source: Tutorials/RietPlot/PublicationPlot.htm @ 3696

Last change on this file since 3696 was 3598, checked in by toby, 3 years ago

add publ plotting tutorial

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25  <o:Author>Von Dreele</o:Author>
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382        mso-font-signature:0 268435456 0 0 -2147483648 0;}
383@font-face
384        {font-family:"MS Mincho";
385        mso-font-charset:78;
386        mso-generic-font-family:auto;
387        mso-font-pitch:variable;
388        mso-font-signature:-536870145 1791491579 18 0 131231 0;}
389@font-face
390        {font-family:"MS Mincho";
391        mso-font-charset:78;
392        mso-generic-font-family:auto;
393        mso-font-pitch:variable;
394        mso-font-signature:-536870145 1791491579 18 0 131231 0;}
395@font-face
396        {font-family:Cambria;
397        panose-1:2 4 5 3 5 4 6 3 2 4;
398        mso-font-charset:0;
399        mso-generic-font-family:auto;
400        mso-font-pitch:variable;
401        mso-font-signature:-536870145 1073743103 0 0 415 0;}
402@font-face
403        {font-family:Tahoma;
404        panose-1:2 11 6 4 3 5 4 4 2 4;
405        mso-font-charset:0;
406        mso-generic-font-family:auto;
407        mso-font-pitch:variable;
408        mso-font-signature:-520082689 -1073717157 41 0 66047 0;}
409 /* Style Definitions */
410p.MsoNormal, li.MsoNormal, div.MsoNormal
411        {mso-style-unhide:no;
412        mso-style-qformat:yes;
413        mso-style-parent:"";
414        margin:0in;
415        margin-bottom:.0001pt;
416        mso-pagination:widow-orphan;
417        font-size:12.0pt;
418        font-family:"Times New Roman";
419        mso-fareast-font-family:"MS Mincho";
420        mso-fareast-theme-font:minor-fareast;}
421h1
422        {mso-style-priority:9;
423        mso-style-unhide:no;
424        mso-style-qformat:yes;
425        mso-style-link:"Heading 1 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:1;
432        font-size:24.0pt;
433        font-family:"Times New Roman";
434        mso-fareast-font-family:"MS Mincho";
435        mso-fareast-theme-font:minor-fareast;
436        font-weight:bold;}
437h2
438        {mso-style-noshow:yes;
439        mso-style-priority:9;
440        mso-style-qformat:yes;
441        mso-style-link:"Heading 2 Char";
442        mso-margin-top-alt:auto;
443        margin-right:0in;
444        mso-margin-bottom-alt:auto;
445        margin-left:0in;
446        mso-pagination:widow-orphan;
447        mso-outline-level:2;
448        font-size:18.0pt;
449        font-family:"Times New Roman";
450        mso-fareast-font-family:"MS Mincho";
451        mso-fareast-theme-font:minor-fareast;
452        font-weight:bold;}
453h3
454        {mso-style-noshow:yes;
455        mso-style-priority:9;
456        mso-style-qformat:yes;
457        mso-style-link:"Heading 3 Char";
458        mso-margin-top-alt:auto;
459        margin-right:0in;
460        mso-margin-bottom-alt:auto;
461        margin-left:0in;
462        mso-pagination:widow-orphan;
463        mso-outline-level:3;
464        font-size:13.5pt;
465        font-family:"Times New Roman";
466        mso-fareast-font-family:"MS Mincho";
467        mso-fareast-theme-font:minor-fareast;
468        font-weight:bold;}
469h4
470        {mso-style-noshow:yes;
471        mso-style-priority:9;
472        mso-style-qformat:yes;
473        mso-style-link:"Heading 4 Char";
474        mso-style-next:Normal;
475        margin-top:10.0pt;
476        margin-right:0in;
477        margin-bottom:0in;
478        margin-left:0in;
479        margin-bottom:.0001pt;
480        mso-pagination:widow-orphan lines-together;
481        page-break-after:avoid;
482        mso-outline-level:4;
483        font-size:13.0pt;
484        font-family:Calibri;
485        mso-ascii-font-family:Calibri;
486        mso-ascii-theme-font:major-latin;
487        mso-fareast-font-family:"MS Gothic";
488        mso-fareast-theme-font:major-fareast;
489        mso-hansi-font-family:Calibri;
490        mso-hansi-theme-font:major-latin;
491        mso-bidi-font-family:"Times New Roman";
492        mso-bidi-theme-font:major-bidi;
493        color:#4F81BD;
494        mso-themecolor:accent1;
495        font-weight:bold;
496        font-style:italic;}
497h5
498        {mso-style-noshow:yes;
499        mso-style-priority:9;
500        mso-style-qformat:yes;
501        mso-style-link:"Heading 5 Char";
502        mso-margin-top-alt:auto;
503        margin-right:0in;
504        mso-margin-bottom-alt:auto;
505        margin-left:0in;
506        mso-pagination:widow-orphan;
507        mso-outline-level:5;
508        font-size:12.0pt;
509        font-family:"Times New Roman";
510        mso-fareast-font-family:"MS Mincho";
511        mso-fareast-theme-font:minor-fareast;
512        color:#4F4FFF;
513        font-weight:bold;}
514p.MsoTitle, li.MsoTitle, div.MsoTitle
515        {mso-style-noshow:yes;
516        mso-style-priority:10;
517        mso-style-unhide:no;
518        mso-style-qformat:yes;
519        mso-style-link:"Title Char";
520        mso-style-next:Normal;
521        margin-top:0in;
522        margin-right:0in;
523        margin-bottom:15.0pt;
524        margin-left:0in;
525        mso-add-space:auto;
526        mso-pagination:widow-orphan;
527        border:none;
528        mso-border-bottom-alt:solid #4F81BD 1.0pt;
529        mso-border-bottom-themecolor:accent1;
530        padding:0in;
531        mso-padding-alt:0in 0in 4.0pt 0in;
532        font-size:26.0pt;
533        font-family:Calibri;
534        mso-ascii-font-family:Calibri;
535        mso-ascii-theme-font:major-latin;
536        mso-fareast-font-family:"MS Gothic";
537        mso-fareast-theme-font:major-fareast;
538        mso-hansi-font-family:Calibri;
539        mso-hansi-theme-font:major-latin;
540        mso-bidi-font-family:"Times New Roman";
541        mso-bidi-theme-font:major-bidi;
542        color:#17365D;
543        mso-themecolor:text2;
544        mso-themeshade:191;
545        letter-spacing:.25pt;
546        mso-font-kerning:14.0pt;}
547p.MsoTitleCxSpFirst, li.MsoTitleCxSpFirst, div.MsoTitleCxSpFirst
548        {mso-style-noshow:yes;
549        mso-style-priority:10;
550        mso-style-unhide:no;
551        mso-style-qformat:yes;
552        mso-style-link:"Title Char";
553        mso-style-next:Normal;
554        mso-style-type:export-only;
555        margin:0in;
556        margin-bottom:.0001pt;
557        mso-add-space:auto;
558        mso-pagination:widow-orphan;
559        border:none;
560        mso-border-bottom-alt:solid #4F81BD 1.0pt;
561        mso-border-bottom-themecolor:accent1;
562        padding:0in;
563        mso-padding-alt:0in 0in 4.0pt 0in;
564        font-size:26.0pt;
565        font-family:Calibri;
566        mso-ascii-font-family:Calibri;
567        mso-ascii-theme-font:major-latin;
568        mso-fareast-font-family:"MS Gothic";
569        mso-fareast-theme-font:major-fareast;
570        mso-hansi-font-family:Calibri;
571        mso-hansi-theme-font:major-latin;
572        mso-bidi-font-family:"Times New Roman";
573        mso-bidi-theme-font:major-bidi;
574        color:#17365D;
575        mso-themecolor:text2;
576        mso-themeshade:191;
577        letter-spacing:.25pt;
578        mso-font-kerning:14.0pt;}
579p.MsoTitleCxSpMiddle, li.MsoTitleCxSpMiddle, div.MsoTitleCxSpMiddle
580        {mso-style-noshow:yes;
581        mso-style-priority:10;
582        mso-style-unhide:no;
583        mso-style-qformat:yes;
584        mso-style-link:"Title Char";
585        mso-style-next:Normal;
586        mso-style-type:export-only;
587        margin:0in;
588        margin-bottom:.0001pt;
589        mso-add-space:auto;
590        mso-pagination:widow-orphan;
591        border:none;
592        mso-border-bottom-alt:solid #4F81BD 1.0pt;
593        mso-border-bottom-themecolor:accent1;
594        padding:0in;
595        mso-padding-alt:0in 0in 4.0pt 0in;
596        font-size:26.0pt;
597        font-family:Calibri;
598        mso-ascii-font-family:Calibri;
599        mso-ascii-theme-font:major-latin;
600        mso-fareast-font-family:"MS Gothic";
601        mso-fareast-theme-font:major-fareast;
602        mso-hansi-font-family:Calibri;
603        mso-hansi-theme-font:major-latin;
604        mso-bidi-font-family:"Times New Roman";
605        mso-bidi-theme-font:major-bidi;
606        color:#17365D;
607        mso-themecolor:text2;
608        mso-themeshade:191;
609        letter-spacing:.25pt;
610        mso-font-kerning:14.0pt;}
611p.MsoTitleCxSpLast, li.MsoTitleCxSpLast, div.MsoTitleCxSpLast
612        {mso-style-noshow:yes;
613        mso-style-priority:10;
614        mso-style-unhide:no;
615        mso-style-qformat:yes;
616        mso-style-link:"Title Char";
617        mso-style-next:Normal;
618        mso-style-type:export-only;
619        margin-top:0in;
620        margin-right:0in;
621        margin-bottom:15.0pt;
622        margin-left:0in;
623        mso-add-space:auto;
624        mso-pagination:widow-orphan;
625        border:none;
626        mso-border-bottom-alt:solid #4F81BD 1.0pt;
627        mso-border-bottom-themecolor:accent1;
628        padding:0in;
629        mso-padding-alt:0in 0in 4.0pt 0in;
630        font-size:26.0pt;
631        font-family:Calibri;
632        mso-ascii-font-family:Calibri;
633        mso-ascii-theme-font:major-latin;
634        mso-fareast-font-family:"MS Gothic";
635        mso-fareast-theme-font:major-fareast;
636        mso-hansi-font-family:Calibri;
637        mso-hansi-theme-font:major-latin;
638        mso-bidi-font-family:"Times New Roman";
639        mso-bidi-theme-font:major-bidi;
640        color:#17365D;
641        mso-themecolor:text2;
642        mso-themeshade:191;
643        letter-spacing:.25pt;
644        mso-font-kerning:14.0pt;}
645a:link, span.MsoHyperlink
646        {mso-style-priority:99;
647        color:blue;
648        text-decoration:underline;
649        text-underline:single;}
650a:visited, span.MsoHyperlinkFollowed
651        {mso-style-noshow:yes;
652        mso-style-priority:99;
653        color:purple;
654        text-decoration:underline;
655        text-underline:single;}
656p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
657        {mso-style-noshow:yes;
658        mso-style-priority:99;
659        mso-style-link:"Document Map Char";
660        margin:0in;
661        margin-bottom:.0001pt;
662        mso-pagination:widow-orphan;
663        font-size:8.0pt;
664        font-family:Tahoma;
665        mso-fareast-font-family:"MS Mincho";
666        mso-fareast-theme-font:minor-fareast;}
667p
668        {mso-style-noshow:yes;
669        mso-style-priority:99;
670        mso-margin-top-alt:auto;
671        margin-right:0in;
672        mso-margin-bottom-alt:auto;
673        margin-left:0in;
674        mso-pagination:widow-orphan;
675        font-size:12.0pt;
676        font-family:"Times New Roman";
677        mso-fareast-font-family:"MS Mincho";
678        mso-fareast-theme-font:minor-fareast;}
679pre
680        {mso-style-noshow:yes;
681        mso-style-priority:99;
682        mso-style-link:"HTML Preformatted Char";
683        margin:0in;
684        margin-bottom:.0001pt;
685        mso-pagination:widow-orphan;
686        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;
687        font-size:10.0pt;
688        font-family:"Courier New";
689        mso-fareast-font-family:"Times New Roman";}
690p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
691        {mso-style-noshow:yes;
692        mso-style-priority:99;
693        mso-style-link:"Balloon Text Char";
694        margin:0in;
695        margin-bottom:.0001pt;
696        mso-pagination:widow-orphan;
697        font-size:8.0pt;
698        font-family:Tahoma;
699        mso-fareast-font-family:"MS Mincho";
700        mso-fareast-theme-font:minor-fareast;}
701span.MsoPlaceholderText
702        {mso-style-noshow:yes;
703        mso-style-priority:99;
704        mso-style-unhide:no;
705        color:gray;}
706p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
707        {mso-style-noshow:yes;
708        mso-style-priority:1;
709        mso-style-unhide:no;
710        mso-style-qformat:yes;
711        mso-style-parent:"";
712        margin:0in;
713        margin-bottom:.0001pt;
714        mso-pagination:widow-orphan;
715        font-size:12.0pt;
716        font-family:"Times New Roman";
717        mso-fareast-font-family:"MS Mincho";
718        mso-fareast-theme-font:minor-fareast;}
719p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
720        {mso-style-noshow:yes;
721        mso-style-priority:34;
722        mso-style-unhide:no;
723        mso-style-qformat:yes;
724        margin-top:0in;
725        margin-right:0in;
726        margin-bottom:0in;
727        margin-left:.5in;
728        margin-bottom:.0001pt;
729        mso-add-space:auto;
730        mso-pagination:widow-orphan;
731        font-size:12.0pt;
732        font-family:"Times New Roman";
733        mso-fareast-font-family:"MS Mincho";
734        mso-fareast-theme-font:minor-fareast;}
735p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst
736        {mso-style-noshow:yes;
737        mso-style-priority:34;
738        mso-style-unhide:no;
739        mso-style-qformat:yes;
740        mso-style-type:export-only;
741        margin-top:0in;
742        margin-right:0in;
743        margin-bottom:0in;
744        margin-left:.5in;
745        margin-bottom:.0001pt;
746        mso-add-space:auto;
747        mso-pagination:widow-orphan;
748        font-size:12.0pt;
749        font-family:"Times New Roman";
750        mso-fareast-font-family:"MS Mincho";
751        mso-fareast-theme-font:minor-fareast;}
752p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle
753        {mso-style-noshow:yes;
754        mso-style-priority:34;
755        mso-style-unhide:no;
756        mso-style-qformat:yes;
757        mso-style-type:export-only;
758        margin-top:0in;
759        margin-right:0in;
760        margin-bottom:0in;
761        margin-left:.5in;
762        margin-bottom:.0001pt;
763        mso-add-space:auto;
764        mso-pagination:widow-orphan;
765        font-size:12.0pt;
766        font-family:"Times New Roman";
767        mso-fareast-font-family:"MS Mincho";
768        mso-fareast-theme-font:minor-fareast;}
769p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast
770        {mso-style-noshow:yes;
771        mso-style-priority:34;
772        mso-style-unhide:no;
773        mso-style-qformat:yes;
774        mso-style-type:export-only;
775        margin-top:0in;
776        margin-right:0in;
777        margin-bottom:0in;
778        margin-left:.5in;
779        margin-bottom:.0001pt;
780        mso-add-space:auto;
781        mso-pagination:widow-orphan;
782        font-size:12.0pt;
783        font-family:"Times New Roman";
784        mso-fareast-font-family:"MS Mincho";
785        mso-fareast-theme-font:minor-fareast;}
786span.MsoIntenseReference
787        {mso-style-priority:32;
788        mso-style-unhide:no;
789        mso-style-qformat:yes;
790        font-variant:small-caps;
791        color:#C0504D;
792        mso-themecolor:accent2;
793        letter-spacing:.25pt;
794        font-weight:bold;
795        text-decoration:underline;
796        text-underline:single;}
797span.Heading1Char
798        {mso-style-name:"Heading 1 Char";
799        mso-style-priority:9;
800        mso-style-unhide:no;
801        mso-style-locked:yes;
802        mso-style-link:"Heading 1";
803        mso-ansi-font-size:24.0pt;
804        mso-bidi-font-size:24.0pt;
805        font-family:"Times New Roman";
806        mso-ascii-font-family:"Times New Roman";
807        mso-fareast-font-family:"MS Mincho";
808        mso-fareast-theme-font:minor-fareast;
809        mso-hansi-font-family:"Times New Roman";
810        mso-bidi-font-family:"Times New Roman";
811        mso-font-kerning:18.0pt;
812        font-weight:bold;}
813span.Heading2Char
814        {mso-style-name:"Heading 2 Char";
815        mso-style-noshow:yes;
816        mso-style-priority:9;
817        mso-style-unhide:no;
818        mso-style-locked:yes;
819        mso-style-link:"Heading 2";
820        mso-ansi-font-size:18.0pt;
821        mso-bidi-font-size:18.0pt;
822        font-family:"Times New Roman";
823        mso-ascii-font-family:"Times New Roman";
824        mso-fareast-font-family:"MS Mincho";
825        mso-fareast-theme-font:minor-fareast;
826        mso-hansi-font-family:"Times New Roman";
827        mso-bidi-font-family:"Times New Roman";
828        font-weight:bold;}
829span.Heading3Char
830        {mso-style-name:"Heading 3 Char";
831        mso-style-noshow:yes;
832        mso-style-priority:9;
833        mso-style-unhide:no;
834        mso-style-locked:yes;
835        mso-style-link:"Heading 3";
836        mso-ansi-font-size:13.5pt;
837        mso-bidi-font-size:13.5pt;
838        font-family:"Times New Roman";
839        mso-ascii-font-family:"Times New Roman";
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1250
1251<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1252
1253<div class=WordSection1>
1254
1255<h1>Create a Publication-Ready Rietveld Plot </h1>
1256
1257<p class=MsoNormal>In this exercise a plot will be created in a form intended
1258for publication from a “finished” refinement in GSAS-II.</p>
1259
1260<h2>Step 1: Read in the project file</h2>
1261
1262<p class=MsoListParagraph style='text-indent:-.25in;mso-list:l1 level1 lfo2'><![if !supportLists]><span
1263style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span
1264style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]>Use
1265the <b style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
1266mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:
1267Cambria;mso-bidi-theme-font:minor-latin'>File/Open Project</span></b> menu item
1268to GSAS-II project file <span class=SpellE>PubPlotTest.gpx</span>. (If you used
1269<span style='mso-fareast-font-family:Cambria;mso-fareast-theme-font:minor-latin'>the
1270</span><b style='mso-bidi-font-weight:normal'><span style='font-family:Cambria;
1271mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Cambria;mso-fareast-theme-font:
1272minor-latin;mso-hansi-theme-font:minor-latin'>Help/Download tutorial</span></b><span
1273style='mso-fareast-font-family:Cambria;mso-fareast-theme-font:minor-latin'>
1274menu entry to open this page with the recommended downloading of the exercise
1275files, then the you should see this file in the file browser. If not, you can
1276manually download it from <a
1277href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RietPlot/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RietPlot/data/</a>;
1278in this case you will need to navigate to the download location manually.)<br
1279style='mso-special-character:line-break'>
1280<![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
1281<![endif]></span></p>
1282
1283<p class=MsoNormal>At this point the <b style='mso-bidi-font-weight:normal'><span
1284style='font-family:Cambria;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1285minor-latin;mso-bidi-font-family:Cambria;mso-bidi-theme-font:minor-latin'>GSAS-II
1286data tree</span></b> window will have several entries. If the PWDR entry is not
1287selected (as below), click on it. <span style="mso-spacerun:yes"> </span></p>
1288
1289<p class=MsoNormal><span style='mso-no-proof:yes'><o:p>&nbsp;</o:p></span></p>
1290
1291<p class=MsoNormal><span style="mso-spacerun:yes"> </span><span
1292style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype id="_x0000_t75"
1293 coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe"
1294 filled="f" stroked="f">
1295 <v:stroke joinstyle="miter"/>
1296 <v:formulas>
1297  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1298  <v:f eqn="sum @0 1 0"/>
1299  <v:f eqn="sum 0 0 @1"/>
1300  <v:f eqn="prod @2 1 2"/>
1301  <v:f eqn="prod @3 21600 pixelWidth"/>
1302  <v:f eqn="prod @3 21600 pixelHeight"/>
1303  <v:f eqn="sum @0 0 1"/>
1304  <v:f eqn="prod @6 1 2"/>
1305  <v:f eqn="prod @7 21600 pixelWidth"/>
1306  <v:f eqn="sum @8 21600 0"/>
1307  <v:f eqn="prod @7 21600 pixelHeight"/>
1308  <v:f eqn="sum @10 21600 0"/>
1309 </v:formulas>
1310 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1311 <o:lock v:ext="edit" aspectratio="t"/>
1312</v:shapetype><v:shape id="Picture_x0020_30" o:spid="_x0000_i1033" type="#_x0000_t75"
1313 style='width:481pt;height:311pt;visibility:visible;mso-wrap-style:square'>
1314 <v:imagedata src="PublicationPlot_files/image001.png" o:title=""/>
1315</v:shape><![endif]--><![if !vml]><img border=0 width=483 height=313
1316src="PublicationPlot_files/image002.png" v:shapes="Picture_x0020_30"><![endif]><o:p></o:p></span></p>
1317
1318<p class=MsoNormal><span style='mso-no-proof:yes'><span
1319style="mso-spacerun:yes"> </span></span></p>
1320
1321<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1322
1323<p class=MsoNormal><span class=GramE>and</span> the plot window will show the
1324powder pattern along with the fit:</p>
1325
1326<p class=MsoNormal><span style="mso-spacerun:yes"> </span><span
1327style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_34"
1328 o:spid="_x0000_i1032" type="#_x0000_t75" style='width:408pt;height:341pt;
1329 visibility:visible;mso-wrap-style:square'>
1330 <v:imagedata src="PublicationPlot_files/image003.png" o:title=""/>
1331</v:shape><![endif]--><![if !vml]><img border=0 width=410 height=343
1332src="PublicationPlot_files/image004.png" v:shapes="Picture_x0020_34"><![endif]></span></p>
1333
1334<h2>Step 2: Format Plot </h2>
1335
1336<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_35" o:spid="_x0000_s1030"
1337 type="#_x0000_t75" style='position:absolute;margin-left:-17.1pt;margin-top:1053pt;
1338 width:34.1pt;height:32pt;z-index:251658240;visibility:visible;
1339 mso-wrap-style:square;mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;
1340 mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0;
1341 mso-position-horizontal:right;mso-position-horizontal-relative:margin;
1342 mso-position-vertical:absolute;mso-position-vertical-relative:margin'>
1343 <v:imagedata src="PublicationPlot_files/image005.png" o:title=""/>
1344 <w:wrap type="square" anchorx="margin" anchory="margin"/>
1345</v:shape><![endif]--><![if !vml]><img width=36 height=34
1346src="PublicationPlot_files/image006.png" align=right hspace=9 v:shapes="Picture_x0020_35"><![endif]>The
1347plot above can be improved a bit, for example by moving the difference curve
1348down so it can be seen more clearly. First click on the <span
1349style="mso-spacerun:yes"> </span>“Shrink Y” yellow tool bar button (shown to
1350right) to make some room at the bottom of the plot. </p>
1351
1352<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1353
1354<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_36" o:spid="_x0000_s1029"
1355 type="#_x0000_t75" style='position:absolute;margin-left:-7.8pt;margin-top:1in;
1356 width:43.4pt;height:24.3pt;z-index:251659264;visibility:visible;
1357 mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
1358 mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1359 mso-wrap-distance-bottom:0;mso-position-horizontal:right;
1360 mso-position-horizontal-relative:margin;mso-position-vertical:absolute;
1361 mso-position-vertical-relative:margin;mso-width-percent:0;
1362 mso-height-percent:0;mso-width-relative:margin;mso-height-relative:margin'>
1363 <v:imagedata src="PublicationPlot_files/image007.png" o:title=""/>
1364 <w:wrap type="square" anchorx="margin" anchory="margin"/>
1365</v:shape><![endif]--><![if !vml]><img width=45 height=26
1366src="PublicationPlot_files/image008.png" align=right hspace=9 v:shapes="Picture_x0020_36"><![endif]>Make
1367sure that the zoom or pan buttons are not selected. Then click with the left
1368mouse button on the cyan different curve and while holding the button down,
1369drag the difference curve down a little bit. This will now be too close to the
1370blue reflection tick marks, so they can be dragged down as well, by clicking on
1371them, moving the mouse with the button down and releasing the button when the
1372tick marks are in the chosen spot. Note that if the drag operation does not
1373work, then zoom or pan mode is very likely selected, or the PWDR item has not
1374been selected from the tree. </p>
1375
1376<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1377
1378<p class=MsoNormal>We can make the plot a bit more compact, by either using “Zoom”
1379to draw a box around the region to be displayed or by pressing the “Home”
1380button. I used zoom to get this:</p>
1381
1382<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1383 id="Picture_x0020_38" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:411pt;
1384 height:351pt;visibility:visible;mso-wrap-style:square'>
1385 <v:imagedata src="PublicationPlot_files/image009.png" o:title=""/>
1386</v:shape><![endif]--><![if !vml]><img border=0 width=413 height=353
1387src="PublicationPlot_files/image010.png" v:shapes="Picture_x0020_38"><![endif]></span></p>
1388
1389<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1390
1391<h2>Step 3: Magnification Regions <o:p></o:p></h2>
1392
1393<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_62" o:spid="_x0000_s1028"
1394 type="#_x0000_t75" style='position:absolute;margin-left:74.8pt;margin-top:549pt;
1395 width:126pt;height:68.5pt;z-index:251660288;visibility:visible;
1396 mso-wrap-style:square;mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;
1397 mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0;
1398 mso-position-horizontal:right;mso-position-horizontal-relative:margin;
1399 mso-position-vertical:absolute;mso-position-vertical-relative:margin'>
1400 <v:imagedata src="PublicationPlot_files/image011.png" o:title=""/>
1401 <w:wrap type="square" anchorx="margin" anchory="margin"/>
1402</v:shape><![endif]--><![if !vml]><img width=128 height=71
1403src="PublicationPlot_files/image012.png" align=right hspace=9 v:shapes="Picture_x0020_62"><![endif]>While
1404not particularly important for the plot above, <span class=GramE>many datasets
1405are dominated by a few intense peaks</span> and it can be of significant value
1406to increase the scale in other regions. <span class=GramE>To add magnification via
1407the mouse, first turn off the zoom mode, if on.</span> Move the mouse to around
140860 degrees (vertically, anywhere inside the axes) and press “a” to add a
1409magnification region. A line appears on the plot and a magnification region is
1410added to the data window, as shown to right. Another way to add magnification
1411is with the “Add a magnification region” button. Press that to add a second
1412region. This adds a region starting somewhere around the middle of the pattern.
1413Change the location of this to around 40 degrees, if needed and the magnification
1414factors to 1.5 and 2.5 respectively. The window and plot will look as below.</p>
1415
1416<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1417 id="Picture_x0020_63" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:480pt;
1418 height:308pt;visibility:visible;mso-wrap-style:square'>
1419 <v:imagedata src="PublicationPlot_files/image013.png" o:title=""/>
1420</v:shape><![endif]--><![if !vml]><img border=0 width=482 height=310
1421src="PublicationPlot_files/image014.png" v:shapes="Picture_x0020_63"><![endif]></span><span
1422style="mso-spacerun:yes"> </span><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1423 id="Picture_x0020_65" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:435pt;
1424 height:372pt;visibility:visible;mso-wrap-style:square'>
1425 <v:imagedata src="PublicationPlot_files/image015.png" o:title=""/>
1426</v:shape><![endif]--><![if !vml]><img border=0 width=437 height=374
1427src="PublicationPlot_files/image016.png" v:shapes="Picture_x0020_65"><![endif]></span></p>
1428
1429<h2>Step 4: Customize the Publication Plot<o:p></o:p></h2>
1430
1431<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_66" o:spid="_x0000_s1027"
1432 type="#_x0000_t75" style='position:absolute;margin-left:-33pt;margin-top:45pt;
1433 width:18.2pt;height:25.45pt;z-index:251661312;visibility:visible;
1434 mso-wrap-style:square;mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;
1435 mso-wrap-distance-right:9pt;mso-wrap-distance-bottom:0;
1436 mso-position-horizontal:right;mso-position-horizontal-relative:margin;
1437 mso-position-vertical:absolute;mso-position-vertical-relative:margin'>
1438 <v:imagedata src="PublicationPlot_files/image017.png" o:title=""/>
1439 <w:wrap type="square" anchorx="margin" anchory="margin"/>
1440</v:shape><![endif]--><![if !vml]><img width=20 height=27
1441src="PublicationPlot_files/image018.png" align=right hspace=9 v:shapes="Picture_x0020_66"><![endif]>Press
1442the “P” button to the right of the toolbar. This opens a window where aspects
1443of the plot can be customized, as below. Note that as changes are made in the
1444controls at the top of the window, these changes are displayed immediately.
1445Also note the addition of <span class=GramE>a</span> additional difference plot
1446at the bottom. This shows the weighted difference between the observed and
1447calculated diffraction pattern ([<span class=SpellE>obs-cal</span>]/sigma); the
1448square of this is what is actually minimized. </p>
1449
1450<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1451 id="Picture_x0020_67" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:498pt;
1452 height:487pt;visibility:visible;mso-wrap-style:square'>
1453 <v:imagedata src="PublicationPlot_files/image019.png" o:title=""/>
1454</v:shape><![endif]--><![if !vml]><img border=0 width=500 height=489
1455src="PublicationPlot_files/image020.png" v:shapes="Picture_x0020_67"><![endif]></span></p>
1456
1457<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1458
1459<p class=MsoNormal>As examples of the types of changes that can be made here: </p>
1460
1461<p class=MsoListParagraphCxSpFirst style='text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
1462style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1463Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1464</span></span></span><![endif]>Most journals will want larger lettering for
1465labels so change the text size to 18</p>
1466
1467<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
1468style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1469Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1470</span></span></span><![endif]>We can use <span class=SpellE>LaTeX</span>
1471symbols in the phase caption, so let’s change that to $\<span class=SpellE>rm</span>\alpha-LaB_6$
1472</p>
1473
1474<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
1475style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1476Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1477</span></span></span><![endif]>Click on “Include in legend” for <span
1478class=SpellE>obs</span> and <span class=SpellE>calc</span> to include them in
1479the legend</p>
1480
1481<p class=MsoListParagraphCxSpMiddle style='text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
1482style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1483Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1484</span></span></span><![endif]>Click on the cyan square for the diff color and
1485choose something more to your liking (brown here)</p>
1486
1487<p class=MsoListParagraphCxSpLast style='text-indent:-.25in;mso-list:l0 level1 lfo7'><![if !supportLists]><span
1488style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1489Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
1490</span></span></span><![endif]>Make the symbols and lines a bit more visible
1491(when the plot is shrunk) by changing the symbols to an “x”, the size to 10, <span
1492class=GramE>the</span> line widths to 1.5 and the tick width to 2.5. </p>
1493
1494<p class=MsoNormal>The plot now appears as below:</p>
1495
1496<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1497 id="Picture_x0020_68" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:501pt;
1498 height:496pt;visibility:visible;mso-wrap-style:square'>
1499 <v:imagedata src="PublicationPlot_files/image021.png" o:title=""/>
1500</v:shape><![endif]--><![if !vml]><img border=0 width=503 height=498
1501src="PublicationPlot_files/image022.png" v:shapes="Picture_x0020_68"><![endif]></span></p>
1502
1503<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1504
1505<p class=MsoNormal><!--[if gte vml 1]><v:shape id="Picture_x0020_69" o:spid="_x0000_s1026"
1506 type="#_x0000_t75" style='position:absolute;margin-left:60.1pt;margin-top:0;
1507 width:111.3pt;height:115.8pt;z-index:251662336;visibility:visible;
1508 mso-wrap-style:square;mso-width-percent:0;mso-height-percent:0;
1509 mso-wrap-distance-left:9pt;mso-wrap-distance-top:0;mso-wrap-distance-right:9pt;
1510 mso-wrap-distance-bottom:0;mso-position-horizontal:right;
1511 mso-position-horizontal-relative:margin;mso-position-vertical:top;
1512 mso-position-vertical-relative:margin;mso-width-percent:0;
1513 mso-height-percent:0;mso-width-relative:margin;mso-height-relative:margin'>
1514 <v:imagedata src="PublicationPlot_files/image023.png" o:title=""/>
1515 <w:wrap type="square" anchorx="margin" anchory="margin"/>
1516</v:shape><![endif]--><![if !vml]><img width=113 height=118
1517src="PublicationPlot_files/image024.png" align=right hspace=9 v:shapes="Picture_x0020_69"><![endif]>The
1518export format can be selected using the pull-down menu for file format (shown
1519to right). When the save button (at bottom) is used a file will be written in
1520this format. The plot can be exported as a bitmap file by selecting an export
1521format of <span class=SpellE>png</span> or <span class=SpellE>tif</span>, but better
1522is to use <span class=SpellE>pdf</span> or <span class=SpellE>svg</span>, as
1523these are vector formats and there will be no degradation of plot due to pixilation.
1524This is to be preferred where possible. </p>
1525
1526<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1527
1528<p class=MsoNormal>Sample .<span class=SpellE>pdf</span> (<a
1529href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RietPlot/examples/PubPlotTest.pdf">PubPlotTest.pdf</a>)
1530and .<span class=SpellE>png</span> (<a
1531href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RietPlot/examples/PubPlotTest.png">PubPlotTest.png</a>)
1532files can be found in this directory<span class=GramE>: <span style='mso-fareast-font-family:
1533Cambria;mso-fareast-theme-font:minor-latin'><span
1534style="mso-spacerun:yes"> </span></span></span><span style='mso-fareast-font-family:
1535Cambria;mso-fareast-theme-font:minor-latin'><a
1536href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RietPlot/examples/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RietPlot/examples/</a></span></p>
1537
1538<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1539
1540<p class=MsoNormal>The remaining formats allow the plot to be exported to other
1541plotting programs where further customization is <span class=GramE>possible</span>.
1542The Grace and Igor Pro programs both allow input of values and plotting
1543instructions (I am interested to hear of any others) and are supported as
1544export formats (see below). For other programs, such as Origin, the data in the
1545plot can be read from the .<span class=SpellE>csv</span> version of the file, but
1546the user must construct the plot <span class=GramE>themself</span>. </p>
1547
1548<h2>Step 5: Export to Grace<o:p></o:p></h2>
1549
1550<p class=MsoNormal>The <a
1551href="https://en.wikipedia.org/wiki/Grace_(plotting_tool)">Grace program</a>
1552(originally called XMGR) is a free open-source WYSIWYG plotting tool. While <a
1553href="http://plasma-gate.weizmann.ac.il/Grace/">Grace</a> has not been updated
1554in about a decade and is not easy to run on all platforms, the excellent <a
1555href="https://sourceforge.net/projects/qtgrace/"><span class=SpellE>QtGrace</span>
1556port</a> runs on Windows, Mac and Linux and is easy to download and install
1557from here: <a href="https://sourceforge.net/projects/qtgrace/files/">https://sourceforge.net/projects/qtgrace/files/</a>.
1558There is also a GTK port of Grace that is likely of greatest interest to Linux
1559users: <a href="https://sourceforge.net/projects/gracegtk/"><span class=SpellE>GraceGTK</span></a>
1560(not tested). </p>
1561
1562<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1563
1564<p class=MsoNormal>To export to Grace select the “Grace input file, <span
1565class=SpellE>agr</span>” for File format and press <span class=GramE>Save</span>.
1566Below shows the screen in <span class=SpellE>QtGrace</span> after reading the .<span
1567class=SpellE>agr</span> file produced here. This can be annotated and
1568extensively modified within Grace. </p>
1569
1570<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1571 id="Picture_x0020_70" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:370pt;
1572 height:291pt;visibility:visible;mso-wrap-style:square'>
1573 <v:imagedata src="PublicationPlot_files/image025.png" o:title=""/>
1574</v:shape><![endif]--><![if !vml]><img border=0 width=372 height=293
1575src="PublicationPlot_files/image026.png" v:shapes="Picture_x0020_70"><![endif]></span></p>
1576
1577<h2>Step 6: Export to Igor Pro<o:p></o:p></h2>
1578
1579<p class=MsoNormal><a href="https://www.wavemetrics.com/products/igorpro">Igor
1580Pro</a> is commercial software (and not cheap) but it is widely used in some
1581circles and also does a great job for creating high-quality graphics. A free 30-day
1582version demo is available. </p>
1583
1584<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1585
1586<p class=MsoNormal>To export to Igor Pro select the “Igor Pro input file, <span
1587class=SpellE>itx</span>” for File format and press <span class=GramE>Save</span>.
1588Below is the Igor window after reading the .<span class=SpellE>itx</span> file.
1589Note that it is easy to move the Intensity label and change the text in the
1590legend, etc. Inset plots and many other features are available within Igor Pro.
1591</p>
1592
1593<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1594
1595<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1596 id="Picture_x0020_71" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:373pt;
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