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| 3 | <title>EXPGUI Alumina Tutorial, part #5</title> |
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| 15 | <? |
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| 16 | include("/var/www/include/navigation.inc"); |
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| 17 | include("/var/www/include/utility.inc"); |
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| 18 | ?> |
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| 19 | <blockquote> |
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| 20 | |
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| 21 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 22 | <TR><TH><A Href="index.html">Intro</A> |
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| 23 | </TH><TH><A Href="alumina6.html">Next page</A> |
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| 24 | </TH><TH><A Href="alumina4.html">Previous page</A> |
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| 25 | </TH></TR></TABLE><BR CLEAR=ALL> |
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| 26 | |
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| 27 | |
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| 28 | <CENTER> |
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| 29 | <H1><HR noshade width="75%" size="2" align="center"> |
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| 30 | GSAS/EXPGUI Alumina tutorial (part 5)<BR> |
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| 31 | Initial Fitting: Refine Scale Factor and Background |
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| 32 | <HR noshade width="75%" size="2" align="center"> |
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| 33 | </H1> |
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| 34 | </CENTER> |
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| 35 | <I>At this point we are almost |
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| 36 | ready to start fitting parameters, but before we do that |
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| 37 | the POWPREF program must be run. In GSAS, each data point has a list |
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| 38 | of reflections that contribute to that data point. This assignment must |
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| 39 | be made in POWPREF before the least squares fit can be performed in the |
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| 40 | GSAS program GENLES. The program must also be rerun if a new phase or |
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| 41 | histogram is added to the refinement. POWPREF should also be rerun if the |
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| 42 | lattice constants or profile terms change significantly. |
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| 43 | </I> |
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| 44 | <P> |
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| 45 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 46 | We want to refine the background and the scale factor to get started. |
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| 47 | The scaling parameters are |
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| 48 | shown on the Scaling panel, shown below. |
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| 49 | GSAS offers us an overall scale factor for each histogram, plus a |
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| 50 | phase fraction scale factor for each phase. |
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| 51 | These two factors have exactly |
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| 52 | the same effect for a single-phase refinement, so only one can be used. |
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| 53 | By default, the scale factor refinement flag is turned on and the phase |
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| 54 | fraction is off. This is what we will use. |
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| 55 | <P><img alt="tutorial screen dump" src="5a.gif" align=RIGHT> |
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| 56 | <BR clear=all> |
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| 57 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 58 | The other change that we will make in the default refinement options |
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| 59 | is to lower the number of refinement cycles to 2. Also, make sure the "Extract |
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| 60 | F<sub>obs</sub>" check box on the least-squares pane is selected. |
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| 61 | <P><img alt="tutorial screen dump" src="5b.gif" align=RIGHT> |
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| 62 | <BR clear=all> |
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| 63 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 64 | |
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| 65 | We are now ready to start running programs. First run POWPREF by pressing |
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| 66 | the POWPREF button on the beige tool bar (or selecting the POWPREF option |
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| 67 | in the Powder menu list.) That causes a window, such as the one below to open |
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| 68 | as POWPREF runs. |
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| 69 | <P><img alt="tutorial screen dump" src="5c.gif" align=RIGHT><P> |
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| 70 | <BR clear=all> |
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| 71 | When POWPREF has completed, press the ENTER key to continue and the |
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| 72 | window should close. |
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| 73 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 74 | |
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| 75 | <P><img alt="tutorial screen dump" src="5d.gif" align=RIGHT><P> |
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| 76 | The POWPREF program makes changes to the experiment (.EXP) file and |
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| 77 | this is noted by EXPGUI by the display of the warning message to the right. |
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| 78 | At this point you do want to accept the changes made by POWPREF, so |
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| 79 | click "Load New" and EXPGUI will reread the revised file. |
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| 80 | <BR clear=all> |
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| 81 | <P><blockquote><I> |
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| 82 | By default, this window is shown every time the experiment file is |
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| 83 | modified by any GSAS program. This allows the file to be "rolled back" to |
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| 84 | the previous version, in case of a disastrous refinement run, by pressing |
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| 85 | "Continue with old." However, some EXPGUI users find it annoying to be asked |
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| 86 | this question all the time. In the EXPGUI Options menu, there is a menu item |
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| 87 | called "Autoload EXP". If the "Autoload EXP" option is checked, the |
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| 88 | experiment file will always be read automatically, but then it is no longer |
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| 89 | possible to roll back erroneous steps so easily. |
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| 90 | </I></blockquote> |
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| 91 | |
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| 92 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 93 | Note that the displayed history record has been updated to reflect the running |
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| 94 | of POWPREF. |
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| 95 | <P><img alt="tutorial screen dump" src="5e.gif" align=RIGHT> |
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| 96 | <BR clear=all> |
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| 97 | <P><HR noshade width="50%" size="4" align="center"><P> |
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| 98 | We can now initiate the refinement, by launching the GENLES program to |
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| 99 | optimize the scale factor and background parameters. The output from this |
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| 100 | run is shown below. |
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| 101 | <P><img alt="tutorial screen dump" src="5f.gif" align=RIGHT> |
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| 102 | <BR clear=all> |
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| 103 | After the refinement completes, press Enter to continue and then press "Load |
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| 104 | new" on the "Reload?" window. |
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| 105 | <P><blockquote><I> |
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| 106 | The output from the GENLES run shows several points worth noting. |
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| 107 | First note that the number of variables (varied parameters) is 7, |
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| 108 | from the scale factor plus the 6 background terms. Note that the |
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| 109 | initial weighted R-factor (wRp or Rwp) and Chi-squared values are |
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| 110 | 99% and 258, respectively but drop to 72% and 134, respectively after a cycle |
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| 111 | of refinement. In the first cycle of refinement, there are very large shifts |
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| 112 | in the parameters, but the parameters converge in the second cycle. |
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| 113 | This is noted by the sum[(shift/esd)**2] term which is 855 in the first cycle, |
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| 114 | but 0 in the second cycle. Note that shifts become insignificant when they are |
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| 115 | small with respect to the esd (standard uncertainty), so a value of 855 |
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| 116 | means that at least some of the parameters made very large shifts in the |
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| 117 | first cycle. Note that GSAS does not compute the R-factor or Chi-squared terms |
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| 118 | after the second refinement cycle. |
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| 119 | </I></blockquote> |
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| 120 | <HR> |
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| 121 | Previous: <A HREF="alumina4.html"> |
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| 122 | Change Background Function |
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| 123 | </A> |
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| 124 | <BR> |
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| 125 | Next step: <A HREF="alumina6.html"> |
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| 126 | Plotting the Initial Fit |
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| 127 | </A> |
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| 128 | |
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| 129 | <HR> |
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| 130 | </blockquote> |
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| 131 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
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| 132 | <font size=-1><? lastmod(); ?> |
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| 133 | <BR>$Revision: 684 $ $Date: 2009-12-04 23:10:17 +0000 (Fri, 04 Dec 2009) $</font> |
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| 134 | </body> |
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| 135 | </html> |
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