source: trunk/doc/expguic.html @ 953

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remove NIST refs; review space in dir warn; use PGPLOT_DIR on win-NT, etc.; doc updates; tkcon problems on windows, add open console; move update menu from help

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1<html>
2<head>
3   <title>EXPGUI</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
5   GSAS, EXPGUI">
6</HEAD>
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15
16<?
17   include("/var/www/include/navigation.inc");
18   include("/var/www/include/utility.inc");
19?>
20<blockquote><font face="arial, helvetica, sans-serif">
21
22<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
23<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
24</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
25</TH><TH><A Href="expgui7.html">Previous page</A>
26</TH></TR></TABLE><BR CLEAR=ALL>
27
28<center><h1>
29<HR noshade width="75%" size="2" align="center">
30EXPGUI, Menu Contents
31<HR noshade width="75%" size="2" align="center">
32</h1></center>
33
34<h2>C. Menu Contents</h2>
35Note that the figures on this page are likely to be out of date with
36respect to the text. The text is updated more frequently. Also, note
37that not all menu options are available in Windows.
38
39<a name="1"></a>
40<H3>C.1 File Menu</H3>
41<BLOCKQUOTE>
42The options on the File menu as is the custom contains the commands
43for reading and writing experiment files, as well as starting
44and ending the program.
45<DL>
46<DT>Open<DD>
47        Select an existing GSAS experiment to be used. If a name is entered
48        that does not exists, it is possible to create a new
49        experiment file from scratch.
50<DT>expnam<DD>
51Equivalent to Open, included since this is the command used in other
52GSAS shells to select GSAS experiments.
53<DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S).
54<DT>Save As<DD>Saves modifications to the current experiment file to disk
55        under a new file name
56<DT>Reread .EXP file<DD>Reread the last saved version of the
57  experiment file from disk.
58<DT>Update GSAS/EXPGUI<DD>This queries the EXPGUI software repository
59  to see if any files in EXPGUI or GSAS has been updated. It then
60  offers the program user the option to update these files. The update
61  will fail if the user does not have permission to change the EXPGUI
62  or GSAS files. In this case, a system administrator may be needed.
63<DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
64<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
65<DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
66</DL>
67<img SRC="m1.gif" BORDER=3 alt="EXPGUI Screen snapshot">
68</BLOCKQUOTE>
69
70<a name="2"></a>
71<h3>C.2 Options Menu</h3>
72<BLOCKQUOTE>
73This menu contains options that determine how EXPGUI runs.
74<a name="archive"></a>
75<DL>
76<DT>archive EXP<DD>
77  Toggles archiving of .EXP files. When on, files are
78        saved before they are overwritten by EXPGUI as a file
79        named <I>EXPNAM</I>.Oxx where xx is a pair of hexidecimal
80        digits (01, 02,..., 09, 0A,... OF, 10,... FF).
81        Each time that EXPGUI archives a file, note is placed in the .LST file
82        so that the saved file name can be associated with
83        the refinement stage. Turning this option off, prevents EXPGUI
84        from creating these <I>EXPNAM</I>.Oxx archive files, but
85        the will still be created by EXPEDT, GENLES,...
86<P>
87<DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are
88         shown in a separate window. When it is not set, the results are
89        written in the .LST file. Note that on Windows, LSTVIEW can interfere
90        with putting output into the DISAGL window. The solution is to
91        close LSTVIEW before running DISAGL.
92
93<a name="Autoupdate"></a>
94<DT>Autoload EXP<DD>Normally EXPGUI prompts before rereading the EXP
95file when GENLES, POWPREF,... or other GSAS programs run
96If this option is set, the new file is automatically read without a prompt.
97The advantage of leaving this option off, is that
98you can opt to not load the
99revised .EXP file, which means that you reject the last set of changes.
100This is useful if
101GENLES blows up or you have done something wrong. The advantage
102of turning "autoload EXP" on is
103that there is one less thing to do when running GSAS programs.
104Note that it is still possible to reverse changes, if
105<a href="#archive">archive files</A>, but this may require more effort.
106
107<a name="execprompt"></a>
108<DT>Prompt after GSAS run<DD>
109<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
110By default, GSAS programs are run in a separate window
111and after the program completes, the window remains open until enter is
112pressed in the window. Turning the "Prompt after GSAS run" option off, causes
113the window to be closed immediately after the program completes, saving
114some effort but obliterating any error messages or other evidence of problems.
115
116<a name="Autoicon"></a>
117<DT>Iconify during GSAS<DD>
118If this option is turned on, the main EXPGUI window is shrunk to an icon
119(minimized) while GSAS programs are running and EXPGUI is suspended.
120The author prefers this mode, since there is no reason to have the
121screen cluttered with EXPGUI when it can't be used,
122but this is an option so that the mode can be turned off by those people
123who find this behavior annoying.
124
125<a name="AutostartGRWND"></a>
126<DT>Autostart GRWND
127<DD>
128This option is available on Windows-95, -98 and -ME to deal with a operating
129system quirk that prevents the starting of the GRWND.EXE program,
130needed for graphics in GSAS programs such as POWPLOT, RAWPLOT, EXPEDT,...
131(this program is not needed for EXPGUI graphics, such as LIVEPLOT). It
132is not understood why this error happens or how to prevent it. One cure
133is to start this GRWND.EXE program before starting the GSAS program.
134If this option is selected, each time a GSAS program is started, a separate
135program TLIST.EXE is used to check if GRWND.EXE is running. If it is not,
136EXPGUI will start this program before starting the requested GSAS program.
137
138<a name="sortatoms"></a>
139<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
140        Atoms may be displayed sorted by number, atom type, site multiplity,
141        occupancy, or by x, y or z coordinate
142<P>
143Clicking on the heading above the atoms list cycles with the left
144mouse button cycles through the atom sort modes. Clicking with
145the right mouse button resets the atom sort mode to "number".
146
147<a name="sorthist"></a>
148<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
149        Histogram, Scaling and Profile panes
150
151        Histograms may be sorted by histogram number, histogram type,
152        original bank number, or diffraction angle/wavelength
153<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
154        When this mode is off, it is possible to modify parameters
155        and refinement flags for only a single histogram. For other settings,
156        it is possible to modify parameters and flags for groups of
157        histograms (see help for Mouse actions).
158
159        It does not make sense, however, to globally modify
160        instrument-related parameters and flags for different histogram types.
161        So global actions can be limited to a single class of histogram types
162        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
163        for groups of similar histograms. Thus, if this mode is set to "All"
164        the Histogram and Profile panes are disabled.
165<DT>Override backspace<DD>This option is available in UNIX only, as there are different
166        ways that backspace can be implemented. When option is set
167        as "On," the backspace key is overridden to send a "delete"
168        character. If backspace does not work in a program such as
169        EXPEDT, change try the other setting for this option.
170
171<a name="setfont"></a>
172<DT>Set Screen Font
173<DD>
174This menu changes the fonts used in most sections of EXPGUI.
175Note that this setting can be saved with the
176SaveOptions menu option (below) so that EXPGUI automatically
177starts with the chosen font.
178
179<a name="exptoolout"></a>
180<DT>Show EXPTOOL output<DD>
181Normally EXPGUI does not show the output from EXPTOOL, when
182actions like adding atoms, phases or histograms is performed.
183If an error is detected, the output is shown. If
184there are problems with adding phases, atoms, histograms... and
185a window showing an error does not appear,
186this option should be set to "on" so the output from EXPTOOL is
187always shown.
188
189<DT>Save Options<DD>Save the current values for "Override backspace",
190        <a href="#sortatoms">"Sort atoms by"</a>,
191        <a href="#sorthist">"Sort histograms by"</a>,
192        <a href="#archive">"archive EXP"</a>,
193        <a href="#Autoupdate">"Autoload EXP"</a>,
194        <a href="#setfont">"Set Screen Font"</a>,
195        and
196        <a href="#Autoicon">"Iconify during GSAS"</a>
197       
198        in file ~/.gsas_config (or c:\gsas.config on Windows).
199<DT>Save Position<DD>Saves the current screen position of the EXPGUI
200  window as the starting point for future runs of EXPGUI in
201        in file ~/.gsas_config (or c:\gsas.config on Windows).
202
203<DT>liveplot_options<DD>Used to set options for
204<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
205for example, the histogram to be plotted
206<DT>Assign app to .EXP files<DD>(on Mac only) When selected, this
207  causes .EXP files to be linked (via the file resource fork) to the
208  EXPGUI applescript. This also causes the .EXP files to be displayed
209  with a GSAS icon.
210 
211</DL>
212<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
213</BLOCKQUOTE>
214
215<a name="3"></a>
216<h3>C.3 Powder Menu</h3>
217<BLOCKQUOTE>
218This menu contains links to GSAS programs used for powder diffraction
219analysis.
220<DL>
221<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
222<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
223<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
224<DT>powplot<DD>Display powder patterns
225<DT>rawplot<DD>Plot powder data
226<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
227<DT>tofnorm<DD>Normalize a TOF spectrum
228<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
229<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
230to fit a background function to a set of fixed background points.
231<DT><a HREF="excledt.html">excledt</a>
232<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
233to set the upper and lower limits for a histogram, as well as
234edit excluded regions.
235</DL>
236<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
237</BLOCKQUOTE>
238
239<a name="4"></a>
240<h3>C.4 Single Crystal Menu</h3>
241<BLOCKQUOTE>
242This menu contains links to GSAS programs used for
243single-rystal diffraction analysis.
244<DL>
245<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
246<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
247<DT>scabs<DD>Single crystal absorption
248<DT>scmerge<DD>Sort and merge single crystal data
249<DT>sxtldata<DD>Prepare generic single crystal data
250</DL>
251<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
252</BLOCKQUOTE>
253
254<a name="5"></a>
255<h3>C.5 Graphics Menu</h3>
256<BLOCKQUOTE>
257This menu contains links to several GSAS and
258two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
259and widplt)
260programs used for graphical display of data and results.
261<DL>
262<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
263        and then compute with FOURIER
264<DT>polfplot<DD>Display polefigures
265<DT>powplot<DD>Display powder patterns
266<DT>ortep<DD>Draw crystal structure
267<DT>rawplot<DD>Plot powder data
268<DT>fourier<DD>Generate Fourier map
269<DT>forsrh<DD>Search Fourier map for peaks
270<DT><a HREF="liveplot.html#liveplot">liveplot</a>
271<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
272to create a plot of powder data
273with zooming, automatic update and other nice features.
274<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
275<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
276</DL>
277<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
278</BLOCKQUOTE>
279
280<a name="6"></a>
281<h3>C.6 Results Menu</h3>
282<BLOCKQUOTE>
283This menu contains links to several GSAS and
284one non-GSAS (lstview)
285programs used for analysis of results.
286<DL>
287<DT>bijcalc<DD>Thermal parameter analysis
288<DT>disagl<DD>Distance/angle calculations
289<DT>reflist<DD>List reflection data
290<DT>geometry<DD>Molecular geometry calculations
291<DT>hstdmp<DD>List powder histogram data
292<DT>istats<DD>HKL Intensity statistics
293<DT>rcalc<DD>Compute reflection resuduals
294<DT>composition<DD>Computes the chemical composition of a unit cell
295accounting for site multiplicies and occupancies
296<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
297<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
298chains, for use in restraints.
299</DL>
300<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
301</BLOCKQUOTE>
302
303<a name="7"></a>
304<h3>C.7 Calculations Menu</h3>
305<BLOCKQUOTE>
306This menu contains programs for useful crystallographic computations.
307<DL>
308<DT>cllchg<DD>Transform unit cell
309<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
310<DT>rducll<DD>Unit cell reduction
311<DT>spcgroup<DD>Space group symbol interpreter
312<DT>unimol<DD>Unique molecule assembler
313</DL>
314<img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot">
315</BLOCKQUOTE>
316
317<a name="8"></a>
318<h3>C.8 Import/Export Menu</h3>
319<BLOCKQUOTE>
320This menu contains utilities for importing information into GSAS and
321exporting.
322<DL>
323<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
324file is used in MSI software such as Cerius and InsightII.
325<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
326<DT>hklsort<DD>Prepare HKL tables
327<DT>pubtable<DD>Prepare atom parameter tables
328<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
329<DT>cad4rd<DD>Prepare CAD4 single crystal data
330<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
331<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
332<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
333<DT>sxtldata<DD>Prepare generic single crystal data
334<DT>gsas2pdb<DD>
335Import (using GSAS2PDB & EXPEDT) and export coordinates (for
336macromolecular phases) to/from Protein Data Base files
337<DT>ref2asc<DD>
338Exports a GSAS reflection file to ASCII for use in non-GSAS programs
339<DT>ref2bin<DD>
340Imports an ASCII reflection file to the GSAS binary format
341</DL>
342<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
343</BLOCKQUOTE>
344
345<a name="9"></a>
346<h3>C.9 Macro Menu
347<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
348</h3>
349<BLOCKQUOTE>
350The macro capability allows actions performed in EXPGUI to be captured into a
351file as a series of Tcl command.
352It is then possible to repeat the actions in a macro repeatedly
353by replaying the macro. Note that macro files can be edited and
354Tcl/Tk commands can be added to the macros to expand capabilities.
355As an example, this code
356<blockquote><TT><PRE>
357runAddHist Data.raw 11BM-12D.INS 1 1 T 59.9995
358runAddHist Data.raw 11BM-12D.INS 2 2 T 57.9995
359runAddHist Data.raw 11BM-12D.INS 3 3 T 55.9995
360runAddHist Data.raw 11BM-12D.INS 4 4 T 53.9995
361</PRE></TT></blockquote>
362can be modified to prompt for a file name and then use it in a macro:
363<blockquote><TT><PRE>
364set DataFile [tk_getOpenFile -defaultextension .raw]
365runAddHist $DataFile 11BM-12D.INS 1 1 T 59.9995
366runAddHist $DataFile 11BM-12D.INS 2 2 T 57.9995
367runAddHist $DataFile 11BM-12D.INS 3 3 T 55.9995
368runAddHist $DataFile 11BM-12D.INS 4 4 T 53.9995
369</blockquote></TT></DL>
370<DL>
371<DT>Record EXPGUI macro<DD>
372When this option is turned on, subsequent actions are recorded into the
373selected macro file.
374<DT>Add comment to macro<DD>
375If this option is selected, a window is opened where a string can be typed.
376This information is then entered at the current point within the macro file
377as a comment.
378<DT>Replay macro line-at-a-time<DD>
379When this option is used, a macro file is selected by the user; the
380contents of the macro file is displayed, and button can be pressed to execute
381each command in the macro file. By clicking on a line in a macro file, that line
382will be the next to be run, so that sections of the file can be skipped over
383or repeated. The macro can also be edited within the file viewer window.
384<DT>Replay macro all at once<DD>
385When this option is used, a macro file is selected by the user, and then
386all commands in the macro file are executed. A status window is opened that
387shows the number of refinement cycles, Chi<sup>2</sup> and the last sum of
388shifts and also allows macros to be aborted. Note that any GSAS run in progress
389will run to completion before the Abort is invoked.
390Note that <A href="#Autoupdate">Autoload EXP</A> is temporarily set to
391on and <A href="#execprompt">Prompt after GSAS run</A>
392is temporarily set to off, when this command is invoked, so that the macro
393runs without need for prompts.
394
395<DT>Show GSAS output in window<DD>
396When this option is selected, GSAS programs are run in a separate window
397that is created for each program run -- even during macro execution.
398When this option is deselected, output from GSAS programs is placed in a
399separate file
400(<I>XXXXXXXX</I>_mac.LST where <I>XXXXXXXX</I> is the experiment name)
401and LSTVIEW is opened to view the output from that .LST file.
402</DL>
403</BLOCKQUOTE>
404<hr>
405<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
406<TR><TH><A  Href="expgui.html">EXPGUI top</A>
407</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
408</TH><TH><A Href="expgui7.html">Previous page</A>
409</TH></TR></TABLE>
410
411<P>
412<font size=-1><? lastmod(); ?> </font>
413<br>
414$Revision: 953 $ $Date: 2010-03-11 20:00:14 +0000 (Thu, 11 Mar 2010) $
415</blockquote>
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