Changeset 1115 for branches/sandbox/doc


Ignore:
Timestamp:
Feb 26, 2011 9:47:37 PM (11 years ago)
Author:
toby
Message:

scan .EXP files for GENLES blowups; update web pages

Location:
branches/sandbox/doc
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • branches/sandbox/doc/expgui.html

    r973 r1115  
    1616EXPGUI<BR>
    1717A Graphical User Interface for
    18 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
     18<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
    1919GSAS</A>
    2020<HR noshade width="75%" size="2" align="center">
     
    3434<P><P>
    3535EXPGUI is a graphical interface for the
    36 Los Alamos
    37 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
    38 GSAS</A> package.
     36<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
     37package, developed at Los Alamos and maintained now at Argonne.
    3938EXPGUI does two things:
    4039it can be used to directly modify the GSAS
     
    117116A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
    118117Los Alamos National Laboratory Report LAUR 86-748 (2000).
    119 <A HREF="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.pdf">
     118<A
     119  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
    120120[link to PDF copy of manual]
    121121</A>
     
    154154are used. The File/Save operation is done automatically before any GSAS
    155155programs, such as GENLES or EXPEDT, are run.
     156<P>
     157<A name="badexp">
     158The GSAS refinement program, GENLES, will sometimes "blow up", where the
     159  program changes varied parameters to values very far from their
     160  correct values. This occurs when parameters are highly correlated,
     161  are refining to values that are not allowed, or some of the refined parameters have
     162  very little impact on the quality of the fit. When this happens,
     163  invalid values are written to the GSAS experiment file that contain
     164  either asterisks (****) or the string "NAN" (not a number). Such
     165  files cannot be used for additional GENLES runs.
     166  <P>
     167  When EXPGUI reads a .EXP file it scans it for evidence of a previous
     168  failure of a GENLES refinement and warns if a problem is
     169  noted. Please note that this scan is not perfect and occasionally
     170  you may be warned in cases where the file is fine (if possible,
     171  please send such .EXP file to Brian Toby so this scan can be improved.)
     172  When such a "bad" .EXP file is located, one can "revert" to an
     173  archived copy of a previous experiment file (with suffix .Oxx). This
     174  can be done with the Revert menu item in the File menu. Note that
     175clicking on a file in the file selection window causes it to be
     176scanned and shows the status of that refinement. Also note that
     177usually the last good archived file has settings that will produce the same bad
     178refinement, so it is necessary to either revert further back, or to
     179change the refinement options before running GENLES.
    156180<P>
    157181
     
    681705<A name=tcltk>
    682706<H2>
    683 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
     707<A Href="http://www.tcl.tk">
    684708Tcl/Tk</A></H2>
    685709The
    686 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
     710<A Href="http://www.tcl.tk">
    687711Tcl/Tk program</A> is a platform-independent scripting language that is
    688712used to implement most of EXPGUI. This software is available for free
    689 and must be loaded in order to use EXPGUI. See the
    690 installation notes for
    691 <A HREF="expgui_Win_readme.html">Windows</A>,
    692 and for
    693 <A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this.
     713and must be loaded in order to use EXPGUI. A somewhat out of date
     714version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
     715more recent versions can be used, but note that the BLT package (see
     716below) is needed for all features of EXPGUI.
    694717While learning Tcl/Tk is a great thing to do, it is not a requirement
    695718for using or installing EXPGUI.
    696 
    697 <A name=winexec>
    698 <H3>
    699 WINEXEC</H3>
    700 <UL>
    701 The WINEXEC package is needed under Windows-95 and its offspring
    702 (-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation
    703 notes</A> for more details.
    704 </UL>
    705719
    706720<A name=blt>
     
    715729If this is the case, a message,
    716730"BLT Setup Error: could not access a Blt_ routine...", will be displayed.
    717 This is most common in UNIX and is discussed further in the
    718 <A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see
    719 <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
    720 http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
    721 </A> for more information on installation of BLT.
     731Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
    722732</UL>
    723733
     
    727737<UL>
    728738The
    729 <A HREF="www.hume.com">Hume
     739<A HREF="http://www.hume.com">Hume
    730740</A>
    731741Linear Algebra Tcl Package,
    732 <A HREF="www.hume.com">
     742<A HREF="http://www.hume.com/la/la.html">
    733743La</A>,
    734744is used by the BKGEDIT
     
    739749should not happen, since the package is included with the EXPGUI files.
    740750So if get this error you probably have an incomplete installation.
    741 Note that the La package requires Tcl/Tk version 8.1 or higher, so that if
    742 you are using an older version of Tcl/Tk, you will need to upgrade.
    743 See the installation instructions for
    744 <A HREF="expgui_Win_readme.html">Windows</A>,
    745 and for
    746 <A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk.
     751</UL>
     752
     753<A name=winexec>
     754<H3>
     755WINEXEC</H3>
     756<UL>
     757The WINEXEC package was needed under Windows-95 and its offspring
     758(-98 and -ME). It was found in older versions of EXPGUI, but is no
     759  longer included.
    747760</UL>
    748761
     
    750763Acknowledgments</H2>
    751764Praise to Larson and
    752 Von Dreele for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
     765Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
    753766for Tcl/Tk,
    754 Przemek Klosowski</A>
     767Przemek Klosowski
    755768for convincing me to learn Tcl/Tk
    756 and Jonathan Wasserman for helping get this project started.
    757 Thanks also to
     769and Jonathan Wasserman for helping me get this project started.
     770Thanks also to
     771Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
     772bond-distance restraints module and the (soon to come) rigid body editor;
    758773Pamela Whitfield of the NRC (Canada) for writing large
    759774sections of the
     
    763778code and to John Cowgill for the "Export to GRACE" code.
    764779<P>
    765 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
     780<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
    766781GSAS</A>
    767782is written by Allen C. Larson and Robert B. Von Dreele while at
     
    770785<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
    771786EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
    772 <A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>
    773 with help from Jonathan Wasserman.
     787<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
    774788
    775789<P><hr><blockquote>
     
    786800software.
    787801
    788 <P>The author of EXPGUI is a U.S. Government employee which means that
     802<P>EXPGUI was written by a U.S. Government employee, which means that
    789803EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write
    790804new sections and make them available to the rest of the world.
     
    793807expressed or implied, or assumes any liability or responsibility
    794808for the use of this information or the software described
    795 here. Brand names cited herein are used for
    796 identification purposes and do not constitute an endorsement by NIST.
     809here.
    797810</blockquote>
    798811
  • branches/sandbox/doc/expgui_intro.html

    r971 r1115  
    7070Customization notes</A>
    7171<LI>
    72 <A HREF="tutorial3/index.html">
     72<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
    7373A well-annotated CW neutron tutorial (Alumina).</A>
    7474<B><I>A very good place to start!</I></B>
    7575<LI>
    76 <A HREF="tutorial1/index.html">
     76<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">
    7777A TOF Tutorial Example (Nickel)</A>
    7878<LI>
    79 <A HREF="tutorial2/index.html">
     79<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">
    8080A CW Neutron Tutorial Example (Garnet)</A>
    8181</UL>
     
    164164<p><br><B>Who is to blame for EXPGUI?</B>
    165165<blockquote>The initial version of the GUI part of EXPGUI was created by
    166 Jonathan Wasserman (thanks Jon!) <a href="http://www.ncnr.nist.gov/staff/toby/">Brian
     166Jonathan Wasserman (thanks Jon!) Brian
    167167Toby</a> is irresponsible for the rest.</blockquote>
    168168
     
    170170<blockquote>Gee, you want to add some features... Great! You have all the
    171171EXPGUI sources and
    172 <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">Tcl/Tk</A>
    173 is free. Oh, you want me to do it. Well, please
     172Tcl/Tk is free. Oh, you want me to do it. Well, please
    174173ask and I will try. In particular, I am looking for good ideas on
    175174how to design GUI's for different aspects of experiment editing,
     
    177176
    178177<p><br><B>Mailing List</B>
    179 <blockquote>If you would like to get news about EXPGUI, please send
    180 <a href="mailto:brian.toby@anl.gov?subject=EXPGUI Mailing List">Brian.Toby@ANL.GOV</a> e-mail. The mailing list is not active at present, but
    181 I hope to use it again to provide
     178<blockquote>If you would like to get news about EXPGUI, please
     179<a href="http://www.aps.anl.gov/mailman/listinfo/expgui">see this
     180link</a>.
     181The mailing list is used only to provide
    182182information about updates and bug fixes.
    183183</blockquote>
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