source: trunk/doc/expgui.html @ 26

Last change on this file since 26 was 26, checked in by toby, 11 years ago

# on 1999/01/13 04:36:53, toby did:
move cd command later
change profile widths to smaller boxes
put Fobs extract button names into expgui(ExtractSettingsRadiobuttons?)
Change Global mode to "Multiple hist. selection"

  • Property rcs:author set to toby
  • Property rcs:date set to 1999/01/13 04:36:53
  • Property rcs:lines set to +62 -2
  • Property rcs:rev set to 1.2
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 14.8 KB
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1<!-- add lstview liveplot and widplt sections (see tkGSAS.html) --!>
2<html>
3<head>
4<title>EXPGUI</title>
5</head>
6<body>
7
8<center>
9<h1>
10Using EXPGUI</h1></center>
11
12<h2>Introduction</h2> 
13EXPGUI allows two types of actions:
14it allows the different
15GSAS programs such as EXPEDT, GENLES, FOURIER,...
16to be run,
17and it can be used to directly modify the GSAS
18experiment file without using EXPEDT.
19Programs are invoked either through use of the menu bar
20<center><B>
21<br>The menu bar.
22<br><img SRC="menubar.gif" BORDER=3 >
23</center></B>
24or by "pressing" a button on the button bar. The button bar
25simply provides an easy way to access commonly used
26actions on the menu bar. Users can configure the menu
27bar to include their own preferred actions and, with
28some knowledge of the program and Tcl/Tk,
29add their own commands to the menu bar or button bar.
30
31<center><B>
32<br>The button bar.
33<br><img SRC="buttonbar.gif" BORDER=3 >
34</center></B>
35
36<P>
37Different sections of the .EXP file can be edited by selecting different
38panels or pages from the tabbed list. These tabs will have slightly different
39appearance depending on the packages
40available with your local version of Tcl/Tk.
41<center><B>
42<br>The panel tabs using the Tix package.
43<br><img SRC="panebar1.gif"  BORDER=3 >
44</center></B>
45<center><B>
46<br>The panel tabs without the Tix package.
47<br><img SRC="panebar2.gif" BORDER=3 >
48</center></B>
49If the Tix package is loaded on your machine, it will be
50used, but if it is not, EXPGUI will run fine without it.
51<P>
52This documentation will describe the different actions that
53can be accomplished with the different panels and the
54contents of the menus.
55<hr>
56
57<h2>1. LS Controls panel</h2>
58<DL><DL>
59<p>The LS Controls panel shows information about the
60current experiment, typically found in the EXPEDT "Least
61Squares Controls" options.
62<P>
63Note that the order that histograms appear in this
64panel is determined by the "Sort histograms by" option in
65the Options Menu.
66<img SRC="1.gif" align=TEXTTOP>
67</DL></DL>
68<P>
69<h2>2. Phase panel</h2> 
70<DL><DL>
71The phase panel is used to edit information
72about the phase or phases found in the experiment
73file. The cell and atomic damping and refinement
74flags can be changed here. Note that if a
75single atom is selected using the mouse, the information
76for that atom can be edited. If a group of atoms is
77selected
78<A href="#mouseactions">(see Mouse Actions)</A>
79the damping and refinement flags
80for all the selected atom can be changed at one time.
81<P>
82Note that the order that atoms appear in this panel is
83determined by the "Sort Atoms by" option in the Options
84Menu.
85<img SRC="2.gif" align=TEXTTOP>
86</DL></DL>
87
88<h2>3. Histogram panel</h2> 
89<DL><DL>
90The histogram panel is used to edit background
91and diffractometer constants for a histogram, as well as
92set damping and refinement flags for these parameters.
93<P>
94If
95<A href="#multiplehistogram">
96"Multiple Histogram Selection" mode</A> is set to "All",
97this panel is disabled. For other settings of this mode,
98groups of histograms can be selected and modified
99collectively.
100<P>
101Note that the order that histograms appear in this
102panel is determined by the "Sort histograms by" option in
103the Options Menu.
104<img SRC="3.gif" align=TEXTTOP>
105</DL></DL>
106
107<h2>4. Scaling panel</h2> 
108<DL><DL>
109The Scaling panel is used to edit the scale factor for a
110histogram as well as the phase fractions for each phase
111present in that histogram. Damping and refinement flags
112can also be set here.
113<P>
114If
115<A href="#multiplehistogram">
116"Multiple Histogram Selection" mode</A> is set to
117any value other than "Off,"
118groups of histograms can be selected and modified
119collectively.
120<P>
121Note that the order that histograms appear in this
122panel is determined by the "Sort histograms by" option in
123the Options Menu.
124<img SRC="4.gif" align=TEXTTOP>
125</DL></DL>
126
127<h2>5. Profile panel</h2> 
128<DL><DL>
129The Profile panel is used to edit the profile values for
130each phase present in a histogram as well as set
131the refinement flags and a damping value for each phase.
132<P>
133If
134<A href="#multiplehistogram">
135"Multiple Histogram Selection" mode</A> is set to "All",
136this panel is disabled. For other settings of this mode,
137profile values and settings can be collectively
138modified for groups of histograms.
139<P>
140Note that the order that histograms appear in this
141panel is determined by the "Sort histograms by" option in
142the Options Menu.
143<img SRC="5.gif" align=TEXTTOP>
144</DL></DL>
145
146<a name="multiplehistogram">
147<h2>6. Multiple Histogram Selection</h2></a>
148<DL><DL>
149This mode allows parameters to be changed for groups of
150histograms.
151When the "Multiple Histogram Selection" mode is off,
152it is possible to modify parameters
153and refinement flags for only a single histogram, but
154the other settings allow groups of histograms
155to be selected and modified.
156<A href="#mouseactions">(see Mouse Actions)</A>.
157
158It does not make sense, however, to globally modify
159instrument-related parameters and flags for different
160histogram types.
161So global actions can be limited to a single class
162of histogram types (e.g. TOF, CW Neutron,...), which
163allows these parameters to be set for groups of
164similar histograms. Thus, if this mode is set to "All"
165the Histogram and Profile panels are disabled.
166<P>
167The setting for "Multiple Histogram Selection" mode is
168selected using the "Multiple Hist. Selection" item on the
169Options menu.
170<p>
171<a name="mouseactions">
172</DL></DL>
173<h2>7. Mouse Actions</h2></a>
174<DL><DL>
175A range of atoms or (in multiple selection mode) histograms may be
176selected by dragging (holding down) the left mouse button. It is also
177possible to select a range by using the Shift key with the left mouse
178button. To select or deselect individual entries, use the Control key
179with the left mouse button. The right mouse button selects all
180entries.
181</DL></DL>
182
183<h2>8. Menus</h2>
184A description of the EXPGUI menus follows along with a very
185brief description of the function of each menu option.
186Note that an option may appear under more than one menu.
187<H3>8.1 File Menu</H3>
188<DL><DL>
189The options on the File menu as is the custom contains the commands
190for reading and writing experiment files, as well as starting
191and ending the program.
192<DL>
193<DT>
194expnam
195<DD>
196        Select an existing GSAS experiment to be used
197<DT>Save<DD>Saves modifications to the current experiment file to disk
198<DT>Save As<DD>Saves modifications to the current experiment file to disk
199        under a new file name
200<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
201<DT>New_expnam<DD>Create a new GSAS experiment from scratch
202<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
203<DT>exit<DD>Exit EXPGUI
204</DL>
205<img SRC="m1.gif" BORDER=3 >
206</DL></DL>
207
208<h3>8.2 Options Menu</h3>
209<DL><DL>
210This menu contains options that determine how EXPGUI runs.
211<DL>
212<DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
213        saved prior to each save or run of expedt in a file named
214        [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX)
215        or in a file named [expnam].ZIP or  [expnam].xxx (Windows)
216<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" page
217        Atoms may be displayed sorted by atom number, atom type,
218        or by x, y or z
219
220<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
221        Histogram, Scaling and Profile pages
222
223        Histograms may be sorted by histogram number, histogram type,
224        original bank number, or diffraction angle/wavelength
225<DT>Multiple hist. selection<DD>When this mode is off, it is possible to modify parameters
226        and refinement flags for only a single histogram. For other settings,
227        it is possible to modify parameters and flags for groups of
228        histograms (see help for Mouse actions).
229
230        It does not make sense, however, to globally modify
231        instrument-related parameters and flags for different histogram types.
232        So global actions can be limited to a single class of histogram types
233        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
234        for groups of similar histograms. Thus, if this mode is set to "All"
235        the Histogram and Profile pages are disabled.
236<DT>Override backspace<DD>This option is available in UNIX only, as there are different
237        ways that backspace can be implemented. When option is set
238        as "On," the backspace key is overridden to send a "delete"
239        character. If backspace does not work in a program such as
240        EXPEDT, change try the other setting for this option.
241<DT>liveplot_options<DD>Used to set options for liveplot,
242for example, the histogram to be plotted
243</DL>
244<img SRC="m2.gif" align=TEXTTOP>
245</DL></DL>
246
247<h3>8.3 Powder Menu</h3>
248<DL><DL>
249This menu contains links to GSAS programs used for powder diffraction
250analysis.
251<DL>
252<DT>expedt<DD>Run GSAS experiment editor
253<DT>powpref<DD>Powder data preparation
254<DT>genles<DD>Run GSAS experiment editor
255<DT>powplot<DD>Display powder patterns
256<DT>rawplot<DD>Plot powder data
257<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
258<DT>tofnorm<DD>Normalize a TOF spectrum
259</DL>
260<img SRC="m3.gif" align=TEXTTOP>
261</DL></DL>
262
263<h3>8.4 Single Crystal Menu</h3>
264<DL><DL>
265This menu contains links to GSAS programs used for
266single-rystal diffraction analysis.
267<DL>
268<DT>expedt<DD>Run GSAS experiment editor
269<DT>powpref<DD>Powder data preparation
270<DT>scabs<DD>Single crystal absorption
271<DT>scmerge<DD>Sort and merge single crystal data
272<DT>sxtldata<DD>Prepare generic single crystal data
273</DL>
274<img SRC="m4.gif" align=TEXTTOP>
275</DL></DL>
276
277<h3>8.5 Graphics Menu</h3>
278<DL><DL>
279This menu contains links to several GSAS and
280two non-GSAS (liveplot and widplt)
281programs used for graphical display of data and results.
282<DL>
283<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
284        and then compute with FOURIER
285<DT>polfplot<DD>Display polefigures
286<DT>powplot<DD>Display powder patterns
287<DT>ortep<DD>Draw crystal structure
288<DT>rawplot<DD>Plot powder data
289<DT>fourier<DD>Generate Fourier map
290<DT>forsrh<DD>Search Fourier map for peaks
291<DT>liveplot<DD>Create a plot of powder data
292with zooming, automatic update and other nice features.
293<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
294</DL>
295<img SRC="m5.gif" align=TEXTTOP
296</DL></DL>
297
298<h3>8.6 Results Menu</h3>
299<DL><DL>
300This menu contains links to several GSAS and
301one non-GSAS (lstview)
302programs used for analysis of results.
303<DL>
304<DT>bijcalc<DD>Thermal parameter analysis
305<DT>disagl<DD>Distance/angle calculations
306<DT>reflist<DD>List reflection data
307<DT>geometry<DD>Molecular geometry calculations
308<DT>hstdmp<DD>List powder histogram data
309<DT>istats<DD>HKL Intensity statistics
310<DT>rcalc<DD>Compute reflection resuduals
311<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
312</DL>
313<img SRC="m6.gif" align=TEXTTOP>
314</DL></DL>
315
316<h3>8.7 Calculations Menu</h3>
317<DL><DL>
318This menu contains programs for useful crystallographic computations.
319<DL>
320<DT>cllchg<DD>Transform unit cell
321<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
322<DT>rducll<DD>Unit cell reduction
323<DT>spcgroup<DD>Space group symbol interpreter
324<DT>unimol<DD>Unique molecule assembler
325</DL>
326<img SRC="m7.gif" align=TEXTTOP>
327</DL></DL>
328
329<h3>8.8 Import/Export Menu</h3>
330<DL><DL>
331This menu contains utilities for importing information into GSAS and
332exporting.
333<DL>
334<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
335<DT>hklsort<DD>Prepare HKL tables
336<DT>pubtable<DD>Prepare atom parameter tables
337<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
338<DT>cad4rd<DD>Prepare CAD4 single crystal data
339<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
340<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
341<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
342<DT>sxtldata<DD>Prepare generic single crystal data
343</DL>
344<img SRC="m8.gif" align=TEXTTOP>
345</DL></DL>
346
347<h2>9. EXPGUI Utility Programs</h2></a>
348<DL><DL>
349<P><B>LSTVIEW</B>
350
351<P>lstview is used to browse through the GSAS output listing. It is
352invoked by the "lstview" command in the GUI.
353<CENTER><IMG SRC="http://rrdjazz.nist.gov/~toby/textview.gif"></CENTER>
354
355
356<P><B>LIVEPLOT</B>
357
358<P>liveplot shows the observed, calculated and difference plots for powder
359refinements. The plot is updated as the refinement progresses. The mouse can
360be used to zoom in on sections of the plot.
361<CENTER><IMG SRC="http://rrdjazz.nist.gov/~toby/liveplot.gif"></CENTER>
362<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
363LIVEPLOT can now be enhanced to superimpose peak locations for
364input unit cells or peaks from JCPDS/ICDD entries.
365See the <A HREF="http://rrdjazz.nist.gov/~toby/tkGSAS_cfg.html#liveplot">
366LIVEPLOT customization information</A>
367or read file <tt>tkGSAS_cfg.html</tt> in the gsas/tcl directory.
368
369<P><B>WIDPLT</B>
370
371<P>widplt can be used to plot the actual peak widths generated by the profile
372parameters used in GSAS. It is possible to define reference curves
373that are loaded automatically.
374<CENTER><IMG SRC="http://rrdjazz.nist.gov/~toby/widplt.gif"></CENTER>
375<BR> 
376</DL></DL>
377
378<H2>
379Acknowledgements</H2>
380Praise to Larson and <A HREF="http://strider.lansce.lanl.gov/mlnsc/scientists/vondreele.html">Von
381Dreele</A> for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
382for Tcl/Tk and <A HREF="http://rrdjazz.nist.gov/przemek.html">Przemek Klosowski</A>
383for convincing me to learn Tcl/Tk.
384<hr>
385GSAS is written by Allen C. Larson and Robert B. Von Dreele,  MS-H805,
386Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions
387or kudos concerning GSAS should be sent to Robert B. Von Dreele at
388<A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A>
389<P>GSAS is Copyright, 1984-1997, The Regents of the University of California.
390The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
391by the Los Alamos National Laboratory, which is operated by the University
392of California for the U.S. Department of Energy. The U.S. Government is
393licensed to use, reproduce, and distribute this software. Permission is
394granted to the public to copy and use this software without charge, provided
395that this notice and any statement of authorship are reproduced on all
396copies. Neither the Government nor the University makes any warranty, express
397or implied, or assumes any liability or responsibility for the use of this
398software.
399<P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
400<A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> 
401with help from Jonathan Wasserman.
402
403<P>EXPGUI is not subject to copyright. Have fun with it.
404
405<p>Neither the U.S. Government nor any author makes any warranty,
406expressed or implied, or assumes any liability or responsibility
407for the use of this information or the software described
408here. Brand names cited here are used for
409identification purposes and do not consitute an endorsement by NIST.
410
411<p><a href="http://rrdjazz.nist.gov/~toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
412<br>
413$Revision: 26 $ $Date: 2009-12-04 22:59:08 +0000 (Fri, 04 Dec 2009) $
414</body>
415</html>
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