Changeset 269 for trunk

Timestamp:

Dec 4, 2009 5:03:14 PM (14 years ago)

Author:

toby

Message:

# on 2000/08/21 19:27:43, toby did:
describe coordinate import routines
pretty up page

File:

• trunk/doc/expgui2.html (modified) (4 diffs, 3 props)

trunk/doc/expgui2.html

@@ -21 +21 @@
 <hr>
 
+<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
+<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
+</TH><TH><A Href="expgui3.html">Next page</A>
+</TH><TH><A Href="expgui1.html">Previous page</A>
+</TH></TR></TABLE><BR CLEAR=ALL>
+
 <center><h1>
-EXPGUI
+EXPGUI, part 2
 </h1></center>
-<A Href="expgui.html">EXPGUI top</A>
+
 
 <h3>A.2 Phase Pane</h3> 
@@ -50 +56 @@
 determined by the 
 <a href="expguic.html#sortatoms">"Sort Atoms by"</a> option 
-in the Options Menu. The parameter used for sorting is designated 
+in the Options Menu. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
+The parameter used for sorting is designated 
 with a "*" on the title line above the atoms. 
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
 Clicking on this title line rotates through the sorting modes.
 </DL></DL>
@@ -57 +65 @@
 <P>
 <img SRC="2a.gif" align=LEFT>
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
 If one or more atoms have been selected
 <A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
@@ -65 +74 @@
 Note that no changes are actually made, until the 
 "Transform Coordinates", "Set Occupancies",... buttons are pressed.
+<br clear=all>
+<P>
+<a name="addphase">
+</a><h4>A.2.1 Add Phase</h4> 
+<DL><DL>
+When the "Add Phase" button is pressed, a dialog is created where the 
+space group and unit cell constants can be entered (below). 
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
+By using the 
+"Import phase from:" button at the lower right, one can read this information,
+as well as atomic parameters, from a file. 
+The button to the right of the "Import phase from:" button selects 
+the file format to be used. See the <A HREF="expgui_cfg.html#import">
+customization information</A> for more details.
+<BR>
+<img SRC="2b.gif" align=TEXTTOP><P>
+<img SRC="2c.gif" align=LEFT>
+After the "Continue" button is pressed, the spacegroup is checked and the 
+generated symmetry operators are shown. These should be checked carefully,
+as GSAS will correctly generate a variety of standard and non-standard
+spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
+describe different (non-standard) space groups.
+<br clear=all><P>
+The EXPTOOL program is then run and the output is optionally displayed.
+If atom coordinates have been read from a file, along with the 
+cell and space group, the "add new atoms" dialog is then shown, with the
+atoms displayed (as below.)
+If the file contains atoms that should not be included 
+in the .EXP file, the "Use" button to the 
+right of each atom can be deselected to prevent the atom from being used. 
+<img SRC="2d.gif" align=LEFT>
+<br clear=all><P>
+<img SRC="2b1.gif" align=LEFT>
+In the case of reading PowderCell .CEL files, the code may 
+have to translate coordinates to shift from an Origin 1 setting 
+to an Origin 2 setting. (GSAS, like many other crystallography programs, 
+assumes that if a center of symmetry is present, it is located at the origin.)
+If this is done a message like the one to the left is displayed. 
+
+<br clear=all><P>
+</DL></DL>
+<h4>A.2.2 Add Atoms</h4> 
+<DL><DL>
+When the "Add New Atoms" button is pressed, a table is generated, 
+as seen below, to enter atoms. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
+The "Import atoms from:" button can 
+be used to read atoms from a file. 
+The button to the right of the "Import atoms from:" button selects 
+the file format to be used. See the <A HREF="expgui_cfg.html#import">
+customization information</A> for more details.
+Note that unlike in the 
+<a href="http:#addphase">Add Phase</a> section, the space group 
+and cell parameters in the file are ignored. The "Use" button to the 
+right of each atom can be deselected to prevent the atom from being used. 
+<img SRC="2e.gif" align=LEFT>
+
+<br clear=all><P>
+</DL></DL>
+<h4>
+A.2.3 Replace Phase
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
+</h4> 
+<DL><DL>
+The "Replace Phase" is used to change the space group and 
+possibly unit cell for a phase. The input dialog, shown below, shows
+the current space group and unit cell parameters.
+By using the 
+"Import phase from:" button at the lower right, one can read this information,
+as well as atomic parameters, from a file. 
+The button to the right of the "Import phase from:" button selects 
+the file format to be used. See the <A HREF="expgui_cfg.html#import">
+customization information</A> for more details.
+<img SRC="2f.gif" align=TEXTTOP>
+<br clear=all><P>
+
+Once the 
+"Continue button is pressed, the space group is checked,
+as is shown in the <a href="http:#addphase">Add Phase</a> section.
+A table is then generated for input of atoms, very similar to
+that in the <a href="http:#addphase">Add Phase</a> section.
+If atom coordinates have been read from a file these atoms
+are included in the table.
+It should be noted that when a phase is replaced in EXPGUI, all atoms in 
+that phase are erased. If the current atom positions are to be 
+retained, the "Reenter current atoms" box in the initial 
+"Replace phase" dialog should be checked, these atoms will also 
+be included in the table.
+<P>
+Note that no changes are made until after the "Continue" button 
+is pressed on the "Enter Atoms" dialog, so that is is safe to 
+press "Cancel" at any point.
 
 <br clear=all>
+</DL></DL>
 <hr>
-<A Href="expgui.html">EXPGUI top</A>
+<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
+<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
+</TH><TH><A Href="expgui3.html">Next page</A>
+</TH><TH><A Href="expgui1.html">Previous page</A>
+</TH></TR></TABLE>
 
-<p><a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
+<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
 <br>
 $Revision$ $Date$