Changeset 523

Dec 4, 2009 5:07:35 PM (11 years ago)

# on 2002/01/22 21:06:17, toby did:
improve utility section
coordinate import/export section

1 edited


  • trunk/doc/expgui.html

    • Property rcs:date changed from 2001/12/19 18:55:42 to 2002/01/22 21:06:17
    • Property rcs:lines changed from +27 -20 to +147 -33
    • Property rcs:rev changed from 1.22 to 1.23
    r503 r523  
    74 <TR><TH BGCOLOR="#F0F0F0">Utilities:</TH>
     74<TR><TH BGCOLOR="#F0F0F0" rowspan=2>Utilities:</TH>
    7575<TH><A Href="liveplot.html">LIVEPLOT</A></TH>
    7676<TH><A Href="liveplot.html">BKGEDIT</A></TH>
    7777<TH><A Href="excledt.html">EXCLEDT</A></TH>
     80<TH><A Href="#WIDPLT">WIDPLT</A></TH>
     81<TH><A Href="#ABSPLT">ABSPLT</A></TH>
    7984<TR><TH BGCOLOR="#F0F0F0">Installation Notes:</TH>
    344349This menu contains links to several GSAS and
    345 two non-GSAS (LIVEPLOT and WIDPLT)
    346 programs used for graphical display of data and results.
     350non-GSAS programs (such as LIVEPLOT and WIDPLT)
     351used for graphical display of data and results.
    353358This menu contains links to several GSAS and
    354359one non-GSAS (LSTVIEW)
    355 programs used for analysis of results.
     360programs that are used for analysis of results.
    372 </DL></DL>
    374 <h2>D. EXPGUI Utility Programs</h2></a>
     378<h2>D. EXPGUI Utility Features</h2></a>
     379EXPGUI adds a number of useful functions to the GSAS package. Some,
     380but not all, of these features are graphically oriented.
    376382<br clear=all>
    380386LSTVIEW is used to browse through the GSAS output listing. It is
    381 invoked by the "lstview" command in the GUI.
     387invoked by the "lstview" command in the GUI.
     388<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
     389to shorten the .LST file by removing older results from the beginning
     390of the file.
     391<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
     392as a function of the cycle number.
    382393<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
    386397<H3>D.2 LIVEPLOT</H3>
    388 LIVEPLOT shows the observed, calculated and difference plots for powder
     399<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated
     400and difference plots for powder
    389401refinements. The plot is updated as the refinement progresses. The mouse can
    390402be used to zoom in on sections of the plot.
    391403LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
    392 <CENTER><IMG SRC="liveplot.gif" alt="EXPGUI Screen snapshot"></CENTER>
     404<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
    393405<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
    394406LIVEPLOT can now be enhanced to superimpose peak locations for
    395407input unit cells or peaks from JCPDS/ICDD entries.
     408See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
     409further documentation, and in particular, the
    396410See the <A HREF="liveplot.html#customize">
    397 LIVEPLOT customization information</A>
    398 or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory.
    399 <P>
    400 </DL></DL>
    402 <br clear=all>
    403 <H3>D.3 WIDPLT</H3>
    404 <DL><DL>
    405 WIDPLT can be used to plot the actual peak widths generated by the profile
    406 parameters used in GSAS.
    407 It is possible to define reference curves
    408 that are loaded automatically.
    409 WIDPLT uses the <A href="#blt">BLT</A> graphics package.
     411LIVEPLOT customization information</A>.
     414<br clear=all>
     415<H3>D.3 BKGEDIT</H3>
     417<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     418<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to
     419fit a GSAS background function to a set of fixed
     420background points that are input using the mouse.
     421The mouse can also be used to zoom in on sections of the plot.
     422BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
     423<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
     424See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
     425further documentation.
     428<br clear=all>
     429<H3>D.4 EXCLEDT</H3>
     431<A HREF="excledt.html">EXCLEDT</A> is used to edit the
     432range of data used from a histogram. The upper & lower ranges
     433can be adjusted to include more data or use less. Also, it is
     434possible to remove sections of the data (exclude regions) that
     435have known systematic errors that cannot be modeled.
     436EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
     437<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
     438See the <A HREF="excledt.html">EXECLEDT web page</A> for
     439further documentation.
     440<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     441EXCLEDT can now be used to change the simulation range for dummy histograms.
     445<br clear=all>
     446<a name="WIDPLT"></a>
     447<a name="ABSPLT"></a>
     448<H3>D.5 WIDPLT and ABSPLT</H3>
     450WIDPLT is used to plot the peak widths that are generated by a set
     451of GSAS profile terms (constant wavelength equations, only).
     452The parameters from each phase & histogram will be
     453read from the .EXP file. It is also possible to input parameters manually.
     454By creating a special file (<A HREF="expgui_cfg.html#import">
     455described in the customization information</A>), it
     456is possible to define reference curves
     457that are loaded automatically for comparison.
    410458<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
     460ABSPLT is used to plot the absorption/reflectivity correction for a
     461histogram. Values are loaded from the histogram(s), but can be edited manually.
     463WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
    414468<a name="ConvertUnix"></a>
    415469<a name="ConvertWin"></a>
    416 <h3>D.4 File Conversions</h3>
     470<h3>D.6 File Conversions</h3>
    434488<br clear=all>
    435489<a name="Composition"></a>
    436 <h3>D.5 Compute Composition</h3>
     490<h3>D.7 Compute Composition</h3>
    438492The composition box shows the unit cell and asymmetric unit composition
    443497<br clear=all>
    444 <a name="ExportMSI"></a>
    445 <h3>D.6 Export coordinates in MSI .xtl format</h3>
    446 <DL><DL>
    447 The Export/exp2xtl routine writes a .xtl file, as is used in Insight-II and
    448 Cerius2 (Molecular Simulations, Inc.). Note that space groups are not named
    449 exactly the same in the two programs and the origin may need to be specified
    450 as "origin 2", for space groups where the center of symmetry is not at the
    451 origin. It is up to the user to get things right.
    452 </DL></DL>
    454 <br clear=all>
    455498<a name="DeleteHistoryRecords"></a>
    456 <h3>D.7 Delete History Records</h3>
     499<h3>D.8 Delete History Records</h3>
    458501Every time a GSAS program (including EXPGUI) is run, an entry is added to
    469512Also, after records have been deleted, the remaining records can be renumbered
    470513starting with 1, so that the 999 record limit is not reached.
     516<h2>E. Coordinate Export & Import Features</h2></a>
     517EXPGUI can be used to read coordinates in formats not
     518supported in GSAS. Coordinates can also be exported in a variety of
     519formats as well.
     521<A name="import">
     522<h3>E.1 Coordinate Import Formats</h3>
     523Coordinates can be imported using the
     524<A HREF="expgui2.html#addphase">"Add Phase"</A>,
     525<A HREF="expgui2.html#addatoms">"Add Atoms"</A> or
     526<A HREF="expgui2.html#replacephase">"Replace Phase"</A>
     527buttons on the <A HREF="expgui2.html">Phase Pane</A>, by choosing
     528the format from the pull-down list to the right of the
     529"Import atoms/phase from" button. The formats currently supported
     530are listed below.
     531Note that it is relatively easy to add new routines for
     532importing coordinates;
     533see the <A HREF="expgui_cfg.html#import">
     534customization information</A> for more details.
     536<DT><B>Crystallographic Information File (CIF)</B><DD>
     537Coordinates can be read from single block or multiblock CIF files
     538using DDL1. If more than one block containing coordinates is found in the
     539file, a CIF browser is available to help select the desired block.
     540<DT><B>PowderCell .CEL files</B><DD>
     541This format is used by the DOS and Windows PowderCell program, a valuable
     542program for the transformation and visualization of structures.
     543<DT><B>GSAS .EXP files</B><DD>
     544This routine is used to copy coordinates, unit cell parameters and space group
     545information from other GSAS experiment (.EXP) files.
     548<A name="export">
     549<h3>E.2 Coordinate Export Formats</h3>
     550Coordinates can be written using the Import/Export=>"Coord Export" menu.
     551Note that contents of the submenu will depend on the
     552number of export routines found in the EXPGUI directory when the menu
     553is first created, thus it is relatively easy to add new routines for
     554importing coordinates;
     555see the <A HREF="expgui_cfg.html#export">
     556customization information</A> for more details.
     558<DT><B>Crystallographic Information File (CIF)</B><DD>
     559Powder Diffraction Crystallographic Information files (pdCIFs) can
     560be created by the GSAS2CIF program. The GSAS2CIF menu item
     561invokes this program.
     562<a name="ExportMSI"></a>
     563<DT><B>MSI .xtl format</B><DD>
     564This writes a .xtl file, as is used in Insight-II and
     565Cerius2 (Molecular Simulations, Inc.). The routine
     566attempts to convert GSAS space group names properly, as well as
     567correctly label "Origin 2" setting, however, the naming conversion
     568will not work for all valid GSAS space groups. Some effort may be needed
     569by the user to get everything worked out correctly.
     570<a name="ExportSPF"></a>
     571<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
     572This writes a .spf file, as used in
     573<A HREF="">Platon</A> and
     574<A HREF="">Pluton</A> by A. L. Spek.
     575Some attempt is made to get space group naming right, but there is
     576no assurance of quality here.
     577<a name="ExportSHELX"></a>
     578<DT><B>SHELX .ins format</B><DD>
     579This writes coordinates and symmetry, as used in the SHELX-97 program, and
     580perhaps as used some other programs, such as CrystalMaker. In addition to
     581exporing the coordinates and displacement parameters, the fields that
     582are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the
     583wavelength, included as the first number on the CELL "card", is set to the
     584arbitrary value of 1/2.
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