source: trunk/help/gsasII.html @ 457

Last change on this file since 457 was 457, checked in by vondreele, 10 years ago

begin distance angle calcs
move gpxfile routines from GSASIIstruct.py to GSASIIIO.py
move getVCov & ValEsd? to GSASIImath.py
add some text to help/gsasII.html

File size: 103.4 KB
Line 
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22<title>Help for GSAS-II</title>
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25  <o:Author>Von Dreele</o:Author>
26  <o:LastAuthor>Von Dreele</o:LastAuthor>
27  <o:Revision>25</o:Revision>
28  <o:TotalTime>1625</o:TotalTime>
29  <o:Created>2011-11-28T16:49:00Z</o:Created>
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377 /* Style Definitions */
378 p.MsoNormal, li.MsoNormal, div.MsoNormal
379        {mso-style-unhide:no;
380        mso-style-qformat:yes;
381        mso-style-parent:"";
382        margin:0in;
383        margin-bottom:.0001pt;
384        mso-pagination:widow-orphan;
385        font-size:12.0pt;
386        font-family:"Times New Roman","serif";
387        mso-fareast-font-family:"Times New Roman";
388        mso-fareast-theme-font:minor-fareast;}
389h1
390        {mso-style-priority:9;
391        mso-style-unhide:no;
392        mso-style-qformat:yes;
393        mso-style-link:"Heading 1 Char";
394        mso-margin-top-alt:auto;
395        margin-right:0in;
396        mso-margin-bottom-alt:auto;
397        margin-left:0in;
398        mso-pagination:widow-orphan;
399        mso-outline-level:1;
400        font-size:24.0pt;
401        font-family:"Times New Roman","serif";
402        mso-fareast-font-family:"Times New Roman";
403        mso-fareast-theme-font:minor-fareast;
404        font-weight:bold;}
405h2
406        {mso-style-priority:9;
407        mso-style-unhide:no;
408        mso-style-qformat:yes;
409        mso-style-link:"Heading 2 Char";
410        mso-margin-top-alt:auto;
411        margin-right:0in;
412        mso-margin-bottom-alt:auto;
413        margin-left:0in;
414        mso-pagination:widow-orphan;
415        mso-outline-level:2;
416        font-size:18.0pt;
417        font-family:"Times New Roman","serif";
418        mso-fareast-font-family:"Times New Roman";
419        mso-fareast-theme-font:minor-fareast;
420        font-weight:bold;}
421h3
422        {mso-style-priority:9;
423        mso-style-unhide:no;
424        mso-style-qformat:yes;
425        mso-style-link:"Heading 3 Char";
426        mso-margin-top-alt:auto;
427        margin-right:0in;
428        mso-margin-bottom-alt:auto;
429        margin-left:0in;
430        mso-pagination:widow-orphan;
431        mso-outline-level:3;
432        font-size:13.5pt;
433        font-family:"Times New Roman","serif";
434        mso-fareast-font-family:"Times New Roman";
435        mso-fareast-theme-font:minor-fareast;
436        font-weight:bold;}
437h4
438        {mso-style-noshow:yes;
439        mso-style-priority:9;
440        mso-style-qformat:yes;
441        mso-style-link:"Heading 4 Char";
442        mso-style-next:Normal;
443        margin-top:10.0pt;
444        margin-right:0in;
445        margin-bottom:0in;
446        margin-left:0in;
447        margin-bottom:.0001pt;
448        mso-pagination:widow-orphan lines-together;
449        page-break-after:avoid;
450        mso-outline-level:4;
451        font-size:13.0pt;
452        font-family:"Cambria","serif";
453        mso-ascii-font-family:Cambria;
454        mso-ascii-theme-font:major-latin;
455        mso-fareast-font-family:"Times New Roman";
456        mso-fareast-theme-font:major-fareast;
457        mso-hansi-font-family:Cambria;
458        mso-hansi-theme-font:major-latin;
459        mso-bidi-font-family:"Times New Roman";
460        mso-bidi-theme-font:major-bidi;
461        color:#4F81BD;
462        mso-themecolor:accent1;
463        font-weight:bold;
464        font-style:italic;}
465h5
466        {mso-style-noshow:yes;
467        mso-style-priority:9;
468        mso-style-qformat:yes;
469        mso-style-link:"Heading 5 Char";
470        mso-margin-top-alt:auto;
471        margin-right:0in;
472        mso-margin-bottom-alt:auto;
473        margin-left:0in;
474        mso-pagination:widow-orphan;
475        mso-outline-level:5;
476        font-size:12.0pt;
477        font-family:"Times New Roman","serif";
478        mso-fareast-font-family:"Times New Roman";
479        mso-fareast-theme-font:minor-fareast;
480        color:#4F4FFF;
481        font-weight:bold;}
482a:link, span.MsoHyperlink
483        {mso-style-noshow:yes;
484        mso-style-priority:99;
485        color:blue;
486        text-decoration:underline;
487        text-underline:single;}
488a:visited, span.MsoHyperlinkFollowed
489        {mso-style-noshow:yes;
490        mso-style-priority:99;
491        color:purple;
492        text-decoration:underline;
493        text-underline:single;}
494p
495        {mso-style-noshow:yes;
496        mso-style-priority:99;
497        mso-margin-top-alt:auto;
498        margin-right:0in;
499        mso-margin-bottom-alt:auto;
500        margin-left:0in;
501        mso-pagination:widow-orphan;
502        font-size:12.0pt;
503        font-family:"Times New Roman","serif";
504        mso-fareast-font-family:"Times New Roman";
505        mso-fareast-theme-font:minor-fareast;}
506pre
507        {mso-style-noshow:yes;
508        mso-style-priority:99;
509        mso-style-link:"HTML Preformatted Char";
510        margin:0in;
511        margin-bottom:.0001pt;
512        mso-pagination:widow-orphan;
513        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;
514        font-size:10.0pt;
515        font-family:"Courier New";
516        mso-fareast-font-family:"Times New Roman";}
517p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
518        {mso-style-noshow:yes;
519        mso-style-priority:99;
520        mso-style-link:"Balloon Text Char";
521        margin:0in;
522        margin-bottom:.0001pt;
523        mso-pagination:widow-orphan;
524        font-size:8.0pt;
525        font-family:"Tahoma","sans-serif";
526        mso-fareast-font-family:"Times New Roman";
527        mso-fareast-theme-font:minor-fareast;}
528span.MsoPlaceholderText
529        {mso-style-noshow:yes;
530        mso-style-priority:99;
531        mso-style-unhide:no;
532        color:gray;}
533p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
534        {mso-style-noshow:yes;
535        mso-style-priority:34;
536        mso-style-unhide:no;
537        mso-style-qformat:yes;
538        margin-top:0in;
539        margin-right:0in;
540        margin-bottom:0in;
541        margin-left:.5in;
542        margin-bottom:.0001pt;
543        mso-add-space:auto;
544        mso-pagination:widow-orphan;
545        font-size:12.0pt;
546        font-family:"Times New Roman","serif";
547        mso-fareast-font-family:"Times New Roman";
548        mso-fareast-theme-font:minor-fareast;}
549p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
550        {mso-style-noshow:yes;
551        mso-style-priority:34;
552        mso-style-unhide:no;
553        mso-style-qformat:yes;
554        mso-style-type:export-only;
555        margin-top:0in;
556        margin-right:0in;
557        margin-bottom:0in;
558        margin-left:.5in;
559        margin-bottom:.0001pt;
560        mso-add-space:auto;
561        mso-pagination:widow-orphan;
562        font-size:12.0pt;
563        font-family:"Times New Roman","serif";
564        mso-fareast-font-family:"Times New Roman";
565        mso-fareast-theme-font:minor-fareast;}
566p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
567        {mso-style-noshow:yes;
568        mso-style-priority:34;
569        mso-style-unhide:no;
570        mso-style-qformat:yes;
571        mso-style-type:export-only;
572        margin-top:0in;
573        margin-right:0in;
574        margin-bottom:0in;
575        margin-left:.5in;
576        margin-bottom:.0001pt;
577        mso-add-space:auto;
578        mso-pagination:widow-orphan;
579        font-size:12.0pt;
580        font-family:"Times New Roman","serif";
581        mso-fareast-font-family:"Times New Roman";
582        mso-fareast-theme-font:minor-fareast;}
583p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
584        {mso-style-noshow:yes;
585        mso-style-priority:34;
586        mso-style-unhide:no;
587        mso-style-qformat:yes;
588        mso-style-type:export-only;
589        margin-top:0in;
590        margin-right:0in;
591        margin-bottom:0in;
592        margin-left:.5in;
593        margin-bottom:.0001pt;
594        mso-add-space:auto;
595        mso-pagination:widow-orphan;
596        font-size:12.0pt;
597        font-family:"Times New Roman","serif";
598        mso-fareast-font-family:"Times New Roman";
599        mso-fareast-theme-font:minor-fareast;}
600span.Heading1Char
601        {mso-style-name:"Heading 1 Char";
602        mso-style-priority:9;
603        mso-style-unhide:no;
604        mso-style-locked:yes;
605        mso-style-link:"Heading 1";
606        mso-ansi-font-size:14.0pt;
607        mso-bidi-font-size:14.0pt;
608        font-family:"Cambria","serif";
609        mso-ascii-font-family:Cambria;
610        mso-ascii-theme-font:major-latin;
611        mso-fareast-font-family:"Times New Roman";
612        mso-fareast-theme-font:major-fareast;
613        mso-hansi-font-family:Cambria;
614        mso-hansi-theme-font:major-latin;
615        mso-bidi-font-family:"Times New Roman";
616        mso-bidi-theme-font:major-bidi;
617        color:#365F91;
618        mso-themecolor:accent1;
619        mso-themeshade:191;
620        font-weight:bold;}
621span.Heading2Char
622        {mso-style-name:"Heading 2 Char";
623        mso-style-noshow:yes;
624        mso-style-priority:9;
625        mso-style-unhide:no;
626        mso-style-locked:yes;
627        mso-style-link:"Heading 2";
628        mso-ansi-font-size:13.0pt;
629        mso-bidi-font-size:13.0pt;
630        font-family:"Cambria","serif";
631        mso-ascii-font-family:Cambria;
632        mso-ascii-theme-font:major-latin;
633        mso-fareast-font-family:"Times New Roman";
634        mso-fareast-theme-font:major-fareast;
635        mso-hansi-font-family:Cambria;
636        mso-hansi-theme-font:major-latin;
637        mso-bidi-font-family:"Times New Roman";
638        mso-bidi-theme-font:major-bidi;
639        color:#4F81BD;
640        mso-themecolor:accent1;
641        font-weight:bold;}
642span.Heading3Char
643        {mso-style-name:"Heading 3 Char";
644        mso-style-noshow:yes;
645        mso-style-priority:9;
646        mso-style-unhide:no;
647        mso-style-locked:yes;
648        mso-style-link:"Heading 3";
649        mso-ansi-font-size:12.0pt;
650        mso-bidi-font-size:12.0pt;
651        font-family:"Cambria","serif";
652        mso-ascii-font-family:Cambria;
653        mso-ascii-theme-font:major-latin;
654        mso-fareast-font-family:"Times New Roman";
655        mso-fareast-theme-font:major-fareast;
656        mso-hansi-font-family:Cambria;
657        mso-hansi-theme-font:major-latin;
658        mso-bidi-font-family:"Times New Roman";
659        mso-bidi-theme-font:major-bidi;
660        color:#4F81BD;
661        mso-themecolor:accent1;
662        font-weight:bold;}
663span.Heading4Char
664        {mso-style-name:"Heading 4 Char";
665        mso-style-noshow:yes;
666        mso-style-priority:9;
667        mso-style-unhide:no;
668        mso-style-locked:yes;
669        mso-style-link:"Heading 4";
670        mso-ansi-font-size:12.0pt;
671        mso-bidi-font-size:12.0pt;
672        font-family:"Cambria","serif";
673        mso-ascii-font-family:Cambria;
674        mso-ascii-theme-font:major-latin;
675        mso-fareast-font-family:"Times New Roman";
676        mso-fareast-theme-font:major-fareast;
677        mso-hansi-font-family:Cambria;
678        mso-hansi-theme-font:major-latin;
679        mso-bidi-font-family:"Times New Roman";
680        mso-bidi-theme-font:major-bidi;
681        color:#4F81BD;
682        mso-themecolor:accent1;
683        font-weight:bold;
684        font-style:italic;}
685span.Heading5Char
686        {mso-style-name:"Heading 5 Char";
687        mso-style-noshow:yes;
688        mso-style-priority:9;
689        mso-style-unhide:no;
690        mso-style-locked:yes;
691        mso-style-link:"Heading 5";
692        mso-ansi-font-size:12.0pt;
693        mso-bidi-font-size:12.0pt;
694        font-family:"Cambria","serif";
695        mso-ascii-font-family:Cambria;
696        mso-ascii-theme-font:major-latin;
697        mso-fareast-font-family:"Times New Roman";
698        mso-fareast-theme-font:major-fareast;
699        mso-hansi-font-family:Cambria;
700        mso-hansi-theme-font:major-latin;
701        mso-bidi-font-family:"Times New Roman";
702        mso-bidi-theme-font:major-bidi;
703        color:#243F60;
704        mso-themecolor:accent1;
705        mso-themeshade:127;}
706span.HTMLPreformattedChar
707        {mso-style-name:"HTML Preformatted Char";
708        mso-style-noshow:yes;
709        mso-style-priority:99;
710        mso-style-unhide:no;
711        mso-style-locked:yes;
712        mso-style-link:"HTML Preformatted";
713        font-family:"Courier New";
714        mso-ascii-font-family:"Courier New";
715        mso-hansi-font-family:"Courier New";
716        mso-bidi-font-family:"Courier New";}
717span.BalloonTextChar
718        {mso-style-name:"Balloon Text Char";
719        mso-style-noshow:yes;
720        mso-style-priority:99;
721        mso-style-unhide:no;
722        mso-style-locked:yes;
723        mso-style-link:"Balloon Text";
724        mso-ansi-font-size:8.0pt;
725        mso-bidi-font-size:8.0pt;
726        font-family:"Tahoma","sans-serif";
727        mso-ascii-font-family:Tahoma;
728        mso-fareast-font-family:"Times New Roman";
729        mso-fareast-theme-font:minor-fareast;
730        mso-hansi-font-family:Tahoma;
731        mso-bidi-font-family:Tahoma;}
732span.SpellE
733        {mso-style-name:"";
734        mso-spl-e:yes;}
735span.GramE
736        {mso-style-name:"";
737        mso-gram-e:yes;}
738.MsoChpDefault
739        {mso-style-type:export-only;
740        mso-default-props:yes;
741        font-size:10.0pt;
742        mso-ansi-font-size:10.0pt;
743        mso-bidi-font-size:10.0pt;}
744@page WordSection1
745        {size:8.5in 11.0in;
746        margin:1.0in 1.0in 1.0in 1.0in;
747        mso-header-margin:.5in;
748        mso-footer-margin:.5in;
749        mso-paper-source:0;}
750div.WordSection1
751        {page:WordSection1;}
752 /* List Definitions */
753 @list l0
754        {mso-list-id:203979460;
755        mso-list-template-ids:88359672;}
756@list l0:level1
757        {mso-level-number-format:bullet;
758        mso-level-text:\F0B7;
759        mso-level-tab-stop:.5in;
760        mso-level-number-position:left;
761        text-indent:-.25in;
762        mso-ansi-font-size:10.0pt;
763        font-family:Symbol;}
764@list l1
765        {mso-list-id:359092647;
766        mso-list-type:hybrid;
767        mso-list-template-ids:1777530928 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
768@list l1:level1
769        {mso-level-tab-stop:none;
770        mso-level-number-position:left;
771        text-indent:-.25in;}
772@list l1:level2
773        {mso-level-tab-stop:1.0in;
774        mso-level-number-position:left;
775        text-indent:-.25in;}
776@list l1:level3
777        {mso-level-tab-stop:1.5in;
778        mso-level-number-position:left;
779        text-indent:-.25in;}
780@list l1:level4
781        {mso-level-tab-stop:2.0in;
782        mso-level-number-position:left;
783        text-indent:-.25in;}
784@list l1:level5
785        {mso-level-tab-stop:2.5in;
786        mso-level-number-position:left;
787        text-indent:-.25in;}
788@list l1:level6
789        {mso-level-tab-stop:3.0in;
790        mso-level-number-position:left;
791        text-indent:-.25in;}
792@list l1:level7
793        {mso-level-tab-stop:3.5in;
794        mso-level-number-position:left;
795        text-indent:-.25in;}
796@list l1:level8
797        {mso-level-tab-stop:4.0in;
798        mso-level-number-position:left;
799        text-indent:-.25in;}
800@list l1:level9
801        {mso-level-tab-stop:4.5in;
802        mso-level-number-position:left;
803        text-indent:-.25in;}
804@list l2
805        {mso-list-id:656106218;
806        mso-list-type:hybrid;
807        mso-list-template-ids:185874704 67698703 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;}
808@list l2:level1
809        {mso-level-tab-stop:none;
810        mso-level-number-position:left;
811        text-indent:-.25in;}
812@list l2:level2
813        {mso-level-tab-stop:1.0in;
814        mso-level-number-position:left;
815        text-indent:-.25in;}
816@list l2:level3
817        {mso-level-tab-stop:1.5in;
818        mso-level-number-position:left;
819        text-indent:-.25in;}
820@list l2:level4
821        {mso-level-tab-stop:2.0in;
822        mso-level-number-position:left;
823        text-indent:-.25in;}
824@list l2:level5
825        {mso-level-tab-stop:2.5in;
826        mso-level-number-position:left;
827        text-indent:-.25in;}
828@list l2:level6
829        {mso-level-tab-stop:3.0in;
830        mso-level-number-position:left;
831        text-indent:-.25in;}
832@list l2:level7
833        {mso-level-tab-stop:3.5in;
834        mso-level-number-position:left;
835        text-indent:-.25in;}
836@list l2:level8
837        {mso-level-tab-stop:4.0in;
838        mso-level-number-position:left;
839        text-indent:-.25in;}
840@list l2:level9
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1046ol
1047        {margin-bottom:0in;}
1048ul
1049        {margin-bottom:0in;}
1050-->
1051</style>
1052<!--[if gte mso 10]>
1053<style>
1054 /* Style Definitions */
1055 table.MsoNormalTable
1056        {mso-style-name:"Table Normal";
1057        mso-tstyle-rowband-size:0;
1058        mso-tstyle-colband-size:0;
1059        mso-style-noshow:yes;
1060        mso-style-priority:99;
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1066        mso-pagination:widow-orphan;
1067        font-size:10.0pt;
1068        font-family:"Times New Roman","serif";}
1069</style>
1070<![endif]-->
1071<link href=gsasIIfav.png rel="SHORTCUT ICON">
1072<!--[if gte mso 9]><xml>
1073 <o:shapedefaults v:ext="edit" spidmax="7170"/>
1074</xml><![endif]--><!--[if gte mso 9]><xml>
1075 <o:shapelayout v:ext="edit">
1076  <o:idmap v:ext="edit" data="1"/>
1077 </o:shapelayout></xml><![endif]-->
1078</head>
1079
1080<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1081
1082<div class=WordSection1>
1083
1084<h1><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600"
1085 o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f"
1086 stroked="f">
1087 <v:stroke joinstyle="miter"/>
1088 <v:formulas>
1089  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
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1104</v:shapetype><v:shape id="Picture_x0020_2" o:spid="_x0000_s1036" type="#_x0000_t75"
1105 alt="GSAS-II logo" style='position:absolute;margin-left:56pt;margin-top:0;
1106 width:96pt;height:96pt;z-index:1;visibility:visible;mso-wrap-style:square;
1107 mso-wrap-distance-left:0;mso-wrap-distance-top:0;mso-wrap-distance-right:0;
1108 mso-wrap-distance-bottom:0;mso-position-horizontal:right;
1109 mso-position-horizontal-relative:text;mso-position-vertical:absolute;
1110 mso-position-vertical-relative:line' o:allowoverlap="f">
1111 <v:imagedata src="gsas2logo.png"/>
1112 <w:wrap type="square" anchory="line"/>
1113</v:shape><![endif]--><![if !vml]><img width=128 height=128 src=gsas2logo.png
1114align=right alt="GSAS-II logo" v:shapes="Picture_x0020_2"><![endif]><span
1115style='mso-fareast-font-family:"Times New Roman"'>Help for GSAS-II<o:p></o:p></span></h1>
1116
1117<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1118is where to find help on various GSAS-II windows and plots. Note that GSAS-II
1119operates with three windows: the main <a href="#Data_tree">GSAS-II data tree</a>
1120window, which provides a hierarchical view of the current project; the <a
1121href="#Data_Frame">GSAS-II data editing</a> window, which shows the contents of
1122a particular section of the project, where values can be examined and changed;
1123and the <a href="#Plots">GSAS-II Plots</a> window, which shows graphical
1124representations of the results. <o:p></o:p></span></p>
1125
1126<div class=MsoNormal align=center style='text-align:center'><span
1127style='mso-fareast-font-family:"Times New Roman"'>
1128
1129<hr size=2 width="100%" align=center>
1130
1131</span></div>
1132
1133<div class=MsoNormal align=center style='text-align:center'><span
1134style='mso-fareast-font-family:"Times New Roman"'>
1135
1136<hr size=2 width="100%" align=center>
1137
1138</span></div>
1139
1140<h2><a name="Data_tree"><span style='mso-fareast-font-family:"Times New Roman"'>1.
1141GSAS-II data tree</span></a><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h2>
1142
1143<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1144is a hierarchical view of the data items in your GSAS-II project (name.gpx).
1145Clicking on any item in the window opens a view where information in that item
1146can be viewed or edited. For example, the <a href="#Sample_Parameters">&quot;Sample
1147Parameters&quot;</a> item contains information about how data were collected,
1148such as the sample temperature <a href="#Sample_Parameters">(see below)</a>. <o:p></o:p></span></p>
1149
1150<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
1151
1152<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1153menus associated with this window provide access to many features of GSAS-II,
1154as outlined below: <o:p></o:p></span></p>
1155
1156<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
1157style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1158style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
1159&#8216;<b style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211;</p>
1160
1161<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1162auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1163style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1164style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1165style='mso-bidi-font-weight:normal'>Open project&#8230;</b> - Open a previously
1166saved GSAS-II project file (name.gpx). If you currently have a project file
1167open, you are asked if it is OK to over write it; Cancel will cancel the
1168process.</p>
1169
1170<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1171auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1172style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1173style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1174style='mso-bidi-font-weight:normal'>Save project</b> &#8211; Save the current
1175project. If a file name is shown after &#8216;Loaded <span class=GramE>Data:&#8217;<span
1176style='mso-fareast-font-family:"Times New Roman"'>,</span></span><span
1177style='mso-fareast-font-family:"Times New Roman"'> it will be saved there.
1178Otherwise, you will be prompted for a new name in a file dialog (you may change
1179directory as well). If the file exists, you will be asked if it OK to
1180overwrite.</span></p>
1181
1182<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1183auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1184style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
1185style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1186style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Save
1187As&#8230;</span></b><span style='mso-fareast-font-family:"Times New Roman"'> -
1188Save the current project to a new file. A file dialog will be shown to enter
1189the name (and change directory if desired). If the file exists, you will be
1190asked if it OK to overwrite.</span></p>
1191
1192<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1193auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1194style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
1195style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1196style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Close
1197project</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
1198&#8211; Close the current project; you will be asked if you want to save it
1199first.</span></p>
1200
1201<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1202auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1203style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
1204style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1205style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Exit</span></b><span
1206style='mso-fareast-font-family:"Times New Roman"'> &#8211; Exit the GSAS-II
1207program; if there is a current project you will be asked if you want to save it
1208first. Pressing the red X in the upper right (Windows) also exits (no save
1209option) GSAS-II; useful for escaping from GSAS-II if needed.</span></p>
1210
1211<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
1212style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1213style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
1214&#8216;<b style='mso-bidi-font-weight:normal'>Data</b>&#8217; &#8211; </p>
1215
1216<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1217auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1218style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1219style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1220style='mso-bidi-font-weight:normal'>Read powder data&#8230;</b> - Read in
1221powder diffraction patterns (multiple patterns can be selected). GSAS-II can
1222read most of the old GSAS powder format files with the position in <span
1223class=SpellE>centidegrees</span> 2-theta. It can also read &#8220;<span
1224class=SpellE>xye</span>&#8221; format files used by <span class=SpellE>topas</span>
1225where the position is in degrees 2-theta. As each file is read, an old GSAS
1226style &#8220;instrument parameter file&#8221; is searched for; if not found a <span
1227class=SpellE>CuK</span><span style='font-family:Symbol'>a</span> laboratory
1228data set is assumed. </p>
1229
1230<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1231auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1232style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1233style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1234style='mso-bidi-font-weight:normal'>Read image data&#8230;</b> - Read in 2-D
1235powder diffraction images (multiple patterns can be selected). GSAS-II can read
1236many different image file formats including MAR345 files, Quantum ADSC files,
1237and tiff files from Perkin-Elmer, Pilatus, and GE. Although many of these
1238formats have data fields that should contain relevant information for the
1239exposure (e.g. wavelength), these are rarely filled in correctly by the data
1240acquisition software. Thus, you should have separately noted this information
1241as it will be needed</p>
1242
1243<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1244auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1245style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
1246style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1247style='mso-bidi-font-weight:normal'>Read Powder Pattern Peaks&#8230;</b> - Read
1248in a list of powder pattern peak positions as either a d-spacing table or a set
1249of 2<span style='font-family:Symbol'>Q</span> positions; these can be used in
1250GSAS-II powder pattern indexing. </p>
1251
1252<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1253auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1254style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
1255style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1256style='mso-bidi-font-weight:normal'>Read single crystal data&#8230;</b> - </p>
1257
1258<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1259auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1260style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
1261style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1262style='mso-bidi-font-weight:normal'>Sum powder data</b> - </p>
1263
1264<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1265auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1266style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
1267style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1268style='mso-bidi-font-weight:normal'>Sum image data</b> - </p>
1269
1270<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1271auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1272style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>g.<span
1273style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1274style='mso-bidi-font-weight:normal'>Add phase</b> - </p>
1275
1276<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1277auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1278style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>h.<span
1279style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1280style='mso-bidi-font-weight:normal'>Delete phase</b> - </p>
1281
1282<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1283auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1284style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>i.<span
1285style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1286</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Rename
1287data</b> - </p>
1288
1289<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1290auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1291style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>j.<span
1292style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1293</span></span></span><![endif]><b style='mso-bidi-font-weight:normal'>Delete
1294data</b> - </p>
1295
1296<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
1297style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1298style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
1299&#8216;<b style='mso-bidi-font-weight:normal'>Calculate</b>&#8217; &#8211; </p>
1300
1301<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1302auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1303style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1304style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1305style='mso-bidi-font-weight:normal'>Make new PDFs</b> - </p>
1306
1307<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1308auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1309style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1310style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1311style='mso-bidi-font-weight:normal'>View LS <span class=SpellE>parms</span></b>
1312- </p>
1313
1314<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1315auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1316style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
1317style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1318style='mso-bidi-font-weight:normal'>Refine</b> - </p>
1319
1320<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1321auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1322style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
1323style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1324style='mso-bidi-font-weight:normal'>Sequential refine</b> - </p>
1325
1326<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1327auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1328style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
1329style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1330style='mso-bidi-font-weight:normal'>Solve</b> - </p>
1331
1332<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
1333style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1334style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
1335&#8216;<b style='mso-bidi-font-weight:normal'>Import</b>&#8217; &#8211; </p>
1336
1337<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1338auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1339style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1340style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1341style='mso-bidi-font-weight:normal'>Import GSAS Exp phase&#8230;</b> - </p>
1342
1343<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1344auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1345style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1346style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1347style='mso-bidi-font-weight:normal'>Import PDB phase&#8230;</b> - </p>
1348
1349<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1350auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1351style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
1352style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1353style='mso-bidi-font-weight:normal'>Import CIF phase&#8230;</b> - </p>
1354
1355<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1356auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1357style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
1358style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1359style='mso-bidi-font-weight:normal'>Import HKLs&#8230;</b> - </p>
1360
1361<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l4 level1 lfo2'><![if !supportLists]><span
1362style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
1363style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Menu
1364&#8216;<b style='mso-bidi-font-weight:normal'>Export</b>&#8217; &#8211;</p>
1365
1366<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1367auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1368style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1369style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1370style='mso-bidi-font-weight:normal'>Export Powder Patterns&#8230;</b> - </p>
1371
1372<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1373auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1374style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1375style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1376style='mso-bidi-font-weight:normal'>Export All Peak Lists&#8230;</b> - </p>
1377
1378<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1379auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1380style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
1381style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1382style='mso-bidi-font-weight:normal'>Export HKLs&#8230;</b> - </p>
1383
1384<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1385auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1386style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
1387style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1388style='mso-bidi-font-weight:normal'>Export PDF&#8230;</b> - </p>
1389
1390<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1391auto;text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1392style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>e.<span
1393style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1394style='mso-bidi-font-weight:normal'>Export Phase&#8230;</b> - </p>
1395
1396<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1397text-indent:-.25in;mso-list:l4 level2 lfo2'><![if !supportLists]><span
1398style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>f.<span
1399style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1400style='mso-bidi-font-weight:normal'>Export CIF&#8230;</b> - </p>
1401
1402<div class=MsoNormal align=center style='text-align:center'><span
1403style='mso-fareast-font-family:"Times New Roman"'>
1404
1405<hr size=2 width="100%" align=center>
1406
1407</span></div>
1408
1409<div class=MsoNormal align=center style='text-align:center'><span
1410style='mso-fareast-font-family:"Times New Roman"'>
1411
1412<hr size=2 width="100%" align=center>
1413
1414</span></div>
1415
1416<h2><a name="Data_Frame"><span style='mso-fareast-font-family:"Times New Roman"'>2.
1417GSAS-II Data Editing Window</span></a><span style='mso-fareast-font-family:
1418"Times New Roman"'><o:p></o:p></span></h2>
1419
1420<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Different
1421information is displayed in the Data Editing Window, depending on which section
1422of the <a href="#Data_tree">data tree</a> is selected. For example, clicking on
1423the &quot;Notebook&quot; entry of the tree brings up the Notebook editing
1424window described below. <o:p></o:p></span></p>
1425
1426<h4><a name=Notebook><span style='mso-fareast-font-family:"Times New Roman"'>Notebook</span></a><span
1427style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
1428
1429<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1430window provides a place for you to enter whatever text commentary you wish.
1431Each time you enter this window, a date/time entry is provided for you. A
1432possibly useful technique is to select a portion of the console window after a
1433refinement completes (it will contain refinement results with residuals, new
1434values &amp; <span class=SpellE>esds</span>) and paste it into this Notebook
1435window so it becomes a part of your project file.<o:p></o:p></span></p>
1436
1437<h4><a name=Controls><span style='mso-fareast-font-family:"Times New Roman"'>Controls</span></a><span
1438style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
1439
1440<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1441window provides the main controls for the major calculations in GSAS-II. At
1442present only Refinement Controls are presented. <o:p></o:p></span></p>
1443
1444<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Two
1445of the main refinement tools are the <span class=SpellE><span class=GramE>fortran</span></span>
1446MINPACK <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
1447algorithms wrapped in python as provided in the <span class=SpellE>Scipy</span>
1448package and a third one is a python version utilizing only the <span
1449class=SpellE>numpy</span> package. The purpose is to </span>minimize the sum of
1450the squares of M<span style='mso-fareast-font-family:"Times New Roman"'>
1451nonlinear functions in N variables by a modification of the <span class=SpellE>Levenberg</span>-Marquardt
1452algorithm. The <span class=SpellE>lmdif</span> and <span class=SpellE>lmder</span>
1453routines were written by </span>Burton S. <span class=SpellE>Garbow</span>,
1454Kenneth E. <span class=SpellE>Hillstrom</span>, <span class=GramE>Jorge</span>
1455J. <span class=GramE>More (Argonne National Laboratory, 1980).</span> The
1456python/numpy version was developed by us based on the material in Numerical
1457Recipes (Press, Flannery, <span class=SpellE><span class=GramE>Teulosky</span></span>
1458&amp; <span class=SpellE>Vetterling</span>) for the <span class=SpellE>Levenberg</span>-Marquardt
1459algorithm.<span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1460
1461<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
1462
1463<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
1464style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1465style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1466style='mso-fareast-font-family:"Times New Roman"'>Select whether the refinement
1467uses &#8216;analytic <span class=SpellE>Jacobian</span>&#8217;, &#8216;analytic
1468Hessian&#8217; or &#8216;numeric&#8217; derivatives. The latter is slower and
1469perhaps a bit less accurate, but may be needed if the analytic functions are
1470not fully developed. The <span class=SpellE>Jacobian</span> matrix is shaped N x
1471M (parameters x observations) and is much larger than the Hessian matrix which
1472is shaped M x M (parameters x parameters). Generally use &#8216;analytic
1473Hessian&#8217; for routine work.<o:p></o:p></span></p>
1474
1475<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
1476style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1477style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1478style='mso-fareast-font-family:"Times New Roman"'>Select &#8216;Min
1479delta-M/M&#8217; for convergence; the refinement will stop when the change in
1480the minimization function is less than this value. Set Min delta-M/M = 1.0 to
1481force just a single cycle to be performed. A value less than 10<sup>-4</sup>
1482(the default) generally gives no better result. The allowed range is 10<sup>-9</sup>
1483to 1.0.<o:p></o:p></span></p>
1484
1485<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
1486style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span
1487style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1488style='mso-fareast-font-family:"Times New Roman"'>If &#8216;analytic Jacobean&#8217;
1489is chosen then select &#8216;Initial shift factor&#8217; for the first cycle of
1490refinement. This value is modified by the least squares routine. The allowed
1491range is 10<sup>-5</sup> to 100. Smaller values may be needed if your initial <span
1492class=GramE>refinement</span> trials immediately diverge, however make sure
1493your starting parameter values are &#8216;reasonable&#8217;. The selected
1494default (=1.0) normally gives good performance.<o:p></o:p></span></p>
1495
1496<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
1497style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>4.<span
1498style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1499style='mso-fareast-font-family:"Times New Roman"'>If &#8216;analytic Hessian&#8217;
1500is chosen then select &#8216;Max cycles&#8217;, the maximum number of least
1501squares cycles to be performed. Choices are given in the pull down selection;
1502the default is 3 cycles.<o:p></o:p></span></p>
1503
1504<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l5 level1 lfo4'><![if !supportLists]><span
1505style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>5.<span
1506style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1507style='mso-fareast-font-family:"Times New Roman"'>Select data for sequential
1508refinement; the data sets may be done in &#8216;reverse order&#8217;. <o:p></o:p></span></p>
1509
1510<h4><span style='mso-fareast-font-family:"Times New Roman"'>Covariance<o:p></o:p></span></h4>
1511
1512<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1513window is blank; the GSASII Plots window &#8216;<a href="#Covariance">Covariance&#8217;</a>
1514shows a graphical representation of the variance-covariance matrix <o:p></o:p></span></p>
1515
1516<h4><a name=Constraints><span style='mso-fareast-font-family:"Times New Roman"'>Constraints<o:p></o:p></span></a></h4>
1517
1518<span style='mso-bookmark:Constraints'></span>
1519
1520<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1521window shows the constraints to be used in a refinement. It is organized into
1522three tabbed pages. &#8216;Phase constraints&#8217; contain those involving
1523parameters that describe aspects of the crystalline phases to be used in the
1524refinement (e.g. atom coordinates, thermal motion and site fraction
1525parameters). &#8216;Histogram/Phase constraints&#8217; are those which describe
1526aspects of the pattern that depend on both the phase and the data set used in
1527the refinement (e.g. </span><span style='font-family:Symbol;mso-fareast-font-family:
1528"Times New Roman"'>m</span><span style='mso-fareast-font-family:"Times New Roman"'>strain
1529and crystallite size parameters). &#8216;Histogram constraints&#8217; are those
1530that depend only on the data set (e.g. profile coefficients U<span class=GramE>,V,W,X</span>
1531and Y).<o:p></o:p></span></p>
1532
1533<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
1534
1535<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l6 level1 lfo6'><![if !supportLists]><span
1536style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1537style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1538style='mso-fareast-font-family:"Times New Roman"'>Select the tab for the
1539parameter types you wish to constrain. Each will have the same possibilities in
1540the &#8216;Edit menu.<o:p></o:p></span></p>
1541
1542<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l6 level1 lfo6'><![if !supportLists]><span
1543style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1544style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1545style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
1546style='mso-bidi-font-weight:normal'>Edit</b>&#8217; &#8211; <o:p></o:p></span></p>
1547
1548<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1549auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
1550style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>a.<span
1551style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1552class=GramE><b style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:
1553"Times New Roman"'>Add</span></b></span><b style='mso-bidi-font-weight:normal'><span
1554style='mso-fareast-font-family:"Times New Roman"'> Hold</span></b><span
1555style='mso-fareast-font-family:"Times New Roman"'> &#8211; select a parameter
1556that you wish to remain fixed although other parameters of the same type may be
1557selected as a group for refinement. For example, if the space group for a phase
1558has a polar axis (e.g. the b-axis in P2<sub>1</sub>), then one atom y-parameter
1559is arbitrary and should be selected for a Hold to keep the structure from
1560drifting up or down the y-axis during refinement. If selected, a dialog box
1561will appear showing the list of available parameters; select one and then OK to
1562implement it, Cancel will cancel the operation. The held parameter will be
1563shown in the constraint window with the keyword &#8216;FIXED&#8217;. A Delete
1564button can be used to remove it.<o:p></o:p></span></p>
1565
1566<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1567auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
1568style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>b.<span
1569style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1570style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
1571equivalence</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
1572&#8211; select a list of parameters that should have the same value (possibly
1573with a non-unitary multiplier for some). Examples are a list of atoms with the
1574same thermal motion <span class=SpellE>Uiso</span>, sets of profile
1575coefficients U<span class=GramE>,V,W</span> across multiple data sets. If
1576selected, a dialog box will appear with a list of the available parameters.
1577Select one and press OK; a second dialog box will appear with only those
1578parameters that can be made equivalent to the first one. Choose those and press
1579OK. Cancel in either dialog will cancel the operation. The equivalenced
1580parameters will show as an equation of the form M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>=0;
1581usually M1=1.0 and M2=-1.0, but can be changed via the &#8216;Edit&#8217;
1582button. The keyword &#8216;EQUIV&#8217; marks it as <span class=GramE>an
1583equivalence</span>. A Delete button can be used to remove it.<o:p></o:p></span></p>
1584
1585<p class=MsoListParagraphCxSpMiddle style='margin-left:1.0in;mso-add-space:
1586auto;text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
1587style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>c.<span
1588style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1589style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
1590constraint</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
1591&#8211; select a list of parameters whose sum (with possible non-unitary
1592multipliers) is fixed. For example, the sum of site fractions for atoms on the
1593same site could be fixed to unity. If selected, a dialog box will appear with a
1594list of the available parameters. Select one and press OK; a second dialog box
1595will appear with only those parameters that can be used in a constraint with
1596the first one. Choose those and press OK. Cancel in either dialog will cancel
1597the operation. The equivalenced parameters will show as an equation of the form
1598M<sub>1</sub>*P<sub>1</sub>+M<sub>2</sub>*P<sub>2</sub>+&#8230;=C; the multipliers
1599M1, <span class=GramE>M2, &#8230;</span> and C can be changed via the
1600&#8216;Edit&#8217; button. The keyword &#8216;CONSTR&#8217; marks it as a
1601constraint. A Delete button can be used to remove it.<o:p></o:p></span></p>
1602
1603<p class=MsoListParagraphCxSpLast style='margin-left:1.0in;mso-add-space:auto;
1604text-indent:-.25in;mso-list:l6 level2 lfo6'><![if !supportLists]><span
1605style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>d.<span
1606style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><b
1607style='mso-bidi-font-weight:normal'><span style='mso-fareast-font-family:"Times New Roman"'>Add
1608function</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
1609&#8211; this is very similar the &#8220;Add constraint&#8221; type except that
1610the result of the sum can be varied in the refinement. The keyword
1611&#8216;FUNCT&#8217; marks it as a function; the &#8216;Refine?&#8217; box
1612indicates your choice to refine the result of the sum. A Delete button can be
1613used to remove it.<o:p></o:p></span></p>
1614
1615<h4><a name=Restraints><span style='mso-fareast-font-family:"Times New Roman"'>Restraints</span></a><span
1616style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
1617
1618<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1619window... <o:p></o:p></span></p>
1620
1621<h4><a name=Limits><span style='mso-fareast-font-family:"Times New Roman"'>Limits</span></a><span
1622style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></h4>
1623
1624<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1625window shows the limits in position to be used in any fitting for this powder
1626pattern. The &#8216;original&#8217; values are obtained from the minimum &amp;
1627maximum values in the powder pattern. You can modify &#8216;changed&#8217; as
1628needed.<o:p></o:p></span></p>
1629
1630<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
1631
1632<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l1 level1 lfo8'><![if !supportLists]><span
1633style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1634style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1635style='mso-fareast-font-family:"Times New Roman"'>Menu &#8216;<b
1636style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
1637style='mso-bidi-font-weight:normal'>Copy</b> - this copies the limits shown to
1638other selected powder patterns. If used, a dialog box (Copy Limits) will appear
1639showing the list of available powder patterns, you can copy the limits to any
1640or all of them; select &#8216;All&#8217; to copy them to all patterns. Then
1641select &#8216;OK&#8217; to do the copy; &#8216;Cancel&#8217; to cancel the
1642operation.<o:p></o:p></span></p>
1643
1644<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l1 level1 lfo8'><![if !supportLists]><span
1645style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span
1646style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
1647style='mso-fareast-font-family:"Times New Roman"'>You can change <span
1648class=SpellE>Tmin</span> and <span class=SpellE>Tmax</span> in the
1649&#8216;changed&#8217; row as needed. Use the mouse to select the value to be
1650changed (the background on the box will be blue or have a black border or a
1651vertical bar will appear in the value), then enter the new value and press
1652Enter or click the mouse elsewhere in the Background window. This will set the
1653new value.<o:p></o:p></span></p>
1654
1655<h4><span style='mso-fareast-font-family:"Times New Roman"'>Texture Control
1656Window<o:p></o:p></span></h4>
1657
1658<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1659window... <o:p></o:p></span></p>
1660
1661<h4><span style='mso-fareast-font-family:"Times New Roman"'>Image Masks<o:p></o:p></span></h4>
1662
1663<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1664window... <o:p></o:p></span></p>
1665
1666<h4><span style='mso-fareast-font-family:"Times New Roman"'>Atoms Control
1667Window<o:p></o:p></span></h4>
1668
1669<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1670window... <o:p></o:p></span></p>
1671
1672<h3><span style='mso-fareast-font-family:"Times New Roman"'>Diffraction Data
1673Control Window<o:p></o:p></span></h3>
1674
1675<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1676window... <o:p></o:p></span></p>
1677
1678<h3><span style='mso-fareast-font-family:"Times New Roman"'>Draw Atoms Control
1679Window<o:p></o:p></span></h3>
1680
1681<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1682window... <o:p></o:p></span></p>
1683
1684<h3><span style='mso-fareast-font-family:"Times New Roman"'>Pawley Control
1685Window<o:p></o:p></span></h3>
1686
1687<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1688window... <o:p></o:p></span></p>
1689
1690<h3><a name=Images><span style='mso-fareast-font-family:"Times New Roman"'>Images
1691Control<o:p></o:p></span></a></h3>
1692
1693<span style='mso-bookmark:Images'></span>
1694
1695<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1696window... <o:p></o:p></span></p>
1697
1698<h3><span style='mso-fareast-font-family:"Times New Roman"'>PDF Controls
1699Control Window<o:p></o:p></span></h3>
1700
1701<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1702window... <o:p></o:p></span></p>
1703
1704<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1705
1706<h3>Phase Windows</h3>
1707
1708<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>When
1709a phase is selected from the <a href="#Data_tree">data tree</a>, parameters are
1710show from that selected phase in a tabbed window. Clicking on the tab raises
1711the windows listed below. <o:p></o:p></span></p>
1712
1713<h4><a name=General><u>General</u> Phase Parameters</a></h4>
1714
1715<span style='mso-bookmark:General'></span>
1716
1717<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
1718is used for overall parameters describing the phase such as the space group,
1719the unit cell parameters and overall parameters for the atom present in the
1720phase. <a name=Data><o:p></o:p></a></span></p>
1721
1722<h4><span style='mso-bookmark:Data'>Sample <u>Data</u></span></h4>
1723
1724<span style='mso-bookmark:Data'></span>
1725
1726<h4><a name=Texture><u>Texture</u> Parameters</a></h4>
1727
1728<h4><span style='mso-bookmark:Texture'><a name=Atoms><u>Atom</u> Parameter<u>s</u></a></span></h4>
1729
1730<span style='mso-bookmark:Atoms'></span>
1731
1732<h4><span style='mso-bookmark:Texture'><a name="Draw_Options"><u>Draw Options</u></a></span></h4>
1733
1734<span style='mso-bookmark:Draw_Options'></span>
1735
1736<h4><span style='mso-bookmark:Texture'><a name="Draw_Atoms"><u>Draw Atoms</u></a></span></h4>
1737
1738<span style='mso-bookmark:Draw_Atoms'></span>
1739
1740<h3><span style='mso-bookmark:Texture'>Powder Histogram Windows</span></h3>
1741
1742<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1743"Times New Roman"'>When a powder diffraction data set (histogram) is selected
1744from the </span></span><a href="#Data_tree"><span style='mso-bookmark:Texture'><span
1745style='mso-fareast-font-family:"Times New Roman"'>data tree</span></span><span
1746style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
1747style='mso-fareast-font-family:"Times New Roman"'>, a variety of subcategories
1748in the tree are shown. The items that are shown depend on the data set type.
1749Selecting a subcategory raises the window listed below. <o:p></o:p></span></span></p>
1750
1751<h4><span style='mso-bookmark:Texture'><a name=Comments></a><a name=""></a><span
1752style='mso-bookmark:Comments'><u>Comments</u></span></span></h4>
1753
1754<span style='mso-bookmark:Comments'></span>
1755
1756<h4><span style='mso-bookmark:Texture'><a name=Background><span
1757style='mso-fareast-font-family:"Times New Roman"'>Background</span></a></span><span
1758style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1759
1760<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1761"Times New Roman"'>This window shows the choice of background function and
1762coefficients to be used in fitting this powder pattern.<o:p></o:p></span></span></p>
1763
1764<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1765"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
1766
1767<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
1768style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
1769"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1770</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Menu
1771&#8216;<b style='mso-bidi-font-weight:normal'>File</b>&#8217; &#8211; <b
1772style='mso-bidi-font-weight:normal'>Copy</b> &#8211; this copies the background
1773parameters shown to other selected powder patterns. If used, a dialog box (Copy
1774Parameters) will appear showing the list of available powder patterns, you can
1775copy the background parameters to any or all of them; select &#8216;All&#8217;
1776to copy them to all patterns. Then select &#8216;OK&#8217; to do the copy;
1777&#8216;Cancel&#8217; to cancel the operation.<o:p></o:p></span></span></p>
1778
1779<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
1780style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
1781"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1782</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
1783can select a different Background function from the pull down tab.<o:p></o:p></span></span></p>
1784
1785<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
1786style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
1787"Times New Roman"'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1788</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
1789can choose to refine/not refine the background coefficients.<o:p></o:p></span></span></p>
1790
1791<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
1792style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
1793"Times New Roman"'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1794</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
1795can select the number of background coefficients to be used (1-36).<o:p></o:p></span></span></p>
1796
1797<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l7 level1 lfo10'><span
1798style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
1799"Times New Roman"'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1800</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
1801can change individual background coefficient values. Enter the value then press
1802Enter or click the mouse elsewhere in the Background window. This will set the
1803new value.<o:p></o:p></span></span></p>
1804
1805<h4><span style='mso-bookmark:Texture'><a name="Instrument_Parameters"><span
1806style='mso-fareast-font-family:"Times New Roman"'>Instrument Parameters</span></a></span><span
1807style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1808
1809<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1810"Times New Roman"'>This window... <o:p></o:p></span></span></p>
1811
1812<h4><span style='mso-bookmark:Texture'><a name="Sample_Parameters"><span
1813style='mso-fareast-font-family:"Times New Roman"'>Sample Parameters</span></a></span><span
1814style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1815
1816<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1817"Times New Roman"'>This window... <o:p></o:p></span></span></p>
1818
1819<h4><span style='mso-bookmark:Texture'><a name="Peak_List"></a><a
1820name="Powder_Peaks"><span style='mso-bookmark:Peak_List'><span
1821style='mso-fareast-font-family:"Times New Roman"'>Peak List</span></span></a></span><span
1822style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1823
1824<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1825"Times New Roman"'>This window shows the list of peaks that will be used by the
1826peak fitting refinement. It is filled by picking peaks in the powder pattern
1827displayed in the GSASII Plots window as a sequence of &#8216;+&#8217; marks.
1828See </span></span><a href="#Powder_Patterns"><span style='mso-bookmark:Texture'><span
1829style='mso-fareast-font-family:"Times New Roman"'>Powder Patterns</span></span><span
1830style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
1831style='mso-fareast-font-family:"Times New Roman"'> below for details for what
1832can be done on this plot.<o:p></o:p></span></span></p>
1833
1834<h4><span style='mso-bookmark:Texture'><a name="Index_Peaks"><span
1835style='mso-fareast-font-family:"Times New Roman"'>Index Peak List</span></a></span><span
1836style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1837
1838<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1839"Times New Roman"'>This window shows the list of peaks that will be used for
1840indexing (see </span></span><a href="#Unit_Cells_List"><span style='mso-bookmark:
1841Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Unit Cells
1842List</span></span><span style='mso-bookmark:Texture'></span></a><span
1843style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>).
1844It must be filled before indexing can proceed. When indexing is completed, this
1845display will show the resulting <span class=SpellE>hkl</span> values for every
1846indexed reflection along with the calculated d-spacing (&#8216;d-<span
1847class=SpellE>calc</span>&#8217;) for the selected unit cell in </span></span><a
1848href="#Unit_Cells_List"><span style='mso-bookmark:Texture'><span
1849style='mso-fareast-font-family:"Times New Roman"'>Unit Cells List</span></span><span
1850style='mso-bookmark:Texture'></span></a><span style='mso-bookmark:Texture'><span
1851style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></span></p>
1852
1853<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1854"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
1855
1856<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l3 level1 lfo12'><span
1857style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
1858"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1859</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>Menu
1860&#8216;<b style='mso-bidi-font-weight:normal'>Operations</b>&#8217; &#8211; <b
1861style='mso-bidi-font-weight:normal'>Load/Reload</b> &#8211; loads the peak
1862positions &amp; intensities from the </span></span><a href="#Peak_List"><span
1863style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Peak
1864List</span></span><span style='mso-bookmark:Texture'></span></a><span
1865style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
1866to make them available for the indexing routine. The d-<span class=SpellE>obs</span>
1867is obtained from Bragg&#8217;s Law after applying the Zero correction shown on
1868the </span></span><a href="#Instrument_Parameters"><span style='mso-bookmark:
1869Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Instrument
1870Parameters</span></span><span style='mso-bookmark:Texture'></span></a><span
1871style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
1872table to the position shown here.<o:p></o:p></span></span></p>
1873
1874<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l3 level1 lfo12'><span
1875style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
1876"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1877</span></span></span><![endif]><span style='mso-fareast-font-family:"Times New Roman"'>You
1878may deselect individual peaks from indexing by <span class=SpellE>unchecking</span>
1879the corresponding &#8216;use&#8217; box.<o:p></o:p></span></span></p>
1880
1881<h4><span style='mso-bookmark:Texture'><a name="Cell_Indexing_Refine"><span
1882style='mso-fareast-font-family:"Times New Roman"'>Unit Cells List</span></a></span><span
1883style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1884
1885<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1886"Times New Roman"'>This window... <o:p></o:p></span></span></p>
1887
1888<h4><span style='mso-bookmark:Texture'><a name="Reflection_List"><span
1889style='mso-fareast-font-family:"Times New Roman"'>Reflection List</span></a></span><span
1890style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1891
1892<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1893"Times New Roman"'>This window... <o:p></o:p></span></span></p>
1894
1895<div class=MsoNormal align=center style='text-align:center'><span
1896style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
1897
1898<hr size=2 width="100%" align=center>
1899
1900</span></span></div>
1901
1902<div class=MsoNormal align=center style='text-align:center'><span
1903style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'>
1904
1905<hr size=2 width="100%" align=center>
1906
1907</span></span></div>
1908
1909<h2><span style='mso-bookmark:Texture'><a name=Plots><span style='mso-fareast-font-family:
1910"Times New Roman"'>3. GSAS-II Plots Window</span></a></span><span
1911style='mso-bookmark:Plots'></span><span style='mso-bookmark:Texture'><span
1912style='mso-fareast-font-family:"Times New Roman";font-weight:normal'> </span></span><span
1913style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h2>
1914
1915<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1916"Times New Roman"'>This window presents all the graphical material as a
1917multipage tabbed set of plots utilizing the <span class=SpellE>matplotlib</span>
1918python package. Each page has a tool bar (at bottom in Windows) with the
1919controls<o:p></o:p></span></span></p>
1920
1921<p class=MsoNormal><span style='mso-bookmark:Texture'></span><span
1922style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman";
1923mso-no-proof:yes'><img border=0 width=225 height=31 id="_x0000_i1032"
1924src=graphbar.jpg></span></span><span style='mso-bookmark:Texture'><span
1925style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></p>
1926
1927<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1928"Times New Roman"'>These are Home, Back, Forward, Pan, Zoom, Save and Help,
1929respectively. <o:p></o:p></span></span></p>
1930
1931<ul type=disc>
1932 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
1933     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
1934     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Home:
1935     returns the plot to the initial scaling <o:p></o:p></span></span></li>
1936 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
1937     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
1938     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Back:
1939     returns the plot to the previous scaling <o:p></o:p></span></span></li>
1940 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
1941     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
1942     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Forward:
1943     reverses the action in the previous press(es) of the Back button <o:p></o:p></span></span></li>
1944 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
1945     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
1946     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Pan:
1947     allows you to control panning across the plot (press left mouse button)
1948     and zooming (press right mouse button), <o:p></o:p></span></span></li>
1949 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
1950     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
1951     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Zoom:
1952     allows you to select a portion of the plot (press right mouse button &amp;
1953     drag for zoom box) for the next plot. <o:p></o:p></span></span></li>
1954 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
1955     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
1956     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Save:
1957     allows you to save the currently displayed plot in one of several
1958     graphical formats suitable for printing or insertion in a document. The <o:p></o:p></span></span></li>
1959 <li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
1960     mso-list:l0 level1 lfo13;tab-stops:list .5in'><span style='mso-bookmark:
1961     Texture'><span style='mso-fareast-font-family:"Times New Roman"'>Help:
1962     accesses GSASII help on the specific plot type. <o:p></o:p></span></span></li>
1963</ul>
1964
1965<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1966"Times New Roman"'><o:p>&nbsp;</o:p></span></span></p>
1967
1968<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1969"Times New Roman"'>Below the toolbar may be a status bar that on the left may
1970show either an instruction for a keyed input or a pull down selection of keyed
1971input; on the right may be displayed position dependent information that is
1972updated as the mouse is moved over the plot region.<o:p></o:p></span></span></p>
1973
1974<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1975"Times New Roman"'><o:p>&nbsp;</o:p></span></span></p>
1976
1977<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1978"Times New Roman"'>The specific types of plots that are pages in the GSASII
1979Plots windows are next.<o:p></o:p></span></span></p>
1980
1981<h4><span style='mso-bookmark:Texture'><a name="Powder_Patterns"><span
1982style='mso-fareast-font-family:"Times New Roman"'>Powder Patterns</span></a></span><span
1983style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1984
1985<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1986"Times New Roman"'>The powder patterns that are part of your project are shown
1987on this page. They can be displayed as a stack of powder patterns, just a
1988single pattern or as a contour image of the peak intensities. What can be done
1989here will depend on which is displayed and on which item in the GSAS-II data
1990tree you have selected.<o:p></o:p></span></span></p>
1991
1992<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
1993"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
1994
1995<h4><span style='mso-bookmark:Texture'><a name=Covariance><span
1996style='mso-fareast-font-family:"Times New Roman"'>Covariance</span></a></span><span
1997style='mso-bookmark:Texture'><span style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></span></h4>
1998
1999<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2000"Times New Roman"'>The variance-covariance matrix as a color coded array is
2001shown on this page. The color bar to the right shows the range of <span
2002class=SpellE>covariances</span> (-1 to 1) and corresponding colors. The
2003parameter names are to the right and the parameter numbers are below the plot.<o:p></o:p></span></span></p>
2004
2005<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2006"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
2007
2008<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l2 level1 lfo15'><span
2009style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
2010"Times New Roman"'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2011</span></span></span><![endif]>Move the mouse cursor across the plot. If on a
2012diagonal cell, the parameter name, value and <span class=SpellE>esd</span> is
2013shown both as a tool tip and in the right hand portion of the status bar. If
2014the cursor is off the diagonal, the two parameter names and their covariance
2015are shown in the tool tip and the status bar.</span></p>
2016
2017<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l2 level1 lfo15'><span
2018style='mso-bookmark:Texture'><![if !supportLists]><span style='mso-fareast-font-family:
2019"Times New Roman"'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
2020</span></span></span><![endif]><span class=GramE>Type &#8216;s&#8217;</span>
2021&#8211; A color scheme selection dialog is shown. Select a color scheme and
2022press <span class=GramE>OK,</span> the new color scheme will be plotted. The
2023default is &#8216;<span class=SpellE>RdYlGn</span>&#8217;.</span></p>
2024
2025<h4><span style='mso-bookmark:Texture'><a name="Structure_Factors"><span
2026style='mso-fareast-font-family:"Times New Roman"'>Structure Factors </span></a></span></h4>
2027
2028<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2029"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
2030
2031<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2032"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
2033
2034<h4><span style='mso-bookmark:Texture'><a name="Powder_Lines"><span
2035style='mso-fareast-font-family:"Times New Roman"'>Powder Lines </span></a></span></h4>
2036
2037<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2038"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
2039
2040<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2041"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
2042
2043<h4><span style='mso-bookmark:Texture'><a name="Peak_Widths"><span
2044style='mso-fareast-font-family:"Times New Roman"'>Peak Widths </span></a></span></h4>
2045
2046<p class=MsoNormal><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2047"Times New Roman"'>This plot shows... <o:p></o:p></span></span></p>
2048
2049<h5><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2050"Times New Roman"'>What can I do here?<o:p></o:p></span></span></h5>
2051
2052<h4><span style='mso-bookmark:Texture'><span style='mso-fareast-font-family:
2053"Times New Roman"'>Texture </span></span></h4>
2054
2055<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2056plot shows... <o:p></o:p></span></p>
2057
2058<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2059
2060<h4><a name="Sequential_refinement"><span style='mso-fareast-font-family:"Times New Roman"'>Sequential
2061refinement </span></a></h4>
2062
2063<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2064plot shows... <o:p></o:p></span></p>
2065
2066<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2067
2068<h4><a name="2D_Powder_Image"><span style='mso-fareast-font-family:"Times New Roman"'>2D
2069Powder Image </span></a></h4>
2070
2071<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2072plot shows... <o:p></o:p></span></p>
2073
2074<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2075
2076<h4><a name="2D_Integration"><span style='mso-fareast-font-family:"Times New Roman"'>2D
2077Integration </span></a></h4>
2078
2079<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2080plot shows... <o:p></o:p></span></p>
2081
2082<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2083
2084<h4><a name="2D_Transformed_Powder_Image"><span style='mso-fareast-font-family:
2085"Times New Roman"'>2D Transformed Powder Image </span></a></h4>
2086
2087<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2088plot shows... <o:p></o:p></span></p>
2089
2090<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2091
2092<h4><a name=Mustrain><span style='mso-fareast-font-family:"Times New Roman"'>Mustrain
2093</span></a></h4>
2094
2095<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2096plot shows... <o:p></o:p></span></p>
2097
2098<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2099
2100<h4><a name=Size><span style='mso-fareast-font-family:"Times New Roman"'>Size </span></a></h4>
2101
2102<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2103plot shows... <o:p></o:p></span></p>
2104
2105<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2106
2107<h4><a name="Preferred_orientation"><span style='mso-fareast-font-family:"Times New Roman"'>Preferred
2108Orientation </span></a></h4>
2109
2110<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2111plot shows... <o:p></o:p></span></p>
2112
2113<h5><span style='mso-fareast-font-family:"Times New Roman"'>What can I do here?<o:p></o:p></span></h5>
2114
2115<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2116
2117<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2118
2119<div class=MsoNormal align=center style='text-align:center'><span
2120style='mso-fareast-font-family:"Times New Roman"'>
2121
2122<hr size=2 width="100%" align=center>
2123
2124</span></div>
2125
2126<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><!-- hhmts start -->Last
2127modified: Tue Nov 22 13:19:47 CST 2011 <o:p></o:p></span></p>
2128
2129<!-- hhmts end --></div>
2130
2131</body>
2132
2133</html>
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