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1<html>
2<head>
3   <title>EXPGUI Alumina Tutorial, part #2</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="alumina3.html">Next page</A>
24</TH><TH><A Href="alumina1.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 2)<BR>
31Adding a phase
32<HR noshade width="75%" size="2" align="center">
33</H1>
34</CENTER>
35<I>When a GSAS experiment file is first created, a fair amount of information
36must be supplied before the refinement of parameters can be started. At a
37minimum, a crystallographic phase must be defined, a set of diffraction
38data must be loaded and a starting values for experimental parameters
39must be defined. Fortunately, this can be a fairly simple operation
40with GSAS and EXPGUI.
41</I>
42<P>
43This page shows how a crystallographic phase is
44specified in EXPGUI. For a mixture, this step would be repeated for
45each crystallographic phase. If an impurity is identified in a later
46stage of the refinement, this step can be run at that point to define
47this additional crystallographic phase. GSAS allows up to nine crystallographic
48phases to be included in a model.
49<P><HR noshade width="50%" size="4" align="center"><P>
50
51To enter information about a crystallographic phase, modify
52crystallographic parameters, or select crystallographic parameters
53to be optimized the "Phase" panel must be selected by clicking on the
54"Phase" tab in the upper left of the EXPGUI window. The window then appears
55as shown just below this text.
56<P><img alt="tutorial screen dump" src="2a.gif" align=RIGHT>
57<BR clear=all><P>
58<blockquote><I>
59
60It should be noted that the Phase panel will have a slightly different
61appearance after one or more phases have been entered,
62(<a href="#withphase">see below</a>).
63</I></blockquote>
64<P><HR noshade width="50%" size="4" align="center"><P>
65
66The next step is to press the "Add Phase" button in the upper left.
67The "Add New Phase" window, shown immediately below, is then generated.
68<P><img alt="tutorial screen dump" src="2b.gif" align=RIGHT>
69<BR clear=all>
70<img alt="tutorial screen dump" src="2c.gif" align=RIGHT>
71Information about the phase can be added directly into the boxes,
72or phase information can be read from a file. For this exercise,
73we will read unit cell parameters, the space group and atom parameters
74from a CIF file. This means that we need to select the "Crystallographic
75Information File (CIF)"
76format from
77the options by pressing the file format button
78in the lower right-hand corner.
79<BR clear=all>
80<P><HR noshade width="50%" size="4" align="center"><P>
81
82When the "Import Phase from" button is pressed, an "open file"
83window is created (this window has a slightly different appearance,
84but the same function in Windows). On this window, the file to be read is
85selected, and then the "Read" button is pressed.
86<P><img alt="tutorial screen dump" src="2d.gif" align=RIGHT>
87<BR clear=all>
88<P><HR noshade width="50%" size="4" align="center"><P>
89
90The CIF is then read and the unit cell information is included
91in the appropriate entry boxes, as shown below.
92If this input is acceptable, press "Continue".
93<P><img alt="tutorial screen dump" src="2e.gif" align=RIGHT>
94<BR clear=all>
95<P><HR noshade width="50%" size="4" align="center"><P>
96
97One of the places where errors occur in the preparation of GSAS input
98is in the entering of space group symbols. For this reason, after the
99"Continue" button is pressed, a window such as the one below, is
100created to help you confirm that the correct space group has been entered.
101<P><img alt="tutorial screen dump" src="2f.gif" align=RIGHT>
102<BR clear=all>
103<blockquote><I>
104<P>It is recommended that you read through this information to check that
105this is correct. As an example of a possible error, if one entered the
106corundum example in the rhombohedral setting,
107rather than the hexagonal setting,
108then the space group should be entered as "R -3 c R" (where the final R
109indicates the rhombohedral setting). The listing of lattice centering vectors
110is only appropriate for the hexagonal (centered) cell.
111</I></blockquote>
112<P><HR noshade width="50%" size="4" align="center"><P>
113
114Since the symmetry information is correct in this example, press the "Continue"
115button on the "check symmetry" window. At this point, since atom
116coordinates were read from the CIF file, the "add new atoms" window is
117opened and the atom coordinates are entered into the appropriate boxes,
118as seen below. Press the "Add Atoms" button at the lower left to continue.
119<P><img alt="tutorial screen dump" src="2g.gif" align=RIGHT>
120<BR clear=all>
121<blockquote><I>
122Note that if atoms were not being read in from a file,
123it would now be necessary
124to press the "Add New Atoms" button to input atoms to the phase.
125In this case, there would be no atoms entered into the window.
126</I></blockquote>
127<P><HR noshade width="50%" size="4" align="center"><P>
128After pressing the "Add Atoms" button, the two atoms are added to the
129experiment and the phase panel appears, as below.
130<a name="withphase">
131<P><img alt="tutorial screen dump" src="2h.gif" align=RIGHT>
132</a>
133<BR clear=all>
134<HR>
135Previous: <A HREF="alumina1.html">
136Creating an Experiment File</A>
137<BR>
138Next step: <A HREF="alumina3.html">
139Add data file to the Experiment</A>
140
141<HR>
142</blockquote>
143<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
144<font size=-1><? lastmod(); ?> 
145<BR>$Revision: 930 $ $Date: 2009-12-04 23:14:35 +0000 (Fri, 04 Dec 2009) $</font>
146</body>
147</html>
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