Changeset 523

Timestamp:

Dec 4, 2009 5:07:35 PM (14 years ago)

Author:

toby

Message:

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

File:

• trunk/doc/expgui.html (modified) (10 diffs, 3 props)

trunk/doc/expgui.html

@@ -72 +72 @@
 <TH>&nbsp;</TH>
 </TR>
-<TR><TH BGCOLOR="#F0F0F0">Utilities:</TH>
+<TR><TH BGCOLOR="#F0F0F0" rowspan=2>Utilities:</TH>
 <TH><A Href="liveplot.html">LIVEPLOT</A></TH>
 <TH><A Href="liveplot.html">BKGEDIT</A></TH>
 <TH><A Href="excledt.html">EXCLEDT</A></TH>
+</TR>
+<TR>
+<TH><A Href="#WIDPLT">WIDPLT</A></TH>
+<TH><A Href="#ABSPLT">ABSPLT</A></TH>
+<TH>&nbsp;</TH>
 </TR>
 <TR><TH BGCOLOR="#F0F0F0">Installation Notes:</TH>
@@ -343 +348 @@
 <DL><DL>
 This menu contains links to several GSAS and 
-two non-GSAS (LIVEPLOT and WIDPLT)
-programs used for graphical display of data and results.
+non-GSAS programs (such as LIVEPLOT and WIDPLT)
+used for graphical display of data and results.
 </DL></DL>
 
@@ -353 +358 @@
 This menu contains links to several GSAS and 
 one non-GSAS (LSTVIEW)
-programs used for analysis of results.
+programs that are used for analysis of results.
 </DL></DL>
 
@@ -370 +375 @@
 exporting.
 </DL></DL>
-</DL></DL>
-
-<h2>D. EXPGUI Utility Programs</h2></a>
+
+<h2>D. EXPGUI Utility Features</h2></a>
+EXPGUI adds a number of useful functions to the GSAS package. Some,
+but not all, of these features are graphically oriented.
 
 <br clear=all>
@@ -379 +385 @@
 <DL><DL>
 LSTVIEW is used to browse through the GSAS output listing. It is
-invoked by the "lstview" command in the GUI.
+invoked by the "lstview" command in the GUI. 
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
+to shorten the .LST file by removing older results from the beginning
+of the file.
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
+as a function of the cycle number.
 <CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
 </DL></DL>
@@ -386 +397 @@
 <H3>D.2 LIVEPLOT</H3>
 <DL><DL>
-LIVEPLOT shows the observed, calculated and difference plots for powder
+<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated 
+and difference plots for powder
 refinements. The plot is updated as the refinement progresses. The mouse can 
 be used to zoom in on sections of the plot. 
 LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
-<CENTER><IMG SRC="liveplot.gif" alt="EXPGUI Screen snapshot"></CENTER>
+<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
 LIVEPLOT can now be enhanced to superimpose peak locations for 
 input unit cells or peaks from JCPDS/ICDD entries. 
+See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
+further documentation, and in particular, the
 See the <A HREF="liveplot.html#customize">
-LIVEPLOT customization information</A> 
-or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory.
-<P>
-</DL></DL>
-
-<br clear=all>
-<H3>D.3 WIDPLT</H3>
-<DL><DL>
-WIDPLT can be used to plot the actual peak widths generated by the profile
-parameters used in GSAS. 
-It is possible to define reference curves 
-that are loaded automatically. 
-WIDPLT uses the <A href="#blt">BLT</A> graphics package.
+LIVEPLOT customization information</A>.
+<P>
+</DL></DL>
+<br clear=all>
+<H3>D.3 BKGEDIT</H3>
+<DL><DL>
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
+<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to 
+fit a GSAS background function to a set of fixed 
+background points that are input using the mouse.
+The mouse can also be used to zoom in on sections of the plot. 
+BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
+<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
+See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
+further documentation.
+<P>
+</DL></DL>
+<br clear=all>
+<H3>D.4 EXCLEDT</H3>
+<DL><DL>
+<A HREF="excledt.html">EXCLEDT</A> is used to edit the
+range of data used from a histogram. The upper & lower ranges
+can be adjusted to include more data or use less. Also, it is 
+possible to remove sections of the data (exclude regions) that
+have known systematic errors that cannot be modeled.
+EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
+<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
+See the <A HREF="excledt.html">EXECLEDT web page</A> for
+further documentation.
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
+EXCLEDT can now be used to change the simulation range for dummy histograms.
+<P>
+</DL></DL>
+
+<br clear=all>
+<a name="WIDPLT"></a>
+<a name="ABSPLT"></a>
+<H3>D.5 WIDPLT and ABSPLT</H3>
+<DL><DL>
+WIDPLT is used to plot the peak widths that are generated by a set
+of GSAS profile terms (constant wavelength equations, only). 
+The parameters from each phase & histogram will be
+read from the .EXP file. It is also possible to input parameters manually.
+By creating a special file (<A HREF="expgui_cfg.html#import">
+described in the customization information</A>), it
+is possible to define reference curves 
+that are loaded automatically for comparison.
 <CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
+<P>
+ABSPLT is used to plot the absorption/reflectivity correction for a
+histogram. Values are loaded from the histogram(s), but can be edited manually.
+<P>
+WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
+
 </DL></DL>
 
@@ -414 +468 @@
 <a name="ConvertUnix"></a>
 <a name="ConvertWin"></a>
-<h3>D.4 File Conversions</h3> 
+<h3>D.6 File Conversions</h3> 
 <DL><DL>
 <P>
@@ -434 +488 @@
 <br clear=all>
 <a name="Composition"></a>
-<h3>D.5 Compute Composition</h3> 
+<h3>D.7 Compute Composition</h3> 
 <DL><DL>
 The composition box shows the unit cell and asymmetric unit composition
@@ -442 +496 @@
 
 <br clear=all>
-<a name="ExportMSI"></a>
-<h3>D.6 Export coordinates in MSI .xtl format</h3> 
-<DL><DL>
-The Export/exp2xtl routine writes a .xtl file, as is used in Insight-II and
-Cerius2 (Molecular Simulations, Inc.). Note that space groups are not named 
-exactly the same in the two programs and the origin may need to be specified
-as "origin 2", for space groups where the center of symmetry is not at the 
-origin. It is up to the user to get things right.
-</DL></DL>
-
-<br clear=all>
 <a name="DeleteHistoryRecords"></a>
-<h3>D.7 Delete History Records</h3> 
+<h3>D.8 Delete History Records</h3> 
 <DL><DL>
 Every time a GSAS program (including EXPGUI) is run, an entry is added to 
@@ -469 +512 @@
 Also, after records have been deleted, the remaining records can be renumbered
 starting with 1, so that the 999 record limit is not reached.
+</DL></DL>
+
+<h2>E. Coordinate Export & Import Features</h2></a>
+EXPGUI can be used to read coordinates in formats not 
+supported in GSAS. Coordinates can also be exported in a variety of 
+formats as well. 
+
+<A name="import">
+<h3>E.1 Coordinate Import Formats</h3> 
+Coordinates can be imported using the 
+<A HREF="expgui2.html#addphase">"Add Phase"</A>, 
+<A HREF="expgui2.html#addatoms">"Add Atoms"</A> or
+<A HREF="expgui2.html#replacephase">"Replace Phase"</A> 
+buttons on the <A HREF="expgui2.html">Phase Pane</A>, by choosing
+the format from the pull-down list to the right of the 
+"Import atoms/phase from" button. The formats currently supported
+are listed below.
+Note that it is relatively easy to add new routines for 
+importing coordinates;
+see the <A HREF="expgui_cfg.html#import">
+customization information</A> for more details.
+<DL><DL>
+<DT><B>Crystallographic Information File (CIF)</B><DD>
+Coordinates can be read from single block or multiblock CIF files
+using DDL1. If more than one block containing coordinates is found in the
+file, a CIF browser is available to help select the desired block.
+<DT><B>PowderCell .CEL files</B><DD>
+This format is used by the DOS and Windows PowderCell program, a valuable 
+program for the transformation and visualization of structures.
+<DT><B>GSAS .EXP files</B><DD>
+This routine is used to copy coordinates, unit cell parameters and space group
+information from other GSAS experiment (.EXP) files.
+</DL></DL>
+
+<A name="export">
+<h3>E.2 Coordinate Export Formats</h3> 
+Coordinates can be written using the Import/Export=>"Coord Export" menu.
+Note that contents of the submenu will depend on the 
+number of export routines found in the EXPGUI directory when the menu 
+is first created, thus it is relatively easy to add new routines for 
+importing coordinates;
+see the <A HREF="expgui_cfg.html#export">
+customization information</A> for more details.
+<DL><DL>
+<DT><B>Crystallographic Information File (CIF)</B><DD>
+Powder Diffraction Crystallographic Information files (pdCIFs) can 
+be created by the GSAS2CIF program. The GSAS2CIF menu item 
+invokes this program.
+<a name="ExportMSI"></a>
+<DT><B>MSI .xtl format</B><DD>
+This writes a .xtl file, as is used in Insight-II and
+Cerius2 (Molecular Simulations, Inc.). The routine 
+attempts to convert GSAS space group names properly, as well as 
+correctly label "Origin 2" setting, however, the naming conversion
+will not work for all valid GSAS space groups. Some effort may be needed
+by the user to get everything worked out correctly.
+<a name="ExportSPF"></a>
+<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
+This writes a .spf file, as used in 
+<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.cryst.chem.uu.nl/platon/">Platon</A> and 
+<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.cryst.chem.uu.nl/platon/">Pluton</A> by A. L. Spek.
+Some attempt is made to get space group naming right, but there is
+no assurance of quality here.
+<a name="ExportSHELX"></a>
+<DT><B>SHELX .ins format</B><DD>
+This writes coordinates and symmetry, as used in the SHELX-97 program, and
+perhaps as used some other programs, such as CrystalMaker. In addition to 
+exporing the coordinates and displacement parameters, the fields that
+are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the 
+wavelength, included as the first number on the CELL "card", is set to the
+arbitrary value of 1/2.
 </DL></DL>