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213
214<div class=WordSection1>
215
216<h1>Stacking Fault Simulations – III</h1>
217
218<p class=MsoNormal>Here we continue the simulation of kaolinites started in
219Stacking Faults-II. If you have not done this exercise and finished by saving
220the project file (kaolinite.gpx) please do that first as this exercise uses the
221results of that exercise. The data we are trying to simulated is from a less
222well ordered kaolinite from Washington County, Georgia (Clay Minerals Society
223Standard KGa-1b) collected with CuKa radiation on a Bruker instrument and thus
224in the Bruker RAW file format. The KGa-1b sample contains a small amount of
225anatase (TiO<sub>2</sub>).</p>
226
227<p class=MsoNormal>If you have not done so already, start GSAS-II and open your
228kaolinite.gpx file.</p>
229
230<h2>Part 1. Create a new phase</h2>
231
232<p class=MsoNormal>We will need a new ‘faulted’ phase for the simulation of the
233Georgia (Ga-1b) kaolinite pattern. Do <b><span style='font-family:"Calibri",sans-serif'>Data/Add
234new phase</span></b> and give it a name (I chose ‘<b><span style='font-family:
235"Calibri",sans-serif'>Georgia</span></b>’); the General tab will be displayed.
236Change the <b><span style='font-family:"Calibri",sans-serif'>Phase type</span></b>
237to <b><span style='font-family:"Calibri",sans-serif'>faulted</span></b>; the
238page will be redrawn and a new tab (Layers) will appear. Select it.</p>
239
240<p class=MsoNormal><img width=624 height=370 id="Picture 1"
241src="Stacking%20Faults-III_files/image002.gif"> We need to enter the kaolinite
242abc* lattice parameters; these can be obtained from the kaolinite.gpx project file.
243Do <b><span style='font-family:"Calibri",sans-serif'>Operations/Copy phase cell</span></b>;
244a file selection dialog will appear showing <b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b>.
245Select it and then select <b><span style='font-family:"Calibri",sans-serif'>kaolinite
246abc*</span></b> from the next popup window; the Layers tab will be redrawn with
247the new lattice parameters.</p>
248
249<p class=MsoNormal><img width=624 height=365 id="Picture 2"
250src="Stacking%20Faults-III_files/image004.gif"></p>
251
252<p class=MsoNormal>We’ll add the layers in a moment.</p>
253
254<h2>Part 2. Import powder data to simulate.</h2>
255
256<p class=MsoNormal>The powder data from the Ga-1b (kaolinite from Washington
257Cty., Georgia) is what we are going to simulate; do <b><span style='font-family:
258"Calibri",sans-serif'>Import/Powder Data/from Bruker RAW file</span></b>.
259Select <b><span style='font-family:"Calibri",sans-serif'>KGA1-CONT.RAW</span></b>;
260answer <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> for
261question about the file. We will use the internal default instrument
262parameters; press <b><span style='font-family:"Calibri",sans-serif'>Cancel</span></b>
263on the file selection dialog and select <b><span style='font-family:"Calibri",sans-serif'>Defaults
264for CuKa lab data</span></b> from the next popup. The next popup asks about the
265phases to be included.</p>
266
267<p class=MsoNormal><img width=320 height=299 id="Picture 3"
268src="Stacking%20Faults-III_files/image006.gif"></p>
269
270<p class=MsoNormal>Select <b><span style='font-family:"Calibri",sans-serif'>Georgia</span></b>
271which is the faulted phase created in Step 1. The pattern will be displayed.</p>
272
273<p class=MsoNormal><img width=624 height=535 id="Picture 4"
274src="Stacking%20Faults-III_files/image008.gif"></p>
275
276<p class=MsoNormal>It covers 2-70° 2&#920; and shows some of the obvious
277characteristics of stacking faults, especially the sharp rise/sloping
278background feature at 20-30° 2&#920;. We want to limit the range for the
279simulation to be <b><span style='font-family:"Calibri",sans-serif'>10-52</span></b>°
2802&#920; (do this in <b><span style='font-family:"Calibri",sans-serif'>Limits</span></b>
281under <b><span style='font-family:"Calibri",sans-serif'>PWDR KGA1-CONT.RAW Scan
2821</span></b>), set the first background coefficient to something reasonable (in
283<b><span style='font-family:"Calibri",sans-serif'>Background</span></b> &amp;
284the flat portion &lt; 20° 2&#920; = ~<b><span style='font-family:"Calibri",sans-serif'>80</span></b>).
285In <b><span style='font-family:"Calibri",sans-serif'>Instrument Parameters</span></b>
286change <b><span style='font-family:"Calibri",sans-serif'>W</span></b> to <b><span
287style='font-family:"Calibri",sans-serif'>40</span></b> and in <b><span
288style='font-family:"Calibri",sans-serif'>Sample Parameters</span></b> set the <b><span
289style='font-family:"Calibri",sans-serif'>Histogram scale factor</span></b> to <b><span
290style='font-family:"Calibri",sans-serif'>40</span></b>. Also change <b><span
291style='font-family:"Calibri",sans-serif'>Diffractometer type</span></b> to <b><span
292style='font-family:"Calibri",sans-serif'>Bragg-Brentano</span></b>. The powder
293pattern will show the new limits.</p>
294
295<p class=MsoNormal><img width=624 height=535 id="Picture 5"
296src="Stacking%20Faults-III_files/image010.gif"></p>
297
298<p class=MsoNormal>Finally select the <b><span style='font-family:"Calibri",sans-serif'>Georgia</span></b>
299phase and the <b><span style='font-family:"Calibri",sans-serif'>Data</span></b>
300tab; it will be empty.</p>
301
302<p class=MsoNormal><img width=440 height=192 id="Picture 10"
303src="Stacking%20Faults-III_files/image018.gif"></p>
304
305<p class=MsoNormal>Do <b><span style='font-family:"Calibri",sans-serif'>Edit/Add
306powder histograms</span></b>; a popup will show the available PWDR data sets. Select
307just <b><span style='font-family:"Calibri",sans-serif'>PWDR KGA1-CONT.RAW Scan
3081</span></b> and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
309The Data tab will be redrawn; currently none of this information is of use in
310stacking fault simulations.</p>
311
312<h2>Step 3. Setup layer model for simulation.</h2>
313
314<p class=MsoNormal>We now need to fill the layer data with atoms and develop a
315stacking fault model for the simulation. Select the <b><span style='font-family:
316"Calibri",sans-serif'>Georgia</span></b> phase and the <b><span
317style='font-family:"Calibri",sans-serif'>Layers</span></b> tab.</p>
318
319<p class=MsoNormal><img width=624 height=365 id="Picture 6"
320src="Stacking%20Faults-III_files/image019.gif"></p>
321
322<p class=MsoNormal>To begin we need a kaolinite layer; you can use <b><span
323style='font-family:"Calibri",sans-serif'>Import new layer</span></b> as before.
324Select <b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b>
325and pick <b><span style='font-family:"Calibri",sans-serif'>kaolinite abc*</span></b>
326from the list of phases; the Layers tab will be redrawn showing the atom list
327for the layer.</p>
328
329<p class=MsoNormal><img width=624 height=377 id="Picture 7"
330src="Stacking%20Faults-III_files/image020.gif"></p>
331
332<p class=MsoNormal>Change the <b><span style='font-family:"Calibri",sans-serif'>Layer
333name</span></b> to <b><span style='font-family:"Calibri",sans-serif'>kaolinite
334A</span></b> (the Layers tab will be redrawn).</p>
335
336<p class=MsoNormal>To make a defect structure we need a second layer which will
337be the same as the first one; select <b><span style='font-family:"Calibri",sans-serif'>Add
338new layer</span></b>. The Layers tab will be redrawn again. Scroll down (might
339need a slight tug on an edge to get the scroll to show) to find the new layer.</p>
340
341<p class=MsoNormal> <img width=624 height=377 id="Picture 9"
342src="Stacking%20Faults-III_files/image021.gif"></p>
343
344<p class=MsoNormal>Change the <b><span style='font-family:"Calibri",sans-serif'>Layer
345name</span></b> to something other than ‘Unk’; I used ‘<b><span
346style='font-family:"Calibri",sans-serif'>kaolinite B</span></b>’ (the tab is
347redrawn). Then change the <b><span style='font-family:"Calibri",sans-serif'>Same
348as</span></b> to <b><span style='font-family:"Calibri",sans-serif'>kaolinite A</span></b>;
349that gives it the same set of atom parameters. Finally change all <b><span
350style='font-family:"Calibri",sans-serif'>Dx=-.368, Dy=-.0246 </span></b>and<b><span
351style='font-family:"Calibri",sans-serif'> Dz=1.0</span></b>; this will be the
352same as the triclinic Kaokuk stacking arrangement. Set the kaolinite A-A and
353B-B probabilities to 1.0 and the cross terms to 0.0 to reproduce the ordered
354stacking. </p>
355
356<h2>Step 4. Simulations of Georgia kaolinite</h2>
357
358<p class=MsoNormal>To do the simulation do <b><span style='font-family:"Calibri",sans-serif'>Operations/Simulate
359pattern</span></b> and <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>
360for the next two popups. </p>
361
362<p class=MsoNormal>Artioli, M<img width=624 height=535 id="Picture 11"
363src="Stacking%20Faults-III_files/image022.gif"></p>
364
365<p class=MsoNormal>The result should be nearly identical to the one we obtained
366for Keokuk kaolinite and it does not represent the data very well especially in
367the 20-30° 2&#920; region. The intent of having the 2<sup>nd</sup> kaolinite
368layer is to displace it relative to the first one as a stacking fault. The
369literature has many such models suggested (e.g. see G. Artioli, et al. Clays
370&amp; Clay Min., 43, 438-445, 1995); a simple one is to displace the 2<sup>nd</sup>
371layer by b/3 which places the SiO4 layer in the same alignment with the
372previous AlO6 layer but with effectively a different orientation than for a pair
373of Keokuk layers. Compare the Keokuk stacking (I pressed the <b><span
374style='font-family:"Calibri",sans-serif'>L</span></b> &amp; <b><span
375style='font-family:"Calibri",sans-serif'>F</span></b> keys get labels &amp;
376fade the 2<sup>nd</sup> layer).</p>
377
378<p class=MsoNormal><img width=477 height=356 id="Picture 12"
379src="Stacking%20Faults-III_files/image023.jpg"></p>
380
381<p class=MsoNormal>With the kaolinite A-B <b><span style='font-family:"Calibri",sans-serif'>Dy</span></b>=1/3-0.0246=<b><span
382style='font-family:"Calibri",sans-serif'>0.3087</span></b>.</p>
383
384<p class=MsoNormal><img width=478 height=358 id="Picture 13"
385src="Stacking%20Faults-III_files/image024.jpg"></p>
386
387<p class=MsoNormal>If you carefully compare these two drawings, you can see
388that the orientation of the 2<sup>nd</sup> (faded) layer with the 1<sup>st</sup>
389layer is the virtually same for both but in different directions. You should check
390that the kaolinite B-A and B-B stacking shows the same relationship (change
391kaolinite B-A <b><span style='font-family:"Calibri",sans-serif'>Dy=0.3087</span></b>).
392Next, change all the probabilities to <b><span style='font-family:"Calibri",sans-serif'>0.5</span></b>
393and rerun the simulation.</p>
394
395<p class=MsoNormal>O low; evidently this data <img width=624 height=535
396id="Picture 14" src="Stacking%20Faults-III_files/image025.gif"></p>
397
398<p class=MsoNormal>The 20-30° 2&#920; region is not well reproduced; the
399features are in the wrong place and are too broad. There is probably too much
400disorder in this model. The <b><span style='font-family:"Calibri",sans-serif'>Histogram
401scale factor</span></b> is also too low; evidently this data set was collected
402with at least twice the step time as the Keokuk one. Go change it to <b><span
403style='font-family:"Calibri",sans-serif'>80</span></b> and rerun the
404simulation. I’ve expanded the 20-30° 2&#920; region to see the fit.</p>
405
406<p class=MsoNormal><img width=624 height=535 id="Picture 15"
407src="Stacking%20Faults-III_files/image026.gif"></p>
408
409<p class=MsoNormal>You can use trial &amp; error adjusting the probabilities to
410find a better model. One with kaolinite A-A and kaolinite B-B probability of <b><span
411style='font-family:"Calibri",sans-serif'>0.8</span></b> and the cross terms at <b><span
412style='font-family:"Calibri",sans-serif'>0.2</span></b> gives a reasonable
413simulation.</p>
414
415<p class=MsoNormal><img width=624 height=535 id="Picture 16"
416src="Stacking%20Faults-III_files/image027.gif"></p>
417
418<p class=MsoNormal>The background feature in the 20-30° 2&#920; is reasonably
419well represented with the peaks correctly positioned and with the right
420intensity. One can create more elaborate models using additional stacking
421layers; see the paper by G. Artioli noted above for some choices. This
422completes the stacking fault simulation exercises; save your project file.</p>
423
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