Using EXPGUI

Introduction

EXPGUI allows two types of actions: it allows the different GSAS programs such as EXPEDT, GENLES, FOURIER,... to be run, and it can be used to directly modify the GSAS experiment file without using EXPEDT. Programs are invoked either through use of the menu bar
The menu bar.
or by "pressing" a button on the button bar. The button bar simply provides an easy way to access commonly used actions on the menu bar. Users can configure the menu bar to include their own preferred actions and, with some knowledge of the program and Tcl/Tk, add their own commands to the menu bar or button bar.
The button bar.

Different sections of the .EXP file can be edited by selecting different panels or pages from the tabbed list. These tabs will have slightly different appearance depending on the packages available with your local version of Tcl/Tk.

The panel tabs using the Tix package.

The panel tabs without the Tix package.
If the Tix package is loaded on your machine, it will be used, but if it is not, EXPGUI will run fine without it.

This documentation will describe the different actions that can be accomplished with the different panels and the contents of the menus.

1. LS Controls panel

The LS Controls panel shows information about the current experiment, typically found in the EXPEDT "Least Squares Controls" options.

Note that the order that histograms appear in this panel is determined by the "Sort histograms by" option in the Options Menu.

2. Phase panel

The phase panel is used to edit information about the phase or phases found in the experiment file. The cell and atomic damping and refinement flags can be changed here. Note that if a single atom is selected using the mouse, the information for that atom can be edited. If a group of atoms is selected (see Mouse Actions) the damping and refinement flags for all the selected atom can be changed at one time.

Note that the order that atoms appear in this panel is determined by the "Sort Atoms by" option in the Options Menu.

3. Histogram panel

The histogram panel is used to edit background and diffractometer constants for a histogram, as well as set damping and refinement flags for these parameters.

If "Multiple Histogram Selection" mode is set to "All", this panel is disabled. For other settings of this mode, groups of histograms can be selected and modified collectively.

Note that the order that histograms appear in this panel is determined by the "Sort histograms by" option in the Options Menu.

4. Scaling panel

The Scaling panel is used to edit the scale factor for a histogram as well as the phase fractions for each phase present in that histogram. Damping and refinement flags can also be set here.

If "Multiple Histogram Selection" mode is set to any value other than "Off," groups of histograms can be selected and modified collectively.

Note that the order that histograms appear in this panel is determined by the "Sort histograms by" option in the Options Menu.

5. Profile panel

The Profile panel is used to edit the profile values for each phase present in a histogram as well as set the refinement flags and a damping value for each phase.

If "Multiple Histogram Selection" mode is set to "All", this panel is disabled. For other settings of this mode, profile values and settings can be collectively modified for groups of histograms.

Note that the order that histograms appear in this panel is determined by the "Sort histograms by" option in the Options Menu.

6. Multiple Histogram Selection

This mode allows parameters to be changed for groups of histograms. When the "Multiple Histogram Selection" mode is off, it is possible to modify parameters and refinement flags for only a single histogram, but the other settings allow groups of histograms to be selected and modified. (see Mouse Actions). It does not make sense, however, to globally modify instrument-related parameters and flags for different histogram types. So global actions can be limited to a single class of histogram types (e.g. TOF, CW Neutron,...), which allows these parameters to be set for groups of similar histograms. Thus, if this mode is set to "All" the Histogram and Profile panels are disabled.

The setting for "Multiple Histogram Selection" mode is selected using the "Multiple Hist. Selection" item on the Options menu.

7. Mouse Actions

A range of atoms or (in multiple selection mode) histograms may be selected by dragging (holding down) the left mouse button. It is also possible to select a range by using the Shift key with the left mouse button. To select or deselect individual entries, use the Control key with the left mouse button. The right mouse button selects all entries.

8. Menus

A description of the EXPGUI menus follows along with a very brief description of the function of each menu option. Note that an option may appear under more than one menu.

8.1 File Menu

The options on the File menu as is the custom contains the commands for reading and writing experiment files, as well as starting and ending the program.

expnam: Select an existing GSAS experiment to be used
Save: Saves modifications to the current experiment file to disk
Save As: Saves modifications to the current experiment file to disk under a new file name
Reread .EXP file: Reread the last saved version of the experiment file from disk.
New_expnam: Create a new GSAS experiment from scratch
convert: Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
exit: Exit EXPGUI

8.2 Options Menu

This menu contains options that determine how EXPGUI runs.

archive EXP: Toggles archiving of .EXP files. When on, files are saved prior to each save or run of expedt in a file named [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX) or in a file named [expnam].ZIP or [expnam].xxx (Windows)
Sort atoms by: Determines the order that atoms are displayed on the "Phase" page Atoms may be displayed sorted by atom number, atom type, or by x, y or z
Sort histograms by: Determines the order that histograms are displayed on the Histogram, Scaling and Profile pages Histograms may be sorted by histogram number, histogram type, original bank number, or diffraction angle/wavelength
Multiple hist. selection: When this mode is off, it is possible to modify parameters and refinement flags for only a single histogram. For other settings, it is possible to modify parameters and flags for groups of histograms (see help for Mouse actions). It does not make sense, however, to globally modify instrument-related parameters and flags for different histogram types. So global actions can be limited to a single class of histogram types (e.g. TOF, CW Neutron,...), which allows these parameters to be set for groups of similar histograms. Thus, if this mode is set to "All" the Histogram and Profile pages are disabled.
Override backspace: This option is available in UNIX only, as there are different ways that backspace can be implemented. When option is set as "On," the backspace key is overridden to send a "delete" character. If backspace does not work in a program such as EXPEDT, change try the other setting for this option.
SaveOptions: Save the current values for "Override backspace", "Sort atoms by", "Sort histograms by" and "archive EXP" in file ~/.gsas_config (c:\.gsas_config on Windows).
liveplot_options: Used to set options for liveplot, for example, the histogram to be plotted

8.3 Powder Menu

This menu contains links to GSAS programs used for powder diffraction analysis.

expedt: Run GSAS experiment editor
powpref: Powder data preparation
genles: Run GSAS experiment editor
powplot: Display powder patterns
rawplot: Plot powder data
fitspec: Fit a TOF vanadium scattering spectrum
tofnorm: Normalize a TOF spectrum

8.4 Single Crystal Menu

This menu contains links to GSAS programs used for single-rystal diffraction analysis.

expedt: Run GSAS experiment editor
powpref: Powder data preparation
scabs: Single crystal absorption
scmerge: Sort and merge single crystal data
sxtldata: Prepare generic single crystal data

8.5 Graphics Menu

This menu contains links to several GSAS and two non-GSAS (liveplot and widplt) programs used for graphical display of data and results.

forplot: Display Fourier maps (set Fourier options in EXPEDT and then compute with FOURIER
polfplot: Display polefigures
powplot: Display powder patterns
ortep: Draw crystal structure
rawplot: Plot powder data
fourier: Generate Fourier map
forsrh: Search Fourier map for peaks
liveplot: Create a plot of powder data with zooming, automatic update and other nice features.
widplt: Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file

8.6 Results Menu

This menu contains links to several GSAS and one non-GSAS (lstview) programs used for analysis of results.

bijcalc: Thermal parameter analysis
disagl: Distance/angle calculations
reflist: List reflection data
geometry: Molecular geometry calculations
hstdmp: List powder histogram data
istats: HKL Intensity statistics
rcalc: Compute reflection resuduals
lstview: Create a box with scrollbars containing the current .LST file

8.7 Calculations Menu

This menu contains programs for useful crystallographic computations.

cllchg: Transform unit cell
fprime: Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
rducll: Unit cell reduction
spcgroup: Space group symbol interpreter
unimol: Unique molecule assembler

8.8 Import/Export Menu

This menu contains utilities for importing information into GSAS and exporting.

gsas2cif: Prepare IUCr crystallographic information (CIF) file
hklsort: Prepare HKL tables
pubtable: Prepare atom parameter tables
convert: Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
cad4rd: Prepare CAD4 single crystal data
dbwscnv: Convert a powder diffraction data file from DBWS format
x17bcnv: Convert an energy dispersive diffractogram data file from NSLS X17b
p3r3data: Prepare Siemens/Brucker P3R3 single crystal data
sxtldata: Prepare generic single crystal data

9. EXPGUI Utility Programs

LSTVIEW

lstview is used to browse through the GSAS output listing. It is invoked by the "lstview" command in the GUI.

LIVEPLOT

liveplot 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 can now be enhanced to superimpose peak locations for input unit cells or peaks from JCPDS/ICDD entries. See the LIVEPLOT customization information or read file tkGSAS_cfg.html in the gsas/tcl directory.

WIDPLT

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.

Acknowledgements

Praise to Larson and Von Dreele for GSAS, Ousterhout for Tcl/Tk and Przemek Klosowski for convincing me to learn Tcl/Tk.

GSAS is written by Allen C. Larson and Robert B. Von Dreele, MS-H805, Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions or kudos concerning GSAS should be sent to Robert B. Von Dreele at vondreele@lanl.gov

GSAS is Copyright, 1984-1997, The Regents of the University of California. The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36) by the Los Alamos National Laboratory, which is operated by the University of California for the U.S. Department of Energy. The U.S. Government is licensed to use, reproduce, and distribute this software. Permission is granted to the public to copy and use this software without charge, provided that this notice and any statement of authorship are reproduced on all copies. Neither the Government nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software.

EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research, Brian.Toby@NIST.GOV with help from Jonathan Wasserman.

EXPGUI is not subject to copyright. Have fun with it.

Neither the U.S. Government nor any author makes any warranty, expressed or implied, or assumes any liability or responsibility for the use of this information or the software described here. Brand names cited here are used for identification purposes and do not consitute an endorsement by NIST.

Brian Toby (Brian.Toby@NIST.GOV)
$Revision: 35 $ $Date: 2009-12-04 22:59:17 +0000 (Fri, 04 Dec 2009) $