source: trunk/doc/expguic.html @ 919

Last change on this file since 919 was 919, checked in by toby, 11 years ago

# on 2008/04/15 17:31:53, toby did:
doc new Prompt after GSAS run option
doc macro capability

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  • Property rcs:rev set to 1.17
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3   <title>EXPGUI</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
8A:link {text-decoration:none}
9A:vlink {text-decoration:none}
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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35Note that the figures on this page are likely to be out of date with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 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 experiment file from disk.
57<DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
58<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
59<DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
61<img SRC="m1.gif" BORDER=3 alt="EXPGUI Screen snapshot">
64<a name="2"></a>
65<h3>C.2 Options Menu</h3>
67This menu contains options that determine how EXPGUI runs.
69<a name="archive"></a>
70<DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
71        saved before they are overwritten by EXPGUI as a file
72        named <I>EXPNAM</I>.Oxx where xx is a pair of hexidecimal
73        digits (01, 02,..., 09, 0A,... OF, 10,... FF).
74        Each time that EXPGUI archives a file, note is placed in the .LST file
75        so that the saved file name can be associated with
76        the refinement stage. Turning this option off, prevents EXPGUI
77        from creating these <I>EXPNAM</I>.Oxx archive files, but
78        the will still be created by EXPEDT, GENLES,...
80<DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are
81         shown in a separate window. When it is not set, the results are
82        written in the .LST file. Note that on Windows, LSTVIEW can interfere
83        with putting output into the DISAGL window. The solution is to
84        close LSTVIEW before running DISAGL.
86<a name="Autoupdate"></a>
87<DT>Autoload EXP<DD>Normally EXPGUI prompts before rereading the EXP
88file when GENLES, POWPREF,... or other GSAS programs run
89If this option is set, the new file is automatically read without a prompt.
90The advantage of leaving this option off, is that
91you can opt to not load the
92revised .EXP file, which means that you reject the last set of changes.
93This is useful if
94GENLES blows up or you have done something wrong. The advantage
95of turning "autoload EXP" on is
96that there is one less thing to do when running GSAS programs.
97Note that it is still possible to reverse changes, if
98<a href="#archive">archive files</A>, but this may require more effort.
100<a name="Autoicon"></a>
101<DT>Iconify during GSAS<DD>
102If this option is turned on, the main EXPGUI window is shrunk to an icon
103(minimized) while GSAS programs are running and EXPGUI is suspended.
104The author prefers this mode, since there is no reason to have the
105screen cluttered with EXPGUI when it can't be used,
106but this is an option so that the mode can be turned off by those people
107who find this behavior annoying.
109<a name="execprompt"></a>
110<DT>Prompt after GSAS run<DD>
111<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
112By default, GSAS programs are run in a separate window
113and after the program completes, the window remains open until enter is
114pressed in the window. Turning the "Prompt after GSAS run" option off, causes
115the window to be closed immediately after the program completes, saving
116some effort but obliterating any error messages or other evidence of problems.
118<a name="AutostartGRWND"></a>
119<DT>Autostart GRWND
121This option is available on Windows-95, -98 and -ME to deal with a operating
122system quirk that prevents the starting of the GRWND.EXE program,
123needed for graphics in GSAS programs such as POWPLOT, RAWPLOT, EXPEDT,...
124(this program is not needed for EXPGUI graphics, such as LIVEPLOT). It
125is not understood why this error happens or how to prevent it. One cure
126is to start this GRWND.EXE program before starting the GSAS program.
127If this option is selected, each time a GSAS program is started, a separate
128program TLIST.EXE is used to check if GRWND.EXE is running. If it is not,
129EXPGUI will start this program before starting the requested GSAS program.
131<a name="sortatoms"></a>
132<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
133        Atoms may be displayed sorted by number, atom type, site multiplity,
134        occupancy, or by x, y or z coordinate
136Clicking on the heading above the atoms list cycles with the left
137mouse button cycles through the atom sort modes. Clicking with
138the right mouse button resets the atom sort mode to "number".
140<a name="sorthist"></a>
141<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
142        Histogram, Scaling and Profile panes
144        Histograms may be sorted by histogram number, histogram type,
145        original bank number, or diffraction angle/wavelength
146<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
147        When this mode is off, it is possible to modify parameters
148        and refinement flags for only a single histogram. For other settings,
149        it is possible to modify parameters and flags for groups of
150        histograms (see help for Mouse actions).
152        It does not make sense, however, to globally modify
153        instrument-related parameters and flags for different histogram types.
154        So global actions can be limited to a single class of histogram types
155        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
156        for groups of similar histograms. Thus, if this mode is set to "All"
157        the Histogram and Profile panes are disabled.
158<DT>Override backspace<DD>This option is available in UNIX only, as there are different
159        ways that backspace can be implemented. When option is set
160        as "On," the backspace key is overridden to send a "delete"
161        character. If backspace does not work in a program such as
162        EXPEDT, change try the other setting for this option.
164<a name="setfont"></a>
165<DT>Set Screen Font
167This menu changes the fonts used in most sections of EXPGUI.
168Note that this setting can be saved with the
169SaveOptions menu option (below) so that EXPGUI automatically
170starts with the chosen font.
172<a name="exptoolout"></a>
173<DT>Show EXPTOOL output<DD>
174Normally EXPGUI does not show the output from EXPTOOL, when
175actions like adding atoms, phases or histograms is performed.
176If an error is detected, the output is shown. If
177there are problems with adding phases, atoms, histograms... and
178a window showing an error does not appear,
179this option should be set to "on" so the output from EXPTOOL is
180always shown.
182<DT>SaveOptions<DD>Save the current values for "Override backspace",
183        <a href="#sortatoms">"Sort atoms by"</a>,
184        <a href="#sorthist">"Sort histograms by"</a>,
185        <a href="#archive">"archive EXP"</a>,
186        <a href="#Autoupdate">"Autoload EXP"</a>,
187        <a href="#setfont">"Set Screen Font"</a>,
188        and
189        <a href="#Autoicon">"Iconify during GSAS"</a>
191        in file ~/.gsas_config (or c:\gsas.config on Windows).
192<DT>liveplot_options<DD>Used to set options for
193<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
194for example, the histogram to be plotted
196<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
199<a name="3"></a>
200<h3>C.3 Powder Menu</h3>
202This menu contains links to GSAS programs used for powder diffraction
205<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
206<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
207<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
208<DT>powplot<DD>Display powder patterns
209<DT>rawplot<DD>Plot powder data
210<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
211<DT>tofnorm<DD>Normalize a TOF spectrum
212<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
213<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
214to fit a background function to a set of fixed background points.
215<DT><a HREF="excledt.html">excledt</a>
216<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
217to set the upper and lower limits for a histogram, as well as
218edit excluded regions.
220<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
223<a name="4"></a>
224<h3>C.4 Single Crystal Menu</h3>
226This menu contains links to GSAS programs used for
227single-rystal diffraction analysis.
229<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
230<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
231<DT>scabs<DD>Single crystal absorption
232<DT>scmerge<DD>Sort and merge single crystal data
233<DT>sxtldata<DD>Prepare generic single crystal data
235<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
238<a name="5"></a>
239<h3>C.5 Graphics Menu</h3>
241This menu contains links to several GSAS and
242two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
243and widplt)
244programs used for graphical display of data and results.
246<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
247        and then compute with FOURIER
248<DT>polfplot<DD>Display polefigures
249<DT>powplot<DD>Display powder patterns
250<DT>ortep<DD>Draw crystal structure
251<DT>rawplot<DD>Plot powder data
252<DT>fourier<DD>Generate Fourier map
253<DT>forsrh<DD>Search Fourier map for peaks
254<DT><a HREF="liveplot.html#liveplot">liveplot</a>
255<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
256to create a plot of powder data
257with zooming, automatic update and other nice features.
258<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
259<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
261<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
264<a name="6"></a>
265<h3>C.6 Results Menu</h3>
267This menu contains links to several GSAS and
268one non-GSAS (lstview)
269programs used for analysis of results.
271<DT>bijcalc<DD>Thermal parameter analysis
272<DT>disagl<DD>Distance/angle calculations
273<DT>reflist<DD>List reflection data
274<DT>geometry<DD>Molecular geometry calculations
275<DT>hstdmp<DD>List powder histogram data
276<DT>istats<DD>HKL Intensity statistics
277<DT>rcalc<DD>Compute reflection resuduals
278<DT>composition<DD>Computes the chemical composition of a unit cell
279accounting for site multiplicies and occupancies
280<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
281<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
282chains, for use in restraints.
284<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
287<a name="7"></a>
288<h3>C.7 Calculations Menu</h3>
290This menu contains programs for useful crystallographic computations.
292<DT>cllchg<DD>Transform unit cell
293<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
294<DT>rducll<DD>Unit cell reduction
295<DT>spcgroup<DD>Space group symbol interpreter
296<DT>unimol<DD>Unique molecule assembler
298<img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot">
301<a name="8"></a>
302<h3>C.8 Import/Export Menu</h3>
304This menu contains utilities for importing information into GSAS and
307<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
308file is used in MSI software such as Cerius and InsightII.
309<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
310<DT>hklsort<DD>Prepare HKL tables
311<DT>pubtable<DD>Prepare atom parameter tables
312<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
313<DT>cad4rd<DD>Prepare CAD4 single crystal data
314<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
315<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
316<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
317<DT>sxtldata<DD>Prepare generic single crystal data
319Import (using GSAS2PDB & EXPEDT) and export coordinates (for
320macromolecular phases) to/from Protein Data Base files
322Exports a GSAS reflection file to ASCII for use in non-GSAS programs
324Imports an ASCII reflection file to the GSAS binary format
326<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
329<a name="9"></a>
330<h3>C.9 Macro Menu
331<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
334The macro capability allows actions performed in EXPGUI to be captured into a
335file as a series of Tcl command.
336It is then possible to repeat the actions in a macro repeatedly
337by replaying the macro. Note that macro files can be edited and
338Tcl/Tk commands can be added to the macros to expand capabilities.
339As an example, this code
341runAddHist Data.raw 11BM-12D.INS 1 1 T 59.9995
342runAddHist Data.raw 11BM-12D.INS 2 2 T 57.9995
343runAddHist Data.raw 11BM-12D.INS 3 3 T 55.9995
344runAddHist Data.raw 11BM-12D.INS 4 4 T 53.9995
346can be modified to prompt for a file name and then use it in a macro:
348set DataFile [tk_getOpenFile -defaultextension .raw]
349runAddHist $DataFile 11BM-12D.INS 1 1 T 59.9995
350runAddHist $DataFile 11BM-12D.INS 2 2 T 57.9995
351runAddHist $DataFile 11BM-12D.INS 3 3 T 55.9995
352runAddHist $DataFile 11BM-12D.INS 4 4 T 53.9995
355<DT>Record EXPGUI macro<DD>
356When this option is turned on, subsequent actions are recorded into the
357selected macro file.
358<DT>Add comment to macro<DD>
359If this option is selected, a window is opened where a string can be typed.
360This information is then entered at the current point within the macro file
361as a comment.
362<DT>Replay macro line-at-a-time<DD>
363When this option is used, a macro file is selected by the user; the
364contents of the macro file is displayed, and button can be pressed to execute
365each command in the macro file. By clicking on a line in a macro file, that line
366will be the next to be run, so that sections of the file can be skipped over
367or repeated. The macro can also be edited within the file viewer window.
368<DT>Replay macro all at once<DD>
369When this option is used, a macro file is selected by the user, and then
370all commands in the macro file are executed. A status window is opened that
371shows the number of refinement cycles, Chi<sup>2</sup> and the last sum of
372shifts and also allows macros to be aborted. Note that any GSAS run in progress
373will run to completion before the Abort is invoked.
374Note that <A href="#Autoupdate">Autoload EXP</A> is temporarily set to
375on and <A href="#execprompt">Prompt after GSAS run</A>
376is temporarily set to off, when this command is invoked, so that the macro
377runs without need for prompts.
379<DT>Show GSAS output in window<DD>
380When this option is selected, GSAS programs are run in a separate window
381that is created for each program run -- even during macro execution.
382When this option is deselected, output from GSAS programs is placed in a
383separate file
384(<I>XXXXXXXX</I>_mac.LST where <I>XXXXXXXX</I> is the experiment name)
385and LSTVIEW is opened to view the output from that .LST file.
390<TR><TH><A  Href="expgui.html">EXPGUI top</A>
391</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
392</TH><TH><A Href="expgui7.html">Previous page</A>
396<font size=-1><? lastmod(); ?> </font>
398$Revision: 919 $ $Date: 2009-12-04 23:14:19 +0000 (Fri, 04 Dec 2009) $
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