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1<html>
2<head>
3   <title>EXPGUI Alumina Tutorial, part #5</title>
4</head>
5
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15<?
16   include("/var/www/include/navigation.inc");
17   include("/var/www/include/utility.inc");
18?>
19<blockquote>
20
21<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
22<TR><TH><A  Href="index.html">Intro</A> 
23</TH><TH><A Href="alumina6.html">Next page</A>
24</TH><TH><A Href="alumina4.html">Previous page</A>
25</TH></TR></TABLE><BR CLEAR=ALL>
26
27
28<CENTER>
29<H1><HR noshade width="75%" size="2" align="center">
30GSAS/EXPGUI Alumina tutorial (part 5)<BR>
31Initial Fitting: Refine Scale Factor and Background
32<HR noshade width="75%" size="2" align="center">
33</H1>
34</CENTER>
35<I>At this point we are almost
36ready to start fitting parameters, but before we do that
37the POWPREF program must be run. In GSAS, each data point has a list
38of reflections that contribute to that data point. This assignment must
39be made in POWPREF before the least squares fit can be performed in the
40GSAS program GENLES. The program must also be rerun if a new phase or
41histogram is added to the refinement. POWPREF should also be rerun if the
42lattice constants or profile terms change significantly.
43</I>
44<P>
45<P><HR noshade width="50%" size="4" align="center"><P>
46We want to refine the background and the scale factor to get started.
47The scaling parameters are
48shown on the Scaling panel, shown below.
49GSAS offers us an overall scale factor for each histogram, plus a
50phase fraction scale factor for each phase.
51These two factors have exactly
52the same effect for a single-phase refinement, so only one can be used.
53By default, the scale factor refinement flag is turned on and the phase
54fraction is off. This is what we will use.
55<P><img alt="tutorial screen dump" src="5a.gif" align=RIGHT>
56<BR clear=all>
57<P><HR noshade width="50%" size="4" align="center"><P>
58The other change that we will make in the default refinement options
59is to lower the number of refinement cycles to 2. Also, make sure the "Extract
60F<sub>obs</sub>" check box on the least-squares pane is selected.
61<P><img alt="tutorial screen dump" src="5b.gif" align=RIGHT>
62<BR clear=all>
63<P><HR noshade width="50%" size="4" align="center"><P>
64
65We are now ready to start running programs. First run POWPREF by pressing
66the POWPREF button on the beige tool bar (or selecting the POWPREF option
67in the Powder menu list.) That causes a window, such as the one below to open
68as POWPREF runs.
69<P><img alt="tutorial screen dump" src="5c.gif" align=RIGHT><P>
70<BR clear=all>
71When POWPREF has completed, press the ENTER key to continue and the
72window should close.
73<P><HR noshade width="50%" size="4" align="center"><P>
74
75<P><img alt="tutorial screen dump" src="5d.gif" align=RIGHT><P>
76The POWPREF program makes changes to the experiment (.EXP) file and
77this is noted by EXPGUI by the display of the warning message to the right.
78At this point you do want to accept the changes made by POWPREF, so
79click "Load New" and EXPGUI will reread the revised file.
80<BR clear=all>
81<P><blockquote><I>
82By default, this window is shown every time the experiment file is
83modified by any GSAS program. This allows the file to be "rolled back" to
84the previous version, in case of a disastrous refinement run, by pressing
85"Continue with old." However, some EXPGUI users find it annoying to be asked
86this question all the time. In the EXPGUI Options menu, there is a menu item
87called "Autoload EXP". If the "Autoload EXP" option is checked, the
88experiment file will always be read automatically, but then it is no longer
89possible to roll back erroneous steps so easily.
90</I></blockquote>
91
92<P><HR noshade width="50%" size="4" align="center"><P>
93Note that the displayed history record has been updated to reflect the running
94of POWPREF.
95<P><img alt="tutorial screen dump" src="5e.gif" align=RIGHT>
96<BR clear=all>
97<P><HR noshade width="50%" size="4" align="center"><P>
98We can now initiate the refinement, by launching the GENLES program to
99optimize the scale factor and background parameters. The output from this
100run is shown below.
101<P><img alt="tutorial screen dump" src="5f.gif" align=RIGHT>
102<BR clear=all>
103After the refinement completes, press Enter to continue and then press "Load
104new" on the "Reload?" window.
105<P><blockquote><I>
106The output from the GENLES run shows several points worth noting.
107First note that the number of variables (varied parameters) is 7,
108from the scale factor plus the 6 background terms. Note that the
109initial weighted R-factor (wRp or Rwp) and Chi-squared values are
11099% and 258, respectively but drop to 72% and 134, respectively after a cycle
111of refinement. In the first cycle of refinement, there are very large shifts
112in the parameters, but the parameters converge in the second cycle.
113This is noted by the sum[(shift/esd)**2] term which is 855 in the first cycle,
114but 0 in the second cycle. Note that shifts become insignificant when they are
115small with respect to the esd (standard uncertainty), so a value of 855
116means that at least some of the parameters made very large shifts in the
117first cycle. Note that GSAS does not compute the R-factor or Chi-squared terms
118after the second refinement cycle.
119</I></blockquote>
120<HR>
121Previous: <A HREF="alumina4.html">
122Change Background Function
123</A>
124<BR>
125Next step: <A HREF="alumina6.html">
126Plotting the Initial Fit
127</A>
128
129<HR>
130</blockquote>
131<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
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133<BR>$Revision: 930 $ $Date: 2009-12-04 23:14:35 +0000 (Fri, 04 Dec 2009) $</font>
134</body>
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