source: trunk/help/Charge Flipping in GSAS.htm @ 1535

Last change on this file since 1535 was 1535, checked in by toby, 7 years ago

address missing images in jaderite charge flip

  • Property svn:mime-type set to text/html
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378        mso-style-link:"Heading 1 Char";
379        mso-margin-top-alt:auto;
380        margin-right:0in;
381        mso-margin-bottom-alt:auto;
382        margin-left:0in;
383        mso-pagination:widow-orphan;
384        mso-outline-level:1;
385        font-size:24.0pt;
386        font-family:"Times New Roman","serif";
387        mso-fareast-font-family:"Times New Roman";
388        mso-fareast-theme-font:minor-fareast;
389        font-weight:bold;}
390h2
391        {mso-style-priority:9;
392        mso-style-unhide:no;
393        mso-style-qformat:yes;
394        mso-style-link:"Heading 2 Char";
395        mso-margin-top-alt:auto;
396        margin-right:0in;
397        mso-margin-bottom-alt:auto;
398        margin-left:0in;
399        mso-pagination:widow-orphan;
400        mso-outline-level:2;
401        font-size:18.0pt;
402        font-family:"Times New Roman","serif";
403        mso-fareast-font-family:"Times New Roman";
404        mso-fareast-theme-font:minor-fareast;
405        font-weight:bold;}
406h3
407        {mso-style-priority:9;
408        mso-style-unhide:no;
409        mso-style-qformat:yes;
410        mso-style-link:"Heading 3 Char";
411        mso-margin-top-alt:auto;
412        margin-right:0in;
413        mso-margin-bottom-alt:auto;
414        margin-left:0in;
415        mso-pagination:widow-orphan;
416        mso-outline-level:3;
417        font-size:13.5pt;
418        font-family:"Times New Roman","serif";
419        mso-fareast-font-family:"Times New Roman";
420        mso-fareast-theme-font:minor-fareast;
421        font-weight:bold;}
422h4
423        {mso-style-priority:9;
424        mso-style-unhide:no;
425        mso-style-qformat:yes;
426        mso-style-link:"Heading 4 Char";
427        margin-top:10.0pt;
428        margin-right:0in;
429        margin-bottom:0in;
430        margin-left:0in;
431        margin-bottom:.0001pt;
432        mso-pagination:widow-orphan;
433        page-break-after:avoid;
434        mso-outline-level:4;
435        font-size:13.0pt;
436        font-family:"Cambria","serif";
437        mso-fareast-font-family:"Times New Roman";
438        mso-fareast-theme-font:minor-fareast;
439        mso-bidi-font-family:"Times New Roman";
440        color:#4F81BD;
441        font-weight:bold;
442        font-style:italic;}
443h5
444        {mso-style-priority:9;
445        mso-style-unhide:no;
446        mso-style-qformat:yes;
447        mso-style-link:"Heading 5 Char";
448        mso-margin-top-alt:auto;
449        margin-right:0in;
450        mso-margin-bottom-alt:auto;
451        margin-left:0in;
452        mso-pagination:widow-orphan;
453        mso-outline-level:5;
454        font-size:12.0pt;
455        font-family:"Times New Roman","serif";
456        mso-fareast-font-family:"Times New Roman";
457        mso-fareast-theme-font:minor-fareast;
458        color:#4F4FFF;
459        font-weight:bold;}
460p.MsoTitle, li.MsoTitle, div.MsoTitle
461        {mso-style-noshow:yes;
462        mso-style-priority:10;
463        mso-style-unhide:no;
464        mso-style-qformat:yes;
465        mso-style-link:"Title Char";
466        margin-top:0in;
467        margin-right:0in;
468        margin-bottom:15.0pt;
469        margin-left:0in;
470        mso-pagination:widow-orphan;
471        font-size:26.0pt;
472        font-family:"Cambria","serif";
473        mso-fareast-font-family:"Times New Roman";
474        mso-fareast-theme-font:minor-fareast;
475        mso-bidi-font-family:"Times New Roman";
476        color:#17365D;
477        letter-spacing:.25pt;}
478a:link, span.MsoHyperlink
479        {mso-style-noshow:yes;
480        mso-style-priority:99;
481        color:blue;
482        text-decoration:underline;
483        text-underline:single;}
484a:visited, span.MsoHyperlinkFollowed
485        {mso-style-noshow:yes;
486        mso-style-priority:99;
487        color:purple;
488        text-decoration:underline;
489        text-underline:single;}
490p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
491        {mso-style-noshow:yes;
492        mso-style-priority:99;
493        mso-style-link:"Document Map Char";
494        margin:0in;
495        margin-bottom:.0001pt;
496        mso-pagination:widow-orphan;
497        font-size:8.0pt;
498        font-family:"Tahoma","sans-serif";
499        mso-fareast-font-family:"Times New Roman";
500        mso-fareast-theme-font:minor-fareast;}
501p
502        {mso-style-noshow:yes;
503        mso-style-priority:99;
504        mso-margin-top-alt:auto;
505        margin-right:0in;
506        mso-margin-bottom-alt:auto;
507        margin-left:0in;
508        mso-pagination:widow-orphan;
509        font-size:12.0pt;
510        font-family:"Times New Roman","serif";
511        mso-fareast-font-family:"Times New Roman";
512        mso-fareast-theme-font:minor-fareast;}
513pre
514        {mso-style-noshow:yes;
515        mso-style-priority:99;
516        mso-style-link:"HTML Preformatted Char";
517        margin:0in;
518        margin-bottom:.0001pt;
519        mso-pagination:widow-orphan;
520        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;
521        font-size:10.0pt;
522        font-family:"Courier New";
523        mso-fareast-font-family:"Times New Roman";
524        mso-fareast-theme-font:minor-fareast;}
525p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
526        {mso-style-noshow:yes;
527        mso-style-priority:99;
528        mso-style-link:"Balloon Text Char";
529        margin:0in;
530        margin-bottom:.0001pt;
531        mso-pagination:widow-orphan;
532        font-size:8.0pt;
533        font-family:"Tahoma","sans-serif";
534        mso-fareast-font-family:"Times New Roman";
535        mso-fareast-theme-font:minor-fareast;}
536span.MsoPlaceholderText
537        {mso-style-noshow:yes;
538        mso-style-priority:99;
539        mso-style-unhide:no;
540        color:gray;}
541p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
542        {mso-style-noshow:yes;
543        mso-style-priority:1;
544        mso-style-unhide:no;
545        mso-style-qformat:yes;
546        margin:0in;
547        margin-bottom:.0001pt;
548        mso-pagination:widow-orphan;
549        font-size:12.0pt;
550        font-family:"Times New Roman","serif";
551        mso-fareast-font-family:"Times New Roman";
552        mso-fareast-theme-font:minor-fareast;}
553p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
554        {mso-style-noshow:yes;
555        mso-style-priority:34;
556        mso-style-unhide:no;
557        mso-style-qformat:yes;
558        margin-top:0in;
559        margin-right:0in;
560        margin-bottom:0in;
561        margin-left:.5in;
562        margin-bottom:.0001pt;
563        mso-pagination:widow-orphan;
564        font-size:12.0pt;
565        font-family:"Times New Roman","serif";
566        mso-fareast-font-family:"Times New Roman";
567        mso-fareast-theme-font:minor-fareast;}
568span.MsoIntenseReference
569        {mso-style-priority:32;
570        mso-style-unhide:no;
571        mso-style-qformat:yes;
572        font-variant:small-caps;
573        color:#C0504D;
574        letter-spacing:.25pt;
575        font-weight:bold;
576        text-decoration:underline;
577        text-underline:single;}
578span.Heading1Char
579        {mso-style-name:"Heading 1 Char";
580        mso-style-priority:9;
581        mso-style-unhide:no;
582        mso-style-locked:yes;
583        mso-style-link:"Heading 1";
584        font-family:"Times New Roman","serif";
585        mso-ascii-font-family:"Times New Roman";
586        mso-hansi-font-family:"Times New Roman";
587        mso-bidi-font-family:"Times New Roman";
588        font-weight:bold;}
589span.Heading2Char
590        {mso-style-name:"Heading 2 Char";
591        mso-style-noshow:yes;
592        mso-style-priority:9;
593        mso-style-unhide:no;
594        mso-style-locked:yes;
595        mso-style-link:"Heading 2";
596        font-family:"Times New Roman","serif";
597        mso-ascii-font-family:"Times New Roman";
598        mso-hansi-font-family:"Times New Roman";
599        mso-bidi-font-family:"Times New Roman";
600        font-weight:bold;}
601span.Heading3Char
602        {mso-style-name:"Heading 3 Char";
603        mso-style-noshow:yes;
604        mso-style-priority:9;
605        mso-style-unhide:no;
606        mso-style-locked:yes;
607        mso-style-link:"Heading 3";
608        font-family:"Times New Roman","serif";
609        mso-ascii-font-family:"Times New Roman";
610        mso-hansi-font-family:"Times New Roman";
611        mso-bidi-font-family:"Times New Roman";
612        font-weight:bold;}
613span.Heading4Char
614        {mso-style-name:"Heading 4 Char";
615        mso-style-noshow:yes;
616        mso-style-priority:9;
617        mso-style-unhide:no;
618        mso-style-locked:yes;
619        mso-style-link:"Heading 4";
620        font-family:"Cambria","serif";
621        mso-ascii-font-family:Cambria;
622        mso-hansi-font-family:Cambria;
623        color:#4F81BD;
624        font-weight:bold;
625        font-style:italic;}
626span.Heading5Char
627        {mso-style-name:"Heading 5 Char";
628        mso-style-noshow:yes;
629        mso-style-priority:9;
630        mso-style-unhide:no;
631        mso-style-locked:yes;
632        mso-style-link:"Heading 5";
633        font-family:"Times New Roman","serif";
634        mso-ascii-font-family:"Times New Roman";
635        mso-hansi-font-family:"Times New Roman";
636        mso-bidi-font-family:"Times New Roman";
637        color:#4F4FFF;
638        font-weight:bold;}
639span.HTMLPreformattedChar
640        {mso-style-name:"HTML Preformatted Char";
641        mso-style-noshow:yes;
642        mso-style-priority:99;
643        mso-style-unhide:no;
644        mso-style-locked:yes;
645        mso-style-link:"HTML Preformatted";
646        font-family:"Courier New";
647        mso-ascii-font-family:"Courier New";
648        mso-hansi-font-family:"Courier New";
649        mso-bidi-font-family:"Courier New";}
650span.TitleChar
651        {mso-style-name:"Title Char";
652        mso-style-priority:10;
653        mso-style-unhide:no;
654        mso-style-locked:yes;
655        mso-style-link:Title;
656        font-family:"Cambria","serif";
657        mso-ascii-font-family:Cambria;
658        mso-hansi-font-family:Cambria;
659        color:#17365D;
660        letter-spacing:.25pt;}
661span.DocumentMapChar
662        {mso-style-name:"Document Map Char";
663        mso-style-noshow:yes;
664        mso-style-priority:99;
665        mso-style-unhide:no;
666        mso-style-locked:yes;
667        mso-style-link:"Document Map";
668        font-family:"Tahoma","sans-serif";
669        mso-ascii-font-family:Tahoma;
670        mso-hansi-font-family:Tahoma;
671        mso-bidi-font-family:Tahoma;}
672span.BalloonTextChar
673        {mso-style-name:"Balloon Text Char";
674        mso-style-noshow:yes;
675        mso-style-priority:99;
676        mso-style-unhide:no;
677        mso-style-locked:yes;
678        mso-style-link:"Balloon Text";
679        font-family:"Tahoma","sans-serif";
680        mso-ascii-font-family:Tahoma;
681        mso-hansi-font-family:Tahoma;
682        mso-bidi-font-family:Tahoma;}
683p.msotitlecxspfirst, li.msotitlecxspfirst, div.msotitlecxspfirst
684        {mso-style-name:msotitlecxspfirst;
685        mso-style-noshow:yes;
686        mso-style-priority:99;
687        mso-style-unhide:no;
688        margin:0in;
689        margin-bottom:.0001pt;
690        mso-pagination:widow-orphan;
691        font-size:26.0pt;
692        font-family:"Cambria","serif";
693        mso-fareast-font-family:"Times New Roman";
694        mso-fareast-theme-font:minor-fareast;
695        mso-bidi-font-family:"Times New Roman";
696        color:#17365D;
697        letter-spacing:.25pt;}
698p.msotitlecxspmiddle, li.msotitlecxspmiddle, div.msotitlecxspmiddle
699        {mso-style-name:msotitlecxspmiddle;
700        mso-style-noshow:yes;
701        mso-style-priority:99;
702        mso-style-unhide:no;
703        margin:0in;
704        margin-bottom:.0001pt;
705        mso-pagination:widow-orphan;
706        font-size:26.0pt;
707        font-family:"Cambria","serif";
708        mso-fareast-font-family:"Times New Roman";
709        mso-fareast-theme-font:minor-fareast;
710        mso-bidi-font-family:"Times New Roman";
711        color:#17365D;
712        letter-spacing:.25pt;}
713p.msotitlecxsplast, li.msotitlecxsplast, div.msotitlecxsplast
714        {mso-style-name:msotitlecxsplast;
715        mso-style-noshow:yes;
716        mso-style-priority:99;
717        mso-style-unhide:no;
718        margin-top:0in;
719        margin-right:0in;
720        margin-bottom:15.0pt;
721        margin-left:0in;
722        mso-pagination:widow-orphan;
723        font-size:26.0pt;
724        font-family:"Cambria","serif";
725        mso-fareast-font-family:"Times New Roman";
726        mso-fareast-theme-font:minor-fareast;
727        mso-bidi-font-family:"Times New Roman";
728        color:#17365D;
729        letter-spacing:.25pt;}
730p.msolistparagraphcxspfirst, li.msolistparagraphcxspfirst, div.msolistparagraphcxspfirst
731        {mso-style-name:msolistparagraphcxspfirst;
732        mso-style-noshow:yes;
733        mso-style-priority:99;
734        mso-style-unhide:no;
735        margin-top:0in;
736        margin-right:0in;
737        margin-bottom:0in;
738        margin-left:.5in;
739        margin-bottom:.0001pt;
740        mso-pagination:widow-orphan;
741        font-size:12.0pt;
742        font-family:"Times New Roman","serif";
743        mso-fareast-font-family:"Times New Roman";
744        mso-fareast-theme-font:minor-fareast;}
745p.msolistparagraphcxspmiddle, li.msolistparagraphcxspmiddle, div.msolistparagraphcxspmiddle
746        {mso-style-name:msolistparagraphcxspmiddle;
747        mso-style-noshow:yes;
748        mso-style-priority:99;
749        mso-style-unhide:no;
750        margin-top:0in;
751        margin-right:0in;
752        margin-bottom:0in;
753        margin-left:.5in;
754        margin-bottom:.0001pt;
755        mso-pagination:widow-orphan;
756        font-size:12.0pt;
757        font-family:"Times New Roman","serif";
758        mso-fareast-font-family:"Times New Roman";
759        mso-fareast-theme-font:minor-fareast;}
760p.msolistparagraphcxsplast, li.msolistparagraphcxsplast, div.msolistparagraphcxsplast
761        {mso-style-name:msolistparagraphcxsplast;
762        mso-style-noshow:yes;
763        mso-style-priority:99;
764        mso-style-unhide:no;
765        margin-top:0in;
766        margin-right:0in;
767        margin-bottom:0in;
768        margin-left:.5in;
769        margin-bottom:.0001pt;
770        mso-pagination:widow-orphan;
771        font-size:12.0pt;
772        font-family:"Times New Roman","serif";
773        mso-fareast-font-family:"Times New Roman";
774        mso-fareast-theme-font:minor-fareast;}
775p.msochpdefault, li.msochpdefault, div.msochpdefault
776        {mso-style-name:msochpdefault;
777        mso-style-noshow:yes;
778        mso-style-priority:99;
779        mso-style-unhide:no;
780        mso-margin-top-alt:auto;
781        margin-right:0in;
782        mso-margin-bottom-alt:auto;
783        margin-left:0in;
784        mso-pagination:widow-orphan;
785        font-size:10.0pt;
786        font-family:"Calibri","sans-serif";
787        mso-fareast-font-family:"Times New Roman";
788        mso-fareast-theme-font:minor-fareast;
789        mso-bidi-font-family:Calibri;}
790span.SpellE
791        {mso-style-name:"";
792        mso-spl-e:yes;}
793span.GramE
794        {mso-style-name:"";
795        mso-gram-e:yes;}
796.MsoChpDefault
797        {mso-style-type:export-only;
798        mso-default-props:yes;
799        font-size:10.0pt;
800        mso-ansi-font-size:10.0pt;
801        mso-bidi-font-size:10.0pt;
802        font-family:"Calibri","sans-serif";
803        mso-ascii-font-family:Calibri;
804        mso-hansi-font-family:Calibri;
805        mso-bidi-font-family:Calibri;}
806@page WordSection1
807        {size:8.5in 11.0in;
808        margin:1.0in 1.0in 1.0in 1.0in;
809        mso-header-margin:.5in;
810        mso-footer-margin:.5in;
811        mso-paper-source:0;}
812div.WordSection1
813        {page:WordSection1;}
814 /* List Definitions */
815 @list l0
816        {mso-list-id:82917343;
817        mso-list-type:hybrid;
818        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
819@list l0:level1
820        {mso-level-tab-stop:none;
821        mso-level-number-position:left;
822        margin-left:.75in;
823        text-indent:-.25in;}
824@list l0:level2
825        {mso-level-number-format:alpha-lower;
826        mso-level-tab-stop:none;
827        mso-level-number-position:left;
828        margin-left:1.25in;
829        text-indent:-.25in;}
830@list l0:level3
831        {mso-level-number-format:roman-lower;
832        mso-level-tab-stop:none;
833        mso-level-number-position:right;
834        margin-left:1.75in;
835        text-indent:-9.0pt;}
836@list l0:level4
837        {mso-level-tab-stop:none;
838        mso-level-number-position:left;
839        margin-left:2.25in;
840        text-indent:-.25in;}
841@list l0:level5
842        {mso-level-number-format:alpha-lower;
843        mso-level-tab-stop:none;
844        mso-level-number-position:left;
845        margin-left:2.75in;
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1204-->
1205</style>
1206<!--[if gte mso 10]>
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1224 <o:shapedefaults v:ext="edit" spidmax="1026"/>
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1229</head>
1230
1231<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1232
1233<div class=WordSection1>
1234
1235<h1><span style='mso-fareast-font-family:"Times New Roman"'>MC/SA in GSAS-II<o:p></o:p></span></h1>
1236
1237<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
1238
1239<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1240of <span class=SpellE>jadarite</span> (aka “kryptonite”) from powder
1241diffraction data via charge flipping. This structure was originally solved by Pam
1242Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>
1243
1244<p class=MsoNormal>If you have not done so already, <a
1245href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
1246(I called it <span class=SpellE>jadarite.gpx</span>) you saved from the second
1247part of the <a href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing
1248exercise</a>. If you didn’t do that exercise, do it now.</p>
1249
1250<h2><span class=GramE>Step 1.</span> Setup for Pawley refinement</h2>
1251
1252<p class=MsoNormal>There are a number of steps that must be done in preparation
1253for a Pawley refinement after having completed the unit cell indexing and new
1254phase creation. These cover two things: one is to prepare the powder pattern
1255(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1256
1257<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1258style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1259style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1260<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1261mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1262in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1263region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
1264Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1265mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1266symbol;mso-symbol-font-family:Symbol'>Q</span></span>. It is an area relatively
1267clear of peaks and makes a good place to end the calculations with a reflection
1268set of ~1Å resolution as needed for charge flipping. Enter <b style='mso-bidi-font-weight:
1269normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1270minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for <span
1271class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1272"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1273minor-latin'>Tmax</span></b></span> as the upper limit and make a note of the
1274exact d-spacing (0.9945Å) using the mouse cursor on the plot.</p>
1275
1276<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1277style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1278style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1279<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1280mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1281Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1282style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1283mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1284style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1285mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1286profile</span></b> to recover the default values. The peak fitting done earlier
1287is over a much more limited range of 2<span style='font-family:Symbol;
1288mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1289mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1290symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that will
1291not extrapolate well over the wider range to be used in the Pawley refinement.
1292We will refine them again later.</p>
1293
1294<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1295style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1296style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1297<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1298mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Sample
1299Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1300normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1301minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
1302
1303<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1304style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1305style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1306to <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'>Phases/kryptonite</span></b>
1308to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1309"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1310minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1311normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1312minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b>
1313box and enter the d-spacing (0.9945) into the <b style='mso-bidi-font-weight:
1314normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1315minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
1316box.</p>
1317
1318<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1319style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1320mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1321
1322<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1323 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1324 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1325 <v:stroke joinstyle="miter"/>
1326 <v:formulas>
1327  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1328  <v:f eqn="sum @0 1 0"/>
1329  <v:f eqn="sum 0 0 @1"/>
1330  <v:f eqn="prod @2 1 2"/>
1331  <v:f eqn="prod @3 21600 pixelWidth"/>
1332  <v:f eqn="prod @3 21600 pixelHeight"/>
1333  <v:f eqn="sum @0 0 1"/>
1334  <v:f eqn="prod @6 1 2"/>
1335  <v:f eqn="prod @7 21600 pixelWidth"/>
1336  <v:f eqn="sum @8 21600 0"/>
1337  <v:f eqn="prod @7 21600 pixelHeight"/>
1338  <v:f eqn="sum @10 21600 0"/>
1339 </v:formulas>
1340 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1341 <o:lock v:ext="edit" aspectratio="t"/>
1342</v:shapetype><v:shape id="_x0000_i1047" type="#_x0000_t75" style='width:542.25pt;
1343 height:356.25pt;visibility:visible;mso-wrap-style:square'>
1344 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image001.png" o:title=""/>
1345</v:shape><![endif]--><![if !vml]><img border=0 width=723 height=475
1346src="Charge%20Flipping%20in%20GSAS_files/image002.gif" v:shapes="_x0000_i1047"><![endif]></span></p>
1347
1348<p class=MsoNormal>Next find the <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'>Data</span></b> tab; it will be empty except
1351for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1352style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1353mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1354dialog box will appear</p>
1355
1356<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1357 id="_x0000_i1046" type="#_x0000_t75" style='width:259.5pt;height:252pt;
1358 visibility:visible;mso-wrap-style:square'>
1359 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image003.png" o:title=""/>
1360</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1361src="Charge%20Flipping%20in%20GSAS_files/image004.gif" v:shapes="_x0000_i1046"><![endif]></span></p>
1362
1363<p class=MsoNormal>Select either choice; the desired data set will be added to
1364this phase for analysis. The data tab now shows the new data set; check the <b
1365style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1366mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1367button to see the full information</p>
1368
1369<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1370 id="Picture_x0020_25" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:359.25pt;
1371 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1372 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image005.png" o:title=""/>
1373</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=535
1374src="Charge%20Flipping%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
1375
1376<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1377contents. This is the location for all the phase dependent parameters for this
1378histogram. Notice that it includes phase fraction, size &amp; <span
1379class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1380and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1381intended for protein work where a significant region of the structure is
1382disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1383surfaces</p>
1384
1385<p class=MsoNormal><span class=GramE>and</span> preferred orientation
1386correction curves.</p>
1387
1388<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1389style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1390mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1391empty except for column headings. <span class=GramE>Do</span> <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'>Operations/Pawley
1394create</span></b>; this makes the reflection set over the range covered by
1395setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1396mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1397class=SpellE>dmin</span></span></b>. The table should list reflections 0-629.
1398Select and check the <b style='mso-bidi-font-weight:normal'><span
1399style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1400mso-hansi-theme-font:minor-latin'>refine</span></b> column using the same
1401technique you used for the peak list. </p>
1402
1403<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1404 id="Picture_x0020_4" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:375pt;
1405 height:225pt;visibility:visible;mso-wrap-style:square'>
1406 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image007.png" o:title=""/>
1407</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1408src="Charge%20Flipping%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
1409
1410<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1411you didn’t skip a step as it might not work correctly if you did.</p>
1412
1413<h2>Step 2 Pawley refinement</h2>
1414
1415<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1416normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1417minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1418the main GSAS-II data tree window. Before it begins a backup of the project
1419file is made; the name will be jadarite.bck0.gpx. It can be used to recover
1420from a bad refinement. A progress dialog box will appear showing the residual
1421as the refinement proceeds. My refinement completed with <span class=SpellE>Rwp</span>
1422~15.5%; a dialog box appears asking if you wish to load the result. Press <b
1423style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1424mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1425To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
1426the width and height).</p>
1427
1428<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1429 id="Picture_x0020_5" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1430 height:450pt;visibility:visible;mso-wrap-style:square'>
1431 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/>
1432</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1433src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
1434
1435<p class=MsoNormal>It is evident from examining the plot that improvement can
1436be had by refining the lattice parameters. Go to <b style='mso-bidi-font-weight:
1437normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1438minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> in
1439the GSAS-II data tree and check the <b style='mso-bidi-font-weight:normal'><span
1440style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1441mso-hansi-theme-font:minor-latin'>Refine unit cell</span></b> box. Repeat <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'>Calculate/Refine</span></b>.
1444I obtained a new residual of 10.36%.</p>
1445
1446<p class=MsoNormal>Now select <b style='mso-bidi-font-weight:normal'><span
1447style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1448mso-hansi-theme-font:minor-latin'>Instrument parameters</span></b> for the PWDR
1449data set in the GSAS-II data tree and check <b style='mso-bidi-font-weight:
1450normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1451minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,<b style='mso-bidi-font-weight:
1452normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1453minor-latin;mso-hansi-theme-font:minor-latin'> V</span></b>,<b
1454style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1455mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> W</span></b>,<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'> <span
1458class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1459style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1460mso-hansi-theme-font:minor-latin'> Y</span></b>. Repeat <b style='mso-bidi-font-weight:
1461normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1462minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I
1463obtained an improved residual of 9.7% with a much better fit at the high angle
1464part of the pattern.</p>
1465
1466<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1467 id="Picture_x0020_8" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1468 height:450pt;visibility:visible;mso-wrap-style:square'>
1469 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image011.png" o:title=""/>
1470</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1471src="Charge%20Flipping%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
1472
1473<p class=MsoNormal>This may be good enough to try charge flipping.</p>
1474
1475<h2>Step 3 Charge flipping</h2>
1476
1477<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1478Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1479mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>
1480and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1481"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1482minor-latin'>Charge flip controls</span></b> in the middle of the <b
1483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1484mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1485tab.</p>
1486
1487<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1488mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1489"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1490</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1491style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1492mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1493style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1494mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
149511bmb_6231.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1496set to be used those in <b style='mso-bidi-font-weight:normal'><span
1497style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1498mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1499data set; these should match the Pawley reflection set.</p>
1500
1501<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1502mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1503"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1504</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1505style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1506mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1507style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1508mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1509controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1510style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1511mso-hansi-theme-font:minor-latin'>10%</span></b>. This controls the map search
1512routine.</p>
1513
1514<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1515style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1516mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1517element</span></b>; if selected a periodic table appears – select an element or
1518‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1519mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1520The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1521mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1522defines the map spacing and thus the extent of the reflection set; the observed
1523reflection set is zero filled to this limit for charge flipping. The <b
1524style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1525mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1526and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1527mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1528determine the lower threshold and upper limit for charge flipping,
1529respectively. The latter is used to avoid “Uranium solutions” in the result.
1530Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1531"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1532minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1533ones. The default (<b style='mso-bidi-font-weight:normal'><span
1534style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1535mso-hansi-theme-font:minor-latin'>20</span></b>) is suitable for kryptonite.</p>
1536
1537<p class=MsoNormal>When ready select <b style='mso-bidi-font-weight:normal'><span
1538style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1539mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b>; a
1540progress bar dialog will appear that tracks the residual found in each charge
1541flipping cycle. It will quickly drop to some level and then perhaps drop again
1542into the 20-30% range for a successful charge flipping run. Press <b
1543style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1544mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b>
1545to stop the charge flipping; a peak list and a drawing of the solution will
1546appear. One of my runs gave</p>
1547
1548<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1549 id="Picture_x0020_7" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt;
1550 height:225pt;visibility:visible;mso-wrap-style:square'>
1551 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/>
1552</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1553src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
1554
1555<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1556
1557<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1558 id="Picture_x0020_1" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:338.25pt;
1559 height:289.5pt;visibility:visible;mso-wrap-style:square'>
1560 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image015.png" o:title=""
1561  croptop="2431f" cropbottom="25578f" cropleft="38673f" cropright="11746f"/>
1562</v:shape><![endif]--><![if !vml]><img border=0 width=451 height=386
1563src="Charge%20Flipping%20in%20GSAS_files/image016.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
1564
1565<p class=MsoNormal>The result looks very promising! Charge flipping operates
1566without regard to symmetry and GSAS-II attempts to locate the map with respect
1567to the symmetry elements from the computed reflection phases. Errors in these
1568phases can disrupt this process so that the map and peak positions are offset
1569from their true positions. To discover this and fix it, rotate the drawing
1570around to check that atom positions are related via the inversion center (the
1571multicolored cross in the center of the cell. NB: only works if structure has
1572an inversion center!). Avoid motions with the right mouse button pressed, this
1573moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:normal'><span
1574style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1575mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the cross to the
1576cell center. If you find an offset to the map, orient it so the offset is
1577horizontal or vertical and then press the <b style='mso-bidi-font-weight:normal'><span
1578style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1579mso-hansi-theme-font:minor-latin'>L</span></b>, <b style='mso-bidi-font-weight:
1580normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1581minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>, <b
1582style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1583mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1584or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1585mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1586keys to shift the map and peaks as needed. The shift is in resolution units
1587(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1588peak positions in the table are updated as the offset is changed. In this case,
1589I needed just a single step to correct the map offset. NB: you can use these
1590keys to move the result anywhere you wish, e.g. to select a different origin
1591for the structure but pay attention to the location of symmetry elements.</p>
1592
1593<h2>Step 4 Obtain solution from charge flip result</h2>
1594
1595<p class=MsoNormal>The next step is to extract the unique peak positions from
1596the map and make atoms out of them. The map peak list is sorted with the
1597highest peak first; you can change the sorting to be along any of the column
1598headings in the table by a single click on the desired heading. The <span
1599class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1600"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1601minor-latin'>dzero</span></b></span> column gives the distance of each peak
1602from the origin. The menu items under Map peaks give you several tools to aid
1603in the peak selection <span class=GramE>process,</span> we will just use a
1604couple in this example. I have chosen to proceed by sorting the atoms by <span
1605class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1606"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1607minor-latin'>dzero</span></b></span>, selecting all and then finding the unique
1608ones. </p>
1609
1610<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1611mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1612"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1613</span></span></span><![endif]>Do a single click on the <span class=SpellE><b
1614style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1615mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b></span>
1616column heading. This will sort the peaks in increasing distance from the
1617origin.</p>
1618
1619<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1620mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1621"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1622</span></span></span><![endif]>Do a single click on the upper left (empty) box
1623of the table. All entries will be colored grey indicating their selection.</p>
1624
1625<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1626mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1627"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1628</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1629style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1630mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
1631should select (grey) 13 out of 52 peak positions in the table and all should be
1632near the top of the list. They will be colored green in the plot. If more are
1633selected then check the map offset – it may need a slight correction.</p>
1634
1635<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1636 id="Picture_x0020_9" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:337.5pt;
1637 height:379.5pt;visibility:visible;mso-wrap-style:square'>
1638 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image017.png" o:title=""/>
1639</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=506
1640src="Charge%20Flipping%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_9"><![endif]></span></p>
1641
1642<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1643style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1644mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1645peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1646selected positions and the <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'>Atoms</span></b> table will now have 13 new H
1649atoms. We are looking for heavier atoms in the formula NaSiO<sub>8</sub>B<sub>3</sub>LiH
1650so 13 atoms should correspond to all but the Li &amp; H atoms.</p>
1651
1652<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1653 id="Picture_x0020_10" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:338.25pt;
1654 height:291.75pt;visibility:visible;mso-wrap-style:square'>
1655 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image019.png" o:title=""
1656  croptop="3527f" cropbottom="24386f" cropleft="38043f" cropright="12462f"/>
1657</v:shape><![endif]--><![if !vml]><img border=0 width=451 height=389
1658src="Charge%20Flipping%20in%20GSAS_files/image029.jpg" v:shapes="Picture_x0020_10"><![endif]></span></p>
1659
1660<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1661 id="Picture_x0020_11" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1662 height:292.5pt;visibility:visible;mso-wrap-style:square'>
1663 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image021.png" o:title=""/>
1664</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=390
1665src="Charge%20Flipping%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_11"><![endif]></span></p>
1666
1667<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1668identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1669normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1670minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1671may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1672style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1673mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1674them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1675style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1676mso-hansi-theme-font:minor-latin'>Alt</span></b> key (or <b style='mso-bidi-font-weight:
1677normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1678minor-latin;mso-hansi-theme-font:minor-latin'>Shift/Ctrl</span></b> keys) down
1679and then selecting a position in the table with the <b style='mso-bidi-font-weight:
1680normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1681minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. On
1682Linux machines the <b style='mso-bidi-font-weight:normal'><span
1683style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1684mso-hansi-theme-font:minor-latin'>Alt</span></b> key may have been hijacked by
1685the operating system; use <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'>Shift/Ctrl</span></b> instead to move atoms.
1688My list is now </p>
1689
1690<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1691 id="Picture_x0020_12" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1692 height:295.5pt;visibility:visible;mso-wrap-style:square'>
1693 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image023.png" o:title=""/>
1694</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=394
1695src="Charge%20Flipping%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_12"><![endif]></span></p>
1696
1697<p class=MsoNormal>Do an <b style='mso-bidi-font-weight:normal'><span
1698style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1699mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b> from the <b
1700style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1701mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1702menu to make the drawing reflect the change in atom ordering.</p>
1703
1704<p class=MsoNormal>To proceed, one could select an atom and see its bonding
1705pattern with its neighbors to identify it. Then pick its neighbors and identify
1706them continuing on until all atoms are identified. In my case this would be:</p>
1707
1708<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1709mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1710"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1711</span></span></span><![endif]>Pick M50; it is bonded to 4 neighbors (one is in
1712next cell) as a tetrahedron. Probably Si. Change its Type. The plot will change
1713the green (as selected) ball to a gold colored one (the color assigned to Si).
1714You may have to rock the structure slightly to make the change happen.</p>
1715
1716<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1717mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1718"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1719</span></span></span><![endif]>Pick its neighbors and change them to O atoms. A
1720shift left mouse button on each will select them. The atoms will change from
1721green to red.</p>
1722
1723<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1724mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1725"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1726</span></span></span><![endif]>Pick an O-atom neighbor; it will be a B-atom.</p>
1727
1728<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1729mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1730"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1731</span></span></span><![endif]>And so on until each atom is identified. NB: the
1732Na atom will be relatively isolated.</p>
1733
1734<p class=MsoNormal>When I finished my structure looked like</p>
1735
1736<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1737 id="Picture_x0020_13" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:526.5pt;
1738 height:6in;visibility:visible;mso-wrap-style:square'>
1739 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image025.png" o:title=""
1740  croptop="2450f" cropbottom="26950f" cropleft="39199f" cropright="11167f"/>
1741</v:shape><![endif]--><![if !vml]><img border=0 width=702 height=576
1742src="Charge%20Flipping%20in%20GSAS_files/image026.jpg" v:shapes="Picture_x0020_13"><![endif]></span></p>
1743
1744<p class=MsoNormal>The original charge flipping solution is still visible and
1745the atoms are now identified.</p>
1746
1747<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1748 id="Picture_x0020_18" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
1749 height:290.25pt;visibility:visible;mso-wrap-style:square'>
1750 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image027.png" o:title=""/>
1751</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=387
1752src="Charge%20Flipping%20in%20GSAS_files/image028.gif" v:shapes="Picture_x0020_18"><![endif]></span></p>
1753
1754<p class=MsoNormal>Interestingly the atoms identified exactly matched with the
1755magnitudes of the charge flip map peaks with Si &amp; Na at the top and B at
1756the bottom.</p>
1757
1758<p class=MsoNormal>Now one can safely remove the map peaks (do <b
1759style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1760mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1761peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1762style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1763mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
1764charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1765style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1766mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
1767normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1768minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
1769style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1770mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1771tab). After dressing up the drawing by making the Na atom van der Waals spheres
1772and the rest as balls and sticks I have a nice drawing of the structure
1773(without the Li and H atoms though).</p>
1774
1775<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1776 id="Picture_x0020_15" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:525.75pt;
1777 height:398.25pt;visibility:visible;mso-wrap-style:square'>
1778 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image029.png" o:title=""
1779  croptop="2054f" cropbottom="23166f" cropleft="37518f" cropright="9679f"/>
1780</v:shape><![endif]--><![if !vml]><img border=0 width=701 height=531
1781src="Charge%20Flipping%20in%20GSAS_files/image030.jpg" v:shapes="Picture_x0020_15"><![endif]></span></p>
1782
1783<p class=MsoNormal>Save the project file; the next step is to complete the
1784structure by finding the Li and H atoms and then doing the <span class=SpellE>Rietveld</span>
1785refinement on the completed structure.</p>
1786
1787<h2>Step 5 Complete the structure</h2>
1788
1789<p class=MsoNormal>To complete the structure you will need to perform a
1790preliminary <span class=SpellE>Rietveld</span> refinement. This will make the
1791atom positions more accurate and prepare a set of calculated structure factors
1792needed to generate a difference Fourier map good enough to reveal the Li atom
1793position and maybe the H-atom as well. There are a number of steps needed to
1794set all the controls from the previous Pawley refinement to get a successful
1795start for the <span class=SpellE>Rietveld</span> refinement.</p>
1796
1797<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1798mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1799"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1800</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1801style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1802mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
1803GSAS-II data tree and uncheck all <b style='mso-bidi-font-weight:normal'><span
1804style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1805mso-hansi-theme-font:minor-latin'>Refine</span></b> boxes. You don’t want to
1806start with these when the scale factor is unknown.</p>
1807
1808<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1809mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1810"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1811</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1812style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1813mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
1814style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1815mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1816scale factor</span></b> box. This is the scale factor for the data set. You may
1817want to change the <b style='mso-bidi-font-weight:normal'><span
1818style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1819mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to 1000. That
1820will put the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1821"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1822minor-latin'>Sample X</span></b> displacement on a proper scale when you refine
1823it later.</p>
1824
1825<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1826mso-list:l4 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1827"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1828</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1829style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1830mso-hansi-theme-font:minor-latin'>Phases/kryptonite General</span></b> tab and
1831uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1832mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
1833cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
1834style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1835mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
1836latter is most important; if you forget you will just get another Pawley
1837refinement!</p>
1838
1839<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1840style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1841mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1842GSAS-II data tree menu; all that was refined is scale and background. I got <span
1843class=GramE>a</span> <span class=SpellE>Rwp</span> ~31%. The plot shows clear
1844intensity differences; the atom positions obviously need refinement.</p>
1845
1846<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1847 id="Picture_x0020_16" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1848 height:450pt;visibility:visible;mso-wrap-style:square'>
1849 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image031.png" o:title=""/>
1850</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1851src="Charge%20Flipping%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
1852
1853<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
1854obvious.</p>
1855
1856<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
1857style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1858mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> and select the <b
1859style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1860mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1861tab. The double click the <b style='mso-bidi-font-weight:normal'><span
1862style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1863mso-hansi-theme-font:minor-latin'>refine</span></b> column heading, a dialog
1864box will appear, select the <b style='mso-bidi-font-weight:normal'><span
1865style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1866mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and press <b
1867style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1868mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1869The atoms table will show the refinement controls</p>
1870
1871<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1872 id="Picture_x0020_17" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
1873 height:225pt;visibility:visible;mso-wrap-style:square'>
1874 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image033.png" o:title=""/>
1875</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1876src="Charge%20Flipping%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_17"><![endif]></span></p>
1877
1878<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1879style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1880mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
1881class=SpellE>Rwp</span> is now ~15%. You can now safely refine lattice
1882parameters (in 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'>General</span></b> tab for <b
1885style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1886mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>)
1887and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1888mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1889parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
1890style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1891mso-hansi-theme-font:minor-latin'>U</span></b>, <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'>V</span></b>, <b
1894style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1895mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
1896<span class=GramE><b style='mso-bidi-font-weight:normal'><span
1897style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1898mso-hansi-theme-font:minor-latin'>X</span></b></span> &amp; <b
1899style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1900mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>.
1901My refinement improved slightly to Rwp~14.5%. Let’s see if a difference Fourier
1902map will show anything.<br>
1903Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1904mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite
1905General</span></b> <span class=GramE>tab ;</span> the <b style='mso-bidi-font-weight:
1906normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1907minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b>
1908are midway down the window.</p>
1909
1910<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1911mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
1912"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1913</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
1914normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1915minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
1916style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1917mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
1918for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1919mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
1920
1921<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1922mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
1923"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1924</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1925style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1926mso-hansi-theme-font:minor-latin'>PWDR 11bmb_6231.fxye Bank 1</span></b> for
1927the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1928mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1929set from</span></b> item (the only choice). The Fourier calculation will use
1930the structure factors shown in the <b style='mso-bidi-font-weight:normal'><span
1931style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1932mso-hansi-theme-font:minor-latin'>Reflection list</span></b> item for this PWDR
1933data set.</p>
1934
1935<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1936mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
1937"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1938</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1939style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1940mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
1941style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1942mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1943tab window. The map will be computed via fast Fourier techniques and is very
1944fast. A few lines summarizing the map is printed on the console, the structure
1945plot may show a single green dot somewhere (it could be hidden beneath an
1946atom!), this is the highest point in the map.</p>
1947
1948<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1949mso-list:l2 level1 lfo12'><![if !supportLists]><span style='mso-fareast-font-family:
1950"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1951</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1952style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1953mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
1954style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1955mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
1956level</span></b> slider until something appears on the map.</p>
1957
1958<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1959 id="Picture_x0020_19" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:274.5pt;
1960 height:337.5pt;visibility:visible;mso-wrap-style:square'>
1961 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image035.png" o:title=""/>
1962</v:shape><![endif]--><![if !vml]><img border=0 width=366 height=450
1963src="Charge%20Flipping%20in%20GSAS_files/image036.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
1964
1965<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1966 id="Picture_x0020_20" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:349.5pt;
1967 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1968 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image037.png" o:title=""
1969  croptop="5231f" cropbottom="8930f" cropleft="11448f" cropright="20374f"/>
1970</v:shape><![endif]--><![if !vml]><img border=0 width=466 height=399
1971src="Charge%20Flipping%20in%20GSAS_files/image038.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
1972
1973<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
1974whose size are proportional to the electron density. These are the Li atom
1975positions. There are several ways within GSAS-II to add it to the atom list.
1976One is to do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1977"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1978minor-latin'>Compute/Search map</span></b> in the <b style='mso-bidi-font-weight:
1979normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1980minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab and then
1981find them in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1982"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1983minor-latin'>Map peaks</span></b> tab much the same way we did earlier in this
1984exercise. Another is to get the atom position directly from the map, we will do
1985that now.</p>
1986
1987<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1988mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
1989"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1990</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1991style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1992mso-hansi-theme-font:minor-latin'>Phases/kryptonite Atoms</span></b> tab.</p>
1993
1994<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1995mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
1996"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1997</span></span></span><![endif]>Using the mouse, position the multicolored cross
1998directly in the center of one of the presumed Li atom peaks. Rotate the drawing
1999around with the left mouse button and shift the cross with the right mouse
2000button. You can zoom in using the roll wheel on the mouse (or else use the <b
2001style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2002mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
2003distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
2004style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2005mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
2006lacks a wheel).</p>
2007
2008<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2009 id="Picture_x0020_21" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:350.25pt;
2010 height:302.25pt;visibility:visible;mso-wrap-style:square'>
2011 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image039.png" o:title=""
2012  cropbottom="13787f" cropleft="10923f" cropright="20900f"/>
2013</v:shape><![endif]--><![if !vml]><img border=0 width=467 height=403
2014src="Charge%20Flipping%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_21"><![endif]></span></p>
2015
2016<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2017mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2018"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2019</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
2020style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2021mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>, a white
2022ball will appear at the selected position and an H-atom (name = <b
2023style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2024mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
2025will be appended to the end of the atom list.</p>
2026
2027<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
2028mso-list:l3 level1 lfo14'><![if !supportLists]><span style='mso-fareast-font-family:
2029"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2030</span></span></span><![endif]>Change its <b style='mso-bidi-font-weight:normal'><span
2031style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2032mso-hansi-theme-font:minor-latin'>Type</span></b> to <b style='mso-bidi-font-weight:
2033normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2034minor-latin;mso-hansi-theme-font:minor-latin'>Li</span></b>, it will be renamed
2035and the ball color/size will change to that for Li.</p>
2036
2037<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2038 id="Picture_x0020_22" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:348pt;
2039 height:297pt;visibility:visible;mso-wrap-style:square'>
2040 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image041.png" o:title=""
2041  croptop="374f" cropbottom="13600f" cropleft="10817f" cropright="20795f"/>
2042</v:shape><![endif]--><![if !vml]><img border=0 width=464 height=396
2043src="Charge%20Flipping%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_22"><![endif]></span></p>
2044
2045<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2046 id="Picture_x0020_23" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2047 height:225pt;visibility:visible;mso-wrap-style:square'>
2048 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image043.png" o:title=""/>
2049</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
2050src="Charge%20Flipping%20in%20GSAS_files/image044.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
2051
2052<p class=MsoNormal>Change the <b style='mso-bidi-font-weight:normal'><span
2053style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2054mso-hansi-theme-font:minor-latin'>refine</span></b> flag to <b
2055style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2056mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2057for the Li atom and repeat <b style='mso-bidi-font-weight:normal'><span
2058style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2059mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
2060GSAS-II data tree window. My residual <span class=SpellE>Rwp</span> dropped to
2061~11.3%. Next set all <b style='mso-bidi-font-weight:normal'><span
2062style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2063mso-hansi-theme-font:minor-latin'>refine</span></b> flags to <b
2064style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2065mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>XU</span></b>
2066and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2067"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2068minor-latin'>Calculate/Refine</span></b>. My residual is now <span
2069class=SpellE>Rwp</span> ~10.8%. Maybe we can find the H-atom.</p>
2070
2071<p class=MsoNormal>From the <b style='mso-bidi-font-weight:normal'><span
2072style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2073mso-hansi-theme-font:minor-latin'>General</span></b> tab, Do <b
2074style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2075mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
2076map</span></b> and adjust the <b style='mso-bidi-font-weight:normal'><span
2077style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2078mso-hansi-theme-font:minor-latin'>Contour level</span></b> in the <b
2079style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2080mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw options</span></b>
2081tab.</p>
2082
2083<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2084 id="Picture_x0020_24" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:348pt;
2085 height:302.25pt;visibility:visible;mso-wrap-style:square'>
2086 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image045.png" o:title=""
2087  cropbottom="13413f" cropleft="10818f" cropright="21005f"/>
2088</v:shape><![endif]--><![if !vml]><img border=0 width=464 height=403
2089src="Charge%20Flipping%20in%20GSAS_files/image046.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
2090
2091<p class=MsoNormal>I moved the cross to a very interesting feature of the map
2092and zoomed in a bit. This may be the H-atom, <b style='mso-bidi-font-weight:
2093normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2094minor-latin;mso-hansi-theme-font:minor-latin'>Insert view point</span></b> from
2095the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2096mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2097tab and change the <b style='mso-bidi-font-weight:normal'><span
2098style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2099mso-hansi-theme-font:minor-latin'>Type</span></b> to <b style='mso-bidi-font-weight:
2100normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2101minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b> (I know it is H
2102already but this step changes the name from <b style='mso-bidi-font-weight:
2103normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2104minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>). Repeat the
2105Calculate/Refine without varying any of the H-atom parameters; my final <span
2106class=SpellE>Rwp</span> = 10.69% (you don’t get much improvement for adding an
2107H-atom to an oxide structure).</p>
2108
2109</div>
2110
2111</body>
2112
2113</html>
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