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1<html>
2<head>
3   <title>EXPGUI</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
5   GSAS, EXPGUI">
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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35Note that the figures on this page are likely to be out of date with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 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)
60</DL>
61<img SRC="m1.gif" BORDER=3 alt="EXPGUI Screen snapshot">
62</BLOCKQUOTE>
63
64<a name="2"></a>
65<h3>C.2 Options Menu</h3>
66<BLOCKQUOTE>
67This menu contains options that determine how EXPGUI runs.
68<a name="archive"></a>
69<DL>
70<DT>archive EXP<DD>
71  Toggles archiving of .EXP files. When on, files are
72        saved before they are overwritten by EXPGUI as a file
73        named <I>EXPNAM</I>.Oxx where xx is a pair of hexidecimal
74        digits (01, 02,..., 09, 0A,... OF, 10,... FF).
75        Each time that EXPGUI archives a file, note is placed in the .LST file
76        so that the saved file name can be associated with
77        the refinement stage. Turning this option off, prevents EXPGUI
78        from creating these <I>EXPNAM</I>.Oxx archive files, but
79        the will still be created by EXPEDT, GENLES,...
80<P>
81<DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are
82         shown in a separate window. When it is not set, the results are
83        written in the .LST file. Note that on Windows, LSTVIEW can interfere
84        with putting output into the DISAGL window. The solution is to
85        close LSTVIEW before running DISAGL.
86
87<a name="Autoupdate"></a>
88<DT>Autoload EXP<DD>Normally EXPGUI prompts before rereading the EXP
89file when GENLES, POWPREF,... or other GSAS programs run
90If this option is set, the new file is automatically read without a prompt.
91The advantage of leaving this option off, is that
92you can opt to not load the
93revised .EXP file, which means that you reject the last set of changes.
94This is useful if
95GENLES blows up or you have done something wrong. The advantage
96of turning "autoload EXP" on is
97that there is one less thing to do when running GSAS programs.
98Note that it is still possible to reverse changes, if
99<a href="#archive">archive files</A>, but this may require more effort.
100
101<a name="execprompt"></a>
102<DT>Prompt after GSAS run<DD>
103<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
104By default, GSAS programs are run in a separate window
105and after the program completes, the window remains open until enter is
106pressed in the window. Turning the "Prompt after GSAS run" option off, causes
107the window to be closed immediately after the program completes, saving
108some effort but obliterating any error messages or other evidence of problems.
109
110<a name="Autoicon"></a>
111<DT>Iconify during GSAS<DD>
112If this option is turned on, the main EXPGUI window is shrunk to an icon
113(minimized) while GSAS programs are running and EXPGUI is suspended.
114The author prefers this mode, since there is no reason to have the
115screen cluttered with EXPGUI when it can't be used,
116but this is an option so that the mode can be turned off by those people
117who find this behavior annoying.
118
119<a name="AutostartGRWND"></a>
120<DT>Autostart GRWND
121<DD>
122This option is available on Windows-95, -98 and -ME to deal with a operating
123system quirk that prevents the starting of the GRWND.EXE program,
124needed for graphics in GSAS programs such as POWPLOT, RAWPLOT, EXPEDT,...
125(this program is not needed for EXPGUI graphics, such as LIVEPLOT). It
126is not understood why this error happens or how to prevent it. One cure
127is to start this GRWND.EXE program before starting the GSAS program.
128If this option is selected, each time a GSAS program is started, a separate
129program TLIST.EXE is used to check if GRWND.EXE is running. If it is not,
130EXPGUI will start this program before starting the requested GSAS program.
131
132<a name="sortatoms"></a>
133<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
134        Atoms may be displayed sorted by number, atom type, site multiplity,
135        occupancy, or by x, y or z coordinate
136<P>
137Clicking on the heading above the atoms list cycles with the left
138mouse button cycles through the atom sort modes. Clicking with
139the right mouse button resets the atom sort mode to "number".
140
141<a name="sorthist"></a>
142<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
143        Histogram, Scaling and Profile panes
144
145        Histograms may be sorted by histogram number, histogram type,
146        original bank number, or diffraction angle/wavelength
147<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
148        When this mode is off, it is possible to modify parameters
149        and refinement flags for only a single histogram. For other settings,
150        it is possible to modify parameters and flags for groups of
151        histograms (see help for Mouse actions).
152
153        It does not make sense, however, to globally modify
154        instrument-related parameters and flags for different histogram types.
155        So global actions can be limited to a single class of histogram types
156        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
157        for groups of similar histograms. Thus, if this mode is set to "All"
158        the Histogram and Profile panes are disabled.
159<DT>Override backspace<DD>This option is available in UNIX only, as there are different
160        ways that backspace can be implemented. When option is set
161        as "On," the backspace key is overridden to send a "delete"
162        character. If backspace does not work in a program such as
163        EXPEDT, change try the other setting for this option.
164
165<a name="setfont"></a>
166<DT>Set Screen Font
167<DD>
168This menu changes the fonts used in most sections of EXPGUI.
169Note that this setting can be saved with the
170SaveOptions menu option (below) so that EXPGUI automatically
171starts with the chosen font.
172
173<a name="exptoolout"></a>
174<DT>Show EXPTOOL output<DD>
175Normally EXPGUI does not show the output from EXPTOOL, when
176actions like adding atoms, phases or histograms is performed.
177If an error is detected, the output is shown. If
178there are problems with adding phases, atoms, histograms... and
179a window showing an error does not appear,
180this option should be set to "on" so the output from EXPTOOL is
181always shown.
182
183<DT>Save Options<DD>Save the current values for "Override backspace",
184        <a href="#sortatoms">"Sort atoms by"</a>,
185        <a href="#sorthist">"Sort histograms by"</a>,
186        <a href="#archive">"archive EXP"</a>,
187        <a href="#Autoupdate">"Autoload EXP"</a>,
188        <a href="#setfont">"Set Screen Font"</a>,
189        and
190        <a href="#Autoicon">"Iconify during GSAS"</a>
191       
192        in file ~/.gsas_config (or c:\gsas.config on Windows).
193<DT>Save Position<DD>Saves the current screen position of the EXPGUI
194  window as the starting point for future runs of EXPGUI in
195        in file ~/.gsas_config (or c:\gsas.config on Windows).
196
197<DT>liveplot_options<DD>Used to set options for
198<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
199for example, the histogram to be plotted
200<DT>Assign app to .EXP files<DD>(on Mac only) When selected, this
201  causes .EXP files to be linked (via the file resource fork) to the
202  EXPGUI applescript. This also causes the .EXP files to be displayed
203  with a GSAS icon.
204 
205</DL>
206<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
207</BLOCKQUOTE>
208
209<a name="3"></a>
210<h3>C.3 Powder Menu</h3>
211<BLOCKQUOTE>
212This menu contains links to GSAS programs used for powder diffraction
213analysis.
214<DL>
215<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
216<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
217<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
218<DT>powplot<DD>Display powder patterns
219<DT>rawplot<DD>Plot powder data
220<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
221<DT>tofnorm<DD>Normalize a TOF spectrum
222<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
223<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
224to fit a background function to a set of fixed background points.
225<DT><a HREF="excledt.html">excledt</a>
226<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
227to set the upper and lower limits for a histogram, as well as
228edit excluded regions.
229</DL>
230<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
231</BLOCKQUOTE>
232
233<a name="4"></a>
234<h3>C.4 Single Crystal Menu</h3>
235<BLOCKQUOTE>
236This menu contains links to GSAS programs used for
237single-rystal diffraction analysis.
238<DL>
239<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
240<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
241<DT>scabs<DD>Single crystal absorption
242<DT>scmerge<DD>Sort and merge single crystal data
243<DT>sxtldata<DD>Prepare generic single crystal data
244</DL>
245<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
246</BLOCKQUOTE>
247
248<a name="5"></a>
249<h3>C.5 Graphics Menu</h3>
250<BLOCKQUOTE>
251This menu contains links to several GSAS and
252two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
253and widplt)
254programs used for graphical display of data and results.
255<DL>
256<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
257        and then compute with FOURIER
258<DT>polfplot<DD>Display polefigures
259<DT>powplot<DD>Display powder patterns
260<DT>ortep<DD>Draw crystal structure
261<DT>rawplot<DD>Plot powder data
262<DT>fourier<DD>Generate Fourier map
263<DT>forsrh<DD>Search Fourier map for peaks
264<DT><a HREF="liveplot.html#liveplot">liveplot</a>
265<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
266to create a plot of powder data
267with zooming, automatic update and other nice features.
268<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
269<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
270</DL>
271<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
272</BLOCKQUOTE>
273
274<a name="6"></a>
275<h3>C.6 Results Menu</h3>
276<BLOCKQUOTE>
277This menu contains links to several GSAS and
278one non-GSAS (lstview)
279programs used for analysis of results.
280<DL>
281<DT>bijcalc<DD>Thermal parameter analysis
282<DT>disagl<DD>Distance/angle calculations
283<DT>reflist<DD>List reflection data
284<DT>geometry<DD>Molecular geometry calculations
285<DT>hstdmp<DD>List powder histogram data
286<DT>istats<DD>HKL Intensity statistics
287<DT>rcalc<DD>Compute reflection resuduals
288<DT>composition<DD>Computes the chemical composition of a unit cell
289accounting for site multiplicies and occupancies
290<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
291<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
292chains, for use in restraints.
293</DL>
294<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
295</BLOCKQUOTE>
296
297<a name="7"></a>
298<h3>C.7 Calculations Menu</h3>
299<BLOCKQUOTE>
300This menu contains programs for useful crystallographic computations.
301<DL>
302<DT>cllchg<DD>Transform unit cell
303<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
304<DT>rducll<DD>Unit cell reduction
305<DT>spcgroup<DD>Space group symbol interpreter
306<DT>unimol<DD>Unique molecule assembler
307</DL>
308<img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot">
309</BLOCKQUOTE>
310
311<a name="8"></a>
312<h3>C.8 Import/Export Menu</h3>
313<BLOCKQUOTE>
314This menu contains utilities for importing information into GSAS and
315exporting.
316<DL>
317<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
318file is used in MSI software such as Cerius and InsightII.
319<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
320<DT>hklsort<DD>Prepare HKL tables
321<DT>pubtable<DD>Prepare atom parameter tables
322<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
323<DT>cad4rd<DD>Prepare CAD4 single crystal data
324<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
325<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
326<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
327<DT>sxtldata<DD>Prepare generic single crystal data
328<DT>gsas2pdb<DD>
329Import (using GSAS2PDB & EXPEDT) and export coordinates (for
330macromolecular phases) to/from Protein Data Base files
331<DT>ref2asc<DD>
332Exports a GSAS reflection file to ASCII for use in non-GSAS programs
333<DT>ref2bin<DD>
334Imports an ASCII reflection file to the GSAS binary format
335</DL>
336<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
337</BLOCKQUOTE>
338
339<a name="9"></a>
340<h3>C.9 Macro Menu
341<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
342</h3>
343<BLOCKQUOTE>
344The macro capability allows actions performed in EXPGUI to be captured into a
345file as a series of Tcl command.
346It is then possible to repeat the actions in a macro repeatedly
347by replaying the macro. Note that macro files can be edited and
348Tcl/Tk commands can be added to the macros to expand capabilities.
349As an example, this code
350<blockquote><TT><PRE>
351runAddHist Data.raw 11BM-12D.INS 1 1 T 59.9995
352runAddHist Data.raw 11BM-12D.INS 2 2 T 57.9995
353runAddHist Data.raw 11BM-12D.INS 3 3 T 55.9995
354runAddHist Data.raw 11BM-12D.INS 4 4 T 53.9995
355</PRE></TT></blockquote>
356can be modified to prompt for a file name and then use it in a macro:
357<blockquote><TT><PRE>
358set DataFile [tk_getOpenFile -defaultextension .raw]
359runAddHist $DataFile 11BM-12D.INS 1 1 T 59.9995
360runAddHist $DataFile 11BM-12D.INS 2 2 T 57.9995
361runAddHist $DataFile 11BM-12D.INS 3 3 T 55.9995
362runAddHist $DataFile 11BM-12D.INS 4 4 T 53.9995
363</blockquote></TT></DL>
364<DL>
365<DT>Record EXPGUI macro<DD>
366When this option is turned on, subsequent actions are recorded into the
367selected macro file.
368<DT>Add comment to macro<DD>
369If this option is selected, a window is opened where a string can be typed.
370This information is then entered at the current point within the macro file
371as a comment.
372<DT>Replay macro line-at-a-time<DD>
373When this option is used, a macro file is selected by the user; the
374contents of the macro file is displayed, and button can be pressed to execute
375each command in the macro file. By clicking on a line in a macro file, that line
376will be the next to be run, so that sections of the file can be skipped over
377or repeated. The macro can also be edited within the file viewer window.
378<DT>Replay macro all at once<DD>
379When this option is used, a macro file is selected by the user, and then
380all commands in the macro file are executed. A status window is opened that
381shows the number of refinement cycles, Chi<sup>2</sup> and the last sum of
382shifts and also allows macros to be aborted. Note that any GSAS run in progress
383will run to completion before the Abort is invoked.
384Note that <A href="#Autoupdate">Autoload EXP</A> is temporarily set to
385on and <A href="#execprompt">Prompt after GSAS run</A>
386is temporarily set to off, when this command is invoked, so that the macro
387runs without need for prompts.
388
389<DT>Show GSAS output in window<DD>
390When this option is selected, GSAS programs are run in a separate window
391that is created for each program run -- even during macro execution.
392When this option is deselected, output from GSAS programs is placed in a
393separate file
394(<I>XXXXXXXX</I>_mac.LST where <I>XXXXXXXX</I> is the experiment name)
395and LSTVIEW is opened to view the output from that .LST file.
396</DL>
397</BLOCKQUOTE>
398<hr>
399<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
400<TR><TH><A  Href="expgui.html">EXPGUI top</A>
401</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
402</TH><TH><A Href="expgui7.html">Previous page</A>
403</TH></TR></TABLE>
404
405<P>
406<font size=-1><? lastmod(); ?> </font>
407<br>
408$Revision: 944 $ $Date: 2010-03-09 05:59:02 +0000 (Tue, 09 Mar 2010) $
409</blockquote>
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