source: Tutorials/MCsimanneal/MCSA in GSAS.htm @ 4271

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finish web tutorials for now

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407   Name="List Paragraph"/>
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410   Name="Intense Quote"/>
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413  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
414  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
415  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
416  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
417  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
418  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
419  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
420  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
421  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
422  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
423  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
424  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
425  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
426  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
427  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
428  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
429  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
430  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
431  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
432  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
433  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
434  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
435  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
436  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
437  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
438  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
439  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
440  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
441  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
442  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
443  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
444  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
445  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
446  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
447  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
448  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
449  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
450  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
451  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
452  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
453  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
454  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
455  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
456  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
457  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
458  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
459  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
460  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
461  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
462  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
463  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
464  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
465  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
466  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
467  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
468  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
469  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
470  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
471  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
472  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
473  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
474  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
475  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
476  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
477  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
478  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
479  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
480  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
481  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
482  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
483  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
484  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
485  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
486  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
487  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
488  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
489  <w:LsdException Locked="false" Priority="19" QFormat="true"
490   Name="Subtle Emphasis"/>
491  <w:LsdException Locked="false" Priority="21" QFormat="true"
492   Name="Intense Emphasis"/>
493  <w:LsdException Locked="false" Priority="31" QFormat="true"
494   Name="Subtle Reference"/>
495  <w:LsdException Locked="false" Priority="32" QFormat="true"
496   Name="Intense Reference"/>
497  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
498  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
499   UnhideWhenUsed="true" Name="Bibliography"/>
500  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
501   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
502  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
503  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
504  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
505  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
506  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
507  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
508  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
509  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
510  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
511  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
512  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
513  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
514  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
515  <w:LsdException Locked="false" Priority="46"
516   Name="Grid Table 1 Light Accent 1"/>
517  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
518  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
519  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
520  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
521  <w:LsdException Locked="false" Priority="51"
522   Name="Grid Table 6 Colorful Accent 1"/>
523  <w:LsdException Locked="false" Priority="52"
524   Name="Grid Table 7 Colorful Accent 1"/>
525  <w:LsdException Locked="false" Priority="46"
526   Name="Grid Table 1 Light Accent 2"/>
527  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
528  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
529  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
530  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
531  <w:LsdException Locked="false" Priority="51"
532   Name="Grid Table 6 Colorful Accent 2"/>
533  <w:LsdException Locked="false" Priority="52"
534   Name="Grid Table 7 Colorful Accent 2"/>
535  <w:LsdException Locked="false" Priority="46"
536   Name="Grid Table 1 Light Accent 3"/>
537  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
538  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
539  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
540  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
541  <w:LsdException Locked="false" Priority="51"
542   Name="Grid Table 6 Colorful Accent 3"/>
543  <w:LsdException Locked="false" Priority="52"
544   Name="Grid Table 7 Colorful Accent 3"/>
545  <w:LsdException Locked="false" Priority="46"
546   Name="Grid Table 1 Light Accent 4"/>
547  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
548  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
549  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
550  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
551  <w:LsdException Locked="false" Priority="51"
552   Name="Grid Table 6 Colorful Accent 4"/>
553  <w:LsdException Locked="false" Priority="52"
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557  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
558  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
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560  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
561  <w:LsdException Locked="false" Priority="51"
562   Name="Grid Table 6 Colorful Accent 5"/>
563  <w:LsdException Locked="false" Priority="52"
564   Name="Grid Table 7 Colorful Accent 5"/>
565  <w:LsdException Locked="false" Priority="46"
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567  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
568  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
569  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
570  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
571  <w:LsdException Locked="false" Priority="51"
572   Name="Grid Table 6 Colorful Accent 6"/>
573  <w:LsdException Locked="false" Priority="52"
574   Name="Grid Table 7 Colorful Accent 6"/>
575  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
576  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
577  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
578  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
579  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
580  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
581  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
582  <w:LsdException Locked="false" Priority="46"
583   Name="List Table 1 Light Accent 1"/>
584  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
585  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
586  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
587  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
588  <w:LsdException Locked="false" Priority="51"
589   Name="List Table 6 Colorful Accent 1"/>
590  <w:LsdException Locked="false" Priority="52"
591   Name="List Table 7 Colorful Accent 1"/>
592  <w:LsdException Locked="false" Priority="46"
593   Name="List Table 1 Light Accent 2"/>
594  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
595  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
596  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
597  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
598  <w:LsdException Locked="false" Priority="51"
599   Name="List Table 6 Colorful Accent 2"/>
600  <w:LsdException Locked="false" Priority="52"
601   Name="List Table 7 Colorful Accent 2"/>
602  <w:LsdException Locked="false" Priority="46"
603   Name="List Table 1 Light Accent 3"/>
604  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
605  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
606  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
607  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
608  <w:LsdException Locked="false" Priority="51"
609   Name="List Table 6 Colorful Accent 3"/>
610  <w:LsdException Locked="false" Priority="52"
611   Name="List Table 7 Colorful Accent 3"/>
612  <w:LsdException Locked="false" Priority="46"
613   Name="List Table 1 Light Accent 4"/>
614  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
615  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
616  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
617  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
618  <w:LsdException Locked="false" Priority="51"
619   Name="List Table 6 Colorful Accent 4"/>
620  <w:LsdException Locked="false" Priority="52"
621   Name="List Table 7 Colorful Accent 4"/>
622  <w:LsdException Locked="false" Priority="46"
623   Name="List Table 1 Light Accent 5"/>
624  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
625  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
626  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
627  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
628  <w:LsdException Locked="false" Priority="51"
629   Name="List Table 6 Colorful Accent 5"/>
630  <w:LsdException Locked="false" Priority="52"
631   Name="List Table 7 Colorful Accent 5"/>
632  <w:LsdException Locked="false" Priority="46"
633   Name="List Table 1 Light Accent 6"/>
634  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
635  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
636  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
637  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
638  <w:LsdException Locked="false" Priority="51"
639   Name="List Table 6 Colorful Accent 6"/>
640  <w:LsdException Locked="false" Priority="52"
641   Name="List Table 7 Colorful Accent 6"/>
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783        mso-pagination:widow-orphan;
784        font-size:26.0pt;
785        font-family:"Cambria",serif;
786        mso-fareast-font-family:"Times New Roman";
787        mso-fareast-theme-font:minor-fareast;
788        mso-bidi-font-family:"Times New Roman";
789        color:#17365D;
790        letter-spacing:.25pt;}
791a:link, span.MsoHyperlink
792        {mso-style-noshow:yes;
793        mso-style-priority:99;
794        color:blue;
795        text-decoration:underline;
796        text-underline:single;}
797a:visited, span.MsoHyperlinkFollowed
798        {mso-style-noshow:yes;
799        mso-style-priority:99;
800        color:purple;
801        text-decoration:underline;
802        text-underline:single;}
803p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
804        {mso-style-noshow:yes;
805        mso-style-priority:99;
806        mso-style-link:"Document Map Char";
807        margin:0in;
808        margin-bottom:.0001pt;
809        mso-pagination:widow-orphan;
810        font-size:8.0pt;
811        font-family:"Tahoma",sans-serif;
812        mso-fareast-font-family:"Times New Roman";
813        mso-fareast-theme-font:minor-fareast;}
814p
815        {mso-style-noshow:yes;
816        mso-style-priority:99;
817        mso-margin-top-alt:auto;
818        margin-right:0in;
819        mso-margin-bottom-alt:auto;
820        margin-left:0in;
821        mso-pagination:widow-orphan;
822        font-size:12.0pt;
823        font-family:"Times New Roman",serif;
824        mso-fareast-font-family:"Times New Roman";
825        mso-fareast-theme-font:minor-fareast;}
826pre
827        {mso-style-noshow:yes;
828        mso-style-priority:99;
829        mso-style-link:"HTML Preformatted Char";
830        margin:0in;
831        margin-bottom:.0001pt;
832        mso-pagination:widow-orphan;
833        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;
834        font-size:10.0pt;
835        font-family:"Courier New";
836        mso-fareast-font-family:"Times New Roman";
837        mso-fareast-theme-font:minor-fareast;}
838p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
839        {mso-style-noshow:yes;
840        mso-style-priority:99;
841        mso-style-link:"Balloon Text Char";
842        margin:0in;
843        margin-bottom:.0001pt;
844        mso-pagination:widow-orphan;
845        font-size:8.0pt;
846        font-family:"Tahoma",sans-serif;
847        mso-fareast-font-family:"Times New Roman";
848        mso-fareast-theme-font:minor-fareast;}
849span.MsoPlaceholderText
850        {mso-style-noshow:yes;
851        mso-style-priority:99;
852        mso-style-unhide:no;
853        color:gray;}
854p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
855        {mso-style-noshow:yes;
856        mso-style-priority:1;
857        mso-style-unhide:no;
858        mso-style-qformat:yes;
859        margin:0in;
860        margin-bottom:.0001pt;
861        mso-pagination:widow-orphan;
862        font-size:12.0pt;
863        font-family:"Times New Roman",serif;
864        mso-fareast-font-family:"Times New Roman";
865        mso-fareast-theme-font:minor-fareast;}
866p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
867        {mso-style-noshow:yes;
868        mso-style-priority:34;
869        mso-style-unhide:no;
870        mso-style-qformat:yes;
871        margin-top:0in;
872        margin-right:0in;
873        margin-bottom:0in;
874        margin-left:.5in;
875        margin-bottom:.0001pt;
876        mso-pagination:widow-orphan;
877        font-size:12.0pt;
878        font-family:"Times New Roman",serif;
879        mso-fareast-font-family:"Times New Roman";
880        mso-fareast-theme-font:minor-fareast;}
881span.MsoIntenseReference
882        {mso-style-priority:32;
883        mso-style-unhide:no;
884        mso-style-qformat:yes;
885        font-variant:small-caps;
886        color:#C0504D;
887        letter-spacing:.25pt;
888        font-weight:bold;
889        text-decoration:underline;
890        text-underline:single;}
891span.Heading1Char
892        {mso-style-name:"Heading 1 Char";
893        mso-style-priority:9;
894        mso-style-unhide:no;
895        mso-style-locked:yes;
896        mso-style-link:"Heading 1";
897        font-family:"Times New Roman",serif;
898        mso-ascii-font-family:"Times New Roman";
899        mso-hansi-font-family:"Times New Roman";
900        mso-bidi-font-family:"Times New Roman";
901        font-weight:bold;}
902span.Heading2Char
903        {mso-style-name:"Heading 2 Char";
904        mso-style-noshow:yes;
905        mso-style-priority:9;
906        mso-style-unhide:no;
907        mso-style-locked:yes;
908        mso-style-link:"Heading 2";
909        font-family:"Times New Roman",serif;
910        mso-ascii-font-family:"Times New Roman";
911        mso-hansi-font-family:"Times New Roman";
912        mso-bidi-font-family:"Times New Roman";
913        font-weight:bold;}
914span.Heading3Char
915        {mso-style-name:"Heading 3 Char";
916        mso-style-noshow:yes;
917        mso-style-priority:9;
918        mso-style-unhide:no;
919        mso-style-locked:yes;
920        mso-style-link:"Heading 3";
921        font-family:"Times New Roman",serif;
922        mso-ascii-font-family:"Times New Roman";
923        mso-hansi-font-family:"Times New Roman";
924        mso-bidi-font-family:"Times New Roman";
925        font-weight:bold;}
926span.Heading4Char
927        {mso-style-name:"Heading 4 Char";
928        mso-style-noshow:yes;
929        mso-style-priority:9;
930        mso-style-unhide:no;
931        mso-style-locked:yes;
932        mso-style-link:"Heading 4";
933        font-family:"Cambria",serif;
934        mso-ascii-font-family:Cambria;
935        mso-hansi-font-family:Cambria;
936        color:#4F81BD;
937        font-weight:bold;
938        font-style:italic;}
939span.Heading5Char
940        {mso-style-name:"Heading 5 Char";
941        mso-style-noshow:yes;
942        mso-style-priority:9;
943        mso-style-unhide:no;
944        mso-style-locked:yes;
945        mso-style-link:"Heading 5";
946        font-family:"Times New Roman",serif;
947        mso-ascii-font-family:"Times New Roman";
948        mso-hansi-font-family:"Times New Roman";
949        mso-bidi-font-family:"Times New Roman";
950        color:#4F4FFF;
951        font-weight:bold;}
952span.HTMLPreformattedChar
953        {mso-style-name:"HTML Preformatted Char";
954        mso-style-noshow:yes;
955        mso-style-priority:99;
956        mso-style-unhide:no;
957        mso-style-locked:yes;
958        mso-style-link:"HTML Preformatted";
959        font-family:"Courier New";
960        mso-ascii-font-family:"Courier New";
961        mso-hansi-font-family:"Courier New";
962        mso-bidi-font-family:"Courier New";}
963p.msonormal0, li.msonormal0, div.msonormal0
964        {mso-style-name:msonormal;
965        mso-style-noshow:yes;
966        mso-style-priority:99;
967        mso-style-unhide:no;
968        mso-margin-top-alt:auto;
969        margin-right:0in;
970        mso-margin-bottom-alt:auto;
971        margin-left:0in;
972        mso-pagination:widow-orphan;
973        font-size:12.0pt;
974        font-family:"Times New Roman",serif;
975        mso-fareast-font-family:"Times New Roman";
976        mso-fareast-theme-font:minor-fareast;}
977span.TitleChar
978        {mso-style-name:"Title Char";
979        mso-style-priority:10;
980        mso-style-unhide:no;
981        mso-style-locked:yes;
982        mso-style-link:Title;
983        font-family:"Cambria",serif;
984        mso-ascii-font-family:Cambria;
985        mso-hansi-font-family:Cambria;
986        color:#17365D;
987        letter-spacing:.25pt;}
988span.DocumentMapChar
989        {mso-style-name:"Document Map Char";
990        mso-style-noshow:yes;
991        mso-style-priority:99;
992        mso-style-unhide:no;
993        mso-style-locked:yes;
994        mso-style-link:"Document Map";
995        font-family:"Tahoma",sans-serif;
996        mso-ascii-font-family:Tahoma;
997        mso-hansi-font-family:Tahoma;
998        mso-bidi-font-family:Tahoma;}
999span.BalloonTextChar
1000        {mso-style-name:"Balloon Text Char";
1001        mso-style-noshow:yes;
1002        mso-style-priority:99;
1003        mso-style-unhide:no;
1004        mso-style-locked:yes;
1005        mso-style-link:"Balloon Text";
1006        font-family:"Tahoma",sans-serif;
1007        mso-ascii-font-family:Tahoma;
1008        mso-hansi-font-family:Tahoma;
1009        mso-bidi-font-family:Tahoma;}
1010p.msotitlecxspfirst, li.msotitlecxspfirst, div.msotitlecxspfirst
1011        {mso-style-name:msotitlecxspfirst;
1012        mso-style-noshow:yes;
1013        mso-style-priority:99;
1014        mso-style-unhide:no;
1015        margin:0in;
1016        margin-bottom:.0001pt;
1017        mso-pagination:widow-orphan;
1018        font-size:26.0pt;
1019        font-family:"Cambria",serif;
1020        mso-fareast-font-family:"Times New Roman";
1021        mso-fareast-theme-font:minor-fareast;
1022        mso-bidi-font-family:"Times New Roman";
1023        color:#17365D;
1024        letter-spacing:.25pt;}
1025p.msotitlecxspmiddle, li.msotitlecxspmiddle, div.msotitlecxspmiddle
1026        {mso-style-name:msotitlecxspmiddle;
1027        mso-style-noshow:yes;
1028        mso-style-priority:99;
1029        mso-style-unhide:no;
1030        margin:0in;
1031        margin-bottom:.0001pt;
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.msotitlecxsplast, li.msotitlecxsplast, div.msotitlecxsplast
1041        {mso-style-name:msotitlecxsplast;
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:15.0pt;
1048        margin-left:0in;
1049        mso-pagination:widow-orphan;
1050        font-size:26.0pt;
1051        font-family:"Cambria",serif;
1052        mso-fareast-font-family:"Times New Roman";
1053        mso-fareast-theme-font:minor-fareast;
1054        mso-bidi-font-family:"Times New Roman";
1055        color:#17365D;
1056        letter-spacing:.25pt;}
1057p.msolistparagraphcxspfirst, li.msolistparagraphcxspfirst, div.msolistparagraphcxspfirst
1058        {mso-style-name:msolistparagraphcxspfirst;
1059        mso-style-noshow:yes;
1060        mso-style-priority:99;
1061        mso-style-unhide:no;
1062        margin-top:0in;
1063        margin-right:0in;
1064        margin-bottom:0in;
1065        margin-left:.5in;
1066        margin-bottom:.0001pt;
1067        mso-pagination:widow-orphan;
1068        font-size:12.0pt;
1069        font-family:"Times New Roman",serif;
1070        mso-fareast-font-family:"Times New Roman";
1071        mso-fareast-theme-font:minor-fareast;}
1072p.msolistparagraphcxspmiddle, li.msolistparagraphcxspmiddle, div.msolistparagraphcxspmiddle
1073        {mso-style-name:msolistparagraphcxspmiddle;
1074        mso-style-noshow:yes;
1075        mso-style-priority:99;
1076        mso-style-unhide:no;
1077        margin-top:0in;
1078        margin-right:0in;
1079        margin-bottom:0in;
1080        margin-left:.5in;
1081        margin-bottom:.0001pt;
1082        mso-pagination:widow-orphan;
1083        font-size:12.0pt;
1084        font-family:"Times New Roman",serif;
1085        mso-fareast-font-family:"Times New Roman";
1086        mso-fareast-theme-font:minor-fareast;}
1087p.msolistparagraphcxsplast, li.msolistparagraphcxsplast, div.msolistparagraphcxsplast
1088        {mso-style-name:msolistparagraphcxsplast;
1089        mso-style-noshow:yes;
1090        mso-style-priority:99;
1091        mso-style-unhide:no;
1092        margin-top:0in;
1093        margin-right:0in;
1094        margin-bottom:0in;
1095        margin-left:.5in;
1096        margin-bottom:.0001pt;
1097        mso-pagination:widow-orphan;
1098        font-size:12.0pt;
1099        font-family:"Times New Roman",serif;
1100        mso-fareast-font-family:"Times New Roman";
1101        mso-fareast-theme-font:minor-fareast;}
1102p.msochpdefault, li.msochpdefault, div.msochpdefault
1103        {mso-style-name:msochpdefault;
1104        mso-style-noshow:yes;
1105        mso-style-priority:99;
1106        mso-style-unhide:no;
1107        mso-margin-top-alt:auto;
1108        margin-right:0in;
1109        mso-margin-bottom-alt:auto;
1110        margin-left:0in;
1111        mso-pagination:widow-orphan;
1112        font-size:10.0pt;
1113        font-family:"Calibri",sans-serif;
1114        mso-fareast-font-family:"Times New Roman";
1115        mso-fareast-theme-font:minor-fareast;}
1116span.SpellE
1117        {mso-style-name:"";
1118        mso-spl-e:yes;}
1119span.GramE
1120        {mso-style-name:"";
1121        mso-gram-e:yes;}
1122.MsoChpDefault
1123        {mso-style-type:export-only;
1124        mso-default-props:yes;
1125        font-size:10.0pt;
1126        mso-ansi-font-size:10.0pt;
1127        mso-bidi-font-size:10.0pt;
1128        font-family:"Calibri",sans-serif;
1129        mso-ascii-font-family:Calibri;
1130        mso-hansi-font-family:Calibri;
1131        mso-bidi-font-family:Calibri;}
1132@page WordSection1
1133        {size:8.5in 11.0in;
1134        margin:1.0in 1.0in 1.0in 1.0in;
1135        mso-header-margin:.5in;
1136        mso-footer-margin:.5in;
1137        mso-paper-source:0;}
1138div.WordSection1
1139        {page:WordSection1;}
1140 /* List Definitions */
1141 @list l0
1142        {mso-list-id:608973138;
1143        mso-list-type:hybrid;
1144        mso-list-template-ids:-1449999034 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1145@list l0:level1
1146        {mso-level-tab-stop:none;
1147        mso-level-number-position:left;
1148        text-indent:-.25in;}
1149@list l0:level2
1150        {mso-level-number-format:alpha-lower;
1151        mso-level-tab-stop:none;
1152        mso-level-number-position:left;
1153        text-indent:-.25in;}
1154@list l0:level3
1155        {mso-level-number-format:roman-lower;
1156        mso-level-tab-stop:none;
1157        mso-level-number-position:right;
1158        text-indent:-9.0pt;}
1159@list l0:level4
1160        {mso-level-tab-stop:none;
1161        mso-level-number-position:left;
1162        text-indent:-.25in;}
1163@list l0:level5
1164        {mso-level-number-format:alpha-lower;
1165        mso-level-tab-stop:none;
1166        mso-level-number-position:left;
1167        text-indent:-.25in;}
1168@list l0:level6
1169        {mso-level-number-format:roman-lower;
1170        mso-level-tab-stop:none;
1171        mso-level-number-position:right;
1172        text-indent:-9.0pt;}
1173@list l0:level7
1174        {mso-level-tab-stop:none;
1175        mso-level-number-position:left;
1176        text-indent:-.25in;}
1177@list l0:level8
1178        {mso-level-number-format:alpha-lower;
1179        mso-level-tab-stop:none;
1180        mso-level-number-position:left;
1181        text-indent:-.25in;}
1182@list l0:level9
1183        {mso-level-number-format:roman-lower;
1184        mso-level-tab-stop:none;
1185        mso-level-number-position:right;
1186        text-indent:-9.0pt;}
1187@list l1
1188        {mso-list-id:1022125565;
1189        mso-list-type:hybrid;
1190        mso-list-template-ids:-482838388 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
1191@list l1:level1
1192        {mso-level-tab-stop:none;
1193        mso-level-number-position:left;
1194        margin-left:1.0in;
1195        text-indent:-.25in;}
1196@list l1:level2
1197        {mso-level-number-format:alpha-lower;
1198        mso-level-tab-stop:none;
1199        mso-level-number-position:left;
1200        margin-left:1.5in;
1201        text-indent:-.25in;}
1202@list l1:level3
1203        {mso-level-number-format:roman-lower;
1204        mso-level-tab-stop:none;
1205        mso-level-number-position:right;
1206        margin-left:2.0in;
1207        text-indent:-9.0pt;}
1208@list l1:level4
1209        {mso-level-tab-stop:none;
1210        mso-level-number-position:left;
1211        margin-left:2.5in;
1212        text-indent:-.25in;}
1213@list l1:level5
1214        {mso-level-number-format:alpha-lower;
1215        mso-level-tab-stop:none;
1216        mso-level-number-position:left;
1217        margin-left:3.0in;
1218        text-indent:-.25in;}
1219@list l1:level6
1220        {mso-level-number-format:roman-lower;
1221        mso-level-tab-stop:none;
1222        mso-level-number-position:right;
1223        margin-left:3.5in;
1224        text-indent:-9.0pt;}
1225@list l1:level7
1226        {mso-level-tab-stop:none;
1227        mso-level-number-position:left;
1228        margin-left:4.0in;
1229        text-indent:-.25in;}
1230@list l1:level8
1231        {mso-level-number-format:alpha-lower;
1232        mso-level-tab-stop:none;
1233        mso-level-number-position:left;
1234        margin-left:4.5in;
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1271</head>
1272
1273<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1274
1275<div class=WordSection1>
1276
1277<h1><span style='mso-fareast-font-family:"Times New Roman"'>MC/SA in GSAS-II<o:p></o:p></span></h1>
1278
1279<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction: <o:p></o:p></span></h2>
1280
1281<p class=MsoNormal>In these exercises you will use GSAS-II to solve the
1282structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
1283diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
1284were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
1285and were originally collected on NSLS beam line X3b1. The MC/SA technique is
1286needed in these cases because as you will see the data does not extend very far
1287in 2&#920; so one cannot use charge flipping to solve them. The steps for each
1288begin with peak selection and fitting, then indexing to identify the lattice
1289parameters. A Pawley refinement is used to obtain a set of structure factors
1290needed for the MC/SA runs. We will use previously developed models for the two
1291molecules; I used the freeware program Avogadro (<a
1292href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1293to create them.</p>
1294
1295<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1296
1297<h2>Step 1. Import powder data for 3-aminoquinoline</h2>
1298
1299<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1300style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1301style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1302the <b style='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-theme-font:
1304minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1305to read the data file into the current GSAS-II project. Change the file
1306directory to <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1307style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1308mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>MCsimanneal</span></b></span><b
1309style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1310mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1311minor-latin'>/data</span></b><span style='font-family:"Calibri",sans-serif;
1312mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1313minor-latin'> to find the file; you may need to change the file type to <b
1314style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired file.</span></p>
1315
1316<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1317style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1318style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1319the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1320style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1321mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Quinoli.gda</span></b></span><span
1322style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1323mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> data</span>
1324file in the first dialog and press <b style='mso-bidi-font-weight:normal'><span
1325style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1326mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
1327There will be a Dialog box asking <b style='mso-bidi-font-weight:normal'><span
1328style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1329mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is this the
1330file you want?</span></b> Press <b style='mso-bidi-font-weight:normal'><span
1331style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1332mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
1333button to proceed.</p>
1334
1335<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1336style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1337style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1338the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1339mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1340minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b> instrument
1341parameter file in the second dialog and press <b style='mso-bidi-font-weight:
1342normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1343minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
1344You’ll have to change the file type to <b style='mso-bidi-font-weight:normal'><span
1345style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1346mso-hansi-theme-font:minor-latin'>*.<span class=SpellE>instprm</span></span></b>
1347(GSAS-II instrument parameter file). The powder pattern will immediately
1348appear.</p>
1349
1350<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1351 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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1372 <v:imagedata src="MCSA%20in%20GSAS_files/image002.png" o:title=""/>
1373</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1374src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_1"><![endif]></span></p>
1375
1376<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1377
1378<p class=MsoListParagraph>Notice that the pattern extends only to a minimum
1379d-spacing of ~1.81Å; this is not far enough to use charge flipping which needs
13801Å or better. </p>
1381
1382<h2>Step 2. Peak picking &amp; fitting</h2>
1383
1384<p class=MsoNormal>Next you need to select limits so that ~20 peaks are
1385selected for indexing; go to <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'>Limits</span></b> and choose <b
1388style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1389mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>9-25</span></b>°
13902&#920;. Next go to <b style='mso-bidi-font-weight:normal'><span
1391style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1392mso-hansi-theme-font:minor-latin'>Peak List</span></b> and pick all the peaks
1393you can see between the limits. This is most easily done by hand as the <b
1394style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1395mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Auto search</span></b>
1396routine gives a lot of spurious peaks for this rather noisy and weak data; I
1397picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
1398normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1399minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span>
1400</span></b>to fit them (it will ask to save the project; I called it ‘<b
1401style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1402mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1403minor-latin'>2-amino</span></b>’). You will need to refine at least <b
1404style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1405mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1406&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1407mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1408in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1409mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1410Parameters</span></b> along with <span class=SpellE><b style='mso-bidi-font-weight:
1411normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1412minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span> &amp; <span
1413class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1414"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1415minor-latin'>int</span></b></span> in the <b style='mso-bidi-font-weight:normal'><span
1416style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1417mso-hansi-theme-font:minor-latin'>Peak List</span></b> to get a reasonable fit
1418suitable for indexing.</p>
1419
1420<h2>Step 3. Indexing</h2>
1421
1422<p class=MsoNormal>Next go to <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'>Index Peak List</span></b> and do <b
1425style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1426mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1427to set up the peaks for indexing. Then go to <b style='mso-bidi-font-weight:
1428normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1429minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
1430indexing. The most likely <span class=SpellE>Bravais</span> lattice for these
1431small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try
1432both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
1433style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1434mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>).
1435Click on <B>Cell Index/Refine/Index Cell</B>. The correct unit
1436cell should almost immediately appear with an M20 ~370 with a=7.748, b=7.650,
1437c=12.736, Vol=755.01. NB: your solution may have a &amp; b switched. Do <b
1438style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1439mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cell
1440Index/Refine/Copy Cell</span></b>; you can then try various space groups. Press
1441the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1442mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show HKL
1443positions</span></b> to see the lines with extinctions (Hint: it’s <b
1444style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1445mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub>
14462<sub>1</sub> 2<sub>1</sub></span></b>).
1447Under the <B>General</B> tab, change the space group to <B>P 21 21 21</B>.
1448You can then do <b style='mso-bidi-font-weight:
1449normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1450minor-latin;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
1451to improve the lattice parameters with M20 ~380. Finally do <b
1452style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1453mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cell
1454Index/Refine/Make new phase</span></b> to create the phase; I named it <b
1455style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1456mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
1457
1458<h2>Step 4. Setup for Pawley refinement</h2>
1459
1460<p class=MsoNormal>There are a number of steps that must be done in preparation
1461for a Pawley refinement after having completed the unit cell indexing and new
1462phase creation. These cover two things: one is to prepare the powder pattern
1463(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1464
1465<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1466style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1467style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1468<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1469mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1470in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1471region at the end of the data is readily seen. This is ~37deg 2<span
1472style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
1473"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
1474style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>;
1475there are a few zero points at the end that need to be excluded. Use the right
1476mouse button and pick a point just inside the end avoiding the zeros. Make a
1477note of the exact d-spacing (for me 1.8126) using the mouse cursor on the plot.</p>
1478
1479<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1480style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1481style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1482<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1483mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1484Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1485style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1486mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1487style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1489profile</span></b> to recover the default values. The peak fitting done earlier
1490is over a more limited range of 2<span style='font-family:Symbol;mso-ascii-font-family:
1491"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
1492mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
1493Symbol'>Q</span></span> giving values that will not extrapolate well over the
1494wider range to be used in the Pawley refinement. We may refine them again
1495later.</p>
1496
1497<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1498style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1499style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1500<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1501mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1502Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1503normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1504minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
1505
1506<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1507style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1508style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1509to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1510mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b>
1511to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1512"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1513minor-latin'>Pawley controls</span></b> under the <B>General</B> tab.
1514Check the <b style='mso-bidi-font-weight:
1515normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1516minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement?</span></b>
1517box, enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1518style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1519mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1.8126</span></b>)
1520into the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1521mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1522class=SpellE>dmin</span></span></b> box and set the <b style='mso-bidi-font-weight:
1523normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1524minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Pawley
1525neg. wt.</span></b><span style='mso-spacerun:yes'>  </span><span class=GramE>to</span>
1526<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1527mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1528minor-latin'>0.001</span></b>. This will suppress possible negative Pawley
1529reflection intensities.</p>
1530
1531<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1532style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1533mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1534
1535<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1536 id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:468pt;
1537 height:263.25pt;visibility:visible;mso-wrap-style:square'>
1538 <v:imagedata src="MCSA%20in%20GSAS_files/image006.png" o:title=""/>
1539</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=351
1540src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
1541
1542<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1543
1544<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1545style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1546mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1547for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1548style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1549mso-hansi-theme-font:minor-latin'>Edit Phase/Add powder histograms</span></b>;
1550a dialog box will appear</p>
1551
1552<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1553 id="Picture_x0020_3" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:241.5pt;
1554 height:228.75pt;visibility:visible;mso-wrap-style:square'>
1555 <v:imagedata src="MCSA%20in%20GSAS_files/image010.png" o:title=""/>
1556</v:shape><![endif]--><![if !vml]><img border=0 width=322 height=305
1557src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
1558
1559<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1560
1561<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1562style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1563mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Set All</span></b>
1564and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1565mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1566minor-latin'>OK</span></b>; the desired data set will be added to this phase
1567for analysis. The data tab now shows the new data set.</p>
1568
1569<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1570 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
1571 height:263.25pt;visibility:visible;mso-wrap-style:square'>
1572 <v:imagedata src="MCSA%20in%20GSAS_files/image014.png" o:title=""/>
1573</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=351
1574src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
1575
1576<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1577
1578<p class=MsoNormal>This is the location for all the phase dependent parameters
1579for this histogram. Notice that it includes phase fraction, size &amp; <span
1580class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1581and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1582intended for protein work where a significant region of the structure is
1583disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1584surfaces and preferred orientation correction curves.</p>
1585
1586<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1587style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1588mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1589empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1590style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1591mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1592makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1593normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1594minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
1595The table should list reflections 0-91. Select and check the <b
1596style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1597mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1598column using the same technique you used for the peak list. </p>
1599
1600<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1601 id="Picture_x0020_5" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1602 height:345pt;visibility:visible;mso-wrap-style:square'>
1603 <v:imagedata src="MCSA%20in%20GSAS_files/image018.png" o:title=""/>
1604</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=460
1605src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
1606
1607<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1608
1609<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1610you didn’t skip a step as it might not work correctly if you did.</p>
1611
1612<h2>Step 5. Pawley refinement</h2>
1613
1614<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1615normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1616minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1617the main GSAS-II data tree window. Before it begins a backup of the project
1618file is made; the name will be <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'>aminoquinoline.bck0.gpx</span></b>. It can be
1621used to recover from a bad refinement. A progress dialog box will appear
1622showing the residual as the refinement proceeds. My refinement (after 2-3
1623tries) completed with <span class=SpellE>Rwp</span> ~13%; a dialog box appears
1624asking if you wish to load the result. Press <b style='mso-bidi-font-weight:
1625normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1626minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot
1627select the PWDR line in the GSAS-II data tree (I’ve adjusted the width and
1628height).</p>
1629
1630<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1631 id="Picture_x0020_6" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
1632 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1633 <v:imagedata src="MCSA%20in%20GSAS_files/image022.png" o:title=""/>
1634</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1635src="MCSA%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
1636
1637<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1638
1639<p class=MsoNormal>I’ve expanded the vertical scale to show the fit; it is
1640evident from examining the plot that improvement can be had by improving the
1641background model. One easy way to fit that broad hump is to add a peak to the
1642background. Go to <b style='mso-bidi-font-weight:normal'><span
1643style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1644mso-hansi-theme-font:minor-latin'>Background</span></b> and set <b
1645style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1646mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. peaks</span></b>
1647to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1648mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>,
1649then change <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1650style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1651mso-hansi-theme-font:minor-latin'>pos</span></b></span> to <b style='mso-bidi-font-weight:
1652normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1653minor-latin;mso-hansi-theme-font:minor-latin'>19</span></b>, <span
1654class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1655"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1656minor-latin'>int</span></b></span> to <b style='mso-bidi-font-weight:normal'><span
1657style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1658mso-hansi-theme-font:minor-latin'>100000</span></b> and <b style='mso-bidi-font-weight:
1659normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1660minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b
1661style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1662mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>;
1663for the peak only refine <b style='mso-bidi-font-weight:normal'><span
1664style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1665mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b
1666style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1667mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1668class=SpellE>coeff</span>.</span></b> to <b style='mso-bidi-font-weight:normal'><span
1669style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1670mso-hansi-theme-font:minor-latin'>5</span></b>; the window shows</p>
1671
1672<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1673 id="Picture_x0020_7" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1674 height:207.75pt;visibility:visible;mso-wrap-style:square'>
1675 <v:imagedata src="MCSA%20in%20GSAS_files/image026.png" o:title=""/>
1676</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=277
1677src="MCSA%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
1678
1679<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1680
1681<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
1682style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1683mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1684class=SpellE>Rwp</span> fell to ~10%. In <b style='mso-bidi-font-weight:normal'><span
1685style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1686mso-hansi-theme-font:minor-latin'>Background</span></b> select <span
1687class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1688"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1689minor-latin'>pos</span></b></span> &amp; <b style='mso-bidi-font-weight:normal'><span
1690style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1691mso-hansi-theme-font:minor-latin'>sig</span></b> for refinement and in <b
1692style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1693mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1694Parameters</span></b> select <b style='mso-bidi-font-weight:normal'><span
1695style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1696mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
1697normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1698minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> for refinement; then
1699do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1700mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate
1701/Refine</span></b> again. I got Rwp~8.3% at convergence and the fit looked like</p>
1702
1703<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1704
1705<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1706 id="Picture_x0020_8" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
1707 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1708 <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
1709</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1710src="MCSA%20in%20GSAS_files/image025.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
1711
1712<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1713
1714<p class=MsoNormal>This may be good enough to try Monte Carlo/Simulated
1715Annealing.</p>
1716
1717<h2>Step 6. Setup for Monte Carlo/Simulated Annealing</h2>
1718
1719<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
1720rings with one N-substituted position and an amino side group</p>
1721
1722<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1723 id="Picture_x0020_9" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:142.5pt;
1724 height:93.75pt;visibility:visible;mso-wrap-style:square'>
1725 <v:imagedata src="MCSA%20in%20GSAS_files/image017.png" o:title="" croptop="20629f"
1726  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
1727</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
1728src="MCSA%20in%20GSAS_files/image027.jpg" v:shapes="Picture_x0020_9"><![endif]></span></p>
1729
1730<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
1731and orientation of this object in the unit cell; it has no internal degrees of
1732freedom. Thus we need to determine essentially six parameters. To do this in
1733GSAS-II we need to put a model of this molecule in as a rigid body. One must
1734create the model outside of GSAS-II, it has no facilities for model building. I
1735used the Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1736package for this and created a simple xyz Cartesian coordinate file for it (if
1737you have Avogadro or something equivalent you can try this for yourself). To
1738start go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1739"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1740minor-latin'>Rigid bodies</span></b> in the main GSAS-II data tree. You will
1741see a window with two tabs; select <b style='mso-bidi-font-weight:normal'><span
1742style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1743mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
1744style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1745mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit
1746Body/Import XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:
1747normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1748minor-latin;mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and
1749select <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1750style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1751mso-hansi-theme-font:minor-latin'>aminoquinoline.xyz</span></b></span>. The <b
1752style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1753mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b>
1754window will show</p>
1755
1756<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1757 id="Picture_x0020_31" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1758 height:419.25pt;visibility:visible;mso-wrap-style:square'>
1759 <v:imagedata src="MCSA%20in%20GSAS_files/image028.png" o:title=""/>
1760</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=559
1761src="MCSA%20in%20GSAS_files/image029.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1762
1763<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1764
1765<p class=MsoNormal>You should change the <b style='mso-bidi-font-weight:normal'><span
1766style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1767mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
1768meaningful, I used <b style='mso-bidi-font-weight:normal'><span
1769style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1770mso-hansi-theme-font:minor-latin'>amino</span></b>.<o:p></o:p></p>
1771
1772<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
1773style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1774mso-hansi-theme-font:minor-latin'>Plot?</span></b> box a drawing will appear</p>
1775
1776<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1777 id="Picture_x0020_32" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
1778 height:406.5pt;visibility:visible;mso-wrap-style:square'>
1779 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
1780</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=542
1781src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1782
1783<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1784
1785<p class=MsoNormal>The orientation is determined by rotation and translation
1786about a coordinate system centered on C1 and defined by the vectors C1-C2 and
1787C1-C3. The C1-C2 vector defines the X-axis (red), the cross product of C1-C2 and
1788C1-C3 defines the Z-axis (blue; default view direction) and the Y-axis is
1789defined as Z-axis cross X-axis (green; down toward C5). You can change these
1790via the pull downs
1791next to <B>Orientation reference non-H atoms A-B-C</B> 
1792(you can’t pick the same atom for two of these so pick them
1793appropriately; I chose C2, C3 &amp; C6). At each choice the structure will be
1794transformed accordingly. My new model is</p>
1795
1796<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1797 id="_x0000_i1041" type="#_x0000_t75" style='width:468pt;height:404.25pt;
1798 visibility:visible;mso-wrap-style:square'>
1799 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
1800</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
1801src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="_x0000_i1041"><![endif]></span></p>
1802
1803<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1804
1805<p class=MsoNormal>The molecular coordinate system has been changed by you
1806assignment of reference atoms. The C2-C3 vector is now the X-axis (red), the
1807C2-C6 vector is ~ the Y-axis (green) and the Z-axis (blue) is ~normal to the
1808molecular plane. The rigid body coordinates reflect this change</p>
1809
1810<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1811 id="_x0000_i1040" type="#_x0000_t75" style='width:468pt;height:420.75pt;
1812 visibility:visible;mso-wrap-style:square'>
1813 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title=""/>
1814</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=561
1815src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="_x0000_i1040"><![endif]></span></p>
1816
1817<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The Cart z values are
1818all close to zero and C3 has only a nonzero Cart x. Notice that the model
1819includes H-atoms; they are not really needed for MC/SA and will just make
1820computation times a bit longer than necessary. They can be removed by selecting
1821the <B>Strip H-atoms box</B>; for now leave them in. </p>
1822
1823<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1824
1825<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1826style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1827mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> and select
1828the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1829mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA</span></b>
1830tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1831"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1832minor-latin'>MC/SA/Add rigid body</span></b>; select the only choice (<b
1833style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1834mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>)
1835from the popup selection box. The MC/SA window shows</p>
1836
1837<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1838 id="_x0000_i1039" type="#_x0000_t75" style='width:468pt;height:212.25pt;
1839 visibility:visible;mso-wrap-style:square'>
1840 <v:imagedata src="MCSA%20in%20GSAS_files/image042.png" o:title=""/>
1841</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=283
1842src="MCSA%20in%20GSAS_files/image044.gif" v:shapes="_x0000_i1039"><![endif]></span></p>
1843
1844<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1845
1846<p class=MsoNormal>And the plot shows the molecular XYZ-axes lined up along the
1847crystal <span class=SpellE>abc</span>-axes; this is expected from our choice of
1848molecular reference atoms (C2, C3 &amp; C6).</p>
1849
1850<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1851 id="Picture_x0020_33" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1852 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1853 <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
1854</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
1855src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1856
1857<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1858
1859<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
1860whose centers fall within the unit cell; the reference one is that in the lower
1861right corner with C2 at the origin. You can enter values in the <span
1862class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1863"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1864minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
1865the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
1866style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1867mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
1868or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1869style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1870mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
1871style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
1872molecule. Each of these parameters has a defined range for the MC/SA
1873optimization run we are about to do; they define the multidimensional search
1874volume. Within that volume will be a number of correct solutions to the
1875structure problem all related by translational and space group symmetry. One
1876can limit this volume by choosing more limited ranges, but here we’ll just go
1877with the default. We want to optimize the position and orientation of this
1878molecule; check the <b style='mso-bidi-font-weight:normal'><span
1879style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1880mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
1881normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1882minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <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'>z</span></b>
1885boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1886"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1887minor-latin'>AV</span></b> from the <span class=SpellE><b style='mso-bidi-font-weight:
1888normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1889minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
1890class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1891"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1892minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
1893style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b>
1895pulldown. The MC/SA window should look like</p>
1896
1897<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1898 id="Picture_x0020_34" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1899 height:204.75pt;visibility:visible;mso-wrap-style:square'>
1900 <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
1901</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=273
1902src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_34"><![endif]></span><span
1903style='mso-spacerun:yes'> </span></p>
1904
1905<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1906
1907<p class=MsoNormal>This completes the set up for MC/SA processing. </p>
1908
1909<h2>Step 7. Monte Carlo/Simulated Annealing</h2>
1910
1911<p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
1912style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1913mso-hansi-theme-font:minor-latin'>General</span></b> tab; the MC/SA controls
1914are at the bottom of the window. To begin the setup of these controls, select a
1915source of the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1916"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1917minor-latin'>Reflection set</span></b> to be used in the MC/SA runs. The choice
1918is to use either the Pawley reflections or the Reflection List for the PWDR
1919data set. If you choose <b style='mso-bidi-font-weight:normal'><span
1920style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1921mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
1922structure factors will be Pawley model values, <span class=SpellE>Fsq</span>(<span
1923class=SpellE>hkl</span>) in Pawley table, and the covariance matrix developed
1924from the refinement will be used for peak overlap effects in the MC/SA
1925calculations. Alternatively, if you choose <b style='mso-bidi-font-weight:normal'><span
1926style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1927mso-hansi-theme-font:minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span>
1928Bank 1 </span></b>then the structure factors will be those, <span class=SpellE>Fosq</span>
1929in Reflection table, extracted during the Pawley refinement and the peak FWHMs
1930will be used for peak overlap effects in the MC/SA calculations. Notice that
1931the Pawley <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) values
1932are the same as the <span class=SpellE>Fcsq</span> Reflection List values. Here
1933I chose <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1934mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR <span
1935class=SpellE>Quinoli.gda</span> Bank 1 </span></b>for the <b style='mso-bidi-font-weight:
1936normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1937minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it
1938gives slightly better performance in MC/SA.</p>
1939
1940<p class=MsoNormal>Next, you need to set the minimum d-spacing (<b
1941style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>d-min</span></b>).
1943Smaller values gives minima in the MC/SA minimization surface that are more
1944sharply defined (thus harder to locate), while larger values yield insufficient
1945numbers of reflections to give sufficient redundancy in the calculations. One
1946should have 5-8 reflections for each MC/SA parameter; in this case 35-50
1947reflections are needed. If you examine the reflection list (either <b
1948style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1949mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley</span></b>
1950or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1951mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1952List</span></b>) you’ll see that a <b style='mso-bidi-font-weight:normal'><span
1953style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1954mso-hansi-theme-font:minor-latin'>d-min</span></b> of <b style='mso-bidi-font-weight:
1955normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1956minor-latin;mso-hansi-theme-font:minor-latin'>2.5</span></b> will give
1957sufficient reflections.</p>
1958
1959<p class=MsoNormal>Lastly, you need to set the run controls. I used <b
1960style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1961mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>500</span></b>
1962for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1963mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
1964this is the number of random tries at each “temperature” in the annealing schedule.
1965I also used <b style='mso-bidi-font-weight:normal'><span style='font-family:
1966"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1967minor-latin'>4 MC/SA runs</span></b> When done the <b style='mso-bidi-font-weight:
1968normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1969minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> window should
1970look like</p>
1971
1972<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1973 id="Picture_x0020_35" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1974 height:223.5pt;visibility:visible;mso-wrap-style:square'>
1975 <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
1976</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=298
1977src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1978
1979<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1980
1981<p class=MsoNormal>When ready, you can start the MC/SA calculation by doing <b
1982style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1983mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>
1984from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1985mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1986window menu. A progress bar will appear that shows the MC/SA residual (an
1987R-factor) as the calculation progresses through the annealing schedule as well
1988as indicating which MC/SA run is being done. When it finishes, control is
1989shifted to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1990"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1991minor-latin'>MC/SA</span></b> window which gives a list of the solutions it
1992found at the bottom of the window (scroll down to see them).</p>
1993
1994<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1995 id="Picture_x0020_36" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1996 height:253.5pt;visibility:visible;mso-wrap-style:square'>
1997 <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
1998</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=338
1999src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
2000
2001<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2002
2003<p class=MsoNormal>The one with the lowest residual is already chosen and the
2004corresponding structure is drawn</p>
2005
2006<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2007 id="Picture_x0020_37" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
2008 height:405pt;visibility:visible;mso-wrap-style:square'>
2009 <v:imagedata src="MCSA%20in%20GSAS_files/image082.png" o:title=""/>
2010</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=540
2011src="MCSA%20in%20GSAS_files/image083.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
2012
2013<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2014
2015<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
2016good solution with a very low Residual (~7.2%). This problem typically gives
2017suitable solutions with Residuals of 7%; if you had stripped the H-atoms, the
2018best residual is ~10%. If your cell indexing resulted in <span class=GramE>a
2019&amp;</span> b swapped, you should view the structure along a (red). If no good
2020solution appears (e.g. molecules clashing &amp; high residuals), then you
2021should just rerun MC/SA perhaps using more runs or more trials.</p>
2022
2023<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
2024
2025<p class=MsoNormal>The MC/SA calculations can take advantage of multicore
2026machines. First set the number of cores by doing <b style='mso-bidi-font-weight:
2027normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2028minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Preferences</span></b>;
2029select <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
2030style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2031mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Multiprocessing_cores</span></b></span>
2032from the pulldown and enter the number you wish to use (I suggest Maxcores-1).
2033Then press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
2034style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2035mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b></span><b
2036style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2037mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2038minor-latin'> current settings</span></b>; your choice becomes available immediately
2039and is then set for all your future uses of GSAS-II. <span
2040style='mso-spacerun:yes'> </span>Go to the <B>General</B> tab and
2041select
2042<b style='mso-bidi-font-weight:normal'><span
2043style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2044mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Compute/Multi
2045MC/SA</span></b> to use it.</p>
2046
2047<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2048
2049<p class=MsoNormal>Be sure to set the <b style='mso-bidi-font-weight:normal'><span
2050style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2051mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
2052want to retain; the others will be cleared before the next MC/SA run starts.
2053When you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
2054normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2055minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span> it; the
2056parameters will be copied to the appropriate boxes in the upper part of the
2057MC/SA window and the structure is drawn again. Next we want to refine this
2058solution so go back to the <b style='mso-bidi-font-weight:normal'><span
2059style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2060mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
2061
2062<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
2063and rerunning the MC/SA calculations. This is done by checking the <b
2064style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2065mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA Refine</span></b>
2066box under the <B>General</B> tab. Using 10% of the ranges reduces the search volume in this case by ~6
2067orders of magnitude so that the true minimum is much easier to find. Now rerun <b
2068style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2069mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
2070be sure to select the best one before starting. The residual might drop to a
2071much lower level. This refinement can be repeated with tighter restriction on
2072the ranges. My result (no improvement on 7%) was</p>
2073
2074<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2075 id="Picture_x0020_38" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
2076 height:257.25pt;visibility:visible;mso-wrap-style:square'>
2077 <v:imagedata src="MCSA%20in%20GSAS_files/image084.png" o:title=""/>
2078</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=343
2079src="MCSA%20in%20GSAS_files/image085.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
2080
2081<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2082
2083<p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>7.2%</span>!)
2084and the structure</p>
2085
2086<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2087 id="Picture_x0020_39" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
2088 height:402.75pt;visibility:visible;mso-wrap-style:square'>
2089 <v:imagedata src="MCSA%20in%20GSAS_files/image086.png" o:title=""/>
2090</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=537
2091src="MCSA%20in%20GSAS_files/image087.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
2092
2093<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2094
2095<p class=MsoNormal>Has a different origin choice (a &amp; b might also be
2096switched) than the published one </p>
2097
2098<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2099 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:288.75pt;
2100 height:225.75pt;visibility:visible;mso-wrap-style:square'>
2101 <v:imagedata src="MCSA%20in%20GSAS_files/image041.png" o:title="" croptop="14378f"
2102  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
2103</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
2104src="MCSA%20in%20GSAS_files/image088.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
2105
2106<p class=MsoNormal>as drawn by the Mercury program </p>
2107
2108<p class=MsoNormal>(<a
2109href="https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx">https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx</a>).
2110To save this solution to the <b style='mso-bidi-font-weight:normal'><span
2111style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2112mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
2113normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2114minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
2115the drawing will show the new atom positions</p>
2116
2117<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2118 id="Picture_x0020_40" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
2119 height:402.75pt;visibility:visible;mso-wrap-style:square'>
2120 <v:imagedata src="MCSA%20in%20GSAS_files/image089.png" o:title=""/>
2121</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=537
2122src="MCSA%20in%20GSAS_files/image090.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
2123
2124<p class=MsoNormal>And they will be listed in the Atoms table.</p>
2125
2126<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2127 id="Picture_x0020_41" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
2128 height:288.75pt;visibility:visible;mso-wrap-style:square'>
2129 <v:imagedata src="MCSA%20in%20GSAS_files/image091.png" o:title=""/>
2130</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=385
2131src="MCSA%20in%20GSAS_files/image095.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
2132
2133<p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use
2134the rigid body as the data will not support independent atom position
2135refinement.</p>
2136
2137<h2>Step 8. Initial Rietveld refinement</h2>
2138
2139<p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
2140be ready for the first Rietveld refinement: 1) On the <b style='mso-bidi-font-weight:
2141normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2142minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab uncheck
2143the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2144mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley
2145refinement?</span></b> box, 2) check the <b style='mso-bidi-font-weight:normal'><span
2146style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2147mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> box in <b
2148style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2149mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2150Parameters</span></b> and 3) zero both <b style='mso-bidi-font-weight:normal'><span
2151style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2152mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
2153normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2154minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> and uncheck their
2155refine boxes in <b style='mso-bidi-font-weight:normal'><span style='font-family:
2156"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2157minor-latin'>Instrument Parameters</span></b>. Then do <b style='mso-bidi-font-weight:
2158normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2159minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
2160the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
2161was ~12%. Next check the <b style='mso-bidi-font-weight:normal'><span
2162style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2163mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b
2164style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2165mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2166window and in the <b style='mso-bidi-font-weight:normal'><span
2167style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2168mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b
2169style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2170mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b>
2171model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
2172style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2173mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
2174style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2175mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
2176class=GramE>size</span></span></b> and both <span class=SpellE><b
2177style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2178mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
2179boxes and do another <b style='mso-bidi-font-weight:normal'><span
2180style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2181mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice) I got an <span
2182class=SpellE>R<sub>wp</sub></span> ~8.2% for this. We’ve not refined atom
2183positions or thermal parameters; to do this we need to describe the structure
2184as a rigid body.</p>
2185
2186<h2>Step 9. Rigid body model</h2>
2187
2188<p class=MsoNormal>The rigid body itself has already been defined; it was used
2189for the MC/SA structure solution. Now we have to place it in the unit cell
2190matching the atom positions obtained from the MC/SA runs. First go to the <b
2191style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2192mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2193tab and change the <b style='mso-bidi-font-weight:normal'><span
2194style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2195mso-hansi-theme-font:minor-latin'>Style</span></b> to <b style='mso-bidi-font-weight:
2196normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2197minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp; sticks</span></b> and
2198the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2199mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
2200to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2201mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>name</span></b>.
2202Double click on the column headings and select the item from the popup control.
2203Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2204"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2205minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
2206style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2207mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Body/Assign
2208atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
2209normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2210minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
2211style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2212mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
2213body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
2214normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2215minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
2216show</p>
2217
2218<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2219 id="Picture_x0020_42" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
2220 height:195.75pt;visibility:visible;mso-wrap-style:square'>
2221 <v:imagedata src="MCSA%20in%20GSAS_files/image096.png" o:title=""/>
2222</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=261
2223src="MCSA%20in%20GSAS_files/image097.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
2224
2225<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2226
2227<p class=MsoNormal>You will orient the rigid body against the atoms by matching
2228up the 3 reference atoms in the rigid body (C1, C2 &amp; C5) to the
2229corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
2230order; the drawing will show the shift of molecular origin and then its
2231reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight:
2232normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2233minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b> when done; the
2234structure will be drawn with orange bonds indicating that it is now a rigid
2235body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span
2236style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2237mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows the new
2238rigid body</p>
2239
2240<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2241 id="Picture_x0020_43" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2242 height:207pt;visibility:visible;mso-wrap-style:square'>
2243 <v:imagedata src="MCSA%20in%20GSAS_files/image098.png" o:title=""/>
2244</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=276
2245src="MCSA%20in%20GSAS_files/image099.gif" v:shapes="Picture_x0020_43"><![endif]></span></p>
2246
2247<p class=MsoNormal>To refine the rigid body origin position check the <b
2248style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2249mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
2250box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2251"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2252minor-latin'>AV</span></b> from the pull down, choose <span class=SpellE><b
2253style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2254mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Uiso</span></b></span>
2255from the thermal parameter model and check its <b style='mso-bidi-font-weight:
2256normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2257minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b> box. Then do <b
2258style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2259mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2260after a couple of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span>
2261~7.9% and the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2262"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2263minor-latin'>RB Models</span></b> window shows the new parameters</p>
2264
2265<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2266 id="Picture_x0020_44" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
2267 height:3in;visibility:visible;mso-wrap-style:square'>
2268 <v:imagedata src="MCSA%20in%20GSAS_files/image100.png" o:title=""/>
2269</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=288
2270src="MCSA%20in%20GSAS_files/image101.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
2271
2272<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
2273
2274<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2275 id="Picture_x0020_45" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2276 height:401.25pt;visibility:visible;mso-wrap-style:square'>
2277 <v:imagedata src="MCSA%20in%20GSAS_files/image102.png" o:title=""/>
2278</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
2279src="MCSA%20in%20GSAS_files/image103.gif" v:shapes="Picture_x0020_45"><![endif]></span></p>
2280
2281<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
2282Next is a more complex case involving some internal degrees of freedom in the
2283molecule of a-d-lactose.</p>
2284
2285</div>
2286
2287</body>
2288
2289</html>
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