source: trunk/doc/expgui2.html @ 480

Last change on this file since 480 was 454, checked in by toby, 12 years ago

# on 2001/10/14 05:32:26, toby did:
.EXP coord import

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  • Property rcs:date set to 2001/10/14 05:32:26
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  • Property rcs:rev set to 1.10
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 9.1 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 three formats are supported,
92the Crystallographic Information File (CIF),
93.CEL files from PowderCell and importing coordinates from other
94GSAS .EXP files.
95Note that it is relatively easy to add new routines for
96importing coordinates;
97see the <A HREF="expgui_cfg.html#import">
98customization information</A> for more details.
99<BR>
100<img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P>
101<img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot">
102After the "Continue" button is pressed, the spacegroup is checked and the
103generated symmetry operators are shown. These should be checked carefully,
104as GSAS will correctly generate a variety of standard and non-standard
105spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
106describe different (non-standard) space groups.
107<br clear=all><P>
108The EXPTOOL program is then run and the output is
109optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>).
110<P>
111If atom coordinates have been read from a file, along with the
112cell and space group, the "add new atoms" dialog is then shown, with the
113atoms displayed (as below.)
114If the file contains atoms that should not be included
115in the .EXP file, the "Use Flag" button to the
116right of each atom can be deselected to prevent the atom from being used.
117<img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot">
118<br clear=all>
119Atoms will be included in the phase in the order they appear in the table.
120<IMG SRC="new.gif" alt="New!">
121This order can be changed by pressing the buttons in the top row of the
122table, which sorts the atoms according to the selected column. Note that
123if the "Use Flag" button is deselected, the atom appears at the bottom
124of the table.
125<P>
126When the "Add Atoms" button is pressed, the table is scanned for errors
127such as invalid numbers or unknown atom types. If an error is encountered,
128a message is displayed listing the problem(s). Corrections can then be
129made to the table before pressing the "Add Atoms" button again.
130<br clear=all><P>
131<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
132In the case of reading PowderCell .CEL files, the code may
133have to translate coordinates to shift from an Origin 1 setting
134to an Origin 2 setting. (GSAS, like many other crystallography programs,
135assumes that if a center of symmetry is present, it is located at the origin.)
136If this is done, a message like the one to the left is displayed.
137
138<br clear=all><P>
139</DL></DL>
140<a name="addatoms">
141<h4>A.2.2 Add Atoms</h4> 
142<DL><DL>
143When the "Add New Atoms" button is pressed, a table is generated,
144as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!">
145The "Import atoms from:" button can
146be used to read atoms from a file.
147The button to the right of the "Import atoms from:" button selects
148the file format to be used.
149Currently two formats are supported, the Crystallographic Information File (CIF)
150and .CEL files from PowderCell.
151See the <A HREF="expgui_cfg.html#import">
152customization information</A> for more details about importing coordinates.
153Note that unlike in the
154<a href="http:#addphase">Add Phase</a> section, the space group
155and cell parameters in the file are ignored. The "Use" button to the
156right of each atom can be deselected to prevent the atom from being used.
157<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
158<br clear=all><P>
159Atoms will be added to the phase in the order they appear in the table.
160<IMG SRC="new.gif" alt="New!">
161This order can be changed by pressing the buttons in the top row of the
162table, which sorts the atoms according to the selected column. Note that
163if the "Use Flag" button is deselected, the atom appears at the bottom
164of the table.
165<P>
166When the "Add Atoms" button is pressed, the table is scanned for errors
167such as invalid numbers or unknown atom types. If an error is encountered,
168a message is displayed listing the problem(s). Corrections can then be
169made to the table before pressing the "Add Atoms" button again.
170
171<br clear=all><P>
172</DL></DL>
173<a name="replacephase"></a><h4>
174A.2.3 Replace Phase
175<IMG SRC="note.gif" alt="Note!">
176</h4> 
177<DL><DL>
178The "Replace Phase" is used to change the space group and
179possibly unit cell for a phase. The input dialog, shown below, shows
180the current space group and unit cell parameters.
181By using the
182"Import phase from:" button at the lower right, one can read this information,
183as well as atomic parameters, from a file.
184The button to the right of the "Import phase from:" button selects
185the file format to be used.
186Currently two formats are supported, the Crystallographic Information File (CIF)
187and .CEL files from PowderCell.
188See the <A HREF="expgui_cfg.html#import">
189customization information</A> for more details about importing coordinates.
190<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
191<br clear=all><P>
192
193Once the
194"Continue button is pressed, the space group is checked,
195as is shown in the <a href="http:#addphase">Add Phase</a> section.
196A table is then generated for input of atoms, very similar to
197that in the <a href="http:#addphase">Add Phase</a> section.
198If atom coordinates have been read from a file these atoms
199are included in the table.
200It should be noted that when a phase is replaced in EXPGUI, all atoms in
201that phase are erased. If the current atom positions are to be
202retained, the "Reenter current atoms" box in the initial
203"Replace phase" dialog should be checked, these atoms will also
204be included in the table.
205<P>
206Note that no changes are made until after the "Continue" button
207is pressed on the "Enter Atoms" dialog, so that is is safe to
208press "Cancel" at any point.
209
210<br clear=all>
211</DL></DL>
212<hr>
213<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
214<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
215</TH><TH><A Href="expgui3.html">Next page</A>
216</TH><TH><A Href="expgui1.html">Previous page</A>
217</TH></TR></TABLE>
218
219<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
220<br>
221$Revision: 454 $ $Date: 2009-12-04 23:06:26 +0000 (Fri, 04 Dec 2009) $
222</body>
223</html>
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