Changeset 2271 for Tutorials


Ignore:
Timestamp:
May 14, 2016 9:42:20 AM (8 years ago)
Author:
vondreele
Message:
 
Location:
Tutorials/StackingFaults-II
Files:
2 edited

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

    r2267 r2271  
    228228stack with an offset to ideally form a triclinic C1 lattice (Bish & Von
    229229Dreele, 1989, Clay & Clay Min. 37, 289-296) for a sample of the most
    230 ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other locations
    231 evidently have stacking faults so that the peaks are displaced, have peculiar
    232 shapes and are above a varying background. For the exercise we provide a
    233 laboratory Bragg-Brentano pattern of Keokuk kaolinite and a less ordered one
    234 from Washington County, Georgia (Clay Minerals Society Standard KGa-1b)
    235 collected with CuKa radiation on a Bruker instrument and thus in the Bruker RAW
    236 file format. The KGa-1b sample contains a small amount of anatase (TiO<sub>2</sub>)
     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>)
    237237and the Keokuk kaolinite has some dickite (different ordered stacking of
    238238kaolinite layers).</p>
    … …  
    254254The General tab is displayed (notice the presence of Xe in the element table).</p>
    255255
    256 <p class=MsoNormal><img width=930 height=500 id="Picture 8"
     256<p class=MsoNormal><img width=930 height=500
    257257src="Stacking%20Faults%20II_files/image001.gif"></p>
    258258
    … …  
    266266from the Phase Data menu; a new popup will appear.</p>
    267267
    268 <p class=MsoNormal><img width=228 height=268 id="Picture 9"
     268<p class=MsoNormal><img width=228 height=268
    269269src="Stacking%20Faults%20II_files/image002.gif"></p>
    270270
    … …  
    275275be drawn with Al, Si &amp; O atoms only.</p>
    276276
    277 <p class=MsoNormal><img width=479 height=358 id="Picture 10"
     277<p class=MsoNormal><img width=479 height=358
    278278src="Stacking%20Faults%20II_files/image003.jpg"></p>
    279279
    280280<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
    281 style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then double
    282 click the empty upper left corner box of the table. All atoms will turn green.
    283 Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill unit cell</span></b>;
    284 the structure will be redrawn with all atoms that belong in the unit cell.
    285 Finally, double click on the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
     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>
    286286column heading, select <b><span style='font-family:"Calibri",sans-serif'>Al</span></b>
    287287&amp; <b><span style='font-family:"Calibri",sans-serif'>Si</span></b> (they
    … …  
    290290layering along the c-axis (blue line) will be evident.</p>
    291291
    292 <p class=MsoNormal><img width=480 height=359 id="Picture 11"
     292<p class=MsoNormal><img width=480 height=359
    293293src="Stacking%20Faults%20II_files/image004.jpg"></p>
    294294
    … …  
    307307window will appear.</p>
    308308
    309 <p class=MsoNormal><img width=350 height=339 id="Picture 12"
     309<p class=MsoNormal><img width=350 height=339
    310310src="Stacking%20Faults%20II_files/image005.gif"></p>
    311311
    … …  
    317317satisfies the stacking fault requirement. Select it; notice that the space
    318318group is changed to P1. Leave this as the kaolinite layer has no symmetry; in
    319 other circumstances the layer may have an inversion center in which P-1 should
    320 be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
     319other circumstances the layer may have an inversion center in which case P-1
     320should be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
    321321the new lattice parameters will be shown.</p>
    322322
    323 <p class=MsoNormal><img width=350 height=339 id="Picture 13"
     323<p class=MsoNormal><img width=350 height=339
    324324src="Stacking%20Faults%20II_files/image006.gif"></p>
    325325
    … …  
    332332Atoms</span></b> tab to see the resulting structure.</p>
    333333
    334 <p class=MsoNormal><img width=471 height=352 id="Picture 14"
     334<p class=MsoNormal><img width=471 height=352
    335335src="Stacking%20Faults%20II_files/image007.jpg"></p>
    336336
    … …  
    355355the drawing should look like (after some zooming/shifting/rotation).</p>
    356356
    357 <p class=MsoNormal><span style='position:absolute;z-index:251659264;margin-left:
    358 12px;margin-top:104px;width:356px;height:201px'><img width=356 height=201
    359 src="Stacking%20Faults%20II_files/image008.gif"></span><img width=477
    360 height=357 id="Picture 15" src="Stacking%20Faults%20II_files/image009.jpg"></p>
    361 
    362 <p class=MsoNormal>I’ll say more about that diagonal line later. This structure
    363 is now suitable for use in DIFFaX calculations; the cell has a c-axis that is
    364 perpendicular to the ab plane with a length that is the stacking repeat
    365 distance. This is a good place to save your project (I called it ‘<b><span
    366 style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
     357<p class=MsoNormal><span style='position:absolute;z-index:251659264'><img
     358width=477 height=357 src="Stacking%20Faults%20II_files/image009.jpg"></p>
     359
     360<p class=MsoNormal>This structure is now suitable for use in DIFFaX
     361calculations; the cell has a c-axis that is perpendicular to the ab plane with
     362a length that is the stacking repeat distance. This is a good place to save
     363your project (I called it ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
    367364
    368365<h2>Part 2. Set up simulation of ideal kaolinite stacking</h2>
    … …  
    376373for it will immediately appear.</p>
    377374
    378 <p class=MsoNormal><img width=930 height=500 id="Picture 17"
     375<p class=MsoNormal><img width=930 height=500
    379376src="Stacking%20Faults%20II_files/image010.gif"></p>
    380377
    … …  
    384381will appear. Select it.</p>
    385382
    386 <p class=MsoNormal><img width=817 height=484 id="Picture 18"
     383<p class=MsoNormal><img width=817 height=484
    387384src="Stacking%20Faults%20II_files/image011.gif"></p>
    388385
    … …  
    399396the Layers window will be redrawn with the new lattice parameters.</p>
    400397
    401 <p class=MsoNormal><img width=829 height=484 id="Picture 19"
     398<p class=MsoNormal><img width=829 height=484
    402399src="Stacking%20Faults%20II_files/image012.gif"></p>
    403400
    404 <p class=MsoNormal>Next, you need to define the layer. As it would be very
    405 tedious to enter 24 atoms by hand, the alternative is to get them from the
    406 previously created kaolinite abc* phase. Select the <b><span style='font-family:
    407 "Calibri",sans-serif'>Import new layer</span></b> box; the file dialog with <b><span
    408 style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b> will appear.
    409 Select the file and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>;
    410 again a small popup with two phases listed will appear. Again select <b><span
     401<p class=MsoNormal>Next, you need to define the layer. As it would be very tedious
     402to enter 24 atoms by hand, the alternative is to get them from the previously
     403created kaolinite abc* phase. Select the <b><span style='font-family:"Calibri",sans-serif'>Import
     404new layer</span></b> box; the file dialog with <b><span style='font-family:
     405"Calibri",sans-serif'>kaolinite.gpx</span></b> will appear. Select the file and
     406press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>; again
     407a small popup with two phases listed will appear. Again select <b><span
    411408style='font-family:"Calibri",sans-serif'>kaolinite abc*</span></b> and press <b><span
    412409style='font-family:"Calibri",sans-serif'>Ok</span></b>; the Layers page will be
    413410redrawn with a layer (named kaolinite) will be filled out.</p>
    414411
    415 <p class=MsoNormal><img width=829 height=500 id="Picture 20"
     412<p class=MsoNormal><img width=829 height=500
    416413src="Stacking%20Faults%20II_files/image013.gif"></p>
    417414
    … …  
    423420directly above another one.</p>
    424421
    425 <p class=MsoNormal><img width=480 height=359 id="Picture 24"
     422<p class=MsoNormal><img width=480 height=359
    426423src="Stacking%20Faults%20II_files/image014.jpg"></p>
    427424
    428425<p class=MsoNormal>Compare that to the stacking in kaolinite.</p>
    429426
    430 <p class=MsoNormal><img width=480 height=359 id="Picture 26"
     427<p class=MsoNormal><img width=480 height=359
    431428src="Stacking%20Faults%20II_files/image015.jpg"></p>
    432429
    … …  
    459456expands; its plot will also show.</p>
    460457
    461 <p class=MsoNormal><img width=700 height=600 id="Picture 27"
     458<p class=MsoNormal><img width=700 height=600
    462459src="Stacking%20Faults%20II_files/image016.gif"></p>
    463460
    … …  
    483480and the new plot will be displayed (I’ve zoomed in a bit).</p>
    484481
    485 <p class=MsoNormal><img width=700 height=600 id="Picture 29"
     482<p class=MsoNormal><img width=700 height=600
    486483src="Stacking%20Faults%20II_files/image017.gif">.</p>
    487484
    … …  
    491488offset consider the drawing of kaolinite.</p>
    492489
    493 <p class=MsoNormal><span style='position:absolute;z-index:251661312;margin-left:
    494 104px;margin-top:123px;width:46px;height:22px'><img width=46 height=22
    495 src="Stacking%20Faults%20II_files/image018.gif"></span><span style='position:
    496 absolute;z-index:251660288;margin-left:153px;margin-top:135px;width:3px;
    497 height:199px'><img width=3 height=199
    498 src="Stacking%20Faults%20II_files/image019.gif"></span><img width=481
    499 height=360 id="Picture 30" src="Stacking%20Faults%20II_files/image020.jpg"></p>
     490<p class=MsoNormal><span style='position:absolute;z-index:251661312'><span
     491style='position:absolute;z-index:251660288;margin-left:105px;margin-top:127px;
     492width:53px;height:207px'><img width=53 height=207
     493src="Stacking%20Faults%20II_files/image001.gif"></span><img width=481
     494height=360 src="Stacking%20Faults%20II_files/image020.jpg"></p>
    500495
    501496<p class=MsoNormal>The offset Dx is given by the blue arrow in the above
    502497drawing of kaolinite and is in fractional coordinates. Geometry gives</p>
    503498
    504 <p class=MsoNormal><span
    505 style='font-size:12.0pt;font-family:"Times New Roman",serif;position:relative;
    506 top:3.0pt'><img width=106 height=26
    507 src="Stacking%20Faults%20II_files/image021.gif"></span> Or in this case <b><span
    508 style='font-family:"Calibri",sans-serif'>-0.368</span></b>. Set <b><span
     499<p class=MsoNormal><span style='position:relative;top:3pt'><img width=106
     500height=26 src="Stacking%20Faults%20II_files/image021.gif">&nbsp;Or in this case
     501<b><span style='font-family:"Calibri",sans-serif'>-0.368</span></b>. Set <b><span
    509502style='font-family:"Calibri",sans-serif'>Dx</span></b> to this value &amp;
    510503repeat simulation.</p>
    511504
    512 <p class=MsoNormal><img width=700 height=600 id="Picture 33"
     505<p class=MsoNormal><img width=700 height=600
    513506src="Stacking%20Faults%20II_files/image022.gif"></p>
    514507
    … …  
    526519again.</p>
    527520
    528 <p class=MsoNormal><img width=700 height=600 id="Picture 34"
     521<p class=MsoNormal><img width=700 height=600
    529522src="Stacking%20Faults%20II_files/image023.gif"></p>
    530523
    … …  
    532525further hand tweaking of the parameters one can further improve the simulation
    533526but based on what we see here we do have the right description of stacking in
    534 Keokuk kaolinite. Save your project as you will need it for the next part of
    535 the exercise.</p>
     527Keokuk kaolinite. Doing sequence simulations varying each parameter over a
     528small range can be used to help with optimization, but in this case it would be
     529far easier to do a Rietveld refinement for this well ordered kaolinite. Save
     530your project as you will need it for the next part of the exercise.</p>
    536531
    537532</div>
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