- Timestamp:
- May 12, 2016 3:56:52 PM (7 years ago)
- Location:
- Tutorials/StackingFaults-II
- Files:
-
- 5 deleted
- 1 edited
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Tutorials/StackingFaults-II/Stacking faults II.htm
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mso-bidi-font-size:10.0pt; 1104 font-family:"Calibri",sans-serif; 1105 mso-ascii-font-family:Calibri; 1106 mso-ascii-theme-font:minor-latin; 1107 mso-fareast-font-family:Calibri; 1108 mso-fareast-theme-font:minor-latin; 1109 mso-hansi-font-family:Calibri; 1110 mso-hansi-theme-font:minor-latin; 1111 mso-bidi-font-family:"Times New Roman"; 1112 mso-bidi-theme-font:minor-bidi;} 194 {font-size:10.0pt; 195 font-family:"Calibri",sans-serif;} 1113 196 @page WordSection1 1114 197 {size:8.5in 11.0in; 1115 margin:1.0in 1.0in 1.0in 1.0in; 1116 mso-header-margin:.5in; 1117 mso-footer-margin:.5in; 1118 mso-paper-source:0;} 198 margin:1.0in 1.0in 1.0in 1.0in;} 1119 199 div.WordSection1 1120 200 {page:WordSection1;} 1121 201 --> 1122 202 </style> 1123 <!--[if gte mso 10]> 1124 <style> 1125 /* Style Definitions */ 1126 table.MsoNormalTable 1127 {mso-style-name:"Table Normal"; 1128 mso-tstyle-rowband-size:0; 1129 mso-tstyle-colband-size:0; 1130 mso-style-noshow:yes; 1131 mso-style-priority:99; 1132 mso-style-parent:""; 1133 mso-padding-alt:0in 5.4pt 0in 5.4pt; 1134 mso-para-margin:0in; 1135 mso-para-margin-bottom:.0001pt; 1136 mso-pagination:widow-orphan; 1137 font-size:10.0pt; 1138 font-family:"Calibri",sans-serif; 1139 mso-ascii-font-family:Calibri; 1140 mso-ascii-theme-font:minor-latin; 1141 mso-hansi-font-family:Calibri; 1142 mso-hansi-theme-font:minor-latin;} 1143 </style> 1144 <![endif]--><!--[if gte mso 9]><xml> 1145 <o:shapedefaults v:ext="edit" spidmax="1026"/> 1146 </xml><![endif]--><!--[if gte mso 9]><xml> 1147 <o:shapelayout v:ext="edit"> 1148 <o:idmap v:ext="edit" data="1"/> 1149 </o:shapelayout></xml><![endif]--> 203 1150 204 </head> 1151 205 1152 <body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>206 <body lang=EN-US link=blue vlink=purple> 1153 207 1154 208 <div class=WordSection1> … … 1157 211 1158 212 <p class=MsoNormal>In this exercise you will simulate some diffraction patterns 1159 from kaolinite clays. Kaolinite, <span class=GramE>Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(</span>OH)<sub>4</sub>, 1160 is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> <span 1161 class=SpellE>octahedra</span> on one side and SiO<sub>4</sub> <span 1162 class=SpellE>tetrahedra</span> on the other. The layers stack with an offset to 1163 ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span> & Von 213 from kaolinite clays. Kaolinite, Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>, 214 is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> 215 octahedra on one side and SiO<sub>4</sub> tetrahedra on the other. The layers 216 stack with an offset to ideally form a triclinic C1 lattice (Bish & Von 1164 217 Dreele, 1989, Clay & Clay Min. 37, 289-296) for a sample of the most 1165 218 ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other locations … … 1168 221 laboratory Bragg-Brentano pattern of Keokuk kaolinite and a less ordered one 1169 222 from Washington County, Georgia (Clay Minerals Society Standard KGa-1b) 1170 collected with <span class=SpellE>CuKa</span> radiation on a Bruker instrument 1171 and thus in the Bruker RAW file format. The KGa-1b sample contains a small 1172 amount of <span class=SpellE>anatase</span> (TiO<sub>2</sub>) and the Keokuk 1173 kaolinite has some <span class=SpellE>dickite</span> (different ordered stacking 1174 of kaolinite layers).</p> 223 collected with CuKa radiation on a Bruker instrument and thus in the Bruker RAW 224 file format. The KGa-1b sample contains a small amount of anatase (TiO<sub>2</sub>) 225 and the Keokuk kaolinite has some dickite (different ordered stacking of kaolinite 226 layers).</p> 227 228 <p class=MsoNormal>If you have not done so already, start GSAS-II.</p> 229 230 <h2>Part 1. Creating kaolinite layer</h2> 231 232 <p class=MsoNormal>In this initial step we will load in from a cif file the 233 structure of kaolinite, draw it to see the layer structure and then transform 234 it into forms suitable for stacking simulations. To begin do <b><span 235 style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>; 236 from the file dialog select <b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b>. 237 After the are you sure popup, there will be another warning you that 4 atom 238 types (O-H) were not recognized chemical element symbols and they were 239 substituted by Xe to make them obvious in the atom list. Press <b><span 240 style='font-family:"Calibri",sans-serif'>Ok</span></b>; you are offered a 241 chance to change the phase name, I used <b><span style='font-family:"Calibri",sans-serif'>kaolinite</span></b>. 242 The General tab is displayed (notice the presence of Xe in the element table).</p> 243 244 <p class=MsoNormal><img width=930 height=500 id="Picture 1" 245 src="Stacking%20faults%20II_files/image001.gif"></p> 246 247 <p class=MsoNormal>To fix the Xe atoms (they should be O), select <b><span 248 style='font-family:"Calibri",sans-serif'>Atoms</span></b> and then double click 249 the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> column 250 heading; a small popup will appear. Select <b><span style='font-family:"Calibri",sans-serif'>Xe</span></b> 251 & press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; 252 the Xe atoms at the bottom of the atom table will be highlighted. Next select <b><span 253 style='font-family:"Calibri",sans-serif'>Edit/Modify atom parameters</span></b> 254 from the Phase Data menu; a new popup will appear.</p> 255 256 <p class=MsoNormal><img width=228 height=268 id="Picture 2" 257 src="Stacking%20faults%20II_files/image002.gif"></p> 258 259 <p class=MsoNormal>Select <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> 260 & press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; a 261 periodic table of the element will appear. Select <b><span style='font-family: 262 "Calibri",sans-serif'>O</span></b> from the O-atom pulldown; the structure will 263 be drawn with Al, Si & O atoms only.</p> 264 265 <p class=MsoNormal><img width=479 height=358 id="Picture 3" 266 src="Stacking%20faults%20II_files/image003.jpg"></p> 267 268 <p class=MsoNormal>To better visualize the stacking layer, select the <b><span 269 style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then double 270 click the empty upper left corner box of the table. All atoms will turn green. 271 Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill unit cell</span></b>; 272 the structure will be redrawn with all atoms that belong in the unit cell. 273 Finally, double click on the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> 274 column heading, select <b><span style='font-family:"Calibri",sans-serif'>Al</span></b> 275 & <b><span style='font-family:"Calibri",sans-serif'>Si</span></b> (they 276 will turn green) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill 277 CN sphere</span></b>. After a bit of rotating the structure around, the 278 layering along the c-axis (blue line) will be evident.</p> 279 280 <p class=MsoNormal><img width=480 height=359 id="Picture 4" 281 src="Stacking%20faults%20II_files/image004.jpg"></p> 282 283 <p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> tetrahedra and 284 AlO<sub>6</sub> octahedra. Also notice that the next layer (represented by the 285 4 O atoms at the bottom of the above drawing are offset giving a triclinic 286 lattice.</p> 287 288 <p class=MsoNormal>The stacking fault simulation calculation via DIFFaX 289 routines requires that the stacking layers be defined in a coordinate system 290 that has the stacking direction perpendicular to the stacking plane defined as 291 the c-axis. This requires transformation of the unit cell and atom coordinates; 292 a suitable tool exists in GSAS-II to do this. Select the <b><span 293 style='font-family:"Calibri",sans-serif'>General</span></b> tab and do <b><span 294 style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>; a popup 295 window will appear.</p> 296 297 <p class=MsoNormal><img width=350 height=339 id="Picture 5" 298 src="Stacking%20faults%20II_files/image005.gif"></p> 299 300 <p class=MsoNormal>Note that this allows one to transform the structure 301 according to a matrix and then shift the resultant positions along some vector 302 and then select those that are unique according to a selected space group. The 303 pulldown gives a selection of commonly used transformations; we want the last 304 one, <b><span style='font-family:"Calibri",sans-serif'>abc*</span></b>, which 305 satisfies the stacking fault requirement. Select it; notice that the space 306 group is changed to P1. Leave this as the kaolinite layer has no symmetry; in 307 other circumstances the layer may have an inversion center in which P-1 should 308 be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>, 309 the new lattice parameters will be shown.</p> 310 311 <p class=MsoNormal><img width=350 height=339 id="Picture 6" 312 src="Stacking%20faults%20II_files/image006.gif"></p> 313 314 <p class=MsoNormal>The a & b axes stay the same, but c is now smaller (the interlayer 315 distance in kaolinite) and <span style='font-family:Symbol'>a</span> & <span 316 style='font-family:Symbol'>b</span> = 90 (<span style='font-family:Symbol'>g</span> 317 is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; 318 a new phase (kaolinite abc*) will be made. Select it from the GSAS-II data tree 319 and then select the <b><span style='font-family:"Calibri",sans-serif'>Draw 320 Atoms</span></b> tab to see the result.</p> 321 322 <p class=MsoNormal><img width=475 height=355 id="Picture 9" 323 src="Stacking%20faults%20II_files/image007.jpg"></p> 1175 324 1176 325 </div>
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