source: trunk/tutorial3/alumina10.html @ 619

Last change on this file since 619 was 619, checked in by toby, 11 years ago

# on 2002/07/18 20:45:10, toby did:
NIST alumina tutorial

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1<html>
2<head>
3   <title>EXPGUI Alumina Tutorial, part #10</title>
4</head>
5
6<style>
7A:link {text-decoration:none}
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11<BODY BGCOLOR="#FFFFFF"
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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="alumina11.html">Next page</A>
24</TH><TH><A Href="alumina9.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 10)<BR>
31Group U<sub>iso</sub> parameters &<BR>
32Refine coordinates and Overall U<sub>iso</sub>.
33
34<HR noshade width="75%" size="2" align="center">
35</H1>
36</CENTER>
37At this stage in the refinement we have a good fit for the experimental
38parameters, but need to improve the crystallographic model.
39To reduce the number of parameters needed in the initial stages of this
40part of the process, we will define a constraint that requires a
41single overall U<sub>iso</sub> value for all atoms.
42<P><HR noshade width="50%" size="4" align="center"><P>
43
44Note that at this stage in the refinement, the peak shape agrees well, but
45there are significant differences between the observed and computed
46intensities. This implies that the crystallographic model is in some
47way inadequate.
48<P><img alt="tutorial screen dump" src="10a.gif" align=RIGHT>
49<BR clear=all>
50<P><HR noshade width="50%" size="4" align="center"><P>
51
52To group atoms so that they share a single atomic displacement parameter
53(displacement parameter is the preferred name for "temperature factor"),
54the parameters need to be constrained together.
55The Constraints panel allows constraints to be defined to link parameters
56together. At present EXPGUI allows constraints to be created for
57atomic parameters and for profile terms. GSAS implements many other types
58of constraints, but they must be accessed via the GSAS EXPEDT program.
59Press the "New Constraint"
60button at the bottom of the window to create a new constraint on
61atomic parameters.
62
63<P><img alt="tutorial screen dump" src="10b.gif" align=RIGHT>
64<BR clear=all>
65<blockquote><I>
66While it is not needed in this case, in many projects it is best to
67refine an overall displacement parameter in the initial refinements for
68this parameter. In many refinements, there simply are not sufficient
69data to allow every atom to have an independently refined displacement
70parameter, in these circumstances, it is useful to group atoms together
71so that chemically similar atoms are constrained to have the same displacement
72parameter values.
73<P>
74It should be noted that these constraints do not actually require that
75the parameters have the same value. In fact, the constraints require that
76the shifts that applied in future refinement cycles have their ratios
77defined by the constraint values. Thus, for parameters to be contrained to
78be equal, the parameters must start at the same value as well as have
79the constraint ratio set to 1.
80</I></blockquote>
81
82<P><HR noshade width="50%" size="4" align="center"><P>
83<img alt="tutorial screen dump" src="10c.gif" align=RIGHT>
84After pressing the "New Constraint" button, the window to the right
85is created. From top to bottom, the phase is selected as phase 1 (there is
86no other choice in this example), both atoms are selected
87(to select a range of atoms use a mouse "drag" or hold the control key while clicking the [left] mouse button; selecting all atoms can also be done by
88press the right mouse button. Finally select UISO for the parameter, leave
89the multiplier as 1 and press "Save"
90<BR clear=all>
91<P><HR noshade width="50%" size="4" align="center"><P>
92
93The Constraints panel now shows the constraint created in the previous
94step, as seen below.
95<P>
96<img alt="tutorial screen dump" src="10d.gif" align=RIGHT>
97<BR clear=all>
98<P><HR noshade width="50%" size="4" align="center"><P>
99
100Now we are ready to set the refinement flags for the atoms on the Phase panel.
101Select both atoms in the list using the mouse. Select the X flag
102(near the bottom of the panel), this means refine x, y and z, as allowed by
103symmetry. Since the Al atom is on a special position, (0,0,z), only the
104z coordinate will be changed. Likewise the O atom is at a (x,0,1/4) position
105and only the x coordinate will be changed. Also select the U flag to refine
106the displacement (temperature) parameter for the two atoms. The previously
107defined constraint will be applied automatically.
108<P>
109<img alt="tutorial screen dump" src="10e.gif" align=RIGHT>
110<BR clear=all>
111<P><HR noshade width="50%" size="4" align="center"><P>
112
113Refinement of these three atomic parameters
114has a enormous impact on the quality of the fit,
115as seen by the improvement in the agreement seen in the GENLES run below.
116<P>
117<img alt="tutorial screen dump" src="10f.gif" align=RIGHT>
118<BR clear=all>
119<P><HR noshade width="50%" size="4" align="center"><P>
120
121The LIVEPLOT output shows a tremendous improvement in the agreement as well.
122<img alt="tutorial screen dump" src="10g.gif" align=RIGHT>
123<BR clear=all>
124<HR>
125Previous: <A HREF="alumina9.html">
126Initial Fitting of Profile Parameters
127
128</A>
129<BR>
130Next step: <A HREF="alumina11.html">
131Finishing up
132</A>
133
134<HR>
135</blockquote>
136<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
137<font size=-1><? lastmod(); ?> 
138<BR>$Revision: 619 $ $Date: 2009-12-04 23:09:12 +0000 (Fri, 04 Dec 2009) $</font>
139</body>
140</html>
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