Changeset 4296


Ignore:
Timestamp:
Feb 11, 2020 7:39:59 AM (21 months ago)
Author:
vondreele
Message:

Extend tutorial to include use of Compare

Location:
Tutorials/RMCProfile-I
Files:
51 added
2 edited

Legend:

Unmodified
Added
Removed
  • Tutorials/RMCProfile-I/RMCProfile-I.htm

    r4284 r4296  
    2323  <o:Author>vondreele</o:Author>
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    12201220this and subsequent tutorials, we will show how to use GSAS-II in conjunction
    12211221with <span class=SpellE>RMCProfile</span> (“<span class=SpellE>RMCProfile</span>:
    1222 Reverse Monte Carlo for polycrystalline materials”, M.G. Tucker, D.A. Keen, M.T.
    1223 Dove, A.L. Goodwin and Q. Hui, (2007) Jour. Phys.: Cond. Matter, <b
     1222Reverse Monte Carlo for polycrystalline materials”, M.G. Tucker, D.A. Keen,
     1223M.T. Dove, A.L. Goodwin and Q. Hui, (2007) Jour. Phys.: Cond. Matter, <b
    12241224style='mso-bidi-font-weight:normal'>19</b>, 335218. <span class=SpellE>doi</span>:
    12251225<a href="https://doi.org/10.1088/0953-8984/19/33/335218">https://doi.org/10.1088/0953-8984/19/33/335218</a>)
    12261226to fit both powder diffraction data and a pair distribution function (PDF)
    1227 created from it with a “large box” disordered model. <o:p></o:p></span></p>
     1227created from it with a “big box” disordered model. <o:p></o:p></span></p>
    12281228
    12291229<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     
    12721272class=SpellE>RMCProfile</span> tutorial Exercises 1-3, sulfur hexafluoride (SF<sub>6</sub>).
    12731273The average structure of SF<sub>6 </sub>is a molecular crystal at low
    1274 temperatures with the SF<sub>6 </sub>octahedra arranged in a body centered
    1275 cubic lattice with the S-F bonds aligned with the crystal axes. The structural
     1274temperatures with the SF<sub>6 </sub>octahedra arranged in a body centered cubic
     1275lattice with the S-F bonds aligned with the crystal axes. The structural
    12761276frustration induced by close F-F contacts forces the octahedra to locally
    12771277rotate in different directions and this disorder gives rise to considerable
     
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    14371437
     
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    1483 style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
    1484 file (only one there) </span>There will be a Dialog box asking <span
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     1483style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> file
     1484(only one there) </span>There will be a Dialog box asking <span class=GramE><b
    14881485style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14891486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1490 minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
     1487minor-latin'>Is</span></b></span><b style='mso-bidi-font-weight:normal'><span
     1488style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     1489mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> this the
     1490file you want?</span></b> Press <span class=GramE><b style='mso-bidi-font-weight:
     1491normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     1492minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Yes</span></b></span>
     1493button to proceed. You will get the opportunity to change the phase name next
     1494(I left it alone; NB: because of restrictions in <span class=SpellE>RMCProfile</span>
     1495it is important that the phase name not have any spaces); press <b
    14911496style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
    14921497mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
    1493 minor-latin'>Yes</span></b></span> button to proceed. You will get the
    1494 opportunity to change the phase name next (I left it alone; NB: because of
    1495 restrictions in <span class=SpellE>RMCProfile</span> it is important that the
    1496 phase name not have any spaces); press <b style='mso-bidi-font-weight:normal'><span
    1497 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
    1498 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
    1499 to continue. Next is the histogram selection window; this connects the phase to
    1500 the data so it can be used in subsequent calculations.</p>
     1498minor-latin'>OK</span></b> to continue. Next is the histogram selection window;
     1499this connects the phase to the data so it can be used in subsequent
     1500calculations.</p>
    15011501
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    20262026 mso-wrap-style:square'>
    20272027 <v:imagedata src="RMCProfile-I_files/image029.png" o:title=""/>
    20282028</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=289
    2029 src="RMCProfile-I_files/image030.gif" v:shapes="Picture_x0020_16"><![endif]></span><span
     2029src="RMCProfile-I_files/image082.gif" v:shapes="Picture_x0020_16"><![endif]></span><span
    20302030style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    20312031
     
    20872087
    20882088<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2089 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_17" o:spid="_x0000_i1042"
     2089mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_17" o:spid="_x0000_i1051"
    20902090 type="#_x0000_t75" style='width:357.75pt;height:132.75pt;visibility:visible;
    20912091 mso-wrap-style:square'>
    20922092 <v:imagedata src="RMCProfile-I_files/image031.png" o:title=""/>
    20932093</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=177
    2094 src="RMCProfile-I_files/image032.gif" v:shapes="Picture_x0020_17"><![endif]></span><span
     2094src="RMCProfile-I_files/image083.gif" v:shapes="Picture_x0020_17"><![endif]></span><span
    20952095style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    20962096
     
    21052105
    21062106<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2107 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_18" o:spid="_x0000_i1041"
     2107mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_18" o:spid="_x0000_i1050"
    21082108 type="#_x0000_t75" style='width:5in;height:3in;visibility:visible;
    21092109 mso-wrap-style:square'>
    21102110 <v:imagedata src="RMCProfile-I_files/image033.png" o:title=""/>
    21112111</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=288
    2112 src="RMCProfile-I_files/image034.gif" v:shapes="Picture_x0020_18"><![endif]></span><span
     2112src="RMCProfile-I_files/image084.gif" v:shapes="Picture_x0020_18"><![endif]></span><span
    21132113style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    21142114
     
    21222122
    21232123<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2124 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_19" o:spid="_x0000_i1040"
     2124mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_19" o:spid="_x0000_i1049"
    21252125 type="#_x0000_t75" style='width:358.5pt;height:133.5pt;visibility:visible;
    21262126 mso-wrap-style:square'>
    21272127 <v:imagedata src="RMCProfile-I_files/image035.png" o:title=""/>
    21282128</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=178
    2129 src="RMCProfile-I_files/image036.gif" v:shapes="Picture_x0020_19"><![endif]></span><span
     2129src="RMCProfile-I_files/image085.gif" v:shapes="Picture_x0020_19"><![endif]></span><span
    21302130style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    21312131
     
    21382138
    21392139<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2140 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_20" o:spid="_x0000_i1039"
     2140mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_20" o:spid="_x0000_i1048"
    21412141 type="#_x0000_t75" style='width:362.25pt;height:217.5pt;visibility:visible;
    21422142 mso-wrap-style:square'>
    21432143 <v:imagedata src="RMCProfile-I_files/image037.png" o:title=""/>
    21442144</v:shape><![endif]--><![if !vml]><img border=0 width=483 height=290
    2145 src="RMCProfile-I_files/image038.gif" v:shapes="Picture_x0020_20"><![endif]></span><span
     2145src="RMCProfile-I_files/image086.gif" v:shapes="Picture_x0020_20"><![endif]></span><span
    21462146style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    21472147
     
    21542154
    21552155<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2156 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_21" o:spid="_x0000_i1038"
     2156mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_21" o:spid="_x0000_i1047"
    21572157 type="#_x0000_t75" style='width:360.75pt;height:138pt;visibility:visible;
    21582158 mso-wrap-style:square'>
    21592159 <v:imagedata src="RMCProfile-I_files/image039.png" o:title=""/>
    21602160</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=184
    2161 src="RMCProfile-I_files/image040.gif" v:shapes="Picture_x0020_21"><![endif]></span><span
     2161src="RMCProfile-I_files/image087.gif" v:shapes="Picture_x0020_21"><![endif]></span><span
    21622162style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    21632163
     
    21652165class=SpellE>RMCProfile</span> files<o:p></o:p></span></h3>
    21662166
    2167 <p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You
    2168 are now ready to setup the <span class=SpellE>RMCProfile</span> input files<span
     2167<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You are
     2168now ready to setup the <span class=SpellE>RMCProfile</span> input files<span
    21692169class=GramE>..</span> Do </span><b style='mso-bidi-font-weight:normal'><span
    21702170style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     
    21752175
    21762176<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2177 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_23" o:spid="_x0000_i1037"
     2177mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_23" o:spid="_x0000_i1046"
    21782178 type="#_x0000_t75" style='width:292.5pt;height:130.5pt;visibility:visible;
    21792179 mso-wrap-style:square'>
    21802180 <v:imagedata src="RMCProfile-I_files/image041.png" o:title=""/>
    21812181</v:shape><![endif]--><![if !vml]><img border=0 width=390 height=174
    2182 src="RMCProfile-I_files/image042.gif" v:shapes="Picture_x0020_23"><![endif]></span><span
     2182src="RMCProfile-I_files/image088.gif" v:shapes="Picture_x0020_23"><![endif]></span><span
    21832183style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    21842184
     
    21882188
    21892189<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2190 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_24" o:spid="_x0000_i1036"
     2190mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_24" o:spid="_x0000_i1045"
    21912191 type="#_x0000_t75" style='width:361.5pt;height:176.25pt;visibility:visible;
    21922192 mso-wrap-style:square'>
    21932193 <v:imagedata src="RMCProfile-I_files/image043.png" o:title=""/>
    21942194</v:shape><![endif]--><![if !vml]><img border=0 width=482 height=235
    2195 src="RMCProfile-I_files/image044.gif" v:shapes="Picture_x0020_24"><![endif]></span><span
     2195src="RMCProfile-I_files/image089.gif" v:shapes="Picture_x0020_24"><![endif]></span><span
    21962196style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    21972197
     
    22762276
    22772277<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    2278 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_25" o:spid="_x0000_i1035"
     2278mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_25" o:spid="_x0000_i1044"
    22792279 type="#_x0000_t75" style='width:5in;height:133.5pt;visibility:visible;
    22802280 mso-wrap-style:square'>
    22812281 <v:imagedata src="RMCProfile-I_files/image045.png" o:title=""/>
    22822282</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=178
    2283 src="RMCProfile-I_files/image046.gif" v:shapes="Picture_x0020_25"><![endif]></span><span
     2283src="RMCProfile-I_files/image090.gif" v:shapes="Picture_x0020_25"><![endif]></span><span
    22842284style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    22852285
     
    41964196 <w:anchorlock/>
    41974197</v:group><![endif]--><![if !vml]><img width=384 height=387
    4198 src="RMCProfile-I_files/image049.gif" v:shapes="Group_x0020_28 Picture_x0020_27 Picture_x0020_26"><![endif]><!--[if mso & !supportInlineShapes & supportFields]><v:shape
    4199  id="_x0000_i1034" type="#_x0000_t75" style='width:288.35pt;height:290.25pt'>
     4198src="RMCProfile-I_files/image091.gif" v:shapes="Group_x0020_28 Picture_x0020_27 Picture_x0020_26"><![endif]><!--[if mso & !supportInlineShapes & supportFields]><v:shape
     4199 id="_x0000_i1043" type="#_x0000_t75" style='width:288.35pt;height:290.25pt'>
    42004200 <v:imagedata croptop="-65520f" cropbottom="65520f"/>
    42014201</v:shape><span style='mso-element:field-end'></span><![endif]--><span
     
    42084208
    42094209<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4210 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29" o:spid="_x0000_i1033"
     4210mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_29" o:spid="_x0000_i1042"
    42114211 type="#_x0000_t75" style='width:4in;height:289.5pt;visibility:visible;
    42124212 mso-wrap-style:square'>
    42134213 <v:imagedata src="RMCProfile-I_files/image050.png" o:title=""/>
    42144214</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=386
    4215 src="RMCProfile-I_files/image051.gif" v:shapes="Picture_x0020_29"><![endif]></span><span
     4215src="RMCProfile-I_files/image092.gif" v:shapes="Picture_x0020_29"><![endif]></span><span
    42164216style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    42174217
    42184218<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
    4219 G(R) partials plot shows the identity of each feature; the first 2 sharp peaks
    4220 arise from S-F (1.58Å) and F-F (2.20Å) distances within the SF<sub>6</sub>
    4221 octahedron (cf. 1.457Å and 2.06Å, respectively, for the average structure)
    4222 while the broader one at 2.8-3.1 are from F-F intermolecular contacts.<o:p></o:p></span></p>
     4219G(R) partials plot shows the identity of each feature; the first 2 sharp peaks arise
     4220from S-F (1.58Å) and F-F (2.20Å) distances within the SF<sub>6</sub> octahedron
     4221(cf. 1.457Å and 2.06Å, respectively, for the average structure) while the
     4222broader one at 2.8-3.1 are from F-F intermolecular contacts.<o:p></o:p></span></p>
    42234223
    42244224<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     
    42274227
    42284228<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4229 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_31" o:spid="_x0000_i1032"
     4229mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_31" o:spid="_x0000_i1041"
    42304230 type="#_x0000_t75" style='width:287.25pt;height:305.25pt;visibility:visible;
    42314231 mso-wrap-style:square'>
    42324232 <v:imagedata src="RMCProfile-I_files/image052.png" o:title=""/>
    42334233</v:shape><![endif]--><![if !vml]><img border=0 width=383 height=407
    4234 src="RMCProfile-I_files/image053.gif" v:shapes="Picture_x0020_31"><![endif]></span><span
     4234src="RMCProfile-I_files/image093.gif" v:shapes="Picture_x0020_31"><![endif]></span><span
    42354235style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    42364236
     
    42394239the second frame.<o:p></o:p></span></p>
    42404240
    4241 <h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 8. View the
    4242 big box structural model for SF<sub>6</sub><o:p></o:p></span></h3>
     4241<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 8. View the big
     4242box structural model for SF<sub>6</sub><o:p></o:p></span></h3>
    42434243
    42444244<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next,
     
    42854285
    42864286<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4287 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32" o:spid="_x0000_i1031"
     4287mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_32" o:spid="_x0000_i1040"
    42884288 type="#_x0000_t75" style='width:358.5pt;height:183pt;visibility:visible;
    42894289 mso-wrap-style:square'>
    42904290 <v:imagedata src="RMCProfile-I_files/image054.png" o:title=""/>
    42914291</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=244
    4292 src="RMCProfile-I_files/image055.gif" v:shapes="Picture_x0020_32"><![endif]></span><span
     4292src="RMCProfile-I_files/image094.gif" v:shapes="Picture_x0020_32"><![endif]></span><span
    42934293style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    42944294
     
    43134313
    43144314<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4315 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_33" o:spid="_x0000_i1030"
     4315mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_33" o:spid="_x0000_i1039"
    43164316 type="#_x0000_t75" style='width:288.75pt;height:306pt;visibility:visible;
    43174317 mso-wrap-style:square'>
    43184318 <v:imagedata src="RMCProfile-I_files/image056.png" o:title=""/>
    43194319</v:shape><![endif]--><![if !vml]><img border=0 width=385 height=408
    4320 src="RMCProfile-I_files/image057.gif" v:shapes="Picture_x0020_33"><![endif]></span><span
     4320src="RMCProfile-I_files/image095.gif" v:shapes="Picture_x0020_33"><![endif]></span><span
    43214321style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    43224322
     
    43244324the rotational disorder as well as some positional shifting of the SF<sub>6</sub>
    43254325molecules. The stray F atoms are bound to SF<sub>6</sub> molecules in
    4326 neighboring boxes.<o:p></o:p></span></p>
     4326neighboring boxes. <o:p></o:p></span></p>
     4327
     4328<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     4329
     4330<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>NB:
     4331this import facility can be used to load any rmc6f file, e.g. from a <span
     4332class=SpellE>RMCProfile</span> run done outside of GSAS-II; all the plotting
     4333and tools in this and the following steps are available for these big box
     4334models.<o:p></o:p></span></p>
    43274335
    43284336<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 9. View the
     
    43434351
    43444352<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4345 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_34" o:spid="_x0000_i1029"
     4353mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_34" o:spid="_x0000_i1038"
    43464354 type="#_x0000_t75" style='width:282pt;height:322.5pt;visibility:visible;
    43474355 mso-wrap-style:square'>
    43484356 <v:imagedata src="RMCProfile-I_files/image058.png" o:title=""/>
    43494357</v:shape><![endif]--><![if !vml]><img border=0 width=376 height=430
    4350 src="RMCProfile-I_files/image059.gif" v:shapes="Picture_x0020_34"><![endif]></span><span
     4358src="RMCProfile-I_files/image096.gif" v:shapes="Picture_x0020_34"><![endif]></span><span
    43514359style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    43524360
     
    43654373
    43664374<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4367 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_35" o:spid="_x0000_i1028"
     4375mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_35" o:spid="_x0000_i1037"
    43684376 type="#_x0000_t75" style='width:282pt;height:322.5pt;visibility:visible;
    43694377 mso-wrap-style:square'>
    43704378 <v:imagedata src="RMCProfile-I_files/image060.png" o:title=""/>
    43714379</v:shape><![endif]--><![if !vml]><img border=0 width=376 height=430
    4372 src="RMCProfile-I_files/image061.gif" v:shapes="Picture_x0020_35"><![endif]></span><span
     4380src="RMCProfile-I_files/image097.gif" v:shapes="Picture_x0020_35"><![endif]></span><span
    43734381style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    43744382
     
    43874395
    43884396<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4389 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_36" o:spid="_x0000_i1027"
    4390  type="#_x0000_t75" style='width:286.5pt;height:303.75pt;visibility:visible;
    4391  mso-wrap-style:square'>
     4397mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1036" type="#_x0000_t75"
     4398 style='width:286.5pt;height:303.75pt;visibility:visible;mso-wrap-style:square'>
    43924399 <v:imagedata src="RMCProfile-I_files/image062.png" o:title=""/>
    43934400</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=405
    4394 src="RMCProfile-I_files/image063.gif" v:shapes="Picture_x0020_36"><![endif]></span><span
     4401src="RMCProfile-I_files/image098.gif" v:shapes="_x0000_i1036"><![endif]></span><span
    43954402style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    43964403
     
    44114418
    44124419<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4413 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_37" o:spid="_x0000_i1026"
    4414  type="#_x0000_t75" style='width:286.5pt;height:303.75pt;visibility:visible;
    4415  mso-wrap-style:square'>
     4420mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1035" type="#_x0000_t75"
     4421 style='width:286.5pt;height:303.75pt;visibility:visible;mso-wrap-style:square'>
    44164422 <v:imagedata src="RMCProfile-I_files/image064.png" o:title=""/>
    44174423</v:shape><![endif]--><![if !vml]><img border=0 width=382 height=405
    4418 src="RMCProfile-I_files/image065.gif" v:shapes="Picture_x0020_37"><![endif]></span><span
     4424src="RMCProfile-I_files/image099.gif" v:shapes="_x0000_i1035"><![endif]></span><span
    44194425style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
    44204426
     
    44244430
    44254431<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
    4426 mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_38" o:spid="_x0000_i1025"
    4427  type="#_x0000_t75" style='width:4in;height:305.25pt;visibility:visible;
    4428  mso-wrap-style:square'>
     4432mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1034" type="#_x0000_t75"
     4433 style='width:4in;height:305.25pt;visibility:visible;mso-wrap-style:square'>
    44294434 <v:imagedata src="RMCProfile-I_files/image066.png" o:title=""/>
    44304435</v:shape><![endif]--><![if !vml]><img border=0 width=384 height=407
    4431 src="RMCProfile-I_files/image067.gif" v:shapes="Picture_x0020_38"><![endif]></span><span
     4436src="RMCProfile-I_files/image100.gif" v:shapes="_x0000_i1034"><![endif]></span><span
    44324437style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4438
     4439<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
     4440
     4441<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 10. Polyhedral
     4442comparison for the big box model<o:p></o:p></span></h3>
     4443
     4444<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
     4445this step we will examine how the suite of SF<sub>6</sub> molecules deviate
     4446from an ideal octahedron. This analysis is currently restricted to structures
     4447with P1 space group symmetry; this is what we have from Step 8 above. Select </span><b
     4448style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     4449mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
     4450mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases/SF6_1</span></b><span
     4451style='mso-fareast-font-family:"Times New Roman"'> from the data tree; the
     4452General tab will appear.<o:p></o:p></span></p>
     4453
     4454<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4455mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_36" o:spid="_x0000_i1033"
     4456 type="#_x0000_t75" style='width:359.25pt;height:183pt;visibility:visible;
     4457 mso-wrap-style:square'>
     4458 <v:imagedata src="RMCProfile-I_files/image101.png" o:title=""/>
     4459</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=244
     4460src="RMCProfile-I_files/image102.gif" v:shapes="Picture_x0020_36"><![endif]></span><span
     4461style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4462
     4463<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>What
     4464we want is at the bottom of this panel; scroll down to the bottom<o:p></o:p></span></p>
     4465
     4466<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4467mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_37" o:spid="_x0000_i1032"
     4468 type="#_x0000_t75" style='width:357.75pt;height:183pt;visibility:visible;
     4469 mso-wrap-style:square'>
     4470 <v:imagedata src="RMCProfile-I_files/image103.png" o:title=""/>
     4471</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=244
     4472src="RMCProfile-I_files/image104.gif" v:shapes="Picture_x0020_37"><![endif]></span><span
     4473style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4474
     4475<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>At
     4476the very bottom is the control for polyhedral comparison. All that is needed is
     4477to select the central atom (“</span><b style='mso-bidi-font-weight:normal'><span
     4478style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     4479mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
     4480mso-bidi-theme-font:minor-latin'>origin atom type</span></b><span
     4481style='mso-fareast-font-family:"Times New Roman"'>”) and the polyhedral
     4482vertices (“</span><b style='mso-bidi-font-weight:normal'><span
     4483style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     4484mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
     4485mso-bidi-theme-font:minor-latin'>target atom type</span></b><span
     4486style='mso-fareast-font-family:"Times New Roman"'>”). Select </span><b
     4487style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     4488mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
     4489mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>S</span></b><span
     4490style='mso-fareast-font-family:"Times New Roman"'> for the former and </span><b
     4491style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     4492mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
     4493mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>F</span></b><span
     4494style='mso-fareast-font-family:"Times New Roman"'> for the latter. Then do </span><b
     4495style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     4496mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
     4497mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Compute/Compare</span></b><span
     4498style='mso-fareast-font-family:"Times New Roman"'> from the menu; a popup for setting
     4499Distance Angle Controls will appear<o:p></o:p></span></p>
     4500
     4501<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4502mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_38" o:spid="_x0000_i1031"
     4503 type="#_x0000_t75" style='width:206.25pt;height:175.5pt;visibility:visible;
     4504 mso-wrap-style:square'>
     4505 <v:imagedata src="RMCProfile-I_files/image105.png" o:title=""/>
     4506</v:shape><![endif]--><![if !vml]><img border=0 width=275 height=234
     4507src="RMCProfile-I_files/image106.gif" v:shapes="Picture_x0020_38"><![endif]></span><span
     4508style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4509
     4510<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
     4511some cases the bond search factor may need to be adjusted to get the right
     4512number of vertices for the polyhedral; in this case </span><b style='mso-bidi-font-weight:
     4513normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     4514minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
     4515minor-latin;mso-bidi-theme-font:minor-latin'>0.85</span></b><span
     4516style='mso-fareast-font-family:"Times New Roman"'> is fine (NB: in this use the
     4517angle ranges are ignored). Press </span><b style='mso-bidi-font-weight:normal'><span
     4518style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     4519mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
     4520mso-bidi-theme-font:minor-latin'>OK</span></b><span style='mso-fareast-font-family:
     4521"Times New Roman"'>; a progress bar will show the atoms being processed. The
     4522console may show some atoms being skipped because the number of vertices wasn’t
     4523either 4 (tetrahedron) or 6 (octahedron); all are ok here. In this case it
     4524quickly finishes; for larger big box models this calculation can take a number
     4525of minutes. The General tab reappears already scrolled to the bottom<o:p></o:p></span></p>
     4526
     4527<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4528mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_39" o:spid="_x0000_i1030"
     4529 type="#_x0000_t75" style='width:363pt;height:185.25pt;visibility:visible;
     4530 mso-wrap-style:square'>
     4531 <v:imagedata src="RMCProfile-I_files/image107.png" o:title=""/>
     4532</v:shape><![endif]--><![if !vml]><img border=0 width=484 height=247
     4533src="RMCProfile-I_files/image108.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
     4534style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4535
     4536<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>A
     4537new button (</span><b style='mso-bidi-font-weight:normal'><span
     4538style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     4539mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
     4540mso-bidi-theme-font:minor-latin'>Show Plots?</span></b><span style='mso-fareast-font-family:
     4541"Times New Roman"'>) has appeared after the atom selections; press it. A number
     4542of new entries will appear on the plot window; we will discuss each in turn.
     4543Select the </span><b style='mso-bidi-font-weight:normal'><span
     4544style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     4545mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
     4546mso-bidi-theme-font:minor-latin'>Bond</span></b><span style='mso-fareast-font-family:
     4547"Times New Roman"'> tab<o:p></o:p></span></p>
     4548
     4549<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4550mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_40" o:spid="_x0000_i1029"
     4551 type="#_x0000_t75" style='width:363.75pt;height:303.75pt;visibility:visible;
     4552 mso-wrap-style:square'>
     4553 <v:imagedata src="RMCProfile-I_files/image109.png" o:title=""/>
     4554</v:shape><![endif]--><![if !vml]><img border=0 width=485 height=405
     4555src="RMCProfile-I_files/image110.gif" v:shapes="Picture_x0020_40"><![endif]></span><span
     4556style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4557
     4558<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
     4559gives the distribution of S-F bond lengths for all the polyhedral found across
     4560the big box model. It is rough because of the small size of the model. The
     4561console will have listed the average value with the standard uncertainty in
     4562parentheses. <o:p></o:p></span></p>
     4563
     4564<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4565mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_41" o:spid="_x0000_i1028"
     4566 type="#_x0000_t75" style='width:216.75pt;height:66.75pt;visibility:visible;
     4567 mso-wrap-style:square'>
     4568 <v:imagedata src="RMCProfile-I_files/image111.png" o:title=""/>
     4569</v:shape><![endif]--><![if !vml]><img border=0 width=289 height=89
     4570src="RMCProfile-I_files/image112.gif" v:shapes="Picture_x0020_41"><![endif]></span><span
     4571style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4572
     4573<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
     4574select the </span><b style='mso-bidi-font-weight:normal'><span
     4575style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
     4576mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
     4577mso-bidi-theme-font:minor-latin'>Tilts</span></b><span style='mso-fareast-font-family:
     4578"Times New Roman"'> tab<o:p></o:p></span></p>
     4579
     4580<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4581mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_42" o:spid="_x0000_i1027"
     4582 type="#_x0000_t75" style='width:5in;height:300pt;visibility:visible;
     4583 mso-wrap-style:square'>
     4584 <v:imagedata src="RMCProfile-I_files/image113.png" o:title=""/>
     4585</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=400
     4586src="RMCProfile-I_files/image114.gif" v:shapes="Picture_x0020_42"><![endif]></span><span
     4587style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4588
     4589<p class=MsoNormal style='tab-stops:344.95pt'><span style='mso-fareast-font-family:
     4590"Times New Roman"'>This gives the distribution of axial tilts of the SF<sub>6</sub>
     4591molecules from the reference octahedron (aligned along the Cartesian axes).
     4592There is a wide distribution with a roughly average tilt of ~30 <span
     4593class=SpellE>deg</span> (the average tilt is also shown on the console). Next
     4594select </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
     4595"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
     4596"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X-Delta</span></b><span
     4597style='mso-fareast-font-family:"Times New Roman"'>, </span><b style='mso-bidi-font-weight:
     4598normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
     4599minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
     4600minor-latin;mso-bidi-theme-font:minor-latin'>Y-Delta</span></b><span
     4601style='mso-fareast-font-family:"Times New Roman"'> and </span><b
     4602style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     4603mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
     4604mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Z-Delta</span></b><span
     4605style='mso-fareast-font-family:"Times New Roman"'> tabs in turn.<o:p></o:p></span></p>
     4606
     4607<p class=MsoNormal style='tab-stops:344.95pt'><span style='mso-fareast-font-family:
     4608"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_43"
     4609 o:spid="_x0000_i1026" type="#_x0000_t75" style='width:5in;height:300pt;
     4610 visibility:visible;mso-wrap-style:square'>
     4611 <v:imagedata src="RMCProfile-I_files/image115.png" o:title=""/>
     4612</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=400
     4613src="RMCProfile-I_files/image116.gif" v:shapes="Picture_x0020_43"><![endif]></span><span
     4614style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4615
     4616<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I
     4617have made this plot by dragging the respective plot tabs to one of the right
     4618(or left) edges to create a 3 pane plot. These show the displacement of the F
     4619atoms from the ideal octahedral vertices along each Cartesian axis. Here they
     4620are arranged about the zeros fairly tightly. If there were structural
     4621distortions to the octahedra (e.g. <span class=SpellE>Jahn</span>-Teller
     4622distortions) these could show in these plots. Finally select the </span><b
     4623style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
     4624mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
     4625mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Oct tilts</span></b><span
     4626style='mso-fareast-font-family:"Times New Roman"'> tab; a 3D plot will be shown<o:p></o:p></span></p>
     4627
     4628<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
     4629mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_44" o:spid="_x0000_i1025"
     4630 type="#_x0000_t75" style='width:357.75pt;height:298.5pt;visibility:visible;
     4631 mso-wrap-style:square'>
     4632 <v:imagedata src="RMCProfile-I_files/image117.png" o:title=""/>
     4633</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=398
     4634src="RMCProfile-I_files/image118.gif" v:shapes="Picture_x0020_44"><![endif]></span><span
     4635style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
     4636
     4637<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The ‘x’
     4638marks show the directions of the unit vectors about which the SF<sub>6</sub>
     4639molecules are tilted with respect to the reference octahedron. In this case
     4640they are quite random; they cover all directions because the algorithm selects
     4641the shortest F atom to octahedral vertex for the tilt calculation. That could
     4642be any one of the six possible along +/- xyz axes. <o:p></o:p></span></p>
     4643
     4644<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
    44334645
    44344646<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
  • Tutorials/RMCProfile-I/RMCProfile-I_files/filelist.xml

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