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Timestamp:
Jul 28, 2016 2:18:10 PM (5 years ago)
Author:
vondreele
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  • Tutorials/StackingFaults-II/Stacking Faults II.htm

    r2281 r2390  
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     696        mso-fareast-theme-font:minor-fareast;
    40697        font-weight:bold;}
    41698h3
    42         {mso-style-link:"Heading 3 Char";
     699        {mso-style-priority:9;
     700        mso-style-unhide:no;
     701        mso-style-qformat:yes;
     702        mso-style-link:"Heading 3 Char";
     703        mso-margin-top-alt:auto;
    43704        margin-right:0in;
     705        mso-margin-bottom-alt:auto;
    44706        margin-left:0in;
     707        mso-pagination:widow-orphan;
     708        mso-outline-level:3;
    45709        font-size:13.5pt;
    46710        font-family:"Times New Roman",serif;
     711        mso-fareast-font-family:"Times New Roman";
     712        mso-fareast-theme-font:minor-fareast;
    47713        font-weight:bold;}
    48714h4
    49         {mso-style-link:"Heading 4 Char";
     715        {mso-style-priority:9;
     716        mso-style-unhide:no;
     717        mso-style-qformat:yes;
     718        mso-style-link:"Heading 4 Char";
    50719        margin-top:10.0pt;
    51720        margin-right:0in;
     
    53722        margin-left:0in;
    54723        margin-bottom:.0001pt;
     724        mso-pagination:widow-orphan;
    55725        page-break-after:avoid;
     726        mso-outline-level:4;
    56727        font-size:13.0pt;
    57728        font-family:"Cambria",serif;
     729        mso-fareast-font-family:"Times New Roman";
     730        mso-fareast-theme-font:minor-fareast;
    58731        color:#4F81BD;
    59732        font-weight:bold;
    60733        font-style:italic;}
    61734h5
    62         {mso-style-link:"Heading 5 Char";
     735        {mso-style-priority:9;
     736        mso-style-unhide:no;
     737        mso-style-qformat:yes;
     738        mso-style-link:"Heading 5 Char";
     739        mso-margin-top-alt:auto;
    63740        margin-right:0in;
     741        mso-margin-bottom-alt:auto;
    64742        margin-left:0in;
     743        mso-pagination:widow-orphan;
     744        mso-outline-level:5;
    65745        font-size:12.0pt;
    66746        font-family:"Times New Roman",serif;
     747        mso-fareast-font-family:"Times New Roman";
     748        mso-fareast-theme-font:minor-fareast;
    67749        color:#4F4FFF;
    68750        font-weight:bold;}
    69751a:link, span.MsoHyperlink
    70         {color:blue;
    71         text-decoration:underline;}
     752        {mso-style-noshow:yes;
     753        mso-style-priority:99;
     754        color:blue;
     755        text-decoration:underline;
     756        text-underline:single;}
    72757a:visited, span.MsoHyperlinkFollowed
    73         {color:purple;
    74         text-decoration:underline;}
     758        {mso-style-noshow:yes;
     759        mso-style-priority:99;
     760        color:purple;
     761        text-decoration:underline;
     762        text-underline:single;}
    75763p.MsoDocumentMap, li.MsoDocumentMap, div.MsoDocumentMap
    76         {mso-style-link:"Document Map Char";
     764        {mso-style-noshow:yes;
     765        mso-style-priority:99;
     766        mso-style-link:"Document Map Char";
    77767        margin:0in;
    78768        margin-bottom:.0001pt;
     769        mso-pagination:widow-orphan;
    79770        font-size:8.0pt;
    80         font-family:"Tahoma",sans-serif;}
     771        font-family:"Tahoma",sans-serif;
     772        mso-fareast-font-family:"Times New Roman";
     773        mso-fareast-theme-font:minor-fareast;}
    81774p
    82         {margin-right:0in;
     775        {mso-style-noshow:yes;
     776        mso-style-priority:99;
     777        mso-margin-top-alt:auto;
     778        margin-right:0in;
     779        mso-margin-bottom-alt:auto;
    83780        margin-left:0in;
     781        mso-pagination:widow-orphan;
    84782        font-size:12.0pt;
    85         font-family:"Times New Roman",serif;}
     783        font-family:"Times New Roman",serif;
     784        mso-fareast-font-family:"Times New Roman";
     785        mso-fareast-theme-font:minor-fareast;}
    86786pre
    87         {mso-style-link:"HTML Preformatted Char";
     787        {mso-style-noshow:yes;
     788        mso-style-priority:99;
     789        mso-style-link:"HTML Preformatted Char";
    88790        margin:0in;
    89791        margin-bottom:.0001pt;
     792        mso-pagination:widow-orphan;
     793        tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt;
    90794        font-size:10.0pt;
    91         font-family:"Courier New";}
     795        font-family:"Courier New";
     796        mso-fareast-font-family:"Times New Roman";
     797        mso-fareast-theme-font:minor-fareast;}
    92798p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
    93         {mso-style-link:"Balloon Text Char";
     799        {mso-style-noshow:yes;
     800        mso-style-priority:99;
     801        mso-style-link:"Balloon Text Char";
    94802        margin:0in;
    95803        margin-bottom:.0001pt;
     804        mso-pagination:widow-orphan;
    96805        font-size:8.0pt;
    97         font-family:"Tahoma",sans-serif;}
     806        font-family:"Tahoma",sans-serif;
     807        mso-fareast-font-family:"Times New Roman";
     808        mso-fareast-theme-font:minor-fareast;}
    98809span.MsoPlaceholderText
    99         {color:gray;}
     810        {mso-style-noshow:yes;
     811        mso-style-priority:99;
     812        mso-style-unhide:no;
     813        color:gray;}
    100814p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
    101         {margin:0in;
     815        {mso-style-priority:1;
     816        mso-style-unhide:no;
     817        mso-style-qformat:yes;
     818        margin:0in;
    102819        margin-bottom:.0001pt;
     820        mso-pagination:widow-orphan;
    103821        font-size:12.0pt;
    104         font-family:"Times New Roman",serif;}
     822        font-family:"Times New Roman",serif;
     823        mso-fareast-font-family:"Times New Roman";
     824        mso-fareast-theme-font:minor-fareast;}
    105825p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
    106         {margin-top:0in;
     826        {mso-style-priority:34;
     827        mso-style-unhide:no;
     828        mso-style-qformat:yes;
     829        margin-top:0in;
    107830        margin-right:0in;
    108831        margin-bottom:0in;
    109832        margin-left:.5in;
    110833        margin-bottom:.0001pt;
     834        mso-pagination:widow-orphan;
    111835        font-size:12.0pt;
    112         font-family:"Times New Roman",serif;}
     836        font-family:"Times New Roman",serif;
     837        mso-fareast-font-family:"Times New Roman";
     838        mso-fareast-theme-font:minor-fareast;}
    113839span.MsoIntenseReference
    114         {font-variant:small-caps;
     840        {mso-style-priority:32;
     841        mso-style-unhide:no;
     842        mso-style-qformat:yes;
     843        font-variant:small-caps;
    115844        color:#C0504D;
    116845        letter-spacing:.25pt;
    117846        font-weight:bold;
    118         text-decoration:underline;}
     847        text-decoration:underline;
     848        text-underline:single;}
    119849span.Heading1Char
    120850        {mso-style-name:"Heading 1 Char";
     851        mso-style-priority:9;
     852        mso-style-unhide:no;
     853        mso-style-locked:yes;
    121854        mso-style-link:"Heading 1";
    122855        font-family:"Times New Roman",serif;
     856        mso-ascii-font-family:"Times New Roman";
     857        mso-hansi-font-family:"Times New Roman";
     858        mso-bidi-font-family:"Times New Roman";
    123859        font-weight:bold;}
    124860span.Heading2Char
    125861        {mso-style-name:"Heading 2 Char";
     862        mso-style-noshow:yes;
     863        mso-style-priority:9;
     864        mso-style-unhide:no;
     865        mso-style-locked:yes;
    126866        mso-style-link:"Heading 2";
    127867        font-family:"Times New Roman",serif;
     868        mso-ascii-font-family:"Times New Roman";
     869        mso-hansi-font-family:"Times New Roman";
     870        mso-bidi-font-family:"Times New Roman";
    128871        font-weight:bold;}
    129872span.Heading3Char
    130873        {mso-style-name:"Heading 3 Char";
     874        mso-style-noshow:yes;
     875        mso-style-priority:9;
     876        mso-style-unhide:no;
     877        mso-style-locked:yes;
    131878        mso-style-link:"Heading 3";
    132879        font-family:"Times New Roman",serif;
     880        mso-ascii-font-family:"Times New Roman";
     881        mso-hansi-font-family:"Times New Roman";
     882        mso-bidi-font-family:"Times New Roman";
    133883        font-weight:bold;}
    134884span.Heading4Char
    135885        {mso-style-name:"Heading 4 Char";
     886        mso-style-noshow:yes;
     887        mso-style-priority:9;
     888        mso-style-unhide:no;
     889        mso-style-locked:yes;
    136890        mso-style-link:"Heading 4";
    137891        font-family:"Cambria",serif;
     892        mso-ascii-font-family:Cambria;
     893        mso-hansi-font-family:Cambria;
    138894        color:#4F81BD;
    139895        font-weight:bold;
     
    141897span.Heading5Char
    142898        {mso-style-name:"Heading 5 Char";
     899        mso-style-noshow:yes;
     900        mso-style-priority:9;
     901        mso-style-unhide:no;
     902        mso-style-locked:yes;
    143903        mso-style-link:"Heading 5";
    144904        font-family:"Times New Roman",serif;
     905        mso-ascii-font-family:"Times New Roman";
     906        mso-hansi-font-family:"Times New Roman";
     907        mso-bidi-font-family:"Times New Roman";
    145908        color:#4F4FFF;
    146909        font-weight:bold;}
    147910span.HTMLPreformattedChar
    148911        {mso-style-name:"HTML Preformatted Char";
     912        mso-style-noshow:yes;
     913        mso-style-priority:99;
     914        mso-style-unhide:no;
     915        mso-style-locked:yes;
    149916        mso-style-link:"HTML Preformatted";
    150         font-family:"Courier New";}
     917        font-family:"Courier New";
     918        mso-ascii-font-family:"Courier New";
     919        mso-hansi-font-family:"Courier New";
     920        mso-bidi-font-family:"Courier New";}
    151921p.msonormal0, li.msonormal0, div.msonormal0
    152922        {mso-style-name:msonormal;
     923        mso-style-unhide:no;
     924        mso-margin-top-alt:auto;
    153925        margin-right:0in;
     926        mso-margin-bottom-alt:auto;
    154927        margin-left:0in;
     928        mso-pagination:widow-orphan;
    155929        font-size:12.0pt;
    156         font-family:"Times New Roman",serif;}
     930        font-family:"Times New Roman",serif;
     931        mso-fareast-font-family:"Times New Roman";
     932        mso-fareast-theme-font:minor-fareast;}
    157933span.DocumentMapChar
    158934        {mso-style-name:"Document Map Char";
     935        mso-style-noshow:yes;
     936        mso-style-priority:99;
     937        mso-style-unhide:no;
     938        mso-style-locked:yes;
    159939        mso-style-link:"Document Map";
    160         font-family:"Tahoma",sans-serif;}
     940        font-family:"Tahoma",sans-serif;
     941        mso-ascii-font-family:Tahoma;
     942        mso-hansi-font-family:Tahoma;
     943        mso-bidi-font-family:Tahoma;}
    161944span.BalloonTextChar
    162945        {mso-style-name:"Balloon Text Char";
     946        mso-style-noshow:yes;
     947        mso-style-priority:99;
     948        mso-style-unhide:no;
     949        mso-style-locked:yes;
    163950        mso-style-link:"Balloon Text";
    164         font-family:"Tahoma",sans-serif;}
     951        font-family:"Tahoma",sans-serif;
     952        mso-ascii-font-family:Tahoma;
     953        mso-hansi-font-family:Tahoma;
     954        mso-bidi-font-family:Tahoma;}
    165955p.msolistparagraphcxspfirst, li.msolistparagraphcxspfirst, div.msolistparagraphcxspfirst
    166956        {mso-style-name:msolistparagraphcxspfirst;
     957        mso-style-unhide:no;
    167958        margin-top:0in;
    168959        margin-right:0in;
     
    170961        margin-left:.5in;
    171962        margin-bottom:.0001pt;
     963        mso-pagination:widow-orphan;
    172964        font-size:12.0pt;
    173         font-family:"Times New Roman",serif;}
     965        font-family:"Times New Roman",serif;
     966        mso-fareast-font-family:"Times New Roman";
     967        mso-fareast-theme-font:minor-fareast;}
    174968p.msolistparagraphcxspmiddle, li.msolistparagraphcxspmiddle, div.msolistparagraphcxspmiddle
    175969        {mso-style-name:msolistparagraphcxspmiddle;
     970        mso-style-unhide:no;
    176971        margin-top:0in;
    177972        margin-right:0in;
     
    179974        margin-left:.5in;
    180975        margin-bottom:.0001pt;
     976        mso-pagination:widow-orphan;
    181977        font-size:12.0pt;
    182         font-family:"Times New Roman",serif;}
     978        font-family:"Times New Roman",serif;
     979        mso-fareast-font-family:"Times New Roman";
     980        mso-fareast-theme-font:minor-fareast;}
    183981p.msolistparagraphcxsplast, li.msolistparagraphcxsplast, div.msolistparagraphcxsplast
    184982        {mso-style-name:msolistparagraphcxsplast;
     983        mso-style-unhide:no;
    185984        margin-top:0in;
    186985        margin-right:0in;
     
    188987        margin-left:.5in;
    189988        margin-bottom:.0001pt;
     989        mso-pagination:widow-orphan;
    190990        font-size:12.0pt;
    191         font-family:"Times New Roman",serif;}
     991        font-family:"Times New Roman",serif;
     992        mso-fareast-font-family:"Times New Roman";
     993        mso-fareast-theme-font:minor-fareast;}
    192994span.GSAS-IItextChar
    193995        {mso-style-name:"GSAS-II text Char";
     996        mso-style-unhide:no;
     997        mso-style-locked:yes;
    194998        mso-style-link:"GSAS-II text";
    195999        font-family:"Times New Roman",serif;
     1000        mso-ascii-font-family:"Times New Roman";
     1001        mso-hansi-font-family:"Times New Roman";
     1002        mso-bidi-font-family:"Times New Roman";
    1961003        font-weight:bold;}
    1971004p.GSAS-IItext, li.GSAS-IItext, div.GSAS-IItext
    1981005        {mso-style-name:"GSAS-II text";
     1006        mso-style-unhide:no;
    1991007        mso-style-link:"GSAS-II text Char";
    2001008        margin:0in;
    2011009        margin-bottom:.0001pt;
     1010        mso-pagination:widow-orphan;
    2021011        font-size:12.0pt;
    2031012        font-family:"Calibri",sans-serif;
     1013        mso-fareast-font-family:"Times New Roman";
     1014        mso-fareast-theme-font:minor-fareast;
     1015        mso-bidi-font-family:"Times New Roman";
    2041016        font-weight:bold;}
    2051017p.msochpdefault, li.msochpdefault, div.msochpdefault
    2061018        {mso-style-name:msochpdefault;
     1019        mso-style-unhide:no;
     1020        mso-margin-top-alt:auto;
    2071021        margin-right:0in;
     1022        mso-margin-bottom-alt:auto;
    2081023        margin-left:0in;
     1024        mso-pagination:widow-orphan;
    2091025        font-size:10.0pt;
    210         font-family:"Calibri",sans-serif;}
     1026        font-family:"Calibri",sans-serif;
     1027        mso-fareast-font-family:"Times New Roman";
     1028        mso-fareast-theme-font:minor-fareast;
     1029        mso-bidi-font-family:"Times New Roman";}
     1030span.SpellE
     1031        {mso-style-name:"";
     1032        mso-spl-e:yes;}
     1033span.GramE
     1034        {mso-style-name:"";
     1035        mso-gram-e:yes;}
    2111036.MsoChpDefault
    212         {font-size:10.0pt;
    213         font-family:"Calibri",sans-serif;}
     1037        {mso-style-type:export-only;
     1038        mso-default-props:yes;
     1039        font-size:10.0pt;
     1040        mso-ansi-font-size:10.0pt;
     1041        mso-bidi-font-size:10.0pt;
     1042        font-family:"Calibri",sans-serif;
     1043        mso-ascii-font-family:Calibri;
     1044        mso-hansi-font-family:Calibri;}
    2141045@page WordSection1
    2151046        {size:8.5in 11.0in;
    216         margin:1.0in 1.0in 1.0in 1.0in;}
     1047        margin:1.0in 1.0in 1.0in 1.0in;
     1048        mso-header-margin:.5in;
     1049        mso-footer-margin:.5in;
     1050        mso-paper-source:0;}
    2171051div.WordSection1
    2181052        {page:WordSection1;}
    2191053-->
    2201054</style>
    221 
     1055<!--[if gte mso 10]>
     1056<style>
     1057 /* Style Definitions */
     1058 table.MsoNormalTable
     1059        {mso-style-name:"Table Normal";
     1060        mso-tstyle-rowband-size:0;
     1061        mso-tstyle-colband-size:0;
     1062        mso-style-noshow:yes;
     1063        mso-style-priority:99;
     1064        mso-style-parent:"";
     1065        mso-padding-alt:0in 5.4pt 0in 5.4pt;
     1066        mso-para-margin:0in;
     1067        mso-para-margin-bottom:.0001pt;
     1068        mso-pagination:widow-orphan;
     1069        font-size:10.0pt;
     1070        font-family:"Calibri",sans-serif;}
     1071</style>
     1072<![endif]--><!--[if gte mso 9]><xml>
     1073 <o:shapedefaults v:ext="edit" spidmax="1026"/>
     1074</xml><![endif]--><!--[if gte mso 9]><xml>
     1075 <o:shapelayout v:ext="edit">
     1076  <o:idmap v:ext="edit" data="1"/>
     1077 </o:shapelayout></xml><![endif]-->
    2221078</head>
    2231079
    224 <body lang=EN-US link=blue vlink=purple>
     1080<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
    2251081
    2261082<div class=WordSection1>
    2271083
    228 <h1>Stacking Fault Simulations – II</h1>
     1084<h1><span style='mso-fareast-font-family:"Times New Roman"'>Stacking Fault
     1085Simulations – II<o:p></o:p></span></h1>
    2291086
    2301087<p class=MsoNormal>In this exercise and the next you will simulate some
    2311088diffraction patterns from kaolinite clays. Kaolinite, Al<sub>2</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub>,
    232 is a 1:1 layer silicate with a single unique sheet with AlO<sub>6</sub>
    233 octahedra on one side and SiO<sub>4</sub> tetrahedra on the other. The layers
    234 stack with an offset to ideally form a triclinic C1 lattice (Bish &amp; Von
    235 Dreele, 1989, Clay &amp; Clay Min. 37, 289-296) for a sample of the most
    236 ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other locations
    237 evidently have stacking faults so that the peaks are displaced, have peculiar
    238 shapes and are above a varying background. For the exercise we provide a
    239 laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with CuKa
    240 radiation on a Bruker instrument and thus in the Bruker RAW file format. The
    241 Keokuk kaolinite has some dickite (different ordered stacking of kaolinite
    242 layers). The next exercise Stacking Faults-III) covers a simple simulation of a
    243 faulted kaolinite from Georgia.</p>
     1089is a 1:<span class=GramE>1 layer</span> silicate with a single unique sheet
     1090with 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
     1092offset 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
     1094most ordered form of kaolinite from Keokuk, Iowa. Kaolinites from other
     1095locations evidently have stacking faults so that the peaks are displaced, have
     1096peculiar shapes and are above a varying background. For the exercise we provide
     1097a laboratory Bragg-Brentano pattern of Keokuk kaolinite collected with <span
     1098class=SpellE>CuKa</span> radiation on a Bruker instrument and thus in the
     1099Bruker RAW file format. The Keokuk kaolinite has some <span class=SpellE>dickite</span>
     1100(different ordered stacking of kaolinite layers). The next exercise Stacking
     1101Faults-III) covers a simple simulation of a faulted kaolinite from Georgia.</p>
    2441102
    2451103<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
    2461104
    247 <h2>Part 1. Creating kaolinite layer</h2>
    248 
    249 <p class=MsoNormal>In this initial step we will load from a cif file the
    250 structure of kaolinite, draw it to see the layer structure and then transform
    251 it into forms suitable for stacking simulations. To begin do <b><span
     1105<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 1. Creating
     1106kaolinite layer<o:p></o:p></span></h2>
     1107
     1108<p class=MsoNormal>In this initial step we will load from a <span class=SpellE>cif</span>
     1109file the structure of kaolinite, draw it to see the layer structure and then
     1110transform it into forms suitable for stacking simulations. To begin do <b><span
    2521111style='font-family:"Calibri",sans-serif'>Import/Phase/from CIF file</span></b>;
    253 from the file dialog select <b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b>.
     1112from the file dialog select <span class=SpellE><b style='mso-bidi-font-weight:
     1113normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1114minor-latin;mso-hansi-theme-font:minor-latin'>StackingFaults</span></b></span><b
     1115style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     1116mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>-II/data/</span></b><span
     1117class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.cif</span></b></span>.
    2541118After the “are you sure” popup, there will be another warning you that 4 atom
    2551119types (‘O-H’) were not recognized chemical element symbols and they were
    256 substituted by Xe to make them obvious in the atom list. Press <b><span
    257 style='font-family:"Calibri",sans-serif'>Ok</span></b>; you are offered a
    258 chance to change the phase name, I used ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’.
    259 The General tab is displayed (notice the presence of Xe in the element table).</p>
    260 
    261 <p class=MsoNormal><img width=930 height=500
    262 src="Stacking%20Faults%20II_files/image001.gif"></p>
    263 
    264 <p class=MsoNormal>To fix the Xe atoms (they should be O), select <b><span
    265 style='font-family:"Calibri",sans-serif'>Atoms</span></b> and then double click
    266 the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> column
    267 heading; a small popup will appear. Select <b><span style='font-family:"Calibri",sans-serif'>Xe</span></b>
    268 &amp; press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
    269 the Xe atoms at the bottom of the atom table will be highlighted. Next select <b><span
     1120substituted by <span class=SpellE>Xe</span> to make them obvious in the atom
     1121list. Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
     1122you are offered a chance to change the phase name, I used ‘<b><span
     1123style='font-family:"Calibri",sans-serif'>kaolinite</span></b>’. The General tab
     1124is displayed (notice the presence of <span class=SpellE>Xe</span> in the
     1125element table).</p>
     1126
     1127<p class=MsoNormal><span style='mso-no-proof:yes'><img width=930 height=500
     1128id="_x0000_i1043" src="Stacking%20Faults%20II_files/image001.gif"></span></p>
     1129
     1130<p class=MsoNormal>To fix the <span class=SpellE>Xe</span> atoms (they should
     1131be O), select <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
     1132and then double click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
     1133column heading; a small popup will appear. Select <span class=SpellE><b><span
     1134style='font-family:"Calibri",sans-serif'>Xe</span></b></span> &amp; press <b><span
     1135style='font-family:"Calibri",sans-serif'>Ok</span></b>; the <span class=SpellE>Xe</span>
     1136atoms at the bottom of the atom table will be highlighted. Next select <b><span
    2701137style='font-family:"Calibri",sans-serif'>Edit/Modify atom parameters</span></b>
    2711138from the Phase Data menu; a new popup will appear. Select <b><span
     
    2761143only.</p>
    2771144
    278 <p class=MsoNormal><img width=479 height=358
    279 src="Stacking%20Faults%20II_files/image003.jpg"></p>
     1145<p class=MsoNormal><span style='mso-no-proof:yes'><img width=479 height=358
     1146id="_x0000_i1042" src="Stacking%20Faults%20II_files/image003.jpg"></span></p>
    2801147
    2811148<p class=MsoNormal>To better visualize the stacking layer, select the <b><span
     
    2911158layering along the c-axis (blue line) will be evident.</p>
    2921159
    293 <p class=MsoNormal><img width=480 height=359
    294 src="Stacking%20Faults%20II_files/image004.jpg"></p>
    295 
    296 <p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> tetrahedra
    297 and AlO<sub>6</sub> octahedra. Also notice that the next layer (represented by
    298 the 4 O atoms at the bottom of the above drawing are offset giving a triclinic
    299 lattice.</p>
    300 
    301 <p class=MsoNormal>The stacking fault simulation calculation via DIFFaX
    302 routines requires that the stacking layers be defined in a coordinate system
    303 that has the stacking direction perpendicular to the stacking plane defined as
    304 the c-axis. This requires transformation of the unit cell and atom coordinates;
    305 a suitable tool exists in GSAS-II to do this. Select the <b><span
    306 style='font-family:"Calibri",sans-serif'>General</span></b> tab and do <b><span
    307 style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>; a popup
    308 window will appear.</p>
    309 
    310 <p class=MsoNormal><img width=350 height=339
    311 src="Stacking%20Faults%20II_files/image005.gif"></p>
     1160<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=359
     1161id="_x0000_i1041" src="Stacking%20Faults%20II_files/image004.jpg"></span></p>
     1162
     1163<p class=MsoNormal>One can easily see the layer of SiO<sub>4</sub> <span
     1164class=SpellE>tetrahedra</span> and AlO<sub>6</sub> <span class=SpellE>octahedra</span>.
     1165Also notice that the next layer (represented by the 4 O atoms at the bottom of
     1166the above drawing are offset giving a triclinic lattice.</p>
     1167
     1168<p class=MsoNormal>The stacking fault simulation calculation via <span
     1169class=SpellE>DIFFaX</span> routines requires that the stacking layers be
     1170defined in a coordinate system that has the stacking direction perpendicular to
     1171the stacking plane defined as the c-axis. This requires transformation of the
     1172unit cell and atom coordinates; a suitable tool exists in GSAS-II to do this.
     1173Select the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
     1174tab and do <b><span style='font-family:"Calibri",sans-serif'>Compute/Transform</span></b>;
     1175a popup window will appear.</p>
     1176
     1177<p class=MsoNormal><span style='mso-no-proof:yes'><img width=350 height=339
     1178id="_x0000_i1040" src="Stacking%20Faults%20II_files/image005.gif"></span></p>
    3121179
    3131180<p class=MsoNormal>Note that this allows one to transform the structure
     
    3151182and then select those that are unique according to a selected space group. The
    3161183pulldown gives a selection of commonly used transformations; we want the last
    317 one, <b><span style='font-family:"Calibri",sans-serif'>abc*</span></b>, which
    318 satisfies the stacking fault requirement. Select it; notice that the space
    319 group is changed to P1. Leave this as the kaolinite layer has no symmetry; in
    320 other circumstances the layer may have an inversion center in which case P-1
    321 should be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
     1184one, <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>abc</span></b></span><b><span
     1185style='font-family:"Calibri",sans-serif'>*</span></b>, which satisfies the
     1186stacking fault requirement. Select it; notice that the space group is changed
     1187to P1. Leave this as the kaolinite layer has no symmetry; in other
     1188circumstances the layer may have an inversion center in which case P-1 should
     1189be used. If you press <b><span style='font-family:"Calibri",sans-serif'>Test</span></b>,
    3221190the new lattice parameters will be shown.</p>
    3231191
    324 <p class=MsoNormal><img width=350 height=339
    325 src="Stacking%20Faults%20II_files/image006.gif"></p>
     1192<p class=MsoNormal><span style='mso-no-proof:yes'><img width=350 height=339
     1193id="_x0000_i1039" src="Stacking%20Faults%20II_files/image006.gif"></span></p>
    3261194
    3271195<p class=MsoNormal>The a &amp; b axes stay the same, but c is now smaller (the
     
    3291197&amp; <span style='font-family:Symbol'>b</span> = 90 (<span style='font-family:
    3301198Symbol'>g</span> is unchanged). Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
    331 a new phase (kaolinite abc*) will be made and its General tab will be shown
    332 immediately. Select the <b><span style='font-family:"Calibri",sans-serif'>Draw
    333 Atoms</span></b> tab to see the resulting structure.</p>
    334 
    335 <p class=MsoNormal><img width=471 height=352
    336 src="Stacking%20Faults%20II_files/image007.jpg"></p>
     1199a new phase (kaolinite <span class=SpellE>abc</span>*) will be made and its
     1200General 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>
     1202
     1203<p class=MsoNormal><span style='mso-no-proof:yes'><img width=471 height=352
     1204id="_x0000_i1038" src="Stacking%20Faults%20II_files/image007.jpg"></span></p>
    3371205
    3381206<p class=MsoNormal>To see what this layer looks like with more of it drawn, you
     
    3421210"Calibri",sans-serif'>increment</span></b> the 1<sup>st</sup> <b><span
    3431211style='font-family:"Calibri",sans-serif'>Choose unit cel</span></b>l and press <b><span
    344 style='font-family:"Calibri",sans-serif'>Ok</span></b>; this will add one unit
    345 cell along x. Now select all the atoms again, do <b><span style='font-family:
    346 "Calibri",sans-serif'>Edit/Add atoms</span></b> and now <b><span
     1212style='font-family:"Calibri",sans-serif'>Ok</span></b>; this will add <span
     1213class=GramE>one unit</span> cell along x. Now select all the atoms again, do <b><span
     1214style='font-family:"Calibri",sans-serif'>Edit/Add atoms</span></b> and now <b><span
    3471215style='font-family:"Calibri",sans-serif'>decrement</span></b> the 1<sup>st</sup>
    3481216<b><span style='font-family:"Calibri",sans-serif'>Choose unit cell</span></b>.
     
    3561224the drawing should look like (after some zooming/shifting/rotation).</p>
    3571225
    358 <p class=MsoNormal><img width=477 height=357
    359 src="Stacking%20Faults%20II_files/image009.jpg"></p>
    360 
    361 <p class=MsoNormal>This structure is now suitable for use in DIFFaX
    362 calculations; the cell has a c-axis that is perpendicular to the ab plane with
    363 a length that is the stacking repeat distance. This is a good place to save
    364 your project (I called it ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
    365 
    366 <h2>Part 2. Set up simulation of ideal kaolinite stacking</h2>
     1226<p class=MsoNormal><span style='mso-no-proof:yes'><img width=477 height=357
     1227id="_x0000_i1037" src="Stacking%20Faults%20II_files/image009.jpg"></span></p>
     1228
     1229<p class=MsoNormal>This structure is now suitable for use in <span
     1230class=SpellE>DIFFaX</span> calculations; the cell has a c-axis that is
     1231perpendicular to the ab plane with a length that is the stacking repeat
     1232distance. This is a good place to save your project (I called it ‘<b><span
     1233style='font-family:"Calibri",sans-serif'>kaolinite’</span></b>).</p>
     1234
     1235<h2><span style='mso-fareast-font-family:"Times New Roman"'>Part 2. Set up
     1236simulation of ideal kaolinite stacking<o:p></o:p></span></h2>
    3671237
    3681238<p class=MsoNormal>In this part of the tutorial we’ll create a stacking model
    369 for Keokuk kaolinite and use DIFFaX to simulate the powder pattern and compare
    370 it to some real data. To begin we need a new phase that we can declare as
    371 “faulted’. In the main GSAS-II data tree menu do <b><span style='font-family:
    372 "Calibri",sans-serif'>Data/Add new phase</span></b>; I named it ‘<b><span
    373 style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The General tab
    374 for it will immediately appear.</p>
    375 
    376 <p class=MsoNormal><img width=930 height=500
    377 src="Stacking%20Faults%20II_files/image010.gif"></p>
     1239for Keokuk kaolinite and use <span class=SpellE>DIFFaX</span> to simulate the
     1240powder pattern and compare it to some real data. To begin we need a new phase
     1241that we can declare as “faulted’. In the main GSAS-II data tree menu do <b><span
     1242style='font-family:"Calibri",sans-serif'>Data/Add new phase</span></b>; I named
     1243it ‘<b><span style='font-family:"Calibri",sans-serif'>Keokuk</span></b>’. The
     1244General tab for it will immediately appear.</p>
     1245
     1246<p class=MsoNormal><span style='mso-no-proof:yes'><img width=930 height=500
     1247id="_x0000_i1036" src="Stacking%20Faults%20II_files/image010.gif"></span></p>
    3781248
    3791249<p class=MsoNormal>Change the <b><span style='font-family:"Calibri",sans-serif'>Phase
     
    3821252will appear. Select it.</p>
    3831253
    384 <p class=MsoNormal><img width=817 height=484
    385 src="Stacking%20Faults%20II_files/image011.gif"></p>
     1254<p class=MsoNormal><span style='mso-no-proof:yes'><img width=817 height=484
     1255id="_x0000_i1035" src="Stacking%20Faults%20II_files/image011.gif"></span></p>
    3861256
    3871257<p class=MsoNormal>We can anticipate (given that kaolinite space group is C1)
    3881258that the <b><span style='font-family:"Calibri",sans-serif'>Diffraction Laue
    3891259symmetry</span></b> is <b><span style='font-family:"Calibri",sans-serif'>-1</span></b>.
    390 We can enter by hand the lattice parameters from the kaolinite abc* phase but
    391 an easier method is available. Do <b><span style='font-family:"Calibri",sans-serif'>Operations/Copy
    392 phase cell</span></b>; a file selection dialog will appear for your current
    393 directory and the file <b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b>
     1260We can enter by hand the lattice parameters from the kaolinite <span
     1261class=SpellE>abc</span>* phase but an easier method is available. Do <b><span
     1262style='font-family:"Calibri",sans-serif'>Operations/Copy phase cell</span></b>;
     1263a file selection dialog will appear for your current directory and the file <span
     1264class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
    3941265should be there. Select it; a small popup will appear listing the available
    395 phases. Choose ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite
    396 abc*</span></b>’ and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>;
    397 the Layers window will be redrawn with the new lattice parameters.</p>
    398 
    399 <p class=MsoNormal><img width=829 height=484
    400 src="Stacking%20Faults%20II_files/image012.gif"></p>
    401 
    402 <p class=MsoNormal>Next, you need to define the layer. As it would be very
    403 tedious to enter 24 atoms by hand, the alternative is to get them from the
    404 previously created kaolinite abc* phase. Select the <b><span style='font-family:
    405 "Calibri",sans-serif'>Import new layer</span></b> box; the file dialog with <b><span
    406 style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b> will appear.
    407 Select the file and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>;
     1266phases. Choose ‘<b><span style='font-family:"Calibri",sans-serif'>kaolinite <span
     1267class=SpellE>abc</span>*</span></b>’ and press <b><span style='font-family:
     1268"Calibri",sans-serif'>Ok</span></b>; the Layers window will be redrawn with the
     1269new lattice parameters.</p>
     1270
     1271<p class=MsoNormal><span style='mso-no-proof:yes'><img width=829 height=484
     1272id="_x0000_i1034" src="Stacking%20Faults%20II_files/image012.gif"></span></p>
     1273
     1274<p class=MsoNormal>Next, you need to define the layer. As it would be very tedious
     1275to enter 24 atoms by hand, the alternative is to get them from the previously
     1276created kaolinite <span class=SpellE>abc</span>* phase. Select the <b><span
     1277style='font-family:"Calibri",sans-serif'>Import new layer</span></b> box; the
     1278file dialog with <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>kaolinite.gpx</span></b></span>
     1279will appear. Select the file and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>;
    4081280again a small popup with two phases listed will appear. Again select <b><span
    409 style='font-family:"Calibri",sans-serif'>kaolinite abc*</span></b> and press <b><span
    410 style='font-family:"Calibri",sans-serif'>Ok</span></b>; the Layers page will be
    411 redrawn with a layer (named kaolinite) will be filled out.</p>
    412 
    413 <p class=MsoNormal><img width=829 height=500
    414 src="Stacking%20Faults%20II_files/image013.gif"></p>
     1281style='font-family:"Calibri",sans-serif'>kaolinite <span class=SpellE>abc</span>*</span></b>
     1282and press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
     1283Layers page will be redrawn with a layer (named kaolinite) will be filled out.</p>
     1284
     1285<p class=MsoNormal><span style='mso-no-proof:yes'><img width=829 height=500
     1286id="_x0000_i1033" src="Stacking%20Faults%20II_files/image013.gif"></span></p>
    4151287
    4161288<p class=MsoNormal>If you move down to the bottom of the page (if there isn’t a
    4171289scroll bar, just grab an edge of the window &amp; shift it slightly) to find
    418 the one line <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer
    419 Transition probabilities</span></b>. Change <b><span style='font-family:"Calibri",sans-serif'>Dz=1.0</span></b>
    420 and press the plot box; the drawing will show a layer of kaolinite stacked
    421 directly above another one.</p>
    422 
    423 <p class=MsoNormal><img width=480 height=359
    424 src="Stacking%20Faults%20II_files/image014.jpg"></p>
     1290the <span class=GramE>one line</span> <b><span style='font-family:"Calibri",sans-serif'>Layer-Layer
     1291Transition probabilities</span></b>. Change <span class=SpellE><b><span
     1292style='font-family:"Calibri",sans-serif'>Dz</span></b></span><b><span
     1293style='font-family:"Calibri",sans-serif'>=1.0</span></b> and press the plot
     1294box; the drawing will show a layer of kaolinite stacked directly above another
     1295one.</p>
     1296
     1297<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=359
     1298id="_x0000_i1032" src="Stacking%20Faults%20II_files/image014.jpg"></span></p>
    4251299
    4261300<p class=MsoNormal>Compare that to the stacking in kaolinite.</p>
    4271301
    428 <p class=MsoNormal><img width=480 height=359
    429 src="Stacking%20Faults%20II_files/image015.jpg"></p>
     1302<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=359
     1303id="_x0000_i1031" src="Stacking%20Faults%20II_files/image015.jpg"></span></p>
    4301304
    4311305<p class=MsoNormal>Notice the effect of the offset. The 1<sup>st</sup> row of
    432 SiO<sub>4</sub> tetrahedra are positioned directly above the AlO<sub>6</sub>
    433 octahedra in the real structure but not in the vertically stacked structure. We
    434 can use a bit of simple geometry to work out what the offset is but first let
    435 us see what happens in the simulation and how it compares to real data.</p>
    436 
    437 <h2>Step 3. Import Keokuk kaolinite data and do 1<sup>st</sup> simulation</h2>
     1306SiO<sub>4</sub> <span class=SpellE>tetrahedra</span> are positioned directly
     1307above the AlO<sub>6</sub> <span class=SpellE>octahedra</span> in the real
     1308structure but not in the vertically stacked structure. We can use a bit of
     1309simple geometry to work out what the offset is but first let us see what
     1310happens in the simulation and how it compares to real data.</p>
     1311
     1312<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Import
     1313Keokuk kaolinite data and do 1<sup>st</sup> simulation<o:p></o:p></span></h2>
    4381314
    4391315<p class=MsoNormal>First we need to import the Keokuk kaolinite powder data; do
    4401316<b><span style='font-family:"Calibri",sans-serif'>Import/Powder Data/from
    4411317Bruker RAW file</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Keokuk
    442 kaolinite.RAW</span></b> from the file dialog box; press <b><span
    443 style='font-family:"Calibri",sans-serif'>Yes</span></b> in the next popup. A
    444 new file dialog appears requesting an instrument parameter file; we will use an
    445 internal default instead. Press <b><span style='font-family:"Calibri",sans-serif'>Cancel</span></b>
    446 and select <b><span style='font-family:"Calibri",sans-serif'>Defaults for CuKa
    447 lab data</span></b> from the next popup. This process will repeat since the RAW
    448 file contains two scans. In the next popup, select only <b><span
    449 style='font-family:"Calibri",sans-serif'>kaolinite abc*</span></b>. There will
    450 be two PWDR scans in the GSAS-II data tree; one covers 2<span style='font-family:
    451 Symbol'>Q</span>= 10-90<span style='font-family:"Calibri",sans-serif'>°</span>
    452 and the other covers 2<span style='font-family:Symbol'>Q</span>=80-150°. Only
    453 the lower part of the first one is going to be used in our simulation work as the
    454 calculations become very time consuming for complex structures and high angle
    455 data. Select <b><span style='font-family:"Calibri",sans-serif'>PWDR Keokuk
    456 kaolinite.RAW Scan 1</span></b> from the GSAS-II data tree make sure it
    457 expands; its plot will also show.</p>
    458 
    459 <p class=MsoNormal><img width=700 height=600
    460 src="Stacking%20Faults%20II_files/image016.gif"></p>
     1318<span class=SpellE>kaolinite.RAW</span></span></b> from the file dialog box;
     1319press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> in the
     1320next popup. A new file dialog appears requesting an instrument parameter file;
     1321we will use an internal default instead. Press <b><span style='font-family:
     1322"Calibri",sans-serif'>Cancel</span></b> and select <b><span style='font-family:
     1323"Calibri",sans-serif'>Defaults for <span class=SpellE>CuKa</span> lab data</span></b>
     1324from the next popup. This process will repeat since the RAW file contains two
     1325scans. In the next popup, select only <b><span style='font-family:"Calibri",sans-serif'>kaolinite
     1326<span class=SpellE>abc</span>*</span></b>. There will be two PWDR scans in the
     1327GSAS-II data tree; one covers 2<span style='font-family:Symbol'>Q</span>= 10-90<span
     1328style='font-family:"Calibri",sans-serif'>°</span> and the other covers 2<span
     1329style='font-family:Symbol'>Q</span>=80-150°. Only the lower part of the first
     1330one is going to be used in our simulation work as the calculations become very
     1331time consuming for complex structures and high angle data. Select <b><span
     1332style='font-family:"Calibri",sans-serif'>PWDR Keokuk <span class=SpellE>kaolinite.RAW</span>
     1333Scan 1</span></b> from the GSAS-II data tree make sure it expands; its plot
     1334will also show.</p>
     1335
     1336<p class=MsoNormal><span style='mso-no-proof:yes'><img width=700 height=600
     1337id="_x0000_i1030" src="Stacking%20Faults%20II_files/image016.gif"></span></p>
    4611338
    4621339<p class=MsoNormal>Go to <b><span style='font-family:"Calibri",sans-serif'>Limits</span></b>
    463 and set <b><span style='font-family:"Calibri",sans-serif'>Tmax</span></b> to <b><span
    464 style='font-family:"Calibri",sans-serif'>52.0</span></b>; that puts the upper limit
    465 in a relatively clear part of the pattern. Then go to Background and set the 1<sup>st</sup>
    466 coefficient to 20 (approximately the background at 2Q=18). Next go to <b><span
    467 style='font-family:"Calibri",sans-serif'>Sample parameters</span></b> and set
    468 the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
    469 to something reasonable (I chose <b><span style='font-family:"Calibri",sans-serif'>20.0</span></b>)
    470 and make sure the <b><span style='font-family:"Calibri",sans-serif'>Diffractometer
    471 type is Bragg-Brentano</span></b>.</p>
     1340and set <span class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Tmax</span></b></span>
     1341to <b><span style='font-family:"Calibri",sans-serif'>52.0</span></b>; that puts
     1342the upper limit in a relatively clear part of the pattern. Then go to
     1343Background and set the 1<sup>st</sup> coefficient to 20 (approximately the
     1344background at 2Q=18). Next go to <b><span style='font-family:"Calibri",sans-serif'>Sample
     1345parameters</span></b> and set the <b><span style='font-family:"Calibri",sans-serif'>Histogram
     1346scale</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
     1348style='font-family:"Calibri",sans-serif'>Diffractometer type is Bragg-Brentano</span></b>.</p>
    4721349
    4731350<p class=MsoNormal>Now we are ready for our 1<sup>st</sup> kaolinite
     
    4811358and the new plot will be displayed (I’ve zoomed in a bit).</p>
    4821359
    483 <p class=MsoNormal><img width=700 height=600
    484 src="Stacking%20Faults%20II_files/image017.gif">.</p>
     1360<p class=MsoNormal><span style='mso-no-proof:yes'><img width=700 height=600
     1361id="_x0000_i1029" src="Stacking%20Faults%20II_files/image017.gif"></span>.</p>
    4851362
    4861363<p class=MsoNormal>As you can see the simulation (green curve) does not fit the
     
    4891366offset consider the drawing of kaolinite.</p>
    4901367
    491 <p class=MsoNormal><img width=480 height=338
    492 src="Stacking%20Faults%20II_files/image002.gif"></p>
    493 
    494 <p class=MsoNormal>The offset Dx is given by the blue arrow in the above
    495 drawing of kaolinite and is in fractional coordinates. Geometry gives</p>
    496 
    497 <p class=MsoNormal><span style='position:relative;top:3pt'><img width=106
    498 height=26 src="Stacking%20Faults%20II_files/image021.gif">&nbsp;Or in this case
    499 <b><span style='font-family:"Calibri",sans-serif'>-0.368</span></b>. Set <b><span
    500 style='font-family:"Calibri",sans-serif'>Dx</span></b> to this value &amp;
    501 repeat simulation.</p>
    502 
    503 <p class=MsoNormal><img width=700 height=600
    504 src="Stacking%20Faults%20II_files/image022.gif"></p>
     1368<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=338
     1369id="_x0000_i1028" src="Stacking%20Faults%20II_files/image002.gif"></span></p>
     1370
     1371<p class=MsoNormal>The offset <span class=SpellE>Dx</span> is given by the blue
     1372arrow in the above drawing of kaolinite and is in fractional coordinates.
     1373Geometry gives<o:p></o:p></p>
     1374
     1375<p class=MsoNormal><span style='position:relative;top:3pt'><span
     1376style='mso-no-proof:yes'><img width=106 height=26 id="_x0000_i1027"
     1377src="Stacking%20Faults%20II_files/image021.gif"></span>&nbsp;Or in this case <b><span
     1378style='font-family:"Calibri",sans-serif'>-0.368</span></b>. Set <span
     1379class=SpellE><b><span style='font-family:"Calibri",sans-serif'>Dx</span></b></span>
     1380to this value &amp; repeat simulation.</p>
     1381
     1382<p class=MsoNormal><span style='mso-no-proof:yes'><img width=700 height=600
     1383id="_x0000_i1026" src="Stacking%20Faults%20II_files/image022.gif"></span></p>
    5051384
    5061385<p class=MsoNormal>There is some improvement but some parts are not very well
    5071386represented. Recall from the triclinic kaolinite lattice parameters that <span
    5081387style='font-family:Symbol'>a</span> was 91.7°; that will produce a small offset
    509 in Dy. Using the same kind of geometry math gives <b><span style='font-family:
    510 "Calibri",sans-serif'>Dy=-0.0246</span></b>. Enter this value &amp; repeat the
    511 simulation again. This gives a much better fit to the observed pattern, but the
    512 simulated peaks are too sharp; this can be fixed by changing the U,V,W
    513 Instrument parameters. I’d just set <b><span style='font-family:"Calibri",sans-serif'>W=40</span></b>
    514 and the <b><span style='font-family:"Calibri",sans-serif'>Histogram scale</span></b>
    515 (in <b><span style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>)
    516 to <b><span style='font-family:"Calibri",sans-serif'>40</span></b> and try
    517 again.</p>
    518 
    519 <p class=MsoNormal><img width=700 height=600
    520 src="Stacking%20Faults%20II_files/image023.gif"></p>
     1388in Dy. Using the same kind of geometry math gives <span class=SpellE><b><span
     1389style='font-family:"Calibri",sans-serif'>Dy</span></b></span><b><span
     1390style='font-family:"Calibri",sans-serif'>=-0.0246</span></b>. Enter this value
     1391&amp; repeat the simulation again. This gives a much better fit to the observed
     1392pattern, but the simulated peaks are too sharp; this can be fixed by changing
     1393the <span class=GramE>U,V</span>,W Instrument parameters. I’d just set <b><span
     1394style='font-family:"Calibri",sans-serif'>W=40</span></b> and the <b><span
     1395style='font-family:"Calibri",sans-serif'>Histogram scale</span></b> (in <b><span
     1396style='font-family:"Calibri",sans-serif'>Sample parameters</span></b>) to <b><span
     1397style='font-family:"Calibri",sans-serif'>40</span></b> and try again.</p>
     1398
     1399<p class=MsoNormal><span style='mso-no-proof:yes'><img width=700 height=600
     1400id="_x0000_i1025" src="Stacking%20Faults%20II_files/image023.gif"></span></p>
    5211401
    5221402<p class=MsoNormal>That is a pretty good fit for a stacking simulation. By
     
    5261406small range can be used to help with optimization, but in this case it would be
    5271407far easier to do a Rietveld refinement for this well ordered kaolinite. Save
    528 your project as you will need it for the next exercise (Stacking Faults-III).</p>
     1408your project as you will need it for the next exercise (Stacking Faults-III).<o:p></o:p></p>
    5291409
    5301410</span></div>
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