source: trunk/help/Charge Flipping in GSAS.htm @ 1002

Last change on this file since 1002 was 1002, checked in by toby, 10 years ago

fix page type

  • Property svn:mime-type set to text/html
File size: 100.9 KB
Line 
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379        mso-margin-bottom-alt:auto;
380        margin-left:0in;
381        mso-pagination:widow-orphan;
382        mso-outline-level:2;
383        font-size:18.0pt;
384        font-family:"Times New Roman","serif";
385        mso-fareast-font-family:"Times New Roman";
386        mso-fareast-theme-font:minor-fareast;
387        font-weight:bold;}
388h3
389        {mso-style-priority:9;
390        mso-style-unhide:no;
391        mso-style-qformat:yes;
392        mso-style-link:"Heading 3 Char";
393        mso-margin-top-alt:auto;
394        margin-right:0in;
395        mso-margin-bottom-alt:auto;
396        margin-left:0in;
397        mso-pagination:widow-orphan;
398        mso-outline-level:3;
399        font-size:13.5pt;
400        font-family:"Times New Roman","serif";
401        mso-fareast-font-family:"Times New Roman";
402        mso-fareast-theme-font:minor-fareast;
403        font-weight:bold;}
404h4
405        {mso-style-priority:9;
406        mso-style-unhide:no;
407        mso-style-qformat:yes;
408        mso-style-link:"Heading 4 Char";
409        margin-top:10.0pt;
410        margin-right:0in;
411        margin-bottom:0in;
412        margin-left:0in;
413        margin-bottom:.0001pt;
414        mso-pagination:widow-orphan;
415        page-break-after:avoid;
416        mso-outline-level:4;
417        font-size:13.0pt;
418        font-family:"Cambria","serif";
419        mso-fareast-font-family:"Times New Roman";
420        mso-fareast-theme-font:minor-fareast;
421        mso-bidi-font-family:"Times New Roman";
422        color:#4F81BD;
423        font-weight:bold;
424        font-style:italic;}
425h5
426        {mso-style-priority:9;
427        mso-style-unhide:no;
428        mso-style-qformat:yes;
429        mso-style-link:"Heading 5 Char";
430        mso-margin-top-alt:auto;
431        margin-right:0in;
432        mso-margin-bottom-alt:auto;
433        margin-left:0in;
434        mso-pagination:widow-orphan;
435        mso-outline-level:5;
436        font-size:12.0pt;
437        font-family:"Times New Roman","serif";
438        mso-fareast-font-family:"Times New Roman";
439        mso-fareast-theme-font:minor-fareast;
440        color:#4F4FFF;
441        font-weight:bold;}
442p.MsoTitle, li.MsoTitle, div.MsoTitle
443        {mso-style-noshow:yes;
444        mso-style-priority:10;
445        mso-style-unhide:no;
446        mso-style-qformat:yes;
447        mso-style-link:"Title Char";
448        margin-top:0in;
449        margin-right:0in;
450        margin-bottom:15.0pt;
451        margin-left:0in;
452        mso-pagination:widow-orphan;
453        font-size:26.0pt;
454        font-family:"Cambria","serif";
455        mso-fareast-font-family:"Times New Roman";
456        mso-fareast-theme-font:minor-fareast;
457        mso-bidi-font-family:"Times New Roman";
458        color:#17365D;
459        letter-spacing:.25pt;}
460a:link, span.MsoHyperlink
461        {mso-style-noshow:yes;
462        mso-style-priority:99;
463        color:blue;
464        text-decoration:underline;
465        text-underline:single;}
466a:visited, span.MsoHyperlinkFollowed
467        {mso-style-noshow:yes;
468        mso-style-priority:99;
469        color:purple;
470        text-decoration:underline;
471        text-underline:single;}
472p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
473        {mso-style-noshow:yes;
474        mso-style-priority:99;
475        mso-style-link:"Document Map Char";
476        margin:0in;
477        margin-bottom:.0001pt;
478        mso-pagination:widow-orphan;
479        font-size:8.0pt;
480        font-family:"Tahoma","sans-serif";
481        mso-fareast-font-family:"Times New Roman";
482        mso-fareast-theme-font:minor-fareast;}
483p
484        {mso-style-noshow:yes;
485        mso-style-priority:99;
486        mso-margin-top-alt:auto;
487        margin-right:0in;
488        mso-margin-bottom-alt:auto;
489        margin-left:0in;
490        mso-pagination:widow-orphan;
491        font-size:12.0pt;
492        font-family:"Times New Roman","serif";
493        mso-fareast-font-family:"Times New Roman";
494        mso-fareast-theme-font:minor-fareast;}
495pre
496        {mso-style-noshow:yes;
497        mso-style-priority:99;
498        mso-style-link:"HTML Preformatted Char";
499        margin:0in;
500        margin-bottom:.0001pt;
501        mso-pagination:widow-orphan;
502        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;
503        font-size:10.0pt;
504        font-family:"Courier New";
505        mso-fareast-font-family:"Times New Roman";
506        mso-fareast-theme-font:minor-fareast;}
507p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
508        {mso-style-noshow:yes;
509        mso-style-priority:99;
510        mso-style-link:"Balloon Text Char";
511        margin:0in;
512        margin-bottom:.0001pt;
513        mso-pagination:widow-orphan;
514        font-size:8.0pt;
515        font-family:"Tahoma","sans-serif";
516        mso-fareast-font-family:"Times New Roman";
517        mso-fareast-theme-font:minor-fareast;}
518span.MsoPlaceholderText
519        {mso-style-noshow:yes;
520        mso-style-priority:99;
521        mso-style-unhide:no;
522        color:gray;}
523p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
524        {mso-style-noshow:yes;
525        mso-style-priority:1;
526        mso-style-unhide:no;
527        mso-style-qformat:yes;
528        margin:0in;
529        margin-bottom:.0001pt;
530        mso-pagination:widow-orphan;
531        font-size:12.0pt;
532        font-family:"Times New Roman","serif";
533        mso-fareast-font-family:"Times New Roman";
534        mso-fareast-theme-font:minor-fareast;}
535p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
536        {mso-style-noshow:yes;
537        mso-style-priority:34;
538        mso-style-unhide:no;
539        mso-style-qformat:yes;
540        margin-top:0in;
541        margin-right:0in;
542        margin-bottom:0in;
543        margin-left:.5in;
544        margin-bottom:.0001pt;
545        mso-pagination:widow-orphan;
546        font-size:12.0pt;
547        font-family:"Times New Roman","serif";
548        mso-fareast-font-family:"Times New Roman";
549        mso-fareast-theme-font:minor-fareast;}
550span.MsoIntenseReference
551        {mso-style-priority:32;
552        mso-style-unhide:no;
553        mso-style-qformat:yes;
554        font-variant:small-caps;
555        color:#C0504D;
556        letter-spacing:.25pt;
557        font-weight:bold;
558        text-decoration:underline;
559        text-underline:single;}
560span.Heading1Char
561        {mso-style-name:"Heading 1 Char";
562        mso-style-priority:9;
563        mso-style-unhide:no;
564        mso-style-locked:yes;
565        mso-style-link:"Heading 1";
566        font-family:"Times New Roman","serif";
567        mso-ascii-font-family:"Times New Roman";
568        mso-hansi-font-family:"Times New Roman";
569        mso-bidi-font-family:"Times New Roman";
570        font-weight:bold;}
571span.Heading2Char
572        {mso-style-name:"Heading 2 Char";
573        mso-style-noshow:yes;
574        mso-style-priority:9;
575        mso-style-unhide:no;
576        mso-style-locked:yes;
577        mso-style-link:"Heading 2";
578        font-family:"Times New Roman","serif";
579        mso-ascii-font-family:"Times New Roman";
580        mso-hansi-font-family:"Times New Roman";
581        mso-bidi-font-family:"Times New Roman";
582        font-weight:bold;}
583span.Heading3Char
584        {mso-style-name:"Heading 3 Char";
585        mso-style-noshow:yes;
586        mso-style-priority:9;
587        mso-style-unhide:no;
588        mso-style-locked:yes;
589        mso-style-link:"Heading 3";
590        font-family:"Times New Roman","serif";
591        mso-ascii-font-family:"Times New Roman";
592        mso-hansi-font-family:"Times New Roman";
593        mso-bidi-font-family:"Times New Roman";
594        font-weight:bold;}
595span.Heading4Char
596        {mso-style-name:"Heading 4 Char";
597        mso-style-noshow:yes;
598        mso-style-priority:9;
599        mso-style-unhide:no;
600        mso-style-locked:yes;
601        mso-style-link:"Heading 4";
602        font-family:"Cambria","serif";
603        mso-ascii-font-family:Cambria;
604        mso-hansi-font-family:Cambria;
605        color:#4F81BD;
606        font-weight:bold;
607        font-style:italic;}
608span.Heading5Char
609        {mso-style-name:"Heading 5 Char";
610        mso-style-noshow:yes;
611        mso-style-priority:9;
612        mso-style-unhide:no;
613        mso-style-locked:yes;
614        mso-style-link:"Heading 5";
615        font-family:"Times New Roman","serif";
616        mso-ascii-font-family:"Times New Roman";
617        mso-hansi-font-family:"Times New Roman";
618        mso-bidi-font-family:"Times New Roman";
619        color:#4F4FFF;
620        font-weight:bold;}
621span.HTMLPreformattedChar
622        {mso-style-name:"HTML Preformatted Char";
623        mso-style-noshow:yes;
624        mso-style-priority:99;
625        mso-style-unhide:no;
626        mso-style-locked:yes;
627        mso-style-link:"HTML Preformatted";
628        font-family:"Courier New";
629        mso-ascii-font-family:"Courier New";
630        mso-hansi-font-family:"Courier New";
631        mso-bidi-font-family:"Courier New";}
632span.TitleChar
633        {mso-style-name:"Title Char";
634        mso-style-priority:10;
635        mso-style-unhide:no;
636        mso-style-locked:yes;
637        mso-style-link:Title;
638        font-family:"Cambria","serif";
639        mso-ascii-font-family:Cambria;
640        mso-hansi-font-family:Cambria;
641        color:#17365D;
642        letter-spacing:.25pt;}
643span.DocumentMapChar
644        {mso-style-name:"Document Map Char";
645        mso-style-noshow:yes;
646        mso-style-priority:99;
647        mso-style-unhide:no;
648        mso-style-locked:yes;
649        mso-style-link:"Document Map";
650        font-family:"Tahoma","sans-serif";
651        mso-ascii-font-family:Tahoma;
652        mso-hansi-font-family:Tahoma;
653        mso-bidi-font-family:Tahoma;}
654span.BalloonTextChar
655        {mso-style-name:"Balloon Text Char";
656        mso-style-noshow:yes;
657        mso-style-priority:99;
658        mso-style-unhide:no;
659        mso-style-locked:yes;
660        mso-style-link:"Balloon Text";
661        font-family:"Tahoma","sans-serif";
662        mso-ascii-font-family:Tahoma;
663        mso-hansi-font-family:Tahoma;
664        mso-bidi-font-family:Tahoma;}
665p.msotitlecxspfirst, li.msotitlecxspfirst, div.msotitlecxspfirst
666        {mso-style-name:msotitlecxspfirst;
667        mso-style-noshow:yes;
668        mso-style-priority:99;
669        mso-style-unhide:no;
670        margin:0in;
671        margin-bottom:.0001pt;
672        mso-pagination:widow-orphan;
673        font-size:26.0pt;
674        font-family:"Cambria","serif";
675        mso-fareast-font-family:"Times New Roman";
676        mso-fareast-theme-font:minor-fareast;
677        mso-bidi-font-family:"Times New Roman";
678        color:#17365D;
679        letter-spacing:.25pt;}
680p.msotitlecxspmiddle, li.msotitlecxspmiddle, div.msotitlecxspmiddle
681        {mso-style-name:msotitlecxspmiddle;
682        mso-style-noshow:yes;
683        mso-style-priority:99;
684        mso-style-unhide:no;
685        margin:0in;
686        margin-bottom:.0001pt;
687        mso-pagination:widow-orphan;
688        font-size:26.0pt;
689        font-family:"Cambria","serif";
690        mso-fareast-font-family:"Times New Roman";
691        mso-fareast-theme-font:minor-fareast;
692        mso-bidi-font-family:"Times New Roman";
693        color:#17365D;
694        letter-spacing:.25pt;}
695p.msotitlecxsplast, li.msotitlecxsplast, div.msotitlecxsplast
696        {mso-style-name:msotitlecxsplast;
697        mso-style-noshow:yes;
698        mso-style-priority:99;
699        mso-style-unhide:no;
700        margin-top:0in;
701        margin-right:0in;
702        margin-bottom:15.0pt;
703        margin-left:0in;
704        mso-pagination:widow-orphan;
705        font-size:26.0pt;
706        font-family:"Cambria","serif";
707        mso-fareast-font-family:"Times New Roman";
708        mso-fareast-theme-font:minor-fareast;
709        mso-bidi-font-family:"Times New Roman";
710        color:#17365D;
711        letter-spacing:.25pt;}
712p.msolistparagraphcxspfirst, li.msolistparagraphcxspfirst, div.msolistparagraphcxspfirst
713        {mso-style-name:msolistparagraphcxspfirst;
714        mso-style-noshow:yes;
715        mso-style-priority:99;
716        mso-style-unhide:no;
717        margin-top:0in;
718        margin-right:0in;
719        margin-bottom:0in;
720        margin-left:.5in;
721        margin-bottom:.0001pt;
722        mso-pagination:widow-orphan;
723        font-size:12.0pt;
724        font-family:"Times New Roman","serif";
725        mso-fareast-font-family:"Times New Roman";
726        mso-fareast-theme-font:minor-fareast;}
727p.msolistparagraphcxspmiddle, li.msolistparagraphcxspmiddle, div.msolistparagraphcxspmiddle
728        {mso-style-name:msolistparagraphcxspmiddle;
729        mso-style-noshow:yes;
730        mso-style-priority:99;
731        mso-style-unhide:no;
732        margin-top:0in;
733        margin-right:0in;
734        margin-bottom:0in;
735        margin-left:.5in;
736        margin-bottom:.0001pt;
737        mso-pagination:widow-orphan;
738        font-size:12.0pt;
739        font-family:"Times New Roman","serif";
740        mso-fareast-font-family:"Times New Roman";
741        mso-fareast-theme-font:minor-fareast;}
742p.msolistparagraphcxsplast, li.msolistparagraphcxsplast, div.msolistparagraphcxsplast
743        {mso-style-name:msolistparagraphcxsplast;
744        mso-style-noshow:yes;
745        mso-style-priority:99;
746        mso-style-unhide:no;
747        margin-top:0in;
748        margin-right:0in;
749        margin-bottom:0in;
750        margin-left:.5in;
751        margin-bottom:.0001pt;
752        mso-pagination:widow-orphan;
753        font-size:12.0pt;
754        font-family:"Times New Roman","serif";
755        mso-fareast-font-family:"Times New Roman";
756        mso-fareast-theme-font:minor-fareast;}
757p.msochpdefault, li.msochpdefault, div.msochpdefault
758        {mso-style-name:msochpdefault;
759        mso-style-noshow:yes;
760        mso-style-priority:99;
761        mso-style-unhide:no;
762        mso-margin-top-alt:auto;
763        margin-right:0in;
764        mso-margin-bottom-alt:auto;
765        margin-left:0in;
766        mso-pagination:widow-orphan;
767        font-size:10.0pt;
768        font-family:"Calibri","sans-serif";
769        mso-fareast-font-family:"Times New Roman";
770        mso-fareast-theme-font:minor-fareast;
771        mso-bidi-font-family:Calibri;}
772span.SpellE
773        {mso-style-name:"";
774        mso-spl-e:yes;}
775span.GramE
776        {mso-style-name:"";
777        mso-gram-e:yes;}
778.MsoChpDefault
779        {mso-style-type:export-only;
780        mso-default-props:yes;
781        font-size:10.0pt;
782        mso-ansi-font-size:10.0pt;
783        mso-bidi-font-size:10.0pt;
784        mso-ascii-font-family:Calibri;
785        mso-hansi-font-family:Calibri;
786        mso-bidi-font-family:Calibri;}
787@page WordSection1
788        {size:8.5in 11.0in;
789        margin:1.0in 1.0in 1.0in 1.0in;
790        mso-header-margin:.5in;
791        mso-footer-margin:.5in;
792        mso-paper-source:0;}
793div.WordSection1
794        {page:WordSection1;}
795 /* List Definitions */
796 @list l0
797        {mso-list-id:82917343;
798        mso-list-type:hybrid;
799        mso-list-template-ids:-1527319822 -2100533712 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
800@list l0:level1
801        {mso-level-tab-stop:none;
802        mso-level-number-position:left;
803        margin-left:.75in;
804        text-indent:-.25in;}
805@list l0:level2
806        {mso-level-number-format:alpha-lower;
807        mso-level-tab-stop:none;
808        mso-level-number-position:left;
809        margin-left:1.25in;
810        text-indent:-.25in;}
811@list l0:level3
812        {mso-level-number-format:roman-lower;
813        mso-level-tab-stop:none;
814        mso-level-number-position:right;
815        margin-left:1.75in;
816        text-indent:-9.0pt;}
817@list l0:level4
818        {mso-level-tab-stop:none;
819        mso-level-number-position:left;
820        margin-left:2.25in;
821        text-indent:-.25in;}
822@list l0:level5
823        {mso-level-number-format:alpha-lower;
824        mso-level-tab-stop:none;
825        mso-level-number-position:left;
826        margin-left:2.75in;
827        text-indent:-.25in;}
828@list l0:level6
829        {mso-level-number-format:roman-lower;
830        mso-level-tab-stop:none;
831        mso-level-number-position:right;
832        margin-left:3.25in;
833        text-indent:-9.0pt;}
834@list l0:level7
835        {mso-level-tab-stop:none;
836        mso-level-number-position:left;
837        margin-left:3.75in;
838        text-indent:-.25in;}
839@list l0:level8
840        {mso-level-number-format:alpha-lower;
841        mso-level-tab-stop:none;
842        mso-level-number-position:left;
843        margin-left:4.25in;
844        text-indent:-.25in;}
845@list l0:level9
846        {mso-level-number-format:roman-lower;
847        mso-level-tab-stop:none;
848        mso-level-number-position:right;
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1210</head>
1211
1212<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1213
1214<div class=WordSection1>
1215
1216<h1><span style='mso-fareast-font-family:"Times New Roman"'>Charge Flipping in
1217GSAS-II - jadarite<o:p></o:p></span></h1>
1218
1219<h1><span style='mso-fareast-font-family:"Times New Roman"'>Prerequisite: <o:p></o:p></span></h1>
1220
1221<p class=MsoNormal>In this exercise you will use GSAS-II to solve the structure
1222of <span class=SpellE>jadarite</span> (aka “kryptonite”) from powder
1223diffraction data via charge flipping. This structure was originally solved by
1224Pam Whitfield from laboratory powder data in the space group P2<sub>1</sub>/c. </p>
1225
1226<p class=MsoNormal>If you have not done so already, <a
1227href="Starting%20GSAS.htm">start GSAS-II</a> and open the GSAS-II project file
1228(I called it <span class=SpellE>jadarite.gpx</span>) you saved from the second
1229part of the <a href="Fit%20Peaks.htm#kryptonite_peak_fit">peak fitting-indexing
1230exercise</a>. If you didn’t do that exercise, do it now.</p>
1231
1232<h2><span class=GramE>Step 1.</span> Setup for Pawley refinement</h2>
1233
1234<p class=MsoNormal>There are a number of steps that must be done in preparation
1235for a Pawley refinement after having completed the unit cell indexing and new
1236phase creation. These cover two things: one is to prepare the powder pattern
1237(reset limits, etc.) and the other is to prepare the phase for the refinement.</p>
1238
1239<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1240style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1241style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1242<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1243mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Limits</span></b>
1244in the GSAS-II data tree for the PWDR data set and expand the plot so that the
1245region near d=1.0Å is readily seen. This is ~24deg 2<span style='font-family:
1246Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1247mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1248symbol;mso-symbol-font-family:Symbol'>Q</span></span>. It is an area relatively
1249clear of peaks and makes a good place to end the calculations with a reflection
1250set of ~1Å resolution as needed for charge flipping. Enter <b style='mso-bidi-font-weight:
1251normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1252minor-latin;mso-hansi-theme-font:minor-latin'>24</span></b> for <span
1253class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1254"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1255minor-latin'>Tmax</span></b></span> as the upper limit and make a note of the
1256exact d-spacing (0.9945Å) using the mouse cursor on the plot.</p>
1257
1258<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1259style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1260style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Select
1261<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1262mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1263Parameters</span></b> and uncheck all <b style='mso-bidi-font-weight:normal'><span
1264style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1265mso-hansi-theme-font:minor-latin'>Refine</span></b> flags and do <b
1266style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1267mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Reset
1268profile</span></b> to recover the default values. The peak fitting done earlier
1269is over a much more limited range of 2<span style='font-family:Symbol;
1270mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:"Times New Roman";
1271mso-char-type:symbol;mso-symbol-font-family:Symbol'><span style='mso-char-type:
1272symbol;mso-symbol-font-family:Symbol'>Q</span></span> giving values that will
1273not extrapolate well over the wider range to be used in the Pawley refinement.
1274We will refine them again later.</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'>3.<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'>Sample
1281Parameters</span></b> and uncheck refinement of <b style='mso-bidi-font-weight:
1282normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1283minor-latin;mso-hansi-theme-font:minor-latin'>Histogram scale factor</span></b>.</p>
1284
1285<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l5 level1 lfo2'><![if !supportLists]><span
1286style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1287style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Go
1288to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1289mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>
1290to find the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1291"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1292minor-latin'>Pawley controls</span></b>. Check the <b style='mso-bidi-font-weight:
1293normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1294minor-latin;mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> box
1295and enter the d-spacing (0.9945) into the <b style='mso-bidi-font-weight:normal'><span
1296style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1297mso-hansi-theme-font:minor-latin'>Pawley <span class=SpellE>dmin</span></span></b>
1298box.</p>
1299
1300<p class=MsoNormal>When done the <b style='mso-bidi-font-weight:normal'><span
1301style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1302mso-hansi-theme-font:minor-latin'>General</span></b> tab should look like</p>
1303
1304<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1305 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1306 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1307 <v:stroke joinstyle="miter"/>
1308 <v:formulas>
1309  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1310  <v:f eqn="sum @0 1 0"/>
1311  <v:f eqn="sum 0 0 @1"/>
1312  <v:f eqn="prod @2 1 2"/>
1313  <v:f eqn="prod @3 21600 pixelWidth"/>
1314  <v:f eqn="prod @3 21600 pixelHeight"/>
1315  <v:f eqn="sum @0 0 1"/>
1316  <v:f eqn="prod @6 1 2"/>
1317  <v:f eqn="prod @7 21600 pixelWidth"/>
1318  <v:f eqn="sum @8 21600 0"/>
1319  <v:f eqn="prod @7 21600 pixelHeight"/>
1320  <v:f eqn="sum @10 21600 0"/>
1321 </v:formulas>
1322 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1323 <o:lock v:ext="edit" aspectratio="t"/>
1324</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_i1047" type="#_x0000_t75"
1325 style='width:545.25pt;height:303.75pt;visibility:visible;mso-wrap-style:square'>
1326 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image001.png" o:title=""/>
1327</v:shape><![endif]--><![if !vml]><img border=0 width=727 height=405
1328src="Charge%20Flipping%20in%20GSAS_files/image002.gif" v:shapes="Picture_x0020_2"><![endif]></span></p>
1329
1330<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1331style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1332mso-hansi-theme-font:minor-latin'>Data</span></b> tab; it will be empty except
1333for a single line of text. Do <b style='mso-bidi-font-weight:normal'><span
1334style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1335mso-hansi-theme-font:minor-latin'>Edit/Add powder histograms</span></b>; a
1336dialog box will appear</p>
1337
1338<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1339 id="Picture_x0020_5" o:spid="_x0000_i1046" type="#_x0000_t75" style='width:259.5pt;
1340 height:252pt;visibility:visible;mso-wrap-style:square'>
1341 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image003.png" o:title=""/>
1342</v:shape><![endif]--><![if !vml]><img border=0 width=346 height=336
1343src="Charge%20Flipping%20in%20GSAS_files/image004.gif" v:shapes="Picture_x0020_5"><![endif]></span></p>
1344
1345<p class=MsoNormal>Select either choice; the desired data set will be added to
1346this phase for analysis. The data tab now shows the new data set; check the <b
1347style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1348mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Show</span></b>
1349button to see the full information</p>
1350
1351<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1352 id="Picture_x0020_6" o:spid="_x0000_i1045" type="#_x0000_t75" style='width:480pt;
1353 height:389.25pt;visibility:visible;mso-wrap-style:square'>
1354 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image005.png" o:title=""/>
1355</v:shape><![endif]--><![if !vml]><img border=0 width=640 height=519
1356src="Charge%20Flipping%20in%20GSAS_files/image006.gif" v:shapes="Picture_x0020_6"><![endif]></span></p>
1357
1358<p class=MsoNormal>I’ve stretched the window slightly to see the entire
1359contents. This is the location for all the phase dependent parameters for this
1360histogram. Notice that it includes phase fraction, size &amp; <span
1361class=SpellE>mustrain</span> as well as preferred orientation, elastic strain
1362and extinction corrections. The <span class=SpellE>Babinet</span> correction is
1363intended for protein work where a significant region of the structure is
1364disordered solvent. There are buttons for plotting size and <span class=SpellE>mustrain</span>
1365surfaces</p>
1366
1367<p class=MsoNormal><span class=GramE>and</span> preferred orientation
1368correction curves.</p>
1369
1370<p class=MsoNormal>Next find the <b style='mso-bidi-font-weight:normal'><span
1371style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1372mso-hansi-theme-font:minor-latin'>Pawley reflections</span></b> tab; it will be
1373empty except for column headings. <span class=GramE>Do</span> <b
1374style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1375mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Operations/Pawley
1376create</span></b>; this makes the reflection set over the range covered by
1377setting <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1378mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Pawley <span
1379class=SpellE>dmin</span></span></b>. The table should list reflections 0-629.
1380Select and check the refine column using the same technique you used for the
1381peak list. </p>
1382
1383<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1384 id="Picture_x0020_4" o:spid="_x0000_i1044" type="#_x0000_t75" style='width:375pt;
1385 height:225pt;visibility:visible;mso-wrap-style:square'>
1386 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image007.png" o:title=""/>
1387</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=300
1388src="Charge%20Flipping%20in%20GSAS_files/image008.gif" v:shapes="Picture_x0020_4"><![endif]></span></p>
1389
1390<p class=MsoNormal>This completes the Pawley refinement setup; be careful that
1391you didn’t skip a step as it might not work correctly if you did.</p>
1392
1393<h2>Step 2 Pawley refinement</h2>
1394
1395<p class=MsoNormal>To start the refinement, do <b style='mso-bidi-font-weight:
1396normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1397minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> on
1398the main GSAS-II data tree window. Before it begins a backup of the project
1399file is made; the name will be jadarite.bck0.gpx. It can be used to recover
1400from a bad refinement. A progress dialog box will appear showing the residual
1401as the refinement proceeds. My refinement completed with <span class=SpellE>Rwp</span>
1402~19.7%; a dialog box appears asking if you wish to load the result. Press <b
1403style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1404mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1405To see the plot select the PWDR line in the GSAS-II data tree (I’ve adjusted
1406the width and height).</p>
1407
1408<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1409 id="Picture_x0020_7" o:spid="_x0000_i1043" type="#_x0000_t75" style='width:525pt;
1410 height:450pt;visibility:visible;mso-wrap-style:square'>
1411 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image009.png" o:title=""/>
1412</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1413src="Charge%20Flipping%20in%20GSAS_files/image010.gif" v:shapes="Picture_x0020_7"><![endif]></span></p>
1414
1415<p class=MsoNormal>It is evident from examining the plot that improvement can
1416be had by refining the lattice parameters. Go to <b style='mso-bidi-font-weight:
1417normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1418minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> in
1419the GSAS-II data tree and check 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'>Refine unit cell</span></b> box. Repeat <b
1422style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1423mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>.
1424I obtained a new residual of 10.73%.</p>
1425
1426<p class=MsoNormal>Now select <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'>Instrument parameters</span></b> for the PWDR
1429data set in the GSAS-II data tree and check <b style='mso-bidi-font-weight:
1430normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1431minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>,<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'> V</span></b>,<b
1434style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1435mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> W</span></b>,<b
1436style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1437mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'> <span
1438class=GramE>X</span> </span></b>&amp;<b style='mso-bidi-font-weight:normal'><span
1439style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1440mso-hansi-theme-font:minor-latin'> Y</span></b>. Repeat <b style='mso-bidi-font-weight:
1441normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1442minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; I
1443obtained an improved residual of 9.7% with a much better fit at the high angle
1444part of the pattern.</p>
1445
1446<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1447 id="Picture_x0020_8" o:spid="_x0000_i1042" type="#_x0000_t75" style='width:525pt;
1448 height:450pt;visibility:visible;mso-wrap-style:square'>
1449 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image011.png" o:title=""/>
1450</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1451src="Charge%20Flipping%20in%20GSAS_files/image012.gif" v:shapes="Picture_x0020_8"><![endif]></span></p>
1452
1453<p class=MsoNormal>This may be good enough to try charge flipping.</p>
1454
1455<h2>Step 3 Charge flipping</h2>
1456
1457<p class=MsoNormal>A few steps are needed to set up for a charge flipping run.
1458Go to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1459mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>
1460and notice the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1461"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1462minor-latin'>Charge flip controls</span></b> in the middle of the <b
1463style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1464mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1465tab.</p>
1466
1467<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1468mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1469"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1470</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1471style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1472mso-hansi-theme-font:minor-latin'>Reflection set from</span></b> to be <b
1473style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1474mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>PWDR
147511bmb_6231.fxye Bank 1</span></b> (the only choice!). This makes the reflection
1476set to be used those in <b style='mso-bidi-font-weight:normal'><span
1477style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1478mso-hansi-theme-font:minor-latin'>Reflection Lists</span></b> under the PWDR
1479data set; these should match the Pawley reflection set.</p>
1480
1481<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1482mso-list:l1 level1 lfo4'><![if !supportLists]><span style='mso-fareast-font-family:
1483"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1484</span></span></span><![endif]>Set the <b style='mso-bidi-font-weight:normal'><span
1485style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1486mso-hansi-theme-font:minor-latin'>Peak cutoff</span></b> (in <b
1487style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1488mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map
1489controls</span></b>) to <b style='mso-bidi-font-weight:normal'><span
1490style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1491mso-hansi-theme-font:minor-latin'>10%</span></b>. This controls the map search
1492routine.</p>
1493
1494<p class=MsoNormal>For powder data it is not usually advisable to select a <b
1495style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1496mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing
1497element</span></b>; if selected a periodic table appears – select an element or
1498‘<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1499mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>None’</span></b>.
1500The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1501mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Resolution</span></b>
1502defines the map spacing and thus the extent of the reflection set; the observed
1503reflection set is zero filled to this limit for charge flipping. The <b
1504style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1505mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-factor</span></b>
1506and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1507mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b>
1508determine the lower threshold and upper limit for charge flipping,
1509respectively. The latter is used to avoid “Uranium solutions” in the result.
1510Set this to <b style='mso-bidi-font-weight:normal'><span style='font-family:
1511"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1512minor-latin'>10-12</span></b> for equal atom problems and larger for heavy atom
1513ones. The default (<b style='mso-bidi-font-weight:normal'><span
1514style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1515mso-hansi-theme-font:minor-latin'>20</span></b>) is suitable for kryptonite.</p>
1516
1517<p class=MsoNormal>When ready select <b style='mso-bidi-font-weight:normal'><span
1518style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1519mso-hansi-theme-font:minor-latin'>Compute/Charge flipping</span></b>; a progress
1520bar dialog will appear that tracks the residual found in each charge flipping
1521cycle. It will quickly drop to some level and then perhaps drop again into the
152220-30% range for a successful charge flipping run. Press <b style='mso-bidi-font-weight:
1523normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1524minor-latin;mso-hansi-theme-font:minor-latin'>Cancel</span></b> to stop the
1525charge flipping; a peak list and a drawing of the solution will appear. One of
1526my runs gave</p>
1527
1528<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1529 id="Picture_x0020_10" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:337.5pt;
1530 height:225pt;visibility:visible;mso-wrap-style:square'>
1531 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image013.png" o:title=""/>
1532</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=300
1533src="Charge%20Flipping%20in%20GSAS_files/image014.gif" v:shapes="Picture_x0020_10"><![endif]></span></p>
1534
1535<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1536
1537<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1538 id="Picture_x0020_1" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:338.25pt;
1539 height:289.5pt;visibility:visible;mso-wrap-style:square'>
1540 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image015.png" o:title=""
1541  croptop="2431f" cropbottom="25578f" cropleft="38673f" cropright="11746f"/>
1542</v:shape><![endif]--><![if !vml]><img border=0 width=451 height=386
1543src="Charge%20Flipping%20in%20GSAS_files/image016.jpg" v:shapes="Picture_x0020_1"><![endif]></span></p>
1544
1545<p class=MsoNormal>The result looks very promising! Charge flipping operates
1546without regard to symmetry and GSAS-II attempts to locate the map with respect
1547to the symmetry elements from the computed reflection phases. Errors in these
1548phases can disrupt this process so that the map and peak positions are offset
1549from their true positions. To discover this and fix it, rotate the drawing
1550around to check that atom positions are related via the inversion center (the
1551multicolored cross in the center of the cell. NB: only works if structure has
1552an inversion center!). Avoid motions with the right mouse button pressed, this
1553moves the cross. To recover, press the ‘<b style='mso-bidi-font-weight:normal'><span
1554style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1555mso-hansi-theme-font:minor-latin'>C</span></b>’ key to reset the cross to the
1556cell center. If you find an offset to the map, orient it so the offset is
1557horizontal or vertical and then press the <b style='mso-bidi-font-weight:normal'><span
1558style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1559mso-hansi-theme-font:minor-latin'>L</span></b>, <b style='mso-bidi-font-weight:
1560normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1561minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>, <b
1562style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1563mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b>
1564or <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1565mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b>
1566keys to shift the map and peaks as needed. The shift is in resolution units
1567(0.5Å) so the fix can only be approximate. Repeat as needed. Notice that the
1568peak positions in the table are updated as the offset is changed. In this case,
1569I needed just a single step to correct the map offset. NB: you can use these
1570keys to move the result anywhere you wish, e.g. to select a different origin
1571for the structure but pay attention to the location of symmetry elements.</p>
1572
1573<h2>Step 4 Obtain solution from charge flip result</h2>
1574
1575<p class=MsoNormal>The next step is to extract the unique peak positions from
1576the map and make atoms out of them. The map peak list is sorted with the
1577highest peak first; you can change the sorting to be along any of the column
1578headings in the table by a single click on the desired heading. The <span
1579class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1580"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1581minor-latin'>dzero</span></b></span> column gives the distance of each peak
1582from the origin. The menu items under Map peaks give you several tools to aid
1583in the peak selection <span class=GramE>process,</span> we will just use a
1584couple in this example. I have chosen to proceed by sorting the atoms by <span
1585class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1586"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1587minor-latin'>dzero</span></b></span>, selecting all and then finding the unique
1588ones. </p>
1589
1590<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1591mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1592"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1593</span></span></span><![endif]>Do a single click on the <span class=SpellE><b
1594style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1595mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>dzero</span></b></span>
1596column heading. This will sort the peaks in increasing distance from the
1597origin.</p>
1598
1599<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1600mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1601"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1602</span></span></span><![endif]>Do a single click on the upper left (empty) box
1603of the table. All entries will be colored grey indicating their selection.</p>
1604
1605<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1606mso-list:l0 level1 lfo6'><![if !supportLists]><span style='mso-fareast-font-family:
1607"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1608</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1609style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1610mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>. That
1611should select (grey) 13 out of 52 peak positions in the table and all should be
1612near the top of the list. They will be colored green in the plot. If more are
1613selected then check the map offset – it may need a slight correction.</p>
1614
1615<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1616 id="Picture_x0020_11" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:337.5pt;
1617 height:379.5pt;visibility:visible;mso-wrap-style:square'>
1618 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image017.png" o:title=""/>
1619</v:shape><![endif]--><![if !vml]><img border=0 width=450 height=506
1620src="Charge%20Flipping%20in%20GSAS_files/image018.gif" v:shapes="Picture_x0020_11"><![endif]></span></p>
1621
1622<p class=MsoNormal>These are now ready to turn into atoms. Do <b
1623style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1624mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1625peaks/Move peaks</span></b>. The drawing will show white balls for each of the
1626selected positions and the <b style='mso-bidi-font-weight:normal'><span
1627style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1628mso-hansi-theme-font:minor-latin'>Atoms</span></b> table will now have 13 new H
1629atoms. We are looking for heavier atoms in the formula NaSiO<sub>8</sub>B<sub>3</sub>LiH
1630so 13 atoms should correspond to all but the Li &amp; H atoms.</p>
1631
1632<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1633 id="Picture_x0020_12" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:338.25pt;
1634 height:291.75pt;visibility:visible;mso-wrap-style:square'>
1635 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image019.png" o:title=""
1636  croptop="3527f" cropbottom="24386f" cropleft="38043f" cropright="12462f"/>
1637</v:shape><![endif]--><![if !vml]><img border=0 width=451 height=389
1638src="Charge%20Flipping%20in%20GSAS_files/image020.jpg" v:shapes="Picture_x0020_12"><![endif]></span></p>
1639
1640<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1641 id="Picture_x0020_13" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:525pt;
1642 height:292.5pt;visibility:visible;mso-wrap-style:square'>
1643 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image021.png" o:title=""/>
1644</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=390
1645src="Charge%20Flipping%20in%20GSAS_files/image022.gif" v:shapes="Picture_x0020_13"><![endif]></span></p>
1646
1647<p class=MsoNormal>The atom names indicate the peak magnitude to aid
1648identification (M100 for the largest in the <b style='mso-bidi-font-weight:
1649normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1650minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> table which
1651may not be one of those moved to the <b style='mso-bidi-font-weight:normal'><span
1652style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1653mso-hansi-theme-font:minor-latin'>Atoms</span></b> table). You can hand sort
1654them by selecting a row with the <b style='mso-bidi-font-weight:normal'><span
1655style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1656mso-hansi-theme-font:minor-latin'>Alt</span></b> key down and then selecting a
1657position in the table with the <b style='mso-bidi-font-weight:normal'><span
1658style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1659mso-hansi-theme-font:minor-latin'>Alt</span></b> key still down. My list is now
1660</p>
1661
1662<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1663 id="Picture_x0020_15" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:525pt;
1664 height:295.5pt;visibility:visible;mso-wrap-style:square'>
1665 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image023.png" o:title=""/>
1666</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=394
1667src="Charge%20Flipping%20in%20GSAS_files/image024.gif" v:shapes="Picture_x0020_15"><![endif]></span></p>
1668
1669<p class=MsoNormal>To <span class=GramE>proceed</span> one could select an atom
1670and see its bonding pattern with its neighbors to identify it. Then pick its
1671neighbors and identify them continuing on until all atoms are identified. In my
1672case this would be:</p>
1673
1674<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1675mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1676"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1677</span></span></span><![endif]>Pick M50; it is bonded to 4 neighbors (one is in
1678next cell) as a tetrahedron. Probably Si. Change its Type. The plot will change
1679the green (as selected) ball to a gold colored one (the color assigned to Si).
1680You may have to rock the structure slightly to make the change happen.</p>
1681
1682<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1683mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1684"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1685</span></span></span><![endif]>Pick its neighbors and change them to O atoms. A
1686shift left mouse button on each will select them. The atoms will change from
1687green to red.</p>
1688
1689<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1690mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1691"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1692</span></span></span><![endif]>Pick an O-atom neighbor; it will be a B-atom.</p>
1693
1694<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1695mso-list:l6 level1 lfo8'><![if !supportLists]><span style='mso-fareast-font-family:
1696"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1697</span></span></span><![endif]>And so on until each atom is identified. NB: the
1698Na atom will be relatively isolated.</p>
1699
1700<p class=MsoNormal>When I finished my structure looked like</p>
1701
1702<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1703 id="_x0000_i1035" type="#_x0000_t75" style='width:526.5pt;height:6in;
1704 visibility:visible;mso-wrap-style:square'>
1705 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image025.png" o:title=""
1706  croptop="2450f" cropbottom="26950f" cropleft="39199f" cropright="11167f"/>
1707</v:shape><![endif]--><![if !vml]><img border=0 width=702 height=576
1708src="Charge%20Flipping%20in%20GSAS_files/image026.jpg" v:shapes="_x0000_i1035"><![endif]></span></p>
1709
1710<p class=MsoNormal>The original charge flipping solution is still visible and
1711the atoms are now identified.</p>
1712
1713<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1714 id="Picture_x0020_18" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:525pt;
1715 height:290.25pt;visibility:visible;mso-wrap-style:square'>
1716 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image027.png" o:title=""/>
1717</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=387
1718src="Charge%20Flipping%20in%20GSAS_files/image028.gif" v:shapes="Picture_x0020_18"><![endif]></span></p>
1719
1720<p class=MsoNormal>Interestingly the atoms identified exactly matched with the
1721magnitudes of the charge flip map peaks with Si &amp; Na at the top and B at
1722the bottom.</p>
1723
1724<p class=MsoNormal>Now one can safely remove the map peaks (do <b
1725style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1726mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map
1727peaks/Clear peaks</span></b> in the <b style='mso-bidi-font-weight:normal'><span
1728style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1729mso-hansi-theme-font:minor-latin'>Map peaks</span></b> tab) and clear the
1730charge flip map (do <span class=GramE><b style='mso-bidi-font-weight:normal'><span
1731style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1732mso-hansi-theme-font:minor-latin'>Clear</span></b></span><b style='mso-bidi-font-weight:
1733normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1734minor-latin;mso-hansi-theme-font:minor-latin'> map</span></b> in the <b
1735style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1736mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1737tab). After dressing up the drawing by making the Na atom van der Waals spheres
1738and the rest as balls and sticks I have a nice drawing of the structure
1739(without the Li and H atoms though).</p>
1740
1741<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1742 id="_x0000_i1033" type="#_x0000_t75" style='width:525.75pt;height:398.25pt;
1743 visibility:visible;mso-wrap-style:square'>
1744 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image029.png" o:title=""
1745  croptop="2054f" cropbottom="23166f" cropleft="37518f" cropright="9679f"/>
1746</v:shape><![endif]--><![if !vml]><img border=0 width=701 height=531
1747src="Charge%20Flipping%20in%20GSAS_files/image030.jpg" v:shapes="_x0000_i1033"><![endif]></span></p>
1748
1749<p class=MsoNormal>Save the project file; the next step is to complete the
1750structure by finding the Li and H atoms and then doing the Rietveld refinement
1751on the completed structure.</p>
1752
1753<h2>Step 5 Complete the structure</h2>
1754
1755<p class=MsoNormal>To complete the structure you will need to perform a
1756preliminary Rietveld refinement. This will make the atom positions more
1757accurate and prepare a set of calculated structure factors needed to generate a
1758difference Fourier map good enough to reveal the Li atom position and maybe the
1759H-atom as well. There are a number of steps needed to set all the controls from
1760the previous Pawley refinement to get a successful start for the Rietveld
1761refinement.</p>
1762
1763<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1764mso-list:l4 level1 lfo9'><![if !supportLists]><span style='mso-fareast-font-family:
1765"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1766</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1767style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1768mso-hansi-theme-font:minor-latin'>Instrument Parameters</span></b> entry in the
1769GSAS-II data tree and uncheck all <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'>Refine</span></b> boxes. You don’t want to
1772start with these when the scale factor is unknown.</p>
1773
1774<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1775mso-list:l4 level1 lfo9'><![if !supportLists]><span style='mso-fareast-font-family:
1776"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1777</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1778style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1779mso-hansi-theme-font:minor-latin'>Sample Parameters</span></b> and check the <b
1780style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1781mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Histogram
1782scale factor</span></b> box. This is the scale factor for the data set. You may
1783want to change the <b style='mso-bidi-font-weight:normal'><span
1784style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1785mso-hansi-theme-font:minor-latin'>Goniometer radius</span></b> to 1000. That
1786will put the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1787"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1788minor-latin'>Sample X</span></b> displacement on a proper scale when you refine
1789it later.</p>
1790
1791<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1792mso-list:l4 level1 lfo9'><![if !supportLists]><span style='mso-fareast-font-family:
1793"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1794</span></span></span><![endif]>Go to <b style='mso-bidi-font-weight:normal'><span
1795style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1796mso-hansi-theme-font:minor-latin'>Phases/kryptonite General</span></b> tab and
1797uncheck <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1798mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Refine unit
1799cell</span></b> and <b style='mso-bidi-font-weight:normal'><span
1800style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1801mso-hansi-theme-font:minor-latin'>Do Pawley refinement</span></b> boxes. The
1802latter is most important; if you forget you will just get another Pawley
1803refinement!</p>
1804
1805<p class=MsoNormal>Now do <b style='mso-bidi-font-weight:normal'><span
1806style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1807mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
1808GSAS-II data tree menu; all that was refined is scale and background. I got <span
1809class=GramE>a</span> <span class=SpellE>Rwp</span> ~31%. The plot shows clear
1810intensity differences; the atom positions obviously need refinement.</p>
1811
1812<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1813 id="Picture_x0020_16" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:525pt;
1814 height:450pt;visibility:visible;mso-wrap-style:square'>
1815 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image031.png" o:title=""/>
1816</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=600
1817src="Charge%20Flipping%20in%20GSAS_files/image032.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
1818
1819<p class=MsoNormal>I’ve shifted &amp; zoomed in to make the differences more
1820obvious.</p>
1821
1822<p class=MsoNormal>Go to <b style='mso-bidi-font-weight:normal'><span
1823style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1824mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b> and select the <b
1825style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1826mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
1827tab. The double click the <b style='mso-bidi-font-weight:normal'><span
1828style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1829mso-hansi-theme-font:minor-latin'>refine</span></b> column heading, a dialog
1830box will appear, select the <b style='mso-bidi-font-weight:normal'><span
1831style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1832mso-hansi-theme-font:minor-latin'>X-coordinates</span></b> box and press <b
1833style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1834mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>.
1835The atoms table will show the refinement controls</p>
1836
1837<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1838 id="Picture_x0020_17" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:525pt;
1839 height:225pt;visibility:visible;mso-wrap-style:square'>
1840 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image033.png" o:title=""/>
1841</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
1842src="Charge%20Flipping%20in%20GSAS_files/image034.gif" v:shapes="Picture_x0020_17"><![endif]></span></p>
1843
1844<p class=MsoNormal>Do <b style='mso-bidi-font-weight:normal'><span
1845style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1846mso-hansi-theme-font:minor-latin'>Calculate/Refine </span></b>again; my <span
1847class=SpellE>Rwp</span> is now ~15%. You can now safely refine lattice
1848parameters (in the <b style='mso-bidi-font-weight:normal'><span
1849style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1850mso-hansi-theme-font:minor-latin'>General</span></b> tab for <b
1851style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1852mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite</span></b>)
1853and the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1854mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Instrument
1855parameters</span></b> <b style='mso-bidi-font-weight:normal'><span
1856style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1857mso-hansi-theme-font:minor-latin'>U</span></b>, <b style='mso-bidi-font-weight:
1858normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1859minor-latin;mso-hansi-theme-font:minor-latin'>V</span></b>, <b
1860style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1861mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>W</span></b>,
1862<span class=GramE><b style='mso-bidi-font-weight:normal'><span
1863style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1864mso-hansi-theme-font:minor-latin'>X</span></b></span> &amp; <b
1865style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1866mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Y</span></b>.
1867My refinement improved slightly to Rwp~14.5%. Let’s see if a difference Fourier
1868map will show anything.<br>
1869Go to the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1870mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Phases/kryptonite
1871General</span></b> <span class=GramE>tab ;</span> the <b style='mso-bidi-font-weight:
1872normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1873minor-latin;mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b>
1874are midway down the window.</p>
1875
1876<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1877mso-list:l2 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1878"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1879</span></span></span><![endif]>Select <span class=SpellE><b style='mso-bidi-font-weight:
1880normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1881minor-latin;mso-hansi-theme-font:minor-latin'>delt</span></b></span><b
1882style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1883mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-F</span></b>
1884for the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1885mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b>.</p>
1886
1887<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1888mso-list:l2 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1889"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1890</span></span></span><![endif]>Select <b style='mso-bidi-font-weight:normal'><span
1891style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1892mso-hansi-theme-font:minor-latin'>PWDR 11bmb_6231.fxye Bank 1</span></b> for the
1893<b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1894mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection
1895set from</span></b> item (the only choice). The Fourier calculation will use
1896the structure factors shown in the <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'>Reflection list</span></b> item for this PWDR
1899data set.</p>
1900
1901<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1902mso-list:l2 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1903"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1904</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1905style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1906mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b> from the <b
1907style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1908mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b>
1909tab window. The map will be computed via fast Fourier techniques and is very
1910fast. A few lines summarizing the map is printed on the console, the structure
1911plot may show a single green dot somewhere (it could be hidden beneath an
1912atom!), this is the highest point in the map.</p>
1913
1914<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1915mso-list:l2 level1 lfo10'><![if !supportLists]><span style='mso-fareast-font-family:
1916"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1917</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1918style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1919mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab and adjust the <b
1920style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1921mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Contour
1922level</span></b> slider until something appears on the map.</p>
1923
1924<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1925 id="Picture_x0020_19" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:274.5pt;
1926 height:337.5pt;visibility:visible;mso-wrap-style:square'>
1927 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image035.png" o:title=""/>
1928</v:shape><![endif]--><![if !vml]><img border=0 width=366 height=450
1929src="Charge%20Flipping%20in%20GSAS_files/image036.gif" v:shapes="Picture_x0020_19"><![endif]></span></p>
1930
1931<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1932 id="Picture_x0020_20" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:349.5pt;
1933 height:299.25pt;visibility:visible;mso-wrap-style:square'>
1934 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image037.png" o:title=""
1935  croptop="5231f" cropbottom="8930f" cropleft="11448f" cropright="20374f"/>
1936</v:shape><![endif]--><![if !vml]><img border=0 width=466 height=399
1937src="Charge%20Flipping%20in%20GSAS_files/image038.jpg" v:shapes="Picture_x0020_20"><![endif]></span></p>
1938
1939<p class=MsoNormal>What <span class=GramE>is</span> drawn here are green dots
1940whose size are proportional to the electron density. These are the Li atom
1941positions. There are several ways within GSAS-II to add it to the atom list.
1942One is to do <b style='mso-bidi-font-weight:normal'><span style='font-family:
1943"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1944minor-latin'>Compute/Search map</span></b> in the <b style='mso-bidi-font-weight:
1945normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1946minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> tab and then
1947find them in the <b style='mso-bidi-font-weight:normal'><span style='font-family:
1948"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1949minor-latin'>Map peaks</span></b> tab much the same way we did earlier in this exercise.
1950Another is to get the atom position directly from the map, we will do that now.</p>
1951
1952<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1953mso-list:l3 level1 lfo11'><![if !supportLists]><span style='mso-fareast-font-family:
1954"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1955</span></span></span><![endif]>Go to the <b style='mso-bidi-font-weight:normal'><span
1956style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1957mso-hansi-theme-font:minor-latin'>Phases/kryptonite Atoms</span></b> tab.</p>
1958
1959<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1960mso-list:l3 level1 lfo11'><![if !supportLists]><span style='mso-fareast-font-family:
1961"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1962</span></span></span><![endif]>Using the mouse, position the multicolored cross
1963directly in the center of one of the presumed Li atom peaks. Rotate the drawing
1964around with the left mouse button and shift the cross with the right mouse
1965button. You can zoom in using the roll wheel on the mouse (or else use the <b
1966style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1967mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Camera
1968distance</span></b> slider in the <b style='mso-bidi-font-weight:normal'><span
1969style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1970mso-hansi-theme-font:minor-latin'>Draw Options</span></b> tab if your mouse
1971lacks a wheel).</p>
1972
1973<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1974 id="Picture_x0020_21" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:350.25pt;
1975 height:302.25pt;visibility:visible;mso-wrap-style:square'>
1976 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image039.png" o:title=""
1977  cropbottom="13787f" cropleft="10923f" cropright="20900f"/>
1978</v:shape><![endif]--><![if !vml]><img border=0 width=467 height=403
1979src="Charge%20Flipping%20in%20GSAS_files/image040.jpg" v:shapes="Picture_x0020_21"><![endif]></span></p>
1980
1981<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1982mso-list:l3 level1 lfo11'><![if !supportLists]><span style='mso-fareast-font-family:
1983"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1984</span></span></span><![endif]>Do <b style='mso-bidi-font-weight:normal'><span
1985style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1986mso-hansi-theme-font:minor-latin'>Edit/Insert view point</span></b>, a white
1987ball will appear at the selected position and an H-atom (name = <b
1988style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
1989mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>)
1990will be appended to the end of the atom list.</p>
1991
1992<p class=MsoListParagraph style='margin-left:.75in;text-indent:-.25in;
1993mso-list:l3 level1 lfo11'><![if !supportLists]><span style='mso-fareast-font-family:
1994"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1995</span></span></span><![endif]>Change its <b style='mso-bidi-font-weight:normal'><span
1996style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
1997mso-hansi-theme-font:minor-latin'>Type</span></b> to <b style='mso-bidi-font-weight:
1998normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
1999minor-latin;mso-hansi-theme-font:minor-latin'>Li</span></b>, it will be renamed
2000and the ball color/size will change to that for Li.</p>
2001
2002<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2003 id="Picture_x0020_22" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:348pt;
2004 height:297pt;visibility:visible;mso-wrap-style:square'>
2005 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image041.png" o:title=""
2006  croptop="374f" cropbottom="13600f" cropleft="10817f" cropright="20795f"/>
2007</v:shape><![endif]--><![if !vml]><img border=0 width=464 height=396
2008src="Charge%20Flipping%20in%20GSAS_files/image042.jpg" v:shapes="Picture_x0020_22"><![endif]></span></p>
2009
2010<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2011 id="Picture_x0020_23" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:525pt;
2012 height:225pt;visibility:visible;mso-wrap-style:square'>
2013 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image043.png" o:title=""/>
2014</v:shape><![endif]--><![if !vml]><img border=0 width=700 height=300
2015src="Charge%20Flipping%20in%20GSAS_files/image044.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
2016
2017<p class=MsoNormal>Change the <b style='mso-bidi-font-weight:normal'><span
2018style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2019mso-hansi-theme-font:minor-latin'>refine</span></b> flag to <b
2020style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2021mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b>
2022for the Li atom and repeat <b style='mso-bidi-font-weight:normal'><span
2023style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2024mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> from the main
2025GSAS-II data tree window. My residual <span class=SpellE>Rwp</span> dropped to
2026~11.3%. Next set all <b style='mso-bidi-font-weight:normal'><span
2027style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2028mso-hansi-theme-font:minor-latin'>refine</span></b> flags to <b
2029style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2030mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>XU</span></b>
2031and repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:
2032"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
2033minor-latin'>Calculate/Refine</span></b>. My residual is now <span
2034class=SpellE>Rwp</span> ~10.8%. Maybe we can find the H-atom.</p>
2035
2036<p class=MsoNormal>From the <b style='mso-bidi-font-weight:normal'><span
2037style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2038mso-hansi-theme-font:minor-latin'>General</span></b> tab, Do <b
2039style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2040mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Fourier
2041map</span></b> and adjust the <b style='mso-bidi-font-weight:normal'><span
2042style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:minor-latin;
2043mso-hansi-theme-font:minor-latin'>Contour level</span></b> in the <b
2044style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2045mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw options</span></b>
2046tab.</p>
2047
2048<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
2049 id="Picture_x0020_24" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:348pt;
2050 height:302.25pt;visibility:visible;mso-wrap-style:square'>
2051 <v:imagedata src="Charge%20Flipping%20in%20GSAS_files/image045.png" o:title=""
2052  cropbottom="13413f" cropleft="10818f" cropright="21005f"/>
2053</v:shape><![endif]--><![if !vml]><img border=0 width=464 height=403
2054src="Charge%20Flipping%20in%20GSAS_files/image046.jpg" v:shapes="Picture_x0020_24"><![endif]></span></p>
2055
2056<p class=MsoNormal>I moved the cross to a very interesting feature of the map
2057and zoomed in a bit. This may be the H-atom, <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'>Insert view point</span></b> from
2060the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri","sans-serif";
2061mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b>
2062tab and change 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'>Type</span></b> to <b style='mso-bidi-font-weight:
2065normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2066minor-latin;mso-hansi-theme-font:minor-latin'>H</span></b> (I know it is H
2067already but this step changes the name from <b style='mso-bidi-font-weight:
2068normal'><span style='font-family:"Calibri","sans-serif";mso-ascii-theme-font:
2069minor-latin;mso-hansi-theme-font:minor-latin'>UNK</span></b>). Repeat the Calculate/Refine
2070without varying any of the H-atom parameters; my final <span class=SpellE>Rwp</span>
2071= 10.69% (you don’t get much improvement for adding an H-atom to an oxide
2072structure).</p>
2073
2074</div>
2075
2076</body>
2077
2078</html>
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