source: Tutorials/StackingFaults-II/Stacking faults II.htm @ 2261

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new stacking faults II tutorial

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216</head>
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218<body lang=EN-US link=blue vlink=purple>
219
220<div class=WordSection1>
221
222<h1>Stacking Fault Simulations – II</h1>
223
224<p class=MsoNormal>In this exercise you will simulate some diffraction patterns
225from kaolinite clays. Kaolinite, Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>,
226is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub>
227octahedra on one side and SiO<sub>4</sub> tetrahedra on the other. The layers
228stack with an offset to ideally form a triclinic C1 lattice (Bish &amp; Von
229Dreele, 1989, Clay &amp; Clay Min. 37, 289-296) for a sample of the most
230ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other locations evidently
231have stacking faults so that the peaks are displaced, have peculiar shapes and
232are above a varying background. For the exercise we provide a laboratory
233Bragg-Brentano pattern of Keokuk kaolinite and a less ordered one from
234Washington County, Georgia (Clay Minerals Society Standard KGa-1b) collected
235with CuKa radiation on a Bruker instrument and thus in the Bruker RAW file
236format. The KGa-1b sample contains a small amount of anatase (TiO<sub>2</sub>)
237and the Keokuk kaolinite has some dickite (different ordered stacking of
238kaolinite layers).</p>
239
240<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
241
242<h2>Part 1. Creating kaolinite layer</h2>
243
244<p class=MsoNormal>In this initial step we will load in from a cif file the
245structure of kaolinite, draw it to see the layer structure and then transform
246it into forms suitable for stacking simulations. To begin do <b><span
247style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>;
248from the file dialog select <b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b>.
249After the “are you sure” popup, there will be another warning you that 4 atom
250types (‘O-H’) were not recognized chemical element symbols and they were
251substituted by Xe to make them obvious in the atom list. Press <b><span
252style='font-family:"Calibri",sans-serif'>Ok</span></b>; you are offered a
253chance to change the phase name, I used ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’.
254The General tab is displayed (notice the presence of Xe in the element table).</p>
255
256<p class=MsoNormal><img width=930 height=500
257src="Stacking%20faults%20II_files/image001.gif"></p>
258
259<p class=MsoNormal>To fix the Xe atoms (they should be O), select <b><span
260style='font-family:"Calibri",sans-serif'>Atoms</span></b> and then double click
261the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> column
262heading; a small popup will appear. Select <b><span style='font-family:"Calibri",sans-serif'>Xe</span></b>
263&amp; press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
264the Xe atoms at the bottom of the atom table will be highlighted. Next select <b><span
265style='font-family:"Calibri",sans-serif'>Edit/Modify atom parameters</span></b>
266from the Phase Data menu; a new popup will appear.</p>
267
268<p class=MsoNormal><img width=228 height=268
269src="Stacking%20faults%20II_files/image002.gif"></p>
270
271<p class=MsoNormal>Select <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
272&amp; press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; a
273periodic table of the element will appear. Select <b><span style='font-family:
274"Calibri",sans-serif'>O</span></b> from the O-atom pulldown; the structure will
275be drawn with Al, Si &amp; O atoms only.</p>
276
277<p class=MsoNormal><img width=479 height=358
278src="Stacking%20faults%20II_files/image003.jpg"></p>
279
280<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
281style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then
282double click the empty upper left corner box of the table. All atoms will turn
283green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill unit
284cell</span></b>; the structure will be redrawn with all atoms that belong in
285the unit cell. Finally, double click on the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
286column heading, select <b><span style='font-family:"Calibri",sans-serif'>Al</span></b>
287&amp; <b><span style='font-family:"Calibri",sans-serif'>Si</span></b> (they
288will turn green) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill
289CN sphere</span></b>. After a bit of rotating the structure around, the
290layering along the c-axis (blue line) will be evident.</p>
291
292<p class=MsoNormal><img width=480 height=359
293src="Stacking%20faults%20II_files/image004.jpg"></p>
294
295<p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> tetrahedra
296and AlO<sub>6</sub> octahedra. Also notice that the next layer (represented by
297the 4 O atoms at the bottom of the above drawing are offset giving a triclinic
298lattice.</p>
299
300<p class=MsoNormal>The stacking fault simulation calculation via DIFFaX
301routines requires that the stacking layers be defined in a coordinate system
302that has the stacking direction perpendicular to the stacking plane defined as
303the c-axis. This requires transformation of the unit cell and atom coordinates;
304a suitable tool exists in GSAS-II to do this. Select the <b><span
305style='font-family:"Calibri",sans-serif'>General</span></b> tab and do <b><span
306style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>; a popup
307window will appear.</p>
308
309<p class=MsoNormal><img width=350 height=339
310src="Stacking%20faults%20II_files/image005.gif"></p>
311
312<p class=MsoNormal>Note that this allows one to transform the structure
313according to a matrix and then shift the resultant positions along some vector
314and then select those that are unique according to a selected space group. The
315pulldown gives a selection of commonly used transformations; we want the last
316one, <b><span style='font-family:"Calibri",sans-serif'>abc*</span></b>, which
317satisfies the stacking fault requirement. Select it; notice that the space
318group is changed to P1. Leave this as the kaolinite layer has no symmetry; in
319other circumstances the layer may have an inversion center in which P-1 should
320be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
321the new lattice parameters will be shown.</p>
322
323<p class=MsoNormal><img width=350 height=339
324src="Stacking%20faults%20II_files/image006.gif"></p>
325
326<p class=MsoNormal>The a &amp; b axes stay the same, but c is now smaller (the
327interlayer distance in kaolinite) and <span style='font-family:Symbol'>a</span>
328&amp; <span style='font-family:Symbol'>b</span> = 90 (<span style='font-family:
329Symbol'>g</span> is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
330a new phase (kaolinite abc*) will be made. Select it from the GSAS-II data tree
331and then select the <b><span style='font-family:"Calibri",sans-serif'>Draw
332Atoms</span></b> tab to see the result.</p>
333
334<p class=MsoNormal><img width=475 height=355
335src="Stacking%20faults%20II_files/image007.jpg"></p>
336
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