Changeset 148


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Timestamp:
Dec 4, 2009 5:01:12 PM (11 years ago)
Author:
toby
Message:

# on 2000/05/18 15:37:38, toby did:
add Tcl/tk logo, general editing
document atomic constraints section
keyboard shortcuts

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1 edited

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  • trunk/doc/expgui.html

    • Property rcs:date changed from 1999/10/11 20:27:39 to 2000/05/18 15:37:38
    • Property rcs:lines changed from +9 -3 to +157 -57
    • Property rcs:rev changed from 1.9 to 1.10
    r115 r148  
    11<html>
    22<head>
    3 <title>EXPGUI</title>
     3   <META NAME="Author" CONTENT="Brian H. Toby">
     4   <title>EXPGUI</title>
    45</head>
    5 <body>
    6 
    7 <center>
    8 <h1>
    9 Using EXPGUI</h1></center>
    10 
    11 <h2>Introduction</h2>
    12 EXPGUI allows two types of actions:
    13 it allows the different
    14 GSAS programs such as EXPEDT, GENLES, FOURIER,...
    15 to be run,
     6<BODY BGCOLOR="#FFFFFF">
     7
     8<A HREF=http://www.ncnr.nist.gov>
     9<IMG SRC="http://www.ncnr.nist.gov/images/ncnrtrans.gif"
     10alt="Link to NIST Center for Neutron Research home page"
     11ALIGN=RIGHT></A>
     12<A HREF=http://www.nist.gov>
     13<IMG SRC="http://www.ncnr.nist.gov/images/webidblue_2lineright.gif"
     14alt="Link to National Institute of Standards & Technology home page"
     15ALIGN=LEFT></A>
     16<CENTER>
     17<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
     18<IMG SRC="tcltklogo100.gif"
     19alt="Link to Tcl/Tk information">
     20</CENTER></A>
     21<hr>
     22
     23<center><h1>
     24EXPGUI<BR>
     25A Graphical User Interface for
     26<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
     27GSAS</A>
     28</h1></center>
     29<P><P>
     30EXPGUI is a graphical interface for the
     31<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
     32GSAS</A> package.
     33It allows two types of actions:
     34the different
     35GSAS</A>
     36programs such as EXPEDT, GENLES, FOURIER,...
     37can be run from a menu or by  pressing buttons,
    1638and it can be used to directly modify the GSAS
    1739experiment file without using EXPEDT.
    18 
    19 <P>
    20 Note that pictures on this page are somewhat out-of-date with respect to the
    21 current software version so they may differ from what is
    22 described in the text.
     40This document describes the functions in EXPGUI.
     41Note that pictures on this page are not updated as frequently as the
     42text.
    2343
    2444<p>
    25 Programs are invoked either through use of the menu bar
     45GSAS programs are invoked either through use of the menu bar
    2646<center><B>
    2747<br>The menu bar.
     
    3050or by "pressing" a button on the button bar. The button bar
    3151simply provides an easy way to access commonly used
    32 actions on the menu bar. Users can configure the menu
    33 bar to include their own preferred actions and, with
     52actions on the menu bar. Users can
     53<A HREF="expgui_cfg.html">
     54configure the menu bar</A> to include their own preferred actions and, with
    3455some knowledge of the program and Tcl/Tk,
    3556add their own commands to the menu bar or button bar.
     
    4263<P>
    4364Different sections of the .EXP file can be edited by selecting different
    44 panels or pages from the tabbed list. These tabs will have slightly different
    45 appearance depending on the packages
    46 available with your local version of Tcl/Tk.
     65panels or pages from the tabbed list.
    4766<center><B>
    48 <br>The panel tabs using the Tix package.
     67<br>The notebook panel tabs.
    4968<br><img SRC="panebar1.gif"  BORDER=3 >
    5069</center></B>
    51 <center><B>
    52 <br>The panel tabs without the Tix package.
    53 <br><img SRC="panebar2.gif" BORDER=3 >
    54 </center></B>
    55 If the Tix package is loaded on your machine, it will be
    56 used, but if it is not, EXPGUI will run fine without it.
    5770<P>
    5871This documentation will describe the different actions that
     
    171184</DL></DL>
    172185
     186<h2>6. Constraints panel</h2>
     187<DL><DL>
     188GSAS offers two types of restraints that can be included in a model.
     189So called "soft constraints" or "restraints" penalize the fit if
     190aspects of a model (for example, bond lengths) differ from selected values.
     191So called "hard constraints" reduce the actual number of
     192parameters in a model,
     193by grouping parameters so that a single shift (possibly scaled) is
     194applied to each parameter in the group.
     195The constraints panel is used to set these "hard constraints."
     196At this time the only constraints that can be set in EXPGUI are on atomic
     197parameters (others can be set in EXPEDT).
     198<P>
     199Note that these constraints are only applied to shifts, so that if two atoms
     200are constrained so that the shift on their occupancy is the same, but
     201the initial occupancies differ, the difference will be maintained as the
     202values refine.
     203<P>
     204<H4>Atom Constraints</H3>
     205The atom constraints editing page appears below. Note that constraints can
     206be listed sorted by constraint number, phase number, lowest atom number or
     207variable by clicking on the buttons at the top of the page.
     208<P>
     209To delete one or more constraints, click on the appropriate checkbuttons in the <B>Delete</B> column and the press the Delete button, below.
     210<img SRC="mc.gif" align=TEXTTOP>
     211Due to the way GSAS implements these constraints, a parameter can be included
     212in only one constraint. Should one or more parameters be constrained twice,
     213an error message is shown as shown below.
     214Note that the constraint number is displayed as red, for constraints that
     215have conflicts in the constraints editing page (see above.)
     216<img SRC="mcerr.gif" align=TEXTTOP>
     217<P>
     218<img SRC="mcedit.gif" align=LEFT>
     219<img SRC="mcvar.gif" align=RIGHT>
     220When the edit button for a constraint is pressed, the constraint is
     221opened for editing. Controls are available to select the phase, variable,
     222multiplier and atom(s). Note that for atom selection, use of the control key
     223and the left mouse button allow individual atoms to be selected or deselected.
     224Shift and the left mouse button allow ranges of atoms to be selected and the
     225right mouse button selects all atoms
     226<A href="#mouseactions">(see Mouse Actions)</A>.
     227<P>
     228Note that it is inappropriate
     229to constrain different types of parameters together, for example X and Uiso.
     230The left-most variable button is the "master" which
     231determines what variable are allowed in the
     232other variable buttons.
     233<P>
     234When the "New Constraint" button is pressed, a blank constraint editing
     235window is opened. Note that any variable to the right may then be selected,
     236including two special codes, Uxx and XYZU. XYZU creates four constraints,
     237requiring the shifts on x, y, z and Uiso to be the same for all the selected
     238atoms. Uxx does the same for the six anisotropic displacement parameters.
     239These special codes are valuable for atoms that share a site.
     240<P>
     241Note that only 100 parameters may be included in a constraint,
     242with one exception. When shifts for Uiso for all atoms in a phase
     243are constrained, this counts as a single parameter. If more than 100
     244parameters are entered for a constraint, an error message is shown.
     245Up to 2000 atomic constraints may be entered.
     246EXPGUI does not warn if you exceed this limit.
     247</DL></DL>
     248
    173249<a name="multiplehistogram">
    174 <h2>6. Multiple Histogram Selection</h2></a>
     250<h2>7. Multiple Histogram Selection</h2></a>
    175251<DL><DL>
    176252This mode allows parameters to be changed for groups of
     
    203279<a name="mouseactions">
    204280</DL></DL>
    205 <h2>7. Mouse Actions</h2></a>
     281<h2>8. Mouse Actions</h2></a>
    206282<DL><DL>
    207283A range of atoms or (in multiple selection mode) histograms may be
     
    213289</DL></DL>
    214290
    215 <h2>8. Menus</h2>
     291<h2>9. Menus</h2>
    216292A description of the EXPGUI menus follows along with a very
    217293brief description of the function of each menu option.
    218294Note that an option may appear under more than one menu.
    219 <H3>8.1 File Menu</H3>
     295<H3>9.1 File Menu</H3>
    220296<DL><DL>
    221297The options on the File menu as is the custom contains the commands
     
    224300<DL>
    225301<DT>expnam<DD>
    226         Select an existing GSAS experiment to be used or create a new
     302        Select an existing GSAS experiment to be used. If a name is entered
     303        that does not exists, it is possible to create a new
    227304        experiment file from scratch.
    228 <DT>Save<DD>Saves modifications to the current experiment file to disk
     305<DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S).
    229306<DT>Save As<DD>Saves modifications to the current experiment file to disk
    230307        under a new file name
    231308<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
     309<DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
    232310<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
    233 <DT>exit<DD>Exit EXPGUI
     311<DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
    234312</DL>
    235313<img SRC="m1.gif" BORDER=3 >
    236314</DL></DL>
    237315
    238 <h3>8.2 Options Menu</h3>
     316<h3>9.2 Options Menu</h3>
    239317<DL><DL>
    240318This menu contains options that determine how EXPGUI runs.
     
    244322        [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX)
    245323        or in a file named [expnam].ZIP or  [expnam].xxx (Windows)
     324<DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are
     325         shown in a separate window. When it is not set, the results are
     326        written in the .LST file.
    246327<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" page
    247328        Atoms may be displayed sorted by atom number, atom type,
     
    273354file when GENLES, POWPREF,... are run (this is so that one can change
    274355the experiment file and rerun with the current input). If this option is
    275 set, the new file is automatically read without a prompt.
     356set, the new file is automatically read without a prompt.
     357This option is not available in Windows.
    276358
    277359<DT>SaveOptions<DD>Save the current values for "Override backspace",
     
    284366</DL></DL>
    285367
    286 <h3>8.3 Powder Menu</h3>
     368<h3>9.3 Powder Menu</h3>
    287369<DL><DL>
    288370This menu contains links to GSAS programs used for powder diffraction
    289371analysis.
    290372<DL>
    291 <DT>expedt<DD>Run GSAS experiment editor
    292 <DT>powpref<DD>Powder data preparation
    293 <DT>genles<DD>Run GSAS experiment editor
     373<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
     374<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
     375<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
    294376<DT>powplot<DD>Display powder patterns
    295377<DT>rawplot<DD>Plot powder data
     
    300382</DL></DL>
    301383
    302 <h3>8.4 Single Crystal Menu</h3>
     384<h3>9.4 Single Crystal Menu</h3>
    303385<DL><DL>
    304386This menu contains links to GSAS programs used for
    305387single-rystal diffraction analysis.
    306388<DL>
    307 <DT>expedt<DD>Run GSAS experiment editor
    308 <DT>powpref<DD>Powder data preparation
     389<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
     390<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
    309391<DT>scabs<DD>Single crystal absorption
    310392<DT>scmerge<DD>Sort and merge single crystal data
     
    314396</DL></DL>
    315397
    316 <h3>8.5 Graphics Menu</h3>
     398<h3>9.5 Graphics Menu</h3>
    317399<DL><DL>
    318400This menu contains links to several GSAS and
     
    336418</DL></DL>
    337419
    338 <h3>8.6 Results Menu</h3>
     420<h3>9.6 Results Menu</h3>
    339421<DL><DL>
    340422This menu contains links to several GSAS and
     
    356438</DL></DL>
    357439
    358 <h3>8.7 Calculations Menu</h3>
     440<h3>9.7 Calculations Menu</h3>
    359441<DL><DL>
    360442This menu contains programs for useful crystallographic computations.
     
    369451</DL></DL>
    370452
    371 <h3>8.8 Import/Export Menu</h3>
     453<h3>9.8 Import/Export Menu</h3>
    372454<DL><DL>
    373455This menu contains utilities for importing information into GSAS and
     
    389471</DL></DL>
    390472
    391 <h2>9. EXPGUI Utility Programs</h2></a>
     473<h2>10. EXPGUI Utility Programs</h2></a>
    392474<DL><DL>
    393475<P><B>LSTVIEW</B>
     
    403485refinements. The plot is updated as the refinement progresses. The mouse can
    404486be used to zoom in on sections of the plot.
     487Liveplot uses the <A href="#blt">BLT</A> graphics package.
    405488<CENTER><IMG SRC="liveplot.gif"></CENTER>
    406489<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     
    417500reflection tickmarks can be displayed by holding the shift key while pressing the left mouse button.
    418501See the installation instructions for installing TCLDUMP.
    419 
    420502<P><B>WIDPLT</B>
    421503
    422 <P>widplt can be used to plot the actual peak widths generated by the profile
    423 parameters used in GSAS. It is possible to define reference curves
    424 that are loaded automatically.
     504<P>WIDPLT can be used to plot the actual peak widths generated by the profile
     505parameters used in GSAS.
     506It is possible to define reference curves
     507that are loaded automatically.
     508WIDPLT uses the <A href="#blt">BLT</A> graphics package.
    425509<CENTER><IMG SRC="widplt.gif"></CENTER>
    426510<BR>
    427511</DL></DL>
     512
     513<A name=blt>
     514<H2>
     515BLT</H2>
     516The BLT graphics package is used by the WIDPLT and LIVEPLOT routines. If the
     517package can not be loaded these routines, an error message,
     518"Error -- Unable to load the BLT package", will be displayed. A frequent
     519problem is the package is installed, but not configured so that common
     520support routines are loaded automatically. If this is the case,
     521a message, "BLT Setup Error: could not access a Blt_ routine...",
     522will be displayed.
     523Please see
     524<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
     525http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
     526</A> for more information on installation of BLT.
    428527
    429528<H2>
     
    437536and Jonathan Wasserman for starting this project.
    438537
    439 <hr>
    440 GSAS is written by Allen C. Larson and <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
     538<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
     539GSAS</A>
     540is written by Allen C. Larson and <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
    441541Robert B. Von Dreele</A>, MS-H805,
    442542Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions
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