source: branches/sandbox/doc/expguic.html @ 1157

Last change on this file since 1157 was 1157, checked in by toby, 10 years ago

liveplot: export to gnuplot; plot I/sigma(I); change title & size of labels; improve tick location; make autoticks standard; expgui: new menu item to create InstParm? file; InstEdit?: bug fixes; remove fprime since not in GSAS anymore; fix 2Theta max bug for CW instruments; updates to doc files

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3   <title>EXPGUI</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
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17   include("/var/www/include/");
18   include("/var/www/include/");
20<blockquote><font face="arial, helvetica, sans-serif">
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>
29<HR noshade width="75%" size="2" align="center">
30EXPGUI, Menu Contents
31<HR noshade width="75%" size="2" align="center">
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35Note that the figures on this page are likely to be out of date with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.
39<a name="1"></a>
40<H3>C.1 File Menu</H3>
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.
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.
51Equivalent to Open (included for historical reasons.)
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>revert<DD>Used to load an <a href="#archive">archived</A>
64    (backup) version of the current .EXP file.
65<DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
66<DT>convert<DD>Convert a standard ASCII file to the direct access
67  format used by GSAS (and for UNIX, the reverse) -- this is not
68  likely to be needed, as GSAS now does most conversions automatically.
69<DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
71<img SRC="m1.gif" BORDER=3 alt="EXPGUI Screen snapshot">
74<a name="2"></a>
75<h3>C.2 Options Menu</h3>
77This menu contains options that determine how EXPGUI runs.
78<a name="archive"></a>
80<DT>archive EXP<DD>
81  Toggles archiving of .EXP files. When on, files are
82        saved before they are overwritten by EXPGUI as a file
83        named <I>EXPNAM</I>.Oxx where xx is a pair of hexidecimal
84        digits (01, 02,..., 09, 0A,... OF, 10,... FF).
85        Each time that EXPGUI archives a file, note is placed in the .LST file
86        so that the saved file name can be associated with
87        the refinement stage. Turning this option off, prevents EXPGUI
88        from creating these <I>EXPNAM</I>.Oxx archive files, but
89        the will still be created by EXPEDT, GENLES,...
91<DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are
92         shown in a separate window. When it is not set, the results are
93        written in the .LST file. Note that on Windows, LSTVIEW can interfere
94        with putting output into the DISAGL window. The solution is to
95        close LSTVIEW before running DISAGL.
97<a name="Autoupdate"></a>
98<DT>Autoload EXP<DD>Normally EXPGUI prompts before rereading the EXP
99file when GENLES, POWPREF,... or other GSAS programs run
100If this option is set, the new file is automatically read without a prompt.
101The advantage of leaving this option off, is that
102you can opt to not load the
103revised .EXP file, which means that you reject the last set of changes.
104This is useful if
105GENLES blows up or you have done something wrong. The reason to 
106turning "autoload EXP" on is
107that there is one less thing to do when running GSAS programs.
108Note that it is still possible to reverse changes, if
109<a href="#archive">archive files</A>, but this may require more
110  effort. See the File/revert menu entry.
111<a name="execprompt"></a>
112<DT>Prompt after GSAS run<DD>
113<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
114By default, GSAS programs are run in a separate window
115and after the program completes, the window remains open until enter is
116pressed in the window. Turning the "Prompt after GSAS run" option off, causes
117the window to be closed immediately after the program completes, saving
118some effort but obliterating any error messages or other evidence of problems.
120<a name="Autoicon"></a>
121<DT>Iconify during GSAS<DD>
122If this option is turned on, the main EXPGUI window is shrunk to an icon
123(minimized) while GSAS programs are running and EXPGUI is suspended.
124The author prefers this mode, since there is no reason to have the
125screen cluttered with EXPGUI when it can't be used,
126but this is an option so that the mode can be turned off by those people
127who find this behavior annoying. It appears this option causes
128  problems on Windows 7.
130<a name="AutostartGRWND"></a>
131<DT>Autostart GRWND
133This option is available on Windows-95, -98 and -ME to deal with a operating
134system quirk that prevents the starting of the GRWND.EXE program,
135needed for graphics in GSAS programs such as POWPLOT, RAWPLOT, EXPEDT,...
136(this program is not needed for EXPGUI graphics, such as LIVEPLOT). It
137is not understood why this error happens or how to prevent it. One cure
138is to start this GRWND.EXE program before starting the GSAS program.
139If this option is selected, each time a GSAS program is started, a separate
140program TLIST.EXE is used to check if GRWND.EXE is running. If it is not,
141EXPGUI will start this program before starting the requested GSAS program.
143<a name="sortatoms"></a>
144<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
145        Atoms may be displayed sorted by number, atom type, site multiplity,
146        occupancy, or by x, y or z coordinate
148Clicking on the heading above the atoms list cycles with the left
149mouse button cycles through the atom sort modes. Clicking with
150the right mouse button resets the atom sort mode to "number".
152<a name="sorthist"></a>
153<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
154        Histogram, Scaling and Profile panes
156        Histograms may be sorted by histogram number, histogram type,
157        original bank number, or diffraction angle/wavelength
158<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
159        When this mode is off, it is possible to modify parameters
160        and refinement flags for only a single histogram. For other settings,
161        it is possible to modify parameters and flags for groups of
162        histograms (see help for Mouse actions).
164        It does not make sense, however, to globally modify
165        instrument-related parameters and flags for different histogram types.
166        So global actions can be limited to a single class of histogram types
167        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
168        for groups of similar histograms. Thus, if this mode is set to "All"
169        the Histogram and Profile panes are disabled.
170<DT>Override backspace<DD>This option is available in UNIX only, as there are different
171        ways that backspace can be implemented. When option is set
172        as "On," the backspace key is overridden to send a "delete"
173        character. If backspace does not work in a program such as
174        EXPEDT, change try the other setting for this option.
176<a name="setfont"></a>
177<DT>Set Screen Font
179This menu changes the fonts used in most sections of EXPGUI.
180Note that this setting can be saved with the
181SaveOptions menu option (below) so that EXPGUI automatically
182starts with the chosen font.
184<a name="exptoolout"></a>
185<DT>Show EXPTOOL output<DD>
186Normally EXPGUI does not show the output from EXPTOOL, when
187actions like adding atoms, phases or histograms is performed.
188If an error is detected, the output is shown. If
189there are problems with adding phases, atoms, histograms... and
190a window showing an error does not appear,
191this option should be set to "on" so the output from EXPTOOL is
192always shown.
194<DT>Save Options<DD>Save the current values for "Override backspace",
195        <a href="#sortatoms">"Sort atoms by"</a>,
196        <a href="#sorthist">"Sort histograms by"</a>,
197        <a href="#archive">"archive EXP"</a>,
198        <a href="#Autoupdate">"Autoload EXP"</a>,
199        <a href="#setfont">"Set Screen Font"</a>,
200        and
201        <a href="#Autoicon">"Iconify during GSAS"</a>
203        in file ~/.gsas_config (or c:\gsas.config on Windows).
204<DT>Save Position<DD>Saves the current screen position of the EXPGUI
205  window as the starting point for future runs of EXPGUI in
206        in file ~/.gsas_config (or c:\gsas.config on Windows).
208<DT>liveplot_options<DD>Used to set options for
209<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
210for example, the histogram to be plotted
211<DT>Assign app to .EXP files<DD>(on Mac only) When selected, this
212  causes .EXP files to be linked (via the file resource fork) to the
213  EXPGUI applescript. This also causes the .EXP files to be displayed
214  with a GSAS icon.
217<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
220<a name="3"></a>
221<h3>C.3 Powder Menu</h3>
223This menu contains links to GSAS programs used for powder diffraction
226<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
227<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
228<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
229<DT>powplot<DD>Display powder patterns
230<DT>rawplot<DD>Plot powder data
231<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
232<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
233<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
234to fit a background function to a set of fixed background points.
235<DT><a HREF="excledt.html">excledt</a>
236<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
237to set the upper and lower limits for a histogram, as well as
238edit excluded regions.
239<DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run
240  GENLES on a set of very similar data files.
241<DT>mustrplot<DD>Plot microstrain results
242<DT><a HREF="expgui.html#INSTEDIT">instedit</A><DD>Invokes the <a HREF="expgui.html#INSTEDIT">instedit</A>
243  to edit an instrument parameter file.
244<DT>New InstParm file<DD>Creates a new instrument parameter file using
245  <a HREF="expgui.html#INSTEDIT">instedit</A>.
249<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
252<a name="4"></a>
253<h3>C.4 Xtal (Single Crystal) Menu</h3>
255This menu contains links to GSAS programs used for
256single-rystal diffraction analysis.
258<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
259<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
260<DT>scabs<DD>Single crystal absorption
261<DT>scmerge<DD>Sort and merge single crystal data
262<DT>sxtldata<DD>Prepare generic single crystal data
264<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
267<a name="5"></a>
268<h3>C.5 Graphics Menu</h3>
270This menu contains links to several GSAS and
271two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
272and widplt)
273programs used for graphical display of data and results.
275<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
276        and then compute with FOURIER
277<DT>polfplot<DD>Display polefigures
278<DT>powplot<DD>Display powder patterns
279<DT>ortep<DD>Draw crystal structure
280<DT>rawplot<DD>Plot powder data
281<DT>fourier<DD>Generate Fourier map
282<DT>forsrh<DD>Search Fourier map for peaks
283<DT>gsas2map<DD>Exports a Fourier map in formats used by other
284  programs (for example Fox and DRAWxtl).
285<DT><a HREF="liveplot.html#liveplot">liveplot</a>
286<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
287to create a plot of powder data
288with zooming, automatic update and other nice features.
289<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
290<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
291<DT><a HREF="expgui.html#ABSPLT">absplt</A>
292<DD>The <a HREF="expgui.html#ABSPLT">absplt</A> program displays the
293  absorption/reflectivity correction curve for values used in a histogram.
294<DT>mustrplot<DD>Plot microstrain results
295<DT>seqplot<DD>Plot results from seqgsas
297<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
300<a name="6"></a>
301<h3>C.6 Results Menu</h3>
303This menu contains links to several GSAS and
304one non-GSAS (lstview)
305programs used for analysis of results.
307<DT>bijcalc<DD>Thermal parameter analysis
308<DT>disagl<DD>Distance/angle calculations
309<DT>disaglviewer<DD>Display results from distance/angle calculations
310  in a graphical browser.
311<DT>reflist<DD>List reflection data
312<DT>geometry<DD>Molecular geometry calculations
313<DT>hstdmp<DD>List powder histogram data
314<DT>istats<DD>HKL Intensity statistics
315<DT>rcalc<DD>Compute reflection resuduals
316<DT>composition<DD>Computes the chemical composition of a unit cell
317accounting for site multiplicies and occupancies
318<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
319<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
320chains, for use in restraints.
321<DT>seqplot<DD>Plot results from seqgsas
323<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
326<a name="7"></a>
327<h3>C.7 Calculations Menu</h3>
329This menu contains programs for useful crystallographic computations.
331<DT>cllchg<DD>Transform unit cell
332<DT>composition<DD>Computes the chemical composition of a unit cell
333accounting for site multiplicies and occupancies
334<DT>rducll<DD>Unit cell reduction
335<DT>spcgroup<DD>Space group symbol interpreter
336<DT>seqgsas<DD>Invokes the sequential GSAS refinement program to run
337  GENLES on a set of very similar data files.
338<DT>seqplot<DD>Plot results from seqgsas
339<DT>unimol<DD>Unique molecule assembler
341<img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot">
344<a name="9"></a>
345<h3>C.8 Macro Menu
346<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
349The macro capability allows actions performed in EXPGUI to be captured into a
350file as a series of Tcl command.
351It is then possible to repeat the actions in a macro repeatedly
352by replaying the macro. Note that macro files can be edited and
353Tcl/Tk commands can be added to the macros to expand capabilities.
354As an example, this code
356runAddHist Data.raw 11BM-12D.INS 1 1 T 59.9995
357runAddHist Data.raw 11BM-12D.INS 2 2 T 57.9995
358runAddHist Data.raw 11BM-12D.INS 3 3 T 55.9995
359runAddHist Data.raw 11BM-12D.INS 4 4 T 53.9995
361can be modified to prompt for a file name and then use it in a macro:
363set DataFile [tk_getOpenFile -defaultextension .raw]
364runAddHist $DataFile 11BM-12D.INS 1 1 T 59.9995
365runAddHist $DataFile 11BM-12D.INS 2 2 T 57.9995
366runAddHist $DataFile 11BM-12D.INS 3 3 T 55.9995
367runAddHist $DataFile 11BM-12D.INS 4 4 T 53.9995
370<DT>Record EXPGUI macro<DD>
371When this option is turned on, subsequent actions are recorded into the
372selected macro file.
373<DT>Add comment to macro<DD>
374If this option is selected, a window is opened where a string can be typed.
375This information is then entered at the current point within the macro file
376as a comment.
377<DT>Replay macro line-at-a-time<DD>
378When this option is used, a macro file is selected by the user; the
379contents of the macro file is displayed, and button can be pressed to execute
380each command in the macro file. By clicking on a line in a macro file, that line
381will be the next to be run, so that sections of the file can be skipped over
382or repeated. The macro can also be edited within the file viewer window.
383<DT>Replay macro all at once<DD>
384When this option is used, a macro file is selected by the user, and then
385all commands in the macro file are executed. A status window is opened that
386shows the number of refinement cycles, Chi<sup>2</sup> and the last sum of
387shifts and also allows macros to be aborted. Note that any GSAS run in progress
388will run to completion before the Abort is invoked.
389Note that <A href="#Autoupdate">Autoload EXP</A> is temporarily set to
390on and <A href="#execprompt">Prompt after GSAS run</A>
391is temporarily set to off, when this command is invoked, so that the macro
392runs without need for prompts.
394<DT>Show GSAS output in window<DD>
395When this option is selected, GSAS programs are run in a separate window
396that is created for each program run -- even during macro execution.
397When this option is deselected, output from GSAS programs is placed in a
398separate file
399(<I>XXXXXXXX</I>_mac.LST where <I>XXXXXXXX</I> is the experiment name)
400and LSTVIEW is opened to view the output from that .LST file.
404<a name="8"></a>
405<h3>C.9 Import/Export Menu</h3>
407This menu contains utilities for importing information into GSAS and
408exporting it to other programs.
410<DT>Coord Export<DD>This provides a series of routines that are used
411to write coordinates and possibly other information to files:<P>
413<DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file
414that documents the current refinement. The CIF contains the
415coordinates for all phases as well as the observed and computed
416diffraction patterns. The templates used by GSAS2CIF can be customized
417to provide a detailed description of the experimental measurements and
418results for use in documenting analysis for publication or
420<DT>coords-only CIF<DD>For export of intermediate results to another
421program, CIF can be a useful exchange format. This routine provides a
422CIF with the current coordinates from one phase and not much else.
423<DT>export to DRAWxtl<DD>This writes a .STR file used in the DRAWxtl
424program and optionally launches DRAWxtl.
425<DT>export to SHELX<DD>This writes coordinates for a selected phase in
426the .INS format used by SHELX and several other programs.
427<DT>export to PLATON<DD>This writes coordinates for a selected phase in
428the .SPF format used by PLATON
429<DT>export test format<DD>This demonstrates how a coordinate export
430routine can be added to EXPGUI. See the <A
431HREF="expgui_cfg.html#export">documentation on this</A> for further
433<DT>export to FOX<DD>This prepares a XML file with coordinates for use
434in the FOX program
435<DT>MSI .xtl<DD>Prepare a .XTL format file of atomic positions. This
436file is used in older Accelrys software such as Cerius and
437Insight-II. It may no longer be of value.
440<DT>CIF Export<DD>This provides a series of routines that are used
441to prepare CIF files:<P>
443<DT>gsas2cif<DD>Prepares IUCr crystallographic information (CIF) file
444that documents the current refinement. The CIF contains the
445coordinates for all phases as well as the observed and computed
446diffraction patterns. The templates used by GSAS2CIF can be customized
447to provide a detailed description of the experimental measurements and
448results for use in documenting analysis for publication or
450<DT>FillTemplate<DD>Used to edit the CIF template files used in GSAS2CIF
451<DT>CIFselect<DD>Used to select interatomic distances and angles to be
452included in the CIF created by GSAS2CIF.
455<DT>hklsort<DD>Prepare HKL tables
456<DT>pubtable<DD>Prepare atom parameter tables
457<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
458<DT>cad4rd<DD>Prepare CAD4 single crystal data
459<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
460<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
461<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
462<DT>sxtldata<DD>Prepare generic single crystal data
464Import (using GSAS2PDB & EXPEDT) and export coordinates (for
465macromolecular phases) to/from Protein Data Base files
467Exports a GSAS reflection file to ASCII for use in non-GSAS programs
469Imports an ASCII reflection file to the GSAS binary format
470<DT>gsas2map<DD>Exports a Fourier map in formats used by other
471  programs (for example Fox and DRAWxtl).
473<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
478<TR><TH><A  Href="expgui.html">EXPGUI top</A>
479</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
480</TH><TH><A Href="expgui7.html">Previous page</A>
484<font size=-1><? lastmod(); ?> </font>
486$Revision: 1157 $ $Date: 2011-07-26 17:47:57 +0000 (Tue, 26 Jul 2011) $
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