source: Tutorials/CIFtutorial/CIFtutorial.html @ 4891

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413  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
414  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
415  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
416  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
417  <w:LsdException Locked="false" Priority="34" QFormat="true"
418   Name="List Paragraph"/>
419  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
420  <w:LsdException Locked="false" Priority="30" QFormat="true"
421   Name="Intense Quote"/>
422  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
423  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
424  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
425  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
426  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
427  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
428  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
429  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
430  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
431  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
432  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
433  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
434  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
435  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
436  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
437  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
438  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
439  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
440  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
441  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
442  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
443  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
444  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
445  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
446  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
447  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
448  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
449  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
450  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
451  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
452  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
453  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
454  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
455  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
456  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
457  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
458  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
459  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
460  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
461  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
462  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
463  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
464  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
465  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
466  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
467  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
468  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
469  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
470  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
471  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
472  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
473  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
474  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
475  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
476  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
477  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
478  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
479  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
480  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
481  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
482  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
483  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
484  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
485  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
486  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
487  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
488  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
489  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
490  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
491  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
492  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
493  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
494  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
495  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
496  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
497  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
498  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
499  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
500  <w:LsdException Locked="false" Priority="19" QFormat="true"
501   Name="Subtle Emphasis"/>
502  <w:LsdException Locked="false" Priority="21" QFormat="true"
503   Name="Intense Emphasis"/>
504  <w:LsdException Locked="false" Priority="31" QFormat="true"
505   Name="Subtle Reference"/>
506  <w:LsdException Locked="false" Priority="32" QFormat="true"
507   Name="Intense Reference"/>
508  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
509  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
510   UnhideWhenUsed="true" Name="Bibliography"/>
511  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
512   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
513  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
514  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
515  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
516  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
517  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
518  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
519  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
520  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
521  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
522  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
523  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
524  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
525  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
526  <w:LsdException Locked="false" Priority="46"
527   Name="Grid Table 1 Light Accent 1"/>
528  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
529  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
530  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
531  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
532  <w:LsdException Locked="false" Priority="51"
533   Name="Grid Table 6 Colorful Accent 1"/>
534  <w:LsdException Locked="false" Priority="52"
535   Name="Grid Table 7 Colorful Accent 1"/>
536  <w:LsdException Locked="false" Priority="46"
537   Name="Grid Table 1 Light Accent 2"/>
538  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
539  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
540  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
541  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
542  <w:LsdException Locked="false" Priority="51"
543   Name="Grid Table 6 Colorful Accent 2"/>
544  <w:LsdException Locked="false" Priority="52"
545   Name="Grid Table 7 Colorful Accent 2"/>
546  <w:LsdException Locked="false" Priority="46"
547   Name="Grid Table 1 Light Accent 3"/>
548  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
549  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
550  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
551  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
552  <w:LsdException Locked="false" Priority="51"
553   Name="Grid Table 6 Colorful Accent 3"/>
554  <w:LsdException Locked="false" Priority="52"
555   Name="Grid Table 7 Colorful Accent 3"/>
556  <w:LsdException Locked="false" Priority="46"
557   Name="Grid Table 1 Light Accent 4"/>
558  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
559  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
560  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
561  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
562  <w:LsdException Locked="false" Priority="51"
563   Name="Grid Table 6 Colorful Accent 4"/>
564  <w:LsdException Locked="false" Priority="52"
565   Name="Grid Table 7 Colorful Accent 4"/>
566  <w:LsdException Locked="false" Priority="46"
567   Name="Grid Table 1 Light Accent 5"/>
568  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
569  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
570  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
571  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
572  <w:LsdException Locked="false" Priority="51"
573   Name="Grid Table 6 Colorful Accent 5"/>
574  <w:LsdException Locked="false" Priority="52"
575   Name="Grid Table 7 Colorful Accent 5"/>
576  <w:LsdException Locked="false" Priority="46"
577   Name="Grid Table 1 Light Accent 6"/>
578  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
579  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
580  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
581  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
582  <w:LsdException Locked="false" Priority="51"
583   Name="Grid Table 6 Colorful Accent 6"/>
584  <w:LsdException Locked="false" Priority="52"
585   Name="Grid Table 7 Colorful Accent 6"/>
586  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
587  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
588  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
589  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
590  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
591  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
592  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
593  <w:LsdException Locked="false" Priority="46"
594   Name="List Table 1 Light Accent 1"/>
595  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
596  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
597  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
598  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
599  <w:LsdException Locked="false" Priority="51"
600   Name="List Table 6 Colorful Accent 1"/>
601  <w:LsdException Locked="false" Priority="52"
602   Name="List Table 7 Colorful Accent 1"/>
603  <w:LsdException Locked="false" Priority="46"
604   Name="List Table 1 Light Accent 2"/>
605  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
606  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
607  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
608  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
609  <w:LsdException Locked="false" Priority="51"
610   Name="List Table 6 Colorful Accent 2"/>
611  <w:LsdException Locked="false" Priority="52"
612   Name="List Table 7 Colorful Accent 2"/>
613  <w:LsdException Locked="false" Priority="46"
614   Name="List Table 1 Light Accent 3"/>
615  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
616  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
617  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
618  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
619  <w:LsdException Locked="false" Priority="51"
620   Name="List Table 6 Colorful Accent 3"/>
621  <w:LsdException Locked="false" Priority="52"
622   Name="List Table 7 Colorful Accent 3"/>
623  <w:LsdException Locked="false" Priority="46"
624   Name="List Table 1 Light Accent 4"/>
625  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
626  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
627  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
628  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
629  <w:LsdException Locked="false" Priority="51"
630   Name="List Table 6 Colorful Accent 4"/>
631  <w:LsdException Locked="false" Priority="52"
632   Name="List Table 7 Colorful Accent 4"/>
633  <w:LsdException Locked="false" Priority="46"
634   Name="List Table 1 Light Accent 5"/>
635  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
636  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
637  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
638  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
639  <w:LsdException Locked="false" Priority="51"
640   Name="List Table 6 Colorful Accent 5"/>
641  <w:LsdException Locked="false" Priority="52"
642   Name="List Table 7 Colorful Accent 5"/>
643  <w:LsdException Locked="false" Priority="46"
644   Name="List Table 1 Light Accent 6"/>
645  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
646  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
647  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
648  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
649  <w:LsdException Locked="false" Priority="51"
650   Name="List Table 6 Colorful Accent 6"/>
651  <w:LsdException Locked="false" Priority="52"
652   Name="List Table 7 Colorful Accent 6"/>
653  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
654   Name="Mention"/>
655  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
656   Name="Smart Hyperlink"/>
657  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
658   Name="Hashtag"/>
659  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
660   Name="Unresolved Mention"/>
661  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
662   Name="Smart Link"/>
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1010</head>
1011
1012<body lang=EN-US link=blue vlink="#954F72" style='tab-interval:.5in;word-wrap:
1013break-word'>
1014
1015<div class=WordSection1>
1016
1017<h1 align=center style='text-align:center'><a name="_GoBack"></a><span
1018style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Tutorial:
1019Preparing a Full CIF<o:p></o:p></span></h1>
1020
1021<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><BL><![if !supportLists]><span
1022style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1023Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1024</span></span></span><![endif]><span dir=LTR></span>Exercise files are found <a
1025href="data" target="_blank">here</a>. The data files are taken from the
1026conclusion of the “<a href="../CWCombined/Combined%20refinement.htm">Combined
1027X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial. <o:p></o:p></p>
1028
1029</BL>
1030
1031<h1><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Background
1032<o:p></o:p></span></h1>
1033
1034<p class=MsoNormal>Crystallography has had a long tradition where experimental
1035data as well as results were reported numerically, so that results could be
1036verified independently as well as utilized. In the past two decades the field
1037has set the standard for data science compared to almost all other areas of
1038physical and biological science through the development of the Crystallographic
1039Information Framework (CIF) which defines a universal format for the reporting
1040of nearly all aspects of a crystallographic fit. This is particularly true for
1041Rietveld fits, where the <span class=SpellE>pdCIF</span> subset of CIF has been
1042developed to capture the observed and computed patterns as well as reflection
1043tables and coordinates as well as interatomic distances and angles. </p>
1044
1045<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1046
1047<p class=MsoNormal>Within GSAS-II, a CIF for a phase <span class=GramE>are</span>
1048available as “quick” coordinate-only file, which provides atom coordinates and
1049displacement parameters, but no uncertainties or other supporting information
1050from the refinement. This is indeed easy with a single menu command. Likewise,
1051a CIF containing only a dataset without phase information can be easily created
1052from the Export menu, but the real power of CIF comes after a project has been
1053completed. Using the “Entire project as…” a “Full CIF” menu command in the
1054Export menu, all results can be reported in a machine and human readable. There
1055are a few steps in generating a full project CIF. This tutorial goes through
1056them and explains what is being done and why. </p>
1057
1058<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1059
1060<p class=MsoNormal>A bit of background on CIF: The format allows a label (a CIF
1061data item, such as _cell_length_a or _publ_author_name) to be associated with
1062either a single value or a column in a table. A collection of data items is
1063placed in a block. For a single-crystal structure, a block will usually contain
1064the coordinates for a phase and the structure factors (experimental data and
1065the matching simulated values) as well as supporting information and derived
1066results. With multiple temperatures, a block would be needed for each setting
1067because, for example, only one set of unit cell dimensions and coordinates can
1068be defined in a block. With powder diffraction, if a single dataset (histogram)
1069is used and only one phase is present, a single block can be used. If either
1070more than one phase is present, or more than one histogram is used, multiple
1071blocks are required. GSAS-II will create single-block CIFs when possible, but
1072otherwise will create a block for the overall refinement plus a block for each
1073histogram and a block for each phase. Referencing information between different
1074blocks requires that each block be labeled with a unique name. These block
1075labels are assembled from a number of fields supplied by the user and a
1076timestamp when the file is created. </p>
1077
1078<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1079
1080<p class=MsoNormal>A tremendous amount of information can be placed into a CIF
1081file. No one is likely to specify all of the field in the IUCr-supplied
1082template, which itself does not include all data items defined in CIF. Some
1083information can be supplied by GSAS-II from what is defined inside a project,
1084data such as symmetry and lattice parameters, but other information, for
1085example synthesis conditions or sample color, must be supplied by the user.
1086This could be done with a simple text editor once the file is created, but the
1087problem that arises from that approach is that it is common that after one has
1088produced the “final” refinement, another idea occurs for a slightly better fit.
1089The approach used in GSAS-II is that as the CIF is generated, copies of
1090template files are made that contain all the user-supplied information. Thus,
1091the CIF can be recreated from the updated project without having to repeat all
1092the work in supplying that information. Also, by saving template files that
1093have setting information that will be common amongst multiple projects (for
1094example, diffraction instrumentation descriptions) these files can be reused,
1095avoiding repetitive tasks.<span style='mso-spacerun:yes'>  </span></p>
1096
1097<h1><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Prerequisite
1098<o:p></o:p></span></h1>
1099
1100<p class=MsoNormal>Before beginning this tutorial, either complete the
1101refinement in the “<a href="../../../CWCombined/Combined%20refinement.htm">Combined
1102X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial or download the
1103GSAS-II project file provided <a href="../../../Scratch/data" target="_blank">here</a>,
1104which provides a two histogram, one phase refinement. </p>
1105
1106<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1107
1108<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
11091. Enter a name for the author of the CIF file. <o:p></o:p></span></h2>
1110
1111<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1112
1113<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
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1116</span></span></span><![endif]><span dir=LTR></span>Select the Controls entry
1117on the data tree and enter the name for the main author for the project and
1118CIF.</p>
1119
1120<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1121
1122<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
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1151
1152<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1153
1154<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
11552: Start the export process<o:p></o:p></span></h2>
1156
1157<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1158
1159<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
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1162</span></span></span><![endif]><span dir=LTR></span>Using the Export menu,
1163select the “Entire project as” menu item and the “Full CIF” submenu option. </p>
1164
1165<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1166
1167<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1174
1175<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1176
1177<p class=MsoNormal>This opens a dialog (exact appearance will depend on the
1178operating system you are using) where you can select a name for the file to be
1179created. </p>
1180
1181<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1190
1191<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1192
1193<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
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1196</span></span></span><![endif]><span dir=LTR></span>Enter a name for the file
1197if you wish to override the default name and press Save. If that file exists, you
1198will need to agree to overwrite it or to select a new name. </p>
1199
1200<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1201
1202<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
12033: Select instrument name(s)<o:p></o:p></span></h2>
1204
1205<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1206
1207<p class=MsoNormal>Before a CIF can be created, each histogram must have
1208associated with it an instrument name. Note that the instrument name appears in
1209the Sample Parameters tree entry for each histogram. If any instrument does not
1210have a name, the dialog below is displayed. </p>
1211
1212<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1213
1214<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1215 id="Picture_x0020_20" o:spid="_x0000_i1042" type="#_x0000_t75" alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1216 style='width:165pt;height:155pt;visibility:visible;mso-wrap-style:square'>
1217 <v:imagedata src="CIFtutorial.fld/image024.png" o:title="Graphical user interface, application&#10;&#10;Description automatically generated"/>
1218</v:shape><![endif]--><![if !vml]><img border=0 width=165 height=155
1219src="CIFtutorial.fld/image024.png"
1220alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1221v:shapes="Picture_x0020_20"><![endif]></span></p>
1222
1223<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1224
1225<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1226
1227<p class=MsoNormal>Ideally the instrument name will be unique, so the
1228combination of the name and a timestamp will create an identifier that is
1229unlikely to be repeated. The instrument name should also allow the data source
1230to be identified should there be several similar instruments within an
1231institution, but the details for naming are left as a local decision. Inclusion
1232of an institution name is a good idea, so an ideal name might be “Univ. of
1233Mars, Curiosity II”. While in this case the two histograms are from different
1234instruments, the down arrow (<span style='font-family:Symbol;mso-ascii-font-family:
1235"Times New Roman";mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;
1236mso-symbol-font-family:Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:
1237Symbol'>Ú</span></span>) button will copy the entered name to all fields below,
1238simplifying the data entry task, when appropriate. </p>
1239
1240<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1241
1242<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1243style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1244Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1245</span></span></span><![endif]><span dir=LTR></span>Enter names for each
1246instrument and then press OK.</p>
1247
1248<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1249
1250<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1251 id="Picture_x0020_22" o:spid="_x0000_i1041" type="#_x0000_t75" alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1252 style='width:202pt;height:192pt;visibility:visible;mso-wrap-style:square'>
1253 <v:imagedata src="CIFtutorial.fld/image025.png" o:title="Graphical user interface, text, application&#10;&#10;Description automatically generated"/>
1254</v:shape><![endif]--><![if !vml]><img border=0 width=202 height=192
1255src="CIFtutorial.fld/image025.png"
1256alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1257v:shapes="Picture_x0020_22"><![endif]></span></p>
1258
1259<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
12604: Bond distance/Angle criteria<o:p></o:p></span></h2>
1261
1262<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1263
1264<p class=MsoNormal>One significant part of a CIF is the computation of bond
1265distances and angles. For this there is a set of atomic radii for each phase
1266along with a tolerance factor. When the CIF creation is initially invoked, the
1267dialog below is shown for each phase:</p>
1268
1269<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1270
1271<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1272 id="Picture_x0020_5" o:spid="_x0000_i1040" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1273 style='width:180pt;height:164pt;visibility:visible;mso-wrap-style:square'>
1274 <v:imagedata src="CIFtutorial.fld/image007.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1275</v:shape><![endif]--><![if !vml]><img border=0 width=180 height=164
1276src="CIFtutorial.fld/image007.png"
1277alt="Graphical user interface&#10;&#10;Description automatically generated"
1278v:shapes="Picture_x0020_5"><![endif]></span></p>
1279
1280<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1281
1282<p class=MsoNormal>This dialog will not be shown again, unless invoked
1283manually. To explain what these numbers mean, distances between Pb and O atoms
1284will be reported when their interatomic distance is less than or equal to
1285(1.95+1.09)*0.85 Å (=2.584 Å) and O-Pb-X or X-O-Pb angles will be reported if
1286the Pb-O distance is less than or equal to (1.75+0.89)*0.85 Å (=2.244 Å) <i>and</i>
1287the O-X or Pb-X is within the requirement for that pair of atoms as well (in
1288this case X could be O, Pb or S). </p>
1289
1290<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1291
1292<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1293style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1294Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1295</span></span></span><![endif]><span dir=LTR></span>At this point no changes
1296are needed, so simply press OK.</p>
1297
1298<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1299
1300<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
13015. <span class=GramE>Conditions</span> warning<o:p></o:p></span></h2>
1302
1303<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1304
1305<p class=MsoNormal>Note that when a histogram is created in GSAS-II, unless
1306pressure and temperature values are reported in the metadata in a standardized
1307fashion (this is uncommon), the sample temperature defaults to 300 K and the
1308ambient pressure to 0.1 MPa. It is likely that these values do not describe the
1309actual data collection conditions. Since they will be included in the CIF, they
1310should be updated with more appropriate values.</p>
1311
1312<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1313
1314<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1315 id="Picture_x0020_23" o:spid="_x0000_i1039" type="#_x0000_t75" alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1316 style='width:220pt;height:87pt;visibility:visible;mso-wrap-style:square'>
1317 <v:imagedata src="CIFtutorial.fld/image026.png" o:title="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"/>
1318</v:shape><![endif]--><![if !vml]><img border=0 width=220 height=87
1319src="CIFtutorial.fld/image026.png"
1320alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1321v:shapes="Picture_x0020_23"><![endif]></span></p>
1322
1323<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1324
1325<p class=MsoNormal>The warning above will be shown every time the code for CIF
1326generation code is initiated, unless the sample temperature has been set to a
1327value other than 300 K for each histogram. If indeed the histogram temperature/pressure
1328values are correct, this warning may be ignored. Note that the Command<span
1329class=GramE>/“</span>Copy Selected” menu command may be useful to change a
1330value in multiple histograms in one operation. <o:p></o:p></p>
1331
1332<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1333
1334<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1335style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1336Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1337</span></span></span><![endif]><span dir=LTR></span>Press Cancel to stop the
1338export</p>
1339
1340<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1341
1342<p class=MsoNormal>In this case it is of particular importance to note the data
1343collection temperatures. The neutron dataset was collected at cryogenic
1344temperatures, while the x-ray data were collected under ambient conditions. </p>
1345
1346<p class=MsoListParagraphCxSpFirst style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1347
1348<p class=MsoListParagraphCxSpLast style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1349style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1350Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1351</span></span></span><![endif]><span dir=LTR></span>Change the temperature
1352values in each histogram, as shown below. Note that ideally, temperature and
1353pressure values will be available to GSAS-II in a data file’s metadata and will
1354be set in the Sample Parameters automatically, but this is seldom the case.</p>
1355
1356<p class=MsoNormal style='margin-left:0in'><o:p>&nbsp;</o:p></p>
1357
1358<p class=MsoNormal style='margin-left:0in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1359 id="Picture_x0020_24" o:spid="_x0000_i1038" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1360 style='width:292pt;height:279pt;visibility:visible;mso-wrap-style:square'>
1361 <v:imagedata src="CIFtutorial.fld/image027.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1362</v:shape><![endif]--><![if !vml]><img border=0 width=292 height=279
1363src="CIFtutorial.fld/image027.png"
1364alt="Graphical user interface&#10;&#10;Description automatically generated"
1365v:shapes="Picture_x0020_24"><![endif]></span></p>
1366
1367<p class=MsoNormal style='margin-left:0in'><o:p>&nbsp;</o:p></p>
1368
1369<p class=MsoNormal style='margin-left:0in'><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1370 id="Picture_x0020_25" o:spid="_x0000_i1037" type="#_x0000_t75" alt="Graphical user interface, table&#10;&#10;Description automatically generated"
1371 style='width:291pt;height:280pt;visibility:visible;mso-wrap-style:square'>
1372 <v:imagedata src="CIFtutorial.fld/image028.png" o:title="Graphical user interface, table&#10;&#10;Description automatically generated"/>
1373</v:shape><![endif]--><![if !vml]><img border=0 width=291 height=280
1374src="CIFtutorial.fld/image028.png"
1375alt="Graphical user interface, table&#10;&#10;Description automatically generated"
1376v:shapes="Picture_x0020_25"><![endif]></span></p>
1377
1378<p class=MsoNormal style='margin-left:0in'><o:p>&nbsp;</o:p></p>
1379
1380<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1381
1382<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
13836. Restart the export process<o:p></o:p></span></h2>
1384
1385<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'><o:p>&nbsp;</o:p></span></h2>
1386
1387<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1388style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1389Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1390</span></span></span><![endif]><span dir=LTR></span>As before, use the Export
1391menu and select the “Entire project as” menu item and the “Full CIF” submenu
1392option. If you use the same file name as in Part 2, you will likely need to say
1393yes to overwrite the file. </p>
1394
1395<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1396
1397<p class=MsoNormal>Note that the windows opened previously in steps 3-5 will
1398not occur again, since the requested information has been provided. <o:p></o:p></p>
1399
1400<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1401
1402<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
14037. Specifying CIF Contents. <o:p></o:p></span></h2>
1404
1405<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1406
1407<p class=MsoNormal>Once the previous steps have been performed, a window such
1408as the one below is shown. Note that the “Edit CIF Author” button opens a
1409dialog window, where the information supplied in Part 1 can be changed. The
1410“Edit Instrument Name(s)” button reopens the window shown in Part 3.</p>
1411
1412<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1413
1414<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1415 id="Picture_x0020_7" o:spid="_x0000_i1036" type="#_x0000_t75" alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1416 style='width:194pt;height:298pt;visibility:visible;mso-wrap-style:square'>
1417 <v:imagedata src="CIFtutorial.fld/image009.png" o:title="Graphical user interface, text, application&#10;&#10;Description automatically generated"/>
1418</v:shape><![endif]--><![if !vml]><img border=0 width=194 height=298
1419src="CIFtutorial.fld/image009.png"
1420alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1421v:shapes="Picture_x0020_7"><![endif]></span></p>
1422
1423<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1424
1425<p class=MsoNormal>Note that for every other section of the window, there is
1426are a pair of buttons labeled “Select Template File” and “Edit Template.” A
1427default template file is selected initially, and information can be included in
1428that template with the “Edit Template” button, as will be shown below. Note
1429that there are four types of template files for (1) overall information; (2)
1430phase information; (3) powder diffraction data and instrumentation details; and
1431(4) single-crystal diffraction data and instrumentation details. Note that data
1432items that are set by GSAS-II directly (for example, lattice parameters and
1433space group information for a phase) are not included in the template. </p>
1434
1435<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1436
1437<p class=MsoNormal>The information you specify to place in a template is
1438included in the GSAS-II project (.<span class=SpellE>gpx</span>) file so that
1439if you perform a new refinement, all of the template edits you have made are
1440used automatically when a new CIF is created. </p>
1441
1442<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1443
1444<p class=MsoNormal>As you are editing each template, you can save that
1445information in a file. There are two reasons for doing this. One is that by
1446saving the information as a file you potentially create a customized template
1447file. Use of this file in the future for a different project can save you
1448considerable time, as an example, when documenting a diffractometer. Also, if a
1449file is saved, instead of keeping all of the template contents in the .<span
1450class=SpellE>gpx</span> file, only the name of the template file is saved,
1451reducing the project file size slightly. (The default template files range from
14521K to 4K bytes in size, so this not usually very significant savings.) Once a
1453customized template file has been created, use the “Select Template File”
1454button to select it in place of the default. </p>
1455
1456<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1457
1458<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1459style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1460Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1461</span></span></span><![endif]><span dir=LTR></span>Edit the Publication
1462template by pressing the “Edit Template” button closest to the top of the
1463window [just below the “Publication (overall) template” heading] a window
1464similar to the one below is created. </p>
1465
1466<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1467
1468<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1469 id="Picture_x0020_9" o:spid="_x0000_i1035" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1470 style='width:169pt;height:225pt;visibility:visible;mso-wrap-style:square'>
1471 <v:imagedata src="CIFtutorial.fld/image010.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1472</v:shape><![endif]--><![if !vml]><img border=0 width=169 height=225
1473src="CIFtutorial.fld/image010.png"
1474alt="Graphical user interface&#10;&#10;Description automatically generated"
1475v:shapes="Picture_x0020_9"><![endif]></span></p>
1476
1477<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1478
1479<p class=MsoNormal>A few notes on the arrangement of this window, which is a
1480bit easier to use if manually resized, as below. </p>
1481
1482<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1483 id="Picture_x0020_10" o:spid="_x0000_i1034" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1484 style='width:269pt;height:200pt;visibility:visible;mso-wrap-style:square'>
1485 <v:imagedata src="CIFtutorial.fld/image011.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1486</v:shape><![endif]--><![if !vml]><img border=0 width=269 height=200
1487src="CIFtutorial.fld/image011.png"
1488alt="Graphical user interface&#10;&#10;Description automatically generated"
1489v:shapes="Picture_x0020_10"><![endif]></span><span
1490style='mso-spacerun:yes'> </span></p>
1491
1492<p class=MsoNormal>Note that this contains three CIF items, _<span
1493class=SpellE>publ_author_name</span>, _<span class=SpellE>publ_author_footnote</span>
1494and _<span class=SpellE>publ_author_address</span>, in a table (loop_). Note
1495the “Add row” button to the upper left which allows additional rows to be added
1496to the table. The remainder of this template is a series of CIF items that
1497accept a single value. Most CIF items are tagged with a help button, marked
1498with a question mark. That indicates that that CIF item is defined in a CIF
1499dictionary. The definition can be looked up by pressing that help button or by
1500allowing the mouse to stay stationary on a CIF item name for a few seconds
1501which causes the definition text to appear as a tool tip, as below,</p>
1502
1503<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1504 id="Picture_x0020_11" o:spid="_x0000_i1033" type="#_x0000_t75" alt="A picture containing graphical user interface&#10;&#10;Description automatically generated"
1505 style='width:205pt;height:96pt;visibility:visible;mso-wrap-style:square'>
1506 <v:imagedata src="CIFtutorial.fld/image012.png" o:title="A picture containing graphical user interface&#10;&#10;Description automatically generated"/>
1507</v:shape><![endif]--><![if !vml]><img border=0 width=205 height=96
1508src="CIFtutorial.fld/image012.png"
1509alt="A picture containing graphical user interface&#10;&#10;Description automatically generated"
1510v:shapes="Picture_x0020_11"><![endif]></span></p>
1511
1512<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1513
1514<p class=MsoNormal>or clicking on the button displays the same information at
1515the bottom of the window, as below.</p>
1516
1517<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1518 id="Picture_x0020_12" o:spid="_x0000_i1032" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated with medium confidence"
1519 style='width:257pt;height:165pt;visibility:visible;mso-wrap-style:square'>
1520 <v:imagedata src="CIFtutorial.fld/image013.png" o:title="Graphical user interface&#10;&#10;Description automatically generated with medium confidence"/>
1521</v:shape><![endif]--><![if !vml]><img border=0 width=257 height=165
1522src="CIFtutorial.fld/image013.png"
1523alt="Graphical user interface&#10;&#10;Description automatically generated with medium confidence"
1524v:shapes="Picture_x0020_12"><![endif]></span></p>
1525
1526<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1527
1528<p class=MsoNormal>Note that each text entry box has a small right-angle bracket
1529(looking a bit like an inverted L) at the lower right corner. This can be used
1530to resize the text entry box to allow viewing a longer line of text and/or
1531several lines of text. </p>
1532
1533<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1534
1535<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1536style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1537Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1538</span></span></span><![endif]><span dir=LTR></span>Press the “Add row” button to
1539create entries for a second author. </p>
1540
1541<p class=MsoListParagraphCxSpMiddle style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1542style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1543Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1544</span></span></span><![endif]><span dir=LTR></span>Enlarge the width of either
1545of the _<span class=SpellE>publ_author_name</span> entry boxes as well as the
1546height and width of the _<span class=SpellE>publ_author_address</span> item to
1547accommodate more text. </p>
1548
1549<p class=MsoListParagraphCxSpLast style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1550style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1551Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1552</span></span></span><![endif]><span dir=LTR></span>Add text to describe
1553authorship, such as what has been done below (authorship of the original
1554Anglesite, aka PbSO<sub>4</sub>, crystal structure). Note that as is described
1555in the CIF definition, author names are supplied as last name, first name. </p>
1556
1557<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1558
1559<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1560 id="Picture_x0020_13" o:spid="_x0000_i1031" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1561 style='width:331pt;height:277pt;visibility:visible;mso-wrap-style:square'>
1562 <v:imagedata src="CIFtutorial.fld/image014.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1563</v:shape><![endif]--><![if !vml]><img border=0 width=331 height=277
1564src="CIFtutorial.fld/image014.png"
1565alt="Graphical user interface&#10;&#10;Description automatically generated"
1566v:shapes="Picture_x0020_13"><![endif]></span></p>
1567
1568<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1569
1570<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1571style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1572Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1573</span></span></span><![endif]><span dir=LTR></span>After completing all
1574appropriate CIF items that would be appropriate for this work, press the “Use”
1575button to close the window, saving the entries into the project file. </p>
1576
1577<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1578
1579<p class=MsoNormal>Note that the window contents changes to indicate that the
1580template information is no longer from a file. </p>
1581
1582<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1583 id="Picture_x0020_14" o:spid="_x0000_i1030" type="#_x0000_t75" alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1584 style='width:148pt;height:86pt;visibility:visible;mso-wrap-style:square'>
1585 <v:imagedata src="CIFtutorial.fld/image015.png" o:title="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1586  croptop="910f" cropbottom="38375f"/>
1587</v:shape><![endif]--><![if !vml]><img border=0 width=148 height=86
1588src="CIFtutorial.fld/image006.png"
1589alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1590v:shapes="Picture_x0020_14"><![endif]></span></p>
1591
1592<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1593
1594<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
15958. Edit Phase Information including Distances and Angles. <o:p></o:p></span></h2>
1596
1597<p class=MsoNormal>The phase template contains a relatively small number of
1598items that can document information about a phase, as shown below. If one
1599produced several projects all using the same sample, it might make sense to
1600produce a template file that might be used for that sample in all projects. </p>
1601
1602<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1603
1604<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1605style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1606Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1607</span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
1608button in the Phase section of the “Edit CIF settings” window and the window
1609below appears. Enter any information desired. Press “Use” when done.<o:p></o:p></p>
1610
1611<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1612
1613<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1614
1615<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1616 id="Picture_x0020_26" o:spid="_x0000_i1029" type="#_x0000_t75" alt="Diagram&#10;&#10;Description automatically generated with medium confidence"
1617 style='width:214pt;height:316pt;visibility:visible;mso-wrap-style:square'>
1618 <v:imagedata src="CIFtutorial.fld/image008.png" o:title="Diagram&#10;&#10;Description automatically generated with medium confidence"/>
1619</v:shape><![endif]--><![if !vml]><img border=0 width=214 height=316
1620src="CIFtutorial.fld/image008.png"
1621alt="Diagram&#10;&#10;Description automatically generated with medium confidence"
1622v:shapes="Picture_x0020_26"><![endif]></span></p>
1623
1624<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1625
1626<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1627
1628<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1629style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1630Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1631</span></span></span><![endif]><span dir=LTR></span>Press the “Set
1632distance/angle publication flag” and the window below appears. </p>
1633
1634<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1635
1636<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1637 id="Picture_x0020_16" o:spid="_x0000_i1028" type="#_x0000_t75" alt="Table&#10;&#10;Description automatically generated"
1638 style='width:257pt;height:325pt;visibility:visible;mso-wrap-style:square'>
1639 <v:imagedata src="CIFtutorial.fld/image018.png" o:title="Table&#10;&#10;Description automatically generated"/>
1640</v:shape><![endif]--><![if !vml]><img border=0 width=257 height=325
1641src="CIFtutorial.fld/image018.png"
1642alt="Table&#10;&#10;Description automatically generated" v:shapes="Picture_x0020_16"><![endif]></span></p>
1643
1644<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1645
1646<p class=MsoNormal>This shows the interatomic distances and angles that that
1647occur within the radii specified above. Note that the Pb radius is too small to
1648pick up the coordination of that atom, so we should change that:</p>
1649
1650<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1651
1652<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1653style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1654Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1655</span></span></span><![endif]><span dir=LTR></span>Press the “Done” button to
1656close this window</p>
1657
1658<p class=MsoListParagraphCxSpMiddle style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1659style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1660Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1661</span></span></span><![endif]><span dir=LTR></span>Press the “Edit
1662distance/angle ranges” button to bring up the screen below. Change the bond
1663search factor from 0.85 to 0.9 to increase the search range, as below.</p>
1664
1665<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1666
1667<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1668 id="Picture_x0020_17" o:spid="_x0000_i1027" type="#_x0000_t75" alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1669 style='width:150pt;height:137pt;visibility:visible;mso-wrap-style:square'>
1670 <v:imagedata src="CIFtutorial.fld/image019.png" o:title="Graphical user interface, application&#10;&#10;Description automatically generated"/>
1671</v:shape><![endif]--><![if !vml]><img border=0 width=150 height=137
1672src="CIFtutorial.fld/image019.png"
1673alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1674v:shapes="Picture_x0020_17"><![endif]></span></p>
1675
1676<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1677
1678<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1679style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1680Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1681</span></span></span><![endif]><span dir=LTR></span>Press the “Set
1682distance/angle publication flag” and note the additional distances (but not
1683angles) in the window below. </p>
1684
1685<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1686
1687<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1688 id="Picture_x0020_18" o:spid="_x0000_i1026" type="#_x0000_t75" alt="Table&#10;&#10;Description automatically generated"
1689 style='width:262pt;height:337pt;visibility:visible;mso-wrap-style:square'>
1690 <v:imagedata src="CIFtutorial.fld/image020.png" o:title="Table&#10;&#10;Description automatically generated"/>
1691</v:shape><![endif]--><![if !vml]><img border=0 width=262 height=337
1692src="CIFtutorial.fld/image020.png"
1693alt="Table&#10;&#10;Description automatically generated" v:shapes="Picture_x0020_18"><![endif]></span></p>
1694
1695<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1696
1697<p class=MsoNormal>Note that to obtain the angles around the Pb and O atoms,
1698the values in the right-hand column and/or the angle search factor range must
1699also be extended. </p>
1700
1701<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1702
1703<p class=MsoNormal>Every bond and angle that is listed on the window will be
1704placed in the CIF when written. Note that while distances and angles are shown
1705in the window without uncertainties, if the atom positions have been varied,
1706the values with their uncertainties will be placed in the CIF (in standard
1707crystallographic notation). Also note that in the CIF each distance has an
1708associated _<span class=SpellE>geom_bond_publ_flag</span> value (for angles, _<span
1709class=SpellE>geom_angle_publ_flag</span>). The value for this can be
1710“yes”&nbsp;or “no” and a “yes” value indicates that the value should be placed
1711in a table of bond distances/angles, if generated from the CIF. By default,
1712this flag defaults to “yes<span class=GramE></span> but this can be changed by
1713clicking on the distance or angle button. </p>
1714
1715<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1716
1717<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
17189. Create a Customized Template File. <o:p></o:p></span></h2>
1719
1720<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1721
1722<p class=MsoNormal>For this particular project, since these were data
1723distributed from a round-robin study many years ago, relatively little is
1724documented on the instruments, but as a useful exercise, I recommend opening
1725documenting an instrument that you use frequently (or twist the arm of the
1726instrument scientist at your favorite facility to do so.)<span
1727style='mso-spacerun:yes'>  </span></p>
1728
1729<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1730
1731<p class=MsoListParagraph style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1732style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1733Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1734</span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
1735button for either histogram <span class=GramE>and</span> define as many of the
1736appropriate fields as are appropriate. </p>
1737
1738<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1739
1740<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1741 id="Picture_x0020_19" o:spid="_x0000_i1025" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1742 style='width:233pt;height:243pt;visibility:visible;mso-wrap-style:square'>
1743 <v:imagedata src="CIFtutorial.fld/image021.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1744</v:shape><![endif]--><![if !vml]><img border=0 width=233 height=243
1745src="CIFtutorial.fld/image021.png"
1746alt="Graphical user interface&#10;&#10;Description automatically generated"
1747v:shapes="Picture_x0020_19"><![endif]></span></p>
1748
1749<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1750style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1751Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1752</span></span></span><![endif]><span dir=LTR></span>Press the “Save as
1753template” button and save the file with a name and location that will make this
1754readily available for future use.</p>
1755
1756<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1757
1758<p class=MsoNormal>Note that the next time that “Export… project… to CIF” is
1759used, this template can be used by pressing the “Select Template File” button
1760for that histogram and by doing this all of the information specified
1761previously can be used without additional data entry effort.<span
1762style='mso-spacerun:yes'>  </span></p>
1763
1764<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1765
1766<h2><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>Part
176710. Create the CIF<o:p></o:p></span></h2>
1768
1769<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1770
1771<p class=MsoListParagraphCxSpFirst style='mso-list:l0 level1 lfo2'><![if !supportLists]><span
1772style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1773Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1774</span></span></span><![endif]><span dir=LTR></span>Pressing the “Create CIF”
1775button will cause the CIF to be written. </p>
1776
1777<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1778
1779<p class=MsoNormal>Depending on the number and size of histograms, this can be
1780a fairly large file as it contains observed and computed patterns for each, as
1781well as a reflection table, plus unit cell parameters, symmetry information,
1782coordinates and bond distances and angles for each phase. </p>
1783
1784<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1785
1786<p class=MsoNormal>Note that if the refinement information is changed, for
1787example by introducing a new variable, changing the background model etc. all
1788that need be done to create a CIF with updated information will be to select
1789the “Entire project as” menu item and the “Full CIF” submenu option from the
1790Export menu and then press the “Create CIF” button again. All information
1791generated by GSAS-II will be updated and previously entered will be retained
1792and placed in the new file. </p>
1793
1794<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1795
1796</div>
1797
1798</body>
1799
1800</html>
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