source: trunk/doc/expgui.html @ 25

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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.
54<hr>
55
56<h2>1. LS Controls panel</h2>
57<DL><DL>
58<p>The LS Controls panel shows information about the
59current experiment, typically found in the EXPEDT "Least
60Squares Controls" options.
61<P>
62Note that the order that histograms appear in this
63panel is determined by the "Sort histograms by" option in
64the Options Menu.
65<img SRC="1.gif" align=TEXTTOP>
66</DL></DL>
67<P>
68<h2>2. Phase panel</h2> 
69<DL><DL>
70The phase panel is used to edit information
71about the phase or phases found in the experiment
72file. The cell and atomic damping and refinement
73flags can be changed here. Note that if a
74single atom is selected using the mouse, the information
75for that atom can be edited. If a group of atoms is
76selected
77<A href="#mouseactions">(see Mouse Actions)</A>
78the damping and refinement flags
79for all the selected atom can be changed at one time.
80<P>
81Note that the order that atoms appear in this panel is
82determined by the "Sort Atoms by" option in the Options
83Menu.
84<img SRC="2.gif" align=TEXTTOP>
85</DL></DL>
86
87<h2>3. Histogram panel</h2> 
88<DL><DL>
89The histogram panel is used to edit background
90and diffractometer constants for a histogram, as well as
91set damping and refinement flags for these parameters.
92<P>
93If
94<A href="#multiplehistogram">
95"Multiple Histogram Selection" mode</A> is set to "All",
96this panel is disabled. For other settings of this mode,
97groups of histograms can be selected and modified
98collectively.
99<P>
100Note that the order that histograms appear in this
101panel is determined by the "Sort histograms by" option in
102the Options Menu.
103<img SRC="3.gif" align=TEXTTOP>
104</DL></DL>
105
106<h2>4. Scaling panel</h2> 
107<DL><DL>
108The Scaling panel is used to edit the scale factor for a
109histogram as well as the phase fractions for each phase
110present in that histogram. Damping and refinement flags
111can also be set here.
112<P>
113If
114<A href="#multiplehistogram">
115"Multiple Histogram Selection" mode</A> is set to
116any value other than "Off,"
117groups of histograms can be selected and modified
118collectively.
119<P>
120Note that the order that histograms appear in this
121panel is determined by the "Sort histograms by" option in
122the Options Menu.
123<img SRC="4.gif" align=TEXTTOP>
124</DL></DL>
125
126<h2>5. Profile panel</h2> 
127<DL><DL>
128The Profile panel is used to edit the profile values for
129each phase present in a histogram as well as set
130the refinement flags and a damping value for each phase.
131<P>
132If
133<A href="#multiplehistogram">
134"Multiple Histogram Selection" mode</A> is set to "All",
135this panel is disabled. For other settings of this mode,
136profile values and settings can be collectively
137modified for groups of histograms.
138<P>
139Note that the order that histograms appear in this
140panel is determined by the "Sort histograms by" option in
141the Options Menu.
142<img SRC="5.gif" align=TEXTTOP>
143</DL></DL>
144
145<a name="multiplehistogram">
146<h2>6. Multiple Histogram Selection</h2></a>
147<DL><DL>
148This mode allows parameters to be changed for groups of
149histograms.
150When the "Multiple Histogram Selection" mode is off,
151it is possible to modify parameters
152and refinement flags for only a single histogram, but
153the other settings allow groups of histograms
154to be selected and modified.
155<A href="#mouseactions">(see Mouse Actions)</A>.
156
157It does not make sense, however, to globally modify
158instrument-related parameters and flags for different
159histogram types.
160So global actions can be limited to a single class
161of histogram types (e.g. TOF, CW Neutron,...), which
162allows these parameters to be set for groups of
163similar histograms. Thus, if this mode is set to "All"
164the Histogram and Profile panels are disabled.
165<P>
166The setting for "Multiple Histogram Selection" mode is
167selected using the "Multiple Hist. Selection" item on the
168Options menu.
169<p>
170<a name="mouseactions">
171</DL></DL>
172<h2>7. Mouse Actions</h2></a>
173<DL><DL>
174A range of atoms or (in multiple selection mode) histograms may be
175selected by dragging (holding down) the left mouse button. It is also
176possible to select a range by using the Shift key with the left mouse
177button. To select or deselect individual entries, use the Control key
178with the left mouse button. The right mouse button selects all
179entries.
180</DL></DL>
181
182<h2>8. Menus</h2>
183A description of the EXPGUI menus follows along with a very
184brief description of the function of each menu option.
185Note that an option may appear under more than one menu.
186<H3>8.1 File Menu</H3>
187<DL><DL>
188The options on the File menu as is the custom contains the commands
189for reading and writing experiment files, as well as starting
190and ending the program.
191<DL>
192<DT>
193expnam
194<DD>
195        Select an existing GSAS experiment to be used
196<DT>Save<DD>Saves modifications to the current experiment file to disk
197<DT>Save As<DD>Saves modifications to the current experiment file to disk
198        under a new file name
199<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
200<DT>New_expnam<DD>Create a new GSAS experiment from scratch
201<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
202<DT>exit<DD>Exit EXPGUI
203</DL>
204<img SRC="m1.gif" BORDER=3 >
205</DL></DL>
206
207<h3>8.2 Options Menu</h3>
208<DL><DL>
209This menu contains options that determine how EXPGUI runs.
210<DL>
211<DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
212        saved prior to each save or run of expedt in a file named
213        [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX)
214        or in a file named [expnam].ZIP or  [expnam].xxx (Windows)
215<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" page
216        Atoms may be displayed sorted by atom number, atom type,
217        or by x, y or z
218
219<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
220        Histogram, Scaling and Profile pages
221
222        Histograms may be sorted by histogram number, histogram type,
223        original bank number, or diffraction angle/wavelength
224<DT>Multiple hist. selection<DD>When this mode is off, it is possible to modify parameters
225        and refinement flags for only a single histogram. For other settings,
226        it is possible to modify parameters and flags for groups of
227        histograms (see help for Mouse actions).
228
229        It does not make sense, however, to globally modify
230        instrument-related parameters and flags for different histogram types.
231        So global actions can be limited to a single class of histogram types
232        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
233        for groups of similar histograms. Thus, if this mode is set to "All"
234        the Histogram and Profile pages are disabled.
235<DT>Override backspace<DD>This option is available in UNIX only, as there are different
236        ways that backspace can be implemented. When option is set
237        as "On," the backspace key is overridden to send a "delete"
238        character. If backspace does not work in a program such as
239        EXPEDT, change try the other setting for this option.
240<DT>liveplot_options<DD>Used to set options for liveplot,
241for example, the histogram to be plotted
242</DL>
243<img SRC="m2.gif" align=TEXTTOP>
244</DL></DL>
245
246<h3>8.3 Powder Menu</h3>
247<DL><DL>
248This menu contains links to GSAS programs used for powder diffraction
249analysis.
250<DL>
251<DT>expedt<DD>Run GSAS experiment editor
252<DT>powpref<DD>Powder data preparation
253<DT>genles<DD>Run GSAS experiment editor
254<DT>powplot<DD>Display powder patterns
255<DT>rawplot<DD>Plot powder data
256<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
257<DT>tofnorm<DD>Normalize a TOF spectrum
258</DL>
259<img SRC="m3.gif" align=TEXTTOP>
260</DL></DL>
261
262<h3>8.4 Single Crystal Menu</h3>
263<DL><DL>
264This menu contains links to GSAS programs used for
265single-rystal diffraction analysis.
266<DL>
267<DT>expedt<DD>Run GSAS experiment editor
268<DT>powpref<DD>Powder data preparation
269<DT>scabs<DD>Single crystal absorption
270<DT>scmerge<DD>Sort and merge single crystal data
271<DT>sxtldata<DD>Prepare generic single crystal data
272</DL>
273<img SRC="m4.gif" align=TEXTTOP>
274</DL></DL>
275
276<h3>8.5 Graphics Menu</h3>
277<DL><DL>
278This menu contains links to several GSAS and
279two non-GSAS (liveplot and widplt)
280programs used for graphical display of data and results.
281<DL>
282<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
283        and then compute with FOURIER
284<DT>polfplot<DD>Display polefigures
285<DT>powplot<DD>Display powder patterns
286<DT>ortep<DD>Draw crystal structure
287<DT>rawplot<DD>Plot powder data
288<DT>fourier<DD>Generate Fourier map
289<DT>forsrh<DD>Search Fourier map for peaks
290<DT>liveplot<DD>Create a plot of powder data
291with zooming, automatic update and other nice features.
292<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
293</DL>
294<img SRC="m5.gif" align=TEXTTOP
295</DL></DL>
296
297<h3>8.6 Results Menu</h3>
298<DL><DL>
299This menu contains links to several GSAS and
300one non-GSAS (lstview)
301programs used for analysis of results.
302<DL>
303<DT>bijcalc<DD>Thermal parameter analysis
304<DT>disagl<DD>Distance/angle calculations
305<DT>reflist<DD>List reflection data
306<DT>geometry<DD>Molecular geometry calculations
307<DT>hstdmp<DD>List powder histogram data
308<DT>istats<DD>HKL Intensity statistics
309<DT>rcalc<DD>Compute reflection resuduals
310<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
311</DL>
312<img SRC="m6.gif" align=TEXTTOP>
313</DL></DL>
314
315<h3>8.7 Calculations Menu</h3>
316<DL><DL>
317This menu contains programs for useful crystallographic computations.
318<DL>
319<DT>cllchg<DD>Transform unit cell
320<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
321<DT>rducll<DD>Unit cell reduction
322<DT>spcgroup<DD>Space group symbol interpreter
323<DT>unimol<DD>Unique molecule assembler
324</DL>
325<img SRC="m7.gif" align=TEXTTOP>
326</DL></DL>
327
328<h3>8.8 Import/Export Menu</h3>
329<DL><DL>
330This menu contains utilities for importing information into GSAS and
331exporting.
332<DL>
333<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
334<DT>hklsort<DD>Prepare HKL tables
335<DT>pubtable<DD>Prepare atom parameter tables
336<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
337<DT>cad4rd<DD>Prepare CAD4 single crystal data
338<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
339<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
340<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
341<DT>sxtldata<DD>Prepare generic single crystal data
342</DL>
343<img SRC="m8.gif" align=TEXTTOP>
344</DL></DL>
345<hr>
346<p>Neither the author nor the U.S. Government makes any warranty,
347expressed or implied, or assumes any liability or responsibility
348for the use of this information or the software described
349here. Brand names cited here are used for
350identification purposes and do not consitute an endorsement by NIST.
351<p><a href="http://rrdjazz.nist.gov/~toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
352<br>
353$Revision: 24 $ $Date: 2009-12-04 22:59:05 +0000 (Fri, 04 Dec 2009) $
354</body>
355</html>
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