source: trunk/doc/expgui2.html @ 269

Last change on this file since 269 was 269, checked in by toby, 14 years ago

# on 2000/08/21 19:27:43, toby did:
describe coordinate import routines
pretty up page
  • Property rcs:author set to toby
  • Property rcs:date set to 2000/08/21 19:27:43
  • Property rcs:lines set to +111 -6
  • Property rcs:rev set to 1.4
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 7.0 KB
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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<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>
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>
62Clicking on this title line rotates through the sorting modes.
63</DL></DL>
64<img SRC="2.gif" align=TEXTTOP>
65<P>
66<img SRC="2a.gif" align=LEFT>
67<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
68If one or more atoms have been selected
69<A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
70to transform the atom coordinates, globally set occupancy or Uiso (Uequiv)
71values for the selected atoms, or erase the selected atoms, by pressing the
72"Xform atom(s)" button. It is also possible to transform the selected atoms
73from isotropic to anisotropic, or the reverse.
74Note that no changes are actually made, until the
75"Transform Coordinates", "Set Occupancies",... buttons are pressed.
76<br clear=all>
77<P>
78<a name="addphase">
79</a><h4>A.2.1 Add Phase</h4> 
80<DL><DL>
81When the "Add Phase" button is pressed, a dialog is created where the
82space group and unit cell constants can be entered (below).
83<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
84By using the
85"Import phase from:" button at the lower right, one can read this information,
86as well as atomic parameters, from a file.
87The button to the right of the "Import phase from:" button selects
88the file format to be used. See the <A HREF="expgui_cfg.html#import">
89customization information</A> for more details.
90<BR>
91<img SRC="2b.gif" align=TEXTTOP><P>
92<img SRC="2c.gif" align=LEFT>
93After the "Continue" button is pressed, the spacegroup is checked and the
94generated symmetry operators are shown. These should be checked carefully,
95as GSAS will correctly generate a variety of standard and non-standard
96spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
97describe different (non-standard) space groups.
98<br clear=all><P>
99The EXPTOOL program is then run and the output is optionally displayed.
100If atom coordinates have been read from a file, along with the
101cell and space group, the "add new atoms" dialog is then shown, with the
102atoms displayed (as below.)
103If the file contains atoms that should not be included
104in the .EXP file, the "Use" button to the
105right of each atom can be deselected to prevent the atom from being used.
106<img SRC="2d.gif" align=LEFT>
107<br clear=all><P>
108<img SRC="2b1.gif" align=LEFT>
109In the case of reading PowderCell .CEL files, the code may
110have to translate coordinates to shift from an Origin 1 setting
111to an Origin 2 setting. (GSAS, like many other crystallography programs,
112assumes that if a center of symmetry is present, it is located at the origin.)
113If this is done a message like the one to the left is displayed.
114
115<br clear=all><P>
116</DL></DL>
117<h4>A.2.2 Add Atoms</h4> 
118<DL><DL>
119When the "Add New Atoms" button is pressed, a table is generated,
120as seen below, to enter atoms. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
121The "Import atoms from:" button can
122be used to read atoms from a file.
123The button to the right of the "Import atoms from:" button selects
124the file format to be used. See the <A HREF="expgui_cfg.html#import">
125customization information</A> for more details.
126Note that unlike in the
127<a href="http:#addphase">Add Phase</a> section, the space group
128and cell parameters in the file are ignored. The "Use" button to the
129right of each atom can be deselected to prevent the atom from being used.
130<img SRC="2e.gif" align=LEFT>
131
132<br clear=all><P>
133</DL></DL>
134<h4>
135A.2.3 Replace Phase
136<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
137</h4> 
138<DL><DL>
139The "Replace Phase" is used to change the space group and
140possibly unit cell for a phase. The input dialog, shown below, shows
141the current space group and unit cell parameters.
142By using the
143"Import phase from:" button at the lower right, one can read this information,
144as well as atomic parameters, from a file.
145The button to the right of the "Import phase from:" button selects
146the file format to be used. See the <A HREF="expgui_cfg.html#import">
147customization information</A> for more details.
148<img SRC="2f.gif" align=TEXTTOP>
149<br clear=all><P>
150
151Once the
152"Continue button is pressed, the space group is checked,
153as is shown in the <a href="http:#addphase">Add Phase</a> section.
154A table is then generated for input of atoms, very similar to
155that in the <a href="http:#addphase">Add Phase</a> section.
156If atom coordinates have been read from a file these atoms
157are included in the table.
158It should be noted that when a phase is replaced in EXPGUI, all atoms in
159that phase are erased. If the current atom positions are to be
160retained, the "Reenter current atoms" box in the initial
161"Replace phase" dialog should be checked, these atoms will also
162be included in the table.
163<P>
164Note that no changes are made until after the "Continue" button
165is pressed on the "Enter Atoms" dialog, so that is is safe to
166press "Cancel" at any point.
167
168<br clear=all>
169</DL></DL>
170<hr>
171<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
172<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
173</TH><TH><A Href="expgui3.html">Next page</A>
174</TH><TH><A Href="expgui1.html">Previous page</A>
175</TH></TR></TABLE>
176
177<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
178<br>
179$Revision: 269 $ $Date: 2009-12-04 23:03:14 +0000 (Fri, 04 Dec 2009) $
180</body>
181</html>
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