source: Tutorials/MCsimanneal/MCSA in GSAS.htm @ 1718

Last change on this file since 1718 was 1718, checked in by vondreele, 7 years ago

updating images in tutorials

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406   Name="Intense Quote"/>
407  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
408  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
409  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
410  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
411  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
412  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
413  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
414  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
415  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
416  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
417  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
418  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
419  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
420  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
421  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
422  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
423  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
424  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
425  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
426  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
427  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
428  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
429  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
430  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
431  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
432  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
433  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
434  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
435  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
436  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
437  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
438  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
439  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
440  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
441  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
442  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
443  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
444  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
445  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
446  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
447  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
448  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
449  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
450  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
451  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
452  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
453  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
454  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
455  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
456  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
457  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
458  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
459  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
460  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
461  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
462  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
463  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
464  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
465  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
466  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
467  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
468  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
469  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
470  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
471  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
472  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
473  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
474  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
475  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
476  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
477  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
478  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
479  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
480  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
481  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
482  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
483  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
484  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
485  <w:LsdException Locked="false" Priority="19" QFormat="true"
486   Name="Subtle Emphasis"/>
487  <w:LsdException Locked="false" Priority="21" QFormat="true"
488   Name="Intense Emphasis"/>
489  <w:LsdException Locked="false" Priority="31" QFormat="true"
490   Name="Subtle Reference"/>
491  <w:LsdException Locked="false" Priority="32" QFormat="true"
492   Name="Intense Reference"/>
493  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
494  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
495   UnhideWhenUsed="true" Name="Bibliography"/>
496  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
497   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
498  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
499  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
500  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
501  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
502  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
503  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
504  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
505  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
506  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
507  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
508  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
509  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
510  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
511  <w:LsdException Locked="false" Priority="46"
512   Name="Grid Table 1 Light Accent 1"/>
513  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
514  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
515  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
516  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
517  <w:LsdException Locked="false" Priority="51"
518   Name="Grid Table 6 Colorful Accent 1"/>
519  <w:LsdException Locked="false" Priority="52"
520   Name="Grid Table 7 Colorful Accent 1"/>
521  <w:LsdException Locked="false" Priority="46"
522   Name="Grid Table 1 Light Accent 2"/>
523  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
524  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
525  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
526  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
527  <w:LsdException Locked="false" Priority="51"
528   Name="Grid Table 6 Colorful Accent 2"/>
529  <w:LsdException Locked="false" Priority="52"
530   Name="Grid Table 7 Colorful Accent 2"/>
531  <w:LsdException Locked="false" Priority="46"
532   Name="Grid Table 1 Light Accent 3"/>
533  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
534  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
535  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
536  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
537  <w:LsdException Locked="false" Priority="51"
538   Name="Grid Table 6 Colorful Accent 3"/>
539  <w:LsdException Locked="false" Priority="52"
540   Name="Grid Table 7 Colorful Accent 3"/>
541  <w:LsdException Locked="false" Priority="46"
542   Name="Grid Table 1 Light Accent 4"/>
543  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
544  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
545  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
546  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
547  <w:LsdException Locked="false" Priority="51"
548   Name="Grid Table 6 Colorful Accent 4"/>
549  <w:LsdException Locked="false" Priority="52"
550   Name="Grid Table 7 Colorful Accent 4"/>
551  <w:LsdException Locked="false" Priority="46"
552   Name="Grid Table 1 Light Accent 5"/>
553  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
554  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
555  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
556  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
557  <w:LsdException Locked="false" Priority="51"
558   Name="Grid Table 6 Colorful Accent 5"/>
559  <w:LsdException Locked="false" Priority="52"
560   Name="Grid Table 7 Colorful Accent 5"/>
561  <w:LsdException Locked="false" Priority="46"
562   Name="Grid Table 1 Light Accent 6"/>
563  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
564  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
565  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
566  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
567  <w:LsdException Locked="false" Priority="51"
568   Name="Grid Table 6 Colorful Accent 6"/>
569  <w:LsdException Locked="false" Priority="52"
570   Name="Grid Table 7 Colorful Accent 6"/>
571  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
572  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
573  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
574  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
575  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
576  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
577  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
578  <w:LsdException Locked="false" Priority="46"
579   Name="List Table 1 Light Accent 1"/>
580  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
581  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
582  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
583  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
584  <w:LsdException Locked="false" Priority="51"
585   Name="List Table 6 Colorful Accent 1"/>
586  <w:LsdException Locked="false" Priority="52"
587   Name="List Table 7 Colorful Accent 1"/>
588  <w:LsdException Locked="false" Priority="46"
589   Name="List Table 1 Light Accent 2"/>
590  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
591  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
592  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
593  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
594  <w:LsdException Locked="false" Priority="51"
595   Name="List Table 6 Colorful Accent 2"/>
596  <w:LsdException Locked="false" Priority="52"
597   Name="List Table 7 Colorful Accent 2"/>
598  <w:LsdException Locked="false" Priority="46"
599   Name="List Table 1 Light Accent 3"/>
600  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
601  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
602  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
603  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
604  <w:LsdException Locked="false" Priority="51"
605   Name="List Table 6 Colorful Accent 3"/>
606  <w:LsdException Locked="false" Priority="52"
607   Name="List Table 7 Colorful Accent 3"/>
608  <w:LsdException Locked="false" Priority="46"
609   Name="List Table 1 Light Accent 4"/>
610  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
611  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
612  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
613  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
614  <w:LsdException Locked="false" Priority="51"
615   Name="List Table 6 Colorful Accent 4"/>
616  <w:LsdException Locked="false" Priority="52"
617   Name="List Table 7 Colorful Accent 4"/>
618  <w:LsdException Locked="false" Priority="46"
619   Name="List Table 1 Light Accent 5"/>
620  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
621  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
622  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
623  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
624  <w:LsdException Locked="false" Priority="51"
625   Name="List Table 6 Colorful Accent 5"/>
626  <w:LsdException Locked="false" Priority="52"
627   Name="List Table 7 Colorful Accent 5"/>
628  <w:LsdException Locked="false" Priority="46"
629   Name="List Table 1 Light Accent 6"/>
630  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
631  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
632  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
633  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
634  <w:LsdException Locked="false" Priority="51"
635   Name="List Table 6 Colorful Accent 6"/>
636  <w:LsdException Locked="false" Priority="52"
637   Name="List Table 7 Colorful Accent 6"/>
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783        mso-fareast-font-family:"Times New Roman";
784        mso-fareast-theme-font:minor-fareast;
785        mso-bidi-font-family:"Times New Roman";
786        color:#17365D;
787        letter-spacing:.25pt;}
788a:link, span.MsoHyperlink
789        {mso-style-noshow:yes;
790        mso-style-priority:99;
791        color:blue;
792        text-decoration:underline;
793        text-underline:single;}
794a:visited, span.MsoHyperlinkFollowed
795        {mso-style-noshow:yes;
796        mso-style-priority:99;
797        color:purple;
798        text-decoration:underline;
799        text-underline:single;}
800p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
801        {mso-style-noshow:yes;
802        mso-style-priority:99;
803        mso-style-link:"Document Map Char";
804        margin:0in;
805        margin-bottom:.0001pt;
806        mso-pagination:widow-orphan;
807        font-size:8.0pt;
808        font-family:"Tahoma",sans-serif;
809        mso-fareast-font-family:"Times New Roman";
810        mso-fareast-theme-font:minor-fareast;}
811p
812        {mso-style-noshow:yes;
813        mso-style-priority:99;
814        mso-margin-top-alt:auto;
815        margin-right:0in;
816        mso-margin-bottom-alt:auto;
817        margin-left:0in;
818        mso-pagination:widow-orphan;
819        font-size:12.0pt;
820        font-family:"Times New Roman",serif;
821        mso-fareast-font-family:"Times New Roman";
822        mso-fareast-theme-font:minor-fareast;}
823pre
824        {mso-style-noshow:yes;
825        mso-style-priority:99;
826        mso-style-link:"HTML Preformatted Char";
827        margin:0in;
828        margin-bottom:.0001pt;
829        mso-pagination:widow-orphan;
830        tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
831        font-size:10.0pt;
832        font-family:"Courier New";
833        mso-fareast-font-family:"Times New Roman";
834        mso-fareast-theme-font:minor-fareast;}
835p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
836        {mso-style-noshow:yes;
837        mso-style-priority:99;
838        mso-style-link:"Balloon Text Char";
839        margin:0in;
840        margin-bottom:.0001pt;
841        mso-pagination:widow-orphan;
842        font-size:8.0pt;
843        font-family:"Tahoma",sans-serif;
844        mso-fareast-font-family:"Times New Roman";
845        mso-fareast-theme-font:minor-fareast;}
846span.MsoPlaceholderText
847        {mso-style-noshow:yes;
848        mso-style-priority:99;
849        mso-style-unhide:no;
850        color:gray;}
851p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
852        {mso-style-noshow:yes;
853        mso-style-priority:1;
854        mso-style-unhide:no;
855        mso-style-qformat:yes;
856        margin:0in;
857        margin-bottom:.0001pt;
858        mso-pagination:widow-orphan;
859        font-size:12.0pt;
860        font-family:"Times New Roman",serif;
861        mso-fareast-font-family:"Times New Roman";
862        mso-fareast-theme-font:minor-fareast;}
863p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
864        {mso-style-noshow:yes;
865        mso-style-priority:34;
866        mso-style-unhide:no;
867        mso-style-qformat:yes;
868        margin-top:0in;
869        margin-right:0in;
870        margin-bottom:0in;
871        margin-left:.5in;
872        margin-bottom:.0001pt;
873        mso-pagination:widow-orphan;
874        font-size:12.0pt;
875        font-family:"Times New Roman",serif;
876        mso-fareast-font-family:"Times New Roman";
877        mso-fareast-theme-font:minor-fareast;}
878span.MsoIntenseReference
879        {mso-style-priority:32;
880        mso-style-unhide:no;
881        mso-style-qformat:yes;
882        font-variant:small-caps;
883        color:#C0504D;
884        letter-spacing:.25pt;
885        font-weight:bold;
886        text-decoration:underline;
887        text-underline:single;}
888span.Heading1Char
889        {mso-style-name:"Heading 1 Char";
890        mso-style-priority:9;
891        mso-style-unhide:no;
892        mso-style-locked:yes;
893        mso-style-link:"Heading 1";
894        font-family:"Times New Roman",serif;
895        mso-ascii-font-family:"Times New Roman";
896        mso-hansi-font-family:"Times New Roman";
897        mso-bidi-font-family:"Times New Roman";
898        font-weight:bold;}
899span.Heading2Char
900        {mso-style-name:"Heading 2 Char";
901        mso-style-noshow:yes;
902        mso-style-priority:9;
903        mso-style-unhide:no;
904        mso-style-locked:yes;
905        mso-style-link:"Heading 2";
906        font-family:"Times New Roman",serif;
907        mso-ascii-font-family:"Times New Roman";
908        mso-hansi-font-family:"Times New Roman";
909        mso-bidi-font-family:"Times New Roman";
910        font-weight:bold;}
911span.Heading3Char
912        {mso-style-name:"Heading 3 Char";
913        mso-style-noshow:yes;
914        mso-style-priority:9;
915        mso-style-unhide:no;
916        mso-style-locked:yes;
917        mso-style-link:"Heading 3";
918        font-family:"Times New Roman",serif;
919        mso-ascii-font-family:"Times New Roman";
920        mso-hansi-font-family:"Times New Roman";
921        mso-bidi-font-family:"Times New Roman";
922        font-weight:bold;}
923span.Heading4Char
924        {mso-style-name:"Heading 4 Char";
925        mso-style-noshow:yes;
926        mso-style-priority:9;
927        mso-style-unhide:no;
928        mso-style-locked:yes;
929        mso-style-link:"Heading 4";
930        font-family:"Cambria",serif;
931        mso-ascii-font-family:Cambria;
932        mso-hansi-font-family:Cambria;
933        color:#4F81BD;
934        font-weight:bold;
935        font-style:italic;}
936span.Heading5Char
937        {mso-style-name:"Heading 5 Char";
938        mso-style-noshow:yes;
939        mso-style-priority:9;
940        mso-style-unhide:no;
941        mso-style-locked:yes;
942        mso-style-link:"Heading 5";
943        font-family:"Times New Roman",serif;
944        mso-ascii-font-family:"Times New Roman";
945        mso-hansi-font-family:"Times New Roman";
946        mso-bidi-font-family:"Times New Roman";
947        color:#4F4FFF;
948        font-weight:bold;}
949span.HTMLPreformattedChar
950        {mso-style-name:"HTML Preformatted Char";
951        mso-style-noshow:yes;
952        mso-style-priority:99;
953        mso-style-unhide:no;
954        mso-style-locked:yes;
955        mso-style-link:"HTML Preformatted";
956        font-family:"Courier New";
957        mso-ascii-font-family:"Courier New";
958        mso-hansi-font-family:"Courier New";
959        mso-bidi-font-family:"Courier New";}
960span.TitleChar
961        {mso-style-name:"Title Char";
962        mso-style-priority:10;
963        mso-style-unhide:no;
964        mso-style-locked:yes;
965        mso-style-link:Title;
966        font-family:"Cambria",serif;
967        mso-ascii-font-family:Cambria;
968        mso-hansi-font-family:Cambria;
969        color:#17365D;
970        letter-spacing:.25pt;}
971span.DocumentMapChar
972        {mso-style-name:"Document Map Char";
973        mso-style-noshow:yes;
974        mso-style-priority:99;
975        mso-style-unhide:no;
976        mso-style-locked:yes;
977        mso-style-link:"Document Map";
978        font-family:"Tahoma",sans-serif;
979        mso-ascii-font-family:Tahoma;
980        mso-hansi-font-family:Tahoma;
981        mso-bidi-font-family:Tahoma;}
982span.BalloonTextChar
983        {mso-style-name:"Balloon Text Char";
984        mso-style-noshow:yes;
985        mso-style-priority:99;
986        mso-style-unhide:no;
987        mso-style-locked:yes;
988        mso-style-link:"Balloon Text";
989        font-family:"Tahoma",sans-serif;
990        mso-ascii-font-family:Tahoma;
991        mso-hansi-font-family:Tahoma;
992        mso-bidi-font-family:Tahoma;}
993p.msotitlecxspfirst, li.msotitlecxspfirst, div.msotitlecxspfirst
994        {mso-style-name:msotitlecxspfirst;
995        mso-style-noshow:yes;
996        mso-style-priority:99;
997        mso-style-unhide:no;
998        margin:0in;
999        margin-bottom:.0001pt;
1000        mso-pagination:widow-orphan;
1001        font-size:26.0pt;
1002        font-family:"Cambria",serif;
1003        mso-fareast-font-family:"Times New Roman";
1004        mso-fareast-theme-font:minor-fareast;
1005        mso-bidi-font-family:"Times New Roman";
1006        color:#17365D;
1007        letter-spacing:.25pt;}
1008p.msotitlecxspmiddle, li.msotitlecxspmiddle, div.msotitlecxspmiddle
1009        {mso-style-name:msotitlecxspmiddle;
1010        mso-style-noshow:yes;
1011        mso-style-priority:99;
1012        mso-style-unhide:no;
1013        margin:0in;
1014        margin-bottom:.0001pt;
1015        mso-pagination:widow-orphan;
1016        font-size:26.0pt;
1017        font-family:"Cambria",serif;
1018        mso-fareast-font-family:"Times New Roman";
1019        mso-fareast-theme-font:minor-fareast;
1020        mso-bidi-font-family:"Times New Roman";
1021        color:#17365D;
1022        letter-spacing:.25pt;}
1023p.msotitlecxsplast, li.msotitlecxsplast, div.msotitlecxsplast
1024        {mso-style-name:msotitlecxsplast;
1025        mso-style-noshow:yes;
1026        mso-style-priority:99;
1027        mso-style-unhide:no;
1028        margin-top:0in;
1029        margin-right:0in;
1030        margin-bottom:15.0pt;
1031        margin-left:0in;
1032        mso-pagination:widow-orphan;
1033        font-size:26.0pt;
1034        font-family:"Cambria",serif;
1035        mso-fareast-font-family:"Times New Roman";
1036        mso-fareast-theme-font:minor-fareast;
1037        mso-bidi-font-family:"Times New Roman";
1038        color:#17365D;
1039        letter-spacing:.25pt;}
1040p.msolistparagraphcxspfirst, li.msolistparagraphcxspfirst, div.msolistparagraphcxspfirst
1041        {mso-style-name:msolistparagraphcxspfirst;
1042        mso-style-noshow:yes;
1043        mso-style-priority:99;
1044        mso-style-unhide:no;
1045        margin-top:0in;
1046        margin-right:0in;
1047        margin-bottom:0in;
1048        margin-left:.5in;
1049        margin-bottom:.0001pt;
1050        mso-pagination:widow-orphan;
1051        font-size:12.0pt;
1052        font-family:"Times New Roman",serif;
1053        mso-fareast-font-family:"Times New Roman";
1054        mso-fareast-theme-font:minor-fareast;}
1055p.msolistparagraphcxspmiddle, li.msolistparagraphcxspmiddle, div.msolistparagraphcxspmiddle
1056        {mso-style-name:msolistparagraphcxspmiddle;
1057        mso-style-noshow:yes;
1058        mso-style-priority:99;
1059        mso-style-unhide:no;
1060        margin-top:0in;
1061        margin-right:0in;
1062        margin-bottom:0in;
1063        margin-left:.5in;
1064        margin-bottom:.0001pt;
1065        mso-pagination:widow-orphan;
1066        font-size:12.0pt;
1067        font-family:"Times New Roman",serif;
1068        mso-fareast-font-family:"Times New Roman";
1069        mso-fareast-theme-font:minor-fareast;}
1070p.msolistparagraphcxsplast, li.msolistparagraphcxsplast, div.msolistparagraphcxsplast
1071        {mso-style-name:msolistparagraphcxsplast;
1072        mso-style-noshow:yes;
1073        mso-style-priority:99;
1074        mso-style-unhide:no;
1075        margin-top:0in;
1076        margin-right:0in;
1077        margin-bottom:0in;
1078        margin-left:.5in;
1079        margin-bottom:.0001pt;
1080        mso-pagination:widow-orphan;
1081        font-size:12.0pt;
1082        font-family:"Times New Roman",serif;
1083        mso-fareast-font-family:"Times New Roman";
1084        mso-fareast-theme-font:minor-fareast;}
1085p.msochpdefault, li.msochpdefault, div.msochpdefault
1086        {mso-style-name:msochpdefault;
1087        mso-style-noshow:yes;
1088        mso-style-priority:99;
1089        mso-style-unhide:no;
1090        mso-margin-top-alt:auto;
1091        margin-right:0in;
1092        mso-margin-bottom-alt:auto;
1093        margin-left:0in;
1094        mso-pagination:widow-orphan;
1095        font-size:10.0pt;
1096        font-family:"Calibri",sans-serif;
1097        mso-fareast-font-family:"Times New Roman";
1098        mso-fareast-theme-font:minor-fareast;
1099        mso-bidi-font-family:Calibri;}
1100.MsoChpDefault
1101        {mso-style-type:export-only;
1102        mso-default-props:yes;
1103        font-size:10.0pt;
1104        mso-ansi-font-size:10.0pt;
1105        mso-bidi-font-size:10.0pt;
1106        font-family:"Calibri",sans-serif;
1107        mso-ascii-font-family:Calibri;
1108        mso-hansi-font-family:Calibri;
1109        mso-bidi-font-family:Calibri;}
1110@page WordSection1
1111        {size:8.5in 11.0in;
1112        margin:1.0in 1.0in 1.0in 1.0in;
1113        mso-header-margin:.5in;
1114        mso-footer-margin:.5in;
1115        mso-paper-source:0;}
1116div.WordSection1
1117        {page:WordSection1;}
1118 /* List Definitions */
1119 @list l0
1120        {mso-list-id:608973138;
1121        mso-list-type:hybrid;
1122        mso-list-template-ids:-1449999034 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1123@list l0:level1
1124        {mso-level-tab-stop:none;
1125        mso-level-number-position:left;
1126        text-indent:-.25in;}
1127@list l0:level2
1128        {mso-level-number-format:alpha-lower;
1129        mso-level-tab-stop:none;
1130        mso-level-number-position:left;
1131        text-indent:-.25in;}
1132@list l0:level3
1133        {mso-level-number-format:roman-lower;
1134        mso-level-tab-stop:none;
1135        mso-level-number-position:right;
1136        text-indent:-9.0pt;}
1137@list l0:level4
1138        {mso-level-tab-stop:none;
1139        mso-level-number-position:left;
1140        text-indent:-.25in;}
1141@list l0:level5
1142        {mso-level-number-format:alpha-lower;
1143        mso-level-tab-stop:none;
1144        mso-level-number-position:left;
1145        text-indent:-.25in;}
1146@list l0:level6
1147        {mso-level-number-format:roman-lower;
1148        mso-level-tab-stop:none;
1149        mso-level-number-position:right;
1150        text-indent:-9.0pt;}
1151@list l0:level7
1152        {mso-level-tab-stop:none;
1153        mso-level-number-position:left;
1154        text-indent:-.25in;}
1155@list l0:level8
1156        {mso-level-number-format:alpha-lower;
1157        mso-level-tab-stop:none;
1158        mso-level-number-position:left;
1159        text-indent:-.25in;}
1160@list l0:level9
1161        {mso-level-number-format:roman-lower;
1162        mso-level-tab-stop:none;
1163        mso-level-number-position:right;
1164        text-indent:-9.0pt;}
1165@list l1
1166        {mso-list-id:1022125565;
1167        mso-list-type:hybrid;
1168        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1169@list l1:level1
1170        {mso-level-tab-stop:none;
1171        mso-level-number-position:left;
1172        margin-left:1.0in;
1173        text-indent:-.25in;}
1174@list l1:level2
1175        {mso-level-number-format:alpha-lower;
1176        mso-level-tab-stop:none;
1177        mso-level-number-position:left;
1178        margin-left:1.5in;
1179        text-indent:-.25in;}
1180@list l1:level3
1181        {mso-level-number-format:roman-lower;
1182        mso-level-tab-stop:none;
1183        mso-level-number-position:right;
1184        margin-left:2.0in;
1185        text-indent:-9.0pt;}
1186@list l1:level4
1187        {mso-level-tab-stop:none;
1188        mso-level-number-position:left;
1189        margin-left:2.5in;
1190        text-indent:-.25in;}
1191@list l1:level5
1192        {mso-level-number-format:alpha-lower;
1193        mso-level-tab-stop:none;
1194        mso-level-number-position:left;
1195        margin-left:3.0in;
1196        text-indent:-.25in;}
1197@list l1:level6
1198        {mso-level-number-format:roman-lower;
1199        mso-level-tab-stop:none;
1200        mso-level-number-position:right;
1201        margin-left:3.5in;
1202        text-indent:-9.0pt;}
1203@list l1:level7
1204        {mso-level-tab-stop:none;
1205        mso-level-number-position:left;
1206        margin-left:4.0in;
1207        text-indent:-.25in;}
1208@list l1:level8
1209        {mso-level-number-format:alpha-lower;
1210        mso-level-tab-stop:none;
1211        mso-level-number-position:left;
1212        margin-left:4.5in;
1213        text-indent:-.25in;}
1214@list l1:level9
1215        {mso-level-number-format:roman-lower;
1216        mso-level-tab-stop:none;
1217        mso-level-number-position:right;
1218        margin-left:5.0in;
1219        text-indent:-9.0pt;}
1220ol
1221        {margin-bottom:0in;}
1222ul
1223        {margin-bottom:0in;}
1224-->
1225</style>
1226<!--[if gte mso 10]>
1227<style>
1228 /* Style Definitions */
1229 table.MsoNormalTable
1230        {mso-style-name:"Table Normal";
1231        mso-tstyle-rowband-size:0;
1232        mso-tstyle-colband-size:0;
1233        mso-style-noshow:yes;
1234        mso-style-priority:99;
1235        mso-style-parent:"";
1236        mso-padding-alt:0in 5.4pt 0in 5.4pt;
1237        mso-para-margin:0in;
1238        mso-para-margin-bottom:.0001pt;
1239        mso-pagination:widow-orphan;
1240        font-size:10.0pt;
1241        font-family:"Calibri",sans-serif;}
1242</style>
1243<![endif]--><!--[if gte mso 9]><xml>
1244 <o:shapedefaults v:ext="edit" spidmax="1026"/>
1245</xml><![endif]--><!--[if gte mso 9]><xml>
1246 <o:shapelayout v:ext="edit">
1247  <o:idmap v:ext="edit" data="1"/>
1248 </o:shapelayout></xml><![endif]-->
1249</head>
1250
1251<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1252
1253<div class=WordSection1>
1254
1255<h1><span style='mso-fareast-font-family:"Times New Roman"'>MC/SA in GSAS-II<o:p></o:p></span></h1>
1256
1257<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
1258
1259<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
1260structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
1261diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets were
1262kindly provided by Peter Stephens (SUNY StonyBrook) and were originally
1263collected on NSLS beam line X3b1. The MC/SA technique is needed in these cases
1264because as you will see the data does not extend very far in 2&#920; so one
1265cannot use charge flipping to solve them. The steps for each begin with peak
1266selection and fitting, then indexing to identify the lattice parameters. A
1267Pawley refinement is used to obtain a set of structure factors needed for the
1268MC/SA runs. We will use previously developed models for the two molecules; I
1269used the freeware program Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1270to create them.</p>
1271
1272<p class=MsoNormal>If you have not done so already, <a
1273href="../../../GSASII/help/Starting%20GSAS.htm">start GSAS-II</a>.</p>
1274
1275<h2>Step 1. Import powder data for 3-aminoquinoline</h2>
1276
1277<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1278style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1279style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1280the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1281mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1282Calibri;mso-bidi-theme-font:minor-latin'>Import/Powder Data/from GSAS powder
1283data file</span></b> menu item to read the data file into the current GSAS-II
1284project. Change the file directory to <b style='mso-bidi-font-weight:normal'><span
1285style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1286mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1287minor-latin'>Exercises/MCSA</span></b><span style='font-family:"Calibri",sans-serif;
1288mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1289Calibri;mso-bidi-theme-font:minor-latin'> to find the file; you may need to
1290change the file type to <b style='mso-bidi-font-weight:normal'>All files (*.*)</b>
1291to find the desired file.</span></p>
1292
1293<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1294style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1295style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1296the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1298Calibri;mso-bidi-theme-font:minor-latin'>Quinoli.gda</span></b><span
1299style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1300mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1301minor-latin'> data</span> file in the first dialog and press <b
1302style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1303mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1304Calibri;mso-bidi-theme-font:minor-latin'>Open</span></b>. There will be a
1305Dialog box asking <b style='mso-bidi-font-weight:normal'><span
1306style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1307mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font:
1308minor-latin'>Is this the file you want?</span></b> Press <b style='mso-bidi-font-weight:
1309normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1310minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1311mso-bidi-theme-font:minor-latin'>Yes</span></b> button to proceed.</p>
1312
1313<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1314style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1315style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1316the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1317mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1318Calibri;mso-bidi-theme-font:minor-latin'>BNL-I.instprm</span></b> instrument
1319parameter file in the second dialog and press <b style='mso-bidi-font-weight:
1320normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1321minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;
1322mso-bidi-theme-font:minor-latin'>Open</span></b>. You’ll have to change the
1323file type to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1324"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1325minor-latin'>*.instprm</span></b> (GSAS-II instrument parameter file). The
1326powder pattern will immediately appear.</p>
1327
1328<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1329 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1330 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1331 <v:stroke joinstyle="miter"/>
1332 <v:formulas>
1333  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1334  <v:f eqn="sum @0 1 0"/>
1335  <v:f eqn="sum 0 0 @1"/>
1336  <v:f eqn="prod @2 1 2"/>
1337  <v:f eqn="prod @3 21600 pixelWidth"/>
1338  <v:f eqn="prod @3 21600 pixelHeight"/>
1339  <v:f eqn="sum @0 0 1"/>
1340  <v:f eqn="prod @6 1 2"/>
1341  <v:f eqn="prod @7 21600 pixelWidth"/>
1342  <v:f eqn="sum @8 21600 0"/>
1343  <v:f eqn="prod @7 21600 pixelHeight"/>
1344  <v:f eqn="sum @10 21600 0"/>
1345 </v:formulas>
1346 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1347 <o:lock v:ext="edit" aspectratio="t"/>
1348</v:shapetype><v:shape id="_x0000_i1051" type="#_x0000_t75" style='width:525pt;
1349 height:450pt;visibility:visible;mso-wrap-style:square'>
1350 <v:imagedata src="MCSA%20in%20GSAS_files/image001.png" o:title=""/>
1351</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1352src="MCSA%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1051"><![endif]></span></p>
1353
1354<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1355
1356<p class=MsoListParagraph>Notice that the pattern extends only to a minimum
1357d-spacing of ~1.81Å; this is not far enough to use charge flipping which needs
13581Å or better. </p>
1359
1360<h2>Step 2. Peak picking &amp; fitting</h2>
1361
1362<p class=MsoNormal>Next you need to select limits so that ~20 peaks are
1363selected for indexing; go to <b style='mso-bidi-font-weight:normal'><span
1364style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1365mso-hansi-theme-font:minor-latin'>Limits</span></b> and choose <b
1366style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1367mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>9-25</span></b>°
13682&#920;. Next go to <b style='mso-bidi-font-weight:normal'><span
1369style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1370mso-hansi-theme-font:minor-latin'>Peak List</span></b> and pick all the peaks
1371you can see between the limits. This is most easily done by hand as the <b
1372style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1373mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Auto search</span></b>
1374routine gives a lot of spurious peaks for this rather noisy and weak data; I
1375picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
1376normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1377minor-latin;mso-hansi-theme-font:minor-latin'>Peak fitting/LSQ PeakFit </span></b>to
1378fit them. You will need to vary at least <b style='mso-bidi-font-weight:normal'><span
1379style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1380mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
1381normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1382minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> in <b
1383style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1384mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1385Parameters</span></b> along with <b style='mso-bidi-font-weight:normal'><span
1386style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1387mso-hansi-theme-font:minor-latin'>pos</span></b> &amp; <b style='mso-bidi-font-weight:
1388normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1389minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> in the <b
1390style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1391mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak List</span></b>
1392to get a reasonable fit suitable for indexing.</p>
1393
1394<h2>Step 3. Indexing</h2>
1395
1396<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1397style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1398mso-hansi-theme-font:minor-latin'>Index Peak List</span></b> and do <b
1399style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1400mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1401to set up the peaks for indexing. Then go to <b style='mso-bidi-font-weight:
1402normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1403minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
1404indexing. The most likely Bravais lattice for these small organic molecules is
1405either Orthorhombic-P or Monoclinic-P; you can try both and see what comes out
1406(Hint: it’s <b style='mso-bidi-font-weight:normal'><span style='font-family:
1407"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1408minor-latin'>Orthorhombic-P</span></b>). The correct unit cell should almost
1409immediately appear with an M20 ~330 with a=7.748, b=7.651, c=12.736,
1410Vol=755.01. Do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1411"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1412minor-latin'>Cell Index/Refine/Copy Cell</span></b>; you can then try various
1413space groups. Press the <b style='mso-bidi-font-weight:normal'><span
1414style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1415mso-hansi-theme-font:minor-latin'>Show HKL positions</span></b> to see the
1416lines with extinctions (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
1417style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1418mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub> 2<sub>1</sub> 2<sub>1</sub></span></b>).
1419You can then do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1420"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1421minor-latin'>Cell Index/Refine/Refine Cell</span></b> to improve the lattice
1422parameters with M20 ~380. Finally do <b style='mso-bidi-font-weight:normal'><span
1423style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1424mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Make new phase</span></b>
1425to create the phase; I named it <b style='mso-bidi-font-weight:normal'><span
1426style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1427mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
1428
1429<h2>Step 4. Setup for Pawley refinement</h2>
1430
1431<p class=MsoNormal>There are a number of steps that must be done in preparation
1432for a Pawley refinement after having completed the unit cell indexing and new
1433phase creation. These cover two things: one is to prepare the powder pattern
1434(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1435
1436<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1437style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1438style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1439<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1440mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1441in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1442region at the end of the data is readily seen. This is ~37deg 2<span
1443style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
1444"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
1445style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>;
1446there is a zero point at the end that needs to be excluded. Use the right mouse
1447button and pick a point just inside the end avoiding the zero. Make a note of
1448the exact d-spacing (for me 1.8133) using the mouse cursor on the plot.</p>
1449
1450<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1451style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1452style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1453<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1454mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1455Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1456style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1457mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1458style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1459mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1460profile</span></b> to recover the default values. The peak fitting done earlier
1461is over a more limited range of 2<span style='font-family:Symbol;mso-ascii-font-family:
1462"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
1463mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
1464Symbol'>Q</span></span> giving values that will not extrapolate well over the
1465wider range to be used in the Pawley refinement. We may refine them again
1466later.</p>
1467
1468<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1469style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1470style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1471<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1472mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1473Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1474normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1475minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
1476
1477<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1478style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1479style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1480to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1481mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b>
1482to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1483"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1484minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1485normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1486minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1487box and enter the d-spacing (1.8133) into the <b style='mso-bidi-font-weight:
1488normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1489minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b> box.</p>
1490
1491<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1492style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1493mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1494
1495<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1496 id="Picture_x0020_2" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:465.75pt;
1497 height:375pt;visibility:visible;mso-wrap-style:square'>
1498 <v:imagedata src="MCSA%20in%20GSAS_files/image003.png" o:title=""/>
1499</v:shape><![endif]--><![if !vml]><img border=0 width=621 height=500
1500src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
1501
1502<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1503
1504<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1505style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1506mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1507for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1508style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1509mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1510dialog box will appear</p>
1511
1512<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1513 id="Picture_x0020_3" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:259.5pt;
1514 height:252pt;visibility:visible;mso-wrap-style:square'>
1515 <v:imagedata src="MCSA%20in%20GSAS_files/image005.png" o:title=""/>
1516</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1517src="MCSA%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
1518
1519<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1520
1521<p class=MsoNormal>Select either choice; the desired data set will be added to
1522this phase for analysis. The data tab now shows the new data set; check the <b
1523style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1524mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1525button to see the full information</p>
1526
1527<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1528 id="Picture_x0020_28" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:359.25pt;
1529 height:375pt;visibility:visible;mso-wrap-style:square'>
1530 <v:imagedata src="MCSA%20in%20GSAS_files/image007.png" o:title=""/>
1531</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=500
1532src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1533
1534<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1535
1536<p class=MsoNormal>This is the location for all the phase dependent parameters
1537for this histogram. Notice that it includes phase fraction, size &amp; mustrain
1538as well as preferred orientation, elastic strain and extinction corrections.
1539The Babinet correction is intended for protein work where a significant region
1540of the structure is disordered solvent. There are buttons for plotting size and
1541mustrain surfaces and preferred orientation correction curves.</p>
1542
1543<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1544style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1545mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1546empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1547style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1548mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1549makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1550normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1551minor-latin;mso-hansi-theme-font:minor-latin'>Pawley dmin</span></b>. The table
1552should list reflections 0-91. Select and check the <b style='mso-bidi-font-weight:
1553normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1554minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b> column using
1555the same technique you used for the peak list. </p>
1556
1557<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1558 id="Picture_x0020_5" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:337.5pt;
1559 height:225pt;visibility:visible;mso-wrap-style:square'>
1560 <v:imagedata src="MCSA%20in%20GSAS_files/image009.png" o:title=""/>
1561</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1562src="MCSA%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
1563
1564<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1565
1566<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1567you didn’t skip a step as it might not work correctly if you did.</p>
1568
1569<h2>Step 5. Pawley refinement</h2>
1570
1571<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1572normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1573minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1574the main GSAS-II data tree window. Before it begins a backup of the project
1575file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1576style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1577mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
1578used to recover from a bad refinement. A progress dialog box will appear
1579showing the residual as the refinement proceeds. My refinement completed with
1580Rwp ~12.9%; a dialog box appears asking if you wish to load the result. Press <b
1581style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1582mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1583To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
1584the width and height).</p>
1585
1586<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1587 id="Picture_x0020_6" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:525pt;
1588 height:450pt;visibility:visible;mso-wrap-style:square'>
1589 <v:imagedata src="MCSA%20in%20GSAS_files/image011.png" o:title=""/>
1590</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1591src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
1592
1593<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1594
1595<p class=MsoNormal>I’ve expanded the vertical scale to show the fit; it is
1596evident from examining the plot that improvement can be had by improving the
1597background model. One easy way to fit that broad hump is to add a peak to the
1598background. Go to <b style='mso-bidi-font-weight:normal'><span
1599style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1600mso-hansi-theme-font:minor-latin'>Background</span></b> and set <b
1601style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1602mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. peaks</span></b>
1603to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1604mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>,
1605then change <b style='mso-bidi-font-weight:normal'><span style='font-family:
1606"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1607minor-latin'>pos</span></b> to <b style='mso-bidi-font-weight:normal'><span
1608style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1609mso-hansi-theme-font:minor-latin'>19</span></b>, <b style='mso-bidi-font-weight:
1610normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1611minor-latin;mso-hansi-theme-font:minor-latin'>int</span></b> to <b
1612style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1613mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>
1614and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1615mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1616to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1617mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>100000</span></b>;
1618for the peak only refine <b style='mso-bidi-font-weight:normal'><span
1619style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1620mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b
1621style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1622mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. coeff.</span></b>
1623to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1624mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5</span></b>;
1625the window shows</p>
1626
1627<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1628 id="Picture_x0020_7" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:402pt;
1629 height:197.25pt;visibility:visible;mso-wrap-style:square'>
1630 <v:imagedata src="MCSA%20in%20GSAS_files/image013.png" o:title=""/>
1631</v:shape><![endif]--><![if !vml]><img border=0 width=536 height=263
1632src="MCSA%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
1633
1634<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1635
1636<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
1637style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1638mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my Rwp fell to
1639~8.5%. In <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1640mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Background</span></b>
1641select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1642mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b>
1643&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b>
1645for refinement and in <b style='mso-bidi-font-weight:normal'><span
1646style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1647mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> select <b
1648style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1649mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1650&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1651mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1652for refinement; then do <b style='mso-bidi-font-weight:normal'><span
1653style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1654mso-hansi-theme-font:minor-latin'>Calculate /Refine</span></b> again. I got
1655Rwp~7.5% at convergence and the fit looked like</p>
1656
1657<p class=MsoNormal><span style='mso-no-proof:yes'>c<!--[if gte vml 1]><v:shape
1658 id="Picture_x0020_33" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:525pt;
1659 height:450pt;visibility:visible;mso-wrap-style:square'>
1660 <v:imagedata src="MCSA%20in%20GSAS_files/image015.png" o:title=""/>
1661</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1662src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1663
1664<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1665
1666<p class=MsoNormal>This may be good enough to try Monte Carlo/Simulated
1667Annealing.</p>
1668
1669<h2>Step 6. Setup for Monte Carlo/Simulated Annealing</h2>
1670
1671<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
1672rings with one N-substituted position and an amino side group</p>
1673
1674<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1675 id="Picture_x0020_34" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:142.5pt;
1676 height:93.75pt;visibility:visible;mso-wrap-style:square'>
1677 <v:imagedata src="MCSA%20in%20GSAS_files/image017.png" o:title="" croptop="20629f"
1678  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
1679</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
1680src="MCSA%20in%20GSAS_files/image018.jpg" v:shapes="Picture_x0020_34"><![endif]></span></p>
1681
1682<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
1683and orientation of this object in the unit cell; it has no internal degrees of
1684freedom. Thus we need to determine essentially six parameters. To do this in
1685GSAS-II we need to put a model of this molecule in as a rigid body. One must
1686create the model outside of GSAS-II, it has no facilities for model building. I
1687used the Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1688package for this and created a simple xyz Cartesian coordinate file for it (if
1689you have Avogadro or something equivalent you can try this for yourself). To
1690start go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1691"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1692minor-latin'>Rigid bodies</span></b> in the main GSAS-II data tree. You will
1693see a window with two tabs; select <b style='mso-bidi-font-weight:normal'><span
1694style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1695mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
1696style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1697mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Import
1698XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:normal'><span
1699style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1700mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and select <b
1701style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1702mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>aminoquinoline.xyz</span></b>.
1703The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1704mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b>
1705window will show</p>
1706
1707<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1708 id="Picture_x0020_35" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:300pt;
1709 height:320.25pt;visibility:visible;mso-wrap-style:square'>
1710 <v:imagedata src="MCSA%20in%20GSAS_files/image019.png" o:title=""/>
1711</v:shape><![endif]--><![if !vml]><img border=0 width=400 height=427
1712src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1713
1714<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1715
1716<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
1717style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1718mso-hansi-theme-font:minor-latin'>Plot?</span></b> box a drawing will appear</p>
1719
1720<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1721 id="Picture_x0020_1" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:286.5pt;
1722 height:234pt;visibility:visible;mso-wrap-style:square'>
1723 <v:imagedata src="MCSA%20in%20GSAS_files/image021.png" o:title="" croptop="13685f"
1724  cropbottom="15961f" cropleft="36898f" cropright="13504f"/>
1725</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=312
1726src="MCSA%20in%20GSAS_files/image022.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
1727
1728<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1729
1730<p class=MsoNormal>The orientation is determined by rotation and translation
1731about a coordinate system centered on C1 and defined by the vectors C1-C2 and
1732C1-C3; you can change these via the pull downs (you can’t pick the same atom
1733for two of these so pick them appropriately; I chose C2, C3 &amp; C6). My new
1734model is</p>
1735
1736<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1737 id="Picture_x0020_36" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:4in;
1738 height:234.75pt;visibility:visible;mso-wrap-style:square'>
1739 <v:imagedata src="MCSA%20in%20GSAS_files/image023.png" o:title="" croptop="13609f"
1740  cropbottom="16027f" cropleft="37724f" cropright="12673f"/>
1741</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=313
1742src="MCSA%20in%20GSAS_files/image024.jpg" v:shapes="Picture_x0020_36"><![endif]></span></p>
1743
1744<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1745
1746<p class=MsoNormal>Notice that the model includes H-atoms; they are not really
1747needed for MC/SA and will just make computation times a bit longer than
1748necessary. You should change the <b style='mso-bidi-font-weight:normal'><span
1749style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1750mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
1751meaningful, I used <b style='mso-bidi-font-weight:normal'><span
1752style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1753mso-hansi-theme-font:minor-latin'>amino</span></b>.</p>
1754
1755<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1756style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1757mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> and select
1758the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1759mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA</span></b>
1760tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1761"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1762minor-latin'>MC/SA/Add rigid body</span></b>; select the only choice (<b
1763style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1764mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>)
1765from the popup selection box. The MC/SA window shows</p>
1766
1767<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1768 id="Picture_x0020_37" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:448.5pt;
1769 height:251.25pt;visibility:visible;mso-wrap-style:square'>
1770 <v:imagedata src="MCSA%20in%20GSAS_files/image025.png" o:title=""/>
1771</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=335
1772src="MCSA%20in%20GSAS_files/image026.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
1773
1774<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1775
1776<p class=MsoNormal>And the plot shows the arbitrarily positioned molecules.</p>
1777
1778<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1779 id="Picture_x0020_14" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:4in;
1780 height:232.5pt;visibility:visible;mso-wrap-style:square'>
1781 <v:imagedata src="MCSA%20in%20GSAS_files/image027.png" o:title="" croptop="17592f"
1782  cropbottom="12829f" cropleft="38911f" cropright="11642f"/>
1783</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=310
1784src="MCSA%20in%20GSAS_files/image028.jpg" v:shapes="Picture_x0020_14"><![endif]></span></p>
1785
1786<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1787
1788<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
1789whose centers fall within the unit cell; the reference one is that in the lower
1790left corner with C1 at the origin. You can enter values in the <b
1791style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1792mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>x,y,z</span></b>
1793boxes and see how the structure changes. Similarly, you can enter an angle in <b
1794style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1795mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b>
1796or a vector in the <b style='mso-bidi-font-weight:normal'><span
1797style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1798mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok</span></b><span
1799style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
1800molecule. Each of these parameters has a defined range for the MC/SA
1801optimization run we are about to do; they define the multidimensional search
1802volume. Within that volume will be a number of correct solutions to the
1803structure problem all related by translational and space group symmetry. One
1804can limit this volume by choosing more limited ranges, but here we’ll just go
1805with the default. We want to optimize the position and orientation of this
1806molecule; check the <b style='mso-bidi-font-weight:normal'><span
1807style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1808mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
1809normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1810minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <b
1811style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1812mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>
1813boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1814"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1815minor-latin'>AV</span></b> from the <b style='mso-bidi-font-weight:normal'><span
1816style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1817mso-hansi-theme-font:minor-latin'>Oa</span></b>, <b style='mso-bidi-font-weight:
1818normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1819minor-latin;mso-hansi-theme-font:minor-latin'>Oi,Oj,Ok Vary?</span></b>
1820pulldown. The MC/SA window should look like</p>
1821
1822<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1823 id="Picture_x0020_39" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:448.5pt;
1824 height:193.5pt;visibility:visible;mso-wrap-style:square'>
1825 <v:imagedata src="MCSA%20in%20GSAS_files/image029.png" o:title=""/>
1826</v:shape><![endif]--><![if !vml]><img border=0 width=598 height=258
1827src="MCSA%20in%20GSAS_files/image030.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
1828style='mso-spacerun:yes'> </span></p>
1829
1830<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1831
1832<p class=MsoNormal>This completes the set up for MC/SA processing. </p>
1833
1834<h2>Step 7. Monte Carlo/Simulated Annealing</h2>
1835
1836<p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
1837style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1838mso-hansi-theme-font:minor-latin'>General</span></b> tab; the MC/SA controls
1839are at the bottom of the window. To begin the setup of these controls, select a
1840source of the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1841"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1842minor-latin'>Reflection set</span></b> to be used in the MC/SA runs. The choice
1843is to use either the Pawley reflections or the Reflection List for the PWDR
1844data set. If you choose <b style='mso-bidi-font-weight:normal'><span
1845style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1846mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
1847structure factors will be Pawley model values, Fsq(hkl) in Pawley table, and
1848the covariance matrix developed from the refinement will be used for peak
1849overlap effects in the MC/SA calculations. Alternatively, if you choose <b
1850style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1851mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
1852Quinoli.gda Bank 1 </span></b>then the structure factors will be those, Fosq in
1853Reflection table, extracted during the Pawley refinement and the peak FWHMs
1854will be used for peak overlap effects in the MC/SA calculations. Notice that
1855the Pawley Fsq(hkl) values are the same as the Fcsq Reflection List values.
1856Here I chose <b style='mso-bidi-font-weight:normal'><span style='font-family:
1857"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1858minor-latin'>Pawley reflections</span></b> for the <b style='mso-bidi-font-weight:
1859normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1860minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it
1861give slightly better performance in MC/SA.</p>
1862
1863<p class=MsoNormal>Next, you need to set the minimum d-spacing (<b
1864style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1865mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>d-min</span></b>).
1866Smaller values gives minima in the MC/SA minimization surface that are more
1867sharply defined (thus harder to locate), while larger values yield insufficient
1868numbers of reflections to give sufficient redundancy in the calculations. One
1869should have 5-8 reflections for each MC/SA parameter; in this case 35-50
1870reflections are needed. If you examine the reflection list (either <b
1871style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1872mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley</span></b>
1873or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1874mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1875List</span></b>) you’ll see that a <b style='mso-bidi-font-weight:normal'><span
1876style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1877mso-hansi-theme-font:minor-latin'>d-min</span></b> of <b style='mso-bidi-font-weight:
1878normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1879minor-latin;mso-hansi-theme-font:minor-latin'>2.5</span></b> will give
1880sufficient reflections.</p>
1881
1882<p class=MsoNormal>Lastly, you need to set the run controls. I used <b
1883style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1884mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>500</span></b>
1885for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
1887this is the number of random tries at each “temperature” in the annealing
1888schedule. When done the <b style='mso-bidi-font-weight:normal'><span
1889style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1890mso-hansi-theme-font:minor-latin'>General</span></b> window should look like</p>
1891
1892<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1893 id="Picture_x0020_16" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:7in;
1894 height:375pt;visibility:visible;mso-wrap-style:square'>
1895 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
1896</v:shape><![endif]--><![if !vml]><img border=0 width=672 height=500
1897src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
1898
1899<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1900
1901<p class=MsoNormal>When ready, you can start the MC/SA calculation by doing <b
1902style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1903mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>
1904from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1905mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1906window menu. A progress bar will appear that shows the MC/SA residual (an
1907R-factor) as the calculation progresses through the annealing schedule as well
1908as indicating which MC/SA run is being done. When it finishes, control is
1909shifted to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1910"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1911minor-latin'>MC/SA</span></b> window which gives a list of the solutions it
1912found at the bottom of the window (scroll down to see them).</p>
1913
1914<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1915 id="Picture_x0020_19" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:560.25pt;
1916 height:273.75pt;visibility:visible;mso-wrap-style:square'>
1917 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
1918</v:shape><![endif]--><![if !vml]><img border=0 width=747 height=365
1919src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
1920
1921<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1922
1923<p class=MsoNormal>The one with the lowest residual is already chosen and the
1924corresponding structure is drawn</p>
1925
1926<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1927 id="Picture_x0020_20" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:279.75pt;
1928 height:243.75pt;visibility:visible;mso-wrap-style:square'>
1929 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title="" croptop="11773f"
1930  cropbottom="16530f" cropleft="37715f" cropright="13079f"/>
1931</v:shape><![endif]--><![if !vml]><img border=0 width=373 height=325
1932src="MCSA%20in%20GSAS_files/image036.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
1933
1934<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1935
1936<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
1937good solution with a very low Residual (~4.8%). This problem typically gives
1938suitable solutions with Residuals of 4-5%. If no good solution appears (e.g.
1939molecules clashing), then you should just rerun MC/SA perhaps using more runs
1940or more trials. Be sure to set the <b style='mso-bidi-font-weight:normal'><span
1941style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1942mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
1943want to retain; the others will be cleared before the next MC/SA run starts.
1944When you think you have a good one, <b style='mso-bidi-font-weight:normal'><span
1945style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1946mso-hansi-theme-font:minor-latin'>Select</span></b> it; the parameters will be
1947copied to the appropriate boxes in the upper part of the MC/SA window and the
1948structure is drawn again. Next we want to refine this solution so go back to
1949the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1950mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1951tab.</p>
1952
1953<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
1954and rerunning the MC/SA calculations. This is done by checking the <b
1955style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1956mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
1957box. Using 10% of the ranges reduces the search volume in this case by ~6
1958orders of magnitude so that the true minimum is much easier to find. Now rerun <b
1959style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1960mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
1961be sure to select the best one before starting. The residual should drop to a
1962much lower level. This refinement can be repeated with tighter restriction on
1963the ranges; I used 5% for a final run and got</p>
1964
1965<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1966 id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:569.25pt;
1967 height:285pt;visibility:visible;mso-wrap-style:square'>
1968 <v:imagedata src="MCSA%20in%20GSAS_files/image037.png" o:title=""/>
1969</v:shape><![endif]--><![if !vml]><img border=0 width=759 height=380
1970src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
1971
1972<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1973
1974<p class=MsoNormal>This is clearly a good result (R ~ 0.4%!) and the structure</p>
1975
1976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1977 id="Picture_x0020_23" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:288.75pt;
1978 height:248.25pt;visibility:visible;mso-wrap-style:square'>
1979 <v:imagedata src="MCSA%20in%20GSAS_files/image039.png" o:title="" croptop="11555f"
1980  cropbottom="16469f" cropleft="37988f" cropright="12498f"/>
1981</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=331
1982src="MCSA%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_23"><![endif]></span></p>
1983
1984<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1985
1986<p class=MsoNormal>is identical to the published one</p>
1987
1988<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1989 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:288.75pt;
1990 height:225.75pt;visibility:visible;mso-wrap-style:square'>
1991 <v:imagedata src="MCSA%20in%20GSAS_files/image041.png" o:title="" croptop="14378f"
1992  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
1993</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
1994src="MCSA%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
1995
1996<p class=MsoNormal>as drawn by the Mercury program </p>
1997
1998<p class=MsoNormal>(<a
1999href="https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx">https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx</a>).
2000To save this solution to the <b style='mso-bidi-font-weight:normal'><span
2001style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2002mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
2003normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2004minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
2005the drawing will show the new atom positions</p>
2006
2007<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2008 id="Picture_x0020_25" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:4in;
2009 height:243.75pt;visibility:visible;mso-wrap-style:square'>
2010 <v:imagedata src="MCSA%20in%20GSAS_files/image043.png" o:title="" croptop="12581f"
2011  cropbottom="15938f" cropleft="37111f" cropright="13377f"/>
2012</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=325
2013src="MCSA%20in%20GSAS_files/image044.jpg" v:shapes="Picture_x0020_25"><![endif]></span></p>
2014
2015<p class=MsoNormal>And they will be listed in the Atoms table.</p>
2016
2017<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2018 id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:525pt;
2019 height:225pt;visibility:visible;mso-wrap-style:square'>
2020 <v:imagedata src="MCSA%20in%20GSAS_files/image045.png" o:title=""/>
2021</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
2022src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
2023
2024<p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use
2025the rigid body as the data will not support independent atom position
2026refinement.</p>
2027
2028<h2>Step 8. Initial Rietveld refinement</h2>
2029
2030<p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
2031be ready for the first Rietveld refinement: 1) On the <b style='mso-bidi-font-weight:
2032normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2033minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab uncheck
2034the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2035mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley
2036refinement?</span></b> box, 2) check the <b style='mso-bidi-font-weight:normal'><span
2037style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2038mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> box in <b
2039style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2040mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2041Parameters</span></b> and 3) zero both <b style='mso-bidi-font-weight:normal'><span
2042style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2043mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
2044normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2045minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> and uncheck their
2046refine boxes in <b style='mso-bidi-font-weight:normal'><span style='font-family:
2047"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2048minor-latin'>Instrument Parameters</span></b>. Then do <b style='mso-bidi-font-weight:
2049normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2050minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
2051the main GSAS-II data tree window; my R<sub>wp</sub> was ~9%. Next check the <b
2052style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2053mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
2054cell</span></b> in the <b style='mso-bidi-font-weight:normal'><span
2055style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2056mso-hansi-theme-font:minor-latin'>General</span></b> window and in the <b
2057style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2058mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Data</span></b>
2059window, using the <b style='mso-bidi-font-weight:normal'><span
2060style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2061mso-hansi-theme-font:minor-latin'>uniaxial</span></b> model for mustrain, check
2062both <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2063mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst. size</span></b>
2064&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2065mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b>
2066boxes and do another <b style='mso-bidi-font-weight:normal'><span
2067style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2068mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I got an R<sub>wp</sub>
2069~8.5% for this. We’ve not refined atom positions or thermal parameters; to do
2070this we need to describe the structure as a rigid body.</p>
2071
2072<h2>Step 9. Rigid body model</h2>
2073
2074<p class=MsoNormal>The rigid body itself has already been defined; it was used
2075for the MC/SA structure solution. Now we have to place it in the unit cell
2076matching the atom positions obtained from the MC/SA runs. First go to the <b
2077style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2078mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2079tab and change the <b style='mso-bidi-font-weight:normal'><span
2080style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2081mso-hansi-theme-font:minor-latin'>Style</span></b> to <b style='mso-bidi-font-weight:
2082normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2083minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp; sticks</span></b> and
2084the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2085mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
2086to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2087mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>name</span></b>.
2088Double click on the column headings and select the item from the popup control.
2089Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2090"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2091minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
2092style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2093mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assign
2094atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
2095normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2096minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
2097style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2098mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
2099body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
2100normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2101minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
2102show</p>
2103
2104<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2105 id="Picture_x0020_27" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:337.5pt;
2106 height:218.25pt;visibility:visible;mso-wrap-style:square'>
2107 <v:imagedata src="MCSA%20in%20GSAS_files/image047.png" o:title=""/>
2108</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=291
2109src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
2110
2111<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2112
2113<p class=MsoNormal>You will orient the rigid body against the atoms by matching
2114up the 3 reference atoms in the rigid body (C1, C2 &amp; C5) to the
2115corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
2116order; the drawing will show the shift of molecular origin and then its
2117reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight:
2118normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2119minor-latin;mso-hansi-theme-font:minor-latin'>Ready</span></b> when done; the
2120structure will be drawn with yellow bonds indicating that it is now a rigid
2121body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span
2122style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2123mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows the new
2124rigid body</p>
2125
2126<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2127 id="Picture_x0020_29" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:474.75pt;
2128 height:210pt;visibility:visible;mso-wrap-style:square'>
2129 <v:imagedata src="MCSA%20in%20GSAS_files/image049.png" o:title=""/>
2130</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=280
2131src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
2132
2133<p class=MsoNormal>To refine the rigid body parameters check the <b
2134style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2135mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
2136box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2137"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2138minor-latin'>AV</span></b> from the pull down, choose <b style='mso-bidi-font-weight:
2139normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2140minor-latin;mso-hansi-theme-font:minor-latin'>Uiso</span></b> from the thermal
2141parameter model and check its <b style='mso-bidi-font-weight:normal'><span
2142style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2143mso-hansi-theme-font:minor-latin'>Refine?</span></b> box. Then do <b
2144style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2145mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2146after a couple of refinement runs I got an R<sub>wp</sub> ~7.9% and the <b
2147style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2148mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RBModels</span></b>
2149window shows the new parameters</p>
2150
2151<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2152 id="Picture_x0020_32" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:474.75pt;
2153 height:225.75pt;visibility:visible;mso-wrap-style:square'>
2154 <v:imagedata src="MCSA%20in%20GSAS_files/image051.png" o:title=""/>
2155</v:shape><![endif]--><![if !vml]><img border=0 width=633 height=301
2156src="MCSA%20in%20GSAS_files/image052.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
2157
2158<p class=MsoNormal>and the profile shows the fit</p>
2159
2160<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2161 id="Picture_x0020_31" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:525pt;
2162 height:450pt;visibility:visible;mso-wrap-style:square'>
2163 <v:imagedata src="MCSA%20in%20GSAS_files/image053.png" o:title=""/>
2164</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
2165src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
2166
2167<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
2168Next is a more complex case involving some internal degrees of freedom in the
2169molecule of a-d-lactose.</p>
2170
2171</div>
2172
2173</body>
2174
2175</html>
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