source: trunk/doc/expgui.html @ 115

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# on 1999/10/11 20:27:39, toby did:
document "Group Phases Together" option

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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20Note that pictures on this page are somewhat out-of-date with respect to the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, as seen below. 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, as seen below. 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 to create a submenu. Also on this submenu is an option
197"Group Phases Together" that controls how EXPGUI treats phases having
198the same profile type when multiple histograms are selected. If
199the "Group Phases Together" option is on, then the refinement flags for
200all phases with the same histogram types are grouped together, when possible.
201If this option is off, phases are treated separately.
202<p>
203<a name="mouseactions">
204</DL></DL>
205<h2>7. Mouse Actions</h2></a>
206<DL><DL>
207A range of atoms or (in multiple selection mode) histograms may be
208selected by dragging (holding down) the left mouse button. It is also
209possible to select a range by using the Shift key with the left mouse
210button. To select or deselect individual entries, use the Control key
211with the left mouse button. Pressing the right mouse button selects all
212entries in a list.
213</DL></DL>
214
215<h2>8. Menus</h2>
216A description of the EXPGUI menus follows along with a very
217brief description of the function of each menu option.
218Note that an option may appear under more than one menu.
219<H3>8.1 File Menu</H3>
220<DL><DL>
221The options on the File menu as is the custom contains the commands
222for reading and writing experiment files, as well as starting
223and ending the program.
224<DL>
225<DT>expnam<DD>
226        Select an existing GSAS experiment to be used or create a new
227        experiment file from scratch.
228<DT>Save<DD>Saves modifications to the current experiment file to disk
229<DT>Save As<DD>Saves modifications to the current experiment file to disk
230        under a new file name
231<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
232<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
233<DT>exit<DD>Exit EXPGUI
234</DL>
235<img SRC="m1.gif" BORDER=3 >
236</DL></DL>
237
238<h3>8.2 Options Menu</h3>
239<DL><DL>
240This menu contains options that determine how EXPGUI runs.
241<DL>
242<DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
243        saved prior to each save or run of expedt in a file named
244        [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX)
245        or in a file named [expnam].ZIP or  [expnam].xxx (Windows)
246<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" page
247        Atoms may be displayed sorted by atom number, atom type,
248        or by x, y or z
249
250<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
251        Histogram, Scaling and Profile pages
252
253        Histograms may be sorted by histogram number, histogram type,
254        original bank number, or diffraction angle/wavelength
255<DT><A href="#multiplehistogram">Multiple hist. selection</A><DD>
256        When this mode is off, it is possible to modify parameters
257        and refinement flags for only a single histogram. For other settings,
258        it is possible to modify parameters and flags for groups of
259        histograms (see help for Mouse actions).
260
261        It does not make sense, however, to globally modify
262        instrument-related parameters and flags for different histogram types.
263        So global actions can be limited to a single class of histogram types
264        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
265        for groups of similar histograms. Thus, if this mode is set to "All"
266        the Histogram and Profile pages are disabled.
267<DT>Override backspace<DD>This option is available in UNIX only, as there are different
268        ways that backspace can be implemented. When option is set
269        as "On," the backspace key is overridden to send a "delete"
270        character. If backspace does not work in a program such as
271        EXPEDT, change try the other setting for this option.
272<DT>Autoupdate EXP<DD>Normally EXPGUI prompts before rereading the EXP
273file when GENLES, POWPREF,... are run (this is so that one can change
274the experiment file and rerun with the current input). If this option is
275set, the new file is automatically read without a prompt.
276
277<DT>SaveOptions<DD>Save the current values for "Override backspace",
278        "Sort atoms by", "Sort histograms by" and "archive EXP"
279        in file ~/.gsas_config (c:\.gsas_config on Windows).
280<DT>liveplot_options<DD>Used to set options for liveplot,
281for example, the histogram to be plotted
282</DL>
283<img SRC="m2.gif"  BORDER=3>
284</DL></DL>
285
286<h3>8.3 Powder Menu</h3>
287<DL><DL>
288This menu contains links to GSAS programs used for powder diffraction
289analysis.
290<DL>
291<DT>expedt<DD>Run GSAS experiment editor
292<DT>powpref<DD>Powder data preparation
293<DT>genles<DD>Run GSAS experiment editor
294<DT>powplot<DD>Display powder patterns
295<DT>rawplot<DD>Plot powder data
296<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
297<DT>tofnorm<DD>Normalize a TOF spectrum
298</DL>
299<img SRC="m3.gif"  BORDER=3>
300</DL></DL>
301
302<h3>8.4 Single Crystal Menu</h3>
303<DL><DL>
304This menu contains links to GSAS programs used for
305single-rystal diffraction analysis.
306<DL>
307<DT>expedt<DD>Run GSAS experiment editor
308<DT>powpref<DD>Powder data preparation
309<DT>scabs<DD>Single crystal absorption
310<DT>scmerge<DD>Sort and merge single crystal data
311<DT>sxtldata<DD>Prepare generic single crystal data
312</DL>
313<img SRC="m4.gif"  BORDER=3>
314</DL></DL>
315
316<h3>8.5 Graphics Menu</h3>
317<DL><DL>
318This menu contains links to several GSAS and
319two non-GSAS (liveplot and widplt)
320programs used for graphical display of data and results.
321<DL>
322<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
323        and then compute with FOURIER
324<DT>polfplot<DD>Display polefigures
325<DT>powplot<DD>Display powder patterns
326<DT>ortep<DD>Draw crystal structure
327<DT>rawplot<DD>Plot powder data
328<DT>fourier<DD>Generate Fourier map
329<DT>forsrh<DD>Search Fourier map for peaks
330<DT>liveplot<DD>Create a plot of powder data
331with zooming, automatic update and other nice features.
332<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
333<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
334</DL>
335<img SRC="m5.gif"  BORDER=3>
336</DL></DL>
337
338<h3>8.6 Results Menu</h3>
339<DL><DL>
340This menu contains links to several GSAS and
341one non-GSAS (lstview)
342programs used for analysis of results.
343<DL>
344<DT>bijcalc<DD>Thermal parameter analysis
345<DT>disagl<DD>Distance/angle calculations
346<DT>reflist<DD>List reflection data
347<DT>geometry<DD>Molecular geometry calculations
348<DT>hstdmp<DD>List powder histogram data
349<DT>istats<DD>HKL Intensity statistics
350<DT>rcalc<DD>Compute reflection resuduals
351<DT>composition<DD>Computes the chemical composition of a unit cell
352accounting for site multiplicies and occupancies
353<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
354</DL>
355<img SRC="m6.gif"  BORDER=3>
356</DL></DL>
357
358<h3>8.7 Calculations Menu</h3>
359<DL><DL>
360This menu contains programs for useful crystallographic computations.
361<DL>
362<DT>cllchg<DD>Transform unit cell
363<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
364<DT>rducll<DD>Unit cell reduction
365<DT>spcgroup<DD>Space group symbol interpreter
366<DT>unimol<DD>Unique molecule assembler
367</DL>
368<img SRC="m7.gif" BORDER=3>
369</DL></DL>
370
371<h3>8.8 Import/Export Menu</h3>
372<DL><DL>
373This menu contains utilities for importing information into GSAS and
374exporting.
375<DL>
376<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
377file is used in MSI software such as Cerius and InsightII.
378<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
379<DT>hklsort<DD>Prepare HKL tables
380<DT>pubtable<DD>Prepare atom parameter tables
381<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
382<DT>cad4rd<DD>Prepare CAD4 single crystal data
383<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
384<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
385<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
386<DT>sxtldata<DD>Prepare generic single crystal data
387</DL>
388<img SRC="m8.gif"  BORDER=3>
389</DL></DL>
390
391<h2>9. EXPGUI Utility Programs</h2></a>
392<DL><DL>
393<P><B>LSTVIEW</B>
394
395<P>lstview is used to browse through the GSAS output listing. It is
396invoked by the "lstview" command in the GUI.
397<CENTER><IMG SRC="textview.gif"></CENTER>
398
399
400<P><B>LIVEPLOT</B>
401
402<P>liveplot shows the observed, calculated and difference plots for powder
403refinements. The plot is updated as the refinement progresses. The mouse can
404be used to zoom in on sections of the plot.
405<CENTER><IMG SRC="liveplot.gif"></CENTER>
406<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
407LIVEPLOT can now be enhanced to superimpose peak locations for
408input unit cells or peaks from JCPDS/ICDD entries.
409See the <A HREF="expgui_cfg.html#liveplot">
410LIVEPLOT customization information</A> 
411or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory.
412<P>
413LIVEPLOT gets the current diffraction information by running the TCLDUMP program, if installed, or
414HSTDUMP otherwise. The TCLDUMP program has been optimized for use with LIVEPLOT and offers a number of extra
415options that are not available when HSTDUMP is used: plots can be displayed in the native units (2Theta/TOF/KeV), or
416in d-space or Q; fixed plus fitted background curves are shown in green; if reflection tickmarks are displayed,
417reflection tickmarks can be displayed by holding the shift key while pressing the left mouse button.
418See the installation instructions for installing TCLDUMP.
419
420<P><B>WIDPLT</B>
421
422<P>widplt can be used to plot the actual peak widths generated by the profile
423parameters used in GSAS. It is possible to define reference curves
424that are loaded automatically.
425<CENTER><IMG SRC="widplt.gif"></CENTER>
426<BR> 
427</DL></DL>
428
429<H2>
430Acknowledgements</H2>
431Praise to Larson and
432<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
433Von Dreele</A> for GSAS, <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.scriptics.com/">Ousterhout</A>
434for Tcl/Tk,
435Przemek Klosowski</A>
436for convincing me to learn Tcl/Tk
437and Jonathan Wasserman for starting this project.
438
439<hr>
440GSAS 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">
441Robert B. Von Dreele</A>, MS-H805,
442Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions
443or kudos concerning GSAS should be sent to Robert B. Von Dreele at
444<A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A>
445<P>GSAS is Copyright, 1984-1997, The Regents of the University of California.
446The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
447by the Los Alamos National Laboratory, which is operated by the University
448of California for the U.S. Department of Energy. The U.S. Government is
449licensed to use, reproduce, and distribute this software. Permission is
450granted to the public to copy and use this software without charge, provided
451that this notice and any statement of authorship are reproduced on all
452copies. Neither the Government nor the University makes any warranty, express
453or implied, or assumes any liability or responsibility for the use of this
454software.
455<P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
456<A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> 
457with help from Jonathan Wasserman.
458
459<P>EXPGUI is not subject to copyright. Have fun with it.
460
461<p>Neither the U.S. Government nor any author makes any warranty,
462expressed or implied, or assumes any liability or responsibility
463for the use of this information or the software described
464here. Brand names cited here are used for
465identification purposes and do not consitute an endorsement by NIST.
466
467<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>)
468<br>
469$Revision: 115 $ $Date: 2009-12-04 23:00:39 +0000 (Fri, 04 Dec 2009) $
470</body>
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