source: Tutorials/CIFtutorial/CIFtutorial.html @ 4872

Last change on this file since 4872 was 4872, checked in by toby, 22 months ago

export project to giant ASCII file; add CIF tutorial; set misc svn flags
  • Property svn:mime-type set to text/html
File size: 90.1 KB
Line 
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411  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
412  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
413  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
414  <w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
415  <w:LsdException Locked="false" Priority="34" QFormat="true"
416   Name="List Paragraph"/>
417  <w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
418  <w:LsdException Locked="false" Priority="30" QFormat="true"
419   Name="Intense Quote"/>
420  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
421  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
422  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
423  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
424  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
425  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
426  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
427  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
428  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
429  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
430  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
431  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
432  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
433  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
434  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
435  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
436  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
437  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
438  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
439  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
440  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
441  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
442  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
443  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
444  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
445  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
446  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
447  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
448  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
449  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
450  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
451  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
452  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
453  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
454  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
455  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
456  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
457  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
458  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
459  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
460  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
461  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
462  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
463  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
464  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
465  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
466  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
467  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
468  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
469  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
470  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
471  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
472  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
473  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
474  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
475  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
476  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
477  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
478  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
479  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
480  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
481  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
482  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
483  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
484  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
485  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
486  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
487  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
488  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
489  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
490  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
491  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
492  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
493  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
494  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
495  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
496  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
497  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
498  <w:LsdException Locked="false" Priority="19" QFormat="true"
499   Name="Subtle Emphasis"/>
500  <w:LsdException Locked="false" Priority="21" QFormat="true"
501   Name="Intense Emphasis"/>
502  <w:LsdException Locked="false" Priority="31" QFormat="true"
503   Name="Subtle Reference"/>
504  <w:LsdException Locked="false" Priority="32" QFormat="true"
505   Name="Intense Reference"/>
506  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
507  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
508   UnhideWhenUsed="true" Name="Bibliography"/>
509  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
510   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
511  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
512  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
513  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
514  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
515  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
516  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
517  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
518  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
519  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
520  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
521  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
522  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
523  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
524  <w:LsdException Locked="false" Priority="46"
525   Name="Grid Table 1 Light Accent 1"/>
526  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
527  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
528  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
529  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
530  <w:LsdException Locked="false" Priority="51"
531   Name="Grid Table 6 Colorful Accent 1"/>
532  <w:LsdException Locked="false" Priority="52"
533   Name="Grid Table 7 Colorful Accent 1"/>
534  <w:LsdException Locked="false" Priority="46"
535   Name="Grid Table 1 Light Accent 2"/>
536  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
537  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
538  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
539  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
540  <w:LsdException Locked="false" Priority="51"
541   Name="Grid Table 6 Colorful Accent 2"/>
542  <w:LsdException Locked="false" Priority="52"
543   Name="Grid Table 7 Colorful Accent 2"/>
544  <w:LsdException Locked="false" Priority="46"
545   Name="Grid Table 1 Light Accent 3"/>
546  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
547  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
548  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
549  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
550  <w:LsdException Locked="false" Priority="51"
551   Name="Grid Table 6 Colorful Accent 3"/>
552  <w:LsdException Locked="false" Priority="52"
553   Name="Grid Table 7 Colorful Accent 3"/>
554  <w:LsdException Locked="false" Priority="46"
555   Name="Grid Table 1 Light Accent 4"/>
556  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
557  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
558  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
559  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
560  <w:LsdException Locked="false" Priority="51"
561   Name="Grid Table 6 Colorful Accent 4"/>
562  <w:LsdException Locked="false" Priority="52"
563   Name="Grid Table 7 Colorful Accent 4"/>
564  <w:LsdException Locked="false" Priority="46"
565   Name="Grid Table 1 Light Accent 5"/>
566  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
567  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
568  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
569  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
570  <w:LsdException Locked="false" Priority="51"
571   Name="Grid Table 6 Colorful Accent 5"/>
572  <w:LsdException Locked="false" Priority="52"
573   Name="Grid Table 7 Colorful Accent 5"/>
574  <w:LsdException Locked="false" Priority="46"
575   Name="Grid Table 1 Light Accent 6"/>
576  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
577  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
578  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
579  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
580  <w:LsdException Locked="false" Priority="51"
581   Name="Grid Table 6 Colorful Accent 6"/>
582  <w:LsdException Locked="false" Priority="52"
583   Name="Grid Table 7 Colorful Accent 6"/>
584  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
585  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
586  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
587  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
588  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
589  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
590  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
591  <w:LsdException Locked="false" Priority="46"
592   Name="List Table 1 Light Accent 1"/>
593  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
594  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
595  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
596  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
597  <w:LsdException Locked="false" Priority="51"
598   Name="List Table 6 Colorful Accent 1"/>
599  <w:LsdException Locked="false" Priority="52"
600   Name="List Table 7 Colorful Accent 1"/>
601  <w:LsdException Locked="false" Priority="46"
602   Name="List Table 1 Light Accent 2"/>
603  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
604  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
605  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
606  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
607  <w:LsdException Locked="false" Priority="51"
608   Name="List Table 6 Colorful Accent 2"/>
609  <w:LsdException Locked="false" Priority="52"
610   Name="List Table 7 Colorful Accent 2"/>
611  <w:LsdException Locked="false" Priority="46"
612   Name="List Table 1 Light Accent 3"/>
613  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
614  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
615  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
616  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
617  <w:LsdException Locked="false" Priority="51"
618   Name="List Table 6 Colorful Accent 3"/>
619  <w:LsdException Locked="false" Priority="52"
620   Name="List Table 7 Colorful Accent 3"/>
621  <w:LsdException Locked="false" Priority="46"
622   Name="List Table 1 Light Accent 4"/>
623  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
624  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
625  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
626  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
627  <w:LsdException Locked="false" Priority="51"
628   Name="List Table 6 Colorful Accent 4"/>
629  <w:LsdException Locked="false" Priority="52"
630   Name="List Table 7 Colorful Accent 4"/>
631  <w:LsdException Locked="false" Priority="46"
632   Name="List Table 1 Light Accent 5"/>
633  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
634  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
635  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
636  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
637  <w:LsdException Locked="false" Priority="51"
638   Name="List Table 6 Colorful Accent 5"/>
639  <w:LsdException Locked="false" Priority="52"
640   Name="List Table 7 Colorful Accent 5"/>
641  <w:LsdException Locked="false" Priority="46"
642   Name="List Table 1 Light Accent 6"/>
643  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
644  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
645  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
646  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
647  <w:LsdException Locked="false" Priority="51"
648   Name="List Table 6 Colorful Accent 6"/>
649  <w:LsdException Locked="false" Priority="52"
650   Name="List Table 7 Colorful Accent 6"/>
651  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
652   Name="Mention"/>
653  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
654   Name="Smart Hyperlink"/>
655  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
656   Name="Hashtag"/>
657  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
658   Name="Unresolved Mention"/>
659  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
660   Name="Smart Link"/>
661 </w:LatentStyles>
662</xml><![endif]-->
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771        mso-fareast-theme-font:minor-latin;}
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1197</head>
1198
1199<body lang=EN-US link=blue vlink="#954F72" style='tab-interval:.5in;word-wrap:
1200break-word'>
1201
1202<div class=WordSection1>
1203
1204<h1 align=center style='text-align:center'><a name="_GoBack"></a>Tutorial: Preparing
1205a Full CIF<o:p></o:p></h1>
1206
1207<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><BL><![if !supportLists]><span
1208style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1209Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1210</span></span></span><![endif]><span dir=LTR></span>Exercise files are found <a
1211href="./data" target="_blank">here</a>. The data files are taken
1212from the conclusion of the “<a
1213href="../CWCombined/Combined%20refinement.htm">Combined X-ray/neutron
1214refinement – PbSO<sub>4</sub></a>” tutorial. <o:p></o:p></p>
1215
1216</BL>
1217
1218<h1>Background <o:p></o:p></h1>
1219
1220<p class=MsoNormal>Crystallography has had a long tradition where experimental
1221data as well as results were reported numerically, so that results could be
1222verified independently as well as utilized. In the past two decades the field has
1223set the standard for data science compared to almost all other areas of
1224physical and biological science through the development of the Crystallographic
1225Information Framework (CIF) which defines a universal format for the reporting
1226of nearly all aspects of a crystallographic fit. This is particularly true for
1227Rietveld fits, where the <span class=SpellE>pdCIF</span> subset of CIF has been
1228developed to capture the observed and computed patterns as well as reflection
1229tables and coordinates as well as interatomic distances and angles. </p>
1230
1231<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1232
1233<p class=MsoNormal>Within GSAS-II, a CIF for a phase <span class=GramE>are</span>
1234available as “quick” coordinate-only file, which provides atom coordinates and
1235displacement parameters, but no uncertainties or other supporting information from
1236the refinement. This is indeed easy with a single menu command. Likewise, a CIF
1237containing only a dataset without phase information can be easily created from
1238the Export menu, but the real power of CIF comes after a project has been completed.
1239Using the “Entire project as
” a “Full CIF” menu command in the Export menu,
1240all results can be reported in a machine and human readable. There are a few
1241steps in generating a full project CIF. This tutorial goes through them and
1242explains what is being done and why. </p>
1243
1244<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1245
1246<p class=MsoNormal>A bit of background on CIF: The format allows a label (a CIF
1247data item, such as _cell_length_a or _publ_author_name) to be associated with either a single value or a column
1248in a table. A collection of data items is placed in a block. For a single-crystal
1249structure, a block will usually contain the coordinates for a phase and the
1250structure factors (experimental data and the matching simulated values) as well
1251as supporting information and derived results. With multiple temperatures, a block
1252would be needed for each setting because, for example, only one set of unit
1253cell dimensions and coordinates can be defined in a block. With powder diffraction,
1254if a single dataset (histogram) is used and only one phase is present, a single
1255block can be used. If either more than one phase is present, or more than one
1256histogram is used, multiple blocks are required. GSAS-II will create single-block
1257CIFs when possible, but otherwise will create a block for the overall
1258refinement plus a block for each histogram and a block for each phase. Referencing
1259information between different blocks requires that each block be labeled with a
1260unique name. These block labels are assembled from a number of fields supplied
1261by the user and a timestamp when the file is created. </p>
1262
1263<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1264
1265<p class=MsoNormal>A tremendous amount of information can be placed into a CIF
1266file. No one is likely to specify all of the field in the IUCr-supplied template,
1267which itself does not include all data items defined in CIF. Some information can
1268be supplied by GSAS-II from what is defined inside a project, data such as
1269symmetry and lattice parameters, but other information, for example synthesis
1270conditions or sample color, must be supplied by the user. This could be done
1271with a simple text editor once the file is created, but the problem that arises
1272from that approach is that it is common that after one has produced the “final”
1273refinement, another idea occurs for a slightly better fit. The approach used in
1274GSAS-II is that as the CIF is generated, copies of template files are made that
1275contain all the user-supplied information. Thus, the CIF can be recreated from
1276the updated project without having to repeat all the work in supplying that information.
1277Also, by saving template files that have setting information that will be
1278common amongst multiple projects (for example, diffraction instrumentation
1279descriptions) these files can be reused, avoiding repetitive tasks. <span
1280style='mso-spacerun:yes'> </span></p>
1281
1282<h1>Prerequisite <o:p></o:p></h1>
1283
1284<p class=MsoNormal>Before beginning this tutorial, either complete the
1285refinement in the “<a href="../../../CWCombined/Combined%20refinement.htm">Combined
1286X-ray/neutron refinement – PbSO<sub>4</sub></a>” tutorial or download the GSAS-II
1287project file provided <a href="../../../Scratch/data" target="_blank">here</a>,
1288which provides a two histogram, one phase refinement. </p>
1289
1290<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1291
1292<h2>Part 1. Enter a name for the author of the CIF file. </h2>
1293
1294<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1295
1296<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1297style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1298Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1299</span></span></span><![endif]><span dir=LTR></span>Select the Controls entry
1300on the data tree and enter the name for the main author for the project and
1301CIF.</p>
1302
1303<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1304
1305<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
1306 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
1307 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
1308 <v:stroke joinstyle="miter"/>
1309 <v:formulas>
1310  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1311  <v:f eqn="sum @0 1 0"/>
1312  <v:f eqn="sum 0 0 @1"/>
1313  <v:f eqn="prod @2 1 2"/>
1314  <v:f eqn="prod @3 21600 pixelWidth"/>
1315  <v:f eqn="prod @3 21600 pixelHeight"/>
1316  <v:f eqn="sum @0 0 1"/>
1317  <v:f eqn="prod @6 1 2"/>
1318  <v:f eqn="prod @7 21600 pixelWidth"/>
1319  <v:f eqn="sum @8 21600 0"/>
1320  <v:f eqn="prod @7 21600 pixelHeight"/>
1321  <v:f eqn="sum @10 21600 0"/>
1322 </v:formulas>
1323 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1324 <o:lock v:ext="edit" aspectratio="t"/>
1325</v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1042" type="#_x0000_t75"
1326 alt="GSAS-II Graphical user interface: Entering author name on Controls panel"
1327 style='width:351pt;height:272pt;visibility:visible;mso-wrap-style:square'>
1328 <v:imagedata src="CIFtutorial.fld/image001.png" o:title=" Entering author name on Controls panel"
1329  croptop="3621f" cropbottom="7013f" cropleft="4297f" cropright="4525f"/>
1330</v:shape><![endif]--><![if !vml]><img border=0 width=351 height=272
1331src="CIFtutorial.fld/image002.png"
1332alt="GSAS-II Graphical user interface: Entering author name on Controls panel"
1333v:shapes="Picture_x0020_1"><![endif]></span></p>
1334
1335<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1336
1337<h2>Part 2: Start the export process</h2>
1338
1339<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1340
1341<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1342style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1343Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1344</span></span></span><![endif]><span dir=LTR></span>Using the Export menu,
1345select the “Entire project as” menu item and the “Full CIF” submenu option. </p>
1346
1347<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1348
1349<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1350 id="Picture_x0020_2" o:spid="_x0000_i1041" type="#_x0000_t75" alt="Graphical user interface: menu item for export poject as CIF"
1351 style='width:231pt;height:34pt;visibility:visible;mso-wrap-style:square'>
1352 <v:imagedata src="CIFtutorial.fld/image003.png" o:title=" menu item for export poject as CIF"/>
1353</v:shape><![endif]--><![if !vml]><img border=0 width=231 height=34
1354src="CIFtutorial.fld/image003.png"
1355alt="Graphical user interface: menu item for export poject as CIF" v:shapes="Picture_x0020_2"><![endif]></span></p>
1356
1357<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1358
1359<p class=MsoNormal>This opens a dialog (exact appearance will depend on the
1360operating system you are using) where you can select a name for the file to be
1361created. </p>
1362
1363<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1364 id="Picture_x0020_3" o:spid="_x0000_i1040" type="#_x0000_t75" alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1365 style='width:356pt;height:226pt;visibility:visible;mso-wrap-style:square'>
1366 <v:imagedata src="CIFtutorial.fld/image004.png" o:title="Graphical user interface, application&#10;&#10;Description automatically generated"
1367  croptop="3754f" cropbottom="7578f" cropleft="3746f" cropright="3831f"/>
1368</v:shape><![endif]--><![if !vml]><img border=0 width=356 height=226
1369src="CIFtutorial.fld/image005.png"
1370alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1371v:shapes="Picture_x0020_3"><![endif]></span></p>
1372
1373<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1374
1375<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1376style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1377Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1378</span></span></span><![endif]><span dir=LTR></span>Enter a name for the file
1379if you wish to override the default name and press Save. If that file exists,
1380you will need to agree to overwrite it or to select a new name. </p>
1381
1382<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1383
1384<h2>Part 3: Select instrument name(s)</h2>
1385
1386<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1387
1388<p class=MsoNormal>Before a CIF can be created, each histogram must have associated
1389with it an instrument name. Note that the instrument name appears in the Sample
1390Parameters tree entry for each histogram. If any instrument does not have a
1391name, the dialog below is displayed. </p>
1392
1393<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1394
1395<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1396 id="Picture_x0020_4" o:spid="_x0000_i1039" type="#_x0000_t75" alt="Graphical user interface: enter instrument name&#10;"
1397 style='width:199pt;height:188pt;visibility:visible;mso-wrap-style:square'>
1398 <v:imagedata src="CIFtutorial.fld/image006.png" o:title=" enter instrument name&#10;"/>
1399</v:shape><![endif]--><![if !vml]><img border=0 width=199 height=188
1400src="CIFtutorial.fld/image006.png"
1401alt="Graphical user interface: enter instrument name&#10;" v:shapes="Picture_x0020_4"><![endif]></span></p>
1402
1403<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1404
1405<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1406
1407<p class=MsoNormal>Ideally the instrument name will be unique, so the combination
1408of the name and a timestamp will create an identifier that is unlikely to be
1409repeated. The instrument name should also allow the data source to be
1410identified should there be several similar instruments within an institution,
1411but the details for naming are left as a local decision. Inclusion of an institution
1412name is a good idea, so an ideal name might be “Univ. of Mars, Curiosity II”.
1413While in this case the two histograms are from different instruments, the down
1414arrow (<span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
1415mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
1416Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Ú</span></span>)
1417button will copy the entered name to all fields below, simplifying the data
1418entry task, when appropriate. <o:p></o:p></p>
1419
1420<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1421
1422<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1423style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1424Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1425</span></span></span><![endif]><span dir=LTR></span>Enter names for each instrument
1426and then press OK.</p>
1427
1428<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1429
1430<h2>Part 4: Bond distance/Angle criteria</h2>
1431
1432<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1433
1434<p class=MsoNormal>One significant part of a CIF is the computation of bond
1435distances and angles. For this there is a set of atomic radii for each phase
1436along with a tolerance factor. When the CIF creation is initially invoked, the
1437dialog below is shown for each phase:</p>
1438
1439<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1440
1441<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1442 id="Picture_x0020_5" o:spid="_x0000_i1038" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1443 style='width:180pt;height:164pt;visibility:visible;mso-wrap-style:square'>
1444 <v:imagedata src="CIFtutorial.fld/image007.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1445</v:shape><![endif]--><![if !vml]><img border=0 width=180 height=164
1446src="CIFtutorial.fld/image007.png"
1447alt="Graphical user interface&#10;&#10;Description automatically generated"
1448v:shapes="Picture_x0020_5"><![endif]></span></p>
1449
1450<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1451
1452<p class=MsoNormal>This dialog will not be shown again, unless invoked manually.
1453To explain what these numbers mean, distances between Pb and O atoms will be
1454reported when their interatomic distance is less than or equal to (1.95+1.09)*0.85
1455Å (=2.584 Å) and O-Pb-X or X-O-Pb angles will be reported if the Pb-O distance is
1456less than or equal to (1.75+0.89)*0.85 Å (=2.244 Å) <i>and</i> the O-X or Pb-X
1457is within the requirement for that pair of atoms as well (in this case X could
1458be O, Pb or S). </p>
1459
1460<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1461
1462<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1463style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1464Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1465</span></span></span><![endif]><span dir=LTR></span>In this case no changes are
1466needed, so simply press OK.</p>
1467
1468<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1469
1470<h2>Part 5. <span class=GramE>Conditions</span> warning</h2>
1471
1472<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1473
1474<p class=MsoNormal>Note that when a histogram is created in GSAS-II, unless
1475pressure and temperature values are reported in the metadata in a standardized
1476fashion (this is uncommon), the sample temperature defaults to 300 K and the
1477ambient pressure to 0.1 MPa. It is likely that these values do not describe the
1478actual data collection conditions. Since they will be included in the CIF, they
1479should be updated with more appropriate values.</p>
1480
1481<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1482
1483<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1484 id="Picture_x0020_6" o:spid="_x0000_i1037" type="#_x0000_t75" alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1485 style='width:352pt;height:185pt;visibility:visible;mso-wrap-style:square'>
1486 <v:imagedata src="CIFtutorial.fld/image008.png" o:title="Graphical user interface, text, application&#10;&#10;Description automatically generated"/>
1487</v:shape><![endif]--><![if !vml]><img border=0 width=352 height=185
1488src="CIFtutorial.fld/image008.png"
1489alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1490v:shapes="Picture_x0020_6"><![endif]></span></p>
1491
1492<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1493style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1494Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1495</span></span></span><![endif]><span dir=LTR></span>Press OK to continue.</p>
1496
1497<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1498
1499<p class=MsoNormal>This warning is shown every time the code is CIF generation
1500code is initiated unless the sample temperature has been set to a value other
1501than 300 K for each histogram. Note that the Command<span class=GramE>/“</span>Copy
1502Selected” may be useful to change a value in multiple histograms in one
1503operation. Note that this warning may be ignored if the histogram values are
1504correct. </p>
1505
1506<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1507
1508<h2>Part 6. Specifying CIF Contents. </h2>
1509
1510<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1511
1512<p class=MsoNormal>Once the previous steps have been performed, a window such
1513as the one below is shown. Note that the “Edit CIF Author” button opens a
1514dialog window, where the information supplied in Part 1 can be changed. The “Edit
1515Instrument Name(s)” button reopens the window shown in Part 3.</p>
1516
1517<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1518
1519<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1520 id="Picture_x0020_7" o:spid="_x0000_i1036" type="#_x0000_t75" alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1521 style='width:194pt;height:298pt;visibility:visible;mso-wrap-style:square'>
1522 <v:imagedata src="CIFtutorial.fld/image009.png" o:title="Graphical user interface, text, application&#10;&#10;Description automatically generated"/>
1523</v:shape><![endif]--><![if !vml]><img border=0 width=194 height=298
1524src="CIFtutorial.fld/image009.png"
1525alt="Graphical user interface, text, application&#10;&#10;Description automatically generated"
1526v:shapes="Picture_x0020_7"><![endif]></span></p>
1527
1528<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1529
1530<p class=MsoNormal>Note that for every other section of the window, there is are
1531a pair of buttons labeled “Select Template File” and “Edit Template.” A default
1532template file is selected initially, and information can be included in that
1533template with the “Edit Template” button, as will be shown below. Note that there
1534are four types of template files for (1) overall information; (2) phase
1535information; (3) powder diffraction data and instrumentation details; and (4) single-crystal
1536diffraction data and instrumentation details. Note that data items that are set
1537by GSAS-II directly (for example, lattice parameters and space group
1538information for a phase) are not included in the template. </p>
1539
1540<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1541
1542<p class=MsoNormal>The information you specify to place in a template is included
1543in the GSAS-II project (.<span class=SpellE>gpx</span>) file so that if you
1544perform a new refinement, all of the template edits you have made are used
1545automatically when a new CIF is created. </p>
1546
1547<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1548
1549<p class=MsoNormal>As you are editing each template, you can save that
1550information in a file. There are two reasons for doing this. One is that by
1551saving the information as a file you potentially create a customized template
1552file. Use of this file in the future for a different project can save you considerable
1553time, as an example, when documenting a diffractometer. Also, if a file is
1554saved, instead of keeping all of the template contents in the .<span
1555class=SpellE>gpx</span> file, only the name of the template file is saved,
1556reducing the project file size slightly. (The default template files range from
15571K to 4K bytes in size, so this not usually very significant savings.) Once a customized
1558template file has been created, use the “Select Template File” button to select
1559it in place of the default. </p>
1560
1561<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1562
1563<p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1564style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1565Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1566</span></span></span><![endif]><span dir=LTR></span>Edit the Publication
1567template by pressing the “Edit Template” button closest to the top of the
1568window [just below the “Publication (overall) template” heading] a window similar
1569to the one below is created. </p>
1570
1571<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1572
1573<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1574 id="Picture_x0020_9" o:spid="_x0000_i1035" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1575 style='width:169pt;height:225pt;visibility:visible;mso-wrap-style:square'>
1576 <v:imagedata src="CIFtutorial.fld/image010.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1577</v:shape><![endif]--><![if !vml]><img border=0 width=169 height=225
1578src="CIFtutorial.fld/image010.png"
1579alt="Graphical user interface&#10;&#10;Description automatically generated"
1580v:shapes="Picture_x0020_9"><![endif]></span></p>
1581
1582<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1583
1584<p class=MsoNormal>A few notes on the arrangement of this window, which is a
1585bit easier to use if manually resized, as below. </p>
1586
1587<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1588 id="Picture_x0020_10" o:spid="_x0000_i1034" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1589 style='width:269pt;height:200pt;visibility:visible;mso-wrap-style:square'>
1590 <v:imagedata src="CIFtutorial.fld/image011.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1591</v:shape><![endif]--><![if !vml]><img border=0 width=269 height=200
1592src="CIFtutorial.fld/image011.png"
1593alt="Graphical user interface&#10;&#10;Description automatically generated"
1594v:shapes="Picture_x0020_10"><![endif]></span><span
1595style='mso-spacerun:yes'> </span></p>
1596
1597<p class=MsoNormal>Note that this contains three CIF items, _<span
1598class=SpellE>publ_author_name</span>, _<span class=SpellE>publ_author_footnote</span>
1599and _<span class=SpellE>publ_author_address</span>, in a table (loop_). Note
1600the “Add row” button to the upper left which allows additional rows to be added
1601to the table. The remainder of this template is a series of CIF items that accept
1602a single value. Most CIF items are tagged with a help button, marked with a
1603question mark. That indicates that that CIF item is defined in a CIF
1604dictionary. The definition can be looked up by pressing that help button or by
1605allowing the mouse to stay stationary on a CIF item name for a few seconds
1606which causes the definition text to appear as a tool tip, as below,</p>
1607
1608<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1609 id="Picture_x0020_11" o:spid="_x0000_i1033" type="#_x0000_t75" alt="A picture containing graphical user interface&#10;&#10;Description automatically generated"
1610 style='width:205pt;height:96pt;visibility:visible;mso-wrap-style:square'>
1611 <v:imagedata src="CIFtutorial.fld/image012.png" o:title="A picture containing graphical user interface&#10;&#10;Description automatically generated"/>
1612</v:shape><![endif]--><![if !vml]><img border=0 width=205 height=96
1613src="CIFtutorial.fld/image012.png"
1614alt="A picture containing graphical user interface&#10;&#10;Description automatically generated"
1615v:shapes="Picture_x0020_11"><![endif]></span></p>
1616
1617<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1618
1619<p class=MsoNormal>or clicking on the button displays the same information at
1620the bottom of the window, as below.</p>
1621
1622<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1623 id="Picture_x0020_12" o:spid="_x0000_i1032" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated with medium confidence"
1624 style='width:257pt;height:165pt;visibility:visible;mso-wrap-style:square'>
1625 <v:imagedata src="CIFtutorial.fld/image013.png" o:title="Graphical user interface&#10;&#10;Description automatically generated with medium confidence"/>
1626</v:shape><![endif]--><![if !vml]><img border=0 width=257 height=165
1627src="CIFtutorial.fld/image013.png"
1628alt="Graphical user interface&#10;&#10;Description automatically generated with medium confidence"
1629v:shapes="Picture_x0020_12"><![endif]></span></p>
1630
1631<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1632
1633<p class=MsoNormal>Note that each text entry box has a small right-angle
1634bracket (looking a bit like an inverted L) at the lower right corner. This can
1635be used to resize the text entry box to allow viewing a longer line of text
1636and/or several lines of text. </p>
1637
1638<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1639
1640<p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1641style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1642Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1643</span></span></span><![endif]><span dir=LTR></span>Press the “Add row” button
1644to create entries for a second author. </p>
1645
1646<p class=MsoListParagraphCxSpMiddle style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1647style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1648Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1649</span></span></span><![endif]><span dir=LTR></span>Enlarge the width of either
1650of the _<span class=SpellE>publ_author_name</span> entry boxes as well as the height
1651and width of the _<span class=SpellE>publ_author_address</span> item to accommodate
1652more text. </p>
1653
1654<p class=MsoListParagraphCxSpLast style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1655style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1656Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1657</span></span></span><![endif]><span dir=LTR></span>Add text to describe
1658authorship, such as what has been done below (authorship of the original Anglesite,
1659aka PbSO<sub>4</sub>, crystal structure). Note that as is described in the CIF
1660definition, author names are supplied as last name, first name. </p>
1661
1662<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1663
1664<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1665 id="Picture_x0020_13" o:spid="_x0000_i1031" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1666 style='width:331pt;height:277pt;visibility:visible;mso-wrap-style:square'>
1667 <v:imagedata src="CIFtutorial.fld/image014.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1668</v:shape><![endif]--><![if !vml]><img border=0 width=331 height=277
1669src="CIFtutorial.fld/image014.png"
1670alt="Graphical user interface&#10;&#10;Description automatically generated"
1671v:shapes="Picture_x0020_13"><![endif]></span></p>
1672
1673<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1674
1675<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1676style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1677Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1678</span></span></span><![endif]><span dir=LTR></span>After completing all
1679appropriate CIF items that would be appropriate for this work, press the “Use”
1680button to close the window, saving the entries into the project file. </p>
1681
1682<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1683
1684<p class=MsoNormal>Note that the window contents changes to indicate that the
1685template information is no longer from a file. </p>
1686
1687<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1688 id="Picture_x0020_14" o:spid="_x0000_i1030" type="#_x0000_t75" alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1689 style='width:148pt;height:86pt;visibility:visible;mso-wrap-style:square'>
1690 <v:imagedata src="CIFtutorial.fld/image015.png" o:title="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1691  croptop="910f" cropbottom="38375f"/>
1692</v:shape><![endif]--><![if !vml]><img border=0 width=148 height=86
1693src="CIFtutorial.fld/image016.png"
1694alt="Graphical user interface, text, application, email&#10;&#10;Description automatically generated"
1695v:shapes="Picture_x0020_14"><![endif]></span></p>
1696
1697<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1698
1699<h2>Part 7. Edit Phase Information including Distances and Angles. </h2>
1700
1701<p class=MsoNormal>The phase template contains a relatively small number of
1702items that can document information about a phase, as shown below. Note that _<span
1703class=SpellE>cell_measurement_temperature</span> is probably best used only
1704with single crystal fits. For powder data, the _<span class=SpellE>diffrn_ambient_temperature</span>
1705field will be set with the temperature supplied for Sample Parameters. If one
1706produced several projects all using the same sample, it might make sense to produce
1707a template file that might be used for that sample in all projects. </p>
1708
1709<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1710
1711<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1712 id="Picture_x0020_15" o:spid="_x0000_i1029" type="#_x0000_t75" alt="Diagram&#10;&#10;Description automatically generated with low confidence"
1713 style='width:195pt;height:310pt;visibility:visible;mso-wrap-style:square'>
1714 <v:imagedata src="CIFtutorial.fld/image017.png" o:title="Diagram&#10;&#10;Description automatically generated with low confidence"/>
1715</v:shape><![endif]--><![if !vml]><img border=0 width=195 height=310
1716src="CIFtutorial.fld/image017.png"
1717alt="Diagram&#10;&#10;Description automatically generated with low confidence"
1718v:shapes="Picture_x0020_15"><![endif]></span></p>
1719
1720<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1721
1722<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1723style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1724Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1725</span></span></span><![endif]><span dir=LTR></span>Press the “Set distance/angle
1726publication flag” the window below appears. </p>
1727
1728<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1729
1730<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1731 id="Picture_x0020_16" o:spid="_x0000_i1028" type="#_x0000_t75" alt="Table&#10;&#10;Description automatically generated"
1732 style='width:257pt;height:325pt;visibility:visible;mso-wrap-style:square'>
1733 <v:imagedata src="CIFtutorial.fld/image018.png" o:title="Table&#10;&#10;Description automatically generated"/>
1734</v:shape><![endif]--><![if !vml]><img border=0 width=257 height=325
1735src="CIFtutorial.fld/image018.png"
1736alt="Table&#10;&#10;Description automatically generated" v:shapes="Picture_x0020_16"><![endif]></span></p>
1737
1738<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1739
1740<p class=MsoNormal>This shows the interatomic distances and angles that that
1741occur within the radii specified above. Note that the Pb radius is too small to
1742pick up the coordination of that atom, so we should change that. </p>
1743
1744<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1745
1746<p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1747style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1748Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1749</span></span></span><![endif]><span dir=LTR></span>Press the “Done” button to
1750close this window</p>
1751
1752<p class=MsoListParagraphCxSpMiddle style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1753style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1754Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1755</span></span></span><![endif]><span dir=LTR></span>Press the “Edit distance/angle
1756ranges” button to bring up the screen below. Change the bond search factor from
17570.85 to 0.9 to increase the search range, as below.</p>
1758
1759<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1760
1761<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1762 id="Picture_x0020_17" o:spid="_x0000_i1027" type="#_x0000_t75" alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1763 style='width:150pt;height:137pt;visibility:visible;mso-wrap-style:square'>
1764 <v:imagedata src="CIFtutorial.fld/image019.png" o:title="Graphical user interface, application&#10;&#10;Description automatically generated"/>
1765</v:shape><![endif]--><![if !vml]><img border=0 width=150 height=137
1766src="CIFtutorial.fld/image019.png"
1767alt="Graphical user interface, application&#10;&#10;Description automatically generated"
1768v:shapes="Picture_x0020_17"><![endif]></span></p>
1769
1770<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1771
1772<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1773style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1774Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1775</span></span></span><![endif]><span dir=LTR></span>Press the “Set distance/angle
1776publication flag” and note the additional distances (but not angles) in the
1777window below. <o:p></o:p></p>
1778
1779<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1780
1781<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1782 id="Picture_x0020_18" o:spid="_x0000_i1026" type="#_x0000_t75" alt="Table&#10;&#10;Description automatically generated"
1783 style='width:262pt;height:337pt;visibility:visible;mso-wrap-style:square'>
1784 <v:imagedata src="CIFtutorial.fld/image020.png" o:title="Table&#10;&#10;Description automatically generated"/>
1785</v:shape><![endif]--><![if !vml]><img border=0 width=262 height=337
1786src="CIFtutorial.fld/image020.png"
1787alt="Table&#10;&#10;Description automatically generated" v:shapes="Picture_x0020_18"><![endif]></span></p>
1788
1789<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1790
1791<p class=MsoNormal>Note that to obtain the angles around the Pb and O atoms,
1792the values in the right-hand column and/or the angle search factor range must also
1793be extended. </p>
1794
1795<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1796
1797<p class=MsoNormal>Every bond and angle that is listed on the window will be
1798placed in the CIF when written. Note that while distances and angles are shown
1799in the window without uncertainties, if the atom positions have been varied,
1800the values with their uncertainties will be placed in the CIF (in standard
1801crystallographic notation). Also note that in the CIF each distance has an
1802associated _<span class=SpellE>geom_bond_publ_flag</span> value (for angles, _<span
1803class=SpellE>geom_angle_publ_flag</span>). The value for this can be “yes”&nbsp;or
1804“no” and a “yes” value indicates that the value should be placed in a table of
1805bond distances/angles, if generated from the CIF. By default, this flag
1806defaults to “yes<span class=GramE>”</span> but this can be changed by clicking
1807on the distance or angle button. </p>
1808
1809<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1810
1811<h2>Part 8. Create a Customized Template File. <o:p></o:p></h2>
1812
1813<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1814
1815<p class=MsoNormal>For this particular project, since these were data distributed
1816from a round-robin study many years ago, relatively little is documented on the
1817instruments, but as a useful exercise, I recommend opening documenting an
1818instrument that you use frequently (or twist the arm of the instrument
1819scientist at your favorite facility to do so.) <span
1820style='mso-spacerun:yes'> </span></p>
1821
1822<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1823
1824<p class=MsoListParagraph style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1825style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1826Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1827</span></span></span><![endif]><span dir=LTR></span>Press the “Edit Template”
1828button for either histogram <span class=GramE>and</span> define as many of the
1829appropriate fields as are appropriate. </p>
1830
1831<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1832
1833<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1834 id="Picture_x0020_19" o:spid="_x0000_i1025" type="#_x0000_t75" alt="Graphical user interface&#10;&#10;Description automatically generated"
1835 style='width:233pt;height:243pt;visibility:visible;mso-wrap-style:square'>
1836 <v:imagedata src="CIFtutorial.fld/image021.png" o:title="Graphical user interface&#10;&#10;Description automatically generated"/>
1837</v:shape><![endif]--><![if !vml]><img border=0 width=233 height=243
1838src="CIFtutorial.fld/image021.png"
1839alt="Graphical user interface&#10;&#10;Description automatically generated"
1840v:shapes="Picture_x0020_19"><![endif]></span></p>
1841
1842<p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1843style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1844Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1845</span></span></span><![endif]><span dir=LTR></span>Press the “Save as template”
1846button and save the file with a name and location that will make this readily
1847available for future use.</p>
1848
1849<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1850
1851<p class=MsoNormal>Note that the next time that “Export
 project
 to CIF” is
1852used, this template can be used by pressing the “Select Template File” button
1853for that histogram and by doing this all of the information specified previously
1854can be used without additional data entry effort. <span
1855style='mso-spacerun:yes'> </span></p>
1856
1857<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1858
1859<h2>Part 9. Create the CIF</h2>
1860
1861<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1862
1863<p class=MsoListParagraphCxSpFirst style='mso-list:l1 level1 lfo4'><![if !supportLists]><span
1864style='font-family:Symbol;mso-fareast-font-family:Symbol;mso-bidi-font-family:
1865Symbol'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
1866</span></span></span><![endif]><span dir=LTR></span>Pressing the “Create CIF”
1867button will cause the CIF to be written. </p>
1868
1869<p class=MsoListParagraphCxSpLast style='text-indent:0in;mso-list:none'><o:p>&nbsp;</o:p></p>
1870
1871<p class=MsoNormal>Depending on the number and size of histograms, this can be
1872a fairly large file as it contains observed and computed patterns for each, as
1873well as a reflection table, plus unit cell parameters, symmetry information, coordinates
1874and bond distances and angles for each phase. <o:p></o:p></p>
1875
1876<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1877
1878<p class=MsoNormal>Note that if the refinement information is changed, for
1879example by introducing a new variable, changing the background model etc. all
1880that need be done to create a CIF with updated information will be to select
1881the “Entire project as” menu item and the “Full CIF” submenu option from the
1882Export menu and then press the “Create CIF” button again. All information generated
1883by GSAS-II will be updated and previously entered will be retained and placed
1884in the new file. </p>
1885
1886<p class=MsoNormal><o:p>&nbsp;</o:p></p>
1887
1888</div>
1889
1890</body>
1891
1892</html>
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