoNormal> 
1977Once the background fit has been
1978improved we can then add the position of this peak to the fit.</p>
1979<P></P>
1980
1981<LI>Treat sample broadening.</LI>
1982
1983<P></P><p class=MsoNormal> 
1984Refine <B>Cryst. Size</B> and isotropic <B>microstrain</B> parameters for the
1985CuCr2O4 phase and the isotropic <B>microstrain</B> parameter for the
1986CuO impurity.
1987
1988<P></P><p class=MsoNormal> 
1989It will be easier to start the sequential refinement with a good fit
1990for the sample broadening. For the majority phase, we should consider
1991both crystallite and microstrain broadening. For the CuO impurity,
1992which only has a few visible peaks, refinement of more than one
1993broadening parameter is not likely to succeed and use of either
1994parameter should be fine.
1995Select the <B>CuCr2O4 phase</B> and the <B>Data</B> tab on the top of
1996the window and then select to refine the <B>Cryst. Size</B> and
1997<B>microstrain</B> parameters.
1998Then select the <B>CuO phase</B> (note that the <B>Data</B> tab is
1999still displayed) and select to refine the <B>microstrain</B> parameter.
2000
2001</OL>
2002 
2003<H3>2. Perform additional fit</H3>
2004
2005<P></P><p class=MsoListParagraphCxSpMiddle>
2006Starting an additional refinement (using the Calculate/Refine menu item)
2007with the addition of the six new variables to the refinement improves
2008the fit significantly visually, though the Rw value drops only to ~15.5%.
2009
2010<H3>3. Still more sample parameters.</H3>
2011
2012<OL style='PADDING-LEFT:0.75in' type="A"><LI>
2013  Vary background peak position</LI>
2014 
2015<P></P><p class=MsoNormal> 
2016Selecting the <b>Background</b> sub-item in the
2017<B>PWDR OH_00.fxye Bank 1</b> histogram and click on the checkbox to
2018  refine the position (<B>pos</B>) value for the single background
2019  peak.
2020
2021  <P></P>
2022<LI>Use Uniaxial (010 axis) microstrain broadening for CuCr2O4</LI>
2023
2024<P></P><p class=MsoNormal>Close examination of the pattern shows that
2025the peak widths are still not as well fit as desired. Since strain broadening
2026seems more significant that sample broadening, we could use an anisotropic
2027strain model. Rather than choosing the relatively complex generalized model, we
2028can introduce only two terms with the uniaxial model.<span
2029style='mso-spacerun:yes'>  </span>Trial and error will show that the 010
2030direction works best. Click on the first phase (<b>CuCr2O4</b>) and
2031the <b>Data</b> tab and select <b>uniaxial</b> for the <b>Mustrain
2032model</b> and change the <B>Unique axis, HKL</B> from "0 0 1" to <b>0
20331 0</b>.
2034Select refinement for both <b>Equatorial</b> and <b>Axial
2035mustrain</b>.
2036</OL>
2037
2038<H3>4. Perform additional fit</H3>
2039
2040<P></P><p class=MsoListParagraphCxSpMiddle>
2041Starting an additional refinement (using the Calculate/Refine menu item)
2042with the addition of two more optimized variables to the refinement improves
2043the fit significantly visually and the Rw value drops to <14%, but the
2044additon of the new background parameter causes issues with correlation
2045between the background terms. Considering that we have not refined any
2046atomic parameters, this is an very good fit despite the seemingly high
2047Rw value, as shown in the plot below.  Clicking on the
2048<b>Covariance</b> data tree item shows the
2049GOF=1.08 and the Reduced &#967;<sup>2</sup>=1.16. This is close to
2050ideal.
2051While atomic parameters could now be refined, this is
2052clearly a good enough place to start refinement with all the datasets. </p>
2053
2054<h1>Step III: Prepare for sequential fit. </h1>
2055
2056<P></P>
2057<p class=MsoNormal>
2058<P></P>
2059<p class=MsoNormal>There is one significant way that sequential
2060fitting differs from the usual refinement process. Rather than fitting
2061lattice constants (for which there will be only one set for each phase in the
2062entire refinement), we will use the Hydrostatic/Elastic strain terms
2063(parameters <tt>&lt;p&gt;:&lt;h&gt;:D<I>ij</i></tt>) to treat the change in
2064lattice parameters from histgram to histogram.
2065
2066<P></P>
2067<p class=MsoNormal style='PADDING-LEFT:0.25in'><I>
2068More details:
2069Note that GSAS-II shows the user unit cell parameters in the
2070traditional a, b, c, &#945;, &#946; & &#947; (distances in &#8491, angles in
2071degrees), but computations are performed internally only
2072after converting this cell to
2073a version of the reciprocal lattice tensor we call the "A tensor" or
2074the <tt>A<i>j</i></tt> terms (<a
2075href="https://gsas-ii.readthedocs.io/en/latest/GSASIIutil.html#gsasiilattice-unit-cells">see
2076the GSASIIlattice documentation<a/>).
2077The actual values refined in GSAS-II are the <tt>A<i>j</i></tt> terms, as
2078allowed by unit cell symmetry. There is one set of <tt>A<i>j</i></tt> values
2079for each phase, but to treat the situation where the use of a phase in
2080each histogram may have somewhat different lattice parameters (<a
2081href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWCombined/Combined%20refinement.htm">see
2082the PbSO<sub>4</sub> combined fitting tutorial</a>, where the x-ray and
2083neutron data were collected at different temperatures), GSAS-II
2084defines <tt>D<I>ij</i></tt> terms, labeled as "Hydrostatic/elastic
2085strain coefficients",  for each phase in each histogram and only the unique
2086terms are shown on the Phase "Data" tab. These values
2087are simply added to the <tt>A<i>j</i></tt> terms. When any <tt>D<I>ij</i></tt>
2088terms are non-zero, the changed unit cell parameters are also shown on
2089the "Data" tab and will differ from the unit cell values shown on the
2090"General" tab.
2091</I>
2092
2093<H3>1. Remove refinement of sensitive parameters (lattice, phase
2094fractions, size/&#956;strain, background peak and sample displacement)
2095and add refinement of the <tt>D<I>ij</i></tt> terms.</H3>
2096
2097<p class=MsoNormal style='PADDING-LEFT:0.25in'>
2098For the initial fitting of datasets over a range of conditions, we
2099will want to start from the fitted values we have fit, but until
2100we have reasonably good values for the scale factor, background and
2101lattice parameters, we do not want to refine any thing else.</P>
2102
2103
2104<OL style='PADDING-LEFT:0.75in' type="A">
2105<LI>
2106Select the first phase (<B>CuCr2O4</B>) and on the <B>General</B> tab,
2107click on the <B>Refine unit cell</B> option to turn off refinement. </P> 
2108
2109<p class=MsoListParagraphCxSpMiddle><span style='mso-spacerun:yes'> </span><span
2110style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2111 id="Picture_x0020_64" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:6in;
2112 height:164.25pt;visibility:visible;mso-wrap-style:square'>
2113 <v:imagedata src="SequentialTutorial_files/image017.png" o:title=""/>
2114</v:shape><![endif]--><![if !vml]><img width=576 height=219
2115src="SequentialTutorial_files/image067.png" v:shapes="Picture_x0020_64"><![endif]></span></p>
2116
2117  <P></P>
2118  <LI>On the Data tab (for <B>CuCr2O4</B>), turn <U>off</U> refinement of the <B>Phase
2119  fraction</B>, the <b>size</b> and both the <b>mustrain</b>
2120  parameters. Turn <U>on</U> refinement of the <B>D11, D22</B> and
2121  <B>D33</B> terms to allow the combined lattice parameters to vary.
2122  The Data window should look something like
2123  </p>
2124
2125<p class=MsoListParagraphCxSpMiddle><span style='mso-spacerun:yes'> </span><span
2126style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2127 id="Picture_x0020_65" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:6in;
2128 height:346.5pt;visibility:visible;mso-wrap-style:square'>
2129 <v:imagedata src="SequentialTutorial_files/image019.png" o:title=""/>
2130</v:shape><![endif]--><![if !vml]><img width=576 height=462
2131src="SequentialTutorial_files/image068.png" v:shapes="Picture_x0020_65"><![endif]></span></p>
2132
2133  <P></P>
2134  <LI>
2135  Select the second phase (<B>CuO</B>) and on the
2136Data tab (since that is shown first), turn <U>off</U> refinement of the <B>Phase
2137  fraction</B> and the <b>microstrain</b>
2138  parameters. Turn <U>on</U> refinement of the <B>D11, D22</B> and
2139  <B>D33</B> terms to allow the combined lattice parameters to
2140  vary. We could refine the <B>D13</B> term [which is related to
2141  cos(&#946*) angle for CuO] but the changes to this are small and
2142  since this is a minor phase and few CuO peaks are seen, it is best
2143  to not vary this, at least initially.  The Data window should look
2144  something like </P>
2145
2146<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2147mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_66" o:spid="_x0000_i1048"
2148 type="#_x0000_t75" style='width:6in;height:303pt;visibility:visible;
2149 mso-wrap-style:square'>
2150 <v:imagedata src="SequentialTutorial_files/image021.png" o:title=""/>
2151</v:shape><![endif]--><![if !vml]><img width=576 height=404
2152src="SequentialTutorial_files/image069.png" v:shapes="Picture_x0020_66"><![endif]></span></p>
2153
2154  <P></P>
2155<LI> On the <B>General</B> tab for CuO,
2156click on the <B>Refine unit cell</B> option to turn off refinement of
2157that.
2158
2159  <P></P>
2160<LI> Also
2161at this stage, turn off
2162refinement of the background peak refinement position and width (sig)
2163terms by clicking on the <b>Background</b> histogram tree item and removing
2164checks from the first and third items in the background peaks table
2165(which has only one row). Be sure to click
2166elsewhere in the window before going on to the next step. </p>
2167
2168<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2169mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_67" o:spid="_x0000_i1047"
2170 type="#_x0000_t75" style='width:6in;height:211.5pt;visibility:visible;
2171 mso-wrap-style:square'>
2172 <v:imagedata src="SequentialTutorial_files/image023.png" o:title=""/>
2173</v:shape><![endif]--><![if !vml]><img width=576 height=282
2174src="SequentialTutorial_files/image070.png" v:shapes="Picture_x0020_67"><![endif]></span></p>
2175
2176  <P></P>
2177<LI>Likewise, select the histogram <B>Sample Parameters</B> tree entry
2178and on that window, turn off the refinement flag for <b>Sample X displ.</b> 
2179</p>
2180
2181<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2182mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_68" o:spid="_x0000_i1046"
2183 type="#_x0000_t75" style='width:6in;height:285.75pt;visibility:visible;
2184 mso-wrap-style:square'>
2185 <v:imagedata src="SequentialTutorial_files/image025.png" o:title=""/>
2186</v:shape><![endif]--><![if !vml]><img width=576 height=381
2187src="SequentialTutorial_files/image025.png" v:shapes="Picture_x0020_68"><![endif]></span></p>
2188
2189  <P></P>
2190<LI>At this point the refinement could be repeated to show that the
2191fit does not change significantly. If this is done, one will see
2192small non-zero values for the <tt>D<I>ij</i></tt> terms, but the unit
2193cell parameters displayed on the "Data" tab are not significantly
2194different from those computed without the <tt>D<I>ij</i></tt> values
2195shown on the "General" tab, but due to the larger uncertainties on the
2196CuO unit cell parameters, the <tt>D<I>ij</i></tt> terms are much
2197larger than for CuCr2O4.
2198
2199</OL>
2200
2201<h1>Step IV: Import the remaining datasets.</h1>
2202
2203<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2204
2205<p class=MsoNormal>In this step we bring in the remaining data.
2206Note that the values for the parameters for the newly-read histograms
2207(on the Sample Parameters data item) and the phase/histogram
2208parameters on each phase's Data tab are set to default values, so we
2209copy the values from the first histogram to the new sets.
2210We can then perform an initial sequential fit. </p>
2211
2212<H3>1. Read the remaining datasets.</H3>
2213
2214<P></P>
2215<OL style='PADDING-LEFT:0.75in' type="A"><LI>
2216  Read the
2217remaining datasets using the <B>Import/Powder Data/from GSAS powder data file</span></b>
2218to open a file browser. Again select <b>zip archive</b>
2219and the downloaded <b>SeqTut.zip</b> file. Select all the <b>.fxye</b>
2220files except <b>OH_00.fxye</b> (use of the filter can
2221again be helpful to show just the data files; press <b>Set All</b> and then
2222unselect the one unneeded file or equivalently one can select only the
2223<b>OH_00.fxye</b> file and press <b>Toggle All</b>). The press OK to
2224start reading the datasets.</p>
2225
2226<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2227mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_69" o:spid="_x0000_i1045"
2228 type="#_x0000_t75" style='width:327pt;height:318pt;visibility:visible;
2229 mso-wrap-style:square'>
2230 <v:imagedata src="SequentialTutorial_files/image026.png" o:title=""/>
2231</v:shape><![endif]--><![if !vml]><img width=436 height=424
2232src="SequentialTutorial_files/image026.png" v:shapes="Picture_x0020_69"><![endif]></span></p>
2233
2234<P></P>
2235  <LI>This time one must select the
2236instrument parameter file (because the name does not match the dataset
2237file name). </p>
2238
2239<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2240mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_70" o:spid="_x0000_i1044"
2241 type="#_x0000_t75" style='width:6in;height:221.25pt;visibility:visible;
2242 mso-wrap-style:square'>
2243 <v:imagedata src="SequentialTutorial_files/image027.png" o:title=""/>
2244</v:shape><![endif]--><![if !vml]><img width=576 height=295
2245src="SequentialTutorial_files/image071.png" v:shapes="Picture_x0020_70"><![endif]></span></p>
2246
2247<P></P>
2248  <LI>Set
2249all data sets to use the two phases</span>, as before in <A href="#I.2.C">
2250 step I.2.C</A> (above).</LI>
2251
2252<p class=MsoListParagraphCxSpMiddle>Note that the files will be
2253processed in the order they appear in the tree (or the reverse of that
2254order, as set in Controls). It will be most convenient if the files
2255are imported in a logical sequence, which could require multiple
2256Import operations to read the files in the desired order or to
2257rename files prior to reading so they are listed in the
2258correct order in the file browser. If files are not read in the
2259intended order, it will be necessary to
2260manually change the positions of the tree items (by dragging them in
2261 the tree with
2262the right mouse button pressed).
2263This is not an issue in this example, since the files are listed in a
2264zip file in the order they need to be read, but may be of concern
2265for other cases.
2266</p>
2267
2268<P></P><LI>Optional: Note that the default graphics
2269mode is to display the last dataset read in.<span style='mso-spacerun:yes'> 
2270</span>If you want to see the entire ensemble of data sets, click on the main
2271entry for any of the datasets (for example <b style='mso-bidi-font-weight:normal'><span
2272style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
2273mso-hansi-theme-font:major-latin'>PWDR OH_00.fxye Bank 1</span></b>), click on
2274the frame of the plot window and press the “<b style='mso-bidi-font-weight:
2275normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2276major-latin;mso-hansi-theme-font:major-latin'>m</span></b>” key.<span
2277style='mso-spacerun:yes'>  </span>(Alternately, press the “<b style='mso-bidi-font-weight:
2278normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2279major-latin;mso-hansi-theme-font:major-latin'>K</span></b>” icon from the list
2280at the bottom of plot, between the “floppy disk” and “question mark” icons and
2281then select “<b style='mso-bidi-font-weight:normal'><span style='font-family:
2282"Calibri",sans-serif;mso-ascii-theme-font:major-latin;mso-hansi-theme-font:
2283major-latin'>m: toggle multidata plot</span></b>” from the pop-up window). The
2284‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2285mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>U</span></b>’,
2286’<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2287mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>D</span></b>’,
2288’<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2289mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>R</span></b>’
2290&amp; ‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2291mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>L</span></b>’
2292keys control the appearance of a ‘waterfall plot’. </p>
2293
2294<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2295mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_71" o:spid="_x0000_i1043"
2296 type="#_x0000_t75" style='width:6in;height:370.5pt;visibility:visible;
2297 mso-wrap-style:square'>
2298 <v:imagedata src="SequentialTutorial_files/image029.png" o:title=""/>
2299</v:shape><![endif]--><![if !vml]><img width=576 height=494
2300src="SequentialTutorial_files/image072.png" v:shapes="Picture_x0020_71"><![endif]></span></p>
2301
2302<P></P><LI>You can then select the ‘<b
2303style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2304mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>C</span></b>’
2305key for a contour plot of all the data; use ‘<b style='mso-bidi-font-weight:
2306normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2307major-latin;mso-hansi-theme-font:major-latin'>U</span></b>’ and ‘<b
2308style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2309mso-ascii-theme-font:major-latin;mso-hansi-theme-font:major-latin'>D</span></b>’
2310keys to change the contrast.</p>
2311
2312<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2313mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_72" o:spid="_x0000_i1042"
2314 type="#_x0000_t75" style='width:6in;height:370.5pt;visibility:visible;
2315 mso-wrap-style:square'>
2316 <v:imagedata src="SequentialTutorial_files/image031.png" o:title=""/>
2317</v:shape><![endif]--><![if !vml]><img width=576 height=494
2318src="SequentialTutorial_files/image073.png" v:shapes="Picture_x0020_72"><![endif]></span></p>
2319
2320<p class=MsoListParagraphCxSpLast>Above, I’ve used ‘<b style='mso-bidi-font-weight:
2321normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2322major-latin;mso-hansi-theme-font:major-latin'>D</span></b>’ to increase the
2323contrast &amp; zoomed in to a location that shows the effect of temperature on
2324the peak positions.</p>
2325</OL>
2326<h3>2. Duplicate information across histograms.</h3>
2327
2328<P></P>
2329<OL style='PADDING-LEFT:0.75in' type="A"><LI>
2330To copy
2331the histogram parameters from the first histogram to the new ones:
2332  select the original <B>PWDR OH_00.fxye Bank 1</b> tree entry and then
2333  use menu command <b>Commands/Copy params</b>.
2334  We need to duplicate the values in the <b>Limits</b>,
2335  <b>Background</b> and <b>Sample Parameters</b> sections between all
2336  histograms. The <b>Instrument Parameters</b> have been read from the
2337  instrument parameter file, and have not been changed in this
2338  exercise, so they are already identical.
2339
2340<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
2341
2342<p class=MsoNormal>This opens a dialog box where the sections
2343to be copied are selected. Limits, Background and Sample Parameters
2344  must be selected; there will be no difference if Instrument
2345  Parameters is selected, since the parameters start as identical, so
2346  there also is no harm in copying them. This, the default entries,
2347  selecting all sections, need not be changed. </p>
2348
2349<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2350mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_73" o:spid="_x0000_i1041"
2351 type="#_x0000_t75" style='width:179.25pt;height:241.5pt;visibility:visible;
2352 mso-wrap-style:square'>
2353 <v:imagedata src="SequentialTutorial_files/image033.png" o:title=""/>
2354</v:shape><![endif]--><![if !vml]><img width=239 height=322
2355src="SequentialTutorial_files/image033.png" v:shapes="Picture_x0020_73"><![endif]></span></p>
2356
2357
2358<P></P><LI>
2359  Press <b>OK</B>.
2360  Note that all Sample Parameters are copied, except measurement
2361  information such as setting angles, temperature, etc. </LI>
2362
2363
2364<P></P><LI>
2365  An additional dialog window is shown which
2366asks which histograms should receive the parameters. <span style='mso-bidi-font-weight:
2367bold'>Press <b>Set All</b> to select all remaining histograms
2368and then press<b>OK</b>. </LI>
2369
2370<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
2371
2372<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2373mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_74" o:spid="_x0000_i1040"
2374 type="#_x0000_t75" style='width:203.25pt;height:318pt;visibility:visible;
2375 mso-wrap-style:square'>
2376 <v:imagedata src="SequentialTutorial_files/image034.png" o:title=""/>
2377</v:shape><![endif]--><![if !vml]><img width=271 height=424
2378src="SequentialTutorial_files/image034.png" v:shapes="Picture_x0020_74"><![endif]></span></p>
2379
2380<P></P><p class=MsoListParagraphCxSpLast>To verify that the copy has
2381been performed, examining any of the other histogram plots (e.g. to see the
2382changed lower limit), etc. or view the contents of the various updated sections.
2383
2384
2385<P></P><LI>
2386Next we need to copy the Phase/Histogram parameters
2387within each phase. To do this, select the first phase (<b>CuCr2O4</b>)
2388in the data tree
2389and then the <b>Data</b> tab in the window. Then use the <b>Edit Phase/Copy data</b> menu
2390command, which raises the selction window below.
2391</LI>
2392
2393<p class=MsoListParagraphCxSpMiddle><span style='mso-spacerun:yes'> </span><span
2394style='mso-fareast-language:EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2395 id="Picture_x0020_75" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:250.5pt;
2396 height:318pt;visibility:visible;mso-wrap-style:square'>
2397 <v:imagedata src="SequentialTutorial_files/image035.png" o:title=""/>
2398</v:shape><![endif]--><![if !vml]><img width=334 height=424
2399src="SequentialTutorial_files/image035.png" v:shapes="Picture_x0020_75"><![endif]></span></p>
2400
2401<P></P>
2402<p class=MsoListParagraphCxSpMiddle>
2403Press the <b>Set All</b> button and then press the <b>OK</b> button.</p>
2404
2405<P></P><LI>
2406Repeat the previous step for the CuO phase.
2407Select <B>CuO</B> in the data tree and then copy the Phase/Histogram
2408parameters in its <b>Data</b> tab by again using the <b>Edit
2409Phase/Copy data</b> menu command. Again, select all histograms and
2410then press the <b>OK</b> button.
2411</LI>
2412</OL>
2413
2414
2415<h1>Step V: Setup and start the sequential refinement. </h1>
2416
2417<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2418
2419<p class=MsoNormal>At this point we determine which histograms will be used in
2420the fit and set that the resulting parameters from the results of each refinement
2421will be used for the subsequent refinements.</p>
2422
2423<H3>1. Set overall Controls for a sequential fit and launch it</H3>
2424
2425<P></P>
2426<p class=MsoListParagraphCxSpMiddle>Here we enable sequential mode by
2427setting the histograms to be included, set another control setting
2428(max cycles) and launch the sequential fit.
2429
2430<OL style='PADDING-LEFT:0.75in' type="A"><LI>
2431Select the <B>Controls</b> data tree item, in the window (as shown
2432below) and press the "Sequential Refinement
2433<b>Select data</b>" button.
2434
2435
2436<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2437mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_76" o:spid="_x0000_i1038"
2438 type="#_x0000_t75" style='width:6in;height:167.25pt;visibility:visible;
2439 mso-wrap-style:square'>
2440 <v:imagedata src="SequentialTutorial_files/image036.png" o:title=""/>
2441</v:shape><![endif]--><![if !vml]><img width=576 height=223
2442src="SequentialTutorial_files/image074.png" v:shapes="Picture_x0020_76"><![endif]></span></p>
2443
2444<P></P>
2445<p class=Msonormal>This opens the window where
2446all histograms can be selected. Press <b>Set All</b> and then press
2447<B>OK</B>. Note that the Controls window now lists the number of
2448datasets in the sequential refinement and three new controls below
2449  that. One is the new "Reverse order?" checkbox, which causes
2450the sequential refinement to start with the last histogram, not the first.
2451Sometimes this is useful, but not here. The "Clear previous
2452  seq. results" will remove previous sequential results from a .gpx
2453  file, reducing its size. The "Copy results to next histogram?" is
2454  described in the next section. 
2455
2456<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2457mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_77" o:spid="_x0000_i1037"
2458 type="#_x0000_t75" style='width:6in;height:162pt;visibility:visible;
2459 mso-wrap-style:square'>
2460 <v:imagedata src="SequentialTutorial_files/image038.png" o:title=""/>
2461</v:shape><![endif]--><![if !vml]><img width=576 height=216
2462src="SequentialTutorial_files/image075.png" v:shapes="Picture_x0020_77"><![endif]></span></p>
2463
2464  <P></P><LI>
2465  <B><I>Important:</I></B>
2466  Check the "<b>Copy results to next histogram</b>?" checkbox. When this
2467  is selected, the parameters obtained after fitting each histogram
2468  will be used as the starting point for the next fit, which is
2469  essential here since the lattice parameters change considerably. If
2470  this were not selected, then refinement for <I>each histogram</I> would
2471start with the current parameters for that histogram --
2472these were obtained from fitting the first (~7 K) dataset. If we did that
2473  the first few refinements will go well, but when reaching datasets
2474  where the temperature
2475  was sufficiently different from 7 K, the starting lattice parameters may be
2476  too far off and the refinements will fail. Even if that were not
2477true, since the temperatures are fairly close between datasets in the
2478series,
2479each fit will start with a fairly close to correct set of lattice
2480  parameters and thus fewer cycles of refinement will be needed to get
2481  to the correct values.
2482</p>
2483
2484<P></P><LI>Also on the Controls window, change the <B>Max cycles</B>
2485setting to <B>10</B>. This makes sure that the refinements have enough
2486cycles to fully adjust to the changes in lattice parameters before
2487being used as the starting point for the next refinement. Note that
2488if the refinement converges, no additional cycles are used, so 10 is a
2489maximum that is not likely to be reached.
2490</LI> 
2491
2492</OL>
2493
2494<H3>2. Start the sequential refinement</H3>
2495
2496
2497<p class=MsoListParagraphCxSpMiddle>Start the sequential refinement
2498with the <b>Calculate/Sequential refine</b> menu command (note that
2499once the histograms were selected for a sequential fit in the previous
2500step, the menu command was relabeled from Calculate/Sequential
2501refine.)</P><P></P>
2502<p class=MsoListParagraphCxSpMiddle <p
2503style='PADDING-LEFT:0.25in'><I>Note that a window
2504saying "There were constraint warnings..." will be generated.
2505This is because we have specified a constraint on the phase
2506fractions in <A href="#I.3">step I.3</A>, but we are no longer varying
2507them, so this constraint must be ignored.
2508Also note the discussion on <A href="#VI.1.F">sequential fit
2509constraint modes</A> in step VI, below.
2510This alert is shown to provide a chance to review
2511possible problems with constraints and not continue with the fit,
2512when this indicates that something has been left out from the varied
2513parameters. However, in this case, this phase fraction constraint
2514will be fine to ignore since we do not want to refine phase fractions
2515at this stage. This message will stop being shown when phase fractions
2516are refined again (or if the constraint would be removed). Press
2517"Yes" to continue with this initial sequential fit, as this
2518warning can be ignored.
2519<P></P></I>
2520<p class=MsoListParagraphCxSpMiddle>
2521The refinement may take a few minutes as each of the 17
2522datasets are fit in turn.</p>
2523<h3>3. Accept the sequential refinement results.</h3>
2524
2525<p class=MsoListParagraphCxSpMiddle>When the refinement completes, a window will be displayed where you
2526are asked if you want to load the results, as below.
2527
2528<p class=MsoNormal style='text-indent:.5in'><span style='mso-fareast-language:
2529EN-US;mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_78"
2530 o:spid="_x0000_i1036" type="#_x0000_t75" style='width:274.5pt;height:91.5pt;
2531 visibility:visible;mso-wrap-style:square'>
2532 <v:imagedata src="SequentialTutorial_files/image041.png" o:title=""/>
2533</v:shape><![endif]--><![if !vml]><img width=366 height=122
2534src="SequentialTutorial_files/image041.png" v:shapes="Picture_x0020_78"><![endif]></span></p>
2535
2536<P></P>
2537<p class=MsoListParagraphCxSpFirst>After clicking on <B>OK</B>
2538the Sequential Results item is created in the data tree and is is
2539selected, which displays a summary of the refinement results as a
2540large table, as below.</p>
2541
2542
2543<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2544mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_79" o:spid="_x0000_i1035"
2545 type="#_x0000_t75" style='width:6in;height:247.5pt;visibility:visible;
2546 mso-wrap-style:square'>
2547 <v:imagedata src="SequentialTutorial_files/image042.png" o:title=""/>
2548</v:shape><![endif]--><![if !vml]><img width=576 height=330
2549src="SequentialTutorial_files/image077.png" v:shapes="Picture_x0020_79"><![endif]></span></p>
2550
2551<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
2552
2553<p class=MsoListParagraphCxSpMiddle>The second column shows the weighted profile
2554R-factor, from each fit. This shows a steady increase with temperature, as
2555might be expected if there were a systematic change in some sample parameters,
2556such as strain or background or even atomic coordinates (which have not yet
2557been fit). The &#916;&#967;<sup>2</sup> value in the third column shows the
2558percent improvement in &#967;<sup>2</sup> seen in the last cycle of refinement.
2559(Meaning that if in that cycle the &#916;&#967;<sup>2</sup> value
2560decreases from 4.1 to 4.0, then the value will be 100*(4.1-4.0)/4.0, or
25612.5%; small numbers indicate that the fit converged.). Note that the
2562fits had pretty well stopped improving, so there is no reason to
2563provide further cycles of refinement without adding new variable
2564parameters. </p> 
2565
2566<p class=MsoListParagraphCxSpMiddle><o:p>&nbsp;</o:p></p>
2567
2568<p class=MsoListParagraphCxSpMiddle>Subsequent columns will show any of the
2569sample parameters that vary across the datasets, here only temperature and then
2570the direct cell lattice constants for each phase, generated from the A<i>x</i> and D<i>ij</i> terms. Scrolling further shows columns the values of most
2571parameters that differ by histogram. Note that some parameters (such
2572as the actual D<i>ij</i> terms) are not shown. The choices for which
2573items that are included is determined by the "Hide columns..." command in
2574the"Columns/Rows" menu.
2575</p>
2576
2577<h3>4. Examine the sequential refinement results.</h3>
2578
2579<p class=MsoListParagraphCxSpMiddle>Before going further, it is useful to
2580review the trends in the lattice parameters as a sanity check. This can be done
2581by <span style='mso-bidi-font-weight:bold'>double-clicking on a column of the
2582table</span>, such as the <b style='mso-bidi-font-weight:normal'><span
2583style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:major-latin;
2584mso-hansi-theme-font:major-latin'>0::b</span></b> parameter, which displays
2585this plot:</p>
2586
2587<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2588mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_80" o:spid="_x0000_i1034"
2589 type="#_x0000_t75" style='width:6in;height:370.5pt;visibility:visible;
2590 mso-wrap-style:square'>
2591 <v:imagedata src="SequentialTutorial_files/image044.png" o:title=""/>
2592</v:shape><![endif]--><![if !vml]><img width=576 height=494
2593src="SequentialTutorial_files/image078.png" v:shapes="Picture_x0020_80"><![endif]></span></p>
2594
2595<P></P>
2596<p class=MsoListParagraphCxSpMiddle>Pressing the “<b>K</b>” icon or pressing the “<b>s</b>” key brings up a menu where the x-axis can be selected as
2597Temperature. If the plot fails to update, click on another column and then
2598return to the original column. </p>
2599
2600<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2601mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_81" o:spid="_x0000_i1033"
2602 type="#_x0000_t75" style='width:6in;height:370.5pt;visibility:visible;
2603 mso-wrap-style:square'>
2604 <v:imagedata src="SequentialTutorial_files/image046.png" o:title=""/>
2605</v:shape><![endif]--><![if !vml]><img width=576 height=494
2606src="SequentialTutorial_files/image079.png" v:shapes="Picture_x0020_81"><![endif]></span></p>
2607
2608<p class=MsoListParagraphCxSpLast><o:p>&nbsp;</o:p></p>
2609
2610<h1>Step VI: Continue the sequential refinement. </h1>
2611
2612<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2613
2614<p class=MsoNormal>At this point we wish to continue the refinements
2615using the the current as-refined parameter values as the starting
2616point. This is the default action for the program as the <b>Copy
2617results to next histogram</b> checkbox is automatically unchecked
2618after a successful sequential refinement. Note that
2619in subsequent actions we will use the "Copy flags" menu commands,
2620which copy only refinement flags not parameter values (as opposed to
2621the "Copy" commands used previously, which copy both values and flags.)
2622</p>
2623
2624
2625<h3>1. Restore the parameters that were previously fit.</h3>
2626
2627<OL style='PADDING-LEFT:0.75in' type="A"><LI>
2628Restore the refinement of background parameters as
2629  in the single-histogram fit. Select <B>Background</B> for any
2630  histogram and add the "Peaks in Background" width (<B>sig</B>)
2631  refine flag.
2632  Note that the peak position could be refined as well, but this is
2633  not well-determined by the data since very little of the low-angle
2634  side of the peak is present, so inclusion of this adds to the
2635  refinement instability without any significant improvement to the
2636  fit.
2637  </LI>
2638  <P></P><LI>
2639  After setting the refinement flag, use the
2640  <B>Background/Copy flags</b> menu item to copy these refinement
2641  flags to all other histograms.</LI> 
2642
2643  <P></P><LI>
2644  Likewise, in the <B>Sample Parameters</B> tree item, include the
2645<B>Sample X displ</b> parameter and again
2646use the <b>Copy flags</b> menu command (here in the <B>Command</B> menu).
2647  </LI>
2648 
2649  <P></P><LI>
2650  For the <B>CuCr<sub>2</sub>O<sub>4</sub></B> phase, return to the
2651  <B>Data</B> tab and enable refinement for the <B>phase fraction</B>
2652  and the three <B>broadening</B> terms (isotropic size and equatorial
2653  and axial mustrain). Again use the <B>Edit Phase/Copy flags</b> menu
2654  command to set these flags for all histograms. </LI>
2655
2656  <P></P><LI>
2657  For the <B>CuO</B> phase, also on the <B>Data</B> tab,
2658  enable refinement for the <B>phase fraction</B>
2659  and the single isotropic <B>microstrain broadening</B> term. Also
2660  add refinement of the <B>D13</B> term. Again use the <B>Edit
2661  Phase/Copy flags</b> menu command to set this for all histograms.
2662  </IL>
2663
2664  <P></P><LI>
2665  <A name="VI.1.F"></A>
2666  Select the <B>Constraints</B> data tree item and note that the
2667  second line of controls that appears for sequential fits.
2668  Confirm that the <B>"Wildcard use"</B> setting is <B>"Set hist # to *"</B>.
2669
2670   <P></P>
2671</OL>
2672  <p class=MsoListParagraphCxSpMiddle style='PADDING-LEFT:0.25in'>
2673  <I>Note:
2674  Refinement of phase
2675  fractions requires a constraint as was added in <A href="#I.3">Step
2676  I.3</A>, but for all histograms.
2677  As of version 5038 of GSAS-II three modes were added for constraints
2678  in sequential refinements.
2679  <UL style='PADDING-LEFT:1.0in'>
2680    <LI>In </I>"Ignore unless hist=*"<I> mode (which was
2681  the only mode prior to this version), any constraints with a
2682  specific histogram number specified (such as </I><tt>":0:0:Scale"</tt><I> and
2683  </I><tt>":1:0:Scale"</tt><I> as used previously) would be ignored and a new
2684  constraint defining </I><tt>":0:*:Scale + :1:*:Scale = 1"</tt><I> would be
2685    required.
2686    <LI>There is now a mode </I>"Set hist # to *"<I> where any
2687  constraints are interpreted to apply to all histograms, despite the
2688  supplied number. <LI>The third mode, </I>"Use as supplied", uses both types
2689  of constraints, so differing constraints can be supplied for
2690  different histograms, but if both </I><tt>":0:*:Scale + :1:*:Scale = 1"</tt><I> and
2691  </I><tt>":0:0:Scale + :1:0:Scale = 1"</tt><I> were supplied, an error would occur
2692    because both constraints would be used for histogram 0.
2693    </UL>
2694    </I>
2695 
2696<h3>2. Perform the refinement.</h3>
2697
2698  <p class=MsoListParagraphCxSpMiddle>
2699Start an additional refinement (using the Calculate/Refine menu item).
2700  Now that the full suite of variables is available for fitting
2701  background, peak widths, etc., the fits improve significantly for
2702  the higher temperature datasets. Before, for the highest temperature
2703  datasets, the Rwp values were in the range of 25-30%. After this
2704  fit, all the Rwp values range from 13-17%. Click on a row header to
2705  see a plot of the fit and double-click on a row header to see the
2706convariance matrix plotted.
2707Note that additional columns appear now in the Sequential results
2708table for the newly-added variables. Also
2709included are the weight fractions. Note that the sum of the phase
2710fractions for each histogram are indeed 1.0.
2711</P>
2712
2713<h1>Step VII: Complete the sequential refinement. </h1>
2714
2715<P></P>
2716<p class=MsoListParagraphCxSpFirst>
2717The last thing we will add to the
2718refinement will be atomic parameters. Note that these are handled a bit
2719differently than the previous things we have refined. There is only one set of
2720coordinates for each phase and these will be refined for each histogram, but
2721are saved individually only in the Sequential results table. To update
2722the coordinates shown in the Phase data tree entry, use the "Update
2723Phase from selected" command in the"Columns/Rows" menu. If a row is
2724selected in the table, that will be used. If no rows are selected, you
2725will be prompted to select a histogram.
2726
2727</p>
2728<h3>1. Vary CuCr<sub>2</sub>O<sub>4</sub> coordinates and
2729U<sub>iso</sub> Parameters.</h3>
2730
2731<P></P>
2732<OL style='PADDING-LEFT:0.75in' type="A"><LI>
2733Select the <b>CuCr2O4</b> phase</span> and then the <b>Atoms</b>
2734  tab. Double-click on the <b>refine</b>column label and a refinement
2735  controls dialog opens as below, select <b>X</b> to refine
2736  coordinates and <b>U</b> to refine the atomic displacement (Uiso)
2737  values.
2738  (<I>Note that only the O atom has coordinates that can be refined,
2739  all coordinates for Cu and Cr are fixed by symmetry.
2740  Use of the X flag for Cu and Cr will not cause those coordinates to
2741  change.</I>)
2742  </LI>
2743 
2744<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2745mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_89" o:spid="_x0000_i1026"
2746 type="#_x0000_t75" style='width:171.75pt;height:150pt;visibility:visible;
2747 mso-wrap-style:square'>
2748 <v:imagedata src="SequentialTutorial_files/image059.png" o:title=""/>
2749</v:shape><![endif]--><![if !vml]><img width=229 height=200
2750src="SequentialTutorial_files/image059.png" v:shapes="Picture_x0020_89"><![endif]></span></p>
2751
2752<P></P>
2753 
2754  <LI>Note the change that appears in the refine column of the atoms
2755  table, as below. Since these parameters are shared in all
2756  histograms, no Copy or Copy flags menu item is needed or even is
2757  available for atomic parameters.</LI> 
2758
2759<p class=MsoListParagraphCxSpMiddle><span style='mso-fareast-language:EN-US;
2760mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_90" o:spid="_x0000_i1025"
2761 type="#_x0000_t75" style='width:6in;height:126pt;visibility:visible;
2762 mso-wrap-style:square'>
2763 <v:imagedata src="SequentialTutorial_files/image060.png" o:title=""/>
2764</v:shape><![endif]--><![if !vml]><img width=576 height=168
2765src="SequentialTutorial_files/image085.png" v:shapes="Picture_x0020_90"><![endif]></span></p>
2766
2767  </OL>
2768  <P></P>
2769<h3>2. Perform final sequential fit, including coordinates displacement parameters.</h3>
2770  <P></P>
2771<p class=MsoListParagraphCxSpMiddle> Start
2772the sequential refinement again with the <b>Calculate/Sequential
2773refine</b> menu item. Small but significant improvements are seen for
2774  fits with the higher temperature datasets, with R<sub>wp</sub>
2775values between 13.8 and 16.5. </P>
2776
2777 
2778<p>This completes the sequential refinement tutorial, although a few more things
2779could be attempted to try to further improve the refinement
2780quality. Be sure to keep the final project file,
2781  since this will used in the <b>Parametric Fitting and Pseudo Variables for
2782Sequential Fits</b> tutorial, where functions of fitted parameters are
2783computed and plotted and these results are fitted to equations of state.
2784</p>
2785
2786</div>
2787
2788</body>
2789
2790</html>
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