Changeset 2812


Ignore:
Timestamp:
Apr 27, 2017 11:01:58 AM (5 years ago)
Author:
vondreele
Message:

update Stacking Faults II

Location:
Tutorials/StackingFaults-II
Files:
4 added
1 deleted
3 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/StackingFaults-II/Stacking Faults II.htm

    r2390 r2812  
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    10451062@page WordSection1
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    10861103
    10871104<p class=MsoNormal>In this exercise and the next you will simulate some
    1088 diffraction patterns from kaolinite clays. Kaolinite, Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>,
    1089 is a 1:<span class=GramE>1 layer</span> silicate with a single unique sheet
    1090 with AlO<sub>6</sub> <span class=SpellE>octahedra</span> on one side and SiO<sub>4</sub>
    1091 <span class=SpellE>tetrahedra</span> on the other. The layers stack with an
    1092 offset to ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span>
    1093 &amp; Von Dreele, 1989, Clay &amp; Clay Min. 37, 289-296) for a sample of the
    1094 most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other
    1095 locations evidently have stacking faults so that the peaks are displaced, have
    1096 peculiar shapes and are above a varying background. For the exercise we provide
    1097 a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
     1105diffraction patterns from kaolinite clays. Kaolinite, <span class=GramE>Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(</span>OH)<sub>4</sub>,
     1106is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> <span
     1107class=SpellE>octahedra</span> on one side and SiO<sub>4</sub> <span
     1108class=SpellE>tetrahedra</span> on the other. The layers stack with an offset to
     1109ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span> &amp; Von <span
     1110class=SpellE>Dreele</span>, 1989, Clay &amp; Clay Min. 37, 289-296) for a
     1111sample of the most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from
     1112other locations evidently have stacking faults so that the peaks are displaced,
     1113have peculiar shapes and are above a varying background. For the exercise we
     1114provide a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
    10981115class=SpellE>CuKa</span> radiation on a Bruker instrument and thus in the
    10991116Bruker RAW file format. The Keokuk kaolinite has some <span class=SpellE>dickite</span>
     
    11351152style='font-family:"Calibri",sans-serif'>Ok</span></b>; the <span class=SpellE>Xe</span>
    11361153atoms at the bottom of the atom table will be highlighted. Next select <b><span
    1137 style='font-family:"Calibri",sans-serif'>Edit/Modify atom parameters</span></b>
     1154style='font-family:"Calibri",sans-serif'>Edit/On selected atoms
     1155/Modify parameters</span></b>
    11381156from the Phase Data menu; a new popup will appear. Select <b><span
    11391157style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
     
    11491167style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then
    11501168double click the empty upper left corner box of the table. All atoms will turn
    1151 green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill unit
    1152 cell</span></b>; the structure will be redrawn with all atoms that belong in
    1153 the unit cell. Finally, double click on the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
    1154 column heading, select <b><span style='font-family:"Calibri",sans-serif'>Al</span></b>
    1155 &amp; <b><span style='font-family:"Calibri",sans-serif'>Si</span></b> (they
    1156 will turn green) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill
     1169green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
     1170unit cell</span></b>; the structure will be redrawn with all atoms that belong
     1171in the unit cell. Finally, double click on the <b><span style='font-family:
     1172"Calibri",sans-serif'>Type</span></b> column heading, select <b><span
     1173style='font-family:"Calibri",sans-serif'>Al</span></b> &amp; <b><span
     1174style='font-family:"Calibri",sans-serif'>Si</span></b> (they will turn green)
     1175and then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
    11571176CN sphere</span></b>. After a bit of rotating the structure around, the
    11581177layering along the c-axis (blue line) will be evident.</p>
     
    11701189defined in a coordinate system that has the stacking direction perpendicular to
    11711190the stacking plane defined as the c-axis. This requires transformation of the
    1172 unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this.
    1173 Select the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
    1174 tab and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
     1191unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this. Select
     1192the <b><span style='font-family:"Calibri",sans-serif'>General</span></b> tab
     1193and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
    11751194a popup window will appear.</p>
    11761195
    1177 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=350 height=339
    1178 id="_x0000_i1040" src="Stacking%20Faults%20II_files/image005.gif"></span></p>
     1196<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
     1197 id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
     1198 path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
     1199 <v:stroke joinstyle="miter"/>
     1200 <v:formulas>
     1201  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
     1202  <v:f eqn="sum @0 1 0"/>
     1203  <v:f eqn="sum 0 0 @1"/>
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     1205  <v:f eqn="prod @3 21600 pixelWidth"/>
     1206  <v:f eqn="prod @3 21600 pixelHeight"/>
     1207  <v:f eqn="sum @0 0 1"/>
     1208  <v:f eqn="prod @6 1 2"/>
     1209  <v:f eqn="prod @7 21600 pixelWidth"/>
     1210  <v:f eqn="sum @8 21600 0"/>
     1211  <v:f eqn="prod @7 21600 pixelHeight"/>
     1212  <v:f eqn="sum @10 21600 0"/>
     1213 </v:formulas>
     1214 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
     1215 <o:lock v:ext="edit" aspectratio="t"/>
     1216</v:shapetype><v:shape id="Picture_x0020_20" o:spid="_x0000_i1040" type="#_x0000_t75"
     1217 style='width:262.5pt;height:301.5pt;visibility:visible;mso-wrap-style:square'>
     1218 <v:imagedata src="Stacking%20Faults%20II_files/image001.png" o:title=""/>
     1219</v:shape><![endif]--><![if !vml]><img width=350 height=402
     1220src="Stacking%20Faults%20II_files/image002.gif" v:shapes="Picture_x0020_20"><![endif]></span></p>
    11791221
    11801222<p class=MsoNormal>Note that this allows one to transform the structure
     
    11901232the new lattice parameters will be shown.</p>
    11911233
    1192 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=350 height=339
    1193 id="_x0000_i1039" src="Stacking%20Faults%20II_files/image006.gif"></span></p>
    1194 
    1195 <p class=MsoNormal>The a &amp; b axes stay the same, but c is now smaller (the
    1196 interlayer distance in kaolinite) and <span style='font-family:Symbol'>a</span>
    1197 &amp; <span style='font-family:Symbol'>b</span> = 90 (<span style='font-family:
    1198 Symbol'>g</span> is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
    1199 a new phase (kaolinite <span class=SpellE>abc</span>*) will be made and its
    1200 General tab will be shown immediately. Select the <b><span style='font-family:
    1201 "Calibri",sans-serif'>Draw Atoms</span></b> tab to see the resulting structure.</p>
     1234<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1235 id="Picture_x0020_21" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:262.5pt;
     1236 height:301.5pt;visibility:visible;mso-wrap-style:square'>
     1237 <v:imagedata src="Stacking%20Faults%20II_files/image003.png" o:title=""/>
     1238</v:shape><![endif]--><![if !vml]><img width=350 height=402
     1239src="Stacking%20Faults%20II_files/image004.gif" v:shapes="Picture_x0020_21"><![endif]></span></p>
     1240
     1241<p class=MsoNormal><span class=GramE>The a</span> &amp; b axes stay the same,
     1242but c is now smaller (the interlayer distance in kaolinite) and <span
     1243style='font-family:Symbol'>a</span> &amp; <span style='font-family:Symbol'>b</span>
     1244= 90 (<span style='font-family:Symbol'>g</span> is unchanged). Press <b><span
     1245style='font-family:"Calibri",sans-serif'>Ok</span></b>; a new phase (kaolinite <span
     1246class=SpellE>abc</span>*) will be made and its General tab will be shown
     1247immediately. Select the <b><span style='font-family:"Calibri",sans-serif'>Draw
     1248Atoms</span></b> tab to see the resulting structure.</p>
    12021249
    12031250<p class=MsoNormal><span style='mso-no-proof:yes'><img width=471 height=352
     
    12071254can add more unit cells to the drawing; select all the atoms by double clicking
    12081255the upper left empty box of the Draw atoms table. Do <b><span style='font-family:
    1209 "Calibri",sans-serif'>Edit/Add atoms</span></b> and <b><span style='font-family:
    1210 "Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup> <b><span
    1211 style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l and press <b><span
    1212 style='font-family:"Calibri",sans-serif'>Ok</span></b>; this will add <span
    1213 class=GramE>one unit</span> cell along x. Now select all the atoms again, do <b><span
    1214 style='font-family:"Calibri",sans-serif'>Edit/Add atoms</span></b> and now <b><span
    1215 style='font-family:"Calibri",sans-serif'>decrement</span></b> the 1<sup>st</sup>
    1216 <b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>.
    1217 Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
    1218 drawing will now be 3 unit cells wide along x. Repeat this once more <b><span
     1256"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and <b><span
     1257style='font-family:"Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup>
     1258<b><span style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l
     1259and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; this
     1260will add one unit cell along x. Now select all the atoms again, do <b><span
     1261style='font-family:"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and
     1262now <b><span style='font-family:"Calibri",sans-serif'>decrement</span></b> the
     12631<sup>st</sup> <b><span style='font-family:"Calibri",sans-serif'>Choose unit
     1264cell</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
     1265the drawing will now be 3 unit cells wide along x. Repeat this once more <b><span
    12191266style='font-family:"Calibri",sans-serif'>decrementing</span></b> the 2<sup>nd</sup>
    12201267<b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>
     
    12371284
    12381285<p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
    1239 for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
    1240 powder pattern and compare it to some real data. To begin we need a new phase
    1241 that we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
     1286for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the powder
     1287pattern and compare it to some real data. To begin we need a new phase that we
     1288can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
    12421289style='font-family:"Calibri",sans-serif'>Data/Add new phase</span></b>; I named
    12431290it ‘<b><span style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The
     
    12721319id="_x0000_i1034" src="Stacking%20Faults%20II_files/image012.gif"></span></p>
    12731320
    1274 <p class=MsoNormal>Next, you need to define the layer. As it would be very tedious
    1275 to enter 24 atoms by hand, the alternative is to get them from the previously
    1276 created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
     1321<p class=MsoNormal>Next, you need to define the layer. As it would be very
     1322tedious to enter 24 atoms by hand, the alternative is to get them from the
     1323previously created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
    12771324style='font-family:"Calibri",sans-serif'>Import new layer</span></b> box; the
    12781325file dialog with <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
     
    12831330Layers page will be redrawn with a layer (named kaolinite) will be filled out.</p>
    12841331
    1285 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=829 height=500
    1286 id="_x0000_i1033" src="Stacking%20Faults%20II_files/image013.gif"></span></p>
    1287 
    1288 <p class=MsoNormal>If you move down to the bottom of the page (if there isn’t a
    1289 scroll bar, just grab an edge of the window &amp; shift it slightly) to find
    1290 the <span class=GramE>one line</span> <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer
    1291 Transition probabilities</span></b>. Change <span class=SpellE><b><span
    1292 style='font-family:"Calibri",sans-serif'>Dz</span></b></span><b><span
    1293 style='font-family:"Calibri",sans-serif'>=1.0</span></b> and press the plot
    1294 box; the drawing will show a layer of kaolinite stacked directly above another
    1295 one.</p>
     1332<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
     1333 id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
     1334 height:282.75pt;visibility:visible;mso-wrap-style:square'>
     1335 <v:imagedata src="Stacking%20Faults%20II_files/image005.png" o:title=""/>
     1336</v:shape><![endif]--><![if !vml]><img width=624 height=377
     1337src="Stacking%20Faults%20II_files/image006.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
     1338
     1339<p class=MsoNormal>If you move down to the bottom of the page to find the one
     1340line <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer Transition
     1341probabilities</span></b>. Change <span class=SpellE><b><span style='font-family:
     1342"Calibri",sans-serif'>Dz</span></b></span><b><span style='font-family:"Calibri",sans-serif'>=1.0</span></b>
     1343and press the plot box; the drawing will show a layer of kaolinite stacked
     1344directly above another one.</p>
    12961345
    12971346<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=359
     
    13421391the upper limit in a relatively clear part of the pattern. Then go to
    13431392Background and set the 1<sup>st</sup> coefficient to 20 (approximately the
    1344 background at 2Q=18). Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample
    1345 parameters</span></b> and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram
    1346 scale</span></b> to something reasonable (I chose <b><span style='font-family:
    1347 "Calibri",sans-serif'>20.0</span></b>) and make sure the <b><span
    1348 style='font-family:"Calibri",sans-serif'>Diffractometer type is Bragg-Brentano</span></b>.</p>
     1393background at 2<span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
     1394mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
     1395Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>=18).
     1396Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>
     1397and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
     1398to something reasonable (I chose <b><span style='font-family:"Calibri",sans-serif'>20.0</span></b>)
     1399and make sure the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
     1400type is Bragg-Brentano</span></b>.</p>
    13491401
    13501402<p class=MsoNormal>Now we are ready for our 1<sup>st</sup> kaolinite
     
    13911443&amp; repeat the simulation again. This gives a much better fit to the observed
    13921444pattern, but the simulated peaks are too sharp; this can be fixed by changing
    1393 the <span class=GramE>U,V</span>,W Instrument parameters. I’d just set <b><span
     1445the U<span class=GramE>,V,W</span> Instrument parameters. I’d just set <b><span
    13941446style='font-family:"Calibri",sans-serif'>W=40</span></b> and the <b><span
    13951447style='font-family:"Calibri",sans-serif'>Histogram scale</span></b> (in <b><span
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