source: Tutorials/MCsimanneal/MCSA in GSAS.htm

Last change on this file was 4457, checked in by toby, 18 months ago

add data link to tutorials

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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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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><BL>
1282  <LI>Exercise files are found <A href="./data/" target="_blank">here</a>
1283</BL></P><P></P>
1284
1285  <p class=MsoNormal>In these exercises you will use GSAS-II to solve the
1286structures of 3-aminoquinoline and &#945;-d-lactose monohydrate from powder
1287diffraction data via Monte Carlo/Simulated Annealing (MC/SA). The data sets
1288were kindly provided by Peter Stephens (SUNY <span class=SpellE>StonyBrook</span>)
1289and were originally collected on NSLS beam line X3b1. The MC/SA technique is
1290needed in these cases because as you will see the data does not extend very far
1291in 2&#920; so one cannot use charge flipping to solve them. The steps for each
1292begin with peak selection and fitting, then indexing to identify the lattice
1293parameters. A Pawley refinement is used to obtain a set of structure factors
1294needed for the MC/SA runs. We will use previously developed models for the two
1295molecules; I used the freeware program Avogadro (<a
1296href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1297to create them.</p>
1298
1299<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1300
1301<h2>Step 1. Import powder data for 3-aminoquinoline</h2>
1302
1303<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1304style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1305style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1306the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1307mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1308minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1309to read the data file into the current GSAS-II project. Change the file
1310directory to <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1311style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1312mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>MCsimanneal</span></b></span><b
1313style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1314mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1315minor-latin'>/data</span></b><span style='font-family:"Calibri",sans-serif;
1316mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1317minor-latin'> to find the file; you may need to change the file type to <b
1318style='mso-bidi-font-weight:normal'>All files (*.*)</b> to find the desired file.</span></p>
1319
1320<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1321style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1322style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1323the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1324style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1325mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Quinoli.gda</span></b></span><span
1326style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1327mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> data</span>
1328file in the first dialog and press <b style='mso-bidi-font-weight:normal'><span
1329style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1330mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
1331There will be a Dialog box asking <b style='mso-bidi-font-weight:normal'><span
1332style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1333mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is this the
1334file you want?</span></b> Press <b style='mso-bidi-font-weight:normal'><span
1335style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1336mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b>
1337button to proceed.</p>
1338
1339<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo2'><![if !supportLists]><span
1340style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1341style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1342the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1343mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1344minor-latin'>BNL-<span class=SpellE>I.instprm</span></span></b> instrument
1345parameter file in the second dialog and press <b style='mso-bidi-font-weight:
1346normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1347minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
1348You’ll have to change the file type to <b style='mso-bidi-font-weight:normal'><span
1349style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1350mso-hansi-theme-font:minor-latin'>*.<span class=SpellE>instprm</span></span></b>
1351(GSAS-II instrument parameter file). The powder pattern will immediately
1352appear.</p>
1353
1354<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1355 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
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1368  <v:f eqn="sum @8 21600 0"/>
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1370  <v:f eqn="sum @10 21600 0"/>
1371 </v:formulas>
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1376 <v:imagedata src="MCSA%20in%20GSAS_files/image002.png" o:title=""/>
1377</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1378src="MCSA%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_1"><![endif]></span></p>
1379
1380<p class=MsoListParagraph><o:p>&nbsp;</o:p></p>
1381
1382<p class=MsoListParagraph>Notice that the pattern extends only to a minimum
1383d-spacing of ~1.81Å; this is not far enough to use charge flipping which needs
13841Å or better. </p>
1385
1386<h2>Step 2. Peak picking &amp; fitting</h2>
1387
1388<p class=MsoNormal>Next you need to select limits so that ~20 peaks are
1389selected for indexing; go to <b style='mso-bidi-font-weight:normal'><span
1390style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1391mso-hansi-theme-font:minor-latin'>Limits</span></b> and choose <b
1392style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1393mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>9-25</span></b>°
13942&#920;. Next go to <b style='mso-bidi-font-weight:normal'><span
1395style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1396mso-hansi-theme-font:minor-latin'>Peak List</span></b> and pick all the peaks
1397you can see between the limits. This is most easily done by hand as the <b
1398style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1399mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Auto search</span></b>
1400routine gives a lot of spurious peaks for this rather noisy and weak data; I
1401picked 21 peaks, skipping a few very weak ones. Then use <b style='mso-bidi-font-weight:
1402normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1403minor-latin;mso-hansi-theme-font:minor-latin'>Peak Fitting/<span class=SpellE>PeakFit</span>
1404</span></b>to fit them (it will ask to save the project; I called it ‘<b
1405style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1406mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1407minor-latin'>2-amino</span></b>’). You will need to refine at least <b
1408style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1409mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
1410&amp; <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1411mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>
1412in <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1413mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1414Parameters</span></b> along with <span class=SpellE><b style='mso-bidi-font-weight:
1415normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1416minor-latin;mso-hansi-theme-font:minor-latin'>pos</span></b></span> &amp; <span
1417class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1418"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1419minor-latin'>int</span></b></span> in the <b style='mso-bidi-font-weight:normal'><span
1420style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1421mso-hansi-theme-font:minor-latin'>Peak List</span></b> to get a reasonable fit
1422suitable for indexing.</p>
1423
1424<h2>Step 3. Indexing</h2>
1425
1426<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1427style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1428mso-hansi-theme-font:minor-latin'>Index Peak List</span></b> and do <b
1429style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1430mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Load/Reload</span></b>
1431to set up the peaks for indexing. Then go to <b style='mso-bidi-font-weight:
1432normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1433minor-latin;mso-hansi-theme-font:minor-latin'>Unit Cells List</span></b> for
1434indexing. The most likely <span class=SpellE>Bravais</span> lattice for these
1435small organic molecules is either Orthorhombic-P or Monoclinic-P; you can try
1436both and see what comes out (Hint: it’s <b style='mso-bidi-font-weight:normal'><span
1437style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1438mso-hansi-theme-font:minor-latin'>Orthorhombic-P</span></b>).
1439Click on <B>Cell Index/Refine/Index Cell</B>. The correct unit
1440cell should almost immediately appear with an M20 ~370 with a=7.748, b=7.650,
1441c=12.736, Vol=755.01. NB: your solution may have a &amp; b switched. Do <b
1442style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1443mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cell
1444Index/Refine/Copy Cell</span></b>; you can then try various space groups. Press
1445the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1446mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show HKL
1447positions</span></b> to see the lines with extinctions (Hint: it’s <b
1448style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1449mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>P 2<sub>1</sub>
14502<sub>1</sub> 2<sub>1</sub></span></b>).
1451Under the <B>General</B> tab, change the space group to <B>P 21 21 21</B>.
1452You can then do <b style='mso-bidi-font-weight:
1453normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1454minor-latin;mso-hansi-theme-font:minor-latin'>Cell Index/Refine/Refine Cell</span></b>
1455to improve the lattice parameters with M20 ~380. Finally do <b
1456style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1457mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cell
1458Index/Refine/Make new phase</span></b> to create the phase; I named it <b
1459style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1460mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>3-aminoquinoline</span></b>.</p>
1461
1462<h2>Step 4. Setup for Pawley refinement</h2>
1463
1464<p class=MsoNormal>There are a number of steps that must be done in preparation
1465for a Pawley refinement after having completed the unit cell indexing and new
1466phase creation. These cover two things: one is to prepare the powder pattern
1467(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1468
1469<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1470style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1471style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1472<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1473mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1474in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1475region at the end of the data is readily seen. This is ~37deg 2<span
1476style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
1477"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
1478style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>;
1479there are a few zero points at the end that need to be excluded. Use the right
1480mouse button and pick a point just inside the end avoiding the zeros. Make a
1481note of the exact d-spacing (for me 1.8126) using the mouse cursor on the plot.</p>
1482
1483<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1484style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1485style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1486<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1487mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1488Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1489style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1490mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1491style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1492mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1493profile</span></b> to recover the default values. The peak fitting done earlier
1494is over a more limited range of 2<span style='font-family:Symbol;mso-ascii-font-family:
1495"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
1496mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
1497Symbol'>Q</span></span> giving values that will not extrapolate well over the
1498wider range to be used in the Pawley refinement. We may refine them again
1499later.</p>
1500
1501<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1502style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1503style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1504<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1505mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1506Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1507normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1508minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
1509
1510<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo4'><![if !supportLists]><span
1511style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1512style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1513to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1514mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b>
1515to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1516"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1517minor-latin'>Pawley controls</span></b> under the <B>General</B> tab.
1518Check the <b style='mso-bidi-font-weight:
1519normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1520minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement?</span></b>
1521box, enter the d-spacing (<b style='mso-bidi-font-weight:normal'><span
1522style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1523mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1.8126</span></b>)
1524into the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1526class=SpellE>dmin</span></span></b> box and set the <b style='mso-bidi-font-weight:
1527normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1528minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Pawley
1529neg. wt.</span></b><span style='mso-spacerun:yes'>  </span><span class=GramE>to</span>
1530<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1531mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1532minor-latin'>0.001</span></b>. This will suppress possible negative Pawley
1533reflection intensities.</p>
1534
1535<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1536style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1537mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1538
1539<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1540 id="Picture_x0020_2" o:spid="_x0000_i1051" type="#_x0000_t75" style='width:468pt;
1541 height:263.25pt;visibility:visible;mso-wrap-style:square'>
1542 <v:imagedata src="MCSA%20in%20GSAS_files/image006.png" o:title=""/>
1543</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=351
1544src="MCSA%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
1545
1546<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1547
1548<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1549style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1550mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1551for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1552style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1553mso-hansi-theme-font:minor-latin'>Edit Phase/Add powder histograms</span></b>;
1554a dialog box will appear</p>
1555
1556<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1557 id="Picture_x0020_3" o:spid="_x0000_i1050" type="#_x0000_t75" style='width:241.5pt;
1558 height:228.75pt;visibility:visible;mso-wrap-style:square'>
1559 <v:imagedata src="MCSA%20in%20GSAS_files/image010.png" o:title=""/>
1560</v:shape><![endif]--><![if !vml]><img border=0 width=322 height=305
1561src="MCSA%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_3"><![endif]></span></p>
1562
1563<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1564
1565<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1566style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1567mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Set All</span></b>
1568and then <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1569mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1570minor-latin'>OK</span></b>; the desired data set will be added to this phase
1571for analysis. The data tab now shows the new data set.</p>
1572
1573<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1574 id="Picture_x0020_4" o:spid="_x0000_i1049" type="#_x0000_t75" style='width:468pt;
1575 height:263.25pt;visibility:visible;mso-wrap-style:square'>
1576 <v:imagedata src="MCSA%20in%20GSAS_files/image014.png" o:title=""/>
1577</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=351
1578src="MCSA%20in%20GSAS_files/image016.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
1579
1580<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1581
1582<p class=MsoNormal>This is the location for all the phase dependent parameters
1583for this histogram. Notice that it includes phase fraction, size &amp; <span
1584class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1585and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1586intended for protein work where a significant region of the structure is
1587disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1588surfaces and preferred orientation correction curves.</p>
1589
1590<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1591style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1592mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1593empty except for column headings. Do <b style='mso-bidi-font-weight:normal'><span
1594style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1595mso-hansi-theme-font:minor-latin'>Operations/Pawley create</span></b>; this
1596makes the reflection set over the range covered by setting <b style='mso-bidi-font-weight:
1597normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1598minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>.
1599The table should list reflections 0-91. Select and check the <b
1600style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1601mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>refine</span></b>
1602column using the same technique you used for the peak list. </p>
1603
1604<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1605 id="Picture_x0020_5" o:spid="_x0000_i1048" type="#_x0000_t75" style='width:468pt;
1606 height:345pt;visibility:visible;mso-wrap-style:square'>
1607 <v:imagedata src="MCSA%20in%20GSAS_files/image018.png" o:title=""/>
1608</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=460
1609src="MCSA%20in%20GSAS_files/image020.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
1610
1611<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1612
1613<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1614you didn’t skip a step as it might not work correctly if you did.</p>
1615
1616<h2>Step 5. Pawley refinement</h2>
1617
1618<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1619normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1620minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1621the main GSAS-II data tree window. Before it begins a backup of the project
1622file is made; the name will be <b style='mso-bidi-font-weight:normal'><span
1623style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1624mso-hansi-theme-font:minor-latin'>aminoquinoline.bck0.gpx</span></b>. It can be
1625used to recover from a bad refinement. A progress dialog box will appear
1626showing the residual as the refinement proceeds. My refinement (after 2-3
1627tries) completed with <span class=SpellE>Rwp</span> ~13%; a dialog box appears
1628asking if you wish to load the result. Press <b style='mso-bidi-font-weight:
1629normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1630minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. To see the plot
1631select the PWDR line in the GSAS-II data tree (I’ve adjusted the width and
1632height).</p>
1633
1634<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1635 id="Picture_x0020_6" o:spid="_x0000_i1047" type="#_x0000_t75" style='width:468pt;
1636 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1637 <v:imagedata src="MCSA%20in%20GSAS_files/image022.png" o:title=""/>
1638</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1639src="MCSA%20in%20GSAS_files/image023.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
1640
1641<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1642
1643<p class=MsoNormal>I’ve expanded the vertical scale to show the fit; it is
1644evident from examining the plot that improvement can be had by improving the
1645background model. One easy way to fit that broad hump is to add a peak to the
1646background. Go to <b style='mso-bidi-font-weight:normal'><span
1647style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1648mso-hansi-theme-font:minor-latin'>Background</span></b> and set <b
1649style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1650mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. peaks</span></b>
1651to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1652mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1</span></b>,
1653then change <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1654style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1655mso-hansi-theme-font:minor-latin'>pos</span></b></span> to <b style='mso-bidi-font-weight:
1656normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1657minor-latin;mso-hansi-theme-font:minor-latin'>19</span></b>, <span
1658class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1659"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1660minor-latin'>int</span></b></span> to <b style='mso-bidi-font-weight:normal'><span
1661style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1662mso-hansi-theme-font:minor-latin'>100000</span></b> and <b style='mso-bidi-font-weight:
1663normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1664minor-latin;mso-hansi-theme-font:minor-latin'>sig</span></b> to <b
1665style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1666mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1000</span></b>;
1667for the peak only refine <b style='mso-bidi-font-weight:normal'><span
1668style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1669mso-hansi-theme-font:minor-latin'>int</span></b>. I also set <b
1670style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1671mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. <span
1672class=SpellE>coeff</span>.</span></b> to <b style='mso-bidi-font-weight:normal'><span
1673style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1674mso-hansi-theme-font:minor-latin'>5</span></b>; the window shows</p>
1675
1676<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1677 id="Picture_x0020_7" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:468pt;
1678 height:207.75pt;visibility:visible;mso-wrap-style:square'>
1679 <v:imagedata src="MCSA%20in%20GSAS_files/image026.png" o:title=""/>
1680</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=277
1681src="MCSA%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
1682
1683<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1684
1685<p class=MsoNormal>Do a <b style='mso-bidi-font-weight:normal'><span
1686style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1687mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; my <span
1688class=SpellE>Rwp</span> fell to ~10%. In <b style='mso-bidi-font-weight:normal'><span
1689style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1690mso-hansi-theme-font:minor-latin'>Background</span></b> select <span
1691class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1692"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1693minor-latin'>pos</span></b></span> &amp; <b style='mso-bidi-font-weight:normal'><span
1694style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1695mso-hansi-theme-font:minor-latin'>sig</span></b> for refinement and in <b
1696style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1697mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1698Parameters</span></b> select <b style='mso-bidi-font-weight:normal'><span
1699style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1700mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
1701normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1702minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> for refinement; then
1703do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1704mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate
1705/Refine</span></b> again. I got Rwp~8.3% at convergence and the fit looked like</p>
1706
1707<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1708
1709<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1710 id="Picture_x0020_8" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:468pt;
1711 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1712 <v:imagedata src="MCSA%20in%20GSAS_files/image030.png" o:title=""/>
1713</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1714src="MCSA%20in%20GSAS_files/image025.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
1715
1716<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1717
1718<p class=MsoNormal>This may be good enough to try Monte Carlo/Simulated
1719Annealing.</p>
1720
1721<h2>Step 6. Setup for Monte Carlo/Simulated Annealing</h2>
1722
1723<p class=MsoNormal>The molecular structure of 3-aminoquinoline is two aromatic
1724rings with one N-substituted position and an amino side group</p>
1725
1726<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1727 id="Picture_x0020_9" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:142.5pt;
1728 height:93.75pt;visibility:visible;mso-wrap-style:square'>
1729 <v:imagedata src="MCSA%20in%20GSAS_files/image017.png" o:title="" croptop="20629f"
1730  cropbottom="17428f" cropleft="9893f" cropright="13874f"/>
1731</v:shape><![endif]--><![if !vml]><img border=0 width=190 height=125
1732src="MCSA%20in%20GSAS_files/image027.jpg" v:shapes="Picture_x0020_9"><![endif]></span></p>
1733
1734<p class=MsoNormal>MC/SA structure solution consists of optimizing the position
1735and orientation of this object in the unit cell; it has no internal degrees of
1736freedom. Thus we need to determine essentially six parameters. To do this in
1737GSAS-II we need to put a model of this molecule in as a rigid body. One must
1738create the model outside of GSAS-II, it has no facilities for model building. I
1739used the Avogadro (<a href="http://avogadro.cc/wiki/Main_Page">http://avogadro.cc/wiki/Main_Page</a>)
1740package for this and created a simple xyz Cartesian coordinate file for it (if
1741you have Avogadro or something equivalent you can try this for yourself). To
1742start go to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1743"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1744minor-latin'>Rigid bodies</span></b> in the main GSAS-II data tree. You will
1745see a window with two tabs; select <b style='mso-bidi-font-weight:normal'><span
1746style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1747mso-hansi-theme-font:minor-latin'>Residue rigid bodies</span></b> and then do <b
1748style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1749mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit
1750Body/Import XYZ</span></b>. Change the file type to <b style='mso-bidi-font-weight:
1751normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1752minor-latin;mso-hansi-theme-font:minor-latin'>XYZ file (*.xyz)</span></b> and
1753select <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1754style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1755mso-hansi-theme-font:minor-latin'>aminoquinoline.xyz</span></b></span>. The <b
1756style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1757mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Rigid bodies</span></b>
1758window will show</p>
1759
1760<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1761 id="Picture_x0020_31" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:468pt;
1762 height:419.25pt;visibility:visible;mso-wrap-style:square'>
1763 <v:imagedata src="MCSA%20in%20GSAS_files/image028.png" o:title=""/>
1764</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=559
1765src="MCSA%20in%20GSAS_files/image029.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1766
1767<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1768
1769<p class=MsoNormal>You should change the <b style='mso-bidi-font-weight:normal'><span
1770style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1771mso-hansi-theme-font:minor-latin'>Residue name</span></b> to something
1772meaningful, I used <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'>amino</span></b>.<o:p></o:p></p>
1775
1776<p class=MsoNormal>If you select the <b style='mso-bidi-font-weight:normal'><span
1777style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1778mso-hansi-theme-font:minor-latin'>Plot?</span></b> box a drawing will appear</p>
1779
1780<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1781 id="Picture_x0020_32" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:468pt;
1782 height:406.5pt;visibility:visible;mso-wrap-style:square'>
1783 <v:imagedata src="MCSA%20in%20GSAS_files/image031.png" o:title=""/>
1784</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=542
1785src="MCSA%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1786
1787<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1788
1789<p class=MsoNormal>The orientation is determined by rotation and translation
1790about a coordinate system centered on C1 and defined by the vectors C1-C2 and
1791C1-C3. The C1-C2 vector defines the X-axis (red), the cross product of C1-C2 and
1792C1-C3 defines the Z-axis (blue; default view direction) and the Y-axis is
1793defined as Z-axis cross X-axis (green; down toward C5). You can change these
1794via the pull downs
1795next to <B>Orientation reference non-H atoms A-B-C</B> 
1796(you can’t pick the same atom for two of these so pick them
1797appropriately; I chose C2, C3 &amp; C6). At each choice the structure will be
1798transformed accordingly. My new model is</p>
1799
1800<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1801 id="_x0000_i1041" type="#_x0000_t75" style='width:468pt;height:404.25pt;
1802 visibility:visible;mso-wrap-style:square'>
1803 <v:imagedata src="MCSA%20in%20GSAS_files/image033.png" o:title=""/>
1804</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
1805src="MCSA%20in%20GSAS_files/image034.gif" v:shapes="_x0000_i1041"><![endif]></span></p>
1806
1807<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1808
1809<p class=MsoNormal>The molecular coordinate system has been changed by you
1810assignment of reference atoms. The C2-C3 vector is now the X-axis (red), the
1811C2-C6 vector is ~ the Y-axis (green) and the Z-axis (blue) is ~normal to the
1812molecular plane. The rigid body coordinates reflect this change</p>
1813
1814<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1815 id="_x0000_i1040" type="#_x0000_t75" style='width:468pt;height:420.75pt;
1816 visibility:visible;mso-wrap-style:square'>
1817 <v:imagedata src="MCSA%20in%20GSAS_files/image035.png" o:title=""/>
1818</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=561
1819src="MCSA%20in%20GSAS_files/image038.gif" v:shapes="_x0000_i1040"><![endif]></span></p>
1820
1821<p class=MsoNormal><span style='mso-spacerun:yes'> </span>The Cart z values are
1822all close to zero and C3 has only a nonzero Cart x. Notice that the model
1823includes H-atoms; they are not really needed for MC/SA and will just make
1824computation times a bit longer than necessary. They can be removed by selecting
1825the <B>Strip H-atoms box</B>; for now leave them in. </p>
1826
1827<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1828
1829<p class=MsoNormal>Next go to <b style='mso-bidi-font-weight:normal'><span
1830style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1831mso-hansi-theme-font:minor-latin'>Phases/3-aminoquinoline</span></b> and select
1832the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1833mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA</span></b>
1834tab and do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1835"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1836minor-latin'>MC/SA/Add rigid body</span></b>; select the only choice (<b
1837style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1838mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b>)
1839from the popup selection box. The MC/SA window shows</p>
1840
1841<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1842 id="_x0000_i1039" type="#_x0000_t75" style='width:468pt;height:212.25pt;
1843 visibility:visible;mso-wrap-style:square'>
1844 <v:imagedata src="MCSA%20in%20GSAS_files/image042.png" o:title=""/>
1845</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=283
1846src="MCSA%20in%20GSAS_files/image044.gif" v:shapes="_x0000_i1039"><![endif]></span></p>
1847
1848<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1849
1850<p class=MsoNormal>And the plot shows the molecular XYZ-axes lined up along the
1851crystal <span class=SpellE>abc</span>-axes; this is expected from our choice of
1852molecular reference atoms (C2, C3 &amp; C6).</p>
1853
1854<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1855 id="Picture_x0020_33" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:468pt;
1856 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1857 <v:imagedata src="MCSA%20in%20GSAS_files/image066.png" o:title=""/>
1858</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
1859src="MCSA%20in%20GSAS_files/image046.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1860
1861<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1862
1863<p class=MsoNormal>You see the four equivalent molecules for space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>
1864whose centers fall within the unit cell; the reference one is that in the lower
1865right corner with C2 at the origin. You can enter values in the <span
1866class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1867"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1868minor-latin'>x<span class=GramE>,y,z</span></span></b></span> boxes and see how
1869the structure changes. Similarly, you can enter an angle in <span class=SpellE><b
1870style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1871mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>
1872or a vector in the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1873style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1874mso-hansi-theme-font:minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><span
1875style='mso-spacerun:yes'>  </span>box to see the effects of rotating the
1876molecule. Each of these parameters has a defined range for the MC/SA
1877optimization run we are about to do; they define the multidimensional search
1878volume. Within that volume will be a number of correct solutions to the
1879structure problem all related by translational and space group symmetry. One
1880can limit this volume by choosing more limited ranges, but here we’ll just go
1881with the default. We want to optimize the position and orientation of this
1882molecule; check the <b style='mso-bidi-font-weight:normal'><span
1883style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1884mso-hansi-theme-font:minor-latin'>x</span></b>, <b style='mso-bidi-font-weight:
1885normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1886minor-latin;mso-hansi-theme-font:minor-latin'>y</span></b> &amp; <b
1887style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1888mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>z</span></b>
1889boxes and select <b style='mso-bidi-font-weight:normal'><span style='font-family:
1890"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1891minor-latin'>AV</span></b> from the <span class=SpellE><b style='mso-bidi-font-weight:
1892normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1893minor-latin;mso-hansi-theme-font:minor-latin'>Oa</span></b></span>, <span
1894class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1895"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1896minor-latin'>Oi<span class=GramE>,Oj,Ok</span></span></b></span><b
1897style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1898mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> Vary?</span></b>
1899pulldown. The MC/SA window should look like</p>
1900
1901<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1902 id="Picture_x0020_34" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1903 height:204.75pt;visibility:visible;mso-wrap-style:square'>
1904 <v:imagedata src="MCSA%20in%20GSAS_files/image068.png" o:title=""/>
1905</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=273
1906src="MCSA%20in%20GSAS_files/image048.gif" v:shapes="Picture_x0020_34"><![endif]></span><span
1907style='mso-spacerun:yes'> </span></p>
1908
1909<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1910
1911<p class=MsoNormal>This completes the set up for MC/SA processing. </p>
1912
1913<h2>Step 7. Monte Carlo/Simulated Annealing</h2>
1914
1915<p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span
1916style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1917mso-hansi-theme-font:minor-latin'>General</span></b> tab; the MC/SA controls
1918are at the bottom of the window. To begin the setup of these controls, select a
1919source of the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1920"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1921minor-latin'>Reflection set</span></b> to be used in the MC/SA runs. The choice
1922is to use either the Pawley reflections or the Reflection List for the PWDR
1923data set. If you choose <b style='mso-bidi-font-weight:normal'><span
1924style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1925mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> then the
1926structure factors will be Pawley model values, <span class=SpellE>Fsq</span>(<span
1927class=SpellE>hkl</span>) in Pawley table, and the covariance matrix developed
1928from the refinement will be used for peak overlap effects in the MC/SA
1929calculations. Alternatively, if you choose <b style='mso-bidi-font-weight:normal'><span
1930style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1931mso-hansi-theme-font:minor-latin'>PWDR <span class=SpellE>Quinoli.gda</span>
1932Bank 1 </span></b>then the structure factors will be those, <span class=SpellE>Fosq</span>
1933in Reflection table, extracted during the Pawley refinement and the peak FWHMs
1934will be used for peak overlap effects in the MC/SA calculations. Notice that
1935the Pawley <span class=SpellE>Fsq</span>(<span class=SpellE>hkl</span>) values
1936are the same as the <span class=SpellE>Fcsq</span> Reflection List values. Here
1937I chose <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1938mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR <span
1939class=SpellE>Quinoli.gda</span> Bank 1 </span></b>for the <b style='mso-bidi-font-weight:
1940normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1941minor-latin;mso-hansi-theme-font:minor-latin'>Reflection set</span></b> as it
1942gives slightly better performance in MC/SA.</p>
1943
1944<p class=MsoNormal>Next, you need to set the minimum d-spacing (<b
1945style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1946mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>d-min</span></b>).
1947Smaller values gives minima in the MC/SA minimization surface that are more
1948sharply defined (thus harder to locate), while larger values yield insufficient
1949numbers of reflections to give sufficient redundancy in the calculations. One
1950should have 5-8 reflections for each MC/SA parameter; in this case 35-50
1951reflections are needed. If you examine the reflection list (either <b
1952style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1953mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley</span></b>
1954or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1955mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1956List</span></b>) you’ll see that a <b style='mso-bidi-font-weight:normal'><span
1957style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1958mso-hansi-theme-font:minor-latin'>d-min</span></b> of <b style='mso-bidi-font-weight:
1959normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1960minor-latin;mso-hansi-theme-font:minor-latin'>2.5</span></b> will give
1961sufficient reflections.</p>
1962
1963<p class=MsoNormal>Lastly, you need to set the run controls. I used <b
1964style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1965mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>500</span></b>
1966for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1967mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>No. trials</span></b>;
1968this is the number of random tries at each “temperature” in the annealing schedule.
1969I also used <b style='mso-bidi-font-weight:normal'><span style='font-family:
1970"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1971minor-latin'>4 MC/SA runs</span></b> When done the <b style='mso-bidi-font-weight:
1972normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1973minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> window should
1974look like</p>
1975
1976<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1977 id="Picture_x0020_35" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1978 height:223.5pt;visibility:visible;mso-wrap-style:square'>
1979 <v:imagedata src="MCSA%20in%20GSAS_files/image070.png" o:title=""/>
1980</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=298
1981src="MCSA%20in%20GSAS_files/image050.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1982
1983<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1984
1985<p class=MsoNormal>When ready, you can start the MC/SA calculation by doing <b
1986style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1987mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>
1988from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1989mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1990window menu. A progress bar will appear that shows the MC/SA residual (an
1991R-factor) as the calculation progresses through the annealing schedule as well
1992as indicating which MC/SA run is being done. When it finishes, control is
1993shifted to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1994"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1995minor-latin'>MC/SA</span></b> window which gives a list of the solutions it
1996found at the bottom of the window (scroll down to see them).</p>
1997
1998<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1999 id="Picture_x0020_36" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
2000 height:253.5pt;visibility:visible;mso-wrap-style:square'>
2001 <v:imagedata src="MCSA%20in%20GSAS_files/image052.png" o:title=""/>
2002</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=338
2003src="MCSA%20in%20GSAS_files/image054.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
2004
2005<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2006
2007<p class=MsoNormal>The one with the lowest residual is already chosen and the
2008corresponding structure is drawn</p>
2009
2010<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2011 id="Picture_x0020_37" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
2012 height:405pt;visibility:visible;mso-wrap-style:square'>
2013 <v:imagedata src="MCSA%20in%20GSAS_files/image082.png" o:title=""/>
2014</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=540
2015src="MCSA%20in%20GSAS_files/image083.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
2016
2017<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2018
2019<p class=MsoNormal>If you are lucky (like I was!) then the result is clearly a
2020good solution with a very low Residual (~7.2%). This problem typically gives
2021suitable solutions with Residuals of 7%; if you had stripped the H-atoms, the
2022best residual is ~10%. If your cell indexing resulted in <span class=GramE>a
2023&amp;</span> b swapped, you should view the structure along a (red). If no good
2024solution appears (e.g. molecules clashing &amp; high residuals), then you
2025should just rerun MC/SA perhaps using more runs or more trials.</p>
2026
2027<p class=MsoNormal><span style='mso-spacerun:yes'> </span></p>
2028
2029<p class=MsoNormal>The MC/SA calculations can take advantage of multicore
2030machines. First set the number of cores by doing <b style='mso-bidi-font-weight:
2031normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2032minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>File/Preferences</span></b>;
2033select <span class=SpellE><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'>Multiprocessing_cores</span></b></span>
2036from the pulldown and enter the number you wish to use (I suggest Maxcores-1).
2037Then press <span class=GramE><b style='mso-bidi-font-weight:normal'><span
2038style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2039mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b></span><b
2040style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2041mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
2042minor-latin'> current settings</span></b>; your choice becomes available immediately
2043and is then set for all your future uses of GSAS-II. <span
2044style='mso-spacerun:yes'> </span>Go to the <B>General</B> tab and
2045select
2046<b style='mso-bidi-font-weight:normal'><span
2047style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2048mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Compute/Multi
2049MC/SA</span></b> to use it.</p>
2050
2051<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2052
2053<p class=MsoNormal>Be sure to set the <b style='mso-bidi-font-weight:normal'><span
2054style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2055mso-hansi-theme-font:minor-latin'>Keep</span></b> box for any solutions you
2056want to retain; the others will be cleared before the next MC/SA run starts.
2057When you think you have a good one, <span class=GramE><b style='mso-bidi-font-weight:
2058normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2059minor-latin;mso-hansi-theme-font:minor-latin'>Select</span></b></span> it; the
2060parameters will be copied to the appropriate boxes in the upper part of the
2061MC/SA window and the structure is drawn again. Next we want to refine this
2062solution so go back to the <b style='mso-bidi-font-weight:normal'><span
2063style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2064mso-hansi-theme-font:minor-latin'>General</span></b> tab.</p>
2065
2066<p class=MsoNormal>MC/SA refinement is achieved by narrowing the search ranges
2067and rerunning the MC/SA calculations. This is done by checking the <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'>MC/SA Refine</span></b>
2070box under the <B>General</B> tab. Using 10% of the ranges reduces the search volume in this case by ~6
2071orders of magnitude so that the true minimum is much easier to find. Now rerun <b
2072style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2073mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/MC/SA</span></b>;
2074be sure to select the best one before starting. The residual might drop to a
2075much lower level. This refinement can be repeated with tighter restriction on
2076the ranges. My result (no improvement on 7%) was</p>
2077
2078<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2079 id="Picture_x0020_38" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
2080 height:257.25pt;visibility:visible;mso-wrap-style:square'>
2081 <v:imagedata src="MCSA%20in%20GSAS_files/image084.png" o:title=""/>
2082</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=343
2083src="MCSA%20in%20GSAS_files/image085.gif" v:shapes="Picture_x0020_38"><![endif]></span></p>
2084
2085<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2086
2087<p class=MsoNormal>This is clearly a good result (R ~ <span class=GramE>7.2%</span>!)
2088and the structure</p>
2089
2090<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2091 id="Picture_x0020_39" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
2092 height:402.75pt;visibility:visible;mso-wrap-style:square'>
2093 <v:imagedata src="MCSA%20in%20GSAS_files/image086.png" o:title=""/>
2094</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=537
2095src="MCSA%20in%20GSAS_files/image087.gif" v:shapes="Picture_x0020_39"><![endif]></span></p>
2096
2097<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2098
2099<p class=MsoNormal>Has a different origin choice (a &amp; b might also be
2100switched) than the published one </p>
2101
2102<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2103 id="Picture_x0020_24" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:288.75pt;
2104 height:225.75pt;visibility:visible;mso-wrap-style:square'>
2105 <v:imagedata src="MCSA%20in%20GSAS_files/image041.png" o:title="" croptop="14378f"
2106  cropbottom="21852f" cropleft="3509f" cropright="49103f"/>
2107</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=301
2108src="MCSA%20in%20GSAS_files/image088.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
2109
2110<p class=MsoNormal>as drawn by the Mercury program </p>
2111
2112<p class=MsoNormal>(<a
2113href="https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx">https://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx</a>).
2114To save this solution to the <b style='mso-bidi-font-weight:normal'><span
2115style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2116mso-hansi-theme-font:minor-latin'>Atoms</span></b> list do <b style='mso-bidi-font-weight:
2117normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2118minor-latin;mso-hansi-theme-font:minor-latin'>MC/SA/Move MC/SA solution</span></b>;
2119the drawing will show the new atom positions</p>
2120
2121<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2122 id="Picture_x0020_40" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
2123 height:402.75pt;visibility:visible;mso-wrap-style:square'>
2124 <v:imagedata src="MCSA%20in%20GSAS_files/image089.png" o:title=""/>
2125</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=537
2126src="MCSA%20in%20GSAS_files/image090.gif" v:shapes="Picture_x0020_40"><![endif]></span></p>
2127
2128<p class=MsoNormal>And they will be listed in the Atoms table.</p>
2129
2130<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2131 id="Picture_x0020_41" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
2132 height:288.75pt;visibility:visible;mso-wrap-style:square'>
2133 <v:imagedata src="MCSA%20in%20GSAS_files/image091.png" o:title=""/>
2134</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=385
2135src="MCSA%20in%20GSAS_files/image095.gif" v:shapes="Picture_x0020_41"><![endif]></span></p>
2136
2137<p class=MsoNormal>It is now ready for Rietveld refinement; this needs to use
2138the rigid body as the data will not support independent atom position
2139refinement.</p>
2140
2141<h2>Step 8. Initial Rietveld refinement</h2>
2142
2143<p class=MsoNormal>After a few simple steps the 3-aminoquinoline structure will
2144be ready for the first Rietveld refinement: 1) On the <b style='mso-bidi-font-weight:
2145normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2146minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab uncheck
2147the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2148mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley
2149refinement?</span></b> box, 2) check the <b style='mso-bidi-font-weight:normal'><span
2150style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2151mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b> box in <b
2152style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2153mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
2154Parameters</span></b> and 3) zero both <b style='mso-bidi-font-weight:normal'><span
2155style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2156mso-hansi-theme-font:minor-latin'>X</span></b> &amp; <b style='mso-bidi-font-weight:
2157normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2158minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b> and uncheck their
2159refine boxes in <b style='mso-bidi-font-weight:normal'><span style='font-family:
2160"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2161minor-latin'>Instrument Parameters</span></b>. Then do <b style='mso-bidi-font-weight:
2162normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2163minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from
2164the main GSAS-II data tree window; my <span class=SpellE>R<sub>wp</sub></span>
2165was ~12%. Next check the <b style='mso-bidi-font-weight:normal'><span
2166style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2167mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> in the <b
2168style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2169mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
2170window and in the <b style='mso-bidi-font-weight:normal'><span
2171style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2172mso-hansi-theme-font:minor-latin'>Data</span></b> window, using the <b
2173style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2174mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>uniaxial</span></b>
2175model for <span class=SpellE>mustrain</span>, check both <span class=SpellE><b
2176style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2177mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cryst</span></b></span><b
2178style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2179mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>. <span
2180class=GramE>size</span></span></b> and both <span class=SpellE><b
2181style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2182mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>mustrain</span></b></span>
2183boxes and do another <b style='mso-bidi-font-weight:normal'><span
2184style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2185mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> (twice) I got an <span
2186class=SpellE>R<sub>wp</sub></span> ~8.2% for this. We’ve not refined atom
2187positions or thermal parameters; to do this we need to describe the structure
2188as a rigid body.</p>
2189
2190<h2>Step 9. Rigid body model</h2>
2191
2192<p class=MsoNormal>The rigid body itself has already been defined; it was used
2193for the MC/SA structure solution. Now we have to place it in the unit cell
2194matching the atom positions obtained from the MC/SA runs. First go to the <b
2195style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2196mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b>
2197tab and change the <b style='mso-bidi-font-weight:normal'><span
2198style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2199mso-hansi-theme-font:minor-latin'>Style</span></b> to <b style='mso-bidi-font-weight:
2200normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2201minor-latin;mso-hansi-theme-font:minor-latin'>balls &amp; sticks</span></b> and
2202the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2203mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b>
2204to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2205mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>name</span></b>.
2206Double click on the column headings and select the item from the popup control.
2207Next go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2208"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2209minor-latin'>RB Models</span></b> tab; it will be empty. Do <b
2210style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2211mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit Body/Assign
2212atoms to rigid body</span></b>; then select <b style='mso-bidi-font-weight:
2213normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2214minor-latin;mso-hansi-theme-font:minor-latin'>amino</span></b> in the <b
2215style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2216mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Select rigid
2217body model</span></b> pull down (the only choice). The <b style='mso-bidi-font-weight:
2218normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2219minor-latin;mso-hansi-theme-font:minor-latin'>RB Models</span></b> window will
2220show</p>
2221
2222<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2223 id="Picture_x0020_42" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
2224 height:195.75pt;visibility:visible;mso-wrap-style:square'>
2225 <v:imagedata src="MCSA%20in%20GSAS_files/image096.png" o:title=""/>
2226</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=261
2227src="MCSA%20in%20GSAS_files/image097.gif" v:shapes="Picture_x0020_42"><![endif]></span></p>
2228
2229<p class=MsoNormal><o:p>&nbsp;</o:p></p>
2230
2231<p class=MsoNormal>You will orient the rigid body against the atoms by matching
2232up the 3 reference atoms in the rigid body (C1, C2 &amp; C5) to the
2233corresponding atoms in the structure (C(2), C(3) &amp; C(6)). Do these in
2234order; the drawing will show the shift of molecular origin and then its
2235reorientation as the three atoms are selected. Press <b style='mso-bidi-font-weight:
2236normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2237minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b> when done; the
2238structure will be drawn with orange bonds indicating that it is now a rigid
2239body and not independent atoms. The <b style='mso-bidi-font-weight:normal'><span
2240style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2241mso-hansi-theme-font:minor-latin'>RB Models</span></b> window shows the new
2242rigid body</p>
2243
2244<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2245 id="Picture_x0020_43" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
2246 height:207pt;visibility:visible;mso-wrap-style:square'>
2247 <v:imagedata src="MCSA%20in%20GSAS_files/image098.png" o:title=""/>
2248</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=276
2249src="MCSA%20in%20GSAS_files/image099.gif" v:shapes="Picture_x0020_43"><![endif]></span></p>
2250
2251<p class=MsoNormal>To refine the rigid body origin position check the <b
2252style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2253mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b>
2254box, select <b style='mso-bidi-font-weight:normal'><span style='font-family:
2255"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2256minor-latin'>AV</span></b> from the pull down, choose <span class=SpellE><b
2257style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2258mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Uiso</span></b></span>
2259from the thermal parameter model and check its <b style='mso-bidi-font-weight:
2260normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2261minor-latin;mso-hansi-theme-font:minor-latin'>Refine?</span></b> box. Then do <b
2262style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2263mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>;
2264after a couple of refinement runs I got an <span class=SpellE>R<sub>wp</sub></span>
2265~7.9% and the <b style='mso-bidi-font-weight:normal'><span style='font-family:
2266"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2267minor-latin'>RB Models</span></b> window shows the new parameters</p>
2268
2269<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2270 id="Picture_x0020_44" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
2271 height:3in;visibility:visible;mso-wrap-style:square'>
2272 <v:imagedata src="MCSA%20in%20GSAS_files/image100.png" o:title=""/>
2273</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=288
2274src="MCSA%20in%20GSAS_files/image101.gif" v:shapes="Picture_x0020_44"><![endif]></span></p>
2275
2276<p class=MsoNormal><span class=GramE>and</span> the profile shows the fit</p>
2277
2278<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2279 id="Picture_x0020_45" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
2280 height:401.25pt;visibility:visible;mso-wrap-style:square'>
2281 <v:imagedata src="MCSA%20in%20GSAS_files/image102.png" o:title=""/>
2282</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
2283src="MCSA%20in%20GSAS_files/image103.gif" v:shapes="Picture_x0020_45"><![endif]></span></p>
2284
2285<p class=MsoNormal>This completes the structure analysis for 3-aminoquinoline.
2286Next is a more complex case involving some internal degrees of freedom in the
2287molecule of a-d-lactose.</p>
2288
2289</div>
2290
2291</body>
2292
2293</html>
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