source: Tutorials/RMCProfile-IV/RMCProfile-IV.htm @ 4367

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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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1201<![endif]--><!--[if gte mso 9]><xml>
1202 <o:shapedefaults v:ext="edit" spidmax="1026"/>
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1207</head>
1208
1209<body lang=EN-US link=blue vlink=purple style='tab-interval:.5in'>
1210
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<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction<o:p></o:p></span></h2>
1216
1217<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
1218this tutorial, we will show how to use GSAS-II in conjunction with RMCProfile
1219(“RMCProfile: Reverse Monte Carlo for polycrystalline materials”, M.G. Tucker,
1220D.A. Keen, M.T. Dove, A.L. Goodwin and Q. Hui, (2007) Jour. Phys.: Cond.
1221Matter, <b style='mso-bidi-font-weight:normal'>19</b>, 335218. <span
1222class=SpellE>doi</span>: <a
1223href="https://doi.org/10.1088/0953-8984/19/33/335218">https://doi.org/10.1088/0953-8984/19/33/335218</a>)
1224to do a fit with x-ray powder diffraction data and pair distribution functions
1225(PDF) created from it with a “big box” disordered model. This exercise is very
1226similar to RMCProfile-III except that no neutron data is used and instead a set
1227of bond and angle potentials are used to augment the fitting.<o:p></o:p></span></p>
1228
1229<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1230
1231<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Before
1232getting started you must obtain the most recent Version 6 of the RMCProfile
1233executable (at this writing this is RMCProfile V6.7.6 Beta Serial). Obtain this
1234from <a href="http://www.rmcprofile.org">www.rmcprofile.org</a> by following
1235the prompts from Downloads. This version is available for Windows, Mac OSX and
1236Linux. The download will be a zip file; save it somewhere convenient. Pull from
1237it only the </span><span class=SpellE><span class=SubtitleChar><span
1238style='font-size:11.0pt'>RMCProfile_package</span></span></span><span
1239class=SubtitleChar><span style='font-size:11.0pt'>/exe/rmcprofile.exe</span></span><span
1240style='mso-fareast-font-family:"Times New Roman"'> and place it in the GSASII
1241main directory or in a new subdirectory (e.g. </span><span class=SubtitleChar><span
1242style='font-size:11.0pt'>GSASII/RMCProfile</span></span><span style='mso-fareast-font-family:
1243"Times New Roman"'>); no other files are needed although you may wish to also
1244retrieve the contents of the tutorial subdirectory. It contains </span><span
1245class=SubtitleChar><span style='font-size:11.0pt'>rmcprofilemanual.pdf</span></span><span
1246style='mso-fareast-font-family:"Times New Roman"'> and </span><span
1247class=SubtitleChar><span style='font-size:11.0pt'>rmcprofile_tutorial.pdf</span></span><span
1248style='mso-fareast-font-family:"Times New Roman"'> which may be of interest
1249since the GSAS-II/RMCProfile tutorials are based on the latter.<o:p></o:p></span></p>
1250
1251<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1252
1253<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1254process for using RMCProfile begins with a normal Rietveld refinement of the
1255average structure. For the kind of disordered materials of interest here, this
1256may give bond lengths that are frequently too short for the atoms involved and
1257sometimes extreme apparent thermal motion for some of the atoms. These effects
1258arise because the average structure places these atoms too close to one
1259another; a more localized view would show coordinated atom displacements or
1260reorientation of groups of atoms to avoid the close contacts. RMCProfile is
1261then used to characterize these local displacements by fitting to the
1262diffraction data and its Fourier transform as a PDF.<o:p></o:p></span></p>
1263
1264<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1265
1266<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1267material used in this tutorial is the same as described in the RMCProfile-III
1268tutorial, gallium phosphate (GaPO<sub>4</sub>). GaPO<sub>4</sub> is a
1269piezoelectric crystal of corner sharing GaO<sub>4</sub> and PO<sub>4</sub>
1270tetrahedra arranged as in a doubled c-axis &#945;-quartz structure.<span
1271style='mso-spacerun:yes'>  </span>The average structure determined by Rietveld
1272refinement results in Ga-O and P-O bond lengths that are shorter than implied
1273by the corresponding peak positions in either an x-ray or neutron PDF. The
1274X-ray data used here was obtained at room temperature on beam line I15 at the
1275Diamond light source. The objective here is to use RMCProfile to model the
1276structural distortions that yield the X-ray PDF derived bond lengths and is
1277augmented by potential energy restraints on Ga-O and P-O bond lengths and
1278O-Ga-O and O-P-O bond angles. The result obtained here can be compared to that
1279from the combined x-ray/neutron fitting described in the RMCProfile-III
1280tutorial.<o:p></o:p></span></p>
1281
1282<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1283
1284<p class=MsoNormal>If you have not done so already, start GSAS-II.</p>
1285
1286<h2>Rietveld Refinement of Gallium phosphate (<span style='mso-fareast-font-family:
1287"Times New Roman"'>GaPO<sub>4</sub></span>):</h2>
1288
1289<h3>Step 1: Read in the data file</h3>
1290
1291<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1. </span>Use
1292the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1293mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1294minor-latin'>Import/Powder Data/from GSAS powder data file</span></b> menu item
1295to read the data file into the current GSAS-II project. This read option is set
1296to read any of the powder data formats defined for GSAS (angles in <span
1297class=SpellE>centidegrees</span>, TOF in µsec). Other submenu items will read
1298the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1299style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1300mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1301format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1302style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1303mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1304format (angles in degrees) used by <span class=SpellE>topas</span>, etc.<span
1305style='mso-spacerun:yes'>  </span>In those cases, you would change the file
1306type to <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1307style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1308mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>cif</span></b></span>
1309format or the <span class=SpellE><b style='mso-bidi-font-weight:normal'><span
1310style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1311mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>xye</span></b></span>
1312format (angles in degrees) to see them. Because you used <span
1313style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>the </span><b
1314style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1315mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1316minor-latin;mso-hansi-theme-font:minor-latin'>Help/Download tutorial</span></b><span
1317style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1318menu entry to open this page and downloaded the exercise files (recommended),
1319then the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1320"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1321Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RMCProfile-IV/data/...</span></b><span
1322style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1323entry will bring you to the location where the files have been downloaded. (It
1324is also possible to download them manually from <a
1325href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/</a>.
1326In this case you will need to navigate to the download location manually.)<o:p></o:p></span></p>
1327
1328<p class=MsoNormal><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1329minor-latin'>For this tutorial you should see the data file in the file
1330browser, but if extensions on data files are not the expected ones, you may
1331need to change the file type to </span><b style='mso-bidi-font-weight:normal'><span
1332style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1333mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1334minor-latin;mso-bidi-theme-font:minor-latin'>All files (*.*)</span></b><span
1335style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> to
1336find the desired file.<o:p></o:p></span></p>
1337
1338<p class=MsoNormal><span style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1339minor-latin'>2. Select the </span><b style='mso-bidi-font-weight:normal'><span
1340style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1341mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1342minor-latin;mso-bidi-theme-font:minor-latin'>105870-pe-GaPO4_ed.gsas</span></b><span
1343style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'> </span><span
1344style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1345mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>data</span>
1346file in the first dialog and press <b style='mso-bidi-font-weight:normal'><span
1347style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1348mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Open</span></b>.
1349There will be a dialog box asking <span class=GramE><b style='mso-bidi-font-weight:
1350normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1351minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
1352style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1353mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1354minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1355style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1356mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1357minor-latin'>Yes</span></b></span> button to proceed. <span style='mso-fareast-font-family:
1358"Times New Roman"'><o:p></o:p></span></p>
1359
1360<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1361will be a apparently empty file selection dialog for the instrument parameter
1362file; switch the file type to </span><b style='mso-bidi-font-weight:normal'><span
1363style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1364mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1365mso-bidi-theme-font:minor-latin'>GSAS <span class=SpellE>iparm</span> file (*.<span
1366class=SpellE>prm</span><span class=GramE>,…</span>)</span></b><span
1367style='mso-fareast-font-family:"Times New Roman"'>. Then one file (</span><b
1368style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1369mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1370mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>inst_i15_pdf_april14.prm</span></b><span
1371style='mso-fareast-font-family:"Times New Roman"'>) is shown. Select it; the pattern
1372will be read in and displayed <o:p></o:p></span></p>
1373
1374<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1375mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600"
1376 o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f"
1377 stroked="f">
1378 <v:stroke joinstyle="miter"/>
1379 <v:formulas>
1380  <v:f eqn="if lineDrawn pixelLineWidth 0"/>
1381  <v:f eqn="sum @0 1 0"/>
1382  <v:f eqn="sum 0 0 @1"/>
1383  <v:f eqn="prod @2 1 2"/>
1384  <v:f eqn="prod @3 21600 pixelWidth"/>
1385  <v:f eqn="prod @3 21600 pixelHeight"/>
1386  <v:f eqn="sum @0 0 1"/>
1387  <v:f eqn="prod @6 1 2"/>
1388  <v:f eqn="prod @7 21600 pixelWidth"/>
1389  <v:f eqn="sum @8 21600 0"/>
1390  <v:f eqn="prod @7 21600 pixelHeight"/>
1391  <v:f eqn="sum @10 21600 0"/>
1392 </v:formulas>
1393 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
1394 <o:lock v:ext="edit" aspectratio="t"/>
1395</v:shapetype><v:shape id="Picture_x0020_45" o:spid="_x0000_i1073" type="#_x0000_t75"
1396 style='width:356.25pt;height:242.25pt;visibility:visible;mso-wrap-style:square'>
1397 <v:imagedata src="RMCProfile-IV_files/image001.png" o:title=""/>
1398</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=323
1399src="RMCProfile-IV_files/image002.gif" v:shapes="Picture_x0020_45"><![endif]></span><span
1400style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1401
1402<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Set limits<o:p></o:p></span></h3>
1403
1404<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Since
1405we want to avoid the abrupt jump and (as it turns out) low angle contaminating
1406peaks, we want to set the lower limit to just below the first large visible
1407Bragg peak and the upper limit needs to be set to include just the range with
1408Bragg intensities (&gt;0.4Å); go the </span><b style='mso-bidi-font-weight:
1409normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1410minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1411minor-latin;mso-bidi-theme-font:minor-latin'>Limits</span></b><span
1412style='mso-fareast-font-family:"Times New Roman"'> entry in the GSAS-II data
1413tree.<o:p></o:p></span></p>
1414
1415<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1416mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_46" o:spid="_x0000_i1072"
1417 type="#_x0000_t75" style='width:289.5pt;height:116.25pt;visibility:visible;
1418 mso-wrap-style:square'>
1419 <v:imagedata src="RMCProfile-IV_files/image003.png" o:title=""/>
1420</v:shape><![endif]--><![if !vml]><img border=0 width=386 height=155
1421src="RMCProfile-IV_files/image004.gif" v:shapes="Picture_x0020_46"><![endif]></span><span
1422style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1423
1424<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Change
1425the 1<sup>st</sup> entry to </span><b style='mso-bidi-font-weight:normal'><span
1426style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1427mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1428mso-bidi-theme-font:minor-latin'>2 </span></b><span style='mso-fareast-font-family:
1429"Times New Roman"'>and the second 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'> 25</span></b><span style='mso-fareast-font-family:
1433"Times New Roman"'>; the plot will change by moving the green and red dashed
1434lines.<o:p></o:p></span></p>
1435
1436<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1437mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_47" o:spid="_x0000_i1071"
1438 type="#_x0000_t75" style='width:5in;height:243.75pt;visibility:visible;
1439 mso-wrap-style:square'>
1440 <v:imagedata src="RMCProfile-IV_files/image005.png" o:title=""/>
1441</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=325
1442src="RMCProfile-IV_files/image006.gif" v:shapes="Picture_x0020_47"><![endif]></span><span
1443style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1444
1445<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Import GaPO<sub>4
1446</sub>phase<o:p></o:p></span></h3>
1447
1448<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1449average structure of GaPO<sub>4</sub> is that of a doubled c-axis
1450&#945;-quartz. Space group P3<sub>1</sub>21, a=4.90063 c=11.04809 with 4 atom
1451positions. We can import it from an old <span class=SpellE>gsas</span>
1452experiment file. </span>Use the <b style='mso-bidi-font-weight:normal'><span
1453style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1454mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Import/Phase/from
1455GSAS .EXP file</span></b> menu item to read the phase information for <span
1456style='mso-fareast-font-family:"Times New Roman"'>GaPO<sub>4 </sub></span>into
1457the current GSAS-II project. Other submenu items will read phase information in
1458other formats.<span style='mso-spacerun:yes'>  </span>Because you used <span
1459style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>the </span><b
1460style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1461mso-ascii-theme-font:minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:
1462minor-latin;mso-hansi-theme-font:minor-latin'>Help/Download tutorial</span></b><span
1463style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1464menu entry to open this page and downloaded the exercise files (recommended),
1465then the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1466"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1467Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RMCProfile-IV/data/...</span></b><span
1468style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1469entry will bring you to the location where the files have been downloaded. (It
1470is also possible to download them manually from <a
1471href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/</a>.
1472In this case you will need to navigate to the download location manually.)
1473Select the </span><b style='mso-bidi-font-weight:normal'><span
1474style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1475mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:
1476minor-latin;mso-bidi-theme-font:minor-latin'>GAPO4_XRAY_BAK.EXP</span></b><span
1477style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
1478file (only one there) </span>There will be a dialog box asking <span
1479class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1480"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:
1481minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
1482style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1483mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1484minor-latin'> this the file you want?</span></b> Press <span class=GramE><b
1485style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1486mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:
1487minor-latin'>Yes</span></b></span> button to proceed. You will get the opportunity
1488to change the phase name next (it is very long, I changed it to GaPO4-X; this
1489will be used as the file root for many of the files produced by RMCProfile. NB:
1490because of restrictions in RMCProfile it is important that the phase name not
1491have any spaces); press <b style='mso-bidi-font-weight:normal'><span
1492style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1493mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>
1494to continue. Next is the histogram selection window; this connects the phase to
1495the data so it can be used in subsequent calculations.</p>
1496
1497<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1498mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_48" o:spid="_x0000_i1070"
1499 type="#_x0000_t75" style='width:3in;height:173.25pt;visibility:visible;
1500 mso-wrap-style:square'>
1501 <v:imagedata src="RMCProfile-IV_files/image007.png" o:title=""/>
1502</v:shape><![endif]--><![if !vml]><img border=0 width=288 height=231
1503src="RMCProfile-IV_files/image008.gif" v:shapes="Picture_x0020_48"><![endif]></span><span
1504style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1505
1506<p class=MsoNormal>Select the histogram (or press <b style='mso-bidi-font-weight:
1507normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1508minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Set
1509All</span></b>) and press <b style='mso-bidi-font-weight:normal'><span
1510style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1511mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b>.
1512The General tab for the phase is shown next</p>
1513
1514<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1515mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_5" o:spid="_x0000_i1069"
1516 type="#_x0000_t75" style='width:359.25pt;height:192pt;visibility:visible;
1517 mso-wrap-style:square'>
1518 <v:imagedata src="RMCProfile-IV_files/image009.png" o:title=""/>
1519</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=256
1520src="RMCProfile-IV_files/image010.gif" v:shapes="Picture_x0020_5"><![endif]></span><span
1521style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1522
1523<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 4. Check atom
1524positions<o:p></o:p></span></h3>
1525
1526<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>It is
1527usually wise particularly for trigonal/hexagonal structures, to check the atom
1528positions to be sure atoms are properly placed on special positions. Select the
1529</span><b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1530mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1531mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Atoms</span></b><span
1532style='mso-fareast-font-family:"Times New Roman"'> tab<o:p></o:p></span></p>
1533
1534<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1535mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1068" type="#_x0000_t75"
1536 style='width:359.25pt;height:103.5pt;visibility:visible;mso-wrap-style:square'>
1537 <v:imagedata src="RMCProfile-IV_files/image011.png" o:title=""/>
1538</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=138
1539src="RMCProfile-IV_files/image012.gif" v:shapes="_x0000_i1068"><![endif]></span><span
1540style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1541
1542<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
1543this case the z-position for both Ga and P are not sufficiently precise for use
1544in <span class=SpellE>RMCProfie</span>. The Ga atom is at z=</span><b
1545style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1546mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1547mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1/3</span></b><span
1548style='mso-fareast-font-family:"Times New Roman"'> and the P 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'>5/6</span></b><span
1552style='mso-fareast-font-family:"Times New Roman"'>. Enter the fractions into
1553the respective positions in the table; GSAS-II will do the math to the full
1554double precision available in python. You should get<o:p></o:p></span></p>
1555
1556<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1557mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_50" o:spid="_x0000_i1067"
1558 type="#_x0000_t75" style='width:5in;height:104.25pt;visibility:visible;
1559 mso-wrap-style:square'>
1560 <v:imagedata src="RMCProfile-IV_files/image013.png" o:title=""/>
1561</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=139
1562src="RMCProfile-IV_files/image014.gif" v:shapes="Picture_x0020_50"><![endif]></span><span
1563style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1564
1565<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>If
1566this isn’t done then some of the input to RMCProfile will not be correctly
1567prepared.<o:p></o:p></span></p>
1568
1569<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Set the
1570background<o:p></o:p></span></h3>
1571
1572<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Although
1573there is not much diffuse scattering, the default background will be
1574insufficient for reasonable fitting. Select the </span><b style='mso-bidi-font-weight:
1575normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1576minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1577minor-latin;mso-bidi-theme-font:minor-latin'>Background</span></b><span
1578style='mso-fareast-font-family:"Times New Roman"'> item from the GSAS-II data
1579tree<o:p></o:p></span></p>
1580
1581<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1582mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_6" o:spid="_x0000_i1066"
1583 type="#_x0000_t75" style='width:361.5pt;height:189pt;visibility:visible;
1584 mso-wrap-style:square'>
1585 <v:imagedata src="RMCProfile-IV_files/image015.png" o:title=""/>
1586</v:shape><![endif]--><![if !vml]><img border=0 width=482 height=252
1587src="RMCProfile-IV_files/image016.gif" v:shapes="Picture_x0020_6"><![endif]></span><span
1588style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1589
1590<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Be
1591sure that “</span><b style='mso-bidi-font-weight:normal'><span
1592style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1593mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1594mso-bidi-theme-font:minor-latin'>chebyschev-1</span></b><span style='mso-fareast-font-family:
1595"Times New Roman"'>” is used for the background function; RMCProfile only
1596recognizes that form to compute the background for the diffraction pattern.
1597Select </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1598"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1599"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>6</span></b><span
1600style='mso-fareast-font-family:"Times New Roman"'> for the number of terms.<o:p></o:p></span></p>
1601
1602<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Rietveld
1603refinement<o:p></o:p></span></h3>
1604
1605<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We
1606are now ready for the first Rietveld refinement; select </span><b
1607style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1608mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1609mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1610style='mso-fareast-font-family:"Times New Roman"'> from the main GSAS-II menu.
1611Before it starts a file selection dialog will appear; select a file name (no
1612extension). I chose “</span><b style='mso-bidi-font-weight:normal'><span
1613style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1614mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1615mso-bidi-theme-font:minor-latin'>GaPO4</span></b><span style='mso-fareast-font-family:
1616"Times New Roman"'>”; do not use the phase name for this purpose because
1617RMCProfile will use that as the root for the many files it creates. Also, you
1618should create a new directory for this exercise while in this dialog box; it
1619will be rapidly filled up with RMCProfile files which can lead to considerable
1620confusion if mixed in with other files. For Windows, after navigating to a suitable
1621location, a new directory can be made by a right mouse click and selecting “</span><b
1622style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1623mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1624mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>New/Folder</span></b><span
1625style='mso-fareast-font-family:"Times New Roman"'>” from the popup menu. It
1626will appear with the name “New Folder”; change the name and select it (it will
1627be empty). Other operating systems will have similar methods. Finally press </span><b
1628style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1629mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1630mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Save</span></b><span
1631style='mso-fareast-font-family:"Times New Roman"'> to save the GSAS-II project
1632(GaPO4.gpx) and start the refinement. It will quickly converge to give a
1633reasonable <span class=SpellE>Rwp</span> (~9.8%) <o:p></o:p></span></p>
1634
1635<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1636mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_9" o:spid="_x0000_i1065"
1637 type="#_x0000_t75" style='width:5in;height:244.5pt;visibility:visible;
1638 mso-wrap-style:square'>
1639 <v:imagedata src="RMCProfile-IV_files/image017.png" o:title=""/>
1640</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=326
1641src="RMCProfile-IV_files/image018.gif" v:shapes="Picture_x0020_9"><![endif]></span><span
1642style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1643
1644<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I
1645pressed <span class=GramE>the ‘s’</span> key so that <span class=SpellE>sqrt</span>(intensity)
1646shows on the y-axis; makes things a bit easier to see. It is evident that the
1647lattice parameter as well as the sample broadening terms needs adjusting. Go to
1648the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1649"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1650"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b><span
1651style='mso-fareast-font-family:"Times New Roman"'> tab for the GaPO4-X phase
1652and select </span><span class=GramE><b style='mso-bidi-font-weight:normal'><span
1653style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1654mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1655mso-bidi-theme-font:minor-latin'>Refine</span></b></span><b style='mso-bidi-font-weight:
1656normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1657minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1658minor-latin;mso-bidi-theme-font:minor-latin'> unit cell</span></b><span
1659style='mso-fareast-font-family:"Times New Roman"'>. Then select the </span><b
1660style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1661mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1662mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Data</span></b><span
1663style='mso-fareast-font-family:"Times New Roman"'> tab and select </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'>size</span></b><span
1667style='mso-fareast-font-family:"Times New Roman"'> and </span><span
1668class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1669"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1670"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>microstrain</span></b></span><span
1671style='mso-fareast-font-family:"Times New Roman"'> for refinement. (A word to
1672the wise; set the starting value for size to </span><b style='mso-bidi-font-weight:
1673normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1674minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1675minor-latin;mso-bidi-theme-font:minor-latin'>0.1</span></b><span
1676style='mso-fareast-font-family:"Times New Roman"'> </span><span class=SpellE><span
1677style='font-family:"Arial",sans-serif;mso-fareast-font-family:"Times New Roman"'>&#956;</span><span
1678style='mso-fareast-font-family:"Times New Roman"'>m</span></span><span
1679style='mso-fareast-font-family:"Times New Roman"'>). Then do </span><b
1680style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1681mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1682mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine
1683</span></b><span style='mso-fareast-font-family:"Times New Roman"'>from the
1684main menu. The fit will greatly improve (<span class=SpellE>Rwp</span> ~5.25%)<o:p></o:p></span></p>
1685
1686<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1687mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_10" o:spid="_x0000_i1064"
1688 type="#_x0000_t75" style='width:357.75pt;height:243.75pt;visibility:visible;
1689 mso-wrap-style:square'>
1690 <v:imagedata src="RMCProfile-IV_files/image019.png" o:title=""/>
1691</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=325
1692src="RMCProfile-IV_files/image020.gif" v:shapes="Picture_x0020_10"><![endif]></span><span
1693style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1694
1695<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1696
1697<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
1698finish up add the following parameters:<o:p></o:p></span></p>
1699
1700<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
1701style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1702mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1703mso-bidi-theme-font:minor-latin'>GaPO4-X/Atoms</span></b><span
1704style='mso-fareast-font-family:"Times New Roman"'>: </span><b style='mso-bidi-font-weight:
1705normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1706minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1707minor-latin;mso-bidi-theme-font:minor-latin'>XU</span></b><span
1708style='mso-fareast-font-family:"Times New Roman"'> for all four atoms (GSAS-II
1709recognizes that the Ga &amp; P atoms are fixed in y &amp; z positions).<o:p></o:p></span></p>
1710
1711<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Do </span><b
1712style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1713mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1714mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Calculate/Refine</span></b><span
1715style='mso-fareast-font-family:"Times New Roman"'> from the main menu; the fit
1716will scarcely change (Rwp~5.25%).<o:p></o:p></span></p>
1717
1718<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Draw
1719structure<o:p></o:p></span></h3>
1720
1721<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
1722the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
1723"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1724"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Phases/GaPO4-X/Draw
1725Atoms</span></b><span style='mso-fareast-font-family:"Times New Roman"'> tab;
1726the list will be shown and the four unique atoms drawn on the plot.<o:p></o:p></span></p>
1727
1728<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1729mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_11" o:spid="_x0000_i1063"
1730 type="#_x0000_t75" style='width:5in;height:107.25pt;visibility:visible;
1731 mso-wrap-style:square'>
1732 <v:imagedata src="RMCProfile-IV_files/image021.png" o:title=""/>
1733</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=143
1734src="RMCProfile-IV_files/image022.gif" v:shapes="Picture_x0020_11"><![endif]></span><span
1735style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1736
1737<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1738mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_12" o:spid="_x0000_i1062"
1739 type="#_x0000_t75" style='width:360.75pt;height:245.25pt;visibility:visible;
1740 mso-wrap-style:square'>
1741 <v:imagedata src="RMCProfile-IV_files/image023.png" o:title=""/>
1742</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=327
1743src="RMCProfile-IV_files/image024.gif" v:shapes="Picture_x0020_12"><![endif]></span><span
1744style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1745
1746<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
1747improve this do the following:<o:p></o:p></span></p>
1748
1749<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>1)
1750Double click the empty upper left box in the </span><b style='mso-bidi-font-weight:
1751normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1752minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1753minor-latin;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b><span
1754style='mso-fareast-font-family:"Times New Roman"'> table; all atoms will turn
1755green and the four table rows will be grey (or blue).<o:p></o:p></span></p>
1756
1757<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>2)
1758Under the menu </span><b style='mso-bidi-font-weight:normal'><span
1759style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1760mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1761mso-bidi-theme-font:minor-latin'>Edit Figure</span></b><span style='mso-fareast-font-family:
1762"Times New Roman"'> select </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'>Fill unit cell</span></b><span
1766style='mso-fareast-font-family:"Times New Roman"'>; the figure will be redrawn
1767showing all atoms in the cell.<o:p></o:p></span></p>
1768
1769<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>3)
1770Double click the </span><b style='mso-bidi-font-weight:normal'><span
1771style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1772mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1773mso-bidi-theme-font:minor-latin'>Type</span></b><span style='mso-fareast-font-family:
1774"Times New Roman"'> column heading and select the </span><b style='mso-bidi-font-weight:
1775normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1776minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1777minor-latin;mso-bidi-theme-font:minor-latin'>Ga </span></b><span
1778style='mso-fareast-font-family:"Times New Roman"'>and</span><b
1779style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1780mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1781mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> P</span></b><span
1782style='mso-fareast-font-family:"Times New Roman"'> atom types<o:p></o:p></span></p>
1783
1784<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>4)
1785Under the menu </span><b style='mso-bidi-font-weight:normal'><span
1786style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1787mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1788mso-bidi-theme-font:minor-latin'>Edit Figure</span></b><span style='mso-fareast-font-family:
1789"Times New Roman"'> select </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'>Fill CN-sphere</span></b><span
1793style='mso-fareast-font-family:"Times New Roman"'>; the figure will be redrawn
1794with four O atoms about all Ga and P atoms.<o:p></o:p></span></p>
1795
1796<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1797mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_13" o:spid="_x0000_i1061"
1798 type="#_x0000_t75" style='width:5in;height:244.5pt;visibility:visible;
1799 mso-wrap-style:square'>
1800 <v:imagedata src="RMCProfile-IV_files/image025.png" o:title=""/>
1801</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=326
1802src="RMCProfile-IV_files/image026.gif" v:shapes="Picture_x0020_13"><![endif]></span><span
1803style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1804
1805<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1806we will explore this with <span class=GramE>a</span> RMCProfile simulation. To
1807keep this drawing, you may want to save the GSAS-II project.<o:p></o:p></span></p>
1808
1809<h2><span style='mso-fareast-font-family:"Times New Roman"'>Reverse Monte Carlo
1810Simulation of GaPO<sub>4<o:p></o:p></sub></span></h2>
1811
1812<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>RMCProfile
1813is most effective if a large box is used for the modelling; this requires very
1814long running times (10-20 <span class=SpellE>hrs</span> for GaPO<sub>4</sub>)
1815before a meaningful result is obtained. However, for the purposes of this
1816tutorial, we will be using a smaller box model that converges in a more
1817reasonable time (~10min). The result will clearly fit the data but the model is
1818too small to give enough atom displacements to be meaningful, however this
1819exercise will show you how to set up RMCProfile from within GSAS-II.<o:p></o:p></span></p>
1820
1821<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
1822start select the </span><b style='mso-bidi-font-weight:normal'><span
1823style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1824mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1825mso-bidi-theme-font:minor-latin'>Phases/GaPO4-X/RMC</span></b><span
1826style='mso-fareast-font-family:"Times New Roman"'> tab; if rmcprofile.exe is
1827within the GSASII directory the data window will show<o:p></o:p></span></p>
1828
1829<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1830mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_14" o:spid="_x0000_i1060"
1831 type="#_x0000_t75" style='width:358.5pt;height:253.5pt;visibility:visible;
1832 mso-wrap-style:square'>
1833 <v:imagedata src="RMCProfile-IV_files/image027.png" o:title=""/>
1834</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=338
1835src="RMCProfile-IV_files/image028.gif" v:shapes="Picture_x0020_14"><![endif]></span><span
1836style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1837
1838<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1839
1840<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>At
1841the top is a radio button selection for </span><b style='mso-bidi-font-weight:
1842normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1843minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1844minor-latin;mso-bidi-theme-font:minor-latin'>RMCProfile</span></b><span
1845style='mso-fareast-font-family:"Times New Roman"'> and </span><span
1846class=SpellE><b style='mso-bidi-font-weight:normal'><span style='font-family:
1847"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
1848"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>fullrmc</span></b></span><span
1849style='mso-fareast-font-family:"Times New Roman"'>. The latter is an
1850alternative big box modeling program (not working – under development);
1851RMCProfile is selected by default and all below are its setup controls. There
1852are four major sections (metadata, major controls, restraints &amp; constraints
1853and data controls); we will work through each of these in turn. The information
1854you enter here is retained in the GSAS-II project file so you can easily try
1855alternative setups without having to enter everything over again. <o:p></o:p></span></p>
1856
1857<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 1. Set
1858metadata items<o:p></o:p></span></h3>
1859
1860<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1861entries here are for your convenience; there is no explicit use made of any of
1862them, but they will appear in some of the output files from RMCProfile and of
1863course will show here on subsequent views of this window. Fill out as many of
1864them as you see fit. I entered some things for each as the defaults are
1865somewhat nonsensical.<o:p></o:p></span></p>
1866
1867<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1868mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_15" o:spid="_x0000_i1059"
1869 type="#_x0000_t75" style='width:5in;height:192pt;visibility:visible;
1870 mso-wrap-style:square'>
1871 <v:imagedata src="RMCProfile-IV_files/image115.png" o:title=""/>
1872</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=256
1873src="RMCProfile-IV_files/image029.gif" v:shapes="Picture_x0020_15"><![endif]></span><span
1874style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1875
1876<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Set general
1877controls<o:p></o:p></span></h3>
1878
1879<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The running
1880time is defaulted to </span><b style='mso-bidi-font-weight:normal'><span
1881style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1882mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1883mso-bidi-theme-font:minor-latin'>10</span></b><span style='mso-fareast-font-family:
1884"Times New Roman"'> minutes with a Save interval of </span><b style='mso-bidi-font-weight:
1885normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1886minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1887minor-latin;mso-bidi-theme-font:minor-latin'>1</span></b><span
1888style='mso-fareast-font-family:"Times New Roman"'> minute. At each save time a
1889number of files are written by RMCProfile; these can be viewed by using the
1890Operations/View command (more about this later – don’t bother trying it now,
1891there is nothing to see). For the purposes of this tutorial leave them at their
1892defaults. <o:p></o:p></span></p>
1893
1894<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
1895big box model used by RMCProfile is described as multiples of the unit cell
1896axes. In this case we want a 6x6x4 box so enter </span><b style='mso-bidi-font-weight:
1897normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1898minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1899minor-latin;mso-bidi-theme-font:minor-latin'>6</span></b><span
1900style='mso-fareast-font-family:"Times New Roman"'> for each of </span><b
1901style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1902mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1903mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X-axis</span></b><span
1904style='mso-fareast-font-family:"Times New Roman"'>, </span><b style='mso-bidi-font-weight:
1905normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
1906minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
1907minor-latin;mso-bidi-theme-font:minor-latin'>Y-axis</span></b><span
1908style='mso-fareast-font-family:"Times New Roman"'> and </span><b
1909style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1910mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1911mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>4</span></b><span
1912style='mso-fareast-font-family:"Times New Roman"'> for </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'>Z-axis</span></b><span
1916style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
1917
1918<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1919is to set the order of the atom types in the structure; this is used to
1920construct atom-atom distance restraints on the modelling. The order here (</span><b
1921style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1922mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1923mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ga, P, O</span></b><span
1924style='mso-fareast-font-family:"Times New Roman"'>) is appropriate; if changed
1925the window will repaint updating various entries possibly resetting some
1926entries to defaults. I suggest you decide the order now and then don’t change
1927it later. Set the maximum shift for Ga &amp; P to be </span><b
1928style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1929mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1930mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.05</span></b><span
1931style='mso-fareast-font-family:"Times New Roman"'> (the value for O is OK).
1932When done the window should look like<o:p></o:p></span></p>
1933
1934<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1935mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_16" o:spid="_x0000_i1058"
1936 type="#_x0000_t75" style='width:5in;height:254.25pt;visibility:visible;
1937 mso-wrap-style:square'>
1938 <v:imagedata src="RMCProfile-IV_files/image031.png" o:title=""/>
1939</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=339
1940src="RMCProfile-IV_files/image030.gif" v:shapes="Picture_x0020_16"><![endif]></span><span
1941style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1942
1943<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Skip
1944the next item (Atom swap probabilities). This is for cases in which atoms can
1945exchange sites.<o:p></o:p></span></p>
1946
1947<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Set
1948constraints/restraints<o:p></o:p></span></h3>
1949
1950<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
1951is to set the “Hard” minimum atom-atom separation and the allowed search rage
1952for each of 6 pairs of atom types. Possible values for this table can be
1953obtained in GSAS-II by computing bond lengths although we discovered a good set
1954in the RMCProfile-III tutorial; we will use these here. Suitable values are in
1955sequence for <span class=GramE>Hard</span> min and Search from: </span><b
1956style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1957mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1958mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>4.0, 2.6,
19591.2, 4.0, 1.2, 2.16</span></b><span style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
1960
1961<p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>The
1962<span class=SpellE>to</span></span></span><span style='mso-fareast-font-family:
1963"Times New Roman"'> items are: </span><b style='mso-bidi-font-weight:normal'><span
1964style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1965mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
1966mso-bidi-theme-font:minor-latin'>4.8, 3.4, 2. 4.8, 2.0, 0.0</span></b><span
1967style='mso-fareast-font-family:"Times New Roman"'>. When done the window should
1968look like<o:p></o:p></span></p>
1969
1970<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1971mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_17" o:spid="_x0000_i1057"
1972 type="#_x0000_t75" style='width:359.25pt;height:219pt;visibility:visible;
1973 mso-wrap-style:square'>
1974 <v:imagedata src="RMCProfile-IV_files/image118.png" o:title=""/>
1975</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=292
1976src="RMCProfile-IV_files/image032.gif" v:shapes="Picture_x0020_17"><![endif]></span><span
1977style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
1978
1979<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
1980
1981<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Scroll
1982down to find the section that has “Potential temperature”; these are for bond
1983and angle potentials. We will need 2 of each so press </span><b
1984style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
1985mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
1986mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Add</span></b><span
1987style='mso-fareast-font-family:"Times New Roman"'> (twice) for A-B stretch and </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"'> (again twice) for A-B-C
1992angle potentials; the window will refresh for each press so be patient while it
1993does this. Additional entries will be formed for each; when done the window
1994will look like<o:p></o:p></span></p>
1995
1996<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
1997mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1056" type="#_x0000_t75"
1998 style='width:358.5pt;height:218.25pt;visibility:visible;mso-wrap-style:square'>
1999 <v:imagedata src="RMCProfile-IV_files/image120.png" o:title=""/>
2000</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=291
2001src="RMCProfile-IV_files/image033.gif" v:shapes="_x0000_i1056"><![endif]></span><span
2002style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2003
2004<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We’re
2005wanting </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2006"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2007"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ga-O</span></b><span
2008style='mso-fareast-font-family:"Times New Roman"'> and </span><b
2009style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2010mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2011mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P-O</span></b><span
2012style='mso-fareast-font-family:"Times New Roman"'> stretch potentials 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'>O-Ga-O</span></b><span
2016style='mso-fareast-font-family:"Times New Roman"'> 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-P-O</span></b><span
2020style='mso-fareast-font-family:"Times New Roman"'> angle potentials. Select the
2021Atom-A, Atom-B and Atom-C appropriately to give<o:p></o:p></span></p>
2022
2023<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2024mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1055" type="#_x0000_t75"
2025 style='width:359.25pt;height:219pt;visibility:visible;mso-wrap-style:square'>
2026 <v:imagedata src="RMCProfile-IV_files/image122.png" o:title=""/>
2027</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=292
2028src="RMCProfile-IV_files/image034.gif" v:shapes="_x0000_i1055"><![endif]></span><span
2029style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2030
2031<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
2032enter appropriate Ga-O and P-O bond distances (</span><b style='mso-bidi-font-weight:
2033normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2034minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2035minor-latin;mso-bidi-theme-font:minor-latin'>1.81</span></b><span
2036style='mso-fareast-font-family:"Times New Roman"'> and </span><b
2037style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2038mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2039mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1.51</span></b><span
2040style='mso-fareast-font-family:"Times New Roman"'>) and O-Ga-O and O-P-O angles
2041(the ideal tetrahedral angle </span><b style='mso-bidi-font-weight:normal'><span
2042style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2043mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2044mso-bidi-theme-font:minor-latin'>109.5</span></b><span style='mso-fareast-font-family:
2045"Times New Roman"'>) and set all potentials to </span><b style='mso-bidi-font-weight:
2046normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2047minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2048minor-latin;mso-bidi-theme-font:minor-latin'>2.0</span></b><span
2049style='mso-fareast-font-family:"Times New Roman"'>. Set both search ranges to </span><b
2050style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2051mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2052mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>20</span></b><span
2053style='mso-fareast-font-family:"Times New Roman"'>%. When done you should see<o:p></o:p></span></p>
2054
2055<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2056mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_20" o:spid="_x0000_i1054"
2057 type="#_x0000_t75" style='width:359.25pt;height:219pt;visibility:visible;
2058 mso-wrap-style:square'>
2059 <v:imagedata src="RMCProfile-IV_files/image035.png" o:title=""/>
2060</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=292
2061src="RMCProfile-IV_files/image036.gif" v:shapes="Picture_x0020_20"><![endif]></span><span
2062style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2063
2064<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2065
2066<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 4. Select data
2067to be fitted<o:p></o:p></span></h3>
2068
2069<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We
2070will be using just x-ray data for GaPO<sub>4</sub> for fitting by RMCProfile. The
2071first step is the selection of the x-ray powder pattern (“Bragg”) for
2072processing. This is taken from the PWDR entry in the GSAS-II project and
2073accessed from the pulldown; there is only one “</span><b style='mso-bidi-font-weight:
2074normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2075minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2076minor-latin;mso-bidi-theme-font:minor-latin'>PWDR 105870-pe-GaPO4_ed.gsas Bank
20771</span></b><span style='mso-fareast-font-family:"Times New Roman"'>” that was
2078used earlier in your Rietveld refinement of GaPO<sub>4</sub>. If you had used
2079multiple banks in the Rietveld refinement, all would be shown in the pulldown,
2080but only one can be selected. Set the weight to </span><b style='mso-bidi-font-weight:
2081normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2082minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2083minor-latin;mso-bidi-theme-font:minor-latin'>100</span></b><span
2084style='mso-fareast-font-family:"Times New Roman"'> (NB: smaller numbers means a
2085heavier weight).<o:p></o:p></span></p>
2086
2087<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
2088press the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2089"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2090"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Select</span></b><span
2091style='mso-fareast-font-family:"Times New Roman"'> button for the “</span><span
2092class=SpellE><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'>Xray</span></b></span><b
2095style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2096mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2097mso-hansi-theme-font:minor-latin'> reciprocal space data: <span class=GramE>F(</span>Q)</span></b><span
2098style='mso-fareast-font-family:"Times New Roman"'>” line; a <span class=SpellE>FileDialog</span>
2099should appear. </span>Because you used <span style='mso-fareast-font-family:
2100Calibri;mso-fareast-theme-font:minor-latin'>the </span><b style='mso-bidi-font-weight:
2101normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2102minor-latin;mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin;
2103mso-hansi-theme-font:minor-latin'>Help/Download tutorial</span></b><span
2104style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
2105menu entry to open this page and downloaded the exercise files (recommended),
2106then the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2107"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2108Calibri;mso-fareast-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>RMCProfile-IV/data/...</span></b><span
2109style='mso-fareast-font-family:Calibri;mso-fareast-theme-font:minor-latin'>
2110entry will bring you to the location where the files have been downloaded. (It
2111is also possible to download them manually from <a
2112href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/">https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/RMCProfile-IV/data/</a>.
2113In this case you will need to navigate to the download location manually.)<o:p></o:p></span></p>
2114
2115<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The <span
2116class=SpellE>FileDialog</span> should show<o:p></o:p></span></p>
2117
2118<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2119mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1053" type="#_x0000_t75"
2120 style='width:356.25pt;height:124.5pt;visibility:visible;mso-wrap-style:square'>
2121 <v:imagedata src="RMCProfile-IV_files/image126.png" o:title=""/>
2122</v:shape><![endif]--><![if !vml]><img border=0 width=475 height=166
2123src="RMCProfile-IV_files/image037.gif" v:shapes="_x0000_i1053"><![endif]></span><span
2124style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2125
2126<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
2127</span><b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2128mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2129mso-hansi-theme-font:minor-latin'>gapo4_xray_rmc.fq</span></b><span
2130style='mso-fareast-font-family:"Times New Roman"'>; it will be copied to your
2131working directory. The window will be redrawn; set the weight to </span><b
2132style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2133mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2134mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.1</span></b><span
2135style='mso-fareast-font-family:"Times New Roman"'>. You should also check the </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'>Fit scale
2139factors?</span></b><span style='mso-fareast-font-family:"Times New Roman"'> <span
2140class=GramE>box</span>. When done the window should show<o:p></o:p></span></p>
2141
2142<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2143mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_22" o:spid="_x0000_i1052"
2144 type="#_x0000_t75" style='width:358.5pt;height:218.25pt;visibility:visible;
2145 mso-wrap-style:square'>
2146 <v:imagedata src="RMCProfile-IV_files/image038.png" o:title=""/>
2147</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=291
2148src="RMCProfile-IV_files/image039.gif" v:shapes="Picture_x0020_22"><![endif]></span><span
2149style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2150
2151<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You
2152should do a </span><b style='mso-bidi-font-weight:normal'><span
2153style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2154mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2155mso-bidi-theme-font:minor-latin'>Save project</span></b><span style='mso-fareast-font-family:
2156"Times New Roman"'> here.<o:p></o:p></span></p>
2157
2158<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Setup
2159RMCProfile files<o:p></o:p></span></h3>
2160
2161<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You
2162are now ready to setup the RMCProfile input files. Do </span><b
2163style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2164mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2165mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Setup
2166RMC</span></b><span style='mso-fareast-font-family:"Times New Roman"'> from the
2167menu; the console should report that files were written<o:p></o:p></span></p>
2168
2169<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2170mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1051" type="#_x0000_t75"
2171 style='width:358.5pt;height:90pt;visibility:visible;mso-wrap-style:square'>
2172 <v:imagedata src="RMCProfile-IV_files/image040.png" o:title=""/>
2173</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=120
2174src="RMCProfile-IV_files/image041.gif" v:shapes="_x0000_i1051"><![endif]></span><span
2175style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2176
2177<p class=MsoNormal><span class=GramE><span style='mso-fareast-font-family:"Times New Roman"'>and</span></span><span
2178style='mso-fareast-font-family:"Times New Roman"'> your local directory should
2179now have at least these 9 files<o:p></o:p></span></p>
2180
2181<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2182mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_24" o:spid="_x0000_i1050"
2183 type="#_x0000_t75" style='width:359.25pt;height:234.75pt;visibility:visible;
2184 mso-wrap-style:square'>
2185 <v:imagedata src="RMCProfile-IV_files/image042.png" o:title=""/>
2186</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=313
2187src="RMCProfile-IV_files/image044.gif" v:shapes="Picture_x0020_24"><![endif]></span><span
2188style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2189
2190<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>These
2191text files contain data needed by RMCProfile for the fitting of GaPO<sub>4</sub>.
2192They are:<o:p></o:p></span></p>
2193
2194<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2195style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.back</span></b><span
2196style='mso-fareast-font-family:"Times New Roman"'>- the 6 coefficients for the
2197chebyschev-1 function needed to compute the background for the Bragg pattern<o:p></o:p></span></p>
2198
2199<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2200style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.bragg</span></b><span
2201style='mso-fareast-font-family:"Times New Roman"'> – the powder pattern used in
2202the Rietveld refinement<o:p></o:p></span></p>
2203
2204<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2205style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.dat</span></b><span
2206style='mso-fareast-font-family:"Times New Roman"'> – the RMCProfile controls
2207file; described in full in the RMCProfile User Manual. It can be edited if need
2208be, but remember it is rewritten each time Operations/Setup RMC is done.<o:p></o:p></span></p>
2209
2210<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2211style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.inst</span></b><span
2212style='mso-fareast-font-family:"Times New Roman"'> – the instrument parameter
2213coefficients for the x-ray peak shape function used by GSAS-II and implemented
2214in RMCProfile for computing the Bragg pattern.<o:p></o:p></span></p>
2215
2216<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
2217style='mso-fareast-font-family:"Times New Roman"'>GaPO4-X.rmc6f</span></b><span
2218style='mso-fareast-font-family:"Times New Roman"'> – the big box set of atom
2219positions. It is normally not rewritten when Operations/Setup RMC is done
2220unless the X-axis, Y-axis, or Z-axis lattice multipliers are changed. Most
2221important is that it will contain the set of big box atom positions as updated
2222by RMCProfile according to the Save interval (every 1 min in this case).<o:p></o:p></span></p>
2223
2224<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>You
2225are now ready to run RMCProfile.<o:p></o:p></span></p>
2226
2227<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Run
2228RMCProfile<o:p></o:p></span></h3>
2229
2230<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
2231run RMCProfile from inside GSAS-II, do </span><b style='mso-bidi-font-weight:
2232normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2233minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2234minor-latin;mso-bidi-theme-font:minor-latin'>Operations/Execute</span></b><span
2235style='mso-fareast-font-family:"Times New Roman"'>. You will first see a “nag”
2236note asking you to cite the publication describing RMCProfile; press </span><b
2237style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2238mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2239mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>OK</span></b><span
2240style='mso-fareast-font-family:"Times New Roman"'>. The program will start in a
2241new console window – processing will initially be pretty fast for this case and
2242then slow down as the modelling proceeds. It reports Time used and <span
2243class=GramE>Last</span> saved. Once the latter is nonzero you can view
2244intermediate results to see its progress.<o:p></o:p></span></p>
2245
2246<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2247mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_58" o:spid="_x0000_i1049"
2248 type="#_x0000_t75" style='width:358.5pt;height:187.5pt;visibility:visible;
2249 mso-wrap-style:square'>
2250 <v:imagedata src="RMCProfile-IV_files/image127.png" o:title=""/>
2251</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=250
2252src="RMCProfile-IV_files/image046.gif" v:shapes="Picture_x0020_58"><![endif]></span><span
2253style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2254
2255<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I
2256have captured the initial RMCProfile console output (done by simply clicking
2257anywhere in the window – note the white square. This temporarily stops
2258processing; it can be restarted by pressing any key with the focus on the
2259window). Things to look at are the several chi^2 values; there will be an
2260overall one and one for each of the 3 data sets used in the fitting. The last
2261one “X-ray real-space” is generated within RMCProfile by doing the Fourier
2262transform from the F(Q) input data to form the x-ray g(R) distribution (e.g.
2263the x-ray PDF). Since we’ve set the Fit scale factors option; the “<span
2264class=SpellE>Renorm</span>” values are other than unity. These will approach
22651.0 as the modelling continues. There is also a value for Bond energy
2266calculated from the bonds and angles subject to the potential energy
2267restraints. Do not be surprised if this value rises while RMCProfile runs; that
2268is simply a reflection of the distortions found in this structure. It will peak
2269at about the 4-5 min mark and then decrease after that. Note that you can exit
2270GSAS-II and RMCProfile will continue running. When it finished the console
2271shows (in part)<o:p></o:p></span></p>
2272
2273<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2274mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_59" o:spid="_x0000_i1048"
2275 type="#_x0000_t75" style='width:357.75pt;height:224.25pt;visibility:visible;
2276 mso-wrap-style:square'>
2277 <v:imagedata src="RMCProfile-IV_files/image129.png" o:title=""/>
2278</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=299
2279src="RMCProfile-IV_files/image047.gif" v:shapes="Picture_x0020_59"><![endif]></span><span
2280style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2281
2282<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
2283chi^2 values are now close to unity and not very different from each other;
2284this is what is desired. The bond energy started out at ~8700, peaked at
2285~14,000 and now is ~11,500; this is the effect of the distortions found by
2286RMCProfile.<o:p></o:p></span></p>
2287
2288<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2289
2290<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>After
2291RMCProfile finishes note that the project directory now has ~35 files many of
2292which are just temporary ones created by RMCProfile. We will be looking at just
2293the *.csv files and the GaPO4.rmcf6 file; the latter contains the last atom
2294configuration acceptable by RMCProfile thus representing a best disordered
2295model.<o:p></o:p></span></p>
2296
2297<h3><span style='mso-fareast-font-family:"Times New Roman"'>A note about
2298weights:<o:p></o:p></span></h3>
2299
2300<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The
2301choice of weights for RMCProfile may seem to be arbitrary in these exercises,
2302but I have selected them so that each of the chi^2 values converge to be
2303roughly equal and somewhere near unity. This selection generally gives the best
2304performance in the reverse Monte Carlo calculation and requires some “trial
2305&amp; effort” in selecting the values. If one of the chi^2 values is too large
2306(&gt;&gt;1, i.e. weight too small) at convergence, then adjustments in the
2307structure will have been dominated by moves that lower that chi^2 sometimes at
2308the expense of others. Conversely, if one chi^2 is too small (&gt;&gt;1, i.e.
2309weight too large) then moves will tend to satisfy the others and there will be
2310little sensitivity to that data set. In this case my chosen weights have
2311yielded chi^2 values between 0.5 and 2.0; this is essentially ideal. If they
2312vary by more than an order of magnitude or are much greater or less than unity,
2313you should adjust the weights.<o:p></o:p></span></p>
2314
2315<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Viewing
2316results from RMCProfile<o:p></o:p></span></h3>
2317
2318<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Do </span><b
2319style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2320mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2321mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Operations/View</span></b><span
2322style='mso-fareast-font-family:"Times New Roman"'>; a <span class=SpellE>FileDialog</span>
2323showing only *.csv files will appear<o:p></o:p></span></p>
2324
2325<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2326mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_60" o:spid="_x0000_i1047"
2327 type="#_x0000_t75" style='width:468pt;height:165pt;visibility:visible;
2328 mso-wrap-style:square'>
2329 <v:imagedata src="RMCProfile-IV_files/image131.png" o:title=""/>
2330</v:shape><![endif]--><![if !vml]><img border=0 width=624 height=220
2331src="RMCProfile-IV_files/image048.gif" v:shapes="Picture_x0020_60"><![endif]></span><span
2332style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2333
2334<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>They
2335all should have the same prefix in their name, “GaPO4-X” which is the phase
2336name from the GSAS-II project file. Select any one of them – it doesn’t matter.
2337All of them will be read and their contents displayed as individual plots. For
2338example the chi^2 plot shows the progress of the RMCProfile fit<o:p></o:p></span></p>
2339
2340<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2341mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_61" o:spid="_x0000_i1046"
2342 type="#_x0000_t75" style='width:357pt;height:303pt;visibility:visible;
2343 mso-wrap-style:square'>
2344 <v:imagedata src="RMCProfile-IV_files/image133.png" o:title=""/>
2345</v:shape><![endif]--><![if !vml]><img border=0 width=476 height=404
2346src="RMCProfile-IV_files/image049.gif" v:shapes="Picture_x0020_61"><![endif]></span><span
2347style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2348
2349<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>If
2350you zoom into the end of the run, you can see that RMCProfile is still
2351improving the fit slowly even after 10 minutes of running.<o:p></o:p></span></p>
2352
2353<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2354
2355<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2356mso-no-proof:yes'>Comparing the Bragg plot with the PWDR plot shows that the
2357RMCProfile fit is very similar to the Rietveld fit<o:p></o:p></span></p>
2358
2359<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2360mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1045" type="#_x0000_t75"
2361 style='width:360.75pt;height:382.5pt;visibility:visible;mso-wrap-style:square'>
2362 <v:imagedata src="RMCProfile-IV_files/image055.png" o:title=""/>
2363</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=510
2364src="RMCProfile-IV_files/image050.gif" v:shapes="_x0000_i1045"><![endif]></span><span
2365style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2366
2367<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2368plot was made by dragging one plot tab to the bottom of the screen to create
2369the second frame. <o:p></o:p></span></p>
2370
2371<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2372mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_62" o:spid="_x0000_i1044"
2373 type="#_x0000_t75" style='width:359.25pt;height:307.5pt;visibility:visible;
2374 mso-wrap-style:square'>
2375 <v:imagedata src="RMCProfile-IV_files/image136.png" o:title=""/>
2376</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=410
2377src="RMCProfile-IV_files/image051.gif" v:shapes="Picture_x0020_62"><![endif]></span><span
2378style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2379
2380<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>A consideration
2381of the reciprocal space F(Q) (top) and the x-ray real space g(R) (bottom) plots
2382show reasonable agreement between the RMCProfile model and the data (but not
2383quite as good as we obtained in the RMCProfile-III tutorial – probably an
2384effect of imposing the potential energy restraints.<o:p></o:p></span></p>
2385
2386<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>The bonds
2387and angles subject to potential energy restraints are plotted<o:p></o:p></span></p>
2388
2389<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2390mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_64" o:spid="_x0000_i1043"
2391 type="#_x0000_t75" style='width:357.75pt;height:306pt;visibility:visible;
2392 mso-wrap-style:square'>
2393 <v:imagedata src="RMCProfile-IV_files/image138.png" o:title=""/>
2394</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=408
2395src="RMCProfile-IV_files/image052.gif" v:shapes="Picture_x0020_64"><![endif]></span><span
2396style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2397
2398<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I’ve
2399adjusted the scales to give a better view of the different bond lengths.<o:p></o:p></span></p>
2400
2401<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2402mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_65" o:spid="_x0000_i1042"
2403 type="#_x0000_t75" style='width:359.25pt;height:307.5pt;visibility:visible;
2404 mso-wrap-style:square'>
2405 <v:imagedata src="RMCProfile-IV_files/image140.png" o:title=""/>
2406</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=410
2407src="RMCProfile-IV_files/image053.gif" v:shapes="Picture_x0020_65"><![endif]></span><span
2408style='mso-fareast-font-family:"Times New Roman"'><span
2409style='mso-spacerun:yes'> </span><o:p></o:p></span></p>
2410
2411<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2412
2413<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>On
2414the other hand, the bond angles are essentially the same as the ideal
2415tetrahedral angle but with considerable spread (close to +/- 10 <span
2416class=SpellE>deg</span>).<o:p></o:p></span></p>
2417
2418<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Finally,
2419note that the console gave mean values for the bonds and angles that were
2420restrained by <span class=GramE>potential</span> energy functions.<o:p></o:p></span></p>
2421
2422<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2423mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_63" o:spid="_x0000_i1041"
2424 type="#_x0000_t75" style='width:311.25pt;height:147.75pt;visibility:visible;
2425 mso-wrap-style:square'>
2426 <v:imagedata src="RMCProfile-IV_files/image142.png" o:title=""/>
2427</v:shape><![endif]--><![if !vml]><img border=0 width=415 height=197
2428src="RMCProfile-IV_files/image054.gif" v:shapes="Picture_x0020_63"><![endif]></span><span
2429style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2430
2431<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>These
2432agree pretty well with our supposed values entered for these restraints. If our
2433guesses were wrong then there would be a shift; one can then enter the new
2434values, redo Operations/Setup RMC and then repeat Operation/Execute to rerun
2435RMCProfile which would start where the previous run stopped.<o:p></o:p></span></p>
2436
2437<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 9. View the
2438big box structural model for GaPO4<o:p></o:p></span></h3>
2439
2440<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next,
2441we can view the resulting big box structure. Do </span><b style='mso-bidi-font-weight:
2442normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2443minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2444minor-latin;mso-bidi-theme-font:minor-latin'>Import/Phase/from RMCProfile
2445.rmc6f file</span></b><span style='mso-fareast-font-family:"Times New Roman"'>;
2446a <span class=SpellE>FileDialog</span> box with one entry will show the
2447required file, </span><b style='mso-bidi-font-weight:normal'><span
2448style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2449mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2450mso-bidi-theme-font:minor-latin'>GaPO4-X.rmc6f</span></b><span
2451style='mso-fareast-font-family:"Times New Roman"'>. You will first see a </span><span
2452class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family:
2453"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2454"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Is</span></b></span><b
2455style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2456mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2457mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'> this the
2458file you want</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
2459popup window; select </span><b style='mso-bidi-font-weight:normal'><span
2460style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2461mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2462mso-bidi-theme-font:minor-latin'>Yes</span></b><span style='mso-fareast-font-family:
2463"Times New Roman"'>. Next will be an </span><b style='mso-bidi-font-weight:
2464normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2465minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2466minor-latin;mso-bidi-theme-font:minor-latin'>Edit phase name</span></b><span
2467style='mso-fareast-font-family:"Times New Roman"'> popup. The proposed name is
2468the same as the existing one; GSAS-II will rename this one by adding ‘_1’ to
2469the end. Next will be a popup for </span><b style='mso-bidi-font-weight:normal'><span
2470style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2471mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2472mso-bidi-theme-font:minor-latin'>Add histograms</span></b><span
2473style='mso-fareast-font-family:"Times New Roman"'>; respond </span><b
2474style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2475mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2476mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Cancel</span></b><span
2477style='mso-fareast-font-family:"Times New Roman"'> because you don’t want this
2478phase to be in any subsequent Rietveld refinement. Looking at the </span><b
2479style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2480mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2481mso-hansi-theme-font:minor-latin'>General</span></b><span style='mso-fareast-font-family:
2482"Times New Roman"'> tab for this phase we see it is 6X in <span class=GramE>a
2483&amp;</span> b and 4X in c axes relative to the original and has no symmetry
2484(space group P 1).<o:p></o:p></span></p>
2485
2486<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2487mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_66" o:spid="_x0000_i1040"
2488 type="#_x0000_t75" style='width:359.25pt;height:183pt;visibility:visible;
2489 mso-wrap-style:square'>
2490 <v:imagedata src="RMCProfile-IV_files/image144.png" o:title=""/>
2491</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=244
2492src="RMCProfile-IV_files/image056.gif" v:shapes="Picture_x0020_66"><![endif]></span><span
2493style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2494
2495<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
2496the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2497"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2498"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
2499Atoms</span></b><span style='mso-fareast-font-family:"Times New Roman"'> tab for
2500this phase; a van der Waals ball model will be drawn. You can select the </span><b
2501style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2502mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2503mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ga &amp; P</span></b><span
2504style='mso-fareast-font-family:"Times New Roman"'> atoms &amp; fill 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'>CN-sphere</span></b><span
2508style='mso-fareast-font-family:"Times New Roman"'> for them (does take a long
2509time, &gt;10min – be patient) and then change all the atoms to ball and stick
2510style. The CN-sphere filling works because the RMCProfile structure still has
2511translational symmetry across its 6x6x4 lattice. You should see something like<o:p></o:p></span></p>
2512
2513<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2514mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1039" type="#_x0000_t75"
2515 style='width:360.75pt;height:382.5pt;visibility:visible;mso-wrap-style:square'>
2516 <v:imagedata src="RMCProfile-IV_files/image071.png" o:title=""/>
2517</v:shape><![endif]--><![if !vml]><img border=0 width=481 height=510
2518src="RMCProfile-IV_files/image057.gif" v:shapes="_x0000_i1039"><![endif]></span><span
2519style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2520
2521<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Notice
2522the apparent tilting the PO<sub>4</sub> and GaO<sub>4</sub> tetrahedra. The
2523stray O atoms are bound to PO<sub>4</sub> and GaO<sub>4</sub> tetrahedra in
2524neighboring boxes. <o:p></o:p></span></p>
2525
2526<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2527
2528<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>NB:
2529this import facility can be used to load any rmc6f file, e.g. from a RMCProfile
2530run done outside of GSAS-II; all the plotting and tools in this and the
2531following steps are available for these big box models.<o:p></o:p></span></p>
2532
2533<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 10. View the
2534disordered average structure<o:p></o:p></span></h3>
2535
2536<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>We
2537can compress the big box result back into the original average crystal
2538structure to see how the disordered sites compare with the average ones. Select
2539the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2540"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2541"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>General</span></b><span
2542style='mso-fareast-font-family:"Times New Roman"'> tab for the big box phase
2543(SF6_1) and then do </span><b style='mso-bidi-font-weight:normal'><span
2544style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2545mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2546mso-bidi-theme-font:minor-latin'>Compute/Transform</span></b><span
2547style='mso-fareast-font-family:"Times New Roman"'>. A popup dialog will appear<o:p></o:p></span></p>
2548
2549<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2550mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_67" o:spid="_x0000_i1038"
2551 type="#_x0000_t75" style='width:282pt;height:322.5pt;visibility:visible;
2552 mso-wrap-style:square'>
2553 <v:imagedata src="RMCProfile-IV_files/image147.png" o:title=""/>
2554</v:shape><![endif]--><![if !vml]><img border=0 width=376 height=430
2555src="RMCProfile-IV_files/image058.gif" v:shapes="Picture_x0020_67"><![endif]></span><span
2556style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2557
2558<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2559is the general tool inside GSAS-II for all sorts of structure transformations.
2560Here we will use it to push all the big box atoms back into the average
2561structure unit cell. Recalling that the big box model is 6x6x4 the original
2562unit cell, we simply want to reverse the process. Enter </span><b
2563style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2564mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2565mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>1/6, 1/6<span
2566class=GramE>,1</span>/4</span></b><span style='mso-fareast-font-family:"Times New Roman"'>
2567into the diagonal elements of the M matrix. The GUI will convert them to the
2568decimal equivalent (0.167<span class=GramE>,…</span>). The target space group
2569should be P 1. You should see<o:p></o:p></span></p>
2570
2571<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2572mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="_x0000_i1037" type="#_x0000_t75"
2573 style='width:282pt;height:322.5pt;visibility:visible;mso-wrap-style:square'>
2574 <v:imagedata src="RMCProfile-IV_files/image075.png" o:title=""/>
2575</v:shape><![endif]--><![if !vml]><img border=0 width=376 height=430
2576src="RMCProfile-IV_files/image059.gif" v:shapes="_x0000_i1037"><![endif]></span><span
2577style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2578
2579<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Press
2580</span><b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2581mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2582mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Ok</span></b><span
2583style='mso-fareast-font-family:"Times New Roman"'> to do the transformation. A
2584new phase, “GaPO4-X_1 <span class=SpellE>abc</span>” will be formed as
2585triclinic with cell axes that match the original hexagonal ones. Select </span><b
2586style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2587mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2588mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw Atoms</span></b><span
2589style='mso-fareast-font-family:"Times New Roman"'>; a van der Waals model will
2590appear.<o:p></o:p></span></p>
2591
2592<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2593mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_75" o:spid="_x0000_i1036"
2594 type="#_x0000_t75" style='width:358.5pt;height:380.25pt;visibility:visible;
2595 mso-wrap-style:square'>
2596 <v:imagedata src="RMCProfile-IV_files/image077.png" o:title=""/>
2597</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=507
2598src="RMCProfile-IV_files/image060.gif" v:shapes="Picture_x0020_75"><![endif]></span><span
2599style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2600
2601<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Select
2602the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2603"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2604"Times New Roman";mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Draw
2605Options</span></b><span style='mso-fareast-font-family:"Times New Roman"'> tab
2606and reduce the </span><b style='mso-bidi-font-weight:normal'><span
2607style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2608mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2609mso-bidi-theme-font:minor-latin'>van der Waals scale</span></b><span
2610style='mso-fareast-font-family:"Times New Roman"'> to about </span><b
2611style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2612mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2613mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.05</span></b><span
2614style='mso-fareast-font-family:"Times New Roman"'>.<o:p></o:p></span></p>
2615
2616<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2617mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_68" o:spid="_x0000_i1035"
2618 type="#_x0000_t75" style='width:358.5pt;height:306.75pt;visibility:visible;
2619 mso-wrap-style:square'>
2620 <v:imagedata src="RMCProfile-IV_files/image151.png" o:title=""/>
2621</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=409
2622src="RMCProfile-IV_files/image061.gif" v:shapes="Picture_x0020_68"><![endif]></span><span
2623style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2624
2625<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2626compares pretty well with the original structure with the ellipsoids drawn at
262799% probability. If anything the spread in atom positions is less that what was
2628obtained in the RMCProfile-III tutorial; an effect of the potential energy
2629restraints.<o:p></o:p></span></p>
2630
2631<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2632mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_77" o:spid="_x0000_i1034"
2633 type="#_x0000_t75" style='width:359.25pt;height:381pt;visibility:visible;
2634 mso-wrap-style:square'>
2635 <v:imagedata src="RMCProfile-IV_files/image081.png" o:title=""/>
2636</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=508
2637src="RMCProfile-IV_files/image062.gif" v:shapes="Picture_x0020_77"><![endif]></span><span
2638style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2639
2640<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>However,
2641the O atoms are more widely distributed in space than the P or Ga atoms.<o:p></o:p></span></p>
2642
2643<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2644
2645<h3><span style='mso-fareast-font-family:"Times New Roman"'>Step 11. Polyhedral
2646comparison for the big box model<o:p></o:p></span></h3>
2647
2648<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
2649this step we will examine how the suite of PO<sub>4</sub> and GaO<sub>4</sub>
2650tetrahedra deviate from an ideal tetrahedron. This analysis is currently
2651restricted to structures with P1 space group symmetry; this is what we have
2652from Step 9 above. Select </span><b style='mso-bidi-font-weight:normal'><span
2653style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2654mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2655mso-bidi-theme-font:minor-latin'>Phases/GaPO4-X_1</span></b><span
2656style='mso-fareast-font-family:"Times New Roman"'> from the data tree; the
2657General tab will appear.<o:p></o:p></span></p>
2658
2659<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2660mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_78" o:spid="_x0000_i1033"
2661 type="#_x0000_t75" style='width:5in;height:192.75pt;visibility:visible;
2662 mso-wrap-style:square'>
2663 <v:imagedata src="RMCProfile-IV_files/image083.png" o:title=""/>
2664</v:shape><![endif]--><![if !vml]><img border=0 width=480 height=257
2665src="RMCProfile-IV_files/image063.gif" v:shapes="Picture_x0020_78"><![endif]></span><span
2666style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2667
2668<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>What
2669we want is at the bottom of this panel; scroll down to the bottom<o:p></o:p></span></p>
2670
2671<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2672mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_79" o:spid="_x0000_i1032"
2673 type="#_x0000_t75" style='width:357pt;height:190.5pt;visibility:visible;
2674 mso-wrap-style:square'>
2675 <v:imagedata src="RMCProfile-IV_files/image085.png" o:title=""/>
2676</v:shape><![endif]--><![if !vml]><img border=0 width=476 height=254
2677src="RMCProfile-IV_files/image064.gif" v:shapes="Picture_x0020_79"><![endif]></span><span
2678style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2679
2680<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>At
2681the very bottom is the control for polyhedral comparison. All that is needed is
2682to select the central atom (“</span><b style='mso-bidi-font-weight:normal'><span
2683style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2684mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2685mso-bidi-theme-font:minor-latin'>origin atom type</span></b><span
2686style='mso-fareast-font-family:"Times New Roman"'>”) and the polyhedral
2687vertices (“</span><b style='mso-bidi-font-weight:normal'><span
2688style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2689mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2690mso-bidi-theme-font:minor-latin'>target atom type</span></b><span
2691style='mso-fareast-font-family:"Times New Roman"'>”). Select </span><b
2692style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2693mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2694mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>P</span></b><span
2695style='mso-fareast-font-family:"Times New Roman"'> for the former and </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'>O</span></b><span
2699style='mso-fareast-font-family:"Times New Roman"'> for the latter. Then do </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'>Compute/Compare</span></b><span
2703style='mso-fareast-font-family:"Times New Roman"'> from the menu; a popup for
2704setting Distance Angle Controls will appear<o:p></o:p></span></p>
2705
2706<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2707mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_80" o:spid="_x0000_i1031"
2708 type="#_x0000_t75" style='width:206.25pt;height:196.5pt;visibility:visible;
2709 mso-wrap-style:square'>
2710 <v:imagedata src="RMCProfile-IV_files/image087.png" o:title=""/>
2711</v:shape><![endif]--><![if !vml]><img border=0 width=275 height=262
2712src="RMCProfile-IV_files/image065.gif" v:shapes="Picture_x0020_80"><![endif]></span><span
2713style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2714
2715<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>In
2716some cases the bond search factor may need to be adjusted to get the right
2717number of vertices for the <span class=SpellE>polyhedra</span>; in this case </span><b
2718style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2719mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2720mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>0.85</span></b><span
2721style='mso-fareast-font-family:"Times New Roman"'> is fine (NB: in this use the
2722angle ranges are ignored). Press </span><b style='mso-bidi-font-weight:normal'><span
2723style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2724mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2725mso-bidi-theme-font:minor-latin'>OK</span></b><span style='mso-fareast-font-family:
2726"Times New Roman"'>; a progress bar will show the atoms being processed. The
2727console may show some atoms being skipped because the number of vertices wasn’t
2728either 4 (tetrahedron) or 6 (octahedron); all but one are ok here. Because
2729there are 432 P atoms to be looked at in this big box model, this calculation
2730can take a number of minutes. The General tab reappears already scrolled to the
2731bottom<o:p></o:p></span></p>
2732
2733<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2734mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_39" o:spid="_x0000_i1030"
2735 type="#_x0000_t75" style='width:363pt;height:185.25pt;visibility:visible;
2736 mso-wrap-style:square'>
2737 <v:imagedata src="RMCProfile-IV_files/image089.png" o:title=""/>
2738</v:shape><![endif]--><![if !vml]><img border=0 width=484 height=247
2739src="RMCProfile-IV_files/image066.gif" v:shapes="Picture_x0020_39"><![endif]></span><span
2740style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2741
2742<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>A
2743new button (</span><b style='mso-bidi-font-weight:normal'><span
2744style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2745mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2746mso-bidi-theme-font:minor-latin'>Show Plots?</span></b><span style='mso-fareast-font-family:
2747"Times New Roman"'>) has appeared after the atom selections; press it. A number
2748of new entries will appear on the plot window; we will discuss each in turn.
2749Select the </span><b style='mso-bidi-font-weight:normal'><span
2750style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2751mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2752mso-bidi-theme-font:minor-latin'>Tet P-O Bond for GaPO4-X_1</span></b><span
2753style='mso-fareast-font-family:"Times New Roman"'> tab<o:p></o:p></span></p>
2754
2755<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2756mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_69" o:spid="_x0000_i1029"
2757 type="#_x0000_t75" style='width:358.5pt;height:306.75pt;visibility:visible;
2758 mso-wrap-style:square'>
2759 <v:imagedata src="RMCProfile-IV_files/image158.png" o:title=""/>
2760</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=409
2761src="RMCProfile-IV_files/image067.gif" v:shapes="Picture_x0020_69"><![endif]></span><span
2762style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2763
2764<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2765gives the distribution of the average P-O bond lengths for all the tetrahedra
2766found across the big box model. It is rough because of the small size of the
2767model, but the asymmetry seen in the RMCProfile-III is not present in this P-O
2768bond distribution. The console will have listed the average value with the
2769standard uncertainty in parentheses. <o:p></o:p></span></p>
2770
2771<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2772mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_71" o:spid="_x0000_i1028"
2773 type="#_x0000_t75" style='width:358.5pt;height:90.75pt;visibility:visible;
2774 mso-wrap-style:square'>
2775 <v:imagedata src="RMCProfile-IV_files/image160.png" o:title=""/>
2776</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=121
2777src="RMCProfile-IV_files/image068.gif" v:shapes="Picture_x0020_71"><![endif]></span><span
2778style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2779
2780<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Next
2781select the </span><b style='mso-bidi-font-weight:normal'><span
2782style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
2783mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:minor-latin;
2784mso-bidi-theme-font:minor-latin'>Tet P-O Tilts for GaPO4-X_1</span></b><span
2785style='mso-fareast-font-family:"Times New Roman"'>tab<o:p></o:p></span></p>
2786
2787<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman";
2788mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_72" o:spid="_x0000_i1027"
2789 type="#_x0000_t75" style='width:358.5pt;height:306.75pt;visibility:visible;
2790 mso-wrap-style:square'>
2791 <v:imagedata src="RMCProfile-IV_files/image162.png" o:title=""/>
2792</v:shape><![endif]--><![if !vml]><img border=0 width=478 height=409
2793src="RMCProfile-IV_files/image069.gif" v:shapes="Picture_x0020_72"><![endif]></span><span
2794style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2795
2796<p class=MsoNormal style='tab-stops:344.95pt'><span style='mso-fareast-font-family:
2797"Times New Roman"'>This gives the distribution of axial tilts of the PO<sub>4</sub>
2798molecules from the reference tetrahedron (aligned along the Cartesian axes) and
2799is similar but tighter compared to that found in the RMCProfile-III tutorial.
2800There is an apparent split distribution centered at ~48 <span class=SpellE>deg</span>
2801and ~68 <span class=SpellE>deg</span> (the rather meaningless in this case
2802average tilt is also shown on the console). Next select </span><b
2803style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2804mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2805mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>X-Delta</span></b><span
2806style='mso-fareast-font-family:"Times New Roman"'>, </span><b style='mso-bidi-font-weight:
2807normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:
2808minor-latin;mso-fareast-font-family:"Times New Roman";mso-hansi-theme-font:
2809minor-latin;mso-bidi-theme-font:minor-latin'>Y-Delta</span></b><span
2810style='mso-fareast-font-family:"Times New Roman"'> and </span><b
2811style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2812mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2813mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>Z-Delta</span></b><span
2814style='mso-fareast-font-family:"Times New Roman"'> tabs in turn.<o:p></o:p></span></p>
2815
2816<p class=MsoNormal style='tab-stops:344.95pt'><span style='mso-fareast-font-family:
2817"Times New Roman";mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_73"
2818 o:spid="_x0000_i1026" type="#_x0000_t75" style='width:359.25pt;height:255.75pt;
2819 visibility:visible;mso-wrap-style:square'>
2820 <v:imagedata src="RMCProfile-IV_files/image164.png" o:title=""/>
2821</v:shape><![endif]--><![if !vml]><img border=0 width=479 height=341
2822src="RMCProfile-IV_files/image070.gif" v:shapes="Picture_x0020_73"><![endif]></span><span
2823style='mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>
2824
2825<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>I
2826have made this plot by dragging the respective plot tabs to one of the right
2827(or left) edges to create a 3 pane plot. These show the displacement of the O
2828atoms from the ideal tetrahedral vertices along each Cartesian axis. Here they
2829are arranged about the zeros fairly tightly; the apparent split in the </span><span
2830style='font-family:Symbol;mso-fareast-font-family:"Times New Roman"'>D</span><span
2831style='mso-fareast-font-family:"Times New Roman"'>Y plot may or may not be real.
2832If there were structural distortions to the tetrahedra (e.g. <span
2833class=SpellE>Jahn</span>-Teller distortions) these could show in these plots. <o:p></o:p></span></p>
2834
2835<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>To
2836do the same thing for Ga-O <span class=SpellE>polyhedra</span>, select </span><b
2837style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif;
2838mso-ascii-theme-font:minor-latin;mso-fareast-font-family:"Times New Roman";
2839mso-hansi-theme-font:minor-latin'>Ga</span></b><span style='mso-fareast-font-family:
2840"Times New Roman"'> instead of P for the origin type atom and then do </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'>Compute/Compare</span></b><span
2844style='mso-fareast-font-family:"Times New Roman"'>. Again there will be the </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'>Distance Angle Controls</span></b><span
2848style='mso-fareast-font-family:"Times New Roman"'> popup; no changes needed.
2849The calculation will again take several minutes to complete. When done press
2850the </span><b style='mso-bidi-font-weight:normal'><span style='font-family:
2851"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-fareast-font-family:
2852"Times New Roman";mso-hansi-theme-font:minor-latin'>Show plots?</span></b><span
2853style='mso-fareast-font-family:"Times New Roman"'> <span class=GramE>button</span>;
2854more plots will be added to the plot window. I show both sets of tetrahedral
2855bonds as a stacked plot; the Ga-O bonds are not skewed, either. <span
2856style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape id="Picture_x0020_74"
2857 o:spid="_x0000_i1025" type="#_x0000_t75" style='width:357.75pt;height:288.75pt;
2858 visibility:visible;mso-wrap-style:square'>
2859 <v:imagedata src="RMCProfile-IV_files/image166.png" o:title=""/>
2860</v:shape><![endif]--><![if !vml]><img border=0 width=477 height=385
2861src="RMCProfile-IV_files/image072.gif" v:shapes="Picture_x0020_74"><![endif]></span><o:p></o:p></span></p>
2862
2863<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Similar
2864comparisons can be made with the other plots. NB: if the project is now saved
2865all the data needed to reproduce the plots is also saved; any of them can be
2866seen without redoing the Compare calculation.<o:p></o:p></span></p>
2867
2868<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2869
2870<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>This
2871completes this RMCProfile tutorial; you should save the project.<o:p></o:p></span></p>
2872
2873<h2><span style='mso-fareast-font-family:"Times New Roman"'>Final note<o:p></o:p></span></h2>
2874
2875<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>A
2876production run with enough atoms to give decent statistics would be for a box
2877that is perhaps 12x12x8 the original unit cell and would require a 10-20 hour
2878run time. It would contain several thousand atoms instead of ~2600 as used
2879here. You can further explore this tutorial project by changing the bond and
2880angle potentials to see how that changes the RMCProfile result. In my case,
2881increasing all 4 to 20 from 2 tightened the Ga-O and P-O bond length distributions
2882but had no impact on the O-P-O and O-Ga-O angle distributions. The fit to the g(R)
2883is also poorer (much higher chi^2).<o:p></o:p></span></p>
2884
2885<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2886
2887<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p>&nbsp;</o:p></span></p>
2888
2889<p class=MsoNormal style='tab-stops:317.2pt'><span style='mso-fareast-font-family:
2890"Times New Roman"'><span style='mso-tab-count:1'>                                                                                                          </span><o:p></o:p></span></p>
2891
2892</div>
2893
2894</body>
2895
2896</html>
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