source: trunk/doc/expgui.html @ 329

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# on 2000/10/18 00:11:17, toby did:
add more utilities docs
fixup formatting

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1<html>
2<head>
3   <META NAME="Author" CONTENT="Brian H. Toby">
4   <title>EXPGUI</title>
5</head>
6<BODY BGCOLOR="#FFFFFF">
7
8<A HREF=http://www.ncnr.nist.gov>
9<IMG SRC="http://www.ncnr.nist.gov/images/ncnrtrans.gif" 
10alt="Link to NIST Center for Neutron Research home page"
11ALIGN=RIGHT></A>
12<A HREF=http://www.nist.gov>
13<IMG SRC="http://www.ncnr.nist.gov/images/webidblue_2lineright.gif" 
14alt="Link to National Institute of Standards & Technology home page"
15ALIGN=LEFT></A>
16<CENTER>
17<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
18<IMG SRC="tcltklogo100.gif" 
19alt="Link to Tcl/Tk information">
20</CENTER></A>
21<br clear=all><hr>
22
23<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
24<TR><TH><A Href="expgui1.html">Next page</A>
25</TH></TR></TABLE><BR CLEAR=ALL>
26
27<center><h1>
28EXPGUI<BR>
29A Graphical User Interface for
30<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
31GSAS</A>
32</h1></center>
33<P><P>
34EXPGUI is a graphical interface for the
35<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
36GSAS</A> package.
37It allows two types of actions:
38it can be used to directly modify the GSAS
39experiment file with a graphical user interface (GUI) and
40it can be used to invoke the programs inside the
41GSAS package such as EXPEDT, GENLES, FOURIER...
42These programs can be run from a menu or in many cases by pressing buttons.
43
44<P>
45This documentation describes the different actions that
46can be accomplished with the different panes and the
47contents of the menus. Other documents about EXPGUI are:
48<a name="installation"></A>
49Installation notes for
50<A HREF="expgui_Win_readme.html">Windows</A>,
51and for
52<A HREF="expgui_Unix_readme.html">UNIX</A>,
53<A HREF="expgui_cfg.html">
54Customization notes</A>, a list of <A HREF="expguierr.html">warning, error and informational messages</A>
55and two example tutorials: for
56<A HREF="tutorial1/index.html">
57TOF</A>
58and
59<A HREF="tutorial2/index.html">
60constant-wavelength neutron</A>.
61Note that screen images in this document are not updated as frequently as the
62text.
63<hr>
64
65<h2>A. Experiment file editing</h2>
66<P>
67<DL><DL>
68When an experiment (.EXP) file is read, a copy is made in local
69computer memory. The values in memory can then be edited
70by selecting different
71panes ("pages" or "panels") from the tabbed list, where
72each pane is reserved for a different section of the .EXP file.
73The changes values are written back out to the .EXP file when the
74"File/Save" or "File/Save as" <A Href="expguic.html#1">menu bar options</A>
75are used. The .EXP file is also automatically written before running any GSAS
76programs, such as GENLES or EXPEDT.
77
78<center><B>
79<br>The notebook pane tabs.
80<br><img SRC="panebar1.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
81</center></B>
82More information about each pane can be found using the links below.
83
84<A Href="expgui1.html">
85<h3>A.1 Least Squares (LS) Controls Pane</h3>
86</A><A Href="expgui2.html">
87<h3>A.2 Phase Pane</h3> 
88</A><A Href="expgui3.html">
89<h3>A.3 Histogram pane</h3> 
90</A><A Href="expgui4.html">
91<h3>A.4 Scaling pane</h3> 
92</A><A Href="expgui5.html">
93<h3>A.5 Profile pane</h3> 
94</A><A Href="expgui6.html">
95<h3>A.6 Constraints pane</h3>
96</A><A Href="expgui7.html">
97<h3>A.7 Preferential Orientation Pane</h3>
98</A>
99<P>
100<img SRC="rederror.gif" align=LEFT BORDER=3 alt="EXPGUI Screen snapshot">
101<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
102Values changed in the entry boxes in these panes are
103immediately transferred to the "in memory" copy of the .EXP file, unless
104there is an error in the typed value, (for example if "1..0" is typed, or
105"1.5" is typed where an integer is expected.) When a value is invalid, it is
106not saved. In this case, the text is turned red, to indicate
107that an error is present, as shown in the figure to the left, where "90.000x"
108has been entered for alpha.
109<br clear=all>
110</DL></DL>
111<h2>B. Shortcuts</h2></a>
112<a name="multiplehistogram">
113<h3>B.1 Multiple Histogram Selection</h3></a>
114<DL><DL>
115This mode allows parameters to be changed for groups of
116histograms.
117When the "Multiple Histogram Selection" mode is off,
118it is possible to modify parameters
119and refinement flags for only a single histogram, but
120the other settings allow groups of histograms
121to be selected and modified.
122<A href="#mouseactions">(see Mouse Actions)</A>.
123<P>
124It does not make sense, however, to globally modify
125instrument-related parameters and flags for different
126histogram types.
127So global actions can be limited to a single class
128of histogram types (e.g. TOF, CW Neutron,...), which
129allows these parameters to be set for groups of
130similar histograms. Thus, if this mode is set to "All"
131the Histogram and Profile panes are disabled.
132<P>
133The setting for "Multiple Histogram Selection" mode is
134displayed above each histogram selection box and is
135selected using the "Multiple Hist. Selection" item on the
136Options menu to create a submenu or by clicking on the display.
137Note that another option in this "Multiple Hist. Selection"
138submenu is an option "Group Phases Together" that controls how
139EXPGUI treats phases having
140the same profile type that is used when multiple histograms are selected. If
141the "Group Phases Together" option is on, then the refinement flags for
142all phases with the same histogram types are grouped together, when possible.
143If this option is off, phases are treated separately.
144<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
145If the left mouse button is used to click on the selection mode display,
146the mode is cycled between the available modes. If the right mouse
147button is used, the mode is reset, to disable multiple histogram selection.
148<p>
149<a name="mouseactions">
150</DL></DL>
151<h3>B.2 Mouse Actions</h3></a>
152<DL><DL>
153A range of atoms or (in multiple selection mode) histograms may be
154selected by dragging (holding down) the left mouse button. It is also
155possible to select a range by using the Shift key with the left mouse
156button. To select or deselect individual entries, use the Control key
157with the left mouse button. Pressing the right mouse button selects all
158entries in a list.
159</DL></DL>
160
161<h2>C. Menu Commands and Programs</h2>
162<p>
163GSAS programs are invoked either through use of the menu bar
164<center><B>
165<br>The menu bar.
166<br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
167</center></B>
168or by "pressing" a button on the button bar. The button bar
169simply provides an easy way to access commonly used
170actions on the menu bar. Users can
171<A HREF="expgui_cfg.html">
172configure the menu bar</A> to include their own preferred actions and, with
173some knowledge of the program and Tcl/Tk,
174add their own commands to the menu bar or button bar.
175
176<center><B>
177<br>The button bar.
178<br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
179</center></B>
180
181A description of the EXPGUI menus follows. Use the links to obtain
182more information, including a very
183brief description of the function of each menu option.
184Note that an option may appear under more than one menu.
185
186<DL><DL>
187
188<A Href="expguic.html#1">
189<H3>C.1 File Menu</H3>
190</A>
191<DL><DL>
192The options on the File menu as is the custom contains the commands
193for reading and writing experiment files, as well as starting
194and ending the program.
195</DL></DL>
196
197<A Href="expguic.html#2">
198<h3>C.2 Options Menu</h3>
199</A>
200<DL><DL>
201This menu contains options that determine how EXPGUI runs.
202</DL></DL>
203
204<A Href="expguic.html#3">
205<h3>C.3 Powder Menu</h3>
206</A>
207<DL><DL>
208This menu contains links to GSAS programs used for powder diffraction
209analysis.
210</DL></DL>
211
212<A Href="expguic.html#4">
213<h3>C.4 Single Crystal Menu</h3>
214</A>
215<DL><DL>
216This menu contains links to GSAS programs used for
217single-crystal diffraction analysis.
218</DL></DL>
219
220<A Href="expguic.html#5">
221<h3>C.5 Graphics Menu</h3>
222</A>
223<DL><DL>
224This menu contains links to several GSAS and
225two non-GSAS (liveplot and widplt)
226programs used for graphical display of data and results.
227</DL></DL>
228
229<A Href="expguic.html#6">
230<h3>C.6 Results Menu</h3>
231</A>
232<DL><DL>
233This menu contains links to several GSAS and
234one non-GSAS (lstview)
235programs used for analysis of results.
236</DL></DL>
237
238<A Href="expguic.html#7">
239<h3>C.7 Calculations Menu</h3>
240</A>
241<DL><DL>
242This menu contains programs for useful crystallographic computations.
243</DL></DL>
244
245<A Href="expguic.html#8">
246<h3>C.8 Import/Export Menu</h3>
247</A>
248<DL><DL>
249This menu contains utilities for importing information into GSAS and
250exporting.
251</DL></DL>
252</DL></DL>
253
254<h2>D. EXPGUI Utility Programs</h2></a>
255
256<br clear=all>
257<H3>LSTVIEW</H3>
258
259<DL><DL>
260lstview is used to browse through the GSAS output listing. It is
261invoked by the "lstview" command in the GUI.
262<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
263</DL></DL>
264
265<br clear=all>
266<H3>LIVEPLOT</H3>
267<DL><DL>
268liveplot shows the observed, calculated and difference plots for powder
269refinements. The plot is updated as the refinement progresses. The mouse can
270be used to zoom in on sections of the plot.
271Liveplot uses the <A href="#blt">BLT</A> graphics package.
272<CENTER><IMG SRC="liveplot.gif" alt="EXPGUI Screen snapshot"></CENTER>
273<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
274LIVEPLOT can now be enhanced to superimpose peak locations for
275input unit cells or peaks from JCPDS/ICDD entries.
276See the <A HREF="expgui_cfg.html#liveplot">
277LIVEPLOT customization information</A> 
278or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory.
279<P>
280LIVEPLOT gets the current diffraction information by running the TCLDUMP program, if installed, or
281HSTDUMP otherwise. The TCLDUMP program has been optimized for use with LIVEPLOT and offers a number of extra
282options that are not available when HSTDUMP is used: plots can be displayed in the native units (2Theta/TOF/KeV), or
283in d-space or Q; fixed plus fitted background curves are shown in green; if reflection tickmarks are displayed, <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
284reflection tickmarks can be displayed by pressing "H" or "h" while the
285mouse is near a reflection (holding the shift key while
286pressing the left mouse button also works).
287See the installation instructions for installing TCLDUMP.
288</DL></DL>
289
290<br clear=all>
291<H3>WIDPLT</H3>
292<DL><DL>
293WIDPLT can be used to plot the actual peak widths generated by the profile
294parameters used in GSAS.
295It is possible to define reference curves
296that are loaded automatically.
297WIDPLT uses the <A href="#blt">BLT</A> graphics package.
298<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
299</DL></DL>
300
301<br clear=all>
302<a name="ConvertUnix"></a>
303<h3>Unix File Conversions</h3> 
304<DL><DL>
305In UNIX, GSAS data, experiment and instrument parameter files are expected to
306have a format with exactly 80 characters per line and no line
307separators (no carriage returns or linefeeds). Files in this format
308are called "Direct Access". Normal UNIX files may have any number
309of characters per line and every line is terminated by a line feed character.
310These files are called "sequential".
311EXPGUI uses the convention that all uppercase is used for Direct Access files
312while all lowercase is used for sequential files.
313<P>
314The Unix File Conversion menu is used to convert sequential files to
315direct access for use in GSAS or to convert direct access files to
316sequential, for use in standard UNIX programs, such as editors or e-mail.
317</DL></DL>
318
319<br clear=all>
320<a name="ConvertWin"></a>
321<h3>Windows File Conversions</h3> 
322<DL><DL>
323In Windows, GSAS data, experiment and instrument parameter files are
324expected to have a format with exactly 80 characters per line followed
325by a carriage returns and a linefeed (82 characters total per line).
326Files in this format can be read in "Direct Access" mode. The Convert menu
327in windows can be used to convert files into this format (it can also
328convert UNIX direct access files correctly). The original version of the
329file is retained and renamed.
330<P>
331</DL></DL>
332
333<br clear=all>
334<a name="Composition"></a>
335<h3>Compute Composition</h3> 
336<DL><DL>
337The composition box shows the unit cell and asymmetric unit composition
338for all phases in a material. Site multiplicities and occupancies are
339taken into account.
340</DL></DL>
341
342<br clear=all>
343<a name="ExportMSI"></a>
344<h3>Export coordinates in MSI .xtl format</h3> 
345<DL><DL>
346The Export/exp2xtl routine writes a .xtl file, as is used in Insight-II and
347Cerius2 (Molecular Simulations, Inc.). Note that spacegroups are not named
348exactly the same in the two programs and the origin may need to be specified
349as "origin 2", for spacegroups where the center of symmetry is not at the
350origin. It is up to the user to get things right.
351</DL></DL>
352
353<br clear=all>
354<a name="DeleteHistoryRecords"></a>
355<h3>Delete History Records</h3> 
356<DL><DL>
357Every time a GSAS program (including EXPGUI) is run, an entry is added to
358the "history records" in the .EXP file. After 999 entries have been written,
359no more can be added to the file. Further, reading large numbers of history
360records can slow the GSAS programs
361(this is less of a problem on faster computers). For these reasons, it may be
362a good idea to prune the older history records from the file. If more than 100
363history records are found in an experiment file, EXPGUI suggests that the
364older history entries be deleted. Alternately the File/EraseHistory command
365can be used to invoke the this option.
366<P>
367On the dialog the number of history records to be retained is specified.
368Also, after records have been deleted, the remaining records can be renumbered
369starting with 1, so that the 999 record limit is not reached.
370</DL></DL>
371
372<A name=blt>
373<H2>
374BLT</H2>
375The BLT graphics package is used by the WIDPLT and LIVEPLOT routines. If the
376package can not be loaded these routines, an error message,
377"Error -- Unable to load the BLT package", will be displayed. A frequent
378problem is the package is installed, but not configured so that common
379support routines are loaded automatically. If this is the case,
380a message, "BLT Setup Error: could not access a Blt_ routine...",
381will be displayed.
382Please see
383<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
384http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
385</A> for more information on installation of BLT.
386
387<H2>
388Acknowledgements</H2>
389Praise to Larson and
390<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
391Von Dreele</A> for GSAS, <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.scriptics.com/">Ousterhout</A>
392for Tcl/Tk,
393Przemek Klosowski</A>
394for convincing me to learn Tcl/Tk
395and Jonathan Wasserman for helping get this project started.
396Large sections of the Preferred Orientation GUI were written by
397Pamela Whitfield of the NRC (Canada).
398<P>
399<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
400GSAS</A>
401is 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">
402Robert B. Von Dreele</A>, MS-H805,
403Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions
404or kudos concerning GSAS should be sent to Robert B. Von Dreele at
405<A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A>
406EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
407<A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> 
408with help from Jonathan Wasserman.
409
410<P>GSAS is Copyright, 1984-2000, by
411the Regents of the University of California.
412The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
413by the Los Alamos National Laboratory, which is operated by the University
414of California for the U.S. Department of Energy. The U.S. Government is
415licensed to use, reproduce, and distribute this software. Permission is
416granted to the public to copy and use this software without charge, provided
417that this notice and any statement of authorship are reproduced on all
418copies. Neither the Government nor the University makes any warranty, express
419or implied, or assumes any liability or responsibility for the use of this
420software.
421
422<P>EXPGUI is not subject to copyright. Have fun with it. Modify it. Write
423new sections and make them available to the rest of the world.
424
425<p>Neither the U.S. Government nor any author makes any warranty,
426expressed or implied, or assumes any liability or responsibility
427for the use of this information or the software described
428here. Brand names cited here are used for
429identification purposes and do not consitute an endorsement by NIST.
430
431<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
432<TR><TH><A Href="expgui1.html">Next page</A>
433</TH></TR></TABLE><BR CLEAR=ALL>
434
435<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>)
436<br>
437$Revision: 329 $ $Date: 2009-12-04 23:04:14 +0000 (Fri, 04 Dec 2009) $
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