source: trunk/doc/expgui2.html

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1<html>
2<head>
3   <title>EXPGUI</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
5   GSAS, EXPGUI">
6</HEAD>
7<style>
8A:link {text-decoration:none}
9A:vlink {text-decoration:none}
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15
16<?
17   include("/var/www/include/navigation.inc");
18   include("/var/www/include/utility.inc");
19?>
20<blockquote><font face="arial, helvetica, sans-serif">
21
22<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
23<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
24</TH><TH><A Href="expgui3.html">Next page</A>
25</TH><TH><A Href="expgui1.html">Previous page</A>
26</TH></TR></TABLE><BR CLEAR=ALL>
27
28<center><h1>
29<HR noshade width="75%" size="2" align="center">
30EXPGUI, part 2
31<HR noshade width="75%" size="2" align="center">
32</h1></center>
33
34
35<h3>A.2 Phase Panel</h3> 
36<DL><DL>
37The phase panel is used to edit information
38about the structural model(s) found in the experiment
39file. The flags for refining the unit cell and atomic parameters,
40as well as ther damping values,
41can be set  on this panel. Note that if a
42single atom is selected using the mouse, the information
43for that atom can be edited. If a group of atoms is
44selected
45<A href="expgui.html#mouseactions">(see Mouse Actions)</A>
46the damping and refinement flags
47for all the selected atoms are changed.
48<P>
49If the EXPTOOL program
50<A href="expgui.html#installation">(see the installation instructions)</A>
51is installed, buttons for adding phases and atoms will
52appear on this panel, as seen below. If the
53program is not properly installed, no errors occur, but the buttons
54do not appear.
55<P>
56Note that the order that atoms appear in this panel is
57determined by the
58<a href="expguic.html#sortatoms">"Sort Atoms by"</a> option
59in the Options Menu. <IMG SRC="note.gif" alt="Note!">
60The parameter used for sorting is designated
61with a "*" on the title line above the atoms.
62<IMG SRC="note.gif" alt="Note!">
63Clicking on this title line rotates through the sorting modes.
64</DL></DL>
65<img SRC="2.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
66<P>
67<P>
68<a name="addphase"></a>
69<h4>A.2.1 Modify Unit Cell Parameters
70<IMG SRC="new.gif" alt="New!">
71</h4> 
72<DL><DL>
73<img SRC="2g.gif" align=RIGHT alt="EXPGUI Screen snapshot">
74If the "Edit Cell" button is pressed, the unit cell parameters can be
75changed, as shown to the right. Note that only the parameters allowed
76by symmetry can be changed.
77
78<br clear=all>
79</DL></DL>
80<P>
81<a name="xform"></a>
82<h4>A.2.2 Modify Atom</h4> 
83<DL><DL>
84<img SRC="2a.jpg" align=RIGHT alt="EXPGUI Screen snapshot">
85The "Modify Atom" button ("Modify Atoms" when multiple atoms are
86  selected) provides access to additional options that can
87  transform or modify the selected atom(s) from the phase panel 
88<A href="expgui.html#mouseactions">(see Mouse Actions</A> for
89  information on selecting atoms); this opens the menu window shown to
90  the right.
91Note that changes are made to the coordinates when the buttons on this
92  window (such as
93"Transform Coordinates", "Set Occupancies",...) are pressed.
94<P><B>Modify Coordinates:</B>
95  This is used
96to transform the coordinates coordinates of the selected atoms using a
97set of  transformation relationships.
98 
99<P><B>Reset Multiplicities:</B>
100 When atom positions are edited in EXPGUI, they may be moved off from
101  or onto special positions in the cell, changing the site
102  multiplicity -- but this will not be reflected in the phase
103  display. When atoms are subsequently refined, GENLES will update the
104  multiplcities. Pressing the  "Reset Multiplicities" button cases
105  this to be done right away (I think this may not work if there are no
106  histograms present).
107
108<P><B>Xform Origin 1 to Origin 2:</B> This button is only available for those
109orthorhombic, tetragonal and cubic space groups that are listed in the
110International Tables with two origin settings. (These space groups have
111a location in the unit cell that has higher symmetry than a location of
112a center of symmetry: origin 1 is placed at the highest symmetry location;
113origin 2 is placed at the computationally reasonable location, the center
114of symmetry. GSAS only uses the origin 2 settings.)
115If coordinates have been entered in the origin 1 setting, they may be
116transformed to the origin 2 setting using this button. It is important
117  to select all atoms in the asymmetric unit before using this button.
118
119  <P><B>Modify Occupancies:</B>
120 This allows the occupancy to be set for one or more atoms. It is
121  most convenient for when many atoms will have their occupancy
122  changed at one time.
123
124<P><B>Modify Displacement Parameters:</B>
125  This allows one to set Uiso (or Uequiv) values for the selected
126  atoms (<B>Set U</B>). To change the flag that determines if the
127  selected atom(s) are represented as Isotropic or Anisotropic, press
128  the <B>Set Isotropic</B> or <B>Set Anisotropic</B> buttons.
129
130<P><B>Erase Atoms:</B>
131  The "Erase Atoms" removes the selected atoms from the phase. I
132  usually set the occupancy to 0. instead.
133 
134<P><B>Fix Atom Coordinates:</B>
135When an atom is refined in GSAS, only the coordinates that are not
136defined by site symmetry are refined. However, in some space groups,
137it is necessary to not refine additional coordinates. The most common
138example are polar space groups (P1, P2, P2<sub>1</sub>, C2,  P4, P4<sub>1</sub>, P
1394<sub>2</sub>, P4<sub>3</sub>, I4, I4<sub>1</sub>, P3, P3<sub>1</sub>, P3<sub>2</sub>, R3, P6, P6<sub>1</sub>, P6<sub>5</sub>, P6<sub>2</sub>, P6<sub>4</sub> and
140P6<sub>3</sub> - from
141<a href="http://www.ruppweb.org/Xray/comp/space_instr.htm"> Bernard Rupp's
142web site, http://www.ruppweb.org/Xray/comp/space_instr.htm</A>) where
143one or more coordinates of the origin are not defined by symmetry. In
144these space groups an appropriate number of coordinates must be fixed
145to define the origin. As an example, in P1, one x, one y and one z
146coordinate must not be refined; in space group P2<sub>1</sub>, the
1472<sub>1</sub> screw axis defines the origin at (0,0,z) so one z
148coordinate cannot be varied.
149
150Occasionally, while symmetry may allow
151atom coordinates to be varied, a crystallographer may choose to
152simplify or constrain the representation to fix the atom in a
153particular location and not refine with all allowed degrees of freedom.
154
155<IMG SRC="new.gif" alt="New!">
156 The "Fix Atom Coordinates" buttons allows a flag to be set (or
157cleared) for an atom
158to prevent refinement of selected coordinates, even when the X
159refinement flag is set. Note the addition of an "F" for the x and z
160coordinates of the first atom as shown in the phase panel, above. This
161indicates that x & z have been fixed. When the atom position is
162varied, only y will be optimized.
163
164<br clear=all>
165</DL></DL>
166<P>
167<a name="addphase"></a>
168<h4>A.2.3 Add Phase</h4> 
169<DL><DL>
170When the "Add Phase" button is pressed, a dialog is created where the
171space group and unit cell constants can be entered (below).
172<IMG SRC="note.gif" alt="Note!">
173By using the
174"Import phase from:" button at the lower right, one can read this information,
175as well as atomic parameters, from a file.
176The button to the right of the "Import phase from:" button selects
177the file format to be used.
178See the <A HREF="expgui.html#import">coordinate import discussion</A> 
179for description of available formats.
180Note that it is relatively easy to add new routines for
181importing coordinates;
182see the <A HREF="expgui_cfg.html#import">
183customization information</A> for more details.
184<BR>
185<img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P>
186<img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot">
187After the "Continue" button is pressed, the spacegroup is checked and the
188generated symmetry operators are shown. These should be checked carefully,
189as GSAS will correctly generate a variety of standard and non-standard
190spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
191describe different (non-standard) space groups.
192<br clear=all><P>
193The EXPTOOL program is then run and the output is
194optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>).
195<P>
196If atom coordinates have been read from a file, along with the
197cell and space group, the "add new atoms" dialog is then shown, with the
198atoms displayed (as below.)
199If the file contains atoms that should not be included
200in the .EXP file, the "Use Flag" button to the
201right of each atom can be deselected to prevent the atom from being used.
202<img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot">
203<br clear=all>
204Atoms will be included in the phase in the order they appear in the table.
205<IMG SRC="new.gif" alt="New!">
206This order can be changed by pressing the buttons in the top row of the
207table, which sorts the atoms according to the selected column. Note that
208if the "Use Flag" button is deselected, the atom appears at the bottom
209of the table.
210<P>
211When the "Add Atoms" button is pressed, the table is scanned for errors
212such as invalid numbers or unknown atom types. If an error is encountered,
213a message is displayed listing the problem(s). Corrections can then be
214made to the table before pressing the "Add Atoms" button again.
215<br clear=all><P>
216<img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot">
217In the case of reading PowderCell .CEL files, the code may
218have to translate coordinates to shift from an Origin 1 setting
219to an Origin 2 setting. (GSAS, like many other crystallography programs,
220assumes that if a center of symmetry is present, it is located at the origin.)
221If this is done, a message like the one to the left is displayed.
222
223<br clear=all><P>
224</DL></DL>
225<a name="addatoms">
226<h4>A.2.4 Add Atoms</h4> 
227<DL><DL>
228When the "Add New Atoms" button is pressed, a table is generated,
229as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!">
230The "Import atoms from:" button can
231be used to read atoms from a file.
232The button to the right of the "Import atoms from:" button selects
233the file format to be used.
234See the <A HREF="expgui.html#import">coordinate import discussion</A> 
235for description of available formats and
236the <A HREF="expgui_cfg.html#import">
237customization information</A> for more details about adding
238additional formats.
239Note that unlike in the
240<a href="http:#addphase">Add Phase</a> section, the space group
241and cell parameters in the imported file are ignored. The "Use" button to the
242right of each atom can be deselected to prevent the atom from being used.
243<img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot">
244<br clear=all><P>
245Atoms will be added to the phase in the order they appear in the table.
246<IMG SRC="new.gif" alt="New!">
247This order can be changed by pressing the buttons in the top row of the
248table, which sorts the atoms according to the selected column. Note that
249if the "Use Flag" button is deselected, the atom appears at the bottom
250of the table.
251<P>
252When the "Add Atoms" button is pressed, the table is scanned for errors
253such as invalid numbers or unknown atom types. If an error is encountered,
254a message is displayed listing the problem(s). Corrections can then be
255made to the table before pressing the "Add Atoms" button again.
256
257<br clear=all><P>
258</DL></DL>
259<a name="replacephase"></a>
260<h4>A.2.5 Replace Phase</h4> 
261<DL><DL>
262The "Replace Phase" is used to change the space group and
263possibly unit cell for a phase. The input dialog, shown below, shows
264the current space group and unit cell parameters.
265By using the
266"Import phase from:" button at the lower right, one can read this information,
267as well as atomic parameters, from a file.
268The button to the right of the "Import phase from:" button selects
269the file format to be used.
270See the <A HREF="expgui.html#import">coordinate import discussion</A> 
271for description of available formats and
272the <A HREF="expgui_cfg.html#import">
273customization information</A> for more details about adding
274additional formats.
275<img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot">
276<br clear=all><P>
277
278Once the
279"Continue button is pressed, the space group is checked,
280as is shown in the <a href="http:#addphase">Add Phase</a> section.
281A table is then generated for input of atoms, very similar to
282that in the <a href="http:#addphase">Add Phase</a> section.
283If atom coordinates have been read from a file these atoms
284are included in the table.
285It should be noted that when a phase is replaced in EXPGUI, all atoms in
286that phase are erased. If the current atom positions are to be
287retained, the "Reenter current atoms" box in the initial
288"Replace phase" dialog should be checked, these atoms will also
289be included in the table.
290<P>
291Note that no changes are made until after the "Continue" button
292is pressed on the "Enter Atoms" dialog, so that is is safe to
293press "Cancel" at any point.
294
295<br clear=all>
296</DL></DL>
297<hr>
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299<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
300</TH><TH><A Href="expgui3.html">Next page</A>
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303
304</blockquote>
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