Ignore:
Timestamp:
Jul 8, 2021 1:43:09 PM (21 months ago)
Author:
vondreele
Message:

fix reference to 3rd phase

File:
1 edited

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  • Tutorials/StackingFaults-II/Stacking Faults II.htm

    r4457 r4993  
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    10971086
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     1087<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in;word-wrap:
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    10991089
    11001090<div class=WordSection1>
    … …  
    11031093Simulations – II<o:p></o:p></span></h1>
    11041094
    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
    1110 diffraction 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>,
    1111 is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> <span
    1112 class=SpellE>octahedra</span> on one side and SiO<sub>4</sub> <span
    1113 class=SpellE>tetrahedra</span> on the other. The layers stack with an offset to
    1114 ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span> &amp; Von <span
    1115 class=SpellE>Dreele</span>, 1989, Clay &amp; Clay Min. 37, 289-296) for a
    1116 sample of the most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from
    1117 other locations evidently have stacking faults so that the peaks are displaced,
    1118 have peculiar shapes and are above a varying background. For the exercise we
    1119 provide a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
    1120 class=SpellE>CuKa</span> radiation on a Bruker instrument and thus in the
    1121 Bruker RAW file format. The Keokuk kaolinite has some <span class=SpellE>dickite</span>
    1122 (different ordered stacking of kaolinite layers). The next exercise Stacking
    1123 Faults-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>
     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>
    11261120
    11271121<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 1. Creating
    … …  
    11401134After the “are you sure” popup, there will be another warning you that 4 atom
    11411135types (‘O-H’) were not recognized chemical element symbols and they were
    1142 substituted by <span class=SpellE>Xe</span> to make them obvious in the atom
    1143 list. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
    1144 you are offered a chance to change the phase name, I used ‘<b><span
    1145 style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’. The General tab
    1146 is displayed (notice the presence of <span class=SpellE>Xe</span> in the
    1147 element table).</p>
     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>
    11481140
    11491141<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
    … …  
    11701162 style='width:468pt;height:225pt;visibility:visible;mso-wrap-style:square'>
    11711163 <v:imagedata src="Stacking%20Faults%20II_files/image007.png" o:title=""/>
    1172 </v:shape><![endif]--><![if !vml]><img width=624 height=300
    1173 src="Stacking%20Faults%20II_files/image008.gif" v:shapes="Picture_x0020_9"><![endif]></span></p>
    1174 
    1175 <p class=MsoNormal>To fix the <span class=SpellE>Xe</span> atoms (they should
    1176 be O), select <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
    1177 and then double click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
    1178 column heading; a small popup will appear. Select <span class=SpellE><b><span
    1179 style='font-family:"Calibri",sans-serif'>Xe</span></b></span> &amp; press <b><span
    1180 style='font-family:"Calibri",sans-serif'>Ok</span></b>; the <span class=SpellE>Xe</span>
    1181 atoms at the bottom of the atom table will be highlighted. Next select <b><span
     1164</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=300
     1165src="Stacking%20Faults%20II_files/image001.gif" v:shapes="Picture_x0020_9"><![endif]></span></p>
     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
    11821173style='font-family:"Calibri",sans-serif'>Edit Atoms/On selected atoms
    11831174/Modify
    … …  
    11931184 height:403.5pt;visibility:visible;mso-wrap-style:square'>
    11941185 <v:imagedata src="Stacking%20Faults%20II_files/image009.png" o:title=""/>
    1195 </v:shape><![endif]--><![if !vml]><img width=624 height=538
    1196 src="Stacking%20Faults%20II_files/image010.gif" v:shapes="Picture_x0020_15"><![endif]></span></p>
     1186</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
     1187src="Stacking%20Faults%20II_files/image002.gif" v:shapes="Picture_x0020_15"><![endif]></span></p>
    11971188
    11981189<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
    11991190style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then
    12001191double click the empty upper left corner box of the table. All atoms will turn
    1201 green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
    1202 Figure/Fill unit cell</span></b>; the structure will be redrawn with all atoms
    1203 that belong in the unit cell. Finally, double click on the <b><span
    1204 style='font-family:"Calibri",sans-serif'>Type</span></b> column heading, select
    1205 <b><span style='font-family:"Calibri",sans-serif'>Al</span></b> &amp; <b><span
     1192green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
     1193unit cell</span></b>; the structure will be redrawn with all atoms that belong
     1194in the unit cell. Finally, double click on the <b><span style='font-family:
     1195"Calibri",sans-serif'>Type</span></b> column heading, select <b><span
     1196style='font-family:"Calibri",sans-serif'>Al</span></b> &amp; <b><span
    12061197style='font-family:"Calibri",sans-serif'>Si</span></b> (they will turn green)
    12071198and then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
    … …  
    12131204 height:403.5pt;visibility:visible;mso-wrap-style:square'>
    12141205 <v:imagedata src="Stacking%20Faults%20II_files/image011.png" o:title=""/>
    1215 </v:shape><![endif]--><![if !vml]><img width=624 height=538
    1216 src="Stacking%20Faults%20II_files/image012.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
    1217 
    1218 <p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> <span
    1219 class=SpellE>tetrahedra</span> and AlO<sub>6</sub> <span class=SpellE>octahedra</span>.
    1220 Also notice that the next layer (represented by the 4 O atoms at the bottom of
    1221 the above drawing are offset giving a triclinic lattice.</p>
     1206</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
     1207src="Stacking%20Faults%20II_files/image004.gif" v:shapes="Picture_x0020_16"><![endif]></span></p>
     1208
     1209<p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> tetrahedra
     1210and AlO<sub>6</sub> octahedra. Also notice that the next layer (represented by
     1211the 4 O atoms at the bottom of the above drawing are offset giving a triclinic
     1212lattice.</p>
    12221213
    12231214<p class=MsoNormal>The stacking fault simulation calculation via <span
    … …  
    12341225 height:301.5pt;visibility:visible;mso-wrap-style:square'>
    12351226 <v:imagedata src="Stacking%20Faults%20II_files/image013.png" o:title=""/>
    1236 </v:shape><![endif]--><![if !vml]><img width=350 height=402
    1237 src="Stacking%20Faults%20II_files/image014.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
     1227</v:shape><![endif]--><![if !vml]><img border=0 width=350 height=402
     1228src="Stacking%20Faults%20II_files/image005.gif" v:shapes="Picture_x0020_23"><![endif]></span></p>
    12381229
    12391230<p class=MsoNormal>Note that this allows one to transform the structure
    1240 according to a matrix and then shift the <span class=GramE>resultant</span>
    1241 positions along some vector and then select those that are unique according to
    1242 a selected space group. The pulldown gives a selection of commonly used
    1243 transformations; we want the last one, <span class=SpellE><b><span
    1244 style='font-family:"Calibri",sans-serif'>abc</span></b></span><b><span
     1231according to a matrix and then shift the resultant positions along some vector
     1232and then select those that are unique according to a selected space group. The
     1233pulldown gives a selection of commonly used transformations; we want the last
     1234one, <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>abc</span></b></span><b><span
    12451235style='font-family:"Calibri",sans-serif'>*</span></b>, which satisfies the
    12461236stacking fault requirement. Select it; notice that the space group is changed
    … …  
    12541244 height:301.5pt;visibility:visible;mso-wrap-style:square'>
    12551245 <v:imagedata src="Stacking%20Faults%20II_files/image003.png" o:title=""/>
    1256 </v:shape><![endif]--><![if !vml]><img width=350 height=402
    1257 src="Stacking%20Faults%20II_files/image015.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
    1258 
    1259 <p class=MsoNormal><span class=GramE>The a</span> &amp; b axes stay the same, but
    1260 c is now smaller (the interlayer distance in kaolinite) and <span
    1261 style='font-family:Symbol'>a</span> &amp; <span style='font-family:Symbol'>b</span>
    1262 = 90 (<span style='font-family:Symbol'>g</span> is unchanged). Press <b><span
    1263 style='font-family:"Calibri",sans-serif'>Ok</span></b>; a new phase (kaolinite <span
    1264 class=SpellE>abc</span>*) will be made and its General tab will be shown
    1265 immediately. Select the <b><span style='font-family:"Calibri",sans-serif'>Draw
    1266 Atoms</span></b> tab to see the resulting structure.</p>
     1246</v:shape><![endif]--><![if !vml]><img border=0 width=350 height=402
     1247src="Stacking%20Faults%20II_files/image006.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
     1248
     1249<p class=MsoNormal>The a &amp; b axes stay the same, but c is now smaller (the
     1250interlayer distance in kaolinite) and <span style='font-family:Symbol'>a</span>
     1251&amp; <span style='font-family:Symbol'>b</span> = 90 (<span style='font-family:
     1252Symbol'>g</span> is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
     1253a new phase (kaolinite <span class=SpellE>abc</span>*) will be made and its
     1254General tab will be shown immediately. Select the <b><span style='font-family:
     1255"Calibri",sans-serif'>Draw Atoms</span></b> tab to see the resulting structure.</p>
    12671256
    12681257<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    12701259 height:403.5pt;visibility:visible;mso-wrap-style:square'>
    12711260 <v:imagedata src="Stacking%20Faults%20II_files/image016.png" o:title=""/>
    1272 </v:shape><![endif]--><![if !vml]><img width=624 height=538
    1273 src="Stacking%20Faults%20II_files/image017.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
     1261</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
     1262src="Stacking%20Faults%20II_files/image038.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
    12741263
    12751264<p class=MsoNormal>To see what this layer looks like with more of it drawn, you
    … …  
    12971286 height:404.25pt;visibility:visible;mso-wrap-style:square'>
    12981287 <v:imagedata src="Stacking%20Faults%20II_files/image018.png" o:title=""/>
    1299 </v:shape><![endif]--><![if !vml]><img width=624 height=539
    1300 src="Stacking%20Faults%20II_files/image019.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
     1288</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=539
     1289src="Stacking%20Faults%20II_files/image039.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
    13011290
    13021291<p class=MsoNormal>This structure is now suitable for use in <span
    1303 class=SpellE>DIFFaX</span> calculations; the cell has a c-axis that is perpendicular
    1304 to the ab plane with a length that is the stacking repeat distance. This is a
    1305 good place to save your project (I called it ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
     1292class=SpellE>DIFFaX</span> calculations; the cell has a c-axis that is
     1293perpendicular to the ab plane with a length that is the stacking repeat
     1294distance. This is a good place to save your project (I called it ‘<b><span
     1295style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
    13061296
    13071297<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 2. Set up
    … …  
    13101300<p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
    13111301for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
    1312 powder pattern and compare it to some real data. To begin we need a new phase
    1313 that we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
     1302powder pattern and compare it to some real data. To begin we need a new phase that
     1303we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
    13141304style='font-family:"Calibri",sans-serif'>Data/Add new phase</span></b>; I named
    13151305it ‘<b><span style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The
    … …  
    13201310 height:225pt;visibility:visible;mso-wrap-style:square'>
    13211311 <v:imagedata src="Stacking%20Faults%20II_files/image020.png" o:title=""/>
    1322 </v:shape><![endif]--><![if !vml]><img width=624 height=300
    1323 src="Stacking%20Faults%20II_files/image021.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
     1312</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=300
     1313src="Stacking%20Faults%20II_files/image044.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
    13241314
    13251315<p class=MsoNormal>Change the <b><span style='font-family:"Calibri",sans-serif'>Phase
    … …  
    13321322 height:196.5pt;visibility:visible;mso-wrap-style:square'>
    13331323 <v:imagedata src="Stacking%20Faults%20II_files/image022.png" o:title=""/>
    1334 </v:shape><![endif]--><![if !vml]><img width=624 height=262
    1335 src="Stacking%20Faults%20II_files/image023.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
     1324</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=262
     1325src="Stacking%20Faults%20II_files/image045.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
    13361326
    13371327<p class=MsoNormal>We can anticipate (given that kaolinite space group is C1)
    … …  
    13531343 height:196.5pt;visibility:visible;mso-wrap-style:square'>
    13541344 <v:imagedata src="Stacking%20Faults%20II_files/image024.png" o:title=""/>
    1355 </v:shape><![endif]--><![if !vml]><img width=624 height=262
    1356 src="Stacking%20Faults%20II_files/image025.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
     1345</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=262
     1346src="Stacking%20Faults%20II_files/image046.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
    13571347
    13581348<p class=MsoNormal>Next, you need to define the layer. As it would be very
    … …  
    13641354again a small popup with two phases listed will appear. Again select <b><span
    13651355style='font-family:"Calibri",sans-serif'>kaolinite <span class=SpellE>abc</span>*</span></b>
    1366 and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
    1367 Layers page will be redrawn with a layer (named kaolinite) will be filled out.</p>
     1356and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the Layers
     1357page will be redrawn with a layer (named kaolinite) will be filled out.</p>
    13681358
    13691359<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    13711361 height:238.5pt;visibility:visible;mso-wrap-style:square'>
    13721362 <v:imagedata src="Stacking%20Faults%20II_files/image026.png" o:title=""/>
    1373 </v:shape><![endif]--><![if !vml]><img width=624 height=318
    1374 src="Stacking%20Faults%20II_files/image027.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
     1363</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=318
     1364src="Stacking%20Faults%20II_files/image047.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
    13751365
    13761366<p class=MsoNormal>If you move down to the bottom of the page to find the one
    … …  
    13781368probabilities</span></b>. Change <span class=SpellE><b><span style='font-family:
    13791369"Calibri",sans-serif'>Dz</span></b></span><b><span style='font-family:"Calibri",sans-serif'>=1.0</span></b>
    1380 and press the plot box; the drawing will show a layer of kaolinite stacked directly
    1381 above another one.</p>
     1370and press the plot box; the drawing will show a layer of kaolinite stacked
     1371directly above another one.</p>
    13821372
    13831373<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    13851375 height:403.5pt;visibility:visible;mso-wrap-style:square'>
    13861376 <v:imagedata src="Stacking%20Faults%20II_files/image028.png" o:title=""/>
    1387 </v:shape><![endif]--><![if !vml]><img width=624 height=538
    1388 src="Stacking%20Faults%20II_files/image029.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
     1377</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
     1378src="Stacking%20Faults%20II_files/image048.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
    13891379
    13901380<p class=MsoNormal>Compare that to the stacking in kaolinite.</p>
    … …  
    13941384 height:401.25pt;visibility:visible;mso-wrap-style:square'>
    13951385 <v:imagedata src="Stacking%20Faults%20II_files/image030.png" o:title=""/>
    1396 </v:shape><![endif]--><![if !vml]><img width=624 height=535
    1397 src="Stacking%20Faults%20II_files/image031.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
     1386</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1387src="Stacking%20Faults%20II_files/image049.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
    13981388
    13991389<p class=MsoNormal>Notice the effect of the offset. The 1<sup>st</sup> row of
    1400 SiO<sub>4</sub> <span class=SpellE>tetrahedra</span> are positioned directly
    1401 above the AlO<sub>6</sub> <span class=SpellE>octahedra</span> in the real
    1402 structure but not in the vertically stacked structure. We can use a bit of
    1403 simple geometry to work out what the offset is but first let us see what
    1404 happens in the simulation and how it compares to real data.</p>
     1390SiO<sub>4</sub> tetrahedra are positioned directly above the AlO<sub>6</sub>
     1391octahedra in the real structure but not in the vertically stacked structure. We
     1392can use a bit of simple geometry to work out what the offset is but first let
     1393us see what happens in the simulation and how it compares to real data.</p>
    14051394
    14061395<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Import
    … …  
    14171406"Calibri",sans-serif'>Defaults for <span class=SpellE>CuKa</span> lab data</span></b>
    14181407from the next popup. This process will repeat since the RAW file contains two
    1419 scans. In the next popup, select only <b><span style='font-family:"Calibri",sans-serif'>kaolinite
    1420 <span class=SpellE>abc</span>*</span></b>. There will be two PWDR scans in the
    1421 GSAS-II data tree; one covers 2<span style='font-family:Symbol'>Q</span>= 10-90<span
     1408scans. In the next popup, select only <b><span style='font-family:"Calibri",sans-serif'>Keokuk
     1409</span></b>(3<sup>rd</sup> phase). There will be two PWDR scans in the GSAS-II
     1410data tree; one covers 2<span style='font-family:Symbol'>Q</span>= 10-90<span
    14221411style='font-family:"Calibri",sans-serif'>°</span> and the other covers 2<span
    1423 style='font-family:Symbol'>Q</span>=80-150°. Only the lower part of the first one
    1424 is going to be used in our simulation work as the calculations become very time
    1425 consuming for complex structures and high angle data. Select <b><span
     1412style='font-family:Symbol'>Q</span>=80-150°. Only the lower part of the first
     1413one is going to be used in our simulation work as the calculations become very
     1414time consuming for complex structures and high angle data. Select <b><span
    14261415style='font-family:"Calibri",sans-serif'>PWDR Keokuk <span class=SpellE>kaolinite.RAW</span>
    14271416Scan 1</span></b> from the GSAS-II data tree make sure it expands; its plot
    … …  
    14321421 height:401.25pt;visibility:visible;mso-wrap-style:square'>
    14331422 <v:imagedata src="Stacking%20Faults%20II_files/image032.png" o:title=""/>
    1434 </v:shape><![endif]--><![if !vml]><img width=624 height=535
    1435 src="Stacking%20Faults%20II_files/image033.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
     1423</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1424src="Stacking%20Faults%20II_files/image050.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
    14361425
    14371426<p class=MsoNormal>Go to <b><span style='font-family:"Calibri",sans-serif'>Limits</span></b>
    14381427and set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Tmax</span></b></span>
    14391428to <b><span style='font-family:"Calibri",sans-serif'>52.0</span></b>; that puts
    1440 the upper limit in a relatively clear part of the pattern. Then go to
    1441 Background and set the 1<sup>st</sup> coefficient to 20 (approximately the
    1442 background at 2<span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
    1443 mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
    1444 Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>=18).
     1429the upper limit in a relatively clear part of the pattern. Then go to Background
     1430and set the 1<sup>st</sup> coefficient to 20 (approximately the background at 2<span
     1431style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";mso-hansi-font-family:
     1432"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:Symbol'><span
     1433style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>=18).
    14451434Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>
    14461435and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
    … …  
    14631452 height:401.25pt;visibility:visible;mso-wrap-style:square'>
    14641453 <v:imagedata src="Stacking%20Faults%20II_files/image034.png" o:title=""/>
    1465 </v:shape><![endif]--><![if !vml]><img width=624 height=535
    1466 src="Stacking%20Faults%20II_files/image035.gif" v:shapes="Picture_x0020_34"><![endif]></span>.</p>
     1454</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1455src="Stacking%20Faults%20II_files/image051.gif" v:shapes="Picture_x0020_34"><![endif]></span>.</p>
    14671456
    14681457<p class=MsoNormal>As you can see the simulation (green curve) does not fit the
    … …  
    14751464 height:403.5pt;visibility:visible;mso-wrap-style:square'>
    14761465 <v:imagedata src="Stacking%20Faults%20II_files/image036.png" o:title=""/>
    1477 </v:shape><![endif]--><![if !vml]><img width=624 height=538
    1478 src="Stacking%20Faults%20II_files/image037.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
    1479 
    1480 <p class=MsoNormal>The offset <span class=SpellE>Dx</span> is given by the blue
    1481 arrow in the above drawing of kaolinite and is in fractional coordinates.
    1482 Geometry gives<o:p></o:p></p>
     1466</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=538
     1467src="Stacking%20Faults%20II_files/image052.gif" v:shapes="Picture_x0020_35"><![endif]></span></p>
     1468
     1469<p class=MsoNormal>The offset Dx is given by the blue arrow in the above
     1470drawing of kaolinite and is in fractional coordinates. Geometry gives<o:p></o:p></p>
    14831471
    14841472<p class=MsoNormal><span style='position:relative;top:3pt'><!--[if gte msEquation 12]><m:oMath><i
    … …  
    15031491top:3.0pt;mso-text-raise:-3.0pt;mso-ansi-language:EN-US;mso-fareast-language:
    15041492EN-US;mso-bidi-language:AR-SA'><!--[if gte vml 1]><v:shape id="_x0000_i1025"
    1505  type="#_x0000_t75" style='width:84pt;height:14.25pt'>
    1506  <v:imagedata src="Stacking%20Faults%20II_files/image038.png" o:title=""
     1493 type="#_x0000_t75" style='width:84.25pt;height:14.55pt'>
     1494 <v:imagedata src="Stacking%20Faults%20II_files/image053.png" o:title=""
    15071495  chromakey="white"/>
    15081496</v:shape><![endif]--><![if !vml]><img width=112 height=19
    1509 src="Stacking%20Faults%20II_files/image039.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;Or
     1497src="Stacking%20Faults%20II_files/image054.gif" v:shapes="_x0000_i1025"><![endif]></span><![endif]>&nbsp;Or
    15101498in this case <b><span style='font-family:"Calibri",sans-serif'>-0.368</span></b>.
    1511 Set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Dx</span></b></span>
    1512 to this value &amp; repeat simulation.</p>
     1499Set <b><span style='font-family:"Calibri",sans-serif'>Dx</span></b> to this
     1500value &amp; repeat simulation.</p>
    15131501
    15141502<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
    … …  
    15161504 height:401.25pt;visibility:visible;mso-wrap-style:square'>
    15171505 <v:imagedata src="Stacking%20Faults%20II_files/image040.png" o:title=""/>
    1518 </v:shape><![endif]--><![if !vml]><img width=624 height=535
    1519 src="Stacking%20Faults%20II_files/image041.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
     1506</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1507src="Stacking%20Faults%20II_files/image055.gif" v:shapes="Picture_x0020_36"><![endif]></span></p>
    15201508
    15211509<p class=MsoNormal>There is some improvement but some parts are not very well
    15221510represented. Recall from the triclinic kaolinite lattice parameters that <span
    15231511style='font-family:Symbol'>a</span> was 91.7°; that will produce a small offset
    1524 in Dy. Using the same kind of geometry math gives <span class=SpellE><b><span
    1525 style='font-family:"Calibri",sans-serif'>Dy</span></b></span><b><span
    1526 style='font-family:"Calibri",sans-serif'>=-0.0246</span></b>. Enter this value
    1527 &amp; repeat the simulation again. This gives a much better fit to the observed
    1528 pattern, but the simulated peaks are too sharp; this can be fixed by changing
    1529 the U<span class=GramE>,V,W</span> Instrument parameters. I’d just set <b><span
     1512in Dy. Using the same kind of geometry math gives <b><span style='font-family:
     1513"Calibri",sans-serif'>Dy=-0.0246</span></b>. Enter this value &amp; repeat the
     1514simulation again. This gives a much better fit to the observed pattern, but the
     1515simulated peaks are too sharp; this can be fixed by changing the <span
     1516class=GramE>U,V</span>,W Instrument parameters. I’d just set <b><span
    15301517style='font-family:"Calibri",sans-serif'>W=40</span></b> and the <b><span
    15311518style='font-family:"Calibri",sans-serif'>Histogram scale</span></b> (in <b><span
    … …  
    15371524 height:401.25pt;visibility:visible;mso-wrap-style:square'>
    15381525 <v:imagedata src="Stacking%20Faults%20II_files/image042.png" o:title=""/>
    1539 </v:shape><![endif]--><![if !vml]><img width=624 height=535
    1540 src="Stacking%20Faults%20II_files/image043.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
     1526</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=535
     1527src="Stacking%20Faults%20II_files/image056.gif" v:shapes="Picture_x0020_37"><![endif]></span></p>
    15411528
    15421529<p class=MsoNormal>That is a pretty good fit for a stacking simulation. By
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