source: Tutorials/StackingFaults-II/Stacking Faults II.htm @ 4457

Last change on this file since 4457 was 4457, checked in by toby, 18 months ago

add data link to tutorials

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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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1098<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
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><BL>
1106  <LI>Exercise files are found <A href="./data/" target="_blank">here</a>
1107</BL></P><P></P>
1108
1109<p class=MsoNormal><B>Introduction:</B> In this exercise and the next you will simulate some
1110diffraction 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>,
1111is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> <span
1112class=SpellE>octahedra</span> on one side and SiO<sub>4</sub> <span
1113class=SpellE>tetrahedra</span> on the other. The layers stack with an offset to
1114ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span> &amp; Von <span
1115class=SpellE>Dreele</span>, 1989, Clay &amp; Clay Min. 37, 289-296) for a
1116sample of the most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from
1117other locations evidently have stacking faults so that the peaks are displaced,
1118have peculiar shapes and are above a varying background. For the exercise we
1119provide a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
1120class=SpellE>CuKa</span> radiation on a Bruker instrument and thus in the
1121Bruker RAW file format. The Keokuk kaolinite has some <span class=SpellE>dickite</span>
1122(different ordered stacking of kaolinite layers). The next exercise Stacking
1123Faults-III) covers a simple simulation of a faulted kaolinite from Georgia.</p>
1124
1125<P></P><p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1126
1127<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 1. Creating
1128kaolinite layer<o:p></o:p></span></h2>
1129
1130<p class=MsoNormal>In this initial step we will load from a <span class=SpellE>cif</span>
1131file the structure of kaolinite, draw it to see the layer structure and then
1132transform it into forms suitable for stacking simulations. To begin do <b><span
1133style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>;
1134from the file dialog select <span class=SpellE><b style='mso-bidi-font-weight:
1135normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1136minor-latin;mso-hansi-theme-font:minor-latin'>StackingFaults</span></b></span><b
1137style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1138mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-II/data/</span></b><span
1139class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b></span>.
1140After the “are you sure” popup, there will be another warning you that 4 atom
1141types (‘O-H’) were not recognized chemical element symbols and they were
1142substituted by <span class=SpellE>Xe</span> to make them obvious in the atom
1143list. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1144you are offered a chance to change the phase name, I used ‘<b><span
1145style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’. The General tab
1146is displayed (notice the presence of <span class=SpellE>Xe</span> in the
1147element table).</p>
1148
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1174
1175<p class=MsoNormal>To fix the <span class=SpellE>Xe</span> atoms (they should
1176be O), select <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1177and then double click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1178column heading; a small popup will appear. Select <span class=SpellE><b><span
1179style='font-family:"Calibri",sans-serif'>Xe</span></b></span> &amp; press <b><span
1180style='font-family:"Calibri",sans-serif'>Ok</span></b>; the <span class=SpellE>Xe</span>
1181atoms at the bottom of the atom table will be highlighted. Next select <b><span
1182style='font-family:"Calibri",sans-serif'>Edit Atoms/On selected atoms…/Modify
1183parameters</span></b> from the Phase Data menu; a new popup will appear. Select
1184<b><span style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
1185style='font-family:"Calibri",sans-serif'>Ok</span></b>; a periodic table of the
1186element will appear. Select <b><span style='font-family:"Calibri",sans-serif'>O</span></b>
1187from the O-atom pulldown; the structure will be drawn with Al, Si &amp; O atoms
1188only.</p>
1189
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1196
1197<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
1198style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then
1199double click the empty upper left corner box of the table. All atoms will turn
1200green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1201Figure/Fill unit cell</span></b>; the structure will be redrawn with all atoms
1202that belong in the unit cell. Finally, double click on the <b><span
1203style='font-family:"Calibri",sans-serif'>Type</span></b> column heading, select
1204<b><span style='font-family:"Calibri",sans-serif'>Al</span></b> &amp; <b><span
1205style='font-family:"Calibri",sans-serif'>Si</span></b> (they will turn green)
1206and then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
1207CN sphere</span></b>. After a bit of rotating the structure around, the
1208layering along the c-axis (blue line) will be evident.</p>
1209
1210<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1211 id="Picture_x0020_16" o:spid="_x0000_i1040" type="#_x0000_t75" style='width:468pt;
1212 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1213 <v:imagedata src="Stacking%20Faults%20II_files/image011.png" o:title=""/>
1214</v:shape><![endif]--><![if !vml]><img width=624 height=538
1215src="Stacking%20Faults%20II_files/image012.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
1216
1217<p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> <span
1218class=SpellE>tetrahedra</span> and AlO<sub>6</sub> <span class=SpellE>octahedra</span>.
1219Also notice that the next layer (represented by the 4 O atoms at the bottom of
1220the above drawing are offset giving a triclinic lattice.</p>
1221
1222<p class=MsoNormal>The stacking fault simulation calculation via <span
1223class=SpellE>DIFFaX</span> routines requires that the stacking layers be
1224defined in a coordinate system that has the stacking direction perpendicular to
1225the stacking plane defined as the c-axis. This requires transformation of the
1226unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this.
1227Select the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1228tab and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
1229a popup window will appear.</p>
1230
1231<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1232 id="Picture_x0020_23" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:262.5pt;
1233 height:301.5pt;visibility:visible;mso-wrap-style:square'>
1234 <v:imagedata src="Stacking%20Faults%20II_files/image013.png" o:title=""/>
1235</v:shape><![endif]--><![if !vml]><img width=350 height=402
1236src="Stacking%20Faults%20II_files/image014.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
1237
1238<p class=MsoNormal>Note that this allows one to transform the structure
1239according to a matrix and then shift the <span class=GramE>resultant</span>
1240positions along some vector and then select those that are unique according to
1241a selected space group. The pulldown gives a selection of commonly used
1242transformations; we want the last one, <span class=SpellE><b><span
1243style='font-family:"Calibri",sans-serif'>abc</span></b></span><b><span
1244style='font-family:"Calibri",sans-serif'>*</span></b>, which satisfies the
1245stacking fault requirement. Select it; notice that the space group is changed
1246to P1. Leave this as the kaolinite layer has no symmetry; in other
1247circumstances the layer may have an inversion center in which case P-1 should
1248be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
1249the new lattice parameters will be shown.</p>
1250
1251<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1252 id="Picture_x0020_24" o:spid="_x0000_i1038" type="#_x0000_t75" style='width:262.5pt;
1253 height:301.5pt;visibility:visible;mso-wrap-style:square'>
1254 <v:imagedata src="Stacking%20Faults%20II_files/image003.png" o:title=""/>
1255</v:shape><![endif]--><![if !vml]><img width=350 height=402
1256src="Stacking%20Faults%20II_files/image015.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
1257
1258<p class=MsoNormal><span class=GramE>The a</span> &amp; b axes stay the same, but
1259c is now smaller (the interlayer distance in kaolinite) and <span
1260style='font-family:Symbol'>a</span> &amp; <span style='font-family:Symbol'>b</span>
1261= 90 (<span style='font-family:Symbol'>g</span> is unchanged). Press <b><span
1262style='font-family:"Calibri",sans-serif'>Ok</span></b>; a new phase (kaolinite <span
1263class=SpellE>abc</span>*) will be made and its General tab will be shown
1264immediately. Select the <b><span style='font-family:"Calibri",sans-serif'>Draw
1265Atoms</span></b> tab to see the resulting structure.</p>
1266
1267<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1268 id="Picture_x0020_25" o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;
1269 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1270 <v:imagedata src="Stacking%20Faults%20II_files/image016.png" o:title=""/>
1271</v:shape><![endif]--><![if !vml]><img width=624 height=538
1272src="Stacking%20Faults%20II_files/image017.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
1273
1274<p class=MsoNormal>To see what this layer looks like with more of it drawn, you
1275can add more unit cells to the drawing; select all the atoms by double clicking
1276the upper left empty box of the Draw atoms table. Do <b><span style='font-family:
1277"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and <b><span
1278style='font-family:"Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup>
1279<b><span style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l
1280and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; this
1281will add one unit cell along x. Now select all the atoms again, do <b><span
1282style='font-family:"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and
1283now <b><span style='font-family:"Calibri",sans-serif'>decrement</span></b> the
12841<sup>st</sup> <b><span style='font-family:"Calibri",sans-serif'>Choose unit
1285cell</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1286the drawing will now be 3 unit cells wide along x. Repeat this once more <b><span
1287style='font-family:"Calibri",sans-serif'>decrementing</span></b> the 2<sup>nd</sup>
1288<b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>
1289to give a 3x2 unit cell block of atoms. Double click the <b><span
1290style='font-family:"Calibri",sans-serif'>Style</span></b> column heading and
1291select <b><span style='font-family:"Calibri",sans-serif'>Balls and sticks</span></b>;
1292the drawing should look like (after some zooming/shifting/rotation).</p>
1293
1294<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1295 id="Picture_x0020_26" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:468pt;
1296 height:404.25pt;visibility:visible;mso-wrap-style:square'>
1297 <v:imagedata src="Stacking%20Faults%20II_files/image018.png" o:title=""/>
1298</v:shape><![endif]--><![if !vml]><img width=624 height=539
1299src="Stacking%20Faults%20II_files/image019.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
1300
1301<p class=MsoNormal>This structure is now suitable for use in <span
1302class=SpellE>DIFFaX</span> calculations; the cell has a c-axis that is perpendicular
1303to the ab plane with a length that is the stacking repeat distance. This is a
1304good place to save your project (I called it ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
1305
1306<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 2. Set up
1307simulation of ideal kaolinite stacking<o:p></o:p></span></h2>
1308
1309<p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
1310for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
1311powder pattern and compare it to some real data. To begin we need a new phase
1312that we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
1313style='font-family:"Calibri",sans-serif'>Data/Add new phase</span></b>; I named
1314it ‘<b><span style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The
1315General tab for it will immediately appear.</p>
1316
1317<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1318 id="Picture_x0020_27" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:468pt;
1319 height:225pt;visibility:visible;mso-wrap-style:square'>
1320 <v:imagedata src="Stacking%20Faults%20II_files/image020.png" o:title=""/>
1321</v:shape><![endif]--><![if !vml]><img width=624 height=300
1322src="Stacking%20Faults%20II_files/image021.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
1323
1324<p class=MsoNormal>Change the <b><span style='font-family:"Calibri",sans-serif'>Phase
1325type</span></b> to ‘<b><span style='font-family:"Calibri",sans-serif'>faulted</span></b>’;
1326the General tab will be redrawn and a new tab <b><span style='font-family:"Calibri",sans-serif'>‘Layers</span></b>’
1327will appear. Select it.</p>
1328
1329<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1330 id="Picture_x0020_28" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1331 height:196.5pt;visibility:visible;mso-wrap-style:square'>
1332 <v:imagedata src="Stacking%20Faults%20II_files/image022.png" o:title=""/>
1333</v:shape><![endif]--><![if !vml]><img width=624 height=262
1334src="Stacking%20Faults%20II_files/image023.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1335
1336<p class=MsoNormal>We can anticipate (given that kaolinite space group is C1)
1337that the <b><span style='font-family:"Calibri",sans-serif'>Diffraction Laue
1338symmetry</span></b> is <b><span style='font-family:"Calibri",sans-serif'>-1</span></b>.
1339We can enter by hand the lattice parameters from the kaolinite <span
1340class=SpellE>abc</span>* phase but an easier method is available. Do <b><span
1341style='font-family:"Calibri",sans-serif'>Operations/Copy phase cell</span></b>;
1342a file selection dialog will appear for your current directory and the file <span
1343class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
1344should be there. Select it; a small popup will appear listing the available
1345phases. Choose ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite <span
1346class=SpellE>abc</span>*</span></b>’ and press <b><span style='font-family:
1347"Calibri",sans-serif'>Ok</span></b>; the Layers window will be redrawn with the
1348new lattice parameters.</p>
1349
1350<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1351 id="Picture_x0020_29" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1352 height:196.5pt;visibility:visible;mso-wrap-style:square'>
1353 <v:imagedata src="Stacking%20Faults%20II_files/image024.png" o:title=""/>
1354</v:shape><![endif]--><![if !vml]><img width=624 height=262
1355src="Stacking%20Faults%20II_files/image025.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
1356
1357<p class=MsoNormal>Next, you need to define the layer. As it would be very
1358tedious to enter 24 atoms by hand, the alternative is to get them from the
1359previously created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
1360style='font-family:"Calibri",sans-serif'>Import new layer</span></b> box; the
1361file dialog with <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
1362will appear. Select the file and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>;
1363again a small popup with two phases listed will appear. Again select <b><span
1364style='font-family:"Calibri",sans-serif'>kaolinite <span class=SpellE>abc</span>*</span></b>
1365and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
1366Layers page will be redrawn with a layer (named kaolinite) will be filled out.</p>
1367
1368<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1369 id="Picture_x0020_30" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1370 height:238.5pt;visibility:visible;mso-wrap-style:square'>
1371 <v:imagedata src="Stacking%20Faults%20II_files/image026.png" o:title=""/>
1372</v:shape><![endif]--><![if !vml]><img width=624 height=318
1373src="Stacking%20Faults%20II_files/image027.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
1374
1375<p class=MsoNormal>If you move down to the bottom of the page to find the one
1376line <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer Transition
1377probabilities</span></b>. Change <span class=SpellE><b><span style='font-family:
1378"Calibri",sans-serif'>Dz</span></b></span><b><span style='font-family:"Calibri",sans-serif'>=1.0</span></b>
1379and press the plot box; the drawing will show a layer of kaolinite stacked directly
1380above another one.</p>
1381
1382<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1383 id="Picture_x0020_31" o:spid="_x0000_i1031" type="#_x0000_t75" style='width:468pt;
1384 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1385 <v:imagedata src="Stacking%20Faults%20II_files/image028.png" o:title=""/>
1386</v:shape><![endif]--><![if !vml]><img width=624 height=538
1387src="Stacking%20Faults%20II_files/image029.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1388
1389<p class=MsoNormal>Compare that to the stacking in kaolinite.</p>
1390
1391<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1392 id="Picture_x0020_32" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1393 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1394 <v:imagedata src="Stacking%20Faults%20II_files/image030.png" o:title=""/>
1395</v:shape><![endif]--><![if !vml]><img width=624 height=535
1396src="Stacking%20Faults%20II_files/image031.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1397
1398<p class=MsoNormal>Notice the effect of the offset. The 1<sup>st</sup> row of
1399SiO<sub>4</sub> <span class=SpellE>tetrahedra</span> are positioned directly
1400above the AlO<sub>6</sub> <span class=SpellE>octahedra</span> in the real
1401structure but not in the vertically stacked structure. We can use a bit of
1402simple geometry to work out what the offset is but first let us see what
1403happens in the simulation and how it compares to real data.</p>
1404
1405<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Import
1406Keokuk kaolinite data and do 1<sup>st</sup> simulation<o:p></o:p></span></h2>
1407
1408<p class=MsoNormal>First we need to import the Keokuk kaolinite powder data; do
1409<b><span style='font-family:"Calibri",sans-serif'>Import/Powder Data/from
1410Bruker RAW file</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Keokuk
1411<span class=SpellE>kaolinite.RAW</span></span></b> from the file dialog box;
1412press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> in the
1413next popup. A new file dialog appears requesting an instrument parameter file;
1414we will use an internal default instead. Press <b><span style='font-family:
1415"Calibri",sans-serif'>Cancel</span></b> and select <b><span style='font-family:
1416"Calibri",sans-serif'>Defaults for <span class=SpellE>CuKa</span> lab data</span></b>
1417from the next popup. This process will repeat since the RAW file contains two
1418scans. In the next popup, select only <b><span style='font-family:"Calibri",sans-serif'>kaolinite
1419<span class=SpellE>abc</span>*</span></b>. There will be two PWDR scans in the
1420GSAS-II data tree; one covers 2<span style='font-family:Symbol'>Q</span>= 10-90<span
1421style='font-family:"Calibri",sans-serif'>°</span> and the other covers 2<span
1422style='font-family:Symbol'>Q</span>=80-150°. Only the lower part of the first one
1423is going to be used in our simulation work as the calculations become very time
1424consuming for complex structures and high angle data. Select <b><span
1425style='font-family:"Calibri",sans-serif'>PWDR Keokuk <span class=SpellE>kaolinite.RAW</span>
1426Scan 1</span></b> from the GSAS-II data tree make sure it expands; its plot
1427will also show.</p>
1428
1429<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1430 id="Picture_x0020_33" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:468pt;
1431 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1432 <v:imagedata src="Stacking%20Faults%20II_files/image032.png" o:title=""/>
1433</v:shape><![endif]--><![if !vml]><img width=624 height=535
1434src="Stacking%20Faults%20II_files/image033.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1435
1436<p class=MsoNormal>Go to <b><span style='font-family:"Calibri",sans-serif'>Limits</span></b>
1437and set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Tmax</span></b></span>
1438to <b><span style='font-family:"Calibri",sans-serif'>52.0</span></b>; that puts
1439the upper limit in a relatively clear part of the pattern. Then go to
1440Background and set the 1<sup>st</sup> coefficient to 20 (approximately the
1441background at 2<span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
1442mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
1443Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>=18).
1444Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>
1445and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
1446to something reasonable (I chose <b><span style='font-family:"Calibri",sans-serif'>20.0</span></b>)
1447and make sure the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
1448type is Bragg-Brentano</span></b>.</p>
1449
1450<p class=MsoNormal>Now we are ready for our 1<sup>st</sup> kaolinite
1451simulation. Go to <b><span style='font-family:"Calibri",sans-serif'>Phases/Keokuk</span></b>
1452and select the <b><span style='font-family:"Calibri",sans-serif'>Layers</span></b>
1453tab. Do <b><span style='font-family:"Calibri",sans-serif'>Operations/Simulate
1454pattern</span></b> and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>
1455in the popup. Select the <b><span style='font-family:"Calibri",sans-serif'>Scan
14561</span></b> pattern and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
1457the simulation will finish quickly (press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>)
1458and the new plot will be displayed (I’ve zoomed in a bit).</p>
1459
1460<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1461 id="Picture_x0020_34" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1462 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1463 <v:imagedata src="Stacking%20Faults%20II_files/image034.png" o:title=""/>
1464</v:shape><![endif]--><![if !vml]><img width=624 height=535
1465src="Stacking%20Faults%20II_files/image035.gif" v:shapes="Picture_x0020_34"><![endif]></span>.</p>
1466
1467<p class=MsoNormal>As you can see the simulation (green curve) does not fit the
1468data (blue crosses) at all mostly due to the incorrect layer offset although
1469the 1<sup>st</sup> peak seems to be positioned correctly. To work out the
1470offset consider the drawing of kaolinite.</p>
1471
1472<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1473 id="Picture_x0020_35" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:468pt;
1474 height:403.5pt;visibility:visible;mso-wrap-style:square'>
1475 <v:imagedata src="Stacking%20Faults%20II_files/image036.png" o:title=""/>
1476</v:shape><![endif]--><![if !vml]><img width=624 height=538
1477src="Stacking%20Faults%20II_files/image037.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
1478
1479<p class=MsoNormal>The offset <span class=SpellE>Dx</span> is given by the blue
1480arrow in the above drawing of kaolinite and is in fractional coordinates.
1481Geometry gives<o:p></o:p></p>
1482
1483<p class=MsoNormal><span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><i
1484 style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1485 mso-no-proof:yes'><m:r>Dx</m:r><m:r>= </m:r></span></i><m:f><m:fPr><m:type
1486    m:val="lin"/><span style='font-family:"Cambria Math",serif;mso-ascii-font-family:
1487   "Cambria Math";mso-hansi-font-family:"Cambria Math";font-style:italic;
1488   mso-bidi-font-style:normal;mso-no-proof:yes'><m:ctrlPr></m:ctrlPr></span></m:fPr><m:num><i
1489   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1490   mso-no-proof:yes'><m:r>c</m:r><m:r> </m:r></span></i><m:func><m:funcPr><span
1491     style='font-family:"Cambria Math",serif;mso-ascii-font-family:"Cambria Math";
1492     mso-hansi-font-family:"Cambria Math";font-style:italic;mso-bidi-font-style:
1493     normal;mso-no-proof:yes'><m:ctrlPr></m:ctrlPr></span></m:funcPr><m:fName><span
1494     style='font-family:"Cambria Math",serif;mso-no-proof:yes'><m:r><m:rPr><m:scr
1495        m:val="roman"/><m:sty m:val="p"/></m:rPr>cos</m:r></span></m:fName><m:e><i
1496     style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1497     mso-no-proof:yes'><m:r>&#946;</m:r></span></i></m:e></m:func></m:num><m:den><i
1498   style='mso-bidi-font-style:normal'><span style='font-family:"Cambria Math",serif;
1499   mso-no-proof:yes'><m:r>a</m:r></span></i></m:den></m:f></m:oMath><![endif]--><![if !msEquation]><span
1500style='font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-font-family:
1501"Times New Roman";mso-fareast-theme-font:minor-fareast;position:relative;
1502top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
1503EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
1504 type="#_x0000_t75" style='width:84pt;height:14.25pt'>
1505 <v:imagedata src="Stacking%20Faults%20II_files/image038.png" o:title=""
1506  chromakey="white"/>
1507</v:shape><![endif]--><![if !vml]><img width=112 height=19
1508src="Stacking%20Faults%20II_files/image039.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;Or
1509in this case <b><span style='font-family:"Calibri",sans-serif'>-0.368</span></b>.
1510Set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Dx</span></b></span>
1511to this value &amp; repeat simulation.</p>
1512
1513<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1514 id="Picture_x0020_36" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;
1515 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1516 <v:imagedata src="Stacking%20Faults%20II_files/image040.png" o:title=""/>
1517</v:shape><![endif]--><![if !vml]><img width=624 height=535
1518src="Stacking%20Faults%20II_files/image041.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
1519
1520<p class=MsoNormal>There is some improvement but some parts are not very well
1521represented. Recall from the triclinic kaolinite lattice parameters that <span
1522style='font-family:Symbol'>a</span> was 91.7°; that will produce a small offset
1523in Dy. Using the same kind of geometry math gives <span class=SpellE><b><span
1524style='font-family:"Calibri",sans-serif'>Dy</span></b></span><b><span
1525style='font-family:"Calibri",sans-serif'>=-0.0246</span></b>. Enter this value
1526&amp; repeat the simulation again. This gives a much better fit to the observed
1527pattern, but the simulated peaks are too sharp; this can be fixed by changing
1528the U<span class=GramE>,V,W</span> Instrument parameters. I’d just set <b><span
1529style='font-family:"Calibri",sans-serif'>W=40</span></b> and the <b><span
1530style='font-family:"Calibri",sans-serif'>Histogram scale</span></b> (in <b><span
1531style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>) to <b><span
1532style='font-family:"Calibri",sans-serif'>40</span></b> and try again.</p>
1533
1534<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1535 id="Picture_x0020_37" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:468pt;
1536 height:401.25pt;visibility:visible;mso-wrap-style:square'>
1537 <v:imagedata src="Stacking%20Faults%20II_files/image042.png" o:title=""/>
1538</v:shape><![endif]--><![if !vml]><img width=624 height=535
1539src="Stacking%20Faults%20II_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
1540
1541<p class=MsoNormal>That is a pretty good fit for a stacking simulation. By
1542further hand tweaking of the parameters one can further improve the simulation
1543but based on what we see here we do have the right description of stacking in
1544Keokuk kaolinite. Doing sequence simulations varying each parameter over a
1545small range can be used to help with optimization, but in this case it would be
1546far easier to do a Rietveld refinement for this well ordered kaolinite. Save
1547your project as you will need it for the next exercise (Stacking Faults-III).<o:p></o:p></p>
1548
1549</span></div>
1550
1551</body>
1552
1553</html>
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