Changeset 269


Ignore:
Timestamp:
Dec 4, 2009 5:03:14 PM (11 years ago)
Author:
toby
Message:

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

File:
1 edited

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  • trunk/doc/expgui2.html

    • Property rcs:date changed from 2000/08/04 19:25:35 to 2000/08/21 19:27:43
    • Property rcs:lines changed from +12 -2 to +111 -6
    • Property rcs:rev changed from 1.3 to 1.4
    r259 r269  
    2121<hr>
    2222
     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
    2329<center><h1>
    24 EXPGUI
     30EXPGUI, part 2
    2531</h1></center>
    26 <A Href="expgui.html">EXPGUI top</A>
     32
    2733
    2834<h3>A.2 Phase Pane</h3>
     
    5056determined by the
    5157<a href="expguic.html#sortatoms">"Sort Atoms by"</a> option
    52 in the Options Menu. The parameter used for sorting is designated
     58in the Options Menu. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     59The parameter used for sorting is designated
    5360with a "*" on the title line above the atoms.
     61<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
    5462Clicking on this title line rotates through the sorting modes.
    5563</DL></DL>
     
    5765<P>
    5866<img SRC="2a.gif" align=LEFT>
     67<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
    5968If one or more atoms have been selected
    6069<A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible
     
    6574Note that no changes are actually made, until the
    6675"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. See the <A HREF="expgui_cfg.html#import">
     89customization information</A> for more details.
     90<BR>
     91<img SRC="2b.gif" align=TEXTTOP><P>
     92<img SRC="2c.gif" align=LEFT>
     93After the "Continue" button is pressed, the spacegroup is checked and the
     94generated symmetry operators are shown. These should be checked carefully,
     95as GSAS will correctly generate a variety of standard and non-standard
     96spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32"
     97describe different (non-standard) space groups.
     98<br clear=all><P>
     99The EXPTOOL program is then run and the output is optionally displayed.
     100If atom coordinates have been read from a file, along with the
     101cell and space group, the "add new atoms" dialog is then shown, with the
     102atoms displayed (as below.)
     103If the file contains atoms that should not be included
     104in the .EXP file, the "Use" button to the
     105right of each atom can be deselected to prevent the atom from being used.
     106<img SRC="2d.gif" align=LEFT>
     107<br clear=all><P>
     108<img SRC="2b1.gif" align=LEFT>
     109In the case of reading PowderCell .CEL files, the code may
     110have to translate coordinates to shift from an Origin 1 setting
     111to an Origin 2 setting. (GSAS, like many other crystallography programs,
     112assumes that if a center of symmetry is present, it is located at the origin.)
     113If this is done a message like the one to the left is displayed.
     114
     115<br clear=all><P>
     116</DL></DL>
     117<h4>A.2.2 Add Atoms</h4>
     118<DL><DL>
     119When the "Add New Atoms" button is pressed, a table is generated,
     120as seen below, to enter atoms. <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     121The "Import atoms from:" button can
     122be used to read atoms from a file.
     123The button to the right of the "Import atoms from:" button selects
     124the file format to be used. See the <A HREF="expgui_cfg.html#import">
     125customization information</A> for more details.
     126Note that unlike in the
     127<a href="http:#addphase">Add Phase</a> section, the space group
     128and cell parameters in the file are ignored. The "Use" button to the
     129right of each atom can be deselected to prevent the atom from being used.
     130<img SRC="2e.gif" align=LEFT>
     131
     132<br clear=all><P>
     133</DL></DL>
     134<h4>
     135A.2.3 Replace Phase
     136<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     137</h4>
     138<DL><DL>
     139The "Replace Phase" is used to change the space group and
     140possibly unit cell for a phase. The input dialog, shown below, shows
     141the current space group and unit cell parameters.
     142By using the
     143"Import phase from:" button at the lower right, one can read this information,
     144as well as atomic parameters, from a file.
     145The button to the right of the "Import phase from:" button selects
     146the file format to be used. See the <A HREF="expgui_cfg.html#import">
     147customization information</A> for more details.
     148<img SRC="2f.gif" align=TEXTTOP>
     149<br clear=all><P>
     150
     151Once the
     152"Continue button is pressed, the space group is checked,
     153as is shown in the <a href="http:#addphase">Add Phase</a> section.
     154A table is then generated for input of atoms, very similar to
     155that in the <a href="http:#addphase">Add Phase</a> section.
     156If atom coordinates have been read from a file these atoms
     157are included in the table.
     158It should be noted that when a phase is replaced in EXPGUI, all atoms in
     159that phase are erased. If the current atom positions are to be
     160retained, the "Reenter current atoms" box in the initial
     161"Replace phase" dialog should be checked, these atoms will also
     162be included in the table.
     163<P>
     164Note that no changes are made until after the "Continue" button
     165is pressed on the "Enter Atoms" dialog, so that is is safe to
     166press "Cancel" at any point.
    67167
    68168<br clear=all>
     169</DL></DL>
    69170<hr>
    70 <A Href="expgui.html">EXPGUI top</A>
     171<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
     172<TR><TH><A  Href="expgui.html">EXPGUI top</A>
     173</TH><TH><A Href="expgui3.html">Next page</A>
     174</TH><TH><A Href="expgui1.html">Previous page</A>
     175</TH></TR></TABLE>
    71176
    72 <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>)
     177<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
    73178<br>
    74179$Revision$ $Date$
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