source: trunk/doc/expgui2.html @ 568

Last change on this file since 568 was 568, checked in by toby, 11 years ago

# on 2002/04/12 19:49:04, toby did:
remove identification stuff

  • Property rcs:author set to toby
  • Property rcs:date set to 2002/04/12 19:49:04
  • Property rcs:lines set to +3 -4
  • Property rcs:rev set to 1.13
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 9.1 KB
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1<html>
2<head>
3   <title>EXPGUI</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
5   GSAS, EXPGUI">
6</HEAD>
7<style>
8A:link {text-decoration:none}
9A:vlink {text-decoration:none}
10</style>
11
12<BODY BGCOLOR="#FFFFFF"
13      topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" 
14      text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff">
15
16<?
17   include("/var/www/include/navigation.inc");
18   include("/var/www/include/utility.inc");
19?>
20<blockquote><font face="arial, helvetica, sans-serif">
21
22<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
23<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
24</TH><TH><A Href="expgui3.html">Next page</A>
25</TH><TH><A Href="expgui1.html">Previous page</A>
26</TH></TR></TABLE><BR CLEAR=ALL>
27
28<center><h1>
29<HR noshade width="75%" size="2" align="center">
30EXPGUI, part 2
31<HR noshade width="75%" size="2" align="center">
32</h1></center>
33
34
35<h3>A.2 Phase Pane</h3> 
36<DL><DL>
37The phase pane is used to edit information
38about the structural model(s) found in the experiment
39file. The flags for refining the unit cell and atomic parameters,
40as well as ther damping values,
41can be set  on this pane. Note that if a
42single atom is selected using the mouse, the information
43for that atom can be edited. If a group of atoms is
44selected
45<A href="expgui.html#mouseactions">(see Mouse Actions)</A>
46the damping and refinement flags
47for all the selected atoms are changed.
48<P>
49If the EXPTOOL program
50<A href="expgui.html#installation">(see the installation instructions)</A>
51is installed, buttons for adding phases and atoms will
52appear on this pane, as seen below. If the
53program is not properly installed, no errors occur, but the buttons
54do not appear.
55<P>
56Note that the order that atoms appear in this pane is
57determined by the
58<a href="expguic.html#sortatoms">"Sort Atoms by"</a> option
59in the Options Menu. <IMG SRC="note.gif" alt="Note!">
60The parameter used for sorting is designated
61with a "*" on the title line above the atoms.
62<IMG SRC="note.gif" alt="Note!">
63Clicking on this title line rotates through the sorting modes.
64</DL></DL>
65<img SRC="2.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
66<P>
67<a name="xform"></a>
68<img SRC="2a.gif" align=LEFT alt="EXPGUI Screen snapshot">
69<IMG SRC="note.gif" alt="Note!">
70If one or more atoms have been selected
71<A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
72to transform the atom coordinates, globally set occupancy or Uiso (Uequiv)
73values for the selected atoms, or erase the selected atoms, by pressing the
74"Xform atom(s)" button. It is also possible to transform the selected atoms
75from isotropic to anisotropic, or the reverse.
76<P>
77Note that no changes are actually made, until the
78"Transform Coordinates", "Set Occupancies",... buttons are pressed.
79<br clear=all>
80<P>
81<a name="addphase">
82</a><h4>A.2.1 Add Phase</h4> 
83<DL><DL>
84When the "Add Phase" button is pressed, a dialog is created where the
85space group and unit cell constants can be entered (below).
86<IMG SRC="note.gif" alt="Note!">
87By using the
88"Import phase from:" button at the lower right, one can read this information,
89as well as atomic parameters, from a file.
90The button to the right of the "Import phase from:" button selects
91the file format to be used.
92See the <A HREF="expgui.html#import">coordinate import discussion</A> 
93for description of available formats.
94Note that it is relatively easy to add new routines for
95importing coordinates;
96see the <A HREF="expgui_cfg.html#import">
97customization information</A> for more details.
98<BR>
99<img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P>
100<img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot">
101After the "Continue" button is pressed, the spacegroup is checked and the
102generated symmetry operators are shown. These should be checked carefully,
103as GSAS will correctly generate a variety of standard and non-standard
104spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
105describe different (non-standard) space groups.
106<br clear=all><P>
107The EXPTOOL program is then run and the output is
108optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>).
109<P>
110If atom coordinates have been read from a file, along with the
111cell and space group, the "add new atoms" dialog is then shown, with the
112atoms displayed (as below.)
113If the file contains atoms that should not be included
114in the .EXP file, the "Use Flag" button to the
115right of each atom can be deselected to prevent the atom from being used.
116<img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot">
117<br clear=all>
118Atoms will be included in the phase in the order they appear in the table.
119<IMG SRC="new.gif" alt="New!">
120This order can be changed by pressing the buttons in the top row of the
121table, which sorts the atoms according to the selected column. Note that
122if the "Use Flag" button is deselected, the atom appears at the bottom
123of the table.
124<P>
125When the "Add Atoms" button is pressed, the table is scanned for errors
126such as invalid numbers or unknown atom types. If an error is encountered,
127a message is displayed listing the problem(s). Corrections can then be
128made to the table before pressing the "Add Atoms" button again.
129<br clear=all><P>
130<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
131In the case of reading PowderCell .CEL files, the code may
132have to translate coordinates to shift from an Origin 1 setting
133to an Origin 2 setting. (GSAS, like many other crystallography programs,
134assumes that if a center of symmetry is present, it is located at the origin.)
135If this is done, a message like the one to the left is displayed.
136
137<br clear=all><P>
138</DL></DL>
139<a name="addatoms">
140<h4>A.2.2 Add Atoms</h4> 
141<DL><DL>
142When the "Add New Atoms" button is pressed, a table is generated,
143as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!">
144The "Import atoms from:" button can
145be used to read atoms from a file.
146The button to the right of the "Import atoms from:" button selects
147the file format to be used.
148See the <A HREF="expgui.html#import">coordinate import discussion</A> 
149for description of available formats and
150the <A HREF="expgui_cfg.html#import">
151customization information</A> for more details about adding
152additional formats.
153Note that unlike in the
154<a href="http:#addphase">Add Phase</a> section, the space group
155and cell parameters in the imported file are ignored. The "Use" button to the
156right of each atom can be deselected to prevent the atom from being used.
157<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
158<br clear=all><P>
159Atoms will be added to the phase in the order they appear in the table.
160<IMG SRC="new.gif" alt="New!">
161This order can be changed by pressing the buttons in the top row of the
162table, which sorts the atoms according to the selected column. Note that
163if the "Use Flag" button is deselected, the atom appears at the bottom
164of the table.
165<P>
166When the "Add Atoms" button is pressed, the table is scanned for errors
167such as invalid numbers or unknown atom types. If an error is encountered,
168a message is displayed listing the problem(s). Corrections can then be
169made to the table before pressing the "Add Atoms" button again.
170
171<br clear=all><P>
172</DL></DL>
173<a name="replacephase"></a><h4>
174A.2.3 Replace Phase
175<IMG SRC="note.gif" alt="Note!">
176</h4> 
177<DL><DL>
178The "Replace Phase" is used to change the space group and
179possibly unit cell for a phase. The input dialog, shown below, shows
180the current space group and unit cell parameters.
181By using the
182"Import phase from:" button at the lower right, one can read this information,
183as well as atomic parameters, from a file.
184The button to the right of the "Import phase from:" button selects
185the file format to be used.
186See the <A HREF="expgui.html#import">coordinate import discussion</A> 
187for description of available formats and
188the <A HREF="expgui_cfg.html#import">
189customization information</A> for more details about adding
190additional formats.
191<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
192<br clear=all><P>
193
194Once the
195"Continue button is pressed, the space group is checked,
196as is shown in the <a href="http:#addphase">Add Phase</a> section.
197A table is then generated for input of atoms, very similar to
198that in the <a href="http:#addphase">Add Phase</a> section.
199If atom coordinates have been read from a file these atoms
200are included in the table.
201It should be noted that when a phase is replaced in EXPGUI, all atoms in
202that phase are erased. If the current atom positions are to be
203retained, the "Reenter current atoms" box in the initial
204"Replace phase" dialog should be checked, these atoms will also
205be included in the table.
206<P>
207Note that no changes are made until after the "Continue" button
208is pressed on the "Enter Atoms" dialog, so that is is safe to
209press "Cancel" at any point.
210
211<br clear=all>
212</DL></DL>
213<hr>
214<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
215<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
216</TH><TH><A Href="expgui3.html">Next page</A>
217</TH><TH><A Href="expgui1.html">Previous page</A>
218</TH></TR></TABLE>
219
220<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
221<font size=-1><? lastmod(); ?> </font>
222<br>$Revision: 568 $ $Date: 2009-12-04 23:08:21 +0000 (Fri, 04 Dec 2009) $
223</blockquote>
224</body>
225</html>
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