source: Tutorials/RMCProfile-IV/RMCProfile-IV.htm @ 4633

Last change on this file since 4633 was 4457, checked in by toby, 3 years ago

add data link to tutorials
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407  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
408  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
409  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
410  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
411  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
412  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
413  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
414  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
415  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
416  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
417  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
418  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
419  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
420  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
421  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
422  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
423  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
424  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
425  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
426  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
427  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
428  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
429  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
430  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
431  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
432  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
433  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
434  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
435  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
436  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
437  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
438  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
439  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
440  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
441  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
442  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
443  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
444  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
445  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
446  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
447  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
448  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
449  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
450  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
451  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
452  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
453  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
454  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
455  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
456  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
457  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
458  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
459  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
460  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
461  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
462  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
463  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
464  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
465  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
466  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
467  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
468  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
469  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
470  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
471  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
472  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
473  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
474  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
475  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
476  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
477  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
478  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
479  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
480  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
481  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
482  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
483  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
484  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
485  <w:LsdException Locked="false" Priority="19" QFormat="true"
486   Name="Subtle Emphasis"/>
487  <w:LsdException Locked="false" Priority="21" QFormat="true"
488   Name="Intense Emphasis"/>
489  <w:LsdException Locked="false" Priority="31" QFormat="true"
490   Name="Subtle Reference"/>
491  <w:LsdException Locked="false" Priority="32" QFormat="true"
492   Name="Intense Reference"/>
493  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
494  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
495   UnhideWhenUsed="true" Name="Bibliography"/>
496  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
497   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
498  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
499  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
500  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
501  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
502  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
503  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
504  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
505  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
506  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
507  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
508  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
509  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
510  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
511  <w:LsdException Locked="false" Priority="46"
512   Name="Grid Table 1 Light Accent 1"/>
513  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
514  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
515  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
516  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
517  <w:LsdException Locked="false" Priority="51"
518   Name="Grid Table 6 Colorful Accent 1"/>
519  <w:LsdException Locked="false" Priority="52"
520   Name="Grid Table 7 Colorful Accent 1"/>
521  <w:LsdException Locked="false" Priority="46"
522   Name="Grid Table 1 Light Accent 2"/>
523  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
524  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
525  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
526  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
527  <w:LsdException Locked="false" Priority="51"
528   Name="Grid Table 6 Colorful Accent 2"/>
529  <w:LsdException Locked="false" Priority="52"
530   Name="Grid Table 7 Colorful Accent 2"/>
531  <w:LsdException Locked="false" Priority="46"
532   Name="Grid Table 1 Light Accent 3"/>
533  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
534  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
535  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
536  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
537  <w:LsdException Locked="false" Priority="51"
538   Name="Grid Table 6 Colorful Accent 3"/>
539  <w:LsdException Locked="false" Priority="52"
540   Name="Grid Table 7 Colorful Accent 3"/>
541  <w:LsdException Locked="false" Priority="46"
542   Name="Grid Table 1 Light Accent 4"/>
543  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
544  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
545  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
546  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
547  <w:LsdException Locked="false" Priority="51"
548   Name="Grid Table 6 Colorful Accent 4"/>
549  <w:LsdException Locked="false" Priority="52"
550   Name="Grid Table 7 Colorful Accent 4"/>
551  <w:LsdException Locked="false" Priority="46"
552   Name="Grid Table 1 Light Accent 5"/>
553  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
554  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
555  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
556  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
557  <w:LsdException Locked="false" Priority="51"
558   Name="Grid Table 6 Colorful Accent 5"/>
559  <w:LsdException Locked="false" Priority="52"
560   Name="Grid Table 7 Colorful Accent 5"/>
561  <w:LsdException Locked="false" Priority="46"
562   Name="Grid Table 1 Light Accent 6"/>
563  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
564  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
565  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
566  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
567  <w:LsdException Locked="false" Priority="51"
568   Name="Grid Table 6 Colorful Accent 6"/>
569  <w:LsdException Locked="false" Priority="52"
570   Name="Grid Table 7 Colorful Accent 6"/>
571  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
572  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
573  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
574  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
575  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
576  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
577  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
578  <w:LsdException Locked="false" Priority="46"
579   Name="List Table 1 Light Accent 1"/>
580  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
581  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
582  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
583  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
584  <w:LsdException Locked="false" Priority="51"
585   Name="List Table 6 Colorful Accent 1"/>
586  <w:LsdException Locked="false" Priority="52"
587   Name="List Table 7 Colorful Accent 1"/>
588  <w:LsdException Locked="false" Priority="46"
589   Name="List Table 1 Light Accent 2"/>
590  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
591  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
592  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
593  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
594  <w:LsdException Locked="false" Priority="51"
595   Name="List Table 6 Colorful Accent 2"/>
596  <w:LsdException Locked="false" Priority="52"
597   Name="List Table 7 Colorful Accent 2"/>
598  <w:LsdException Locked="false" Priority="46"
599   Name="List Table 1 Light Accent 3"/>
600  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
601  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
602  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
603  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
604  <w:LsdException Locked="false" Priority="51"
605   Name="List Table 6 Colorful Accent 3"/>
606  <w:LsdException Locked="false" Priority="52"
607   Name="List Table 7 Colorful Accent 3"/>
608  <w:LsdException Locked="false" Priority="46"
609   Name="List Table 1 Light Accent 4"/>
610  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
611  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
612  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
613  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
614  <w:LsdException Locked="false" Priority="51"
615   Name="List Table 6 Colorful Accent 4"/>
616  <w:LsdException Locked="false" Priority="52"
617   Name="List Table 7 Colorful Accent 4"/>
618  <w:LsdException Locked="false" Priority="46"
619   Name="List Table 1 Light Accent 5"/>
620  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
621  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
622  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
623  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
624  <w:LsdException Locked="false" Priority="51"
625   Name="List Table 6 Colorful Accent 5"/>
626  <w:LsdException Locked="false" Priority="52"
627   Name="List Table 7 Colorful Accent 5"/>
628  <w:LsdException Locked="false" Priority="46"
629   Name="List Table 1 Light Accent 6"/>
630  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
631  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
632  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
633  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
634  <w:LsdException Locked="false" Priority="51"
635   Name="List Table 6 Colorful Accent 6"/>
636  <w:LsdException Locked="false" Priority="52"
637   Name="List Table 7 Colorful Accent 6"/>
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1211<div class=WordSection1>
1212
1213<h1><span style='mso-fareast-font-family:"Times New Roman"'>RMCProfile – IV<o:p></o:p></span></h1>
1214
1215<P><BL>
1216  <LI>Exercise files are found <A href="./data/" target="_blank">here</a>
1217</BL></P><P></P>
1218
1219  <h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction<o:p></o:p></span></h2>
1220
1221<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
1222this tutorial, we will show how to use GSAS-II in conjunction with RMCProfile
1223(“RMCProfile: Reverse Monte Carlo for polycrystalline materials”, M.G. Tucker,
1224D.A. Keen, M.T. Dove, A.L. Goodwin and Q. Hui, (2007) Jour. Phys.: Cond.
1225Matter, <b style='mso-bidi-font-weight:normal'>19</b>, 335218. <span
1226class=SpellE>doi</span>: <a
1227href="https://doi.org/10.1088/0953-8984/19/33/335218">https://doi.org/10.1088/0953-8984/19/33/335218</a>)
1228to do a fit with x-ray powder diffraction data and pair distribution functions
1229(PDF) created from it with a “big box” disordered model. This exercise is very
1230similar to RMCProfile-III except that no neutron data is used and instead a set
1231of bond and angle potentials are used to augment the fitting.<o:p></o:p></span></p>
1232
1233<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1234
1235<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Before
1236getting started you must obtain the most recent Version 6 of the RMCProfile
1237executable (at this writing this is RMCProfile V6.7.6 Beta Serial). Obtain this
1238from <a href="http://www.rmcprofile.org">www.rmcprofile.org</a> by following
1239the prompts from Downloads. This version is available for Windows, Mac OSX and
1240Linux. The download will be a zip file; save it somewhere convenient. Pull from
1241it only the </span><span class=SpellE><span class=SubtitleChar><span
1242style='font-size:11.0pt'>RMCProfile_package</span></span></span><span
1243class=SubtitleChar><span style='font-size:11.0pt'>/exe/rmcprofile.exe</span></span><span
1244style='mso-fareast-font-family:"Times New Roman"'> and place it in the GSASII
1245main directory or in a new subdirectory (e.g. </span><span class=SubtitleChar><span
1246style='font-size:11.0pt'>GSASII/RMCProfile</span></span><span style='mso-fareast-font-family:
1247"Times New Roman"'>); no other files are needed although you may wish to also
1248retrieve the contents of the tutorial subdirectory. It contains </span><span
1249class=SubtitleChar><span style='font-size:11.0pt'>rmcprofilemanual.pdf</span></span><span
1250style='mso-fareast-font-family:"Times New Roman"'> and </span><span
1251class=SubtitleChar><span style='font-size:11.0pt'>rmcprofile_tutorial.pdf</span></span><span
1252style='mso-fareast-font-family:"Times New Roman"'> which may be of interest
1253since the GSAS-II/RMCProfile tutorials are based on the latter.<o:p></o:p></span></p>
1254
1255<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1256
1257<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1258process for using RMCProfile begins with a normal Rietveld refinement of the
1259average structure. For the kind of disordered materials of interest here, this
1260may give bond lengths that are frequently too short for the atoms involved and
1261sometimes extreme apparent thermal motion for some of the atoms. These effects
1262arise because the average structure places these atoms too close to one
1263another; a more localized view would show coordinated atom displacements or
1264reorientation of groups of atoms to avoid the close contacts. RMCProfile is
1265then used to characterize these local displacements by fitting to the
1266diffraction data and its Fourier transform as a PDF.<o:p></o:p></span></p>
1267
1268<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1269
1270<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1271material used in this tutorial is the same as described in the RMCProfile-III
1272tutorial, gallium phosphate (GaPO<sub>4</sub>). GaPO<sub>4</sub> is a
1273piezoelectric crystal of corner sharing GaO<sub>4</sub> and PO<sub>4</sub>
1274tetrahedra arranged as in a doubled c-axis &#945;-quartz structure.<span
1275style='mso-spacerun:yes'>  </span>The average structure determined by Rietveld
1276refinement results in Ga-O and P-O bond lengths that are shorter than implied
1277by the corresponding peak positions in either an x-ray or neutron PDF. The
1278X-ray data used here was obtained at room temperature on beam line I15 at the
1279Diamond light source. The objective here is to use RMCProfile to model the
1280structural distortions that yield the X-ray PDF derived bond lengths and is
1281augmented by potential energy restraints on Ga-O and P-O bond lengths and
1282O-Ga-O and O-P-O bond angles. The result obtained here can be compared to that
1283from the combined x-ray/neutron fitting described in the RMCProfile-III
1284tutorial.<o:p></o:p></span></p>
1285
1286<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1287
1288<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1289
1290<h2>Rietveld Refinement of Gallium phosphate (<span style='mso-fareast-font-family:
1291"Times New Roman"'>GaPO<sub>4</sub></span>):</h2>
1292
1293<h3>Step 1: Read in the data file</h3>
1294
1295<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1. </span>Use
1296the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1297mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1298minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1299to read the data file into the current GSAS-II project. This read option is set
1300to read any of the powder data formats defined for GSAS (angles in <span
1301class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
1302the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1303style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1304mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1305format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1306style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1307mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1308format (angles in degrees) used by <span class=SpellE>topas</span>, etc.<span
1309style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1310type to <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1311style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1312mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1313format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1314style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1315mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1316format (angles in degrees) to see them. Because you used <span
1317style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>the </span><b
1318style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1319mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1320minor-latin;mso-hansi-theme-font:minor-latin'>Help/Download tutorial</span></b><span
1321style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1322menu entry to open this page and downloaded the exercise files (recommended),
1323then the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1324"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1325Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RMCProfile-IV/data/...</span></b><span
1326style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1327entry will bring you to the location where the files have been downloaded. (It
1328is also possible to download them manually from <a
1329href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/</a>.
1330In this case you will need to navigate to the download location manually.)<o:p></o:p></span></p>
1331
1332<p class=MsoNormal><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1333minor-latin'>For this tutorial you should see the data file in the file
1334browser, but if extensions on data files are not the expected ones, you may
1335need to change the file type to </span><b style='mso-bidi-font-weight:normal'><span
1336style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1337mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1338minor-latin;mso-bidi-theme-font:minor-latin'>All files (*.*)</span></b><span
1339style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> to
1340find the desired file.<o:p></o:p></span></p>
1341
1342<p class=MsoNormal><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1343minor-latin'>2. Select the </span><b style='mso-bidi-font-weight:normal'><span
1344style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1345mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1346minor-latin;mso-bidi-theme-font:minor-latin'>105870-pe-GaPO4_ed.gsas</span></b><span
1347style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> </span><span
1348style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1349mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>data</span>
1350file in the first dialog and press <b style='mso-bidi-font-weight:normal'><span
1351style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1352mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
1353There will be a dialog box asking <span class=GramE><b style='mso-bidi-font-weight:
1354normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1355minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
1356style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1357mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1358minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1359style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1360mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1361minor-latin'>Yes</span></b></span> button to proceed. <span style='mso-fareast-font-family:
1362"Times New Roman"'><o:p></o:p></span></p>
1363
1364<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1365will be a apparently empty file selection dialog for the instrument parameter
1366file; switch the file type to </span><b style='mso-bidi-font-weight:normal'><span
1367style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1368mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1369mso-bidi-theme-font:minor-latin'>GSAS <span class=SpellE>iparm</span> file (*.<span
1370class=SpellE>prm</span><span class=GramE>,…</span>)</span></b><span
1371style='mso-fareast-font-family:"Times New Roman"'>. Then one file (</span><b
1372style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1373mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1374mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>inst_i15_pdf_april14.prm</span></b><span
1375style='mso-fareast-font-family:"Times New Roman"'>) is shown. Select it; the pattern
1376will be read in and displayed <o:p></o:p></span></p>
1377
1378<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1379mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600"
1380 o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f"
1381 stroked="f">
1382 <v:stroke joinstyle="miter"/>
1383 <v:formulas>
1384  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1385  <v:f eqn="sum @0 1 0"/>
1386  <v:f eqn="sum 0 0 @1"/>
1387  <v:f eqn="prod @2 1 2"/>
1388  <v:f eqn="prod @3 21600 pixelWidth"/>
1389  <v:f eqn="prod @3 21600 pixelHeight"/>
1390  <v:f eqn="sum @0 0 1"/>
1391  <v:f eqn="prod @6 1 2"/>
1392  <v:f eqn="prod @7 21600 pixelWidth"/>
1393  <v:f eqn="sum @8 21600 0"/>
1394  <v:f eqn="prod @7 21600 pixelHeight"/>
1395  <v:f eqn="sum @10 21600 0"/>
1396 </v:formulas>
1397 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1398 <o:lock v:ext="edit" aspectratio="t"/>
1399</v:shapetype><v:shape id="Picture_x0020_45" o:spid="_x0000_i1073" type="#_x0000_t75"
1400 style='width:356.25pt;height:242.25pt;visibility:visible;mso-wrap-style:square'>
1401 <v:imagedata src="RMCProfile-IV_files/image001.png" o:title=""/>
1402</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=323
1403src="RMCProfile-IV_files/image002.gif" v:shapes="Picture_x0020_45"><![endif]></span><span
1404style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1405
1406<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Set limits<o:p></o:p></span></h3>
1407
1408<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Since
1409we want to avoid the abrupt jump and (as it turns out) low angle contaminating
1410peaks, we want to set the lower limit to just below the first large visible
1411Bragg peak and the upper limit needs to be set to include just the range with
1412Bragg intensities (&gt;0.4Å); go the </span><b style='mso-bidi-font-weight:
1413normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1414minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1415minor-latin;mso-bidi-theme-font:minor-latin'>Limits</span></b><span
1416style='mso-fareast-font-family:"Times New Roman"'> entry in the GSAS-II data
1417tree.<o:p></o:p></span></p>
1418
1419<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1420mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_46" o:spid="_x0000_i1072"
1421 type="#_x0000_t75" style='width:289.5pt;height:116.25pt;visibility:visible;
1422 mso-wrap-style:square'>
1423 <v:imagedata src="RMCProfile-IV_files/image003.png" o:title=""/>
1424</v:shape><![endif]--><![if !vml]><img border=0 width=386 height=155
1425src="RMCProfile-IV_files/image004.gif" v:shapes="Picture_x0020_46"><![endif]></span><span
1426style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1427
1428<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Change
1429the 1<sup>st</sup> entry to </span><b style='mso-bidi-font-weight:normal'><span
1430style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1431mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1432mso-bidi-theme-font:minor-latin'>2 </span></b><span style='mso-fareast-font-family:
1433"Times New Roman"'>and the second to</span><b style='mso-bidi-font-weight:normal'><span
1434style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1435mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1436mso-bidi-theme-font:minor-latin'> 25</span></b><span style='mso-fareast-font-family:
1437"Times New Roman"'>; the plot will change by moving the green and red dashed
1438lines.<o:p></o:p></span></p>
1439
1440<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1441mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_47" o:spid="_x0000_i1071"
1442 type="#_x0000_t75" style='width:5in;height:243.75pt;visibility:visible;
1443 mso-wrap-style:square'>
1444 <v:imagedata src="RMCProfile-IV_files/image005.png" o:title=""/>
1445</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=325
1446src="RMCProfile-IV_files/image006.gif" v:shapes="Picture_x0020_47"><![endif]></span><span
1447style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1448
1449<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Import GaPO<sub>4
1450</sub>phase<o:p></o:p></span></h3>
1451
1452<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1453average structure of GaPO<sub>4</sub> is that of a doubled c-axis
1454&#945;-quartz. Space group P3<sub>1</sub>21, a=4.90063 c=11.04809 with 4 atom
1455positions. We can import it from an old <span class=SpellE>gsas</span>
1456experiment file. </span>Use the <b style='mso-bidi-font-weight:normal'><span
1457style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1458mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Import/Phase/from
1459GSAS .EXP file</span></b> menu item to read the phase information for <span
1460style='mso-fareast-font-family:"Times New Roman"'>GaPO<sub>4 </sub></span>into
1461the current GSAS-II project. Other submenu items will read phase information in
1462other formats.<span style='mso-spacerun:yes'>  </span>Because you used <span
1463style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>the </span><b
1464style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1465mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1466minor-latin;mso-hansi-theme-font:minor-latin'>Help/Download tutorial</span></b><span
1467style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1468menu entry to open this page and downloaded the exercise files (recommended),
1469then the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1470"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1471Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RMCProfile-IV/data/...</span></b><span
1472style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1473entry will bring you to the location where the files have been downloaded. (It
1474is also possible to download them manually from <a
1475href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/</a>.
1476In this case you will need to navigate to the download location manually.)
1477Select the </span><b style='mso-bidi-font-weight:normal'><span
1478style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1479mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1480minor-latin;mso-bidi-theme-font:minor-latin'>GAPO4_XRAY_BAK.EXP</span></b><span
1481style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1482file (only one there) </span>There will be a dialog box asking <span
1483class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1484"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1485minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
1486style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1487mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1488minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1489style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1490mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1491minor-latin'>Yes</span></b></span> button to proceed. You will get the opportunity
1492to change the phase name next (it is very long, I changed it to GaPO4-X; this
1493will be used as the file root for many of the files produced by RMCProfile. NB:
1494because of restrictions in RMCProfile it is important that the phase name not
1495have any spaces); press <b style='mso-bidi-font-weight:normal'><span
1496style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1497mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
1498to continue. Next is the histogram selection window; this connects the phase to
1499the data so it can be used in subsequent calculations.</p>
1500
1501<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1502mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_48" o:spid="_x0000_i1070"
1503 type="#_x0000_t75" style='width:3in;height:173.25pt;visibility:visible;
1504 mso-wrap-style:square'>
1505 <v:imagedata src="RMCProfile-IV_files/image007.png" o:title=""/>
1506</v:shape><![endif]--><![if !vml]><img border=0 width=288 height=231
1507src="RMCProfile-IV_files/image008.gif" v:shapes="Picture_x0020_48"><![endif]></span><span
1508style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1509
1510<p class=MsoNormal>Select the histogram (or press <b style='mso-bidi-font-weight:
1511normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1512minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Set
1513All</span></b>) and press <b style='mso-bidi-font-weight:normal'><span
1514style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1515mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
1516The General tab for the phase is shown next</p>
1517
1518<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1519mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5" o:spid="_x0000_i1069"
1520 type="#_x0000_t75" style='width:359.25pt;height:192pt;visibility:visible;
1521 mso-wrap-style:square'>
1522 <v:imagedata src="RMCProfile-IV_files/image009.png" o:title=""/>
1523</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=256
1524src="RMCProfile-IV_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span><span
1525style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1526
1527<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 4. Check atom
1528positions<o:p></o:p></span></h3>
1529
1530<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>It is
1531usually wise particularly for trigonal/hexagonal structures, to check the atom
1532positions to be sure atoms are properly placed on special positions. Select the
1533</span><b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1534mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1535mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b><span
1536style='mso-fareast-font-family:"Times New Roman"'> tab<o:p></o:p></span></p>
1537
1538<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1539mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1068" type="#_x0000_t75"
1540 style='width:359.25pt;height:103.5pt;visibility:visible;mso-wrap-style:square'>
1541 <v:imagedata src="RMCProfile-IV_files/image011.png" o:title=""/>
1542</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=138
1543src="RMCProfile-IV_files/image012.gif" v:shapes="_x0000_i1068"><![endif]></span><span
1544style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1545
1546<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
1547this case the z-position for both Ga and P are not sufficiently precise for use
1548in <span class=SpellE>RMCProfie</span>. The Ga atom is at z=</span><b
1549style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1550mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1551mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1/3</span></b><span
1552style='mso-fareast-font-family:"Times New Roman"'> and the P atom is at z=</span><b
1553style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1554mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1555mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>5/6</span></b><span
1556style='mso-fareast-font-family:"Times New Roman"'>. Enter the fractions into
1557the respective positions in the table; GSAS-II will do the math to the full
1558double precision available in python. You should get<o:p></o:p></span></p>
1559
1560<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1561mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_50" o:spid="_x0000_i1067"
1562 type="#_x0000_t75" style='width:5in;height:104.25pt;visibility:visible;
1563 mso-wrap-style:square'>
1564 <v:imagedata src="RMCProfile-IV_files/image013.png" o:title=""/>
1565</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=139
1566src="RMCProfile-IV_files/image014.gif" v:shapes="Picture_x0020_50"><![endif]></span><span
1567style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1568
1569<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>If
1570this isn’t done then some of the input to RMCProfile will not be correctly
1571prepared.<o:p></o:p></span></p>
1572
1573<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Set the
1574background<o:p></o:p></span></h3>
1575
1576<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Although
1577there is not much diffuse scattering, the default background will be
1578insufficient for reasonable fitting. Select the </span><b style='mso-bidi-font-weight:
1579normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1580minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1581minor-latin;mso-bidi-theme-font:minor-latin'>Background</span></b><span
1582style='mso-fareast-font-family:"Times New Roman"'> item from the GSAS-II data
1583tree<o:p></o:p></span></p>
1584
1585<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1586mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6" o:spid="_x0000_i1066"
1587 type="#_x0000_t75" style='width:361.5pt;height:189pt;visibility:visible;
1588 mso-wrap-style:square'>
1589 <v:imagedata src="RMCProfile-IV_files/image015.png" o:title=""/>
1590</v:shape><![endif]--><![if !vml]><img border=0 width=482 height=252
1591src="RMCProfile-IV_files/image016.gif" v:shapes="Picture_x0020_6"><![endif]></span><span
1592style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1593
1594<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Be
1595sure that “</span><b style='mso-bidi-font-weight:normal'><span
1596style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1597mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1598mso-bidi-theme-font:minor-latin'>chebyschev-1</span></b><span style='mso-fareast-font-family:
1599"Times New Roman"'>” is used for the background function; RMCProfile only
1600recognizes that form to compute the background for the diffraction pattern.
1601Select </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1602"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1603"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>6</span></b><span
1604style='mso-fareast-font-family:"Times New Roman"'> for the number of terms.<o:p></o:p></span></p>
1605
1606<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Rietveld
1607refinement<o:p></o:p></span></h3>
1608
1609<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We
1610are now ready for the first Rietveld refinement; select </span><b
1611style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1612mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1613mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1614style='mso-fareast-font-family:"Times New Roman"'> from the main GSAS-II menu.
1615Before it starts a file selection dialog will appear; select a file name (no
1616extension). I chose “</span><b style='mso-bidi-font-weight:normal'><span
1617style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1618mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1619mso-bidi-theme-font:minor-latin'>GaPO4</span></b><span style='mso-fareast-font-family:
1620"Times New Roman"'>”; do not use the phase name for this purpose because
1621RMCProfile will use that as the root for the many files it creates. Also, you
1622should create a new directory for this exercise while in this dialog box; it
1623will be rapidly filled up with RMCProfile files which can lead to considerable
1624confusion if mixed in with other files. For Windows, after navigating to a suitable
1625location, a new directory can be made by a right mouse click and selecting “</span><b
1626style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1627mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1628mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>New/Folder</span></b><span
1629style='mso-fareast-font-family:"Times New Roman"'>” from the popup menu. It
1630will appear with the name “New Folder”; change the name and select it (it will
1631be empty). Other operating systems will have similar methods. Finally press </span><b
1632style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1633mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1634mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b><span
1635style='mso-fareast-font-family:"Times New Roman"'> to save the GSAS-II project
1636(GaPO4.gpx) and start the refinement. It will quickly converge to give a
1637reasonable <span class=SpellE>Rwp</span> (~9.8%) <o:p></o:p></span></p>
1638
1639<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1640mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9" o:spid="_x0000_i1065"
1641 type="#_x0000_t75" style='width:5in;height:244.5pt;visibility:visible;
1642 mso-wrap-style:square'>
1643 <v:imagedata src="RMCProfile-IV_files/image017.png" o:title=""/>
1644</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=326
1645src="RMCProfile-IV_files/image018.gif" v:shapes="Picture_x0020_9"><![endif]></span><span
1646style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1647
1648<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I
1649pressed <span class=GramE>the ‘s’</span> key so that <span class=SpellE>sqrt</span>(intensity)
1650shows on the y-axis; makes things a bit easier to see. It is evident that the
1651lattice parameter as well as the sample broadening terms needs adjusting. Go to
1652the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1653"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1654"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b><span
1655style='mso-fareast-font-family:"Times New Roman"'> tab for the GaPO4-X phase
1656and select </span><span class=GramE><b style='mso-bidi-font-weight:normal'><span
1657style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1658mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1659mso-bidi-theme-font:minor-latin'>Refine</span></b></span><b style='mso-bidi-font-weight:
1660normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1661minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1662minor-latin;mso-bidi-theme-font:minor-latin'> unit cell</span></b><span
1663style='mso-fareast-font-family:"Times New Roman"'>. Then select the </span><b
1664style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1665mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1666mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Data</span></b><span
1667style='mso-fareast-font-family:"Times New Roman"'> tab and select </span><b
1668style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1669mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1670mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>size</span></b><span
1671style='mso-fareast-font-family:"Times New Roman"'> and </span><span
1672class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1673"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1674"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>microstrain</span></b></span><span
1675style='mso-fareast-font-family:"Times New Roman"'> for refinement. (A word to
1676the wise; set the starting value for size to </span><b style='mso-bidi-font-weight:
1677normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1678minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1679minor-latin;mso-bidi-theme-font:minor-latin'>0.1</span></b><span
1680style='mso-fareast-font-family:"Times New Roman"'> </span><span class=SpellE><span
1681style='font-family:"Arial",sans-serif;mso-fareast-font-family:"Times New Roman"'>&#956;</span><span
1682style='mso-fareast-font-family:"Times New Roman"'>m</span></span><span
1683style='mso-fareast-font-family:"Times New Roman"'>). Then do </span><b
1684style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1685mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1686mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine
1687</span></b><span style='mso-fareast-font-family:"Times New Roman"'>from the
1688main menu. The fit will greatly improve (<span class=SpellE>Rwp</span> ~5.25%)<o:p></o:p></span></p>
1689
1690<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1691mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_10" o:spid="_x0000_i1064"
1692 type="#_x0000_t75" style='width:357.75pt;height:243.75pt;visibility:visible;
1693 mso-wrap-style:square'>
1694 <v:imagedata src="RMCProfile-IV_files/image019.png" o:title=""/>
1695</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=325
1696src="RMCProfile-IV_files/image020.gif" v:shapes="Picture_x0020_10"><![endif]></span><span
1697style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1698
1699<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1700
1701<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
1702finish up add the following parameters:<o:p></o:p></span></p>
1703
1704<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
1705style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1706mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1707mso-bidi-theme-font:minor-latin'>GaPO4-X/Atoms</span></b><span
1708style='mso-fareast-font-family:"Times New Roman"'>: </span><b style='mso-bidi-font-weight:
1709normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1710minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1711minor-latin;mso-bidi-theme-font:minor-latin'>XU</span></b><span
1712style='mso-fareast-font-family:"Times New Roman"'> for all four atoms (GSAS-II
1713recognizes that the Ga &amp; P atoms are fixed in y &amp; z positions).<o:p></o:p></span></p>
1714
1715<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Do </span><b
1716style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1717mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1718mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1719style='mso-fareast-font-family:"Times New Roman"'> from the main menu; the fit
1720will scarcely change (Rwp~5.25%).<o:p></o:p></span></p>
1721
1722<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Draw
1723structure<o:p></o:p></span></h3>
1724
1725<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
1726the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1727"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1728"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases/GaPO4-X/Draw
1729Atoms</span></b><span style='mso-fareast-font-family:"Times New Roman"'> tab;
1730the list will be shown and the four unique atoms drawn on the plot.<o:p></o:p></span></p>
1731
1732<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1733mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11" o:spid="_x0000_i1063"
1734 type="#_x0000_t75" style='width:5in;height:107.25pt;visibility:visible;
1735 mso-wrap-style:square'>
1736 <v:imagedata src="RMCProfile-IV_files/image021.png" o:title=""/>
1737</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=143
1738src="RMCProfile-IV_files/image022.gif" v:shapes="Picture_x0020_11"><![endif]></span><span
1739style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1740
1741<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1742mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_12" o:spid="_x0000_i1062"
1743 type="#_x0000_t75" style='width:360.75pt;height:245.25pt;visibility:visible;
1744 mso-wrap-style:square'>
1745 <v:imagedata src="RMCProfile-IV_files/image023.png" o:title=""/>
1746</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=327
1747src="RMCProfile-IV_files/image024.gif" v:shapes="Picture_x0020_12"><![endif]></span><span
1748style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1749
1750<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
1751improve this do the following:<o:p></o:p></span></p>
1752
1753<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1)
1754Double click the empty upper left box in the </span><b style='mso-bidi-font-weight:
1755normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1756minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1757minor-latin;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b><span
1758style='mso-fareast-font-family:"Times New Roman"'> table; all atoms will turn
1759green and the four table rows will be grey (or blue).<o:p></o:p></span></p>
1760
1761<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>2)
1762Under the menu </span><b style='mso-bidi-font-weight:normal'><span
1763style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1764mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1765mso-bidi-theme-font:minor-latin'>Edit Figure</span></b><span style='mso-fareast-font-family:
1766"Times New Roman"'> select </span><b style='mso-bidi-font-weight:normal'><span
1767style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1768mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1769mso-bidi-theme-font:minor-latin'>Fill unit cell</span></b><span
1770style='mso-fareast-font-family:"Times New Roman"'>; the figure will be redrawn
1771showing all atoms in the cell.<o:p></o:p></span></p>
1772
1773<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>3)
1774Double click the </span><b style='mso-bidi-font-weight:normal'><span
1775style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1776mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1777mso-bidi-theme-font:minor-latin'>Type</span></b><span style='mso-fareast-font-family:
1778"Times New Roman"'> column heading and select the </span><b style='mso-bidi-font-weight:
1779normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1780minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1781minor-latin;mso-bidi-theme-font:minor-latin'>Ga </span></b><span
1782style='mso-fareast-font-family:"Times New Roman"'>and</span><b
1783style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1784mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1785mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> P</span></b><span
1786style='mso-fareast-font-family:"Times New Roman"'> atom types<o:p></o:p></span></p>
1787
1788<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>4)
1789Under the menu </span><b style='mso-bidi-font-weight:normal'><span
1790style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1791mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1792mso-bidi-theme-font:minor-latin'>Edit Figure</span></b><span style='mso-fareast-font-family:
1793"Times New Roman"'> select </span><b style='mso-bidi-font-weight:normal'><span
1794style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1795mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1796mso-bidi-theme-font:minor-latin'>Fill CN-sphere</span></b><span
1797style='mso-fareast-font-family:"Times New Roman"'>; the figure will be redrawn
1798with four O atoms about all Ga and P atoms.<o:p></o:p></span></p>
1799
1800<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1801mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_13" o:spid="_x0000_i1061"
1802 type="#_x0000_t75" style='width:5in;height:244.5pt;visibility:visible;
1803 mso-wrap-style:square'>
1804 <v:imagedata src="RMCProfile-IV_files/image025.png" o:title=""/>
1805</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=326
1806src="RMCProfile-IV_files/image026.gif" v:shapes="Picture_x0020_13"><![endif]></span><span
1807style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1808
1809<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1810we will explore this with <span class=GramE>a</span> RMCProfile simulation. To
1811keep this drawing, you may want to save the GSAS-II project.<o:p></o:p></span></p>
1812
1813<h2><span style='mso-fareast-font-family:"Times New Roman"'>Reverse Monte Carlo
1814Simulation of GaPO<sub>4<o:p></o:p></sub></span></h2>
1815
1816<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>RMCProfile
1817is most effective if a large box is used for the modelling; this requires very
1818long running times (10-20 <span class=SpellE>hrs</span> for GaPO<sub>4</sub>)
1819before a meaningful result is obtained. However, for the purposes of this
1820tutorial, we will be using a smaller box model that converges in a more
1821reasonable time (~10min). The result will clearly fit the data but the model is
1822too small to give enough atom displacements to be meaningful, however this
1823exercise will show you how to set up RMCProfile from within GSAS-II.<o:p></o:p></span></p>
1824
1825<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
1826start select the </span><b style='mso-bidi-font-weight:normal'><span
1827style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1828mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1829mso-bidi-theme-font:minor-latin'>Phases/GaPO4-X/RMC</span></b><span
1830style='mso-fareast-font-family:"Times New Roman"'> tab; if rmcprofile.exe is
1831within the GSASII directory the data window will show<o:p></o:p></span></p>
1832
1833<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1834mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_14" o:spid="_x0000_i1060"
1835 type="#_x0000_t75" style='width:358.5pt;height:253.5pt;visibility:visible;
1836 mso-wrap-style:square'>
1837 <v:imagedata src="RMCProfile-IV_files/image027.png" o:title=""/>
1838</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=338
1839src="RMCProfile-IV_files/image028.gif" v:shapes="Picture_x0020_14"><![endif]></span><span
1840style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1841
1842<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1843
1844<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>At
1845the top is a radio button selection for </span><b style='mso-bidi-font-weight:
1846normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1847minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1848minor-latin;mso-bidi-theme-font:minor-latin'>RMCProfile</span></b><span
1849style='mso-fareast-font-family:"Times New Roman"'> and </span><span
1850class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1851"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1852"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fullrmc</span></b></span><span
1853style='mso-fareast-font-family:"Times New Roman"'>. The latter is an
1854alternative big box modeling program (not working – under development);
1855RMCProfile is selected by default and all below are its setup controls. There
1856are four major sections (metadata, major controls, restraints &amp; constraints
1857and data controls); we will work through each of these in turn. The information
1858you enter here is retained in the GSAS-II project file so you can easily try
1859alternative setups without having to enter everything over again. <o:p></o:p></span></p>
1860
1861<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 1. Set
1862metadata items<o:p></o:p></span></h3>
1863
1864<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1865entries here are for your convenience; there is no explicit use made of any of
1866them, but they will appear in some of the output files from RMCProfile and of
1867course will show here on subsequent views of this window. Fill out as many of
1868them as you see fit. I entered some things for each as the defaults are
1869somewhat nonsensical.<o:p></o:p></span></p>
1870
1871<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1872mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_15" o:spid="_x0000_i1059"
1873 type="#_x0000_t75" style='width:5in;height:192pt;visibility:visible;
1874 mso-wrap-style:square'>
1875 <v:imagedata src="RMCProfile-IV_files/image115.png" o:title=""/>
1876</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=256
1877src="RMCProfile-IV_files/image029.gif" v:shapes="Picture_x0020_15"><![endif]></span><span
1878style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1879
1880<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Set general
1881controls<o:p></o:p></span></h3>
1882
1883<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The running
1884time is defaulted to </span><b style='mso-bidi-font-weight:normal'><span
1885style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1886mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1887mso-bidi-theme-font:minor-latin'>10</span></b><span style='mso-fareast-font-family:
1888"Times New Roman"'> minutes with a Save interval of </span><b style='mso-bidi-font-weight:
1889normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1890minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1891minor-latin;mso-bidi-theme-font:minor-latin'>1</span></b><span
1892style='mso-fareast-font-family:"Times New Roman"'> minute. At each save time a
1893number of files are written by RMCProfile; these can be viewed by using the
1894Operations/View command (more about this later – don’t bother trying it now,
1895there is nothing to see). For the purposes of this tutorial leave them at their
1896defaults. <o:p></o:p></span></p>
1897
1898<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1899big box model used by RMCProfile is described as multiples of the unit cell
1900axes. In this case we want a 6x6x4 box so enter </span><b style='mso-bidi-font-weight:
1901normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1902minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1903minor-latin;mso-bidi-theme-font:minor-latin'>6</span></b><span
1904style='mso-fareast-font-family:"Times New Roman"'> for each of </span><b
1905style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1906mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1907mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X-axis</span></b><span
1908style='mso-fareast-font-family:"Times New Roman"'>, </span><b style='mso-bidi-font-weight:
1909normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1910minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1911minor-latin;mso-bidi-theme-font:minor-latin'>Y-axis</span></b><span
1912style='mso-fareast-font-family:"Times New Roman"'> and </span><b
1913style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1914mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1915mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>4</span></b><span
1916style='mso-fareast-font-family:"Times New Roman"'> for </span><b
1917style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1918mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1919mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Z-axis</span></b><span
1920style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
1921
1922<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1923is to set the order of the atom types in the structure; this is used to
1924construct atom-atom distance restraints on the modelling. The order here (</span><b
1925style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1926mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1927mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ga, P, O</span></b><span
1928style='mso-fareast-font-family:"Times New Roman"'>) is appropriate; if changed
1929the window will repaint updating various entries possibly resetting some
1930entries to defaults. I suggest you decide the order now and then don’t change
1931it later. Set the maximum shift for Ga &amp; P to be </span><b
1932style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1933mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1934mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.05</span></b><span
1935style='mso-fareast-font-family:"Times New Roman"'> (the value for O is OK).
1936When done the window should look like<o:p></o:p></span></p>
1937
1938<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1939mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_16" o:spid="_x0000_i1058"
1940 type="#_x0000_t75" style='width:5in;height:254.25pt;visibility:visible;
1941 mso-wrap-style:square'>
1942 <v:imagedata src="RMCProfile-IV_files/image031.png" o:title=""/>
1943</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=339
1944src="RMCProfile-IV_files/image030.gif" v:shapes="Picture_x0020_16"><![endif]></span><span
1945style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1946
1947<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Skip
1948the next item (Atom swap probabilities). This is for cases in which atoms can
1949exchange sites.<o:p></o:p></span></p>
1950
1951<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Set
1952constraints/restraints<o:p></o:p></span></h3>
1953
1954<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1955is to set the “Hard” minimum atom-atom separation and the allowed search rage
1956for each of 6 pairs of atom types. Possible values for this table can be
1957obtained in GSAS-II by computing bond lengths although we discovered a good set
1958in the RMCProfile-III tutorial; we will use these here. Suitable values are in
1959sequence for <span class=GramE>Hard</span> min and Search from: </span><b
1960style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1961mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1962mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>4.0, 2.6,
19631.2, 4.0, 1.2, 2.16</span></b><span style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
1964
1965<p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>The
1966<span class=SpellE>to</span></span></span><span style='mso-fareast-font-family:
1967"Times New Roman"'> items are: </span><b style='mso-bidi-font-weight:normal'><span
1968style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1969mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1970mso-bidi-theme-font:minor-latin'>4.8, 3.4, 2. 4.8, 2.0, 0.0</span></b><span
1971style='mso-fareast-font-family:"Times New Roman"'>. When done the window should
1972look like<o:p></o:p></span></p>
1973
1974<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1975mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_17" o:spid="_x0000_i1057"
1976 type="#_x0000_t75" style='width:359.25pt;height:219pt;visibility:visible;
1977 mso-wrap-style:square'>
1978 <v:imagedata src="RMCProfile-IV_files/image118.png" o:title=""/>
1979</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=292
1980src="RMCProfile-IV_files/image032.gif" v:shapes="Picture_x0020_17"><![endif]></span><span
1981style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1982
1983<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1984
1985<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Scroll
1986down to find the section that has “Potential temperature”; these are for bond
1987and angle potentials. We will need 2 of each so press </span><b
1988style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1989mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1990mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Add</span></b><span
1991style='mso-fareast-font-family:"Times New Roman"'> (twice) for A-B stretch and </span><b
1992style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1993mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1994mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Add</span></b><span
1995style='mso-fareast-font-family:"Times New Roman"'> (again twice) for A-B-C
1996angle potentials; the window will refresh for each press so be patient while it
1997does this. Additional entries will be formed for each; when done the window
1998will look like<o:p></o:p></span></p>
1999
2000<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2001mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1056" type="#_x0000_t75"
2002 style='width:358.5pt;height:218.25pt;visibility:visible;mso-wrap-style:square'>
2003 <v:imagedata src="RMCProfile-IV_files/image120.png" o:title=""/>
2004</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=291
2005src="RMCProfile-IV_files/image033.gif" v:shapes="_x0000_i1056"><![endif]></span><span
2006style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2007
2008<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We’re
2009wanting </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2010"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2011"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ga-O</span></b><span
2012style='mso-fareast-font-family:"Times New Roman"'> and </span><b
2013style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2014mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2015mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P-O</span></b><span
2016style='mso-fareast-font-family:"Times New Roman"'> stretch potentials and </span><b
2017style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2018mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2019mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>O-Ga-O</span></b><span
2020style='mso-fareast-font-family:"Times New Roman"'> and </span><b
2021style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2022mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2023mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>O-P-O</span></b><span
2024style='mso-fareast-font-family:"Times New Roman"'> angle potentials. Select the
2025Atom-A, Atom-B and Atom-C appropriately to give<o:p></o:p></span></p>
2026
2027<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2028mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1055" type="#_x0000_t75"
2029 style='width:359.25pt;height:219pt;visibility:visible;mso-wrap-style:square'>
2030 <v:imagedata src="RMCProfile-IV_files/image122.png" o:title=""/>
2031</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=292
2032src="RMCProfile-IV_files/image034.gif" v:shapes="_x0000_i1055"><![endif]></span><span
2033style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2034
2035<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
2036enter appropriate Ga-O and P-O bond distances (</span><b style='mso-bidi-font-weight:
2037normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2038minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2039minor-latin;mso-bidi-theme-font:minor-latin'>1.81</span></b><span
2040style='mso-fareast-font-family:"Times New Roman"'> and </span><b
2041style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2042mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2043mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1.51</span></b><span
2044style='mso-fareast-font-family:"Times New Roman"'>) and O-Ga-O and O-P-O angles
2045(the ideal tetrahedral angle </span><b style='mso-bidi-font-weight:normal'><span
2046style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2047mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2048mso-bidi-theme-font:minor-latin'>109.5</span></b><span style='mso-fareast-font-family:
2049"Times New Roman"'>) and set all potentials to </span><b style='mso-bidi-font-weight:
2050normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2051minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2052minor-latin;mso-bidi-theme-font:minor-latin'>2.0</span></b><span
2053style='mso-fareast-font-family:"Times New Roman"'>. Set both search ranges to </span><b
2054style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2055mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2056mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>20</span></b><span
2057style='mso-fareast-font-family:"Times New Roman"'>%. When done you should see<o:p></o:p></span></p>
2058
2059<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2060mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_20" o:spid="_x0000_i1054"
2061 type="#_x0000_t75" style='width:359.25pt;height:219pt;visibility:visible;
2062 mso-wrap-style:square'>
2063 <v:imagedata src="RMCProfile-IV_files/image035.png" o:title=""/>
2064</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=292
2065src="RMCProfile-IV_files/image036.gif" v:shapes="Picture_x0020_20"><![endif]></span><span
2066style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2067
2068<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2069
2070<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 4. Select data
2071to be fitted<o:p></o:p></span></h3>
2072
2073<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We
2074will be using just x-ray data for GaPO<sub>4</sub> for fitting by RMCProfile. The
2075first step is the selection of the x-ray powder pattern (“Bragg”) for
2076processing. This is taken from the PWDR entry in the GSAS-II project and
2077accessed from the pulldown; there is only one “</span><b style='mso-bidi-font-weight:
2078normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2079minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2080minor-latin;mso-bidi-theme-font:minor-latin'>PWDR 105870-pe-GaPO4_ed.gsas Bank
20811</span></b><span style='mso-fareast-font-family:"Times New Roman"'>” that was
2082used earlier in your Rietveld refinement of GaPO<sub>4</sub>. If you had used
2083multiple banks in the Rietveld refinement, all would be shown in the pulldown,
2084but only one can be selected. Set the weight to </span><b style='mso-bidi-font-weight:
2085normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2086minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2087minor-latin;mso-bidi-theme-font:minor-latin'>100</span></b><span
2088style='mso-fareast-font-family:"Times New Roman"'> (NB: smaller numbers means a
2089heavier weight).<o:p></o:p></span></p>
2090
2091<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
2092press the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2093"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2094"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Select</span></b><span
2095style='mso-fareast-font-family:"Times New Roman"'> button for the “</span><span
2096class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2097"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2098"Times New Roman";mso-hansi-theme-font:minor-latin'>Xray</span></b></span><b
2099style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2100mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2101mso-hansi-theme-font:minor-latin'> reciprocal space data: <span class=GramE>F(</span>Q)</span></b><span
2102style='mso-fareast-font-family:"Times New Roman"'>” line; a <span class=SpellE>FileDialog</span>
2103should appear. </span>Because you used <span style='mso-fareast-font-family:
2104Calibri;mso-fareast-theme-font:minor-latin'>the </span><b style='mso-bidi-font-weight:
2105normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2106minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2107mso-hansi-theme-font:minor-latin'>Help/Download tutorial</span></b><span
2108style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
2109menu entry to open this page and downloaded the exercise files (recommended),
2110then the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2111"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2112Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RMCProfile-IV/data/...</span></b><span
2113style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
2114entry will bring you to the location where the files have been downloaded. (It
2115is also possible to download them manually from <a
2116href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/</a>.
2117In this case you will need to navigate to the download location manually.)<o:p></o:p></span></p>
2118
2119<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The <span
2120class=SpellE>FileDialog</span> should show<o:p></o:p></span></p>
2121
2122<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2123mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1053" type="#_x0000_t75"
2124 style='width:356.25pt;height:124.5pt;visibility:visible;mso-wrap-style:square'>
2125 <v:imagedata src="RMCProfile-IV_files/image126.png" o:title=""/>
2126</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=166
2127src="RMCProfile-IV_files/image037.gif" v:shapes="_x0000_i1053"><![endif]></span><span
2128style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2129
2130<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
2131</span><b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2132mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2133mso-hansi-theme-font:minor-latin'>gapo4_xray_rmc.fq</span></b><span
2134style='mso-fareast-font-family:"Times New Roman"'>; it will be copied to your
2135working directory. The window will be redrawn; set the weight to </span><b
2136style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2137mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2138mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.1</span></b><span
2139style='mso-fareast-font-family:"Times New Roman"'>. You should also check the </span><b
2140style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2141mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2142mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Fit scale
2143factors?</span></b><span style='mso-fareast-font-family:"Times New Roman"'> <span
2144class=GramE>box</span>. When done the window should show<o:p></o:p></span></p>
2145
2146<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2147mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_22" o:spid="_x0000_i1052"
2148 type="#_x0000_t75" style='width:358.5pt;height:218.25pt;visibility:visible;
2149 mso-wrap-style:square'>
2150 <v:imagedata src="RMCProfile-IV_files/image038.png" o:title=""/>
2151</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=291
2152src="RMCProfile-IV_files/image039.gif" v:shapes="Picture_x0020_22"><![endif]></span><span
2153style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2154
2155<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You
2156should do a </span><b style='mso-bidi-font-weight:normal'><span
2157style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2158mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2159mso-bidi-theme-font:minor-latin'>Save project</span></b><span style='mso-fareast-font-family:
2160"Times New Roman"'> here.<o:p></o:p></span></p>
2161
2162<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Setup
2163RMCProfile files<o:p></o:p></span></h3>
2164
2165<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You
2166are now ready to setup the RMCProfile input files. Do </span><b
2167style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2168mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2169mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Setup
2170RMC</span></b><span style='mso-fareast-font-family:"Times New Roman"'> from the
2171menu; the console should report that files were written<o:p></o:p></span></p>
2172
2173<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2174mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1051" type="#_x0000_t75"
2175 style='width:358.5pt;height:90pt;visibility:visible;mso-wrap-style:square'>
2176 <v:imagedata src="RMCProfile-IV_files/image040.png" o:title=""/>
2177</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=120
2178src="RMCProfile-IV_files/image041.gif" v:shapes="_x0000_i1051"><![endif]></span><span
2179style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2180
2181<p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>and</span></span><span
2182style='mso-fareast-font-family:"Times New Roman"'> your local directory should
2183now have at least these 9 files<o:p></o:p></span></p>
2184
2185<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2186mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_24" o:spid="_x0000_i1050"
2187 type="#_x0000_t75" style='width:359.25pt;height:234.75pt;visibility:visible;
2188 mso-wrap-style:square'>
2189 <v:imagedata src="RMCProfile-IV_files/image042.png" o:title=""/>
2190</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=313
2191src="RMCProfile-IV_files/image044.gif" v:shapes="Picture_x0020_24"><![endif]></span><span
2192style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2193
2194<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>These
2195text files contain data needed by RMCProfile for the fitting of GaPO<sub>4</sub>.
2196They are:<o:p></o:p></span></p>
2197
2198<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2199style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.back</span></b><span
2200style='mso-fareast-font-family:"Times New Roman"'>- the 6 coefficients for the
2201chebyschev-1 function needed to compute the background for the Bragg pattern<o:p></o:p></span></p>
2202
2203<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2204style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.bragg</span></b><span
2205style='mso-fareast-font-family:"Times New Roman"'> – the powder pattern used in
2206the Rietveld refinement<o:p></o:p></span></p>
2207
2208<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2209style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.dat</span></b><span
2210style='mso-fareast-font-family:"Times New Roman"'> – the RMCProfile controls
2211file; described in full in the RMCProfile User Manual. It can be edited if need
2212be, but remember it is rewritten each time Operations/Setup RMC is done.<o:p></o:p></span></p>
2213
2214<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2215style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.inst</span></b><span
2216style='mso-fareast-font-family:"Times New Roman"'> – the instrument parameter
2217coefficients for the x-ray peak shape function used by GSAS-II and implemented
2218in RMCProfile for computing the Bragg pattern.<o:p></o:p></span></p>
2219
2220<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2221style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.rmc6f</span></b><span
2222style='mso-fareast-font-family:"Times New Roman"'> – the big box set of atom
2223positions. It is normally not rewritten when Operations/Setup RMC is done
2224unless the X-axis, Y-axis, or Z-axis lattice multipliers are changed. Most
2225important is that it will contain the set of big box atom positions as updated
2226by RMCProfile according to the Save interval (every 1 min in this case).<o:p></o:p></span></p>
2227
2228<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You
2229are now ready to run RMCProfile.<o:p></o:p></span></p>
2230
2231<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Run
2232RMCProfile<o:p></o:p></span></h3>
2233
2234<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
2235run RMCProfile from inside GSAS-II, do </span><b style='mso-bidi-font-weight:
2236normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2237minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2238minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Execute</span></b><span
2239style='mso-fareast-font-family:"Times New Roman"'>. You will first see a “nag”
2240note asking you to cite the publication describing RMCProfile; press </span><b
2241style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2242mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2243mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b><span
2244style='mso-fareast-font-family:"Times New Roman"'>. The program will start in a
2245new console window – processing will initially be pretty fast for this case and
2246then slow down as the modelling proceeds. It reports Time used and <span
2247class=GramE>Last</span> saved. Once the latter is nonzero you can view
2248intermediate results to see its progress.<o:p></o:p></span></p>
2249
2250<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2251mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_58" o:spid="_x0000_i1049"
2252 type="#_x0000_t75" style='width:358.5pt;height:187.5pt;visibility:visible;
2253 mso-wrap-style:square'>
2254 <v:imagedata src="RMCProfile-IV_files/image127.png" o:title=""/>
2255</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=250
2256src="RMCProfile-IV_files/image046.gif" v:shapes="Picture_x0020_58"><![endif]></span><span
2257style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2258
2259<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I
2260have captured the initial RMCProfile console output (done by simply clicking
2261anywhere in the window – note the white square. This temporarily stops
2262processing; it can be restarted by pressing any key with the focus on the
2263window). Things to look at are the several chi^2 values; there will be an
2264overall one and one for each of the 3 data sets used in the fitting. The last
2265one “X-ray real-space” is generated within RMCProfile by doing the Fourier
2266transform from the F(Q) input data to form the x-ray g(R) distribution (e.g.
2267the x-ray PDF). Since we’ve set the Fit scale factors option; the “<span
2268class=SpellE>Renorm</span>” values are other than unity. These will approach
22691.0 as the modelling continues. There is also a value for Bond energy
2270calculated from the bonds and angles subject to the potential energy
2271restraints. Do not be surprised if this value rises while RMCProfile runs; that
2272is simply a reflection of the distortions found in this structure. It will peak
2273at about the 4-5 min mark and then decrease after that. Note that you can exit
2274GSAS-II and RMCProfile will continue running. When it finished the console
2275shows (in part)<o:p></o:p></span></p>
2276
2277<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2278mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_59" o:spid="_x0000_i1048"
2279 type="#_x0000_t75" style='width:357.75pt;height:224.25pt;visibility:visible;
2280 mso-wrap-style:square'>
2281 <v:imagedata src="RMCProfile-IV_files/image129.png" o:title=""/>
2282</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=299
2283src="RMCProfile-IV_files/image047.gif" v:shapes="Picture_x0020_59"><![endif]></span><span
2284style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2285
2286<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
2287chi^2 values are now close to unity and not very different from each other;
2288this is what is desired. The bond energy started out at ~8700, peaked at
2289~14,000 and now is ~11,500; this is the effect of the distortions found by
2290RMCProfile.<o:p></o:p></span></p>
2291
2292<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2293
2294<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>After
2295RMCProfile finishes note that the project directory now has ~35 files many of
2296which are just temporary ones created by RMCProfile. We will be looking at just
2297the *.csv files and the GaPO4.rmcf6 file; the latter contains the last atom
2298configuration acceptable by RMCProfile thus representing a best disordered
2299model.<o:p></o:p></span></p>
2300
2301<h3><span style='mso-fareast-font-family:"Times New Roman"'>A note about
2302weights:<o:p></o:p></span></h3>
2303
2304<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
2305choice of weights for RMCProfile may seem to be arbitrary in these exercises,
2306but I have selected them so that each of the chi^2 values converge to be
2307roughly equal and somewhere near unity. This selection generally gives the best
2308performance in the reverse Monte Carlo calculation and requires some “trial
2309&amp; effort” in selecting the values. If one of the chi^2 values is too large
2310(&gt;&gt;1, i.e. weight too small) at convergence, then adjustments in the
2311structure will have been dominated by moves that lower that chi^2 sometimes at
2312the expense of others. Conversely, if one chi^2 is too small (&gt;&gt;1, i.e.
2313weight too large) then moves will tend to satisfy the others and there will be
2314little sensitivity to that data set. In this case my chosen weights have
2315yielded chi^2 values between 0.5 and 2.0; this is essentially ideal. If they
2316vary by more than an order of magnitude or are much greater or less than unity,
2317you should adjust the weights.<o:p></o:p></span></p>
2318
2319<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Viewing
2320results from RMCProfile<o:p></o:p></span></h3>
2321
2322<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Do </span><b
2323style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2324mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2325mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/View</span></b><span
2326style='mso-fareast-font-family:"Times New Roman"'>; a <span class=SpellE>FileDialog</span>
2327showing only *.csv files will appear<o:p></o:p></span></p>
2328
2329<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2330mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_60" o:spid="_x0000_i1047"
2331 type="#_x0000_t75" style='width:468pt;height:165pt;visibility:visible;
2332 mso-wrap-style:square'>
2333 <v:imagedata src="RMCProfile-IV_files/image131.png" o:title=""/>
2334</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=220
2335src="RMCProfile-IV_files/image048.gif" v:shapes="Picture_x0020_60"><![endif]></span><span
2336style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2337
2338<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>They
2339all should have the same prefix in their name, “GaPO4-X” which is the phase
2340name from the GSAS-II project file. Select any one of them – it doesn’t matter.
2341All of them will be read and their contents displayed as individual plots. For
2342example the chi^2 plot shows the progress of the RMCProfile fit<o:p></o:p></span></p>
2343
2344<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2345mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_61" o:spid="_x0000_i1046"
2346 type="#_x0000_t75" style='width:357pt;height:303pt;visibility:visible;
2347 mso-wrap-style:square'>
2348 <v:imagedata src="RMCProfile-IV_files/image133.png" o:title=""/>
2349</v:shape><![endif]--><![if !vml]><img border=0 width=476 height=404
2350src="RMCProfile-IV_files/image049.gif" v:shapes="Picture_x0020_61"><![endif]></span><span
2351style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2352
2353<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>If
2354you zoom into the end of the run, you can see that RMCProfile is still
2355improving the fit slowly even after 10 minutes of running.<o:p></o:p></span></p>
2356
2357<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2358
2359<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2360mso-no-proof:yes'>Comparing the Bragg plot with the PWDR plot shows that the
2361RMCProfile fit is very similar to the Rietveld fit<o:p></o:p></span></p>
2362
2363<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2364mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1045" type="#_x0000_t75"
2365 style='width:360.75pt;height:382.5pt;visibility:visible;mso-wrap-style:square'>
2366 <v:imagedata src="RMCProfile-IV_files/image055.png" o:title=""/>
2367</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=510
2368src="RMCProfile-IV_files/image050.gif" v:shapes="_x0000_i1045"><![endif]></span><span
2369style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2370
2371<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2372plot was made by dragging one plot tab to the bottom of the screen to create
2373the second frame. <o:p></o:p></span></p>
2374
2375<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2376mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_62" o:spid="_x0000_i1044"
2377 type="#_x0000_t75" style='width:359.25pt;height:307.5pt;visibility:visible;
2378 mso-wrap-style:square'>
2379 <v:imagedata src="RMCProfile-IV_files/image136.png" o:title=""/>
2380</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=410
2381src="RMCProfile-IV_files/image051.gif" v:shapes="Picture_x0020_62"><![endif]></span><span
2382style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2383
2384<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>A consideration
2385of the reciprocal space F(Q) (top) and the x-ray real space g(R) (bottom) plots
2386show reasonable agreement between the RMCProfile model and the data (but not
2387quite as good as we obtained in the RMCProfile-III tutorial – probably an
2388effect of imposing the potential energy restraints.<o:p></o:p></span></p>
2389
2390<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The bonds
2391and angles subject to potential energy restraints are plotted<o:p></o:p></span></p>
2392
2393<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2394mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_64" o:spid="_x0000_i1043"
2395 type="#_x0000_t75" style='width:357.75pt;height:306pt;visibility:visible;
2396 mso-wrap-style:square'>
2397 <v:imagedata src="RMCProfile-IV_files/image138.png" o:title=""/>
2398</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=408
2399src="RMCProfile-IV_files/image052.gif" v:shapes="Picture_x0020_64"><![endif]></span><span
2400style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2401
2402<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I’ve
2403adjusted the scales to give a better view of the different bond lengths.<o:p></o:p></span></p>
2404
2405<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2406mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_65" o:spid="_x0000_i1042"
2407 type="#_x0000_t75" style='width:359.25pt;height:307.5pt;visibility:visible;
2408 mso-wrap-style:square'>
2409 <v:imagedata src="RMCProfile-IV_files/image140.png" o:title=""/>
2410</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=410
2411src="RMCProfile-IV_files/image053.gif" v:shapes="Picture_x0020_65"><![endif]></span><span
2412style='mso-fareast-font-family:"Times New Roman"'><span
2413style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
2414
2415<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2416
2417<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>On
2418the other hand, the bond angles are essentially the same as the ideal
2419tetrahedral angle but with considerable spread (close to +/- 10 <span
2420class=SpellE>deg</span>).<o:p></o:p></span></p>
2421
2422<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Finally,
2423note that the console gave mean values for the bonds and angles that were
2424restrained by <span class=GramE>potential</span> energy functions.<o:p></o:p></span></p>
2425
2426<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2427mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_63" o:spid="_x0000_i1041"
2428 type="#_x0000_t75" style='width:311.25pt;height:147.75pt;visibility:visible;
2429 mso-wrap-style:square'>
2430 <v:imagedata src="RMCProfile-IV_files/image142.png" o:title=""/>
2431</v:shape><![endif]--><![if !vml]><img border=0 width=415 height=197
2432src="RMCProfile-IV_files/image054.gif" v:shapes="Picture_x0020_63"><![endif]></span><span
2433style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2434
2435<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>These
2436agree pretty well with our supposed values entered for these restraints. If our
2437guesses were wrong then there would be a shift; one can then enter the new
2438values, redo Operations/Setup RMC and then repeat Operation/Execute to rerun
2439RMCProfile which would start where the previous run stopped.<o:p></o:p></span></p>
2440
2441<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 9. View the
2442big box structural model for GaPO4<o:p></o:p></span></h3>
2443
2444<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next,
2445we can view the resulting big box structure. Do </span><b style='mso-bidi-font-weight:
2446normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2447minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2448minor-latin;mso-bidi-theme-font:minor-latin'>Import/Phase/from RMCProfile
2449.rmc6f file</span></b><span style='mso-fareast-font-family:"Times New Roman"'>;
2450a <span class=SpellE>FileDialog</span> box with one entry will show the
2451required file, </span><b style='mso-bidi-font-weight:normal'><span
2452style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2453mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2454mso-bidi-theme-font:minor-latin'>GaPO4-X.rmc6f</span></b><span
2455style='mso-fareast-font-family:"Times New Roman"'>. You will first see a </span><span
2456class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2457"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2458"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
2459style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2460mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2461mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> this the
2462file you want</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
2463popup window; select </span><b style='mso-bidi-font-weight:normal'><span
2464style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2465mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2466mso-bidi-theme-font:minor-latin'>Yes</span></b><span style='mso-fareast-font-family:
2467"Times New Roman"'>. Next will be an </span><b style='mso-bidi-font-weight:
2468normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2469minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2470minor-latin;mso-bidi-theme-font:minor-latin'>Edit phase name</span></b><span
2471style='mso-fareast-font-family:"Times New Roman"'> popup. The proposed name is
2472the same as the existing one; GSAS-II will rename this one by adding ‘_1’ to
2473the end. Next will be a popup for </span><b style='mso-bidi-font-weight:normal'><span
2474style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2475mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2476mso-bidi-theme-font:minor-latin'>Add histograms</span></b><span
2477style='mso-fareast-font-family:"Times New Roman"'>; respond </span><b
2478style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2479mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2480mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b><span
2481style='mso-fareast-font-family:"Times New Roman"'> because you don’t want this
2482phase to be in any subsequent Rietveld refinement. Looking at the </span><b
2483style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2484mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2485mso-hansi-theme-font:minor-latin'>General</span></b><span style='mso-fareast-font-family:
2486"Times New Roman"'> tab for this phase we see it is 6X in <span class=GramE>a
2487&amp;</span> b and 4X in c axes relative to the original and has no symmetry
2488(space group P 1).<o:p></o:p></span></p>
2489
2490<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2491mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_66" o:spid="_x0000_i1040"
2492 type="#_x0000_t75" style='width:359.25pt;height:183pt;visibility:visible;
2493 mso-wrap-style:square'>
2494 <v:imagedata src="RMCProfile-IV_files/image144.png" o:title=""/>
2495</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=244
2496src="RMCProfile-IV_files/image056.gif" v:shapes="Picture_x0020_66"><![endif]></span><span
2497style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2498
2499<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
2500the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2501"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2502"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
2503Atoms</span></b><span style='mso-fareast-font-family:"Times New Roman"'> tab for
2504this phase; a van der Waals ball model will be drawn. You can select the </span><b
2505style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2506mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2507mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ga &amp; P</span></b><span
2508style='mso-fareast-font-family:"Times New Roman"'> atoms &amp; fill the </span><b
2509style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2510mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2511mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>CN-sphere</span></b><span
2512style='mso-fareast-font-family:"Times New Roman"'> for them (does take a long
2513time, &gt;10min – be patient) and then change all the atoms to ball and stick
2514style. The CN-sphere filling works because the RMCProfile structure still has
2515translational symmetry across its 6x6x4 lattice. You should see something like<o:p></o:p></span></p>
2516
2517<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2518mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1039" type="#_x0000_t75"
2519 style='width:360.75pt;height:382.5pt;visibility:visible;mso-wrap-style:square'>
2520 <v:imagedata src="RMCProfile-IV_files/image071.png" o:title=""/>
2521</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=510
2522src="RMCProfile-IV_files/image057.gif" v:shapes="_x0000_i1039"><![endif]></span><span
2523style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2524
2525<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Notice
2526the apparent tilting the PO<sub>4</sub> and GaO<sub>4</sub> tetrahedra. The
2527stray O atoms are bound to PO<sub>4</sub> and GaO<sub>4</sub> tetrahedra in
2528neighboring boxes. <o:p></o:p></span></p>
2529
2530<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2531
2532<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>NB:
2533this import facility can be used to load any rmc6f file, e.g. from a RMCProfile
2534run done outside of GSAS-II; all the plotting and tools in this and the
2535following steps are available for these big box models.<o:p></o:p></span></p>
2536
2537<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 10. View the
2538disordered average structure<o:p></o:p></span></h3>
2539
2540<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We
2541can compress the big box result back into the original average crystal
2542structure to see how the disordered sites compare with the average ones. Select
2543the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2544"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2545"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b><span
2546style='mso-fareast-font-family:"Times New Roman"'> tab for the big box phase
2547(SF6_1) and then do </span><b style='mso-bidi-font-weight:normal'><span
2548style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2549mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2550mso-bidi-theme-font:minor-latin'>Compute/Transform</span></b><span
2551style='mso-fareast-font-family:"Times New Roman"'>. A popup dialog will appear<o:p></o:p></span></p>
2552
2553<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2554mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_67" o:spid="_x0000_i1038"
2555 type="#_x0000_t75" style='width:282pt;height:322.5pt;visibility:visible;
2556 mso-wrap-style:square'>
2557 <v:imagedata src="RMCProfile-IV_files/image147.png" o:title=""/>
2558</v:shape><![endif]--><![if !vml]><img border=0 width=376 height=430
2559src="RMCProfile-IV_files/image058.gif" v:shapes="Picture_x0020_67"><![endif]></span><span
2560style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2561
2562<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2563is the general tool inside GSAS-II for all sorts of structure transformations.
2564Here we will use it to push all the big box atoms back into the average
2565structure unit cell. Recalling that the big box model is 6x6x4 the original
2566unit cell, we simply want to reverse the process. Enter </span><b
2567style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2568mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2569mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1/6, 1/6<span
2570class=GramE>,1</span>/4</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
2571into the diagonal elements of the M matrix. The GUI will convert them to the
2572decimal equivalent (0.167<span class=GramE>,…</span>). The target space group
2573should be P 1. You should see<o:p></o:p></span></p>
2574
2575<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2576mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1037" type="#_x0000_t75"
2577 style='width:282pt;height:322.5pt;visibility:visible;mso-wrap-style:square'>
2578 <v:imagedata src="RMCProfile-IV_files/image075.png" o:title=""/>
2579</v:shape><![endif]--><![if !vml]><img border=0 width=376 height=430
2580src="RMCProfile-IV_files/image059.gif" v:shapes="_x0000_i1037"><![endif]></span><span
2581style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2582
2583<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Press
2584</span><b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2585mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2586mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ok</span></b><span
2587style='mso-fareast-font-family:"Times New Roman"'> to do the transformation. A
2588new phase, “GaPO4-X_1 <span class=SpellE>abc</span>” will be formed as
2589triclinic with cell axes that match the original hexagonal ones. Select </span><b
2590style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2591mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2592mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b><span
2593style='mso-fareast-font-family:"Times New Roman"'>; a van der Waals model will
2594appear.<o:p></o:p></span></p>
2595
2596<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2597mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_75" o:spid="_x0000_i1036"
2598 type="#_x0000_t75" style='width:358.5pt;height:380.25pt;visibility:visible;
2599 mso-wrap-style:square'>
2600 <v:imagedata src="RMCProfile-IV_files/image077.png" o:title=""/>
2601</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=507
2602src="RMCProfile-IV_files/image060.gif" v:shapes="Picture_x0020_75"><![endif]></span><span
2603style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2604
2605<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
2606the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2607"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2608"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
2609Options</span></b><span style='mso-fareast-font-family:"Times New Roman"'> tab
2610and reduce the </span><b style='mso-bidi-font-weight:normal'><span
2611style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2612mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2613mso-bidi-theme-font:minor-latin'>van der Waals scale</span></b><span
2614style='mso-fareast-font-family:"Times New Roman"'> to about </span><b
2615style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2616mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2617mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.05</span></b><span
2618style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
2619
2620<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2621mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_68" o:spid="_x0000_i1035"
2622 type="#_x0000_t75" style='width:358.5pt;height:306.75pt;visibility:visible;
2623 mso-wrap-style:square'>
2624 <v:imagedata src="RMCProfile-IV_files/image151.png" o:title=""/>
2625</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=409
2626src="RMCProfile-IV_files/image061.gif" v:shapes="Picture_x0020_68"><![endif]></span><span
2627style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2628
2629<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2630compares pretty well with the original structure with the ellipsoids drawn at
263199% probability. If anything the spread in atom positions is less that what was
2632obtained in the RMCProfile-III tutorial; an effect of the potential energy
2633restraints.<o:p></o:p></span></p>
2634
2635<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2636mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_77" o:spid="_x0000_i1034"
2637 type="#_x0000_t75" style='width:359.25pt;height:381pt;visibility:visible;
2638 mso-wrap-style:square'>
2639 <v:imagedata src="RMCProfile-IV_files/image081.png" o:title=""/>
2640</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=508
2641src="RMCProfile-IV_files/image062.gif" v:shapes="Picture_x0020_77"><![endif]></span><span
2642style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2643
2644<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>However,
2645the O atoms are more widely distributed in space than the P or Ga atoms.<o:p></o:p></span></p>
2646
2647<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2648
2649<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 11. Polyhedral
2650comparison for the big box model<o:p></o:p></span></h3>
2651
2652<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
2653this step we will examine how the suite of PO<sub>4</sub> and GaO<sub>4</sub>
2654tetrahedra deviate from an ideal tetrahedron. This analysis is currently
2655restricted to structures with P1 space group symmetry; this is what we have
2656from Step 9 above. Select </span><b style='mso-bidi-font-weight:normal'><span
2657style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2658mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2659mso-bidi-theme-font:minor-latin'>Phases/GaPO4-X_1</span></b><span
2660style='mso-fareast-font-family:"Times New Roman"'> from the data tree; the
2661General tab will appear.<o:p></o:p></span></p>
2662
2663<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2664mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_78" o:spid="_x0000_i1033"
2665 type="#_x0000_t75" style='width:5in;height:192.75pt;visibility:visible;
2666 mso-wrap-style:square'>
2667 <v:imagedata src="RMCProfile-IV_files/image083.png" o:title=""/>
2668</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=257
2669src="RMCProfile-IV_files/image063.gif" v:shapes="Picture_x0020_78"><![endif]></span><span
2670style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2671
2672<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>What
2673we want is at the bottom of this panel; scroll down to the bottom<o:p></o:p></span></p>
2674
2675<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2676mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_79" o:spid="_x0000_i1032"
2677 type="#_x0000_t75" style='width:357pt;height:190.5pt;visibility:visible;
2678 mso-wrap-style:square'>
2679 <v:imagedata src="RMCProfile-IV_files/image085.png" o:title=""/>
2680</v:shape><![endif]--><![if !vml]><img border=0 width=476 height=254
2681src="RMCProfile-IV_files/image064.gif" v:shapes="Picture_x0020_79"><![endif]></span><span
2682style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2683
2684<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>At
2685the very bottom is the control for polyhedral comparison. All that is needed is
2686to select the central atom (“</span><b style='mso-bidi-font-weight:normal'><span
2687style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2688mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2689mso-bidi-theme-font:minor-latin'>origin atom type</span></b><span
2690style='mso-fareast-font-family:"Times New Roman"'>”) and the polyhedral
2691vertices (“</span><b style='mso-bidi-font-weight:normal'><span
2692style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2693mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2694mso-bidi-theme-font:minor-latin'>target atom type</span></b><span
2695style='mso-fareast-font-family:"Times New Roman"'>”). Select </span><b
2696style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2697mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2698mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P</span></b><span
2699style='mso-fareast-font-family:"Times New Roman"'> for the former and </span><b
2700style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2701mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2702mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>O</span></b><span
2703style='mso-fareast-font-family:"Times New Roman"'> for the latter. Then do </span><b
2704style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2705mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2706mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Compute/Compare</span></b><span
2707style='mso-fareast-font-family:"Times New Roman"'> from the menu; a popup for
2708setting Distance Angle Controls will appear<o:p></o:p></span></p>
2709
2710<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2711mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_80" o:spid="_x0000_i1031"
2712 type="#_x0000_t75" style='width:206.25pt;height:196.5pt;visibility:visible;
2713 mso-wrap-style:square'>
2714 <v:imagedata src="RMCProfile-IV_files/image087.png" o:title=""/>
2715</v:shape><![endif]--><![if !vml]><img border=0 width=275 height=262
2716src="RMCProfile-IV_files/image065.gif" v:shapes="Picture_x0020_80"><![endif]></span><span
2717style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2718
2719<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
2720some cases the bond search factor may need to be adjusted to get the right
2721number of vertices for the <span class=SpellE>polyhedra</span>; in this case </span><b
2722style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2723mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2724mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.85</span></b><span
2725style='mso-fareast-font-family:"Times New Roman"'> is fine (NB: in this use the
2726angle ranges are ignored). Press </span><b style='mso-bidi-font-weight:normal'><span
2727style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2728mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2729mso-bidi-theme-font:minor-latin'>OK</span></b><span style='mso-fareast-font-family:
2730"Times New Roman"'>; a progress bar will show the atoms being processed. The
2731console may show some atoms being skipped because the number of vertices wasn’t
2732either 4 (tetrahedron) or 6 (octahedron); all but one are ok here. Because
2733there are 432 P atoms to be looked at in this big box model, this calculation
2734can take a number of minutes. The General tab reappears already scrolled to the
2735bottom<o:p></o:p></span></p>
2736
2737<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2738mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_39" o:spid="_x0000_i1030"
2739 type="#_x0000_t75" style='width:363pt;height:185.25pt;visibility:visible;
2740 mso-wrap-style:square'>
2741 <v:imagedata src="RMCProfile-IV_files/image089.png" o:title=""/>
2742</v:shape><![endif]--><![if !vml]><img border=0 width=484 height=247
2743src="RMCProfile-IV_files/image066.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
2744style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2745
2746<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>A
2747new button (</span><b style='mso-bidi-font-weight:normal'><span
2748style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2749mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2750mso-bidi-theme-font:minor-latin'>Show Plots?</span></b><span style='mso-fareast-font-family:
2751"Times New Roman"'>) has appeared after the atom selections; press it. A number
2752of new entries will appear on the plot window; we will discuss each in turn.
2753Select the </span><b style='mso-bidi-font-weight:normal'><span
2754style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2755mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2756mso-bidi-theme-font:minor-latin'>Tet P-O Bond for GaPO4-X_1</span></b><span
2757style='mso-fareast-font-family:"Times New Roman"'> tab<o:p></o:p></span></p>
2758
2759<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2760mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_69" o:spid="_x0000_i1029"
2761 type="#_x0000_t75" style='width:358.5pt;height:306.75pt;visibility:visible;
2762 mso-wrap-style:square'>
2763 <v:imagedata src="RMCProfile-IV_files/image158.png" o:title=""/>
2764</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=409
2765src="RMCProfile-IV_files/image067.gif" v:shapes="Picture_x0020_69"><![endif]></span><span
2766style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2767
2768<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2769gives the distribution of the average P-O bond lengths for all the tetrahedra
2770found across the big box model. It is rough because of the small size of the
2771model, but the asymmetry seen in the RMCProfile-III is not present in this P-O
2772bond distribution. The console will have listed the average value with the
2773standard uncertainty in parentheses. <o:p></o:p></span></p>
2774
2775<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2776mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_71" o:spid="_x0000_i1028"
2777 type="#_x0000_t75" style='width:358.5pt;height:90.75pt;visibility:visible;
2778 mso-wrap-style:square'>
2779 <v:imagedata src="RMCProfile-IV_files/image160.png" o:title=""/>
2780</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=121
2781src="RMCProfile-IV_files/image068.gif" v:shapes="Picture_x0020_71"><![endif]></span><span
2782style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2783
2784<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
2785select the </span><b style='mso-bidi-font-weight:normal'><span
2786style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2787mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2788mso-bidi-theme-font:minor-latin'>Tet P-O Tilts for GaPO4-X_1</span></b><span
2789style='mso-fareast-font-family:"Times New Roman"'>tab<o:p></o:p></span></p>
2790
2791<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2792mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_72" o:spid="_x0000_i1027"
2793 type="#_x0000_t75" style='width:358.5pt;height:306.75pt;visibility:visible;
2794 mso-wrap-style:square'>
2795 <v:imagedata src="RMCProfile-IV_files/image162.png" o:title=""/>
2796</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=409
2797src="RMCProfile-IV_files/image069.gif" v:shapes="Picture_x0020_72"><![endif]></span><span
2798style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2799
2800<p class=MsoNormal style='tab-stops:344.95pt'><span style='mso-fareast-font-family:
2801"Times New Roman"'>This gives the distribution of axial tilts of the PO<sub>4</sub>
2802molecules from the reference tetrahedron (aligned along the Cartesian axes) and
2803is similar but tighter compared to that found in the RMCProfile-III tutorial.
2804There is an apparent split distribution centered at ~48 <span class=SpellE>deg</span>
2805and ~68 <span class=SpellE>deg</span> (the rather meaningless in this case
2806average tilt is also shown on the console). Next select </span><b
2807style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2808mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2809mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X-Delta</span></b><span
2810style='mso-fareast-font-family:"Times New Roman"'>, </span><b style='mso-bidi-font-weight:
2811normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2812minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2813minor-latin;mso-bidi-theme-font:minor-latin'>Y-Delta</span></b><span
2814style='mso-fareast-font-family:"Times New Roman"'> and </span><b
2815style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2816mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2817mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Z-Delta</span></b><span
2818style='mso-fareast-font-family:"Times New Roman"'> tabs in turn.<o:p></o:p></span></p>
2819
2820<p class=MsoNormal style='tab-stops:344.95pt'><span style='mso-fareast-font-family:
2821"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_73"
2822 o:spid="_x0000_i1026" type="#_x0000_t75" style='width:359.25pt;height:255.75pt;
2823 visibility:visible;mso-wrap-style:square'>
2824 <v:imagedata src="RMCProfile-IV_files/image164.png" o:title=""/>
2825</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=341
2826src="RMCProfile-IV_files/image070.gif" v:shapes="Picture_x0020_73"><![endif]></span><span
2827style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2828
2829<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I
2830have made this plot by dragging the respective plot tabs to one of the right
2831(or left) edges to create a 3 pane plot. These show the displacement of the O
2832atoms from the ideal tetrahedral vertices along each Cartesian axis. Here they
2833are arranged about the zeros fairly tightly; the apparent split in the </span><span
2834style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span><span
2835style='mso-fareast-font-family:"Times New Roman"'>Y plot may or may not be real.
2836If there were structural distortions to the tetrahedra (e.g. <span
2837class=SpellE>Jahn</span>-Teller distortions) these could show in these plots. <o:p></o:p></span></p>
2838
2839<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
2840do the same thing for Ga-O <span class=SpellE>polyhedra</span>, select </span><b
2841style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2842mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2843mso-hansi-theme-font:minor-latin'>Ga</span></b><span style='mso-fareast-font-family:
2844"Times New Roman"'> instead of P for the origin type atom and then do </span><b
2845style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2846mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2847mso-hansi-theme-font:minor-latin'>Compute/Compare</span></b><span
2848style='mso-fareast-font-family:"Times New Roman"'>. Again there will be the </span><b
2849style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2850mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2851mso-hansi-theme-font:minor-latin'>Distance Angle Controls</span></b><span
2852style='mso-fareast-font-family:"Times New Roman"'> popup; no changes needed.
2853The calculation will again take several minutes to complete. When done press
2854the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2855"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2856"Times New Roman";mso-hansi-theme-font:minor-latin'>Show plots?</span></b><span
2857style='mso-fareast-font-family:"Times New Roman"'> <span class=GramE>button</span>;
2858more plots will be added to the plot window. I show both sets of tetrahedral
2859bonds as a stacked plot; the Ga-O bonds are not skewed, either. <span
2860style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_74"
2861 o:spid="_x0000_i1025" type="#_x0000_t75" style='width:357.75pt;height:288.75pt;
2862 visibility:visible;mso-wrap-style:square'>
2863 <v:imagedata src="RMCProfile-IV_files/image166.png" o:title=""/>
2864</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=385
2865src="RMCProfile-IV_files/image072.gif" v:shapes="Picture_x0020_74"><![endif]></span><o:p></o:p></span></p>
2866
2867<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Similar
2868comparisons can be made with the other plots. NB: if the project is now saved
2869all the data needed to reproduce the plots is also saved; any of them can be
2870seen without redoing the Compare calculation.<o:p></o:p></span></p>
2871
2872<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2873
2874<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2875completes this RMCProfile tutorial; you should save the project.<o:p></o:p></span></p>
2876
2877<h2><span style='mso-fareast-font-family:"Times New Roman"'>Final note<o:p></o:p></span></h2>
2878
2879<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>A
2880production run with enough atoms to give decent statistics would be for a box
2881that is perhaps 12x12x8 the original unit cell and would require a 10-20 hour
2882run time. It would contain several thousand atoms instead of ~2600 as used
2883here. You can further explore this tutorial project by changing the bond and
2884angle potentials to see how that changes the RMCProfile result. In my case,
2885increasing all 4 to 20 from 2 tightened the Ga-O and P-O bond length distributions
2886but had no impact on the O-P-O and O-Ga-O angle distributions. The fit to the g(R)
2887is also poorer (much higher chi^2).<o:p></o:p></span></p>
2888
2889<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2890
2891<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2892
2893<p class=MsoNormal style='tab-stops:317.2pt'><span style='mso-fareast-font-family:
2894"Times New Roman"'><span style='mso-tab-count:1'>                                                                                                          </span><o:p></o:p></span></p>
2895
2896</div>
2897
2898</body>
2899
2900</html>
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