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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.
18Programs are invoked either through use of the menu bar
19<center><B>
20<br>The menu bar.
21<br><img SRC="menubar.gif" BORDER=3 >
22</center></B>
23or by "pressing" a button on the button bar. The button bar
24simply provides an easy way to access commonly used
25actions on the menu bar. Users can configure the menu
26bar to include their own preferred actions and, with
27some knowledge of the program and Tcl/Tk,
28add their own commands to the menu bar or button bar.
29
30<center><B>
31<br>The button bar.
32<br><img SRC="buttonbar.gif" BORDER=3 >
33</center></B>
34
35<P>
36Different sections of the .EXP file can be edited by selecting different
37panels or pages from the tabbed list. These tabs will have slightly different
38appearance depending on the packages
39available with your local version of Tcl/Tk.
40<center><B>
41<br>The panel tabs using the Tix package.
42<br><img SRC="panebar1.gif"  BORDER=3 >
43</center></B>
44<center><B>
45<br>The panel tabs without the Tix package.
46<br><img SRC="panebar2.gif" BORDER=3 >
47</center></B>
48If the Tix package is loaded on your machine, it will be
49used, but if it is not, EXPGUI will run fine without it.
50<P>
51This documentation will describe the different actions that
52can be accomplished with the different panels and the
53contents of the menus. Other documents contain:
54<A HREF="http://www.ncnr.nist.gov/~toby/expgui/expgui_Win_readme.html">
55Installation notes for Windows</A>,
56<A HREF="http://www.ncnr.nist.gov/~toby/expgui/expgui_Unix_readme.html">
57Installation notes for UNIX</A> and
58<A HREF="http://www.ncnr.nist.gov/~toby/expgui/expgui_cfg.html">
59Customization notes</A>.
60<hr>
61
62<h2>1. LS Controls panel</h2>
63<DL><DL>
64<p>The LS Controls panel shows information about the
65current experiment, typically found in the EXPEDT "Least
66Squares Controls" options.
67<P>
68Note that the order that histograms appear in this
69panel is determined by the "Sort histograms by" option in
70the Options Menu.
71<img SRC="1.gif" align=TEXTTOP>
72</DL></DL>
73<P>
74<h2>2. Phase panel</h2> 
75<DL><DL>
76The phase panel is used to edit information
77about the phase or phases found in the experiment
78file. The cell and atomic damping and refinement
79flags can be changed here. Note that if a
80single atom is selected using the mouse, the information
81for that atom can be edited. If a group of atoms is
82selected
83<A href="#mouseactions">(see Mouse Actions)</A>
84the damping and refinement flags
85for all the selected atom can be changed at one time.
86<P>
87Note that the order that atoms appear in this panel is
88determined by the "Sort Atoms by" option in the Options
89Menu.
90<img SRC="2.gif" align=TEXTTOP>
91</DL></DL>
92
93<h2>3. Histogram panel</h2> 
94<DL><DL>
95The histogram panel is used to edit background
96and diffractometer constants for a histogram, as well as
97set damping and refinement flags for these parameters.
98<P>
99If
100<A href="#multiplehistogram">
101"Multiple Histogram Selection" mode</A> is set to "All",
102this panel is disabled. For other settings of this mode,
103groups of histograms can be selected and modified
104collectively.
105<P>
106Note that the order that histograms appear in this
107panel is determined by the "Sort histograms by" option in
108the Options Menu.
109<img SRC="3.gif" align=TEXTTOP>
110</DL></DL>
111
112<h2>4. Scaling panel</h2> 
113<DL><DL>
114The Scaling panel is used to edit the scale factor for a
115histogram as well as the phase fractions for each phase
116present in that histogram. Damping and refinement flags
117can also be set here.
118<P>
119If
120<A href="#multiplehistogram">
121"Multiple Histogram Selection" mode</A> is set to
122any value other than "Off,"
123groups of histograms can be selected and modified
124collectively.
125<P>
126Note that the order that histograms appear in this
127panel is determined by the "Sort histograms by" option in
128the Options Menu.
129<img SRC="4.gif" align=TEXTTOP>
130</DL></DL>
131
132<h2>5. Profile panel</h2> 
133<DL><DL>
134The Profile panel is used to edit the profile values for
135each phase present in a histogram as well as set
136the refinement flags and a damping value for each phase.
137<P>
138If
139<A href="#multiplehistogram">
140"Multiple Histogram Selection" mode</A> is set to "All",
141this panel is disabled. For other settings of this mode,
142profile values and settings can be collectively
143modified for groups of histograms.
144<P>
145Note that the order that histograms appear in this
146panel is determined by the "Sort histograms by" option in
147the Options Menu.
148<img SRC="5.gif" align=TEXTTOP>
149</DL></DL>
150
151<a name="multiplehistogram">
152<h2>6. Multiple Histogram Selection</h2></a>
153<DL><DL>
154This mode allows parameters to be changed for groups of
155histograms.
156When the "Multiple Histogram Selection" mode is off,
157it is possible to modify parameters
158and refinement flags for only a single histogram, but
159the other settings allow groups of histograms
160to be selected and modified.
161<A href="#mouseactions">(see Mouse Actions)</A>.
162
163It does not make sense, however, to globally modify
164instrument-related parameters and flags for different
165histogram types.
166So global actions can be limited to a single class
167of histogram types (e.g. TOF, CW Neutron,...), which
168allows these parameters to be set for groups of
169similar histograms. Thus, if this mode is set to "All"
170the Histogram and Profile panels are disabled.
171<P>
172The setting for "Multiple Histogram Selection" mode is
173selected using the "Multiple Hist. Selection" item on the
174Options menu.
175<p>
176<a name="mouseactions">
177</DL></DL>
178<h2>7. Mouse Actions</h2></a>
179<DL><DL>
180A range of atoms or (in multiple selection mode) histograms may be
181selected by dragging (holding down) the left mouse button. It is also
182possible to select a range by using the Shift key with the left mouse
183button. To select or deselect individual entries, use the Control key
184with the left mouse button. The right mouse button selects all
185entries.
186</DL></DL>
187
188<h2>8. Menus</h2>
189A description of the EXPGUI menus follows along with a very
190brief description of the function of each menu option.
191Note that an option may appear under more than one menu.
192<H3>8.1 File Menu</H3>
193<DL><DL>
194The options on the File menu as is the custom contains the commands
195for reading and writing experiment files, as well as starting
196and ending the program.
197<DL>
198<DT>expnam<DD>
199        Select an existing GSAS experiment to be used or create a new
200        experiment file from scratch.
201<DT>Save<DD>Saves modifications to the current experiment file to disk
202<DT>Save As<DD>Saves modifications to the current experiment file to disk
203        under a new file name
204<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
205<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
206<DT>exit<DD>Exit EXPGUI
207</DL>
208<img SRC="m1.gif" BORDER=3 >
209</DL></DL>
210
211<h3>8.2 Options Menu</h3>
212<DL><DL>
213This menu contains options that determine how EXPGUI runs.
214<DL>
215<DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
216        saved prior to each save or run of expedt in a file named
217        [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX)
218        or in a file named [expnam].ZIP or  [expnam].xxx (Windows)
219<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" page
220        Atoms may be displayed sorted by atom number, atom type,
221        or by x, y or z
222
223<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
224        Histogram, Scaling and Profile pages
225
226        Histograms may be sorted by histogram number, histogram type,
227        original bank number, or diffraction angle/wavelength
228<DT>Multiple hist. selection<DD>When this mode is off, it is possible to modify parameters
229        and refinement flags for only a single histogram. For other settings,
230        it is possible to modify parameters and flags for groups of
231        histograms (see help for Mouse actions).
232
233        It does not make sense, however, to globally modify
234        instrument-related parameters and flags for different histogram types.
235        So global actions can be limited to a single class of histogram types
236        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
237        for groups of similar histograms. Thus, if this mode is set to "All"
238        the Histogram and Profile pages are disabled.
239<DT>Override backspace<DD>This option is available in UNIX only, as there are different
240        ways that backspace can be implemented. When option is set
241        as "On," the backspace key is overridden to send a "delete"
242        character. If backspace does not work in a program such as
243        EXPEDT, change try the other setting for this option.
244<DT>SaveOptions<DD>Save the current values for "Override backspace",
245        "Sort atoms by", "Sort histograms by" and "archive EXP"
246        in file ~/.gsas_config (c:\.gsas_config on Windows).
247<DT>liveplot_options<DD>Used to set options for liveplot,
248for example, the histogram to be plotted
249</DL>
250<img SRC="m2.gif"  BORDER=3>
251</DL></DL>
252
253<h3>8.3 Powder Menu</h3>
254<DL><DL>
255This menu contains links to GSAS programs used for powder diffraction
256analysis.
257<DL>
258<DT>expedt<DD>Run GSAS experiment editor
259<DT>powpref<DD>Powder data preparation
260<DT>genles<DD>Run GSAS experiment editor
261<DT>powplot<DD>Display powder patterns
262<DT>rawplot<DD>Plot powder data
263<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
264<DT>tofnorm<DD>Normalize a TOF spectrum
265</DL>
266<img SRC="m3.gif"  BORDER=3>
267</DL></DL>
268
269<h3>8.4 Single Crystal Menu</h3>
270<DL><DL>
271This menu contains links to GSAS programs used for
272single-rystal diffraction analysis.
273<DL>
274<DT>expedt<DD>Run GSAS experiment editor
275<DT>powpref<DD>Powder data preparation
276<DT>scabs<DD>Single crystal absorption
277<DT>scmerge<DD>Sort and merge single crystal data
278<DT>sxtldata<DD>Prepare generic single crystal data
279</DL>
280<img SRC="m4.gif"  BORDER=3>
281</DL></DL>
282
283<h3>8.5 Graphics Menu</h3>
284<DL><DL>
285This menu contains links to several GSAS and
286two non-GSAS (liveplot and widplt)
287programs used for graphical display of data and results.
288<DL>
289<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
290        and then compute with FOURIER
291<DT>polfplot<DD>Display polefigures
292<DT>powplot<DD>Display powder patterns
293<DT>ortep<DD>Draw crystal structure
294<DT>rawplot<DD>Plot powder data
295<DT>fourier<DD>Generate Fourier map
296<DT>forsrh<DD>Search Fourier map for peaks
297<DT>liveplot<DD>Create a plot of powder data
298with zooming, automatic update and other nice features.
299<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
300</DL>
301<img SRC="m5.gif"  BORDER=3>
302</DL></DL>
303
304<h3>8.6 Results Menu</h3>
305<DL><DL>
306This menu contains links to several GSAS and
307one non-GSAS (lstview)
308programs used for analysis of results.
309<DL>
310<DT>bijcalc<DD>Thermal parameter analysis
311<DT>disagl<DD>Distance/angle calculations
312<DT>reflist<DD>List reflection data
313<DT>geometry<DD>Molecular geometry calculations
314<DT>hstdmp<DD>List powder histogram data
315<DT>istats<DD>HKL Intensity statistics
316<DT>rcalc<DD>Compute reflection resuduals
317<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
318</DL>
319<img SRC="m6.gif"  BORDER=3>
320</DL></DL>
321
322<h3>8.7 Calculations Menu</h3>
323<DL><DL>
324This menu contains programs for useful crystallographic computations.
325<DL>
326<DT>cllchg<DD>Transform unit cell
327<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
328<DT>rducll<DD>Unit cell reduction
329<DT>spcgroup<DD>Space group symbol interpreter
330<DT>unimol<DD>Unique molecule assembler
331</DL>
332<img SRC="m7.gif" BORDER=3>
333</DL></DL>
334
335<h3>8.8 Import/Export Menu</h3>
336<DL><DL>
337This menu contains utilities for importing information into GSAS and
338exporting.
339<DL>
340<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
341<DT>hklsort<DD>Prepare HKL tables
342<DT>pubtable<DD>Prepare atom parameter tables
343<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
344<DT>cad4rd<DD>Prepare CAD4 single crystal data
345<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
346<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
347<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
348<DT>sxtldata<DD>Prepare generic single crystal data
349</DL>
350<img SRC="m8.gif"  BORDER=3>
351</DL></DL>
352
353<h2>9. EXPGUI Utility Programs</h2></a>
354<DL><DL>
355<P><B>LSTVIEW</B>
356
357<P>lstview is used to browse through the GSAS output listing. It is
358invoked by the "lstview" command in the GUI.
359<CENTER><IMG SRC="http://www.ncnr.nist.gov/~toby/textview.gif"></CENTER>
360
361
362<P><B>LIVEPLOT</B>
363
364<P>liveplot shows the observed, calculated and difference plots for powder
365refinements. The plot is updated as the refinement progresses. The mouse can
366be used to zoom in on sections of the plot.
367<CENTER><IMG SRC="http://www.ncnr.nist.gov/~toby/liveplot.gif"></CENTER>
368<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
369LIVEPLOT can now be enhanced to superimpose peak locations for
370input unit cells or peaks from JCPDS/ICDD entries.
371See the <A HREF="http://www.ncnr.nist.gov/~toby/expgui/expgui_cfg.html#liveplot">
372LIVEPLOT customization information</A> 
373or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory.
374<P>
375LIVEPLOT gets the current diffraction information by running the TCLDUMP program, if installed, or
376HSTDUMP otherwise. The TCLDUMP program has been optimized for use with LIVEPLOT and offers a number of extra
377options that are not available when HSTDUMP is used: plots can be displayed in the native units (2Theta/TOF/KeV), or
378in d-space or Q; fixed plus fitted background curves are shown in green; if reflection tickmarks are displayed,
379reflection tickmarks can be displayed by holding the shift key while pressing the left mouse button.
380See the installation instructions for installing TCLDUMP.
381
382<P><B>WIDPLT</B>
383
384<P>widplt can be used to plot the actual peak widths generated by the profile
385parameters used in GSAS. It is possible to define reference curves
386that are loaded automatically.
387<CENTER><IMG SRC="http://www.ncnr.nist.gov/~toby/widplt.gif"></CENTER>
388<BR> 
389</DL></DL>
390
391<H2>
392Acknowledgements</H2>
393Praise to Larson and
394<A HREF="http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
395Von Dreele</A> for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
396for Tcl/Tk,
397<A HREF="http://www.ncnr.nist.gov/przemek.html">Przemek Klosowski</A>
398for convincing me to learn Tcl/Tk
399and Jonathan Wasserman for starting this project.
400
401<hr>
402GSAS is written by Allen C. Larson and <A HREF="http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
403Robert B. Von Dreele</A>, MS-H805,
404Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions
405or kudos concerning GSAS should be sent to Robert B. Von Dreele at
406<A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A>
407<P>GSAS is Copyright, 1984-1997, The Regents of the University of California.
408The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
409by the Los Alamos National Laboratory, which is operated by the University
410of California for the U.S. Department of Energy. The U.S. Government is
411licensed to use, reproduce, and distribute this software. Permission is
412granted to the public to copy and use this software without charge, provided
413that this notice and any statement of authorship are reproduced on all
414copies. Neither the Government nor the University makes any warranty, express
415or implied, or assumes any liability or responsibility for the use of this
416software.
417<P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
418<A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> 
419with help from Jonathan Wasserman.
420
421<P>EXPGUI is not subject to copyright. Have fun with it.
422
423<p>Neither the U.S. Government nor any author makes any warranty,
424expressed or implied, or assumes any liability or responsibility
425for the use of this information or the software described
426here. Brand names cited here are used for
427identification purposes and do not consitute an endorsement by NIST.
428
429<p><a href="http://www.ncnr.nist.gov/~toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
430<br>
431$Revision: 66 $ $Date: 2009-12-04 22:59:50 +0000 (Fri, 04 Dec 2009) $
432</body>
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