source: Tutorials/StackingFaults-II/Stacking faults II.htm @ 2256

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204</head>
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206<body lang=EN-US link=blue vlink=purple>
207
208<div class=WordSection1>
209
210<h1>Stacking Fault Simulations – II</h1>
211
212<p class=MsoNormal>In this exercise you will simulate some diffraction patterns
213from kaolinite clays. Kaolinite, Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>,
214is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub>
215octahedra on one side and SiO<sub>4</sub> tetrahedra on the other. The layers
216stack with an offset to ideally form a triclinic C1 lattice (Bish &amp; Von
217Dreele, 1989, Clay &amp; Clay Min. 37, 289-296) for a sample of the most
218ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other locations
219evidently have stacking faults so that the peaks are displaced, have peculiar
220shapes and are above a varying background. For the exercise we provide a
221laboratory Bragg-Brentano pattern of Keokuk kaolinite and a less ordered one
222from Washington County, Georgia (Clay Minerals Society Standard KGa-1b)
223collected with CuKa radiation on a Bruker instrument and thus in the Bruker RAW
224file format. The KGa-1b sample contains a small amount of anatase (TiO<sub>2</sub>)
225and the Keokuk kaolinite has some dickite (different ordered stacking of kaolinite
226layers).</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
233structure of kaolinite, draw it to see the layer structure and then transform
234it into forms suitable for stacking simulations. To begin do <b><span
235style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>;
236from the file dialog select <b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b>.
237After the “are you sure” popup, there will be another warning you that 4 atom
238types (‘O-H’) were not recognized chemical element symbols and they were
239substituted by Xe to make them obvious in the atom list. Press <b><span
240style='font-family:"Calibri",sans-serif'>Ok</span></b>; you are offered a
241chance to change the phase name, I used ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’.
242The 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"
245src="Stacking%20faults%20II_files/image001.gif"></p>
246
247<p class=MsoNormal>To fix the Xe atoms (they should be O), select <b><span
248style='font-family:"Calibri",sans-serif'>Atoms</span></b> and then double click
249the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> column
250heading; a small popup will appear. Select <b><span style='font-family:"Calibri",sans-serif'>Xe</span></b>
251&amp; press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
252the Xe atoms at the bottom of the atom table will be highlighted. Next select <b><span
253style='font-family:"Calibri",sans-serif'>Edit/Modify atom parameters</span></b>
254from the Phase Data menu; a new popup will appear.</p>
255
256<p class=MsoNormal><img width=228 height=268 id="Picture 2"
257src="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&amp; press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; a
261periodic 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
263be drawn with Al, Si &amp; O atoms only.</p>
264
265<p class=MsoNormal><img width=479 height=358 id="Picture 3"
266src="Stacking%20faults%20II_files/image003.jpg"></p>
267
268<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
269style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then double
270click the empty upper left corner box of the table. All atoms will turn green.
271Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill unit cell</span></b>;
272the structure will be redrawn with all atoms that belong in the unit cell.
273Finally, double click on the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
274column heading, select <b><span style='font-family:"Calibri",sans-serif'>Al</span></b>
275&amp; <b><span style='font-family:"Calibri",sans-serif'>Si</span></b> (they
276will turn green) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill
277CN sphere</span></b>. After a bit of rotating the structure around, the
278layering along the c-axis (blue line) will be evident.</p>
279
280<p class=MsoNormal><img width=480 height=359 id="Picture 4"
281src="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
284AlO<sub>6</sub> octahedra. Also notice that the next layer (represented by the
2854 O atoms at the bottom of the above drawing are offset giving a triclinic
286lattice.</p>
287
288<p class=MsoNormal>The stacking fault simulation calculation via DIFFaX
289routines requires that the stacking layers be defined in a coordinate system
290that has the stacking direction perpendicular to the stacking plane defined as
291the c-axis. This requires transformation of the unit cell and atom coordinates;
292a suitable tool exists in GSAS-II to do this. Select the <b><span
293style='font-family:"Calibri",sans-serif'>General</span></b> tab and do <b><span
294style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>; a popup
295window will appear.</p>
296
297<p class=MsoNormal><img width=350 height=339 id="Picture 5"
298src="Stacking%20faults%20II_files/image005.gif"></p>
299
300<p class=MsoNormal>Note that this allows one to transform the structure
301according to a matrix and then shift the resultant positions along some vector
302and then select those that are unique according to a selected space group. The
303pulldown gives a selection of commonly used transformations; we want the last
304one, <b><span style='font-family:"Calibri",sans-serif'>abc*</span></b>, which
305satisfies the stacking fault requirement. Select it; notice that the space
306group is changed to P1. Leave this as the kaolinite layer has no symmetry; in
307other circumstances the layer may have an inversion center in which P-1 should
308be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
309the new lattice parameters will be shown.</p>
310
311<p class=MsoNormal><img width=350 height=339 id="Picture 6"
312src="Stacking%20faults%20II_files/image006.gif"></p>
313
314<p class=MsoNormal>The a &amp; b axes stay the same, but c is now smaller (the interlayer
315distance in kaolinite) and <span style='font-family:Symbol'>a</span> &amp; <span
316style='font-family:Symbol'>b</span> = 90 (<span style='font-family:Symbol'>g</span>
317is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
318a new phase (kaolinite abc*) will be made. Select it from the GSAS-II data tree
319and then select the <b><span style='font-family:"Calibri",sans-serif'>Draw
320Atoms</span></b> tab to see the result.</p>
321
322<p class=MsoNormal><img width=475 height=355 id="Picture 9"
323src="Stacking%20faults%20II_files/image007.jpg"></p>
324
325</div>
326
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