Changeset 1166 for trunk/doc/expgui.html

Timestamp:

Aug 17, 2011 6:17:04 PM (10 years ago)

Author:

toby

Message:

bring sandbox changes over to main release

File:

• trunk/doc/expgui.html (modified) (16 diffs)

trunk/doc/expgui.html

@@ -16 +16 @@
 EXPGUI<BR>
 A Graphical User Interface for 
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
 GSAS</A>
 <HR noshade width="75%" size="2" align="center">
@@ -34 +34 @@
 <P><P>
 EXPGUI is a graphical interface for the 
-Los Alamos
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
-GSAS</A> package. 
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
+package, developed at Los Alamos and maintained now at Argonne. 
 EXPGUI does two things: 
 it can be used to directly modify the GSAS 
@@ -60 +59 @@
 <TH><A Href="expgui4.html">Scaling info</A></TH>
 <TH><A Href="expgui5.html">Profile terms</A></TH>
-<TH><A Href="expgui6.html">Constraints</A></TH>
+<TH><A Href="expgui6.html">Constraints & Restraints</A></TH>
 </TR>
 <TR>
+<TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
 <TH><A Href="expgui7.html">Preferred Orientation</A></TH>
 <TH><A Href="expguic.html">Menus</A></TH>
@@ -117 +117 @@
 A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)", 
 Los Alamos National Laboratory Report LAUR 86-748 (2000).
-<A HREF="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.pdf">
+<A
+  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
 [link to PDF copy of manual]
 </A>
@@ -154 +155 @@
 are used. The File/Save operation is done automatically before any GSAS
 programs, such as GENLES or EXPEDT, are run.
+<P>
+<A name="badexp">
+The GSAS refinement program, GENLES, will sometimes "blow up", where the
+  program changes varied parameters to values very far from their
+  correct values. This occurs when parameters are highly correlated,
+  are refining to values that are not allowed, or some of the refined parameters have
+  very little impact on the quality of the fit. When this happens,
+  invalid values are written to the GSAS experiment file that contain
+  either asterisks (****) or the string "NAN" (not a number). Such
+  files cannot be used for additional GENLES runs.
+  <P>
+  When EXPGUI reads a .EXP file it scans it for evidence of a previous
+  failure of a GENLES refinement and warns if a problem is
+  noted. Please note that this scan is not perfect and occasionally
+  you may be warned in cases where the file is fine (if possible,
+  please send such .EXP file to Brian Toby so this scan can be improved.)
+  When such a "bad" .EXP file is located, one can "revert" to an
+  archived copy of a previous experiment file (with suffix .Oxx). This
+  can be done with the Revert menu item in the File menu. Note that
+clicking on a file in the file selection window causes it to be
+scanned and shows the status of that refinement. Also note that
+usually the last good archived file has settings that will produce the same bad
+refinement, so it is necessary to either revert further back, or to
+change the refinement options before running GENLES. 
 <P>
 
@@ -475 +500 @@
 
 The INSTEDIT utility is used to edit or create an instrument parameter file.
-At this time it can only be used to edit files for 
-constant-wavelength data. The utility can be started from the "Edit File"
-button in the 
+The utility can be started from the "Edit File" button in the 
 <A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the 
-the "instedit" option in the Powder menu. In the latter case, the user
-is given the chance to select an input file. If no file is selected,
-a new, empty, file is created. An example INSTEDIT window appears below.
+the "instedit" option in the Powder menu. Alternately, to create a new
+  instrument parameter file, choose Powder menu option "New InstParm
+  file". (It is also possible 
+  to create a new file using the standard instedit by selecting
+  "Cancel" when asked for an input file.)
+An example INSTEDIT window appears below.
 <P>
 <img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
@@ -593 +619 @@
 records can slow the GSAS programs 
 (this is less of a problem on faster computers). For these reasons, it may be 
-a good idea to prune the older history records from the file. If more than 100
-history records are found in an experiment file, EXPGUI suggests that the
-older history entries be deleted. Alternately the File/EraseHistory command
-can be used to invoke the this option.
+a good idea to prune the older history records from the file.
+The File/EraseHistory command can be used to invoke the this option.
 <P>
 On the dialog the number of history records to be retained is specified. 
@@ -681 +705 @@
 <A name=tcltk>
 <H2>
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
+<A Href="http://www.tcl.tk">
 Tcl/Tk</A></H2>
 The 
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
+<A Href="http://www.tcl.tk">
 Tcl/Tk program</A> is a platform-independent scripting language that is
 used to implement most of EXPGUI. This software is available for free
-and must be loaded in order to use EXPGUI. See the 
-installation notes for 
-<A HREF="expgui_Win_readme.html">Windows</A>,
-and for
-<A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this.
+and must be loaded in order to use EXPGUI. A somewhat out of date
+version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
+more recent versions can be used, but note that the BLT package (see
+below) is needed for all features of EXPGUI.
 While learning Tcl/Tk is a great thing to do, it is not a requirement
 for using or installing EXPGUI.
-
-<A name=winexec>
-<H3>
-WINEXEC</H3>
-<UL>
-The WINEXEC package is needed under Windows-95 and its offspring 
-(-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation 
-notes</A> for more details.
-</UL>
 
 <A name=blt>
@@ -715 +729 @@
 If this is the case, a message, 
 "BLT Setup Error: could not access a Blt_ routine...", will be displayed.
-This is most common in UNIX and is discussed further in the 
-<A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see 
-<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
-http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
-</A> for more information on installation of BLT.
+Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
 </UL>
 
@@ -727 +737 @@
 <UL>
 The
-<A HREF="www.hume.com">Hume 
+<A HREF="http://www.hume.com">Hume 
 </A>
 Linear Algebra Tcl Package, 
-<A HREF="www.hume.com">
+<A HREF="http://www.hume.com/la/la.html">
 La</A>, 
 is used by the BKGEDIT
@@ -739 +749 @@
 should not happen, since the package is included with the EXPGUI files.
 So if get this error you probably have an incomplete installation.
-Note that the La package requires Tcl/Tk version 8.1 or higher, so that if 
-you are using an older version of Tcl/Tk, you will need to upgrade.
-See the installation instructions for
-<A HREF="expgui_Win_readme.html">Windows</A>,
-and for
-<A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk.
+</UL>
+
+<A name=winexec>
+<H3>
+WINEXEC</H3>
+<UL>
+The WINEXEC package was needed under Windows-95 and its offspring 
+(-98 and -ME). It was found in older versions of EXPGUI, but is no
+  longer included.
 </UL>
 
@@ -750 +763 @@
 Acknowledgments</H2>
 Praise to Larson and 
-Von Dreele for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
+Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
 for Tcl/Tk, 
-Przemek Klosowski</A>
+Przemek Klosowski
 for convincing me to learn Tcl/Tk 
-and Jonathan Wasserman for helping get this project started.
-Thanks also to 
+and Jonathan Wasserman for helping me get this project started.
+Thanks also to
+Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
+bond-distance restraints module and the (soon to come) rigid body editor;
 Pamela Whitfield of the NRC (Canada) for writing large 
 sections of the 
@@ -763 +778 @@
 code and to John Cowgill for the "Export to GRACE" code.
 <P>
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
 GSAS</A>
 is written by Allen C. Larson and Robert B. Von Dreele while at 
@@ -770 +785 @@
 <A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
 EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
-<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A> 
-with help from Jonathan Wasserman.
+<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
 
 <P><hr><blockquote>
@@ -786 +800 @@
 software.
 
-<P>The author of EXPGUI is a U.S. Government employee which means that
+<P>EXPGUI was written by a U.S. Government employee, which means that
 EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write 
 new sections and make them available to the rest of the world. 
@@ -793 +807 @@
 expressed or implied, or assumes any liability or responsibility 
 for the use of this information or the software described
-here. Brand names cited herein are used for
-identification purposes and do not constitute an endorsement by NIST.
+here.
 </blockquote>