source: trunk/doc/expgui2.html @ 433

Last change on this file since 433 was 409, checked in by toby, 11 years ago

# on 2001/08/24 18:56:53, toby did:
updates

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  • Property rcs:date set to 2001/08/24 18:56:53
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  • Property rcs:rev set to 1.9
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 9.0 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<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="note.gif" alt="Note!">
59The parameter used for sorting is designated
60with a "*" on the title line above the atoms.
61<IMG SRC="note.gif" alt="Note!">
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="note.gif" alt="Note!">
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="note.gif" alt="Note!">
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 Flag" 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>
115Atoms will be included in the phase in the order they appear in the table.
116<IMG SRC="new.gif" alt="New!">
117This order can be changed by pressing the buttons in the top row of the
118table, which sorts the atoms according to the selected column. Note that
119if the "Use Flag" button is deselected, the atom appears at the bottom
120of the table.
121<P>
122When the "Add Atoms" button is pressed, the table is scanned for errors
123such as invalid numbers or unknown atom types. If an error is encountered,
124a message is displayed listing the problem(s). Corrections can then be
125made to the table before pressing the "Add Atoms" button again.
126<br clear=all><P>
127<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
128In the case of reading PowderCell .CEL files, the code may
129have to translate coordinates to shift from an Origin 1 setting
130to an Origin 2 setting. (GSAS, like many other crystallography programs,
131assumes that if a center of symmetry is present, it is located at the origin.)
132If this is done, a message like the one to the left is displayed.
133
134<br clear=all><P>
135</DL></DL>
136<a name="addatoms">
137<h4>A.2.2 Add Atoms</h4> 
138<DL><DL>
139When the "Add New Atoms" button is pressed, a table is generated,
140as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!">
141The "Import atoms from:" button can
142be used to read atoms from a file.
143The button to the right of the "Import atoms from:" button selects
144the file format to be used.
145Currently two formats are supported, the Crystallographic Information File (CIF)
146and .CEL files from PowderCell.
147See the <A HREF="expgui_cfg.html#import">
148customization information</A> for more details about importing coordinates.
149Note that unlike in the
150<a href="http:#addphase">Add Phase</a> section, the space group
151and cell parameters in the file are ignored. The "Use" button to the
152right of each atom can be deselected to prevent the atom from being used.
153<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
154<br clear=all><P>
155Atoms will be added to the phase in the order they appear in the table.
156<IMG SRC="new.gif" alt="New!">
157This order can be changed by pressing the buttons in the top row of the
158table, which sorts the atoms according to the selected column. Note that
159if the "Use Flag" button is deselected, the atom appears at the bottom
160of the table.
161<P>
162When the "Add Atoms" button is pressed, the table is scanned for errors
163such as invalid numbers or unknown atom types. If an error is encountered,
164a message is displayed listing the problem(s). Corrections can then be
165made to the table before pressing the "Add Atoms" button again.
166
167<br clear=all><P>
168</DL></DL>
169<a name="replacephase"></a><h4>
170A.2.3 Replace Phase
171<IMG SRC="note.gif" alt="Note!">
172</h4> 
173<DL><DL>
174The "Replace Phase" is used to change the space group and
175possibly unit cell for a phase. The input dialog, shown below, shows
176the current space group and unit cell parameters.
177By using the
178"Import phase from:" button at the lower right, one can read this information,
179as well as atomic parameters, from a file.
180The button to the right of the "Import phase from:" button selects
181the file format to be used.
182Currently two formats are supported, the Crystallographic Information File (CIF)
183and .CEL files from PowderCell.
184See the <A HREF="expgui_cfg.html#import">
185customization information</A> for more details about importing coordinates.
186<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
187<br clear=all><P>
188
189Once the
190"Continue button is pressed, the space group is checked,
191as is shown in the <a href="http:#addphase">Add Phase</a> section.
192A table is then generated for input of atoms, very similar to
193that in the <a href="http:#addphase">Add Phase</a> section.
194If atom coordinates have been read from a file these atoms
195are included in the table.
196It should be noted that when a phase is replaced in EXPGUI, all atoms in
197that phase are erased. If the current atom positions are to be
198retained, the "Reenter current atoms" box in the initial
199"Replace phase" dialog should be checked, these atoms will also
200be included in the table.
201<P>
202Note that no changes are made until after the "Continue" button
203is pressed on the "Enter Atoms" dialog, so that is is safe to
204press "Cancel" at any point.
205
206<br clear=all>
207</DL></DL>
208<hr>
209<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
210<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
211</TH><TH><A Href="expgui3.html">Next page</A>
212</TH><TH><A Href="expgui1.html">Previous page</A>
213</TH></TR></TABLE>
214
215<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
216<br>
217$Revision: 409 $ $Date: 2009-12-04 23:05:41 +0000 (Fri, 04 Dec 2009) $
218</body>
219</html>
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