source: trunk/doc/expgui2.html @ 332

Last change on this file since 332 was 332, checked in by toby, 11 years ago

# on 2000/10/18 00:11:17, toby did:
fixup formatting

  • Property rcs:author set to toby
  • Property rcs:date set to 2000/10/18 00:11:17
  • Property rcs:lines set to +2 -2
  • Property rcs:rev set to 1.8
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 7.9 KB
Line 
1<html>
2<head>
3   <META NAME="Author" CONTENT="Brian H. Toby">
4   <title>EXPGUI</title>
5</head>
6<BODY BGCOLOR="#FFFFFF">
7
8<A HREF=http://www.ncnr.nist.gov>
9<IMG SRC="http://www.ncnr.nist.gov/images/ncnrtrans.gif" 
10alt="Link to NIST Center for Neutron Research home page"
11ALIGN=RIGHT></A>
12<A HREF=http://www.nist.gov>
13<IMG SRC="http://www.ncnr.nist.gov/images/webidblue_2lineright.gif" 
14alt="Link to National Institute of Standards & Technology home page"
15ALIGN=LEFT></A>
16<CENTER>
17<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
18<IMG SRC="tcltklogo100.gif" 
19alt="Link to Tcl/Tk information">
20</CENTER></A>
21<br clear=all><hr>
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>
30EXPGUI, part 2
31</h1></center>
32
33
34<h3>A.2 Phase Pane</h3> 
35<DL><DL>
36The phase pane is used to edit information
37about the structural model(s) found in the experiment
38file. The flags for refining the unit cell and atomic parameters,
39as well as ther damping values,
40can be set  on this pane. Note that if a
41single atom is selected using the mouse, the information
42for that atom can be edited. If a group of atoms is
43selected
44<A href="expgui.html#mouseactions">(see Mouse Actions)</A>
45the damping and refinement flags
46for all the selected atoms are changed.
47<P>
48If the EXPTOOL program
49<A href="expgui.html#installation">(see the installation instructions)</A>
50is installed, buttons for adding phases and atoms will
51appear on this pane, as seen below. If the
52program is not properly installed, no errors occur, but the buttons
53do not appear.
54<P>
55Note that the order that atoms appear in this pane is
56determined by the
57<a href="expguic.html#sortatoms">"Sort Atoms by"</a> option
58in the Options Menu. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
59The parameter used for sorting is designated
60with a "*" on the title line above the atoms.
61<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
62Clicking on this title line rotates through the sorting modes.
63</DL></DL>
64<img SRC="2.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
65<P>
66<a name="xform"></a>
67<img SRC="2a.gif" align=LEFT alt="EXPGUI Screen snapshot">
68<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
69If one or more atoms have been selected
70<A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
71to transform the atom coordinates, globally set occupancy or Uiso (Uequiv)
72values for the selected atoms, or erase the selected atoms, by pressing the
73"Xform atom(s)" button. It is also possible to transform the selected atoms
74from isotropic to anisotropic, or the reverse.
75<P>
76Note that no changes are actually made, until the
77"Transform Coordinates", "Set Occupancies",... buttons are pressed.
78<br clear=all>
79<P>
80<a name="addphase">
81</a><h4>A.2.1 Add Phase</h4> 
82<DL><DL>
83When the "Add Phase" button is pressed, a dialog is created where the
84space group and unit cell constants can be entered (below).
85<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
86By using the
87"Import phase from:" button at the lower right, one can read this information,
88as well as atomic parameters, from a file.
89The button to the right of the "Import phase from:" button selects
90the file format to be used.
91Currently two formats are supported, the Crystallographic Information File (CIF)
92and .CEL files from PowderCell.
93See the <A HREF="expgui_cfg.html#import">
94customization information</A> for more details about importing coordinates.
95<BR>
96<img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P>
97<img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot">
98After the "Continue" button is pressed, the spacegroup is checked and the
99generated symmetry operators are shown. These should be checked carefully,
100as GSAS will correctly generate a variety of standard and non-standard
101spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
102describe different (non-standard) space groups.
103<br clear=all><P>
104The EXPTOOL program is then run and the output is
105optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>).
106<P>
107If atom coordinates have been read from a file, along with the
108cell and space group, the "add new atoms" dialog is then shown, with the
109atoms displayed (as below.)
110If the file contains atoms that should not be included
111in the .EXP file, the "Use" button to the
112right of each atom can be deselected to prevent the atom from being used.
113<img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot">
114<br clear=all><P>
115<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
116In the case of reading PowderCell .CEL files, the code may
117have to translate coordinates to shift from an Origin 1 setting
118to an Origin 2 setting. (GSAS, like many other crystallography programs,
119assumes that if a center of symmetry is present, it is located at the origin.)
120If this is done a message like the one to the left is displayed.
121
122<br clear=all><P>
123</DL></DL>
124<a name="addatoms">
125<h4>A.2.2 Add Atoms</h4> 
126<DL><DL>
127When the "Add New Atoms" button is pressed, a table is generated,
128as seen below, to enter atoms. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
129The "Import atoms from:" button can
130be used to read atoms from a file.
131The button to the right of the "Import atoms from:" button selects
132the file format to be used.
133Currently two formats are supported, the Crystallographic Information File (CIF)
134and .CEL files from PowderCell.
135See the <A HREF="expgui_cfg.html#import">
136customization information</A> for more details about importing coordinates.
137Note that unlike in the
138<a href="http:#addphase">Add Phase</a> section, the space group
139and cell parameters in the file are ignored. The "Use" button to the
140right of each atom can be deselected to prevent the atom from being used.
141<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
142
143<br clear=all><P>
144</DL></DL>
145<a name="replacephase"></a><h4>
146A.2.3 Replace Phase
147<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
148</h4> 
149<DL><DL>
150The "Replace Phase" is used to change the space group and
151possibly unit cell for a phase. The input dialog, shown below, shows
152the current space group and unit cell parameters.
153By using the
154"Import phase from:" button at the lower right, one can read this information,
155as well as atomic parameters, from a file.
156The button to the right of the "Import phase from:" button selects
157the file format to be used.
158Currently two formats are supported, the Crystallographic Information File (CIF)
159and .CEL files from PowderCell.
160See the <A HREF="expgui_cfg.html#import">
161customization information</A> for more details about importing coordinates.
162<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
163<br clear=all><P>
164
165Once the
166"Continue button is pressed, the space group is checked,
167as is shown in the <a href="http:#addphase">Add Phase</a> section.
168A table is then generated for input of atoms, very similar to
169that in the <a href="http:#addphase">Add Phase</a> section.
170If atom coordinates have been read from a file these atoms
171are included in the table.
172It should be noted that when a phase is replaced in EXPGUI, all atoms in
173that phase are erased. If the current atom positions are to be
174retained, the "Reenter current atoms" box in the initial
175"Replace phase" dialog should be checked, these atoms will also
176be included in the table.
177<P>
178Note that no changes are made until after the "Continue" button
179is pressed on the "Enter Atoms" dialog, so that is is safe to
180press "Cancel" at any point.
181
182<br clear=all>
183</DL></DL>
184<hr>
185<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
186<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
187</TH><TH><A Href="expgui3.html">Next page</A>
188</TH><TH><A Href="expgui1.html">Previous page</A>
189</TH></TR></TABLE>
190
191<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
192<br>
193$Revision: 332 $ $Date: 2009-12-04 23:04:17 +0000 (Fri, 04 Dec 2009) $
194</body>
195</html>
Note: See TracBrowser for help on using the repository browser.