source: trunk/doc/expgui2.html @ 507

Last change on this file since 507 was 506, checked in by toby, 12 years ago

# on 2001/12/19 18:55:42, toby did:
reformat to match NCNR style

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  • Property rcs:date set to 2001/12/19 18:55:42
  • Property rcs:lines set to +21 -18
  • Property rcs:rev set to 1.11
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 9.2 KB
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1<html>
2<head>
3   <META NAME="Author" CONTENT="Brian H. Toby">
4   <title>EXPGUI</title>
5   <meta name="keywords" content="crystallography, Rietveld, diffraction,
6   GSAS, EXPGUI">
7</HEAD>
8<style>
9A:link {text-decoration:none}
10A:vlink {text-decoration:none}
11</style>
12
13<BODY BGCOLOR="#FFFFFF"
14      topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" 
15      text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff">
16
17<?
18   include("/var/www/include/navigation.inc");
19   include("/var/www/include/utility.inc");
20?>
21<blockquote><font face="arial, helvetica, sans-serif">
22
23<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
24<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
25</TH><TH><A Href="expgui3.html">Next page</A>
26</TH><TH><A Href="expgui1.html">Previous page</A>
27</TH></TR></TABLE><BR CLEAR=ALL>
28
29<center><h1>
30<HR noshade width="75%" size="2" align="center">
31EXPGUI, part 2
32<HR noshade width="75%" size="2" align="center">
33</h1></center>
34
35
36<h3>A.2 Phase Pane</h3> 
37<DL><DL>
38The phase pane is used to edit information
39about the structural model(s) found in the experiment
40file. The flags for refining the unit cell and atomic parameters,
41as well as ther damping values,
42can be set  on this pane. Note that if a
43single atom is selected using the mouse, the information
44for that atom can be edited. If a group of atoms is
45selected
46<A href="expgui.html#mouseactions">(see Mouse Actions)</A>
47the damping and refinement flags
48for all the selected atoms are changed.
49<P>
50If the EXPTOOL program
51<A href="expgui.html#installation">(see the installation instructions)</A>
52is installed, buttons for adding phases and atoms will
53appear on this pane, as seen below. If the
54program is not properly installed, no errors occur, but the buttons
55do not appear.
56<P>
57Note that the order that atoms appear in this pane is
58determined by the
59<a href="expguic.html#sortatoms">"Sort Atoms by"</a> option
60in the Options Menu. <IMG SRC="note.gif" alt="Note!">
61The parameter used for sorting is designated
62with a "*" on the title line above the atoms.
63<IMG SRC="note.gif" alt="Note!">
64Clicking on this title line rotates through the sorting modes.
65</DL></DL>
66<img SRC="2.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
67<P>
68<a name="xform"></a>
69<img SRC="2a.gif" align=LEFT alt="EXPGUI Screen snapshot">
70<IMG SRC="note.gif" alt="Note!">
71If one or more atoms have been selected
72<A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
73to transform the atom coordinates, globally set occupancy or Uiso (Uequiv)
74values for the selected atoms, or erase the selected atoms, by pressing the
75"Xform atom(s)" button. It is also possible to transform the selected atoms
76from isotropic to anisotropic, or the reverse.
77<P>
78Note that no changes are actually made, until the
79"Transform Coordinates", "Set Occupancies",... buttons are pressed.
80<br clear=all>
81<P>
82<a name="addphase">
83</a><h4>A.2.1 Add Phase</h4> 
84<DL><DL>
85When the "Add Phase" button is pressed, a dialog is created where the
86space group and unit cell constants can be entered (below).
87<IMG SRC="note.gif" alt="Note!">
88By using the
89"Import phase from:" button at the lower right, one can read this information,
90as well as atomic parameters, from a file.
91The button to the right of the "Import phase from:" button selects
92the file format to be used.
93Currently three formats are supported,
94the Crystallographic Information File (CIF),
95.CEL files from PowderCell and importing coordinates from other
96GSAS .EXP files.
97Note that it is relatively easy to add new routines for
98importing coordinates;
99see the <A HREF="expgui_cfg.html#import">
100customization information</A> for more details.
101<BR>
102<img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P>
103<img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot">
104After the "Continue" button is pressed, the spacegroup is checked and the
105generated symmetry operators are shown. These should be checked carefully,
106as GSAS will correctly generate a variety of standard and non-standard
107spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
108describe different (non-standard) space groups.
109<br clear=all><P>
110The EXPTOOL program is then run and the output is
111optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>).
112<P>
113If atom coordinates have been read from a file, along with the
114cell and space group, the "add new atoms" dialog is then shown, with the
115atoms displayed (as below.)
116If the file contains atoms that should not be included
117in the .EXP file, the "Use Flag" button to the
118right of each atom can be deselected to prevent the atom from being used.
119<img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot">
120<br clear=all>
121Atoms will be included in the phase in the order they appear in the table.
122<IMG SRC="new.gif" alt="New!">
123This order can be changed by pressing the buttons in the top row of the
124table, which sorts the atoms according to the selected column. Note that
125if the "Use Flag" button is deselected, the atom appears at the bottom
126of the table.
127<P>
128When the "Add Atoms" button is pressed, the table is scanned for errors
129such as invalid numbers or unknown atom types. If an error is encountered,
130a message is displayed listing the problem(s). Corrections can then be
131made to the table before pressing the "Add Atoms" button again.
132<br clear=all><P>
133<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
134In the case of reading PowderCell .CEL files, the code may
135have to translate coordinates to shift from an Origin 1 setting
136to an Origin 2 setting. (GSAS, like many other crystallography programs,
137assumes that if a center of symmetry is present, it is located at the origin.)
138If this is done, a message like the one to the left is displayed.
139
140<br clear=all><P>
141</DL></DL>
142<a name="addatoms">
143<h4>A.2.2 Add Atoms</h4> 
144<DL><DL>
145When the "Add New Atoms" button is pressed, a table is generated,
146as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!">
147The "Import atoms from:" button can
148be used to read atoms from a file.
149The button to the right of the "Import atoms from:" button selects
150the file format to be used.
151Currently two formats are supported, the Crystallographic Information File (CIF)
152and .CEL files from PowderCell.
153See the <A HREF="expgui_cfg.html#import">
154customization information</A> for more details about importing coordinates.
155Note that unlike in the
156<a href="http:#addphase">Add Phase</a> section, the space group
157and cell parameters in the file are ignored. The "Use" button to the
158right of each atom can be deselected to prevent the atom from being used.
159<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
160<br clear=all><P>
161Atoms will be added to the phase in the order they appear in the table.
162<IMG SRC="new.gif" alt="New!">
163This order can be changed by pressing the buttons in the top row of the
164table, which sorts the atoms according to the selected column. Note that
165if the "Use Flag" button is deselected, the atom appears at the bottom
166of the table.
167<P>
168When the "Add Atoms" button is pressed, the table is scanned for errors
169such as invalid numbers or unknown atom types. If an error is encountered,
170a message is displayed listing the problem(s). Corrections can then be
171made to the table before pressing the "Add Atoms" button again.
172
173<br clear=all><P>
174</DL></DL>
175<a name="replacephase"></a><h4>
176A.2.3 Replace Phase
177<IMG SRC="note.gif" alt="Note!">
178</h4> 
179<DL><DL>
180The "Replace Phase" is used to change the space group and
181possibly unit cell for a phase. The input dialog, shown below, shows
182the current space group and unit cell parameters.
183By using the
184"Import phase from:" button at the lower right, one can read this information,
185as well as atomic parameters, from a file.
186The button to the right of the "Import phase from:" button selects
187the file format to be used.
188Currently two formats are supported, the Crystallographic Information File (CIF)
189and .CEL files from PowderCell.
190See the <A HREF="expgui_cfg.html#import">
191customization information</A> for more details about importing coordinates.
192<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
193<br clear=all><P>
194
195Once the
196"Continue button is pressed, the space group is checked,
197as is shown in the <a href="http:#addphase">Add Phase</a> section.
198A table is then generated for input of atoms, very similar to
199that in the <a href="http:#addphase">Add Phase</a> section.
200If atom coordinates have been read from a file these atoms
201are included in the table.
202It should be noted that when a phase is replaced in EXPGUI, all atoms in
203that phase are erased. If the current atom positions are to be
204retained, the "Reenter current atoms" box in the initial
205"Replace phase" dialog should be checked, these atoms will also
206be included in the table.
207<P>
208Note that no changes are made until after the "Continue" button
209is pressed on the "Enter Atoms" dialog, so that is is safe to
210press "Cancel" at any point.
211
212<br clear=all>
213</DL></DL>
214<hr>
215<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
216<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
217</TH><TH><A Href="expgui3.html">Next page</A>
218</TH><TH><A Href="expgui1.html">Previous page</A>
219</TH></TR></TABLE>
220
221<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
222<br>
223$Revision: 506 $ $Date: 2009-12-04 23:07:18 +0000 (Fri, 04 Dec 2009) $
224</blockquote>
225</body>
226</html>
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