source: trunk/doc/expguic.html @ 565

Last change on this file since 565 was 522, checked in by toby, 12 years ago

# on 2002/01/22 21:05:34, toby did:
add newer (mostly MM) programs

  • Property rcs:author set to toby
  • Property rcs:date set to 2002/01/22 21:05:34
  • Property rcs:lines set to +10 -1
  • Property rcs:rev set to 1.13
  • Property rcs:state set to Exp
  • Property svn:keywords set to Author Date Revision Id
File size: 12.6 KB
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1<html>
2<head>
3   <META NAME="Author" CONTENT="Brian H. Toby">
4   <title>EXPGUI</title>
5   <meta name="keywords" content="crystallography, Rietveld, diffraction,
6   GSAS, EXPGUI">
7</HEAD>
8<style>
9A:link {text-decoration:none}
10A:vlink {text-decoration:none}
11</style>
12
13<BODY BGCOLOR="#FFFFFF"
14      topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" 
15      text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff">
16
17<?
18   include("/var/www/include/navigation.inc");
19   include("/var/www/include/utility.inc");
20?>
21<blockquote><font face="arial, helvetica, sans-serif">
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<BR>(Utilities)</A>
26</TH><TH><A Href="expgui7.html">Previous page</A>
27</TH></TR></TABLE><BR CLEAR=ALL>
28
29<center><h1>
30<HR noshade width="75%" size="2" align="center">
31EXPGUI, Menu Contents
32<HR noshade width="75%" size="2" align="center">
33</h1></center>
34
35<h2>C. Menu Contents</h2>
36Note that the figures on this page are likely to be out of date with
37respect to the text. The text is updated more frequently. Also, note
38that not all menu options are available in Windows.
39
40<a name="1"></a>
41<H3>C.1 File Menu</H3>
42<DL><DL>
43The options on the File menu as is the custom contains the commands
44for reading and writing experiment files, as well as starting
45and ending the program.
46<DL>
47<DT>Open<DD>
48        Select an existing GSAS experiment to be used. If a name is entered
49        that does not exists, it is possible to create a new
50        experiment file from scratch.
51<DT>expnam<DD>
52Equivalent to Open, included since this is the command used in other
53GSAS shells to select GSAS experiments.
54<DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S).
55<DT>Save As<DD>Saves modifications to the current experiment file to disk
56        under a new file name
57<DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk.
58<DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file.
59<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
60<DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C)
61</DL>
62<img SRC="m1.gif" BORDER=3 alt="EXPGUI Screen snapshot">
63</DL></DL>
64
65<a name="2"></a>
66<h3>C.2 Options Menu</h3>
67<DL><DL>
68This menu contains options that determine how EXPGUI runs.
69<DL>
70<a name="archive"></a>
71<DT>archive EXP<DD>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="Autoicon"></a>
102<DT>Iconify during GSAS<DD>
103If this option is turned on, the main EXPGUI window is shrunk to an icon
104(minimized) while GSAS programs are running and EXPGUI is suspended.
105The author prefers this mode, since there is no reason to have the
106screen cluttered with EXPGUI when it can't be used,
107but this is an option so that the mode can be turned off by those people
108who find this behavior annoying.
109
110<a name="sortatoms"></a>
111<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
112        Atoms may be displayed sorted by number, atom type, site multiplity,
113        occupancy, or by x, y or z coordinate
114<P>
115<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
116Clicking on the heading above the atoms list cycles with the left
117mouse button cycles through the atom sort modes. Clicking with
118the right mouse button resets the atom sort mode to "number".
119
120<a name="sorthist"></a>
121<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
122        Histogram, Scaling and Profile panes
123
124        Histograms may be sorted by histogram number, histogram type,
125        original bank number, or diffraction angle/wavelength
126<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
127        When this mode is off, it is possible to modify parameters
128        and refinement flags for only a single histogram. For other settings,
129        it is possible to modify parameters and flags for groups of
130        histograms (see help for Mouse actions).
131
132        It does not make sense, however, to globally modify
133        instrument-related parameters and flags for different histogram types.
134        So global actions can be limited to a single class of histogram types
135        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
136        for groups of similar histograms. Thus, if this mode is set to "All"
137        the Histogram and Profile panes are disabled.
138<DT>Override backspace<DD>This option is available in UNIX only, as there are different
139        ways that backspace can be implemented. When option is set
140        as "On," the backspace key is overridden to send a "delete"
141        character. If backspace does not work in a program such as
142        EXPEDT, change try the other setting for this option.
143
144<a name="setfont"></a>
145<DT>Set Screen Font
146<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
147<DD>
148This menu changes the fonts used in most sections of EXPGUI.
149Note that this setting can be saved with the
150SaveOptions menu option (below) so that EXPGUI automatically
151starts with the chosen font.
152
153<a name="exptoolout"></a>
154<DT>Show EXPTOOL output<DD>
155Normally EXPGUI does not show the output from EXPTOOL, when
156actions like adding atoms, phases or histograms is performed.
157If an error is detected, the output is shown. If
158there are problems with adding phases, atoms, histograms... and
159a window showing an error does not appear,
160this option should be set to "on" so the output from EXPTOOL is
161always shown.
162
163<DT>SaveOptions<DD>Save the current values for "Override backspace",
164        <a href="#sortatoms">"Sort atoms by"</a>,
165        <a href="#sorthist">"Sort histograms by"</a>,
166        <a href="#archive">"archive EXP"</a>,
167        <a href="#Autoupdate">"Autoload EXP"</a>,
168        <a href="#setfont">"Set Screen Font"</a>,
169        and
170        <a href="#Autoicon">"Iconify during GSAS"</a>
171       
172        in file ~/.gsas_config (c:\.gsas_config on Windows).
173<DT>liveplot_options<DD>Used to set options for
174<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
175for example, the histogram to be plotted
176</DL>
177<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
178</DL></DL>
179
180<a name="3"></a>
181<h3>C.3 Powder Menu</h3>
182<DL><DL>
183This menu contains links to GSAS programs used for powder diffraction
184analysis.
185<DL>
186<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
187<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
188<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
189<DT>powplot<DD>Display powder patterns
190<DT>rawplot<DD>Plot powder data
191<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
192<DT>tofnorm<DD>Normalize a TOF spectrum
193<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
194<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
195<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
196to fit a background function to a set of fixed background points.
197<DT><a HREF="excledt.html">excledt</a>
198<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
199<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
200to set the upper and lower limits for a histogram, as well as
201edit excluded regions.
202</DL>
203<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
204</DL></DL>
205
206<a name="4"></a>
207<h3>C.4 Single Crystal Menu</h3>
208<DL><DL>
209This menu contains links to GSAS programs used for
210single-rystal diffraction analysis.
211<DL>
212<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
213<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
214<DT>scabs<DD>Single crystal absorption
215<DT>scmerge<DD>Sort and merge single crystal data
216<DT>sxtldata<DD>Prepare generic single crystal data
217</DL>
218<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
219</DL></DL>
220
221<a name="5"></a>
222<h3>C.5 Graphics Menu</h3>
223<DL><DL>
224This menu contains links to several GSAS and
225two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
226and widplt)
227programs used for graphical display of data and results.
228<DL>
229<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
230        and then compute with FOURIER
231<DT>polfplot<DD>Display polefigures
232<DT>powplot<DD>Display powder patterns
233<DT>ortep<DD>Draw crystal structure
234<DT>rawplot<DD>Plot powder data
235<DT>fourier<DD>Generate Fourier map
236<DT>forsrh<DD>Search Fourier map for peaks
237<DT><a HREF="liveplot.html#liveplot">liveplot</a>
238<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
239to create a plot of powder data
240with zooming, automatic update and other nice features.
241<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
242<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
243</DL>
244<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
245</DL></DL>
246
247<a name="6"></a>
248<h3>C.6 Results Menu</h3>
249<DL><DL>
250This menu contains links to several GSAS and
251one non-GSAS (lstview)
252programs used for analysis of results.
253<DL>
254<DT>bijcalc<DD>Thermal parameter analysis
255<DT>disagl<DD>Distance/angle calculations
256<DT>reflist<DD>List reflection data
257<DT>geometry<DD>Molecular geometry calculations
258<DT>hstdmp<DD>List powder histogram data
259<DT>istats<DD>HKL Intensity statistics
260<DT>rcalc<DD>Compute reflection resuduals
261<DT>composition<DD>Computes the chemical composition of a unit cell
262accounting for site multiplicies and occupancies
263<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
264<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
265chains, for use in restraints.
266</DL>
267<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
268</DL></DL>
269
270<a name="7"></a>
271<h3>C.7 Calculations Menu</h3>
272<DL><DL>
273This menu contains programs for useful crystallographic computations.
274<DL>
275<DT>cllchg<DD>Transform unit cell
276<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
277<DT>rducll<DD>Unit cell reduction
278<DT>spcgroup<DD>Space group symbol interpreter
279<DT>unimol<DD>Unique molecule assembler
280</DL>
281<img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot">
282</DL></DL>
283
284<a name="8"></a>
285<h3>C.8 Import/Export Menu</h3>
286<DL><DL>
287This menu contains utilities for importing information into GSAS and
288exporting.
289<DL>
290<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
291file is used in MSI software such as Cerius and InsightII.
292<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
293<DT>hklsort<DD>Prepare HKL tables
294<DT>pubtable<DD>Prepare atom parameter tables
295<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
296<DT>cad4rd<DD>Prepare CAD4 single crystal data
297<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
298<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
299<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
300<DT>sxtldata<DD>Prepare generic single crystal data
301<DT>gsas2pdb<DD>
302Import (using GSAS2PDB & EXPEDT) and export coordinates (for
303macromolecular phases) to/from Protein Data Base files
304<DT>ref2asc<DD>
305Exports a GSAS reflection file to ASCII for use in non-GSAS programs
306<DT>ref2bin<DD>
307Imports an ASCII reflection file to the GSAS binary format
308</DL>
309<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
310</DL></DL>
311
312
313<hr>
314<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
315<TR><TH><A  Href="expgui.html">EXPGUI top</A>
316</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
317</TH><TH><A Href="expgui7.html">Previous page</A>
318</TH></TR></TABLE>
319
320<a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>)
321<br>
322$Revision: 522 $ $Date: 2009-12-04 23:07:34 +0000 (Fri, 04 Dec 2009) $
323</blockquote>
324</body>
325</html>
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