source: trunk/doc/expgui2.html @ 291

Last change on this file since 291 was 281, checked in by toby, 11 years ago

# on 2000/09/25 20:07:22, toby did:
Add CIF import documentation

  • Property rcs:author set to toby
  • Property rcs:date set to 2000/09/25 20:07:22
  • Property rcs:lines set to +16 -7
  • Property rcs:rev set to 1.5
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 7.4 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.
89Currently two formats are supported, the Crystallographic Information File (CIF)
90and .CEL files from PowderCell.
91See the <A HREF="expgui_cfg.html#import">
92customization information</A> for more details about importing coordinates.
93<BR>
94<img SRC="2b.gif" align=TEXTTOP><P>
95<img SRC="2c.gif" align=LEFT>
96After the "Continue" button is pressed, the spacegroup is checked and the
97generated symmetry operators are shown. These should be checked carefully,
98as GSAS will correctly generate a variety of standard and non-standard
99spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
100describe different (non-standard) space groups.
101<br clear=all><P>
102The EXPTOOL program is then run and the output is optionally displayed.
103If atom coordinates have been read from a file, along with the
104cell and space group, the "add new atoms" dialog is then shown, with the
105atoms displayed (as below.)
106If the file contains atoms that should not be included
107in the .EXP file, the "Use" button to the
108right of each atom can be deselected to prevent the atom from being used.
109<img SRC="2d.gif" align=LEFT>
110<br clear=all><P>
111<img SRC="2b1.gif" align=LEFT>
112In the case of reading PowderCell .CEL files, the code may
113have to translate coordinates to shift from an Origin 1 setting
114to an Origin 2 setting. (GSAS, like many other crystallography programs,
115assumes that if a center of symmetry is present, it is located at the origin.)
116If this is done a message like the one to the left is displayed.
117
118<br clear=all><P>
119</DL></DL>
120<h4>A.2.2 Add Atoms</h4> 
121<DL><DL>
122When the "Add New Atoms" button is pressed, a table is generated,
123as seen below, to enter atoms. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
124The "Import atoms from:" button can
125be used to read atoms from a file.
126The button to the right of the "Import atoms from:" button selects
127the file format to be used.
128Currently two formats are supported, the Crystallographic Information File (CIF)
129and .CEL files from PowderCell.
130See the <A HREF="expgui_cfg.html#import">
131customization information</A> for more details about importing coordinates.
132Note that unlike in the
133<a href="http:#addphase">Add Phase</a> section, the space group
134and cell parameters in the file are ignored. The "Use" button to the
135right of each atom can be deselected to prevent the atom from being used.
136<img SRC="2e.gif" align=LEFT>
137
138<br clear=all><P>
139</DL></DL>
140<h4>
141A.2.3 Replace Phase
142<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
143</h4> 
144<DL><DL>
145The "Replace Phase" is used to change the space group and
146possibly unit cell for a phase. The input dialog, shown below, shows
147the current space group and unit cell parameters.
148By using the
149"Import phase from:" button at the lower right, one can read this information,
150as well as atomic parameters, from a file.
151The button to the right of the "Import phase from:" button selects
152the file format to be used.
153Currently two formats are supported, the Crystallographic Information File (CIF)
154and .CEL files from PowderCell.
155See the <A HREF="expgui_cfg.html#import">
156customization information</A> for more details about importing coordinates.
157<img SRC="2f.gif" align=TEXTTOP>
158<br clear=all><P>
159
160Once the
161"Continue button is pressed, the space group is checked,
162as is shown in the <a href="http:#addphase">Add Phase</a> section.
163A table is then generated for input of atoms, very similar to
164that in the <a href="http:#addphase">Add Phase</a> section.
165If atom coordinates have been read from a file these atoms
166are included in the table.
167It should be noted that when a phase is replaced in EXPGUI, all atoms in
168that phase are erased. If the current atom positions are to be
169retained, the "Reenter current atoms" box in the initial
170"Replace phase" dialog should be checked, these atoms will also
171be included in the table.
172<P>
173Note that no changes are made until after the "Continue" button
174is pressed on the "Enter Atoms" dialog, so that is is safe to
175press "Cancel" at any point.
176
177<br clear=all>
178</DL></DL>
179<hr>
180<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
181<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
182</TH><TH><A Href="expgui3.html">Next page</A>
183</TH><TH><A Href="expgui1.html">Previous page</A>
184</TH></TR></TABLE>
185
186<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
187<br>
188$Revision: 281 $ $Date: 2009-12-04 23:03:26 +0000 (Fri, 04 Dec 2009) $
189</body>
190</html>
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