source: trunk/doc/expgui2.html @ 856

Last change on this file since 856 was 856, checked in by toby, 11 years ago

# on 2005/12/16 00:40:23, toby did:

pane --> panel

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  • Property rcs:date set to 2005/12/16 00:40:23
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  • Property rcs:rev set to 1.15
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
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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 Panel</h3> 
36<DL><DL>
37The phase panel 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 panel. 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 panel, 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 panel 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 make changes to those atoms by pressing the "Xform atom(s)" button.
88This raises the window shown to the right.
89Note that no changes are actually made, until the
90"Transform Coordinates", "Set Occupancies",... buttons are pressed.
91<P>
92This window can be used
93to transform the coordinates coordinates of the selected atoms,
94globally set occupancy or Uiso (Uequiv)
95values for the selected atoms, or erase the selected atoms. by pressing the
96It is also possible to transform the selected atoms
97from isotropic to anisotropic, or the reverse.
98<P>
99<IMG SRC="new.gif" alt="New!">
100The "Xform Origin 1 to Origin 2" button is only available for those
101orthorhombic, tetragonal and cubic space groups that are listed in the
102International Tables with two origin settings. (These space groups have
103a location in the unit cell that has higher symmetry than a location of
104a center of symmetry: origin 1 is placed at the highest symmetry location;
105origin 2 is placed at the computationally reasonable location, the center
106of symmetry. GSAS only uses the origin 2 settings.)
107If coordinates have been entered in the origin 1 setting, they may be
108transformed to the origin 2 setting using this button.
109
110<br clear=all>
111</DL></DL>
112<P>
113<a name="addphase"></a>
114<h4>A.2.3 Add Phase</h4> 
115<DL><DL>
116When the "Add Phase" button is pressed, a dialog is created where the
117space group and unit cell constants can be entered (below).
118<IMG SRC="note.gif" alt="Note!">
119By using the
120"Import phase from:" button at the lower right, one can read this information,
121as well as atomic parameters, from a file.
122The button to the right of the "Import phase from:" button selects
123the file format to be used.
124See the <A HREF="expgui.html#import">coordinate import discussion</A> 
125for description of available formats.
126Note that it is relatively easy to add new routines for
127importing coordinates;
128see the <A HREF="expgui_cfg.html#import">
129customization information</A> for more details.
130<BR>
131<img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P>
132<img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot">
133After the "Continue" button is pressed, the spacegroup is checked and the
134generated symmetry operators are shown. These should be checked carefully,
135as GSAS will correctly generate a variety of standard and non-standard
136spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
137describe different (non-standard) space groups.
138<br clear=all><P>
139The EXPTOOL program is then run and the output is
140optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>).
141<P>
142If atom coordinates have been read from a file, along with the
143cell and space group, the "add new atoms" dialog is then shown, with the
144atoms displayed (as below.)
145If the file contains atoms that should not be included
146in the .EXP file, the "Use Flag" button to the
147right of each atom can be deselected to prevent the atom from being used.
148<img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot">
149<br clear=all>
150Atoms will be included in the phase in the order they appear in the table.
151<IMG SRC="new.gif" alt="New!">
152This order can be changed by pressing the buttons in the top row of the
153table, which sorts the atoms according to the selected column. Note that
154if the "Use Flag" button is deselected, the atom appears at the bottom
155of the table.
156<P>
157When the "Add Atoms" button is pressed, the table is scanned for errors
158such as invalid numbers or unknown atom types. If an error is encountered,
159a message is displayed listing the problem(s). Corrections can then be
160made to the table before pressing the "Add Atoms" button again.
161<br clear=all><P>
162<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
163In the case of reading PowderCell .CEL files, the code may
164have to translate coordinates to shift from an Origin 1 setting
165to an Origin 2 setting. (GSAS, like many other crystallography programs,
166assumes that if a center of symmetry is present, it is located at the origin.)
167If this is done, a message like the one to the left is displayed.
168
169<br clear=all><P>
170</DL></DL>
171<a name="addatoms">
172<h4>A.2.4 Add Atoms</h4> 
173<DL><DL>
174When the "Add New Atoms" button is pressed, a table is generated,
175as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!">
176The "Import atoms from:" button can
177be used to read atoms from a file.
178The button to the right of the "Import atoms from:" button selects
179the file format to be used.
180See the <A HREF="expgui.html#import">coordinate import discussion</A> 
181for description of available formats and
182the <A HREF="expgui_cfg.html#import">
183customization information</A> for more details about adding
184additional formats.
185Note that unlike in the
186<a href="http:#addphase">Add Phase</a> section, the space group
187and cell parameters in the imported file are ignored. The "Use" button to the
188right of each atom can be deselected to prevent the atom from being used.
189<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
190<br clear=all><P>
191Atoms will be added to the phase in the order they appear in the table.
192<IMG SRC="new.gif" alt="New!">
193This order can be changed by pressing the buttons in the top row of the
194table, which sorts the atoms according to the selected column. Note that
195if the "Use Flag" button is deselected, the atom appears at the bottom
196of the table.
197<P>
198When the "Add Atoms" button is pressed, the table is scanned for errors
199such as invalid numbers or unknown atom types. If an error is encountered,
200a message is displayed listing the problem(s). Corrections can then be
201made to the table before pressing the "Add Atoms" button again.
202
203<br clear=all><P>
204</DL></DL>
205<a name="replacephase"></a>
206<h4>A.2.5 Replace Phase</h4> 
207<DL><DL>
208The "Replace Phase" is used to change the space group and
209possibly unit cell for a phase. The input dialog, shown below, shows
210the current space group and unit cell parameters.
211By using the
212"Import phase from:" button at the lower right, one can read this information,
213as well as atomic parameters, from a file.
214The button to the right of the "Import phase from:" button selects
215the file format to be used.
216See the <A HREF="expgui.html#import">coordinate import discussion</A> 
217for description of available formats and
218the <A HREF="expgui_cfg.html#import">
219customization information</A> for more details about adding
220additional formats.
221<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
222<br clear=all><P>
223
224Once the
225"Continue button is pressed, the space group is checked,
226as is shown in the <a href="http:#addphase">Add Phase</a> section.
227A table is then generated for input of atoms, very similar to
228that in the <a href="http:#addphase">Add Phase</a> section.
229If atom coordinates have been read from a file these atoms
230are included in the table.
231It should be noted that when a phase is replaced in EXPGUI, all atoms in
232that phase are erased. If the current atom positions are to be
233retained, the "Reenter current atoms" box in the initial
234"Replace phase" dialog should be checked, these atoms will also
235be included in the table.
236<P>
237Note that no changes are made until after the "Continue" button
238is pressed on the "Enter Atoms" dialog, so that is is safe to
239press "Cancel" at any point.
240
241<br clear=all>
242</DL></DL>
243<hr>
244<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
245<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
246</TH><TH><A Href="expgui3.html">Next page</A>
247</TH><TH><A Href="expgui1.html">Previous page</A>
248</TH></TR></TABLE>
249
250<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
251<font size=-1><? lastmod(); ?> </font>
252<br>$Revision: 856 $ $Date: 2009-12-04 23:13:13 +0000 (Fri, 04 Dec 2009) $
253</blockquote>
254</body>
255</html>
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