source: trunk/doc/expguic.html @ 604

Last change on this file since 604 was 578, checked in by toby, 12 years ago

# on 2002/04/12 19:49:04, toby did:
remove identification stuff

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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35Note that the figures on this page are likely to be out of date with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="sortatoms"></a>
110<DT>Sort atoms by<DD>   Determines the order that atoms are displayed on the "Phase" pane
111        Atoms may be displayed sorted by number, atom type, site multiplity,
112        occupancy, or by x, y or z coordinate
113<P>
114<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
115Clicking on the heading above the atoms list cycles with the left
116mouse button cycles through the atom sort modes. Clicking with
117the right mouse button resets the atom sort mode to "number".
118
119<a name="sorthist"></a>
120<DT>Sort histograms by<DD>Determines the order that histograms are displayed on the
121        Histogram, Scaling and Profile panes
122
123        Histograms may be sorted by histogram number, histogram type,
124        original bank number, or diffraction angle/wavelength
125<DT><A href="expgui.html#multiplehistogram">Multiple hist. selection</A><DD>
126        When this mode is off, it is possible to modify parameters
127        and refinement flags for only a single histogram. For other settings,
128        it is possible to modify parameters and flags for groups of
129        histograms (see help for Mouse actions).
130
131        It does not make sense, however, to globally modify
132        instrument-related parameters and flags for different histogram types.
133        So global actions can be limited to a single class of histogram types
134        (e.g. TOF, CW Neutron,...), which allows these parameters to be set
135        for groups of similar histograms. Thus, if this mode is set to "All"
136        the Histogram and Profile panes are disabled.
137<DT>Override backspace<DD>This option is available in UNIX only, as there are different
138        ways that backspace can be implemented. When option is set
139        as "On," the backspace key is overridden to send a "delete"
140        character. If backspace does not work in a program such as
141        EXPEDT, change try the other setting for this option.
142
143<a name="setfont"></a>
144<DT>Set Screen Font
145<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
146<DD>
147This menu changes the fonts used in most sections of EXPGUI.
148Note that this setting can be saved with the
149SaveOptions menu option (below) so that EXPGUI automatically
150starts with the chosen font.
151
152<a name="exptoolout"></a>
153<DT>Show EXPTOOL output<DD>
154Normally EXPGUI does not show the output from EXPTOOL, when
155actions like adding atoms, phases or histograms is performed.
156If an error is detected, the output is shown. If
157there are problems with adding phases, atoms, histograms... and
158a window showing an error does not appear,
159this option should be set to "on" so the output from EXPTOOL is
160always shown.
161
162<DT>SaveOptions<DD>Save the current values for "Override backspace",
163        <a href="#sortatoms">"Sort atoms by"</a>,
164        <a href="#sorthist">"Sort histograms by"</a>,
165        <a href="#archive">"archive EXP"</a>,
166        <a href="#Autoupdate">"Autoload EXP"</a>,
167        <a href="#setfont">"Set Screen Font"</a>,
168        and
169        <a href="#Autoicon">"Iconify during GSAS"</a>
170       
171        in file ~/.gsas_config (c:\.gsas_config on Windows).
172<DT>liveplot_options<DD>Used to set options for
173<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
174for example, the histogram to be plotted
175</DL>
176<img SRC="m2.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
177</DL></DL>
178
179<a name="3"></a>
180<h3>C.3 Powder Menu</h3>
181<DL><DL>
182This menu contains links to GSAS programs used for powder diffraction
183analysis.
184<DL>
185<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
186<DT>powpref<DD>Powder data preparation (shortcut Alt-P)
187<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
188<DT>powplot<DD>Display powder patterns
189<DT>rawplot<DD>Plot powder data
190<DT>fitspec<DD>Fit a TOF vanadium scattering spectrum
191<DT>tofnorm<DD>Normalize a TOF spectrum
192<DT><a HREF="liveplot.html#bkgedit">bkgedit</a>
193<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
194<DD>Invokes the <a HREF="liveplot.html#bkgedit">BKGEDIT</a> program
195to fit a background function to a set of fixed background points.
196<DT><a HREF="excledt.html">excledt</a>
197<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
198<DD>Invokes the <a HREF="excledt.html">EXCLEDT</a> program
199to set the upper and lower limits for a histogram, as well as
200edit excluded regions.
201</DL>
202<img SRC="m3.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
203</DL></DL>
204
205<a name="4"></a>
206<h3>C.4 Single Crystal Menu</h3>
207<DL><DL>
208This menu contains links to GSAS programs used for
209single-rystal diffraction analysis.
210<DL>
211<DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E)
212<DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G)
213<DT>scabs<DD>Single crystal absorption
214<DT>scmerge<DD>Sort and merge single crystal data
215<DT>sxtldata<DD>Prepare generic single crystal data
216</DL>
217<img SRC="m4.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
218</DL></DL>
219
220<a name="5"></a>
221<h3>C.5 Graphics Menu</h3>
222<DL><DL>
223This menu contains links to several GSAS and
224two non-GSAS (<a HREF="liveplot.html#liveplot">LIVEPLOT</a>,
225and widplt)
226programs used for graphical display of data and results.
227<DL>
228<DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT
229        and then compute with FOURIER
230<DT>polfplot<DD>Display polefigures
231<DT>powplot<DD>Display powder patterns
232<DT>ortep<DD>Draw crystal structure
233<DT>rawplot<DD>Plot powder data
234<DT>fourier<DD>Generate Fourier map
235<DT>forsrh<DD>Search Fourier map for peaks
236<DT><a HREF="liveplot.html#liveplot">liveplot</a>
237<DD>Invokes the <a HREF="liveplot.html#liveplot">LIVEPLOT</a> program
238to create a plot of powder data
239with zooming, automatic update and other nice features.
240<DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software
241<DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file
242</DL>
243<img SRC="m5.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
244</DL></DL>
245
246<a name="6"></a>
247<h3>C.6 Results Menu</h3>
248<DL><DL>
249This menu contains links to several GSAS and
250one non-GSAS (lstview)
251programs used for analysis of results.
252<DL>
253<DT>bijcalc<DD>Thermal parameter analysis
254<DT>disagl<DD>Distance/angle calculations
255<DT>reflist<DD>List reflection data
256<DT>geometry<DD>Molecular geometry calculations
257<DT>hstdmp<DD>List powder histogram data
258<DT>istats<DD>HKL Intensity statistics
259<DT>rcalc<DD>Compute reflection resuduals
260<DT>composition<DD>Computes the chemical composition of a unit cell
261accounting for site multiplicies and occupancies
262<DT>lstview<DD>Create a box with scrollbars containing the current .LST file
263<DT>ramafit<DD>Fits torsion angle distributions, particularly in peptide
264chains, for use in restraints.
265</DL>
266<img SRC="m6.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
267</DL></DL>
268
269<a name="7"></a>
270<h3>C.7 Calculations Menu</h3>
271<DL><DL>
272This menu contains programs for useful crystallographic computations.
273<DL>
274<DT>cllchg<DD>Transform unit cell
275<DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths
276<DT>rducll<DD>Unit cell reduction
277<DT>spcgroup<DD>Space group symbol interpreter
278<DT>unimol<DD>Unique molecule assembler
279</DL>
280<img SRC="m7.gif" BORDER=3 alt="EXPGUI Screen snapshot">
281</DL></DL>
282
283<a name="8"></a>
284<h3>C.8 Import/Export Menu</h3>
285<DL><DL>
286This menu contains utilities for importing information into GSAS and
287exporting.
288<DL>
289<DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This
290file is used in MSI software such as Cerius and InsightII.
291<DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file
292<DT>hklsort<DD>Prepare HKL tables
293<DT>pubtable<DD>Prepare atom parameter tables
294<DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse)
295<DT>cad4rd<DD>Prepare CAD4 single crystal data
296<DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format
297<DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b
298<DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data
299<DT>sxtldata<DD>Prepare generic single crystal data
300<DT>gsas2pdb<DD>
301Import (using GSAS2PDB & EXPEDT) and export coordinates (for
302macromolecular phases) to/from Protein Data Base files
303<DT>ref2asc<DD>
304Exports a GSAS reflection file to ASCII for use in non-GSAS programs
305<DT>ref2bin<DD>
306Imports an ASCII reflection file to the GSAS binary format
307</DL>
308<img SRC="m8.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
309</DL></DL>
310
311
312<hr>
313<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
314<TR><TH><A  Href="expgui.html">EXPGUI top</A>
315</TH><TH><A Href="liveplot.html">Next page<BR>(Utilities)</A>
316</TH><TH><A Href="expgui7.html">Previous page</A>
317</TH></TR></TABLE>
318
319<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
320<font size=-1><? lastmod(); ?> </font>
321<br>
322$Revision: 578 $ $Date: 2009-12-04 23:08:31 +0000 (Fri, 04 Dec 2009) $
323</blockquote>
324</body>
325</html>
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