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1<html>
2<head>
3<title>EXPGUI</title>
4</head>
5<body>
6
7<center>
8<h1>
9Using EXPGUI</h1></center>
10
11<h2>Introduction</h2> 
12EXPGUI allows two types of actions:
13it allows the different
14GSAS programs such as EXPEDT, GENLES, FOURIER,...
15to be run,
16and it can be used to directly modify the GSAS
17experiment file without using EXPEDT.
18
19<P>
20Note that pictures on this page are somewhat out-of-date with respect to the
21current software version so they may differ from what is
22described in the text.
23
24<p>
25Programs are invoked either through use of the menu bar
26<center><B>
27<br>The menu bar.
28<br><img SRC="menubar.gif" BORDER=3 >
29</center></B>
30or by "pressing" a button on the button bar. The button bar
31simply provides an easy way to access commonly used
32actions on the menu bar. Users can configure the menu
33bar to include their own preferred actions and, with
34some knowledge of the program and Tcl/Tk,
35add their own commands to the menu bar or button bar.
36
37<center><B>
38<br>The button bar.
39<br><img SRC="buttonbar.gif" BORDER=3 >
40</center></B>
41
42<P>
43Different sections of the .EXP file can be edited by selecting different
44panels or pages from the tabbed list. These tabs will have slightly different
45appearance depending on the packages
46available with your local version of Tcl/Tk.
47<center><B>
48<br>The panel tabs using the Tix package.
49<br><img SRC="panebar1.gif"  BORDER=3 >
50</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>
55If the Tix package is loaded on your machine, it will be
56used, but if it is not, EXPGUI will run fine without it.
57<P>
58This documentation will describe the different actions that
59can be accomplished with the different panels and the
60contents of the menus. Other documents contain:
61<a name="installation"></A>
62<A HREF="expgui_Win_readme.html">
63Installation notes for Windows</A>,
64<A HREF="expgui_Unix_readme.html">
65Installation notes for UNIX</A> and
66<A HREF="expgui_cfg.html">
67Customization notes</A>.
68<hr>
69
70<h2>1. LS Controls panel</h2>
71<DL><DL>
72<p>The LS Controls panel shows information about the
73current experiment, typically found in the EXPEDT "Least
74Squares Controls" options.
75<P>
76Note that the order that histograms appear in this
77panel is determined by the "Sort histograms by" option in
78the Options Menu.
79<img SRC="1.gif" align=TEXTTOP>
80</DL></DL>
81<P>
82<h2>2. Phase panel</h2> 
83<DL><DL>
84The phase panel is used to edit information
85about the phase or phases found in the experiment
86file. The cell and atomic damping and refinement
87flags can be changed here. Note that if a
88single atom is selected using the mouse, the information
89for that atom can be edited. If a group of atoms is
90selected
91<A href="#mouseactions">(see Mouse Actions)</A>
92the damping and refinement flags
93for all the selected atom can be changed at one time.
94<P>
95If the EXPTOOL program
96<A href="#installation">(see the installation instructions)</A>
97is installed, buttons for adding phases and atoms will
98appear on this panel. If the
99program is not properly installed, no errors occur, but the buttons
100do not appear.
101<P>
102Note that the order that atoms appear in this panel is
103determined by the "Sort Atoms by" option in the Options
104Menu.
105<img SRC="2.gif" align=TEXTTOP>
106</DL></DL>
107
108<h2>3. Histogram panel</h2> 
109<DL><DL>
110The histogram panel is used to edit background
111and diffractometer constants for a histogram, as well as
112set damping and refinement flags for these parameters.
113<P>
114If
115<A href="#multiplehistogram">
116"Multiple Histogram Selection" mode</A> is set to "All",
117this panel is disabled. For other settings of this mode,
118groups of histograms can be selected and modified
119collectively.
120<P>
121If the EXPTOOL program
122<A href="#installation">(see the installation instructions)</A>
123is installed, a button for adding histograms will
124appear on the bottom right on this panel. If the
125program is not properly installed, no errors occur, but the button
126does not appear.
127<P>
128Note that the order that histograms appear in this
129panel is determined by the "Sort histograms by" option in
130the Options Menu.
131<img SRC="3.gif" align=TEXTTOP>
132</DL></DL>
133
134<h2>4. Scaling panel</h2> 
135<DL><DL>
136The Scaling panel is used to edit the scale factor for a
137histogram as well as the phase fractions for each phase
138present in that histogram. Damping and refinement flags
139can also be set here.
140<P>
141If
142<A href="#multiplehistogram">
143"Multiple Histogram Selection" mode</A> is set to
144any value other than "Off,"
145groups of histograms can be selected and modified
146collectively.
147<P>
148Note that the order that histograms appear in this
149panel is determined by the "Sort histograms by" option in
150the Options Menu.
151<img SRC="4.gif" align=TEXTTOP>
152</DL></DL>
153
154<h2>5. Profile panel</h2> 
155<DL><DL>
156The Profile panel is used to edit the profile values for
157each phase present in a histogram as well as set
158the refinement flags and a damping value for each phase.
159<P>
160If
161<A href="#multiplehistogram">
162"Multiple Histogram Selection" mode</A> is set to "All",
163this panel is disabled. For other settings of this mode,
164profile values and settings can be collectively
165modified for groups of histograms.
166<P>
167Note that the order that histograms appear in this
168panel is determined by the "Sort histograms by" option in
169the Options Menu.
170<img SRC="5.gif" align=TEXTTOP>
171</DL></DL>
172
173<a name="multiplehistogram">
174<h2>6. Multiple Histogram Selection</h2></a>
175<DL><DL>
176This mode allows parameters to be changed for groups of
177histograms.
178When the "Multiple Histogram Selection" mode is off,
179it is possible to modify parameters
180and refinement flags for only a single histogram, but
181the other settings allow groups of histograms
182to be selected and modified.
183<A href="#mouseactions">(see Mouse Actions)</A>.
184
185It does not make sense, however, to globally modify
186instrument-related parameters and flags for different
187histogram types.
188So global actions can be limited to a single class
189of histogram types (e.g. TOF, CW Neutron,...), which
190allows these parameters to be set for groups of
191similar histograms. Thus, if this mode is set to "All"
192the Histogram and Profile panels are disabled.
193<P>
194The setting for "Multiple Histogram Selection" mode is
195selected using the "Multiple Hist. Selection" item on the
196Options menu.
197<p>
198<a name="mouseactions">
199</DL></DL>
200<h2>7. Mouse Actions</h2></a>
201<DL><DL>
202A range of atoms or (in multiple selection mode) histograms may be
203selected by dragging (holding down) the left mouse button. It is also
204possible to select a range by using the Shift key with the left mouse
205button. To select or deselect individual entries, use the Control key
206with the left mouse button. Pressing the right mouse button selects all
207entries in a list.
208</DL></DL>
209
210<h2>8. Menus</h2>
211A description of the EXPGUI menus follows along with a very
212brief description of the function of each menu option.
213Note that an option may appear under more than one menu.
214<H3>8.1 File Menu</H3>
215<DL><DL>
216The options on the File menu as is the custom contains the commands
217for reading and writing experiment files, as well as starting
218and ending the program.
219<DL>
220<DT>expnam<DD>
221        Select an existing GSAS experiment to be used or create a new
222        experiment file from scratch.
223<DT>Save<DD>Saves modifications to the current experiment file to disk
224<DT>Save As<DD>Saves modifications to the current experiment file to disk
225        under a new file name
226<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
227<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
228<DT>exit<DD>Exit EXPGUI
229</DL>
230<img SRC="m1.gif" BORDER=3 >
231</DL></DL>
232
233<h3>8.2 Options Menu</h3>
234<DL><DL>
235This menu contains options that determine how EXPGUI runs.
236<DL>
237<DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
238        saved prior to each save or run of expedt in a file named
239        [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX)
240        or in a file named [expnam].ZIP or  [expnam].xxx (Windows)
241<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" page
242        Atoms may be displayed sorted by atom number, atom type,
243        or by x, y or z
244
245<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
246        Histogram, Scaling and Profile pages
247
248        Histograms may be sorted by histogram number, histogram type,
249        original bank number, or diffraction angle/wavelength
250<DT>Multiple hist. selection<DD>When this mode is off, it is possible to modify parameters
251        and refinement flags for only a single histogram. For other settings,
252        it is possible to modify parameters and flags for groups of
253        histograms (see help for Mouse actions).
254
255        It does not make sense, however, to globally modify
256        instrument-related parameters and flags for different histogram types.
257        So global actions can be limited to a single class of histogram types
258        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
259        for groups of similar histograms. Thus, if this mode is set to "All"
260        the Histogram and Profile pages are disabled.
261<DT>Override backspace<DD>This option is available in UNIX only, as there are different
262        ways that backspace can be implemented. When option is set
263        as "On," the backspace key is overridden to send a "delete"
264        character. If backspace does not work in a program such as
265        EXPEDT, change try the other setting for this option.
266<DT>Autoupdate EXP<DD>Normally EXPGUI prompts before rereading the EXP
267file when GENLES, POWPREF,... are run (this is so that one can change
268the experiment file and rerun with the current input). If this option is
269set, the new file is automatically read without a prompt.
270
271<DT>SaveOptions<DD>Save the current values for "Override backspace",
272        "Sort atoms by", "Sort histograms by" and "archive EXP"
273        in file ~/.gsas_config (c:\.gsas_config on Windows).
274<DT>liveplot_options<DD>Used to set options for liveplot,
275for example, the histogram to be plotted
276</DL>
277<img SRC="m2.gif"  BORDER=3>
278</DL></DL>
279
280<h3>8.3 Powder Menu</h3>
281<DL><DL>
282This menu contains links to GSAS programs used for powder diffraction
283analysis.
284<DL>
285<DT>expedt<DD>Run GSAS experiment editor
286<DT>powpref<DD>Powder data preparation
287<DT>genles<DD>Run GSAS experiment editor
288<DT>powplot<DD>Display powder patterns
289<DT>rawplot<DD>Plot powder data
290<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
291<DT>tofnorm<DD>Normalize a TOF spectrum
292</DL>
293<img SRC="m3.gif"  BORDER=3>
294</DL></DL>
295
296<h3>8.4 Single Crystal Menu</h3>
297<DL><DL>
298This menu contains links to GSAS programs used for
299single-rystal diffraction analysis.
300<DL>
301<DT>expedt<DD>Run GSAS experiment editor
302<DT>powpref<DD>Powder data preparation
303<DT>scabs<DD>Single crystal absorption
304<DT>scmerge<DD>Sort and merge single crystal data
305<DT>sxtldata<DD>Prepare generic single crystal data
306</DL>
307<img SRC="m4.gif"  BORDER=3>
308</DL></DL>
309
310<h3>8.5 Graphics Menu</h3>
311<DL><DL>
312This menu contains links to several GSAS and
313two non-GSAS (liveplot and widplt)
314programs used for graphical display of data and results.
315<DL>
316<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
317        and then compute with FOURIER
318<DT>polfplot<DD>Display polefigures
319<DT>powplot<DD>Display powder patterns
320<DT>ortep<DD>Draw crystal structure
321<DT>rawplot<DD>Plot powder data
322<DT>fourier<DD>Generate Fourier map
323<DT>forsrh<DD>Search Fourier map for peaks
324<DT>liveplot<DD>Create a plot of powder data
325with zooming, automatic update and other nice features.
326<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
327<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
328</DL>
329<img SRC="m5.gif"  BORDER=3>
330</DL></DL>
331
332<h3>8.6 Results Menu</h3>
333<DL><DL>
334This menu contains links to several GSAS and
335one non-GSAS (lstview)
336programs used for analysis of results.
337<DL>
338<DT>bijcalc<DD>Thermal parameter analysis
339<DT>disagl<DD>Distance/angle calculations
340<DT>reflist<DD>List reflection data
341<DT>geometry<DD>Molecular geometry calculations
342<DT>hstdmp<DD>List powder histogram data
343<DT>istats<DD>HKL Intensity statistics
344<DT>rcalc<DD>Compute reflection resuduals
345<DT>composition<DD>Computes the chemical composition of a unit cell
346accounting for site multiplicies and occupancies
347<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
348</DL>
349<img SRC="m6.gif"  BORDER=3>
350</DL></DL>
351
352<h3>8.7 Calculations Menu</h3>
353<DL><DL>
354This menu contains programs for useful crystallographic computations.
355<DL>
356<DT>cllchg<DD>Transform unit cell
357<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
358<DT>rducll<DD>Unit cell reduction
359<DT>spcgroup<DD>Space group symbol interpreter
360<DT>unimol<DD>Unique molecule assembler
361</DL>
362<img SRC="m7.gif" BORDER=3>
363</DL></DL>
364
365<h3>8.8 Import/Export Menu</h3>
366<DL><DL>
367This menu contains utilities for importing information into GSAS and
368exporting.
369<DL>
370<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
371file is used in MSI software such as Cerius and InsightII.
372<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
373<DT>hklsort<DD>Prepare HKL tables
374<DT>pubtable<DD>Prepare atom parameter tables
375<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
376<DT>cad4rd<DD>Prepare CAD4 single crystal data
377<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
378<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
379<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
380<DT>sxtldata<DD>Prepare generic single crystal data
381</DL>
382<img SRC="m8.gif"  BORDER=3>
383</DL></DL>
384
385<h2>9. EXPGUI Utility Programs</h2></a>
386<DL><DL>
387<P><B>LSTVIEW</B>
388
389<P>lstview is used to browse through the GSAS output listing. It is
390invoked by the "lstview" command in the GUI.
391<CENTER><IMG SRC="textview.gif"></CENTER>
392
393
394<P><B>LIVEPLOT</B>
395
396<P>liveplot shows the observed, calculated and difference plots for powder
397refinements. The plot is updated as the refinement progresses. The mouse can
398be used to zoom in on sections of the plot.
399<CENTER><IMG SRC="liveplot.gif"></CENTER>
400<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
401LIVEPLOT can now be enhanced to superimpose peak locations for
402input unit cells or peaks from JCPDS/ICDD entries.
403See the <A HREF="expgui_cfg.html#liveplot">
404LIVEPLOT customization information</A> 
405or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory.
406<P>
407LIVEPLOT gets the current diffraction information by running the TCLDUMP program, if installed, or
408HSTDUMP otherwise. The TCLDUMP program has been optimized for use with LIVEPLOT and offers a number of extra
409options that are not available when HSTDUMP is used: plots can be displayed in the native units (2Theta/TOF/KeV), or
410in d-space or Q; fixed plus fitted background curves are shown in green; if reflection tickmarks are displayed,
411reflection tickmarks can be displayed by holding the shift key while pressing the left mouse button.
412See the installation instructions for installing TCLDUMP.
413
414<P><B>WIDPLT</B>
415
416<P>widplt can be used to plot the actual peak widths generated by the profile
417parameters used in GSAS. It is possible to define reference curves
418that are loaded automatically.
419<CENTER><IMG SRC="widplt.gif"></CENTER>
420<BR> 
421</DL></DL>
422
423<H2>
424Acknowledgements</H2>
425Praise to Larson and
426<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
427Von Dreele</A> for GSAS, <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.scriptics.com/">Ousterhout</A>
428for Tcl/Tk,
429Przemek Klosowski</A>
430for convincing me to learn Tcl/Tk
431and Jonathan Wasserman for starting this project.
432
433<hr>
434GSAS 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">
435Robert B. Von Dreele</A>, MS-H805,
436Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions
437or kudos concerning GSAS should be sent to Robert B. Von Dreele at
438<A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A>
439<P>GSAS is Copyright, 1984-1997, The Regents of the University of California.
440The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
441by the Los Alamos National Laboratory, which is operated by the University
442of California for the U.S. Department of Energy. The U.S. Government is
443licensed to use, reproduce, and distribute this software. Permission is
444granted to the public to copy and use this software without charge, provided
445that this notice and any statement of authorship are reproduced on all
446copies. Neither the Government nor the University makes any warranty, express
447or implied, or assumes any liability or responsibility for the use of this
448software.
449<P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
450<A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> 
451with help from Jonathan Wasserman.
452
453<P>EXPGUI is not subject to copyright. Have fun with it.
454
455<p>Neither the U.S. Government nor any author makes any warranty,
456expressed or implied, or assumes any liability or responsibility
457for the use of this information or the software described
458here. Brand names cited here are used for
459identification purposes and do not consitute an endorsement by NIST.
460
461<p><a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
462<br>
463$Revision: 103 $ $Date: 2009-12-04 23:00:27 +0000 (Fri, 04 Dec 2009) $
464</body>
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