source: trunk/doc/expgui2.html @ 678

Last change on this file since 678 was 678, checked in by toby, 11 years ago

# on 2003/04/10 22:22:49, toby did:
add edit cell doc
better formatting

  • Property rcs:author set to toby
  • Property rcs:date set to 2003/04/10 22:22:49
  • Property rcs:lines set to +25 -10
  • Property rcs:rev set to 1.14
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 9.5 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<P>
68<a name="addphase"></a>
69<h4>A.2.1 Modify Unit Cell Parameters
70<IMG SRC="new.gif" alt="New!">
71</h4> 
72<DL><DL>
73<img SRC="2g.gif" align=RIGHT alt="EXPGUI Screen snapshot">
74If the "Edit Cell" button is pressed, the unit cell parameters can be
75changed, as shown to the right. Note that only the parameters allowed
76by symmetry can be changed.
77
78<br clear=all>
79</DL></DL>
80<P>
81<a name="xform"></a>
82<h4>A.2.2 Transform Coordinates</h4> 
83<DL><DL>
84<img SRC="2a.gif" align=RIGHT alt="EXPGUI Screen snapshot">
85If one or more atoms have been selected
86<A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
87to transform the atom coordinates, globally set occupancy or Uiso (Uequiv)
88values for the selected atoms, or erase the selected atoms, by pressing the
89"Xform atom(s)" button. It is also possible to transform the selected atoms
90from isotropic to anisotropic, or the reverse.
91<P>
92Note that no changes are actually made, until the
93"Transform Coordinates", "Set Occupancies",... buttons are pressed.
94
95<br clear=all>
96</DL></DL>
97<P>
98<a name="addphase"></a>
99<h4>A.2.3 Add Phase</h4> 
100<DL><DL>
101When the "Add Phase" button is pressed, a dialog is created where the
102space group and unit cell constants can be entered (below).
103<IMG SRC="note.gif" alt="Note!">
104By using the
105"Import phase from:" button at the lower right, one can read this information,
106as well as atomic parameters, from a file.
107The button to the right of the "Import phase from:" button selects
108the file format to be used.
109See the <A HREF="expgui.html#import">coordinate import discussion</A> 
110for description of available formats.
111Note that it is relatively easy to add new routines for
112importing coordinates;
113see the <A HREF="expgui_cfg.html#import">
114customization information</A> for more details.
115<BR>
116<img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P>
117<img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot">
118After the "Continue" button is pressed, the spacegroup is checked and the
119generated symmetry operators are shown. These should be checked carefully,
120as GSAS will correctly generate a variety of standard and non-standard
121spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
122describe different (non-standard) space groups.
123<br clear=all><P>
124The EXPTOOL program is then run and the output is
125optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>).
126<P>
127If atom coordinates have been read from a file, along with the
128cell and space group, the "add new atoms" dialog is then shown, with the
129atoms displayed (as below.)
130If the file contains atoms that should not be included
131in the .EXP file, the "Use Flag" button to the
132right of each atom can be deselected to prevent the atom from being used.
133<img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot">
134<br clear=all>
135Atoms will be included in the phase in the order they appear in the table.
136<IMG SRC="new.gif" alt="New!">
137This order can be changed by pressing the buttons in the top row of the
138table, which sorts the atoms according to the selected column. Note that
139if the "Use Flag" button is deselected, the atom appears at the bottom
140of the table.
141<P>
142When the "Add Atoms" button is pressed, the table is scanned for errors
143such as invalid numbers or unknown atom types. If an error is encountered,
144a message is displayed listing the problem(s). Corrections can then be
145made to the table before pressing the "Add Atoms" button again.
146<br clear=all><P>
147<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
148In the case of reading PowderCell .CEL files, the code may
149have to translate coordinates to shift from an Origin 1 setting
150to an Origin 2 setting. (GSAS, like many other crystallography programs,
151assumes that if a center of symmetry is present, it is located at the origin.)
152If this is done, a message like the one to the left is displayed.
153
154<br clear=all><P>
155</DL></DL>
156<a name="addatoms">
157<h4>A.2.4 Add Atoms</h4> 
158<DL><DL>
159When the "Add New Atoms" button is pressed, a table is generated,
160as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!">
161The "Import atoms from:" button can
162be used to read atoms from a file.
163The button to the right of the "Import atoms from:" button selects
164the file format to be used.
165See the <A HREF="expgui.html#import">coordinate import discussion</A> 
166for description of available formats and
167the <A HREF="expgui_cfg.html#import">
168customization information</A> for more details about adding
169additional formats.
170Note that unlike in the
171<a href="http:#addphase">Add Phase</a> section, the space group
172and cell parameters in the imported file are ignored. The "Use" button to the
173right of each atom can be deselected to prevent the atom from being used.
174<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
175<br clear=all><P>
176Atoms will be added to the phase in the order they appear in the table.
177<IMG SRC="new.gif" alt="New!">
178This order can be changed by pressing the buttons in the top row of the
179table, which sorts the atoms according to the selected column. Note that
180if the "Use Flag" button is deselected, the atom appears at the bottom
181of the table.
182<P>
183When the "Add Atoms" button is pressed, the table is scanned for errors
184such as invalid numbers or unknown atom types. If an error is encountered,
185a message is displayed listing the problem(s). Corrections can then be
186made to the table before pressing the "Add Atoms" button again.
187
188<br clear=all><P>
189</DL></DL>
190<a name="replacephase"></a>
191<h4>A.2.5 Replace Phase</h4> 
192<DL><DL>
193The "Replace Phase" is used to change the space group and
194possibly unit cell for a phase. The input dialog, shown below, shows
195the current space group and unit cell parameters.
196By using the
197"Import phase from:" button at the lower right, one can read this information,
198as well as atomic parameters, from a file.
199The button to the right of the "Import phase from:" button selects
200the file format to be used.
201See the <A HREF="expgui.html#import">coordinate import discussion</A> 
202for description of available formats and
203the <A HREF="expgui_cfg.html#import">
204customization information</A> for more details about adding
205additional formats.
206<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
207<br clear=all><P>
208
209Once the
210"Continue button is pressed, the space group is checked,
211as is shown in the <a href="http:#addphase">Add Phase</a> section.
212A table is then generated for input of atoms, very similar to
213that in the <a href="http:#addphase">Add Phase</a> section.
214If atom coordinates have been read from a file these atoms
215are included in the table.
216It should be noted that when a phase is replaced in EXPGUI, all atoms in
217that phase are erased. If the current atom positions are to be
218retained, the "Reenter current atoms" box in the initial
219"Replace phase" dialog should be checked, these atoms will also
220be included in the table.
221<P>
222Note that no changes are made until after the "Continue" button
223is pressed on the "Enter Atoms" dialog, so that is is safe to
224press "Cancel" at any point.
225
226<br clear=all>
227</DL></DL>
228<hr>
229<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
230<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
231</TH><TH><A Href="expgui3.html">Next page</A>
232</TH><TH><A Href="expgui1.html">Previous page</A>
233</TH></TR></TABLE>
234
235<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
236<font size=-1><? lastmod(); ?> </font>
237<br>$Revision: 678 $ $Date: 2009-12-04 23:10:11 +0000 (Fri, 04 Dec 2009) $
238</blockquote>
239</body>
240</html>
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