source: trunk/doc/expguic.html @ 441

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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="expgui.html">EXPGUI top</A> 
25</TH><TH><A Href="liveplot.html">Next page (Utilities)</A>
26</TH><TH><A Href="expgui7.html">Previous page</A>
27</TH></TR></TABLE><BR CLEAR=ALL>
28
29<center><h1>
30EXPGUI, Menu Contents
31</h1></center>
32
33<h2>C. Menu Contents</h2>
34Note that the figures on this page are likely to be out of date with
35respect to the text. The text is updated more frequently. Also, note
36that not all menu options are available in Windows.
37
38<a name="1"></a>
39<H3>C.1 File Menu</H3>
40<DL><DL>
41The options on the File menu as is the custom contains the commands
42for reading and writing experiment files, as well as starting
43and ending the program.
44<DL>
45<DT>Open<DD>
46        Select an existing GSAS experiment to be used. If a name is entered
47        that does not exists, it is possible to create a new
48        experiment file from scratch.
49<DT>expnam<DD>
50Equivalent to Open, included since this is the command used in other
51GSAS shells to select GSAS experiments.
52<DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S).
53<DT>Save As<DD>Saves modifications to the current experiment file to disk
54        under a new file name
55<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
56<DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
57<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
58<DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
59</DL>
60<img SRC="m1.gif" BORDER=3 alt="EXPGUI Screen snapshot">
61</DL></DL>
62
63<a name="2"></a>
64<h3>C.2 Options Menu</h3>
65<DL><DL>
66This menu contains options that determine how EXPGUI runs.
67<DL>
68<a name="archive"></a>
69<DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are
70        saved prior to each save or run of EXPEDT.
71        Each time a file is saved a note is placed in the .LST file
72        so that the saved file name can be associated with
73        the refinement stage.
74<P>
75<B>UNIX:</B> Old .EXP files are saved in a compressed file named
76[expnam].EXP.xxx.gz where xxx = 000, 001..., if the the gzip
77program can be run by EXPGUI, or in an uncompressed file named
78[expnam].EXP.xxx if gzip is not available.
79<P>
80Archived files can be loaded by using the File/Open (expnam) command:
81set the "Include Archived Files" checkbox, then select the file to be loaded.
82When an archived file is read, either the same experiment name can be used.
83In which case the archived file will replace the current version of the
84experiment file, or the archived file can be saved under a new name.
85<P>
86<B>Windows:</B> Old .EXP files are saved in a compressed form in
87a file named [expnam].ZIP, if program PKZIP.EXE is found in the
88same directory where EXPGUI is installed (typically c:\gsas\expgui).
89To read the archived files, you will
90need to use PKZIP or WINZIP to extract and rename them.
91If PKZIP is not installed, the files are archived by
92renaming them [expnam]!xxx.EXP. These archived files can be read
93directly by EXPGUI, but you are suggested to save them under
94a new name using the File/"Save As" option.
95<P>
96<DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are
97         shown in a separate window. When it is not set, the results are
98        written in the .LST file. Note that on Windows, LSTVIEW can interfere
99        with putting output into the DISAGL window. The solution is to
100        close LSTVIEW before running DISAGL.
101
102<a name="Autoupdate"></a>
103<DT>Autoload EXP<DD>Normally EXPGUI prompts before rereading the EXP
104file when GENLES, POWPREF,... or other GSAS programs run
105If this option is set, the new file is automatically read without a prompt.
106The advantage of leaving this option off, is that
107you can opt to not load the
108revised .EXP file, which means that you reject the last set of changes.
109This is useful if
110GENLES blows up or you have done something wrong. The advantage
111of turning "autoload EXP" on is
112that there is one less thing to do when running GSAS programs.
113Note that it is still possible to reverse changes, if
114<a href="#archive">archive mode</A> is on, but this may require more effort.
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="sortatoms"></a>
126<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
127        Atoms may be displayed sorted by number, atom type, site multiplity,
128        occupancy, or by x, y or z coordinate
129<P>
130<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
131Clicking on the heading above the atoms list cycles with the left
132mouse button cycles through the atom sort modes. Clicking with
133the right mouse button resets the atom sort mode to "number".
134
135<a name="sorthist"></a>
136<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
137        Histogram, Scaling and Profile panes
138
139        Histograms may be sorted by histogram number, histogram type,
140        original bank number, or diffraction angle/wavelength
141<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
142        When this mode is off, it is possible to modify parameters
143        and refinement flags for only a single histogram. For other settings,
144        it is possible to modify parameters and flags for groups of
145        histograms (see help for Mouse actions).
146
147        It does not make sense, however, to globally modify
148        instrument-related parameters and flags for different histogram types.
149        So global actions can be limited to a single class of histogram types
150        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
151        for groups of similar histograms. Thus, if this mode is set to "All"
152        the Histogram and Profile panes are disabled.
153<DT>Override backspace<DD>This option is available in UNIX only, as there are different
154        ways that backspace can be implemented. When option is set
155        as "On," the backspace key is overridden to send a "delete"
156        character. If backspace does not work in a program such as
157        EXPEDT, change try the other setting for this option.
158
159<a name="setfont"></a>
160<DT>Set Screen Font
161<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
162<DD>
163This menu changes the fonts used in most sections of EXPGUI.
164Note that this setting can be saved with the
165SaveOptions menu option (below) so that EXPGUI automatically
166starts with the chosen font.
167
168<a name="exptoolout"></a>
169<DT>Show EXPTOOL output<DD>
170Normally EXPGUI does not show the output from EXPTOOL, when
171actions like adding atoms, phases or histograms is performed.
172If an error is detected, the output is shown. If
173there are problems with adding phases, atoms, histograms... and
174a window showing an error does not appear,
175this option should be set to "on" so the output from EXPTOOL is
176always shown.
177
178<DT>SaveOptions<DD>Save the current values for "Override backspace",
179        <a href="#sortatoms">"Sort atoms by"</a>,
180        <a href="#sorthist">"Sort histograms by"</a>,
181        <a href="#archive">"archive EXP"</a>,
182        <a href="#Autoupdate">"Autoload EXP"</a>,
183        <a href="#setfont">"Set Screen Font"</a>,
184        and
185        <a href="#Autoicon">"Iconify during GSAS"</a>
186       
187        in file ~/.gsas_config (c:\.gsas_config on Windows).
188<DT>liveplot_options<DD>Used to set options for
189<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
190for example, the histogram to be plotted
191</DL>
192<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
193</DL></DL>
194
195<a name="3"></a>
196<h3>C.3 Powder Menu</h3>
197<DL><DL>
198This menu contains links to GSAS programs used for powder diffraction
199analysis.
200<DL>
201<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
202<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
203<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
204<DT>powplot<DD>Display powder patterns
205<DT>rawplot<DD>Plot powder data
206<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
207<DT>tofnorm<DD>Normalize a TOF spectrum
208<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
209<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
210<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
211to fit a background function to a set of fixed background points.
212<DT><a HREF="excledt.html">excledt</a>
213<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
214<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
215to set the upper and lower limits for a histogram, as well as
216edit excluded regions.
217</DL>
218<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
219</DL></DL>
220
221<a name="4"></a>
222<h3>C.4 Single Crystal Menu</h3>
223<DL><DL>
224This menu contains links to GSAS programs used for
225single-rystal diffraction analysis.
226<DL>
227<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
228<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
229<DT>scabs<DD>Single crystal absorption
230<DT>scmerge<DD>Sort and merge single crystal data
231<DT>sxtldata<DD>Prepare generic single crystal data
232</DL>
233<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
234</DL></DL>
235
236<a name="5"></a>
237<h3>C.5 Graphics Menu</h3>
238<DL><DL>
239This menu contains links to several GSAS and
240two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
241and widplt)
242programs used for graphical display of data and results.
243<DL>
244<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
245        and then compute with FOURIER
246<DT>polfplot<DD>Display polefigures
247<DT>powplot<DD>Display powder patterns
248<DT>ortep<DD>Draw crystal structure
249<DT>rawplot<DD>Plot powder data
250<DT>fourier<DD>Generate Fourier map
251<DT>forsrh<DD>Search Fourier map for peaks
252<DT><a HREF="liveplot.html#liveplot">liveplot</a>
253<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
254to create a plot of powder data
255with zooming, automatic update and other nice features.
256<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
257<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
258</DL>
259<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
260</DL></DL>
261
262<a name="6"></a>
263<h3>C.6 Results Menu</h3>
264<DL><DL>
265This menu contains links to several GSAS and
266one non-GSAS (lstview)
267programs used for analysis of results.
268<DL>
269<DT>bijcalc<DD>Thermal parameter analysis
270<DT>disagl<DD>Distance/angle calculations
271<DT>reflist<DD>List reflection data
272<DT>geometry<DD>Molecular geometry calculations
273<DT>hstdmp<DD>List powder histogram data
274<DT>istats<DD>HKL Intensity statistics
275<DT>rcalc<DD>Compute reflection resuduals
276<DT>composition<DD>Computes the chemical composition of a unit cell
277accounting for site multiplicies and occupancies
278<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
279</DL>
280<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
281</DL></DL>
282
283<a name="7"></a>
284<h3>C.7 Calculations Menu</h3>
285<DL><DL>
286This menu contains programs for useful crystallographic computations.
287<DL>
288<DT>cllchg<DD>Transform unit cell
289<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
290<DT>rducll<DD>Unit cell reduction
291<DT>spcgroup<DD>Space group symbol interpreter
292<DT>unimol<DD>Unique molecule assembler
293</DL>
294<img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot">
295</DL></DL>
296
297<a name="8"></a>
298<h3>C.8 Import/Export Menu</h3>
299<DL><DL>
300This menu contains utilities for importing information into GSAS and
301exporting.
302<DL>
303<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
304file is used in MSI software such as Cerius and InsightII.
305<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
306<DT>hklsort<DD>Prepare HKL tables
307<DT>pubtable<DD>Prepare atom parameter tables
308<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
309<DT>cad4rd<DD>Prepare CAD4 single crystal data
310<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
311<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
312<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
313<DT>sxtldata<DD>Prepare generic single crystal data
314</DL>
315<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
316</DL></DL>
317
318
319<hr>
320<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
321<TR><TH><A  Href="expgui.html">EXPGUI top</A>
322</TH><TH><A Href="liveplot.html">Next page (Utilities)</A>
323</TH><TH><A Href="expgui7.html">Previous page</A>
324</TH></TR></TABLE>
325
326<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
327<br>
328$Revision: 441 $ $Date: 2009-12-04 23:06:13 +0000 (Fri, 04 Dec 2009) $
329</body>
330</html>
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