source: Tutorials/StackingFaults-II/Stacking Faults II.htm @ 4993

Last change on this file since 4993 was 4993, checked in by vondreele, 5 months ago

fix reference to 3rd phase

  • Property svn:mime-type set to text/html
File size: 77.4 KB
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399  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
400  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
401  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
402  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
403  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
404  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
405  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
406  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
407  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
408  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
409  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
410  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
411  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
412  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
413  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
414  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
415  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
416  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
417  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
418  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
419  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
420  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
421  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
422  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
423  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
424  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
425  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
426  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
427  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
428  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
429  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
430  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
431  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
432  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
433  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
434  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
435  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
436  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
437  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
438  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
439  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
440  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
441  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
442  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
443  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
444  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
445  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
446  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
447  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
448  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
449  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
450  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
451  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
452  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
453  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
454  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
455  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
456  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
457  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
458  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
459  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
460  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
461  <w:LsdException Locked="false" Priority="19" QFormat="true"
462   Name="Subtle Emphasis"/>
463  <w:LsdException Locked="false" Priority="21" QFormat="true"
464   Name="Intense Emphasis"/>
465  <w:LsdException Locked="false" Priority="31" QFormat="true"
466   Name="Subtle Reference"/>
467  <w:LsdException Locked="false" Priority="32" QFormat="true"
468   Name="Intense Reference"/>
469  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
470  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
471   UnhideWhenUsed="true" Name="Bibliography"/>
472  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
473   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
474  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
475  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
476  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
477  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
478  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
479  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
480  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
481  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
482  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
483  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
484  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
485  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
486  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
487  <w:LsdException Locked="false" Priority="46"
488   Name="Grid Table 1 Light Accent 1"/>
489  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
490  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
491  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
492  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
493  <w:LsdException Locked="false" Priority="51"
494   Name="Grid Table 6 Colorful Accent 1"/>
495  <w:LsdException Locked="false" Priority="52"
496   Name="Grid Table 7 Colorful Accent 1"/>
497  <w:LsdException Locked="false" Priority="46"
498   Name="Grid Table 1 Light Accent 2"/>
499  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
500  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
501  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
502  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
503  <w:LsdException Locked="false" Priority="51"
504   Name="Grid Table 6 Colorful Accent 2"/>
505  <w:LsdException Locked="false" Priority="52"
506   Name="Grid Table 7 Colorful Accent 2"/>
507  <w:LsdException Locked="false" Priority="46"
508   Name="Grid Table 1 Light Accent 3"/>
509  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
510  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
511  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
512  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
513  <w:LsdException Locked="false" Priority="51"
514   Name="Grid Table 6 Colorful Accent 3"/>
515  <w:LsdException Locked="false" Priority="52"
516   Name="Grid Table 7 Colorful Accent 3"/>
517  <w:LsdException Locked="false" Priority="46"
518   Name="Grid Table 1 Light Accent 4"/>
519  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
520  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
521  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
522  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
523  <w:LsdException Locked="false" Priority="51"
524   Name="Grid Table 6 Colorful Accent 4"/>
525  <w:LsdException Locked="false" Priority="52"
526   Name="Grid Table 7 Colorful Accent 4"/>
527  <w:LsdException Locked="false" Priority="46"
528   Name="Grid Table 1 Light Accent 5"/>
529  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
530  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
531  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
532  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
533  <w:LsdException Locked="false" Priority="51"
534   Name="Grid Table 6 Colorful Accent 5"/>
535  <w:LsdException Locked="false" Priority="52"
536   Name="Grid Table 7 Colorful Accent 5"/>
537  <w:LsdException Locked="false" Priority="46"
538   Name="Grid Table 1 Light Accent 6"/>
539  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
540  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
541  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
542  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
543  <w:LsdException Locked="false" Priority="51"
544   Name="Grid Table 6 Colorful Accent 6"/>
545  <w:LsdException Locked="false" Priority="52"
546   Name="Grid Table 7 Colorful Accent 6"/>
547  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
548  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
549  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
550  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
551  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
552  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
553  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
554  <w:LsdException Locked="false" Priority="46"
555   Name="List Table 1 Light Accent 1"/>
556  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
557  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
558  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
559  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
560  <w:LsdException Locked="false" Priority="51"
561   Name="List Table 6 Colorful Accent 1"/>
562  <w:LsdException Locked="false" Priority="52"
563   Name="List Table 7 Colorful Accent 1"/>
564  <w:LsdException Locked="false" Priority="46"
565   Name="List Table 1 Light Accent 2"/>
566  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
567  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
568  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
569  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
570  <w:LsdException Locked="false" Priority="51"
571   Name="List Table 6 Colorful Accent 2"/>
572  <w:LsdException Locked="false" Priority="52"
573   Name="List Table 7 Colorful Accent 2"/>
574  <w:LsdException Locked="false" Priority="46"
575   Name="List Table 1 Light Accent 3"/>
576  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
577  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
578  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
579  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
580  <w:LsdException Locked="false" Priority="51"
581   Name="List Table 6 Colorful Accent 3"/>
582  <w:LsdException Locked="false" Priority="52"
583   Name="List Table 7 Colorful Accent 3"/>
584  <w:LsdException Locked="false" Priority="46"
585   Name="List Table 1 Light Accent 4"/>
586  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
587  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
588  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
589  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
590  <w:LsdException Locked="false" Priority="51"
591   Name="List Table 6 Colorful Accent 4"/>
592  <w:LsdException Locked="false" Priority="52"
593   Name="List Table 7 Colorful Accent 4"/>
594  <w:LsdException Locked="false" Priority="46"
595   Name="List Table 1 Light Accent 5"/>
596  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
597  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
598  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
599  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
600  <w:LsdException Locked="false" Priority="51"
601   Name="List Table 6 Colorful Accent 5"/>
602  <w:LsdException Locked="false" Priority="52"
603   Name="List Table 7 Colorful Accent 5"/>
604  <w:LsdException Locked="false" Priority="46"
605   Name="List Table 1 Light Accent 6"/>
606  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
607  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
608  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
609  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
610  <w:LsdException Locked="false" Priority="51"
611   Name="List Table 6 Colorful Accent 6"/>
612  <w:LsdException Locked="false" Priority="52"
613   Name="List Table 7 Colorful Accent 6"/>
614  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
615   Name="Mention"/>
616  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
617   Name="Smart Hyperlink"/>
618  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
619   Name="Hashtag"/>
620  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
621   Name="Unresolved Mention"/>
622  <w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
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1079<![endif]--><!--[if gte mso 9]><xml>
1080 <o:shapedefaults v:ext="edit" spidmax="1026"/>
1081</xml><![endif]--><!--[if gte mso 9]><xml>
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1085</head>
1086
1087<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in;word-wrap:
1088break-word'>
1089
1090<div class=WordSection1>
1091
1092<h1><span style='mso-fareast-font-family:"Times New Roman"'>Stacking Fault
1093Simulations – II<o:p></o:p></span></h1>
1094
1095<p class=MsoNormal><BL><span style='font-family:Symbol;mso-ascii-font-family:
1096"Times New Roman";mso-fareast-font-family:"Times New Roman"'>·</span><span
1097style='mso-fareast-font-family:"Times New Roman"'><span
1098style='mso-spacerun:yes'>  </span>Exercise files are found <a href="data/"
1099target="_blank">here</a> <o:p></o:p></span></p>
1100
1101</BL>
1102
1103<p class=MsoNormal><b>Introduction:</b> In this exercise and the next you will
1104simulate some diffraction patterns from kaolinite clays. Kaolinite, Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>,
1105is a 1:<span class=GramE>1 layer</span> silicate with a single unique sheet
1106with AlO<sub>6</sub> octahedra on one side and SiO<sub>4</sub> tetrahedra on
1107the other. The layers stack with an offset to ideally form a triclinic C1
1108lattice (<span class=SpellE>Bish</span> &amp; Von Dreele, 1989, Clay &amp; Clay
1109Min. 37, 289-296) for a sample of the most ordered form of kaolinite from
1110Keokuk, Iowa. Kaolinites from other locations evidently have stacking faults so
1111that the peaks are displaced, have peculiar shapes and are above a varying
1112background. For the exercise we provide a laboratory Bragg-Brentano pattern of
1113Keokuk kaolinite collected with <span class=SpellE>CuKa</span> radiation on a
1114Bruker instrument and thus in the Bruker RAW file format. The Keokuk kaolinite
1115has some dickite (different ordered stacking of kaolinite layers). The next
1116exercise Stacking Faults-III) covers a simple simulation of a faulted kaolinite
1117from Georgia.</p>
1118
1119<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1120
1121<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 1. Creating
1122kaolinite layer<o:p></o:p></span></h2>
1123
1124<p class=MsoNormal>In this initial step we will load from a <span class=SpellE>cif</span>
1125file the structure of kaolinite, draw it to see the layer structure and then
1126transform it into forms suitable for stacking simulations. To begin do <b><span
1127style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>;
1128from the file dialog select <span class=SpellE><b style='mso-bidi-font-weight:
1129normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1130minor-latin;mso-hansi-theme-font:minor-latin'>StackingFaults</span></b></span><b
1131style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1132mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-II/data/</span></b><span
1133class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b></span>.
1134After the “are you sure” popup, there will be another warning you that 4 atom
1135types (‘O-H’) were not recognized chemical element symbols and they were
1136substituted by Xe to make them obvious in the atom list. Press <b><span
1137style='font-family:"Calibri",sans-serif'>Ok</span></b>; you are offered a
1138chance to change the phase name, I used ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’.
1139The General tab is displayed (notice the presence of Xe in the element table).</p>
1140
1141<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
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1166
1167<p class=MsoNormal>To fix the Xe atoms (they should be O), select <b><span
1168style='font-family:"Calibri",sans-serif'>Atoms</span></b> and then double click
1169the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> column
1170heading; a small popup will appear. Select <b><span style='font-family:"Calibri",sans-serif'>Xe</span></b>
1171&amp; press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
1172Xe atoms at the bottom of the atom table will be highlighted. Next select <b><span
1173style='font-family:"Calibri",sans-serif'>Edit Atoms/On selected atoms…/Modify
1174parameters</span></b> from the Phase Data menu; a new popup will appear. Select
1175<b><span style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
1176style='font-family:"Calibri",sans-serif'>Ok</span></b>; a periodic table of the
1177element will appear. Select <b><span style='font-family:"Calibri",sans-serif'>O</span></b>
1178from the O-atom pulldown; the structure will be drawn with Al, Si &amp; O atoms
1179only.</p>
1180
1181<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1182 id="Picture_x0020_15" o:spid="_x0000_i1041" type="#_x0000_t75" style='width:468pt;
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1185</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
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1187
1188<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
1189style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then
1190double click the empty upper left corner box of the table. All atoms will turn
1191green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
1192unit cell</span></b>; the structure will be redrawn with all atoms that belong
1193in the unit cell. Finally, double click on the <b><span style='font-family:
1194"Calibri",sans-serif'>Type</span></b> column heading, select <b><span
1195style='font-family:"Calibri",sans-serif'>Al</span></b> &amp; <b><span
1196style='font-family:"Calibri",sans-serif'>Si</span></b> (they will turn green)
1197and then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
1198CN sphere</span></b>. After a bit of rotating the structure around, the
1199layering along the c-axis (blue line) will be evident.</p>
1200
1201<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1202 id="Picture_x0020_16" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1203 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1204 <v:imagedata src="Stacking%20Faults%20II_files/image011.png" o:title=""/>
1205</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
1206src="Stacking%20Faults%20II_files/image004.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
1207
1208<p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> tetrahedra
1209and AlO<sub>6</sub> octahedra. Also notice that the next layer (represented by
1210the 4 O atoms at the bottom of the above drawing are offset giving a triclinic
1211lattice.</p>
1212
1213<p class=MsoNormal>The stacking fault simulation calculation via <span
1214class=SpellE>DIFFaX</span> routines requires that the stacking layers be
1215defined in a coordinate system that has the stacking direction perpendicular to
1216the stacking plane defined as the c-axis. This requires transformation of the
1217unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this.
1218Select the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1219tab and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
1220a popup window will appear.</p>
1221
1222<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1223 id="Picture_x0020_23" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:262.5pt;
1224 height:301.5pt;visibility:visible;mso-wrap-style:square'>
1225 <v:imagedata src="Stacking%20Faults%20II_files/image013.png" o:title=""/>
1226</v:shape><![endif]--><![if !vml]><img border=0 width=350 height=402
1227src="Stacking%20Faults%20II_files/image005.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
1228
1229<p class=MsoNormal>Note that this allows one to transform the structure
1230according to a matrix and then shift the resultant positions along some vector
1231and then select those that are unique according to a selected space group. The
1232pulldown gives a selection of commonly used transformations; we want the last
1233one, <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>abc</span></b></span><b><span
1234style='font-family:"Calibri",sans-serif'>*</span></b>, which satisfies the
1235stacking fault requirement. Select it; notice that the space group is changed
1236to P1. Leave this as the kaolinite layer has no symmetry; in other
1237circumstances the layer may have an inversion center in which case P-1 should
1238be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
1239the new lattice parameters will be shown.</p>
1240
1241<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1242 id="Picture_x0020_24" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:262.5pt;
1243 height:301.5pt;visibility:visible;mso-wrap-style:square'>
1244 <v:imagedata src="Stacking%20Faults%20II_files/image003.png" o:title=""/>
1245</v:shape><![endif]--><![if !vml]><img border=0 width=350 height=402
1246src="Stacking%20Faults%20II_files/image006.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
1247
1248<p class=MsoNormal>The a &amp; b axes stay the same, but c is now smaller (the
1249interlayer distance in kaolinite) and <span style='font-family:Symbol'>a</span>
1250&amp; <span style='font-family:Symbol'>b</span> = 90 (<span style='font-family:
1251Symbol'>g</span> is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1252a new phase (kaolinite <span class=SpellE>abc</span>*) will be made and its
1253General tab will be shown immediately. Select the <b><span style='font-family:
1254"Calibri",sans-serif'>Draw Atoms</span></b> tab to see the resulting structure.</p>
1255
1256<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1257 id="Picture_x0020_25" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1258 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1259 <v:imagedata src="Stacking%20Faults%20II_files/image016.png" o:title=""/>
1260</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
1261src="Stacking%20Faults%20II_files/image038.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
1262
1263<p class=MsoNormal>To see what this layer looks like with more of it drawn, you
1264can add more unit cells to the drawing; select all the atoms by double clicking
1265the upper left empty box of the Draw atoms table. Do <b><span style='font-family:
1266"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and <b><span
1267style='font-family:"Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup>
1268<b><span style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l
1269and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; this
1270will add one unit cell along x. Now select all the atoms again, do <b><span
1271style='font-family:"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and
1272now <b><span style='font-family:"Calibri",sans-serif'>decrement</span></b> the
12731<sup>st</sup> <b><span style='font-family:"Calibri",sans-serif'>Choose unit
1274cell</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1275the drawing will now be 3 unit cells wide along x. Repeat this once more <b><span
1276style='font-family:"Calibri",sans-serif'>decrementing</span></b> the 2<sup>nd</sup>
1277<b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>
1278to give a 3x2 unit cell block of atoms. Double click the <b><span
1279style='font-family:"Calibri",sans-serif'>Style</span></b> column heading and
1280select <b><span style='font-family:"Calibri",sans-serif'>Balls and sticks</span></b>;
1281the drawing should look like (after some zooming/shifting/rotation).</p>
1282
1283<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1284 id="Picture_x0020_26" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1285 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1286 <v:imagedata src="Stacking%20Faults%20II_files/image018.png" o:title=""/>
1287</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
1288src="Stacking%20Faults%20II_files/image039.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
1289
1290<p class=MsoNormal>This structure is now suitable for use in <span
1291class=SpellE>DIFFaX</span> calculations; the cell has a c-axis that is
1292perpendicular to the ab plane with a length that is the stacking repeat
1293distance. This is a good place to save your project (I called it ‘<b><span
1294style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
1295
1296<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 2. Set up
1297simulation of ideal kaolinite stacking<o:p></o:p></span></h2>
1298
1299<p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
1300for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
1301powder pattern and compare it to some real data. To begin we need a new phase that
1302we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
1303style='font-family:"Calibri",sans-serif'>Data/Add new phase</span></b>; I named
1304it ‘<b><span style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The
1305General tab for it will immediately appear.</p>
1306
1307<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1308 id="Picture_x0020_27" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1309 height:225pt;visibility:visible;mso-wrap-style:square'>
1310 <v:imagedata src="Stacking%20Faults%20II_files/image020.png" o:title=""/>
1311</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=300
1312src="Stacking%20Faults%20II_files/image044.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
1313
1314<p class=MsoNormal>Change the <b><span style='font-family:"Calibri",sans-serif'>Phase
1315type</span></b> to ‘<b><span style='font-family:"Calibri",sans-serif'>faulted</span></b>’;
1316the General tab will be redrawn and a new tab <b><span style='font-family:"Calibri",sans-serif'>‘Layers</span></b>’
1317will appear. Select it.</p>
1318
1319<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1320 id="Picture_x0020_28" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1321 height:196.5pt;visibility:visible;mso-wrap-style:square'>
1322 <v:imagedata src="Stacking%20Faults%20II_files/image022.png" o:title=""/>
1323</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=262
1324src="Stacking%20Faults%20II_files/image045.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1325
1326<p class=MsoNormal>We can anticipate (given that kaolinite space group is C1)
1327that the <b><span style='font-family:"Calibri",sans-serif'>Diffraction Laue
1328symmetry</span></b> is <b><span style='font-family:"Calibri",sans-serif'>-1</span></b>.
1329We can enter by hand the lattice parameters from the kaolinite <span
1330class=SpellE>abc</span>* phase but an easier method is available. Do <b><span
1331style='font-family:"Calibri",sans-serif'>Operations/Copy phase cell</span></b>;
1332a file selection dialog will appear for your current directory and the file <span
1333class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
1334should be there. Select it; a small popup will appear listing the available
1335phases. Choose ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite <span
1336class=SpellE>abc</span>*</span></b>’ and press <b><span style='font-family:
1337"Calibri",sans-serif'>Ok</span></b>; the Layers window will be redrawn with the
1338new lattice parameters.</p>
1339
1340<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1341 id="Picture_x0020_29" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1342 height:196.5pt;visibility:visible;mso-wrap-style:square'>
1343 <v:imagedata src="Stacking%20Faults%20II_files/image024.png" o:title=""/>
1344</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=262
1345src="Stacking%20Faults%20II_files/image046.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
1346
1347<p class=MsoNormal>Next, you need to define the layer. As it would be very
1348tedious to enter 24 atoms by hand, the alternative is to get them from the
1349previously created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
1350style='font-family:"Calibri",sans-serif'>Import new layer</span></b> box; the
1351file dialog with <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
1352will appear. Select the file and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>;
1353again a small popup with two phases listed will appear. Again select <b><span
1354style='font-family:"Calibri",sans-serif'>kaolinite <span class=SpellE>abc</span>*</span></b>
1355and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the Layers
1356page will be redrawn with a layer (named kaolinite) will be filled out.</p>
1357
1358<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1359 id="Picture_x0020_30" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1360 height:238.5pt;visibility:visible;mso-wrap-style:square'>
1361 <v:imagedata src="Stacking%20Faults%20II_files/image026.png" o:title=""/>
1362</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=318
1363src="Stacking%20Faults%20II_files/image047.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
1364
1365<p class=MsoNormal>If you move down to the bottom of the page to find the one
1366line <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer Transition
1367probabilities</span></b>. Change <span class=SpellE><b><span style='font-family:
1368"Calibri",sans-serif'>Dz</span></b></span><b><span style='font-family:"Calibri",sans-serif'>=1.0</span></b>
1369and press the plot box; the drawing will show a layer of kaolinite stacked
1370directly above another one.</p>
1371
1372<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1373 id="Picture_x0020_31" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
1374 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1375 <v:imagedata src="Stacking%20Faults%20II_files/image028.png" o:title=""/>
1376</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
1377src="Stacking%20Faults%20II_files/image048.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1378
1379<p class=MsoNormal>Compare that to the stacking in kaolinite.</p>
1380
1381<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1382 id="Picture_x0020_32" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1383 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1384 <v:imagedata src="Stacking%20Faults%20II_files/image030.png" o:title=""/>
1385</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1386src="Stacking%20Faults%20II_files/image049.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1387
1388<p class=MsoNormal>Notice the effect of the offset. The 1<sup>st</sup> row of
1389SiO<sub>4</sub> tetrahedra are positioned directly above the AlO<sub>6</sub>
1390octahedra in the real structure but not in the vertically stacked structure. We
1391can use a bit of simple geometry to work out what the offset is but first let
1392us see what happens in the simulation and how it compares to real data.</p>
1393
1394<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Import
1395Keokuk kaolinite data and do 1<sup>st</sup> simulation<o:p></o:p></span></h2>
1396
1397<p class=MsoNormal>First we need to import the Keokuk kaolinite powder data; do
1398<b><span style='font-family:"Calibri",sans-serif'>Import/Powder Data/from
1399Bruker RAW file</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Keokuk
1400<span class=SpellE>kaolinite.RAW</span></span></b> from the file dialog box;
1401press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> in the
1402next popup. A new file dialog appears requesting an instrument parameter file;
1403we will use an internal default instead. Press <b><span style='font-family:
1404"Calibri",sans-serif'>Cancel</span></b> and select <b><span style='font-family:
1405"Calibri",sans-serif'>Defaults for <span class=SpellE>CuKa</span> lab data</span></b>
1406from the next popup. This process will repeat since the RAW file contains two
1407scans. In the next popup, select only <b><span style='font-family:"Calibri",sans-serif'>Keokuk
1408</span></b>(3<sup>rd</sup> phase). There will be two PWDR scans in the GSAS-II
1409data tree; one covers 2<span style='font-family:Symbol'>Q</span>= 10-90<span
1410style='font-family:"Calibri",sans-serif'>°</span> and the other covers 2<span
1411style='font-family:Symbol'>Q</span>=80-150°. Only the lower part of the first
1412one is going to be used in our simulation work as the calculations become very
1413time consuming for complex structures and high angle data. Select <b><span
1414style='font-family:"Calibri",sans-serif'>PWDR Keokuk <span class=SpellE>kaolinite.RAW</span>
1415Scan 1</span></b> from the GSAS-II data tree make sure it expands; its plot
1416will also show.</p>
1417
1418<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1419 id="Picture_x0020_33" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
1420 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1421 <v:imagedata src="Stacking%20Faults%20II_files/image032.png" o:title=""/>
1422</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1423src="Stacking%20Faults%20II_files/image050.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1424
1425<p class=MsoNormal>Go to <b><span style='font-family:"Calibri",sans-serif'>Limits</span></b>
1426and set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Tmax</span></b></span>
1427to <b><span style='font-family:"Calibri",sans-serif'>52.0</span></b>; that puts
1428the upper limit in a relatively clear part of the pattern. Then go to Background
1429and set the 1<sup>st</sup> coefficient to 20 (approximately the background at 2<span
1430style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
1431"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
1432style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>=18).
1433Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>
1434and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
1435to something reasonable (I chose <b><span style='font-family:"Calibri",sans-serif'>20.0</span></b>)
1436and make sure the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
1437type is Bragg-Brentano</span></b>.</p>
1438
1439<p class=MsoNormal>Now we are ready for our 1<sup>st</sup> kaolinite
1440simulation. Go to <b><span style='font-family:"Calibri",sans-serif'>Phases/Keokuk</span></b>
1441and select the <b><span style='font-family:"Calibri",sans-serif'>Layers</span></b>
1442tab. Do <b><span style='font-family:"Calibri",sans-serif'>Operations/Simulate
1443pattern</span></b> and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>
1444in the popup. Select the <b><span style='font-family:"Calibri",sans-serif'>Scan
14451</span></b> pattern and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1446the simulation will finish quickly (press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>)
1447and the new plot will be displayed (I’ve zoomed in a bit).</p>
1448
1449<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1450 id="Picture_x0020_34" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1451 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1452 <v:imagedata src="Stacking%20Faults%20II_files/image034.png" o:title=""/>
1453</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1454src="Stacking%20Faults%20II_files/image051.gif" v:shapes="Picture_x0020_34"><![endif]></span>.</p>
1455
1456<p class=MsoNormal>As you can see the simulation (green curve) does not fit the
1457data (blue crosses) at all mostly due to the incorrect layer offset although
1458the 1<sup>st</sup> peak seems to be positioned correctly. To work out the
1459offset consider the drawing of kaolinite.</p>
1460
1461<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1462 id="Picture_x0020_35" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
1463 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1464 <v:imagedata src="Stacking%20Faults%20II_files/image036.png" o:title=""/>
1465</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
1466src="Stacking%20Faults%20II_files/image052.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1467
1468<p class=MsoNormal>The offset Dx is given by the blue arrow in the above
1469drawing of kaolinite and is in fractional coordinates. Geometry gives<o:p></o:p></p>
1470
1471<p class=MsoNormal><span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><i
1472 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1473 mso-no-proof:yes'><m:r>Dx</m:r><m:r>= </m:r></span></i><m:f><m:fPr><m:type
1474    m:val="lin"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family:
1475   "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic;
1476   mso-bidi-font-style:normal;mso-no-proof:yes'><m:ctrlPr></m:ctrlPr></span></m:fPr><m:num><i
1477   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1478   mso-no-proof:yes'><m:r>c</m:r><m:r> </m:r></span></i><m:func><m:funcPr><span
1479     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
1480     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
1481     normal;mso-no-proof:yes'><m:ctrlPr></m:ctrlPr></span></m:funcPr><m:fName><span
1482     style='font-family:"Cambria Math",serif;mso-no-proof:yes'><m:r><m:rPr><m:scr
1483        m:val="roman"/><m:sty m:val="p"/></m:rPr>cos</m:r></span></m:fName><m:e><i
1484     style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1485     mso-no-proof:yes'><m:r>&#946;</m:r></span></i></m:e></m:func></m:num><m:den><i
1486   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1487   mso-no-proof:yes'><m:r>a</m:r></span></i></m:den></m:f></m:oMath><![endif]--><![if !msEquation]><span
1488style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family:
1489"Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative;
1490top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
1491EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
1492 type="#_x0000_t75" style='width:84.25pt;height:14.55pt'>
1493 <v:imagedata src="Stacking%20Faults%20II_files/image053.png" o:title=""
1494  chromakey="white"/>
1495</v:shape><![endif]--><![if !vml]><img width=112 height=19
1496src="Stacking%20Faults%20II_files/image054.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;Or
1497in this case <b><span style='font-family:"Calibri",sans-serif'>-0.368</span></b>.
1498Set <b><span style='font-family:"Calibri",sans-serif'>Dx</span></b> to this
1499value &amp; repeat simulation.</p>
1500
1501<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1502 id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
1503 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1504 <v:imagedata src="Stacking%20Faults%20II_files/image040.png" o:title=""/>
1505</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1506src="Stacking%20Faults%20II_files/image055.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
1507
1508<p class=MsoNormal>There is some improvement but some parts are not very well
1509represented. Recall from the triclinic kaolinite lattice parameters that <span
1510style='font-family:Symbol'>a</span> was 91.7°; that will produce a small offset
1511in Dy. Using the same kind of geometry math gives <b><span style='font-family:
1512"Calibri",sans-serif'>Dy=-0.0246</span></b>. Enter this value &amp; repeat the
1513simulation again. This gives a much better fit to the observed pattern, but the
1514simulated peaks are too sharp; this can be fixed by changing the <span
1515class=GramE>U,V</span>,W Instrument parameters. I’d just set <b><span
1516style='font-family:"Calibri",sans-serif'>W=40</span></b> and the <b><span
1517style='font-family:"Calibri",sans-serif'>Histogram scale</span></b> (in <b><span
1518style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>) to <b><span
1519style='font-family:"Calibri",sans-serif'>40</span></b> and try again.</p>
1520
1521<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1522 id="Picture_x0020_37" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
1523 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1524 <v:imagedata src="Stacking%20Faults%20II_files/image042.png" o:title=""/>
1525</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
1526src="Stacking%20Faults%20II_files/image056.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
1527
1528<p class=MsoNormal>That is a pretty good fit for a stacking simulation. By
1529further hand tweaking of the parameters one can further improve the simulation
1530but based on what we see here we do have the right description of stacking in
1531Keokuk kaolinite. Doing sequence simulations varying each parameter over a
1532small range can be used to help with optimization, but in this case it would be
1533far easier to do a Rietveld refinement for this well ordered kaolinite. Save
1534your project as you will need it for the next exercise (Stacking Faults-III).<o:p></o:p></p>
1535
1536</span></div>
1537
1538</body>
1539
1540</html>
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