Changeset 2812 for Tutorials

Timestamp:

Apr 27, 2017 11:01:58 AM (7 years ago)

Author:

vondreele

Message:

update Stacking Faults II

Location:

Tutorials/StackingFaults-II

Files:

• Stacking Faults II.htm (modified) (23 diffs)
• Stacking Faults II_files/image001.png (added)
• Stacking Faults II_files/image002.gif (modified) (previous)
• Stacking Faults II_files/image003.png (added)
• Stacking Faults II_files/image004.gif (added)
• Stacking Faults II_files/image005.png (added)
• Stacking Faults II_files/image006.gif (modified) (previous)
• Stacking Faults II_files/image018.gif (deleted)

Tutorials/StackingFaults-II/Stacking Faults II.htm

@@ -25 +25 @@
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@@ -637 +638 @@
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@@ -729 +730 @@
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@@ -813 +815 @@
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@@ -921 +925 @@
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@@ -955 +961 @@
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@@ -968 +976 @@
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@@ -1004 +1016 @@
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@@ -1017 +1031 @@
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@@ -1042 +1058 @@
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 @page WordSection1
         {size:8.5in 11.0in;
@@ -1086 +1103 @@
 
 <p class=MsoNormal>In this exercise and the next you will simulate some
-diffraction patterns from kaolinite clays. Kaolinite, Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>,
-is a 1:<span class=GramE>1 layer</span> silicate with a single unique sheet
-with AlO<sub>6</sub> <span class=SpellE>octahedra</span> on one side and SiO<sub>4</sub>
-<span class=SpellE>tetrahedra</span> on the other. The layers stack with an
-offset to ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span>
-&amp; Von Dreele, 1989, Clay &amp; Clay Min. 37, 289-296) for a sample of the
-most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other
-locations evidently have stacking faults so that the peaks are displaced, have
-peculiar shapes and are above a varying background. For the exercise we provide
-a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
+diffraction 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>,
+is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub> <span
+class=SpellE>octahedra</span> on one side and SiO<sub>4</sub> <span
+class=SpellE>tetrahedra</span> on the other. The layers stack with an offset to
+ideally form a triclinic C1 lattice (<span class=SpellE>Bish</span> &amp; Von <span
+class=SpellE>Dreele</span>, 1989, Clay &amp; Clay Min. 37, 289-296) for a
+sample of the most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from
+other locations evidently have stacking faults so that the peaks are displaced,
+have peculiar shapes and are above a varying background. For the exercise we
+provide a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
 class=SpellE>CuKa</span> radiation on a Bruker instrument and thus in the
 Bruker RAW file format. The Keokuk kaolinite has some <span class=SpellE>dickite</span>
@@ -1135 +1152 @@
 style='font-family:"Calibri",sans-serif'>Ok</span></b>; the <span class=SpellE>Xe</span>
 atoms at the bottom of the atom table will be highlighted. Next select <b><span
-style='font-family:"Calibri",sans-serif'>Edit/Modify atom parameters</span></b>
+style='font-family:"Calibri",sans-serif'>Edit/On selected atoms
+/Modify parameters</span></b>
 from the Phase Data menu; a new popup will appear. Select <b><span
 style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
@@ -1149 +1167 @@
 style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and then
 double click the empty upper left corner box of the table. All atoms will turn
-green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill unit
-cell</span></b>; the structure will be redrawn with all atoms that belong in
-the unit cell. Finally, double click on the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
-column heading, select <b><span style='font-family:"Calibri",sans-serif'>Al</span></b>
-&amp; <b><span style='font-family:"Calibri",sans-serif'>Si</span></b> (they
-will turn green) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Fill
+green. Then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
+unit cell</span></b>; the structure will be redrawn with all atoms that belong
+in the unit cell. Finally, double click on the <b><span style='font-family:
+"Calibri",sans-serif'>Type</span></b> column heading, select <b><span
+style='font-family:"Calibri",sans-serif'>Al</span></b> &amp; <b><span
+style='font-family:"Calibri",sans-serif'>Si</span></b> (they will turn green)
+and then do <b><span style='font-family:"Calibri",sans-serif'>Edit Figure/Fill
 CN sphere</span></b>. After a bit of rotating the structure around, the
 layering along the c-axis (blue line) will be evident.</p>
@@ -1170 +1189 @@
 defined in a coordinate system that has the stacking direction perpendicular to
 the stacking plane defined as the c-axis. This requires transformation of the
-unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this.
-Select the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
-tab and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
+unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this. Select
+the <b><span style='font-family:"Calibri",sans-serif'>General</span></b> tab
+and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
 a popup window will appear.</p>
 
-<p class=MsoNormal><span style='mso-no-proof:yes'><img width=350 height=339
-id="_x0000_i1040" src="Stacking%20Faults%20II_files/image005.gif"></span></p>
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
+ id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
+ path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
+ <v:stroke joinstyle="miter"/>
+ <v:formulas>
+  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
+  <v:f eqn="sum @0 1 0"/>
+  <v:f eqn="sum 0 0 @1"/>
+  <v:f eqn="prod @2 1 2"/>
+  <v:f eqn="prod @3 21600 pixelWidth"/>
+  <v:f eqn="prod @3 21600 pixelHeight"/>
+  <v:f eqn="sum @0 0 1"/>
+  <v:f eqn="prod @6 1 2"/>
+  <v:f eqn="prod @7 21600 pixelWidth"/>
+  <v:f eqn="sum @8 21600 0"/>
+  <v:f eqn="prod @7 21600 pixelHeight"/>
+  <v:f eqn="sum @10 21600 0"/>
+ </v:formulas>
+ <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
+ <o:lock v:ext="edit" aspectratio="t"/>
+</v:shapetype><v:shape id="Picture_x0020_20" o:spid="_x0000_i1040" type="#_x0000_t75"
+ style='width:262.5pt;height:301.5pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Stacking%20Faults%20II_files/image001.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img width=350 height=402
+src="Stacking%20Faults%20II_files/image002.gif" v:shapes="Picture_x0020_20"><![endif]></span></p>
 
 <p class=MsoNormal>Note that this allows one to transform the structure
@@ -1190 +1232 @@
 the new lattice parameters will be shown.</p>
 
-<p class=MsoNormal><span style='mso-no-proof:yes'><img width=350 height=339
-id="_x0000_i1039" src="Stacking%20Faults%20II_files/image006.gif"></span></p>
-
-<p class=MsoNormal>The a &amp; b axes stay the same, but c is now smaller (the
-interlayer distance in kaolinite) and <span style='font-family:Symbol'>a</span>
-&amp; <span style='font-family:Symbol'>b</span> = 90 (<span style='font-family:
-Symbol'>g</span> is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
-a new phase (kaolinite <span class=SpellE>abc</span>*) will be made and its
-General tab will be shown immediately. Select the <b><span style='font-family:
-"Calibri",sans-serif'>Draw Atoms</span></b> tab to see the resulting structure.</p>
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_21" o:spid="_x0000_i1039" type="#_x0000_t75" style='width:262.5pt;
+ height:301.5pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Stacking%20Faults%20II_files/image003.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img width=350 height=402
+src="Stacking%20Faults%20II_files/image004.gif" v:shapes="Picture_x0020_21"><![endif]></span></p>
+
+<p class=MsoNormal><span class=GramE>The a</span> &amp; b axes stay the same,
+but c is now smaller (the interlayer distance in kaolinite) and <span
+style='font-family:Symbol'>a</span> &amp; <span style='font-family:Symbol'>b</span>
+= 90 (<span style='font-family:Symbol'>g</span> is unchanged). Press <b><span
+style='font-family:"Calibri",sans-serif'>Ok</span></b>; a new phase (kaolinite <span
+class=SpellE>abc</span>*) will be made and its General tab will be shown
+immediately. Select the <b><span style='font-family:"Calibri",sans-serif'>Draw
+Atoms</span></b> tab to see the resulting structure.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=471 height=352
@@ -1207 +1254 @@
 can add more unit cells to the drawing; select all the atoms by double clicking
 the upper left empty box of the Draw atoms table. Do <b><span style='font-family:
-"Calibri",sans-serif'>Edit/Add atoms</span></b> and <b><span style='font-family:
-"Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup> <b><span
-style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l and press <b><span
-style='font-family:"Calibri",sans-serif'>Ok</span></b>; this will add <span
-class=GramE>one unit</span> cell along x. Now select all the atoms again, do <b><span
-style='font-family:"Calibri",sans-serif'>Edit/Add atoms</span></b> and now <b><span
-style='font-family:"Calibri",sans-serif'>decrement</span></b> the 1<sup>st</sup>
-<b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>.
-Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
-drawing will now be 3 unit cells wide along x. Repeat this once more <b><span
+"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and <b><span
+style='font-family:"Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup>
+<b><span style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l
+and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; this
+will add one unit cell along x. Now select all the atoms again, do <b><span
+style='font-family:"Calibri",sans-serif'>Edit Figure/Add atoms</span></b> and
+now <b><span style='font-family:"Calibri",sans-serif'>decrement</span></b> the
+1<sup>st</sup> <b><span style='font-family:"Calibri",sans-serif'>Choose unit
+cell</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
+the drawing will now be 3 unit cells wide along x. Repeat this once more <b><span
 style='font-family:"Calibri",sans-serif'>decrementing</span></b> the 2<sup>nd</sup>
 <b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>
@@ -1237 +1284 @@
 
 <p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
-for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
-powder pattern and compare it to some real data. To begin we need a new phase
-that we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
+for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the powder
+pattern and compare it to some real data. To begin we need a new phase that we
+can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
 style='font-family:"Calibri",sans-serif'>Data/Add new phase</span></b>; I named
 it ‘<b><span style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The
@@ -1272 +1319 @@
 id="_x0000_i1034" src="Stacking%20Faults%20II_files/image012.gif"></span></p>
 
-<p class=MsoNormal>Next, you need to define the layer. As it would be very tedious
-to enter 24 atoms by hand, the alternative is to get them from the previously
-created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
+<p class=MsoNormal>Next, you need to define the layer. As it would be very
+tedious to enter 24 atoms by hand, the alternative is to get them from the
+previously created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
 style='font-family:"Calibri",sans-serif'>Import new layer</span></b> box; the
 file dialog with <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
@@ -1283 +1330 @@
 Layers page will be redrawn with a layer (named kaolinite) will be filled out.</p>
 
-<p class=MsoNormal><span style='mso-no-proof:yes'><img width=829 height=500
-id="_x0000_i1033" src="Stacking%20Faults%20II_files/image013.gif"></span></p>
-
-<p class=MsoNormal>If you move down to the bottom of the page (if there isn’t a
-scroll bar, just grab an edge of the window &amp; shift it slightly) to find
-the <span class=GramE>one line</span> <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer
-Transition probabilities</span></b>. Change <span class=SpellE><b><span
-style='font-family:"Calibri",sans-serif'>Dz</span></b></span><b><span
-style='font-family:"Calibri",sans-serif'>=1.0</span></b> and press the plot
-box; the drawing will show a layer of kaolinite stacked directly above another
-one.</p>
+<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
+ id="Picture_x0020_22" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
+ height:282.75pt;visibility:visible;mso-wrap-style:square'>
+ <v:imagedata src="Stacking%20Faults%20II_files/image005.png" o:title=""/>
+</v:shape><![endif]--><![if !vml]><img width=624 height=377
+src="Stacking%20Faults%20II_files/image006.gif" v:shapes="Picture_x0020_22"><![endif]></span></p>
+
+<p class=MsoNormal>If you move down to the bottom of the page to find the one
+line <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer Transition
+probabilities</span></b>. Change <span class=SpellE><b><span style='font-family:
+"Calibri",sans-serif'>Dz</span></b></span><b><span style='font-family:"Calibri",sans-serif'>=1.0</span></b>
+and press the plot box; the drawing will show a layer of kaolinite stacked
+directly above another one.</p>
 
 <p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=359
@@ -1342 +1391 @@
 the upper limit in a relatively clear part of the pattern. Then go to
 Background and set the 1<sup>st</sup> coefficient to 20 (approximately the
-background at 2Q=18). Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample
-parameters</span></b> and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram
-scale</span></b> to something reasonable (I chose <b><span style='font-family:
-"Calibri",sans-serif'>20.0</span></b>) and make sure the <b><span
-style='font-family:"Calibri",sans-serif'>Diffractometer type is Bragg-Brentano</span></b>.</p>
+background at 2<span style='font-family:Symbol;mso-ascii-font-family:"Times New Roman";
+mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
+Symbol'><span style='mso-char-type:symbol;mso-symbol-font-family:Symbol'>Q</span></span>=18).
+Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>
+and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
+to something reasonable (I chose <b><span style='font-family:"Calibri",sans-serif'>20.0</span></b>)
+and make sure the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
+type is Bragg-Brentano</span></b>.</p>
 
 <p class=MsoNormal>Now we are ready for our 1<sup>st</sup> kaolinite
@@ -1391 +1443 @@
 &amp; repeat the simulation again. This gives a much better fit to the observed
 pattern, but the simulated peaks are too sharp; this can be fixed by changing
-the <span class=GramE>U,V</span>,W Instrument parameters. I’d just set <b><span
+the U<span class=GramE>,V,W</span> Instrument parameters. I’d just set <b><span
 style='font-family:"Calibri",sans-serif'>W=40</span></b> and the <b><span
 style='font-family:"Calibri",sans-serif'>Histogram scale</span></b> (in <b><span