source: trunk/doc/expguic.html @ 679

Last change on this file since 679 was 679, checked in by toby, 14 years ago

# on 2003/04/10 22:25:03, toby did:
autostart GRWND
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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>
7<style>
8A:link {text-decoration:none}
9A:vlink {text-decoration:none}
10</style>
11
12<BODY BGCOLOR="#FFFFFF"
13      topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" 
14      text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff">
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35Note that the figures on this page are likely to be out of date with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<DL><DL>
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</DL></DL>
63
64<a name="2"></a>
65<h3>C.2 Options Menu</h3>
66<DL><DL>
67This menu contains options that determine how EXPGUI runs.
68<DL>
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,...
79<P>
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.
85
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.
99
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.
108
109<a name="AutostartGRWND"></a>
110<DT>Autostart GRWND
111<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
112<DD>
113This option is available on Windows-95, -98 and -ME to deal with a operating
114system quirk that prevents the starting of the GRWND.EXE program,
115needed for graphics in GSAS programs such as POWPLOT, RAWPLOT, EXPEDT,...
116(this program is not needed for EXPGUI graphics, such as LIVEPLOT). It
117is not understood why this error happens or how to prevent it. One cure
118is to start this GRWND.EXE program before starting the GSAS program.
119If this option is selected, each time a GSAS program is started, a separate
120program TLIST.EXE is used to check if GRWND.EXE is running. If it is not,
121EXPGUI will start this program before starting the requested GSAS program.
122
123<a name="sortatoms"></a>
124<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
125        Atoms may be displayed sorted by number, atom type, site multiplity,
126        occupancy, or by x, y or z coordinate
127<P>
128<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
129Clicking on the heading above the atoms list cycles with the left
130mouse button cycles through the atom sort modes. Clicking with
131the right mouse button resets the atom sort mode to "number".
132
133<a name="sorthist"></a>
134<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
135        Histogram, Scaling and Profile panes
136
137        Histograms may be sorted by histogram number, histogram type,
138        original bank number, or diffraction angle/wavelength
139<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
140        When this mode is off, it is possible to modify parameters
141        and refinement flags for only a single histogram. For other settings,
142        it is possible to modify parameters and flags for groups of
143        histograms (see help for Mouse actions).
144
145        It does not make sense, however, to globally modify
146        instrument-related parameters and flags for different histogram types.
147        So global actions can be limited to a single class of histogram types
148        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
149        for groups of similar histograms. Thus, if this mode is set to "All"
150        the Histogram and Profile panes are disabled.
151<DT>Override backspace<DD>This option is available in UNIX only, as there are different
152        ways that backspace can be implemented. When option is set
153        as "On," the backspace key is overridden to send a "delete"
154        character. If backspace does not work in a program such as
155        EXPEDT, change try the other setting for this option.
156
157<a name="setfont"></a>
158<DT>Set Screen Font
159<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
160<DD>
161This menu changes the fonts used in most sections of EXPGUI.
162Note that this setting can be saved with the
163SaveOptions menu option (below) so that EXPGUI automatically
164starts with the chosen font.
165
166<a name="exptoolout"></a>
167<DT>Show EXPTOOL output<DD>
168Normally EXPGUI does not show the output from EXPTOOL, when
169actions like adding atoms, phases or histograms is performed.
170If an error is detected, the output is shown. If
171there are problems with adding phases, atoms, histograms... and
172a window showing an error does not appear,
173this option should be set to "on" so the output from EXPTOOL is
174always shown.
175
176<DT>SaveOptions<DD>Save the current values for "Override backspace",
177        <a href="#sortatoms">"Sort atoms by"</a>,
178        <a href="#sorthist">"Sort histograms by"</a>,
179        <a href="#archive">"archive EXP"</a>,
180        <a href="#Autoupdate">"Autoload EXP"</a>,
181        <a href="#setfont">"Set Screen Font"</a>,
182        and
183        <a href="#Autoicon">"Iconify during GSAS"</a>
184       
185        in file ~/.gsas_config (c:\.gsas_config on Windows).
186<DT>liveplot_options<DD>Used to set options for
187<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
188for example, the histogram to be plotted
189</DL>
190<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
191</DL></DL>
192
193<a name="3"></a>
194<h3>C.3 Powder Menu</h3>
195<DL><DL>
196This menu contains links to GSAS programs used for powder diffraction
197analysis.
198<DL>
199<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
200<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
201<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
202<DT>powplot<DD>Display powder patterns
203<DT>rawplot<DD>Plot powder data
204<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
205<DT>tofnorm<DD>Normalize a TOF spectrum
206<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
207<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
208<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
209to fit a background function to a set of fixed background points.
210<DT><a HREF="excledt.html">excledt</a>
211<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
212<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
213to set the upper and lower limits for a histogram, as well as
214edit excluded regions.
215</DL>
216<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
217</DL></DL>
218
219<a name="4"></a>
220<h3>C.4 Single Crystal Menu</h3>
221<DL><DL>
222This menu contains links to GSAS programs used for
223single-rystal diffraction analysis.
224<DL>
225<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
226<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
227<DT>scabs<DD>Single crystal absorption
228<DT>scmerge<DD>Sort and merge single crystal data
229<DT>sxtldata<DD>Prepare generic single crystal data
230</DL>
231<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
232</DL></DL>
233
234<a name="5"></a>
235<h3>C.5 Graphics Menu</h3>
236<DL><DL>
237This menu contains links to several GSAS and
238two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
239and widplt)
240programs used for graphical display of data and results.
241<DL>
242<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
243        and then compute with FOURIER
244<DT>polfplot<DD>Display polefigures
245<DT>powplot<DD>Display powder patterns
246<DT>ortep<DD>Draw crystal structure
247<DT>rawplot<DD>Plot powder data
248<DT>fourier<DD>Generate Fourier map
249<DT>forsrh<DD>Search Fourier map for peaks
250<DT><a HREF="liveplot.html#liveplot">liveplot</a>
251<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
252to create a plot of powder data
253with zooming, automatic update and other nice features.
254<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
255<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
256</DL>
257<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
258</DL></DL>
259
260<a name="6"></a>
261<h3>C.6 Results Menu</h3>
262<DL><DL>
263This menu contains links to several GSAS and
264one non-GSAS (lstview)
265programs used for analysis of results.
266<DL>
267<DT>bijcalc<DD>Thermal parameter analysis
268<DT>disagl<DD>Distance/angle calculations
269<DT>reflist<DD>List reflection data
270<DT>geometry<DD>Molecular geometry calculations
271<DT>hstdmp<DD>List powder histogram data
272<DT>istats<DD>HKL Intensity statistics
273<DT>rcalc<DD>Compute reflection resuduals
274<DT>composition<DD>Computes the chemical composition of a unit cell
275accounting for site multiplicies and occupancies
276<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
277<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
278chains, for use in restraints.
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<DT>gsas2pdb<DD>
315Import (using GSAS2PDB & EXPEDT) and export coordinates (for
316macromolecular phases) to/from Protein Data Base files
317<DT>ref2asc<DD>
318Exports a GSAS reflection file to ASCII for use in non-GSAS programs
319<DT>ref2bin<DD>
320Imports an ASCII reflection file to the GSAS binary format
321</DL>
322<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
323</DL></DL>
324
325
326<hr>
327<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
328<TR><TH><A  Href="expgui.html">EXPGUI top</A>
329</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
330</TH><TH><A Href="expgui7.html">Previous page</A>
331</TH></TR></TABLE>
332
333<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
334<font size=-1><? lastmod(); ?> </font>
335<br>
336$Revision: 679 $ $Date: 2009-12-04 23:10:12 +0000 (Fri, 04 Dec 2009) $
337</blockquote>
338</body>
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