source: Tutorials/StackingFaults-II/Stacking Faults II.htm @ 3083

Last change on this file since 3083 was 3083, checked in by vondreele, 4 years ago

update to 2 frame

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402  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
403  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
404  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
405  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
406  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
407  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
408  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
409  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
410  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
411  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
412  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
413  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
414  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
415  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
416  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
417  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
418  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
419  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
420  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
421  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
422  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
423  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
424  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
425  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
426  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
427  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
428  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
429  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
430  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
431  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
432  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
433  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
434  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
435  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
436  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
437  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
438  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
439  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
440  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
441  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
442  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
443  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
444  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
445  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
446  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
447  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
448  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
449  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
450  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
451  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
452  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
453  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
454  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
455  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
456  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
457  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
458  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
459  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
460  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
461  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
462  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
463  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
464  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
465  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
466  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
467  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
468  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
469  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
470  <w:LsdException Locked="false" Priority="19" QFormat="true"
471   Name="Subtle Emphasis"/>
472  <w:LsdException Locked="false" Priority="21" QFormat="true"
473   Name="Intense Emphasis"/>
474  <w:LsdException Locked="false" Priority="31" QFormat="true"
475   Name="Subtle Reference"/>
476  <w:LsdException Locked="false" Priority="32" QFormat="true"
477   Name="Intense Reference"/>
478  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
479  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
480   UnhideWhenUsed="true" Name="Bibliography"/>
481  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
482   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
483  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
484  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
485  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
486  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
487  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
488  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
489  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
490  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
491  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
492  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
493  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
494  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
495  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
496  <w:LsdException Locked="false" Priority="46"
497   Name="Grid Table 1 Light Accent 1"/>
498  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
499  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
500  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
501  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
502  <w:LsdException Locked="false" Priority="51"
503   Name="Grid Table 6 Colorful Accent 1"/>
504  <w:LsdException Locked="false" Priority="52"
505   Name="Grid Table 7 Colorful Accent 1"/>
506  <w:LsdException Locked="false" Priority="46"
507   Name="Grid Table 1 Light Accent 2"/>
508  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
509  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
510  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
511  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
512  <w:LsdException Locked="false" Priority="51"
513   Name="Grid Table 6 Colorful Accent 2"/>
514  <w:LsdException Locked="false" Priority="52"
515   Name="Grid Table 7 Colorful Accent 2"/>
516  <w:LsdException Locked="false" Priority="46"
517   Name="Grid Table 1 Light Accent 3"/>
518  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
519  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
520  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
521  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
522  <w:LsdException Locked="false" Priority="51"
523   Name="Grid Table 6 Colorful Accent 3"/>
524  <w:LsdException Locked="false" Priority="52"
525   Name="Grid Table 7 Colorful Accent 3"/>
526  <w:LsdException Locked="false" Priority="46"
527   Name="Grid Table 1 Light Accent 4"/>
528  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
529  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
530  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
531  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
532  <w:LsdException Locked="false" Priority="51"
533   Name="Grid Table 6 Colorful Accent 4"/>
534  <w:LsdException Locked="false" Priority="52"
535   Name="Grid Table 7 Colorful Accent 4"/>
536  <w:LsdException Locked="false" Priority="46"
537   Name="Grid Table 1 Light Accent 5"/>
538  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
539  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
540  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
541  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
542  <w:LsdException Locked="false" Priority="51"
543   Name="Grid Table 6 Colorful Accent 5"/>
544  <w:LsdException Locked="false" Priority="52"
545   Name="Grid Table 7 Colorful Accent 5"/>
546  <w:LsdException Locked="false" Priority="46"
547   Name="Grid Table 1 Light Accent 6"/>
548  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
549  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
550  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
551  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
552  <w:LsdException Locked="false" Priority="51"
553   Name="Grid Table 6 Colorful Accent 6"/>
554  <w:LsdException Locked="false" Priority="52"
555   Name="Grid Table 7 Colorful Accent 6"/>
556  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
557  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
558  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
559  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
560  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
561  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
562  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
563  <w:LsdException Locked="false" Priority="46"
564   Name="List Table 1 Light Accent 1"/>
565  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
566  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
567  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
568  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
569  <w:LsdException Locked="false" Priority="51"
570   Name="List Table 6 Colorful Accent 1"/>
571  <w:LsdException Locked="false" Priority="52"
572   Name="List Table 7 Colorful Accent 1"/>
573  <w:LsdException Locked="false" Priority="46"
574   Name="List Table 1 Light Accent 2"/>
575  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
576  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
577  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
578  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
579  <w:LsdException Locked="false" Priority="51"
580   Name="List Table 6 Colorful Accent 2"/>
581  <w:LsdException Locked="false" Priority="52"
582   Name="List Table 7 Colorful Accent 2"/>
583  <w:LsdException Locked="false" Priority="46"
584   Name="List Table 1 Light Accent 3"/>
585  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
586  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
587  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
588  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
589  <w:LsdException Locked="false" Priority="51"
590   Name="List Table 6 Colorful Accent 3"/>
591  <w:LsdException Locked="false" Priority="52"
592   Name="List Table 7 Colorful Accent 3"/>
593  <w:LsdException Locked="false" Priority="46"
594   Name="List Table 1 Light Accent 4"/>
595  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
596  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
597  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
598  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
599  <w:LsdException Locked="false" Priority="51"
600   Name="List Table 6 Colorful Accent 4"/>
601  <w:LsdException Locked="false" Priority="52"
602   Name="List Table 7 Colorful Accent 4"/>
603  <w:LsdException Locked="false" Priority="46"
604   Name="List Table 1 Light Accent 5"/>
605  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
606  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
607  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
608  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
609  <w:LsdException Locked="false" Priority="51"
610   Name="List Table 6 Colorful Accent 5"/>
611  <w:LsdException Locked="false" Priority="52"
612   Name="List Table 7 Colorful Accent 5"/>
613  <w:LsdException Locked="false" Priority="46"
614   Name="List Table 1 Light Accent 6"/>
615  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
616  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
617  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
618  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
619  <w:LsdException Locked="false" Priority="51"
620   Name="List Table 6 Colorful Accent 6"/>
621  <w:LsdException Locked="false" Priority="52"
622   Name="List Table 7 Colorful Accent 6"/>
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1090<![endif]--><!--[if gte mso 9]><xml>
1091 <o:shapedefaults v:ext="edit" spidmax="1026"/>
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1099
1100<div class=WordSection1>
1101
1102<h1><span style='mso-fareast-font-family:"Times New Roman"'>Stacking Fault
1103Simulations – II<o:p></o:p></span></h1>
1104
1105<p class=MsoNormal>In this exercise and the next you will simulate some
1106diffraction patterns from kaolinite clays. Kaolinite, <span class=GramE>Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(</span>OH)<sub>4</sub>,
1107is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> <span
1108class=SpellE>octahedra</span> on one side and SiO<sub>4</sub> <span
1109class=SpellE>tetrahedra</span> on the other. The layers stack with an offset to
1110ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span> &amp; Von <span
1111class=SpellE>Dreele</span>, 1989, Clay &amp; Clay Min. 37, 289-296) for a
1112sample of the most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from
1113other locations evidently have stacking faults so that the peaks are displaced,
1114have peculiar shapes and are above a varying background. For the exercise we
1115provide a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
1116class=SpellE>CuKa</span> radiation on a Bruker instrument and thus in the
1117Bruker RAW file format. The Keokuk kaolinite has some <span class=SpellE>dickite</span>
1118(different ordered stacking of kaolinite layers). The next exercise Stacking
1119Faults-III) covers a simple simulation of a faulted kaolinite from Georgia.</p>
1120
1121<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1122
1123<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 1. Creating
1124kaolinite layer<o:p></o:p></span></h2>
1125
1126<p class=MsoNormal>In this initial step we will load from a <span class=SpellE>cif</span>
1127file the structure of kaolinite, draw it to see the layer structure and then
1128transform it into forms suitable for stacking simulations. To begin do <b><span
1129style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>;
1130from the file dialog select <span class=SpellE><b style='mso-bidi-font-weight:
1131normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1132minor-latin;mso-hansi-theme-font:minor-latin'>StackingFaults</span></b></span><b
1133style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1134mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-II/data/</span></b><span
1135class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b></span>.
1136After the “are you sure” popup, there will be another warning you that 4 atom
1137types (‘O-H’) were not recognized chemical element symbols and they were
1138substituted by <span class=SpellE>Xe</span> to make them obvious in the atom
1139list. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1140you are offered a chance to change the phase name, I used ‘<b><span
1141style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’. The General tab
1142is displayed (notice the presence of <span class=SpellE>Xe</span> in the
1143element table).</p>
1144
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1170
1171<p class=MsoNormal>To fix the <span class=SpellE>Xe</span> atoms (they should
1172be O), select <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1173and then double click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1174column heading; a small popup will appear. Select <span class=SpellE><b><span
1175style='font-family:"Calibri",sans-serif'>Xe</span></b></span> &amp; press <b><span
1176style='font-family:"Calibri",sans-serif'>Ok</span></b>; the <span class=SpellE>Xe</span>
1177atoms at the bottom of the atom table will be highlighted. Next select <b><span
1178style='font-family:"Calibri",sans-serif'>Edit Atoms/On selected atoms…/Modify
1179parameters</span></b> from the Phase Data menu; a new popup will appear. Select
1180<b><span style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
1181style='font-family:"Calibri",sans-serif'>Ok</span></b>; a periodic table of the
1182element will appear. Select <b><span style='font-family:"Calibri",sans-serif'>O</span></b>
1183from the O-atom pulldown; the structure will be drawn with Al, Si &amp; O atoms
1184only.</p>
1185
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1192
1193<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
1194style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then
1195double click the empty upper left corner box of the table. All atoms will turn
1196green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1197Figure/Fill unit cell</span></b>; the structure will be redrawn with all atoms
1198that belong in the unit cell. Finally, double click on the <b><span
1199style='font-family:"Calibri",sans-serif'>Type</span></b> column heading, select
1200<b><span style='font-family:"Calibri",sans-serif'>Al</span></b> &amp; <b><span
1201style='font-family:"Calibri",sans-serif'>Si</span></b> (they will turn green)
1202and then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
1203CN sphere</span></b>. After a bit of rotating the structure around, the
1204layering along the c-axis (blue line) will be evident.</p>
1205
1206<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1207 id="Picture_x0020_16" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1208 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1209 <v:imagedata src="Stacking%20Faults%20II_files/image011.png" o:title=""/>
1210</v:shape><![endif]--><![if !vml]><img width=624 height=538
1211src="Stacking%20Faults%20II_files/image012.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
1212
1213<p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> <span
1214class=SpellE>tetrahedra</span> and AlO<sub>6</sub> <span class=SpellE>octahedra</span>.
1215Also notice that the next layer (represented by the 4 O atoms at the bottom of
1216the above drawing are offset giving a triclinic lattice.</p>
1217
1218<p class=MsoNormal>The stacking fault simulation calculation via <span
1219class=SpellE>DIFFaX</span> routines requires that the stacking layers be
1220defined in a coordinate system that has the stacking direction perpendicular to
1221the stacking plane defined as the c-axis. This requires transformation of the
1222unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this.
1223Select the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1224tab and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
1225a popup window will appear.</p>
1226
1227<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1228 id="Picture_x0020_23" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:262.5pt;
1229 height:301.5pt;visibility:visible;mso-wrap-style:square'>
1230 <v:imagedata src="Stacking%20Faults%20II_files/image013.png" o:title=""/>
1231</v:shape><![endif]--><![if !vml]><img width=350 height=402
1232src="Stacking%20Faults%20II_files/image014.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
1233
1234<p class=MsoNormal>Note that this allows one to transform the structure
1235according to a matrix and then shift the <span class=GramE>resultant</span>
1236positions along some vector and then select those that are unique according to
1237a selected space group. The pulldown gives a selection of commonly used
1238transformations; we want the last one, <span class=SpellE><b><span
1239style='font-family:"Calibri",sans-serif'>abc</span></b></span><b><span
1240style='font-family:"Calibri",sans-serif'>*</span></b>, which satisfies the
1241stacking fault requirement. Select it; notice that the space group is changed
1242to P1. Leave this as the kaolinite layer has no symmetry; in other
1243circumstances the layer may have an inversion center in which case P-1 should
1244be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
1245the new lattice parameters will be shown.</p>
1246
1247<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1248 id="Picture_x0020_24" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:262.5pt;
1249 height:301.5pt;visibility:visible;mso-wrap-style:square'>
1250 <v:imagedata src="Stacking%20Faults%20II_files/image003.png" o:title=""/>
1251</v:shape><![endif]--><![if !vml]><img width=350 height=402
1252src="Stacking%20Faults%20II_files/image015.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
1253
1254<p class=MsoNormal><span class=GramE>The a</span> &amp; b axes stay the same, but
1255c is now smaller (the interlayer distance in kaolinite) and <span
1256style='font-family:Symbol'>a</span> &amp; <span style='font-family:Symbol'>b</span>
1257= 90 (<span style='font-family:Symbol'>g</span> is unchanged). Press <b><span
1258style='font-family:"Calibri",sans-serif'>Ok</span></b>; a new phase (kaolinite <span
1259class=SpellE>abc</span>*) will be made and its General tab will be shown
1260immediately. Select the <b><span style='font-family:"Calibri",sans-serif'>Draw
1261Atoms</span></b> tab to see the resulting structure.</p>
1262
1263<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1264 id="Picture_x0020_25" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1265 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1266 <v:imagedata src="Stacking%20Faults%20II_files/image016.png" o:title=""/>
1267</v:shape><![endif]--><![if !vml]><img width=624 height=538
1268src="Stacking%20Faults%20II_files/image017.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
1269
1270<p class=MsoNormal>To see what this layer looks like with more of it drawn, you
1271can add more unit cells to the drawing; select all the atoms by double clicking
1272the upper left empty box of the Draw atoms table. Do <b><span style='font-family:
1273"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and <b><span
1274style='font-family:"Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup>
1275<b><span style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l
1276and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; this
1277will add one unit cell along x. Now select all the atoms again, do <b><span
1278style='font-family:"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and
1279now <b><span style='font-family:"Calibri",sans-serif'>decrement</span></b> the
12801<sup>st</sup> <b><span style='font-family:"Calibri",sans-serif'>Choose unit
1281cell</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1282the drawing will now be 3 unit cells wide along x. Repeat this once more <b><span
1283style='font-family:"Calibri",sans-serif'>decrementing</span></b> the 2<sup>nd</sup>
1284<b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>
1285to give a 3x2 unit cell block of atoms. Double click the <b><span
1286style='font-family:"Calibri",sans-serif'>Style</span></b> column heading and
1287select <b><span style='font-family:"Calibri",sans-serif'>Balls and sticks</span></b>;
1288the drawing should look like (after some zooming/shifting/rotation).</p>
1289
1290<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1291 id="Picture_x0020_26" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1292 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1293 <v:imagedata src="Stacking%20Faults%20II_files/image018.png" o:title=""/>
1294</v:shape><![endif]--><![if !vml]><img width=624 height=539
1295src="Stacking%20Faults%20II_files/image019.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
1296
1297<p class=MsoNormal>This structure is now suitable for use in <span
1298class=SpellE>DIFFaX</span> calculations; the cell has a c-axis that is perpendicular
1299to the ab plane with a length that is the stacking repeat distance. This is a
1300good place to save your project (I called it ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
1301
1302<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 2. Set up
1303simulation of ideal kaolinite stacking<o:p></o:p></span></h2>
1304
1305<p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
1306for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
1307powder pattern and compare it to some real data. To begin we need a new phase
1308that we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
1309style='font-family:"Calibri",sans-serif'>Data/Add new phase</span></b>; I named
1310it ‘<b><span style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The
1311General tab for it will immediately appear.</p>
1312
1313<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1314 id="Picture_x0020_27" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1315 height:225pt;visibility:visible;mso-wrap-style:square'>
1316 <v:imagedata src="Stacking%20Faults%20II_files/image020.png" o:title=""/>
1317</v:shape><![endif]--><![if !vml]><img width=624 height=300
1318src="Stacking%20Faults%20II_files/image021.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
1319
1320<p class=MsoNormal>Change the <b><span style='font-family:"Calibri",sans-serif'>Phase
1321type</span></b> to ‘<b><span style='font-family:"Calibri",sans-serif'>faulted</span></b>’;
1322the General tab will be redrawn and a new tab <b><span style='font-family:"Calibri",sans-serif'>‘Layers</span></b>’
1323will appear. Select it.</p>
1324
1325<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1326 id="Picture_x0020_28" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1327 height:196.5pt;visibility:visible;mso-wrap-style:square'>
1328 <v:imagedata src="Stacking%20Faults%20II_files/image022.png" o:title=""/>
1329</v:shape><![endif]--><![if !vml]><img width=624 height=262
1330src="Stacking%20Faults%20II_files/image023.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1331
1332<p class=MsoNormal>We can anticipate (given that kaolinite space group is C1)
1333that the <b><span style='font-family:"Calibri",sans-serif'>Diffraction Laue
1334symmetry</span></b> is <b><span style='font-family:"Calibri",sans-serif'>-1</span></b>.
1335We can enter by hand the lattice parameters from the kaolinite <span
1336class=SpellE>abc</span>* phase but an easier method is available. Do <b><span
1337style='font-family:"Calibri",sans-serif'>Operations/Copy phase cell</span></b>;
1338a file selection dialog will appear for your current directory and the file <span
1339class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
1340should be there. Select it; a small popup will appear listing the available
1341phases. Choose ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite <span
1342class=SpellE>abc</span>*</span></b>’ and press <b><span style='font-family:
1343"Calibri",sans-serif'>Ok</span></b>; the Layers window will be redrawn with the
1344new lattice parameters.</p>
1345
1346<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1347 id="Picture_x0020_29" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1348 height:196.5pt;visibility:visible;mso-wrap-style:square'>
1349 <v:imagedata src="Stacking%20Faults%20II_files/image024.png" o:title=""/>
1350</v:shape><![endif]--><![if !vml]><img width=624 height=262
1351src="Stacking%20Faults%20II_files/image025.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
1352
1353<p class=MsoNormal>Next, you need to define the layer. As it would be very
1354tedious to enter 24 atoms by hand, the alternative is to get them from the
1355previously created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
1356style='font-family:"Calibri",sans-serif'>Import new layer</span></b> box; the
1357file dialog with <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
1358will appear. Select the file and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>;
1359again a small popup with two phases listed will appear. Again select <b><span
1360style='font-family:"Calibri",sans-serif'>kaolinite <span class=SpellE>abc</span>*</span></b>
1361and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
1362Layers page will be redrawn with a layer (named kaolinite) will be filled out.</p>
1363
1364<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1365 id="Picture_x0020_30" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1366 height:238.5pt;visibility:visible;mso-wrap-style:square'>
1367 <v:imagedata src="Stacking%20Faults%20II_files/image026.png" o:title=""/>
1368</v:shape><![endif]--><![if !vml]><img width=624 height=318
1369src="Stacking%20Faults%20II_files/image027.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
1370
1371<p class=MsoNormal>If you move down to the bottom of the page to find the one
1372line <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer Transition
1373probabilities</span></b>. Change <span class=SpellE><b><span style='font-family:
1374"Calibri",sans-serif'>Dz</span></b></span><b><span style='font-family:"Calibri",sans-serif'>=1.0</span></b>
1375and press the plot box; the drawing will show a layer of kaolinite stacked directly
1376above another one.</p>
1377
1378<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1379 id="Picture_x0020_31" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
1380 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1381 <v:imagedata src="Stacking%20Faults%20II_files/image028.png" o:title=""/>
1382</v:shape><![endif]--><![if !vml]><img width=624 height=538
1383src="Stacking%20Faults%20II_files/image029.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1384
1385<p class=MsoNormal>Compare that to the stacking in kaolinite.</p>
1386
1387<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1388 id="Picture_x0020_32" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1389 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1390 <v:imagedata src="Stacking%20Faults%20II_files/image030.png" o:title=""/>
1391</v:shape><![endif]--><![if !vml]><img width=624 height=535
1392src="Stacking%20Faults%20II_files/image031.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1393
1394<p class=MsoNormal>Notice the effect of the offset. The 1<sup>st</sup> row of
1395SiO<sub>4</sub> <span class=SpellE>tetrahedra</span> are positioned directly
1396above the AlO<sub>6</sub> <span class=SpellE>octahedra</span> in the real
1397structure but not in the vertically stacked structure. We can use a bit of
1398simple geometry to work out what the offset is but first let us see what
1399happens in the simulation and how it compares to real data.</p>
1400
1401<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Import
1402Keokuk kaolinite data and do 1<sup>st</sup> simulation<o:p></o:p></span></h2>
1403
1404<p class=MsoNormal>First we need to import the Keokuk kaolinite powder data; do
1405<b><span style='font-family:"Calibri",sans-serif'>Import/Powder Data/from
1406Bruker RAW file</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Keokuk
1407<span class=SpellE>kaolinite.RAW</span></span></b> from the file dialog box;
1408press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> in the
1409next popup. A new file dialog appears requesting an instrument parameter file;
1410we will use an internal default instead. Press <b><span style='font-family:
1411"Calibri",sans-serif'>Cancel</span></b> and select <b><span style='font-family:
1412"Calibri",sans-serif'>Defaults for <span class=SpellE>CuKa</span> lab data</span></b>
1413from the next popup. This process will repeat since the RAW file contains two
1414scans. In the next popup, select only <b><span style='font-family:"Calibri",sans-serif'>kaolinite
1415<span class=SpellE>abc</span>*</span></b>. There will be two PWDR scans in the
1416GSAS-II data tree; one covers 2<span style='font-family:Symbol'>Q</span>= 10-90<span
1417style='font-family:"Calibri",sans-serif'>°</span> and the other covers 2<span
1418style='font-family:Symbol'>Q</span>=80-150°. Only the lower part of the first one
1419is going to be used in our simulation work as the calculations become very time
1420consuming for complex structures and high angle data. Select <b><span
1421style='font-family:"Calibri",sans-serif'>PWDR Keokuk <span class=SpellE>kaolinite.RAW</span>
1422Scan 1</span></b> from the GSAS-II data tree make sure it expands; its plot
1423will also show.</p>
1424
1425<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1426 id="Picture_x0020_33" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
1427 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1428 <v:imagedata src="Stacking%20Faults%20II_files/image032.png" o:title=""/>
1429</v:shape><![endif]--><![if !vml]><img width=624 height=535
1430src="Stacking%20Faults%20II_files/image033.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1431
1432<p class=MsoNormal>Go to <b><span style='font-family:"Calibri",sans-serif'>Limits</span></b>
1433and set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Tmax</span></b></span>
1434to <b><span style='font-family:"Calibri",sans-serif'>52.0</span></b>; that puts
1435the upper limit in a relatively clear part of the pattern. Then go to
1436Background and set the 1<sup>st</sup> coefficient to 20 (approximately the
1437background at 2<span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
1438mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
1439Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>=18).
1440Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>
1441and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
1442to something reasonable (I chose <b><span style='font-family:"Calibri",sans-serif'>20.0</span></b>)
1443and make sure the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
1444type is Bragg-Brentano</span></b>.</p>
1445
1446<p class=MsoNormal>Now we are ready for our 1<sup>st</sup> kaolinite
1447simulation. Go to <b><span style='font-family:"Calibri",sans-serif'>Phases/Keokuk</span></b>
1448and select the <b><span style='font-family:"Calibri",sans-serif'>Layers</span></b>
1449tab. Do <b><span style='font-family:"Calibri",sans-serif'>Operations/Simulate
1450pattern</span></b> and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>
1451in the popup. Select the <b><span style='font-family:"Calibri",sans-serif'>Scan
14521</span></b> pattern and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1453the simulation will finish quickly (press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>)
1454and the new plot will be displayed (I’ve zoomed in a bit).</p>
1455
1456<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1457 id="Picture_x0020_34" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1458 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1459 <v:imagedata src="Stacking%20Faults%20II_files/image034.png" o:title=""/>
1460</v:shape><![endif]--><![if !vml]><img width=624 height=535
1461src="Stacking%20Faults%20II_files/image035.gif" v:shapes="Picture_x0020_34"><![endif]></span>.</p>
1462
1463<p class=MsoNormal>As you can see the simulation (green curve) does not fit the
1464data (blue crosses) at all mostly due to the incorrect layer offset although
1465the 1<sup>st</sup> peak seems to be positioned correctly. To work out the
1466offset consider the drawing of kaolinite.</p>
1467
1468<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1469 id="Picture_x0020_35" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
1470 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1471 <v:imagedata src="Stacking%20Faults%20II_files/image036.png" o:title=""/>
1472</v:shape><![endif]--><![if !vml]><img width=624 height=538
1473src="Stacking%20Faults%20II_files/image037.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1474
1475<p class=MsoNormal>The offset <span class=SpellE>Dx</span> is given by the blue
1476arrow in the above drawing of kaolinite and is in fractional coordinates.
1477Geometry gives<o:p></o:p></p>
1478
1479<p class=MsoNormal><span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><i
1480 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1481 mso-no-proof:yes'><m:r>Dx</m:r><m:r>= </m:r></span></i><m:f><m:fPr><m:type
1482    m:val="lin"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family:
1483   "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic;
1484   mso-bidi-font-style:normal;mso-no-proof:yes'><m:ctrlPr></m:ctrlPr></span></m:fPr><m:num><i
1485   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1486   mso-no-proof:yes'><m:r>c</m:r><m:r> </m:r></span></i><m:func><m:funcPr><span
1487     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
1488     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
1489     normal;mso-no-proof:yes'><m:ctrlPr></m:ctrlPr></span></m:funcPr><m:fName><span
1490     style='font-family:"Cambria Math",serif;mso-no-proof:yes'><m:r><m:rPr><m:scr
1491        m:val="roman"/><m:sty m:val="p"/></m:rPr>cos</m:r></span></m:fName><m:e><i
1492     style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1493     mso-no-proof:yes'><m:r>&#946;</m:r></span></i></m:e></m:func></m:num><m:den><i
1494   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1495   mso-no-proof:yes'><m:r>a</m:r></span></i></m:den></m:f></m:oMath><![endif]--><![if !msEquation]><span
1496style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family:
1497"Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative;
1498top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
1499EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
1500 type="#_x0000_t75" style='width:84pt;height:14.25pt'>
1501 <v:imagedata src="Stacking%20Faults%20II_files/image038.png" o:title=""
1502  chromakey="white"/>
1503</v:shape><![endif]--><![if !vml]><img width=112 height=19
1504src="Stacking%20Faults%20II_files/image039.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;Or
1505in this case <b><span style='font-family:"Calibri",sans-serif'>-0.368</span></b>.
1506Set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Dx</span></b></span>
1507to this value &amp; repeat simulation.</p>
1508
1509<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1510 id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
1511 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1512 <v:imagedata src="Stacking%20Faults%20II_files/image040.png" o:title=""/>
1513</v:shape><![endif]--><![if !vml]><img width=624 height=535
1514src="Stacking%20Faults%20II_files/image041.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
1515
1516<p class=MsoNormal>There is some improvement but some parts are not very well
1517represented. Recall from the triclinic kaolinite lattice parameters that <span
1518style='font-family:Symbol'>a</span> was 91.7°; that will produce a small offset
1519in Dy. Using the same kind of geometry math gives <span class=SpellE><b><span
1520style='font-family:"Calibri",sans-serif'>Dy</span></b></span><b><span
1521style='font-family:"Calibri",sans-serif'>=-0.0246</span></b>. Enter this value
1522&amp; repeat the simulation again. This gives a much better fit to the observed
1523pattern, but the simulated peaks are too sharp; this can be fixed by changing
1524the U<span class=GramE>,V,W</span> Instrument parameters. I’d just set <b><span
1525style='font-family:"Calibri",sans-serif'>W=40</span></b> and the <b><span
1526style='font-family:"Calibri",sans-serif'>Histogram scale</span></b> (in <b><span
1527style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>) to <b><span
1528style='font-family:"Calibri",sans-serif'>40</span></b> and try again.</p>
1529
1530<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1531 id="Picture_x0020_37" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
1532 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1533 <v:imagedata src="Stacking%20Faults%20II_files/image042.png" o:title=""/>
1534</v:shape><![endif]--><![if !vml]><img width=624 height=535
1535src="Stacking%20Faults%20II_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
1536
1537<p class=MsoNormal>That is a pretty good fit for a stacking simulation. By
1538further hand tweaking of the parameters one can further improve the simulation
1539but based on what we see here we do have the right description of stacking in
1540Keokuk kaolinite. Doing sequence simulations varying each parameter over a
1541small range can be used to help with optimization, but in this case it would be
1542far easier to do a Rietveld refinement for this well ordered kaolinite. Save
1543your project as you will need it for the next exercise (Stacking Faults-III).<o:p></o:p></p>
1544
1545</span></div>
1546
1547</body>
1548
1549</html>
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