source: branches/sandbox/doc/expgui.html @ 1157

Last change on this file since 1157 was 1157, checked in by toby, 10 years ago

liveplot: export to gnuplot; plot I/sigma(I); change title & size of labels; improve tick location; make autoticks standard; expgui: new menu item to create InstParm? file; InstEdit?: bug fixes; remove fprime since not in GSAS anymore; fix 2Theta max bug for CW instruments; updates to doc files

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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
8<BODY BGCOLOR="#FFFFFF"
9      topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" 
10      text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff">
11
12<blockquote><font face="arial, helvetica, sans-serif">
13
14<center><h1>
15<HR noshade width="75%" size="2" align="center">
16EXPGUI<BR>
17A Graphical User Interface for
18<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
19GSAS</A>
20<HR noshade width="75%" size="2" align="center">
21</h1></center>
22<P><P>
23<I><B>
24<blockquote>
25For the impatient, see download/installation instructions for:
26<A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
27Windows</A>,
28<A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallOSX">
29Mac (OS X)</A>, or
30<A HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallLinux">
31Linux</A>
32</blockquote>
33</I></B>
34<P><P>
35EXPGUI is a graphical interface for the
36<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
37package, developed at Los Alamos and maintained now at Argonne.
38EXPGUI does two things:
39it can be used to directly modify the GSAS
40experiment file with a graphical user interface (GUI) and
41it can be used to invoke the programs inside the
42GSAS package such as EXPEDT, GENLES, FOURIER...
43These programs can be run from a menu or in many cases by pressing buttons.
44EXPGUI is written using the
45<A href="#tcltk">Tcl/Tk</A> scripting language.
46<P>
47This web page describes the different actions that
48can be accomplished with the different panels and the
49contents of the menus. The table below contains links to the other
50web accessible documentation.
51<P>
52<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=CENTER>
53<TR><TH BGCOLOR="#F0F0F0" rowspan=3>GUI Sections</TH>
54<TH><A Href="expgui1.html">Least Squares</A></TH>
55<TH><A Href="expgui2.html">Phase info</A></TH>
56<TH><A Href="expgui3.html">Histogram info</A></TH>
57</TR>
58<TR>
59<TH><A Href="expgui4.html">Scaling info</A></TH>
60<TH><A Href="expgui5.html">Profile terms</A></TH>
61<TH><A Href="expgui6.html">Constraints & Restraints</A></TH>
62</TR>
63<TR>
64<TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
65<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
66<TH><A Href="expguic.html">Menus</A></TH>
67<TH>&nbsp;</TH>
68</TR>
69<TR><TH BGCOLOR="#F0F0F0" rowspan=3>Utilities:</TH>
70<TH><A Href="liveplot.html">LIVEPLOT</A></TH>
71<TH><A Href="liveplot.html">BKGEDIT</A></TH>
72<TH><A Href="excledt.html">EXCLEDT</A></TH>
73</TR>
74<TR>
75<TH><A Href="#WIDPLT">WIDPLT</A></TH>
76<TH><A Href="#ABSPLT">ABSPLT</A></TH>
77<TH><A Href="#INSTEDIT">INSTEDIT</A></TH>
78</TR>
79<TR>
80<TH><A Href="gsas2cif.html">CIF export</A></TH>
81<TH>&nbsp;</TH>
82<TH>&nbsp;</TH>
83</TR>
84<TR><TH BGCOLOR="#F0F0F0" rowspan=2>Installation Notes:</TH>
85<TH><A Href="expgui_Unix_readme.html">Unix</A></TH>
86<TH><A Href="expgui_Win_readme.html">Windows</A></TH>
87<TH>
88<A Href="osx.html">Mac OS X</A></TH>
89</TR><TR>
90<TH><A Href="expgui_cfg.html">Customization</A></TH>
91<TH>&nbsp;</TH>
92<TH>&nbsp;</TH>
93</TR>
94<TR><TH BGCOLOR="#F0F0F0">Tutorials:</TH>
95<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
96NIST<BR>Neutron data</A></TH>
97<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
98<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
99</TR>
100<TR><TH BGCOLOR="#F0F0F0">Messages:</TH>
101<TH><A Href="expguierr.html#Error">Error</A></TH>
102<TH><A Href="expguierr.html#Warn">Warning</A></TH>
103<TH><A Href="expguierr.html#Info">Informational</A></TH>
104</TR>
105<TR><TH BGCOLOR="#F0F0F0">Other:</TH>
106<TH><A Href="expgui_intro.html">Introduction</A></TH>
107<TH><A Href="wishlist.html">Recent & Planned<BR>Improvements</A></TH>
108<TH><A Href="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
109<I>J. Appl. Cryst.</i><BR>article</A></TH>
110</TR>
111</TABLE><BR CLEAR=ALL>
112<P>
113<B>Citations.</B>
114The appropriate citations to be used for GSAS and EXPGUI are:
115<UL>
116<LI>
117A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
118Los Alamos National Laboratory Report LAUR 86-748 (2000).
119<A
120  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
121[link to PDF copy of manual]
122</A>
123<LI>
124B. H. Toby, <i>EXPGUI</i>, a graphical user interface for <i>GSAS</i>,
125<i>J. Appl. Cryst.</i> <b>34</b>, 210-213 (2001).
126<A HREF="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
127[link to PDF file]
128</A>
129</UL>
130<P>
131<B>Mailing List.</B>
132There is a mailing list for users of EXPGUI for news about about new
133features, bug fixes in EXPGUI, etc.
134<A href="http://www.aps.anl.gov/mailman/listinfo/expgui">Subscription info</A>
135<P>
136<hr>
137
138<h2>A. Experiment file editing</h2>
139<P>
140<DL><DL>
141When an experiment (.EXP) file is read, a copy is made in local
142computer memory. In most cases, values are changed in this
143"in memory" copy of the experiment file
144as this information is changed by the user on the screen.
145<img SRC="rederror.gif" align=LEFT BORDER=3 alt="EXPGUI Screen snapshot">
146<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
147If there is an error in the typed value, (for example if "1..0" is typed, or
148"1.5" is typed where an integer is expected), these values are
149not saved. In this case, the text is turned red, to indicate
150that an error is present, as shown in the figure to the left, where "90.000x"
151has been entered for alpha.
152The edited version of the experiment file is written back out to
153disk when the "File/Save" or "File/Save as"
154<A Href="expguic.html#1">menu bar options</A>
155are used. The File/Save operation is done automatically before any GSAS
156programs, such as GENLES or EXPEDT, are run.
157<P>
158<A name="badexp">
159The GSAS refinement program, GENLES, will sometimes "blow up", where the
160  program changes varied parameters to values very far from their
161  correct values. This occurs when parameters are highly correlated,
162  are refining to values that are not allowed, or some of the refined parameters have
163  very little impact on the quality of the fit. When this happens,
164  invalid values are written to the GSAS experiment file that contain
165  either asterisks (****) or the string "NAN" (not a number). Such
166  files cannot be used for additional GENLES runs.
167  <P>
168  When EXPGUI reads a .EXP file it scans it for evidence of a previous
169  failure of a GENLES refinement and warns if a problem is
170  noted. Please note that this scan is not perfect and occasionally
171  you may be warned in cases where the file is fine (if possible,
172  please send such .EXP file to Brian Toby so this scan can be improved.)
173  When such a "bad" .EXP file is located, one can "revert" to an
174  archived copy of a previous experiment file (with suffix .Oxx). This
175  can be done with the Revert menu item in the File menu. Note that
176clicking on a file in the file selection window causes it to be
177scanned and shows the status of that refinement. Also note that
178usually the last good archived file has settings that will produce the same bad
179refinement, so it is necessary to either revert further back, or to
180change the refinement options before running GENLES.
181<P>
182
183Since the GSAS experiment file is quite complex,
184values are grouped together by function, approximately
185following the outline of the EXPEDT program.
186Each set of values is given a
187"tabbed panel" on a window that has the appearance of a notebook (see below).
188<center><B>
189<br>The notebook panel tabs.
190<br><img SRC="panebar1.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
191</center></B>
192In some cases, where values are
193too numerous or complex to fit onto the notebook panel, one or more buttons
194may be present on a panel that will create a separate window,
195where the associated values can be modified.
196These values are not recorded in the
197"in memory" copy of the experiment file unless the "Save" button on this window
198is pressed. If "Cancel" is pressed, no changes are made.
199Each notebook panel is listed below with a link to the web page documenting
200that panel.
201
202<A Href="expgui1.html">
203<h3>A.1 Least Squares (LS) Controls Panel</h3>
204</A><A Href="expgui2.html">
205<h3>A.2 Phase Panel</h3> 
206</A><A Href="expgui3.html">
207<h3>A.3 Histogram panel</h3> 
208</A><A Href="expgui4.html">
209<h3>A.4 Scaling panel</h3> 
210</A><A Href="expgui5.html">
211<h3>A.5 Profile panel</h3> 
212</A><A Href="expgui6.html">
213<h3>A.6 Constraints panel</h3>
214</A><A Href="expgui7.html">
215<h3>A.7 Preferential Orientation Panel</h3>
216</A>
217<br clear=all>
218</DL></DL>
219<h2>B. Shortcuts</h2></a>
220<a name="multiplehistogram">
221<h3>B.1 Multiple Histogram Selection</h3></a>
222<DL><DL>
223This mode allows parameters to be changed for groups of
224histograms.
225When the "Multiple Histogram Selection" mode is off,
226it is possible to modify parameters
227and refinement flags for only a single histogram, but
228the other settings allow groups of histograms
229to be selected and modified.
230<A href="#mouseactions">(see Mouse Actions)</A>.
231<P>
232It does not make sense, however, to globally modify
233instrument-related parameters and flags for different
234histogram types.
235So global actions can be limited to a single class
236of histogram types (e.g. TOF, CW Neutron,...), which
237allows these parameters to be set for groups of
238similar histograms. Thus, if this mode is set to "All"
239the Histogram and Profile panels are disabled.
240<P>
241The setting for "Multiple Histogram Selection" mode is
242displayed above each histogram selection box and is
243selected using the "Multiple Hist. Selection" item on the
244Options menu to create a submenu or by clicking on the display.
245Note that another option in this "Multiple Hist. Selection"
246submenu is an option "Group Phases Together" that controls how
247EXPGUI treats phases having
248the same profile type that is used when multiple histograms are selected. If
249the "Group Phases Together" option is on, then the refinement flags for
250all phases with the same histogram types are grouped together, when possible.
251If this option is off, phases are treated separately.
252<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
253If the left mouse button is used to click on the selection mode display,
254the mode is cycled between the available modes. If the right mouse
255button is used, the mode is reset, to disable multiple histogram selection.
256<p>
257<a name="mouseactions">
258</DL></DL>
259<h3>B.2 Mouse Actions</h3></a>
260<DL><DL>
261A range of atoms or (in multiple selection mode) histograms may be
262selected by dragging (holding down) the left mouse button. It is also
263possible to select a range by using the Shift key with the left mouse
264button. To select or deselect individual entries, use the Control key
265with the left mouse button. Pressing the right mouse button selects all
266entries in a list.
267</DL></DL>
268
269<h2>C. Menu Commands and Programs</h2>
270<p>
271GSAS programs are invoked either through use of the menu bar
272<center><B>
273<br>The menu bar.
274<br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
275</center></B>
276or by "pressing" a button on the button bar. The button bar
277simply provides an easy way to access commonly used
278actions on the menu bar. Users can
279<A HREF="expgui_cfg.html">
280configure the menu bar</A> to include their own preferred actions and, with
281some knowledge of the program and Tcl/Tk,
282add their own commands to the menu bar or button bar.
283
284<center><B>
285<br>The button bar.
286<br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
287</center></B>
288
289<h3>Invoking of GSAS programs</h3>
290When GSAS programs are invoked, in most cases EXPGUI is suspended while
291the GSAS program is run in a terminal (or DOS) window. When the terminal
292window is closed, EXPGUI is restarted. If desired (see the
293<A Href="expguic.html#Autoicon">
294"Iconify during GSAS"</A>
295option) while this occurs, EXPGUI can be made into an icon
296to save screen space.
297<P>
298<img src="powpref4a.gif" align=left alt="EXPGUI Screen snapshot">
299Once the GSAS program has finished, if the program has modified
300the .EXP file,
301<a Href="expguierr.html#Overwrite">
302"File has been modified..."</a>message box
303similar to the one to the left is displayed (also see the more complete
304discussion on the <a Href="expguierr.html#Overwrite">messages page</A>.
305Note that this message can be avoided if the
306<A Href="expguic.html#Autoupdate">
307"Autoload EXP"</A>
308option is used.
309<BR clear=all>
310<P>
311Note that in both Windows-95 and Windows-NT, a file named <tt>EXPGUI.LCK</tt>
312is created while the GSAS program runs. The presence of this file is used
313to suspend the LIVEPLOT program, since LIVEPLOT has sometimes crashed
314when run at the same time as GENLES (no such problem has been seen in Unix).
315This file is deleted when the GSAS program completes.
316<P>
317<img src="lock.gif" align=left alt="EXPGUI Screen snapshot">
318In Windows-9x, the <a Href="expgui_Win_readme.html#Winexec">Winexec</a>
319package is used to execute a command that creates a DOS window.
320The GSAS programs are then run by a batch file in this DOS window.
321Due to limitations in Tcl/Tk & Windows, the DOS window runs independently
322of EXPGUI, so the lock file (<tt>EXPGUI.LCK</tt>) is also used to suspend
323EXPGUI. While EXPGUI is waiting, the
324<a Href="expguierr.html#lock">
325Please wait...
326</a>
327window shown to the left is displayed. When the GSAS program completes, the
328lock file is deleted, the window automatically disappears and EXPGUI resumes.
329Should a problem arise where the file is not deleted, EXPGUI can be resumed by
330pressing the "Continue" button.
331
332<BR clear=all>
333<h3>GSAS menus</h3>
334
335A description of the EXPGUI menus follows. Use the links to obtain
336more information, including a very
337brief description of the function of each menu option.
338Note that an option may appear under more than one menu.
339
340<DL><DL>
341
342<A Href="expguic.html#1">
343<H3>C.1 File Menu</H3>
344</A>
345<DL><DL>
346The options on the File menu as is the custom contains the commands
347for reading and writing experiment files, as well as starting, 
348ending and controlling the program.
349</DL></DL>
350
351<A Href="expguic.html#2">
352<h3>C.2 Options Menu</h3>
353</A>
354<DL><DL>
355This menu contains options that determine how EXPGUI runs.
356</DL></DL>
357
358<A Href="expguic.html#3">
359<h3>C.3 Powder Menu</h3>
360</A>
361<DL><DL>
362This menu contains links to GSAS programs used for powder diffraction
363analysis.
364</DL></DL>
365
366<A Href="expguic.html#4">
367<h3>C.4 Single Crystal Menu</h3>
368</A>
369<DL><DL>
370This menu contains links to GSAS programs used for
371single-crystal diffraction analysis.
372</DL></DL>
373
374<A Href="expguic.html#5">
375<h3>C.5 Graphics Menu</h3>
376</A>
377<DL><DL>
378This menu contains links to several GSAS and
379non-GSAS programs (such as LIVEPLOT and WIDPLT)
380used for graphical display of data and results.
381</DL></DL>
382
383<A Href="expguic.html#6">
384<h3>C.6 Results Menu</h3>
385</A>
386<DL><DL>
387This menu contains links to several GSAS and
388one non-GSAS (LSTVIEW)
389programs that are used for analysis of results.
390</DL></DL>
391
392<A Href="expguic.html#7">
393<h3>C.7 Calculations Menu</h3>
394</A>
395<DL><DL>
396This menu contains programs for useful crystallographic computations.
397</DL></DL>
398
399<A Href="expguic.html#8">
400<h3>C.8 Import/Export Menu</h3>
401</A>
402<DL><DL>
403This menu contains utilities for importing information into GSAS and
404exporting.
405</DL></DL>
406
407<h2>D. EXPGUI Utility Features</h2></a>
408EXPGUI adds a number of useful functions to the GSAS package. Some,
409but not all, of these features are graphically oriented.
410
411<br clear=all>
412<a name="LSTVIEW"></a>
413<H3>D.1 LSTVIEW</H3>
414
415<DL><DL>
416LSTVIEW is used to browse through the GSAS output listing. It is
417invoked by the "lstview" command in the GUI.
418<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
419to shorten the .LST file by removing older results from the beginning
420of the file.
421<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
422as a function of the cycle number.
423<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
424</DL></DL>
425
426<br clear=all>
427<H3>D.2 LIVEPLOT</H3>
428<DL><DL>
429<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated
430and difference plots for powder
431refinements. The plot is updated as the refinement progresses. The mouse can
432be used to zoom in on sections of the plot.
433LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
434<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
435<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
436LIVEPLOT can now be enhanced to superimpose peak locations for
437input unit cells or peaks from JCPDS/ICDD entries.
438See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
439further documentation, and in particular, the
440See the <A HREF="liveplot.html#customize">
441LIVEPLOT customization information</A>.
442<P>
443</DL></DL>
444<br clear=all>
445<H3>D.3 BKGEDIT</H3>
446<DL><DL>
447<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
448<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to
449fit a GSAS background function to a set of fixed
450background points that are input using the mouse.
451The mouse can also be used to zoom in on sections of the plot.
452BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
453<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
454See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
455further documentation.
456<P>
457</DL></DL>
458<br clear=all>
459<H3>D.4 EXCLEDT</H3>
460<DL><DL>
461<A HREF="excledt.html">EXCLEDT</A> is used to edit the
462range of data used from a histogram. The upper & lower ranges
463can be adjusted to include more data or use less. Also, it is
464possible to remove sections of the data (exclude regions) that
465have known systematic errors that cannot be modeled.
466EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
467<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
468See the <A HREF="excledt.html">EXECLEDT web page</A> for
469further documentation.
470<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
471EXCLEDT can now be used to change the simulation range for dummy histograms.
472<P>
473</DL></DL>
474
475<br clear=all>
476<a name="WIDPLT"></a>
477<a name="ABSPLT"></a>
478<H3>D.5 WIDPLT and ABSPLT</H3>
479<DL><DL>
480WIDPLT is used to plot the peak widths that are generated by a set
481of GSAS profile terms (constant wavelength equations, only).
482The parameters from each phase & histogram will be
483read from the .EXP file. It is also possible to input parameters manually.
484By creating a special file (<A HREF="expgui_cfg.html#import">
485described in the customization information</A>), it
486is possible to define reference curves
487that are loaded automatically for comparison.
488<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
489<P>
490ABSPLT is used to plot the absorption/reflectivity correction for a
491histogram. Values are loaded from the histogram(s), but can be edited manually.
492<P>
493WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
494</DL></DL>
495
496<br clear=all>
497<a name="INSTEDIT"></a>
498<H3>D.6 INSTEDIT</H3>
499<DL><DL>
500
501The INSTEDIT utility is used to edit or create an instrument parameter file.
502The utility can be started from the "Edit File" button in the
503<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
504the "instedit" option in the Powder menu. Alternately, to create a new
505  instrument parameter file, choose Powder menu option "New InstParm
506  file". (It is also possible
507  to create a new file using the standard instedit by selecting
508  "Cancel" when asked for an input file.)
509An example INSTEDIT window appears below.
510<P>
511<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
512<br clear=all>
513<P>
514Note that an instrument parameter file is used for a single type of data,
515as is selected by the menu button at the top of the window.
516However, multiple sets of parameters may be included in a
517file, to be used for example with differing operating modes for the
518instrument. Each set of parameters is called a bank in GSAS terminology.
519The radiobuttons on the top of the window are used to select
520which bank's parameters will be viewed.
521The "Add Bank" button adds an additional bank to the file.
522<P>
523The parameters are described briefly below, but in more depth in the
524GSAS manual (for example, pages 158-166 for profile parameters and
525page 221-223 for the details of the instrument parameter file.)
526<P>
527<H5>Bank Parameters</H5>
528The parameters available for each bank are:
529<DL>
530<DT>Title<DD>This probably has no real use.
531<DT>Instrument Name<DD>This string is used for creation of CIFs. It is
532best if this name is unique for each instrument.
533<DT>Primary Wavelength<DD>Note, this value is set automatically when
534the radiation type is selected
535<DT>Zero Correction<DD>This is the shift to be applied to 2theta
536values in centidegrees (degrees/100). This value should probably be
537near zero for Debye-Scherrer geometry instruments (unless known from
538calibration) and will almost always be fixed at zero
539for Bragg-Brentano geometry.
540<DT>
541</DL>
542<I>X-ray only parameters</I>
543<DL>
544<DT>Radiation type<DD>Used with x-rays. The value set here
545determines the anomolous dispersion (f' and f'' values) used.
546<DT>Monochromatic/Dual<DD>Used with x-rays. Set to dual when Kalpha1, Kalpha2
547radiation is present.
548<DT>Secondary Wavelength<DD>Used in "dual" wavelength mode.
549Note, this value is set automatically when the radiation type is selected
550<DT>Wavelength Ratio<DD>Typically 0.5 for typical K alpha 1,2 instruments,
551<<I>i.e.</I>when K alpha 1 is double the intensity of K alpha 2.
552<DT>Polarization Correction<DD>There are three modes for this, where the
553first two modes work similarly. The first mode ("Diffracted Beam")
554is most common. The third mode ("None") is used when
555Lorentz-polaraization corrections are applied to the data prior to its input
556to GSAS. See page 144-145 in the GSAS manual for more information on these
557corrections.
558<DT>Polarization Ratio<DD>In "Diffracted Beam" mode:
559typically 0.5 for lab instruments without monochromators and higher for
560instruments with a diffracted beam; the value depends on the monochromator
561take-off angle. Typically slightly below unity (0.9-0.98) for synchrotron
562instruments. Ask the instrument scientist for the appropriate value.
563</DL>
564<P>
565Each bank in the instrument parameter file has one or more sets of
566profile parameters associated. Set number 1 is the default loaded
567when a histogram is added. Increase the number of sets
568using the "Add profile" button. Select the optimal profile type
569for use with your data for this set, but for most flexibility, define
570default values for all useful profile types (type 1 is of use only for
571CW neutron work) and set these values from fitting a standard with
572minimal broodening. Note that profiles can be read from a GSAS experiment
573file using the "Import profile", which raises a dialog
574such as the one below.
575<P>
576<img SRC="instedit2.gif" align=RIGHT alt="EXPGUI Screen snapshot">
577<br clear=all>
578
579
580</DL></DL>
581
582<br clear=all>
583<a name="ConvertUnix"></a>
584<a name="ConvertWin"></a>
585<h3>D.7 File Conversions</h3> 
586<DL><DL>
587<P>
588GSAS data, experiment and instrument parameter files are
589expected to have a format with exactly 80 characters per line followed
590by a carriage return and then a linefeed (82 characters total per line).
591Files in this format can be read in "Direct Access" mode.
592Recent versions of GSAS will attempt to detect and repair files that
593are not in this format, but if the file is incorrectly formatted and
594by chance the length of the file is divisible by 82, the problem in the
595file format will not be detected.
596The Convert menu
597in can be used to convert files into the correct format.
598The original version of the
599file is retained and renamed.
600<P>
601</DL></DL>
602
603<br clear=all>
604<a name="Composition"></a>
605<h3>D.8 Compute Composition</h3> 
606<DL><DL>
607The composition box shows the unit cell and asymmetric unit composition
608for all phases in a material. Site multiplicities and occupancies are
609taken into account.
610</DL></DL>
611
612<br clear=all>
613<a name="DeleteHistoryRecords"></a>
614<h3>D.9 Delete History Records</h3> 
615<DL><DL>
616Every time a GSAS program (including EXPGUI) is run, an entry is added to
617the "history records" in the .EXP file. After 999 entries have been written,
618no more can be added to the file. Further, reading large numbers of history
619records can slow the GSAS programs
620(this is less of a problem on faster computers). For these reasons, it may be
621a good idea to prune the older history records from the file.
622The File/EraseHistory command can be used to invoke the this option.
623<P>
624On the dialog the number of history records to be retained is specified.
625Also, after records have been deleted, the remaining records can be renumbered
626starting with 1, so that the 999 record limit is not reached.
627</DL></DL>
628
629<h2>E. Coordinate Export & Import Features</h2></a>
630EXPGUI can be used to read coordinates in formats not
631supported in GSAS. Coordinates can also be exported in a variety of
632formats as well.
633
634<A name="import">
635<h3>E.1 Coordinate Import Formats</h3> 
636Coordinates can be imported using the
637<A HREF="expgui2.html#addphase">"Add Phase"</A>,
638<A HREF="expgui2.html#addatoms">"Add Atoms"</A> or
639<A HREF="expgui2.html#replacephase">"Replace Phase"</A> 
640buttons on the <A HREF="expgui2.html">Phase Panel</A>, by choosing
641the format from the pull-down list to the right of the
642"Import atoms/phase from" button. The formats currently supported
643are listed below.
644Note that it is relatively easy to add new routines for
645importing coordinates;
646see the <A HREF="expgui_cfg.html#import">
647customization information</A> for more details.
648<DL><DL>
649<DT><B>Crystallographic Information File (CIF)</B><DD>
650Coordinates can be read from single block or multiblock CIF files
651using DDL1. If more than one block containing coordinates is found in the
652file, a CIF browser is available to help select the desired block.
653<DT><B>PowderCell .CEL files</B><DD>
654This format is used by the DOS and Windows PowderCell program, a valuable
655program for the transformation and visualization of structures.
656<DT><B>GSAS .EXP files</B><DD>
657This routine is used to copy coordinates, unit cell parameters and space group
658information from other GSAS experiment (.EXP) files.
659<DT><B>MSI .xtl format</B><DD>
660<a HREF="#ExportMSI">see below</a>
661<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
662<a HREF="#ExportSPF">see below</a>
663
664</DL></DL>
665
666<A name="export">
667<h3>E.2 Coordinate Export Formats</h3> 
668Coordinates can be written using the Import/Export=>"Coord Export" menu.
669Note that contents of the submenu will depend on the
670number of export routines found in the EXPGUI directory when the menu
671is first created, thus it is relatively easy to add new routines for
672importing coordinates;
673see the <A HREF="expgui_cfg.html#export">
674customization information</A> for more details.
675<DL><DL>
676<DT><B>Crystallographic Information File (CIF)</B><DD>
677Powder Diffraction Crystallographic Information files (pdCIFs) can
678be created by the GSAS2CIF program. The GSAS2CIF menu item
679invokes this program.
680<a name="ExportMSI"></a>
681<DT><B>MSI .xtl format</B><DD>
682This writes a .xtl file, as is used in Insight-II and
683Cerius2 (Molecular Simulations, Inc.). The routine
684attempts to convert GSAS space group names properly, as well as
685correctly label "Origin 2" setting, however, the naming conversion
686will not work for all valid GSAS space groups. Some effort may be needed
687by the user to get everything worked out correctly.
688<a name="ExportSPF"></a>
689<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
690This writes a .spf file, as used in
691<A HREF="http://www.cryst.chem.uu.nl/platon/">Platon</A> and
692<A HREF="http://www.cryst.chem.uu.nl/platon/">Pluton</A> by A. L. Spek.
693Some attempt is made to get space group naming right, but there is
694no assurance of quality here.
695<a name="ExportSHELX"></a>
696<DT><B>SHELX .ins format</B><DD>
697This writes coordinates and symmetry, as used in the SHELX-97 program, and
698perhaps as used some other programs, such as CrystalMaker. In addition to
699exporing the coordinates and displacement parameters, the fields that
700are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the
701wavelength, included as the first number on the CELL "card", is set to the
702arbitrary value of 1/2.
703</DL></DL>
704
705<A name=tcltk>
706<H2>
707<A Href="http://www.tcl.tk">
708Tcl/Tk</A></H2>
709The
710<A Href="http://www.tcl.tk">
711Tcl/Tk program</A> is a platform-independent scripting language that is
712used to implement most of EXPGUI. This software is available for free
713and must be loaded in order to use EXPGUI. A somewhat out of date
714version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
715more recent versions can be used, but note that the BLT package (see
716below) is needed for all features of EXPGUI.
717While learning Tcl/Tk is a great thing to do, it is not a requirement
718for using or installing EXPGUI.
719
720<A name=blt>
721<H3>
722BLT Package</H3>
723<UL>
724The BLT graphics package is used by the WIDPLT, LIVEPLOT, BKGEDIT & 
725EXCLEDT routines. If the
726package can not be found by these routines, an error message,
727"Error -- Unable to load the BLT package", will be displayed. It is also
728possible for the package to be installed, but not configured properly.
729If this is the case, a message,
730"BLT Setup Error: could not access a Blt_ routine...", will be displayed.
731Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
732</UL>
733
734<A name=La>
735<H3>
736La (Linear Algebra) Package</H3>
737<UL>
738The
739<A HREF="http://www.hume.com">Hume
740</A>
741Linear Algebra Tcl Package,
742<A HREF="http://www.hume.com/la/la.html">
743La</A>,
744is used by the BKGEDIT
745routine to perform least-squares fitting. If the
746package can not be found, the routine cannot run.
747If the package cannot be found, a message,
748"Error -- Unable to load the La package" will be displayed. This
749should not happen, since the package is included with the EXPGUI files.
750So if get this error you probably have an incomplete installation.
751</UL>
752
753<A name=winexec>
754<H3>
755WINEXEC</H3>
756<UL>
757The WINEXEC package was needed under Windows-95 and its offspring
758(-98 and -ME). It was found in older versions of EXPGUI, but is no
759  longer included.
760</UL>
761
762<H2>
763Acknowledgments</H2>
764Praise to Larson and
765Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
766for Tcl/Tk,
767Przemek Klosowski
768for convincing me to learn Tcl/Tk
769and Jonathan Wasserman for helping me get this project started.
770Thanks also to
771Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
772bond-distance restraints module and the (soon to come) rigid body editor;
773Pamela Whitfield of the NRC (Canada) for writing large
774sections of the
775<A Href="expgui7.html">Preferential Orientation Panel</A>
776and the
777<A Href="expgui6.html">Profile Constraints panel</A>
778code and to John Cowgill for the "Export to GRACE" code.
779<P>
780<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
781GSAS</A>
782is written by Allen C. Larson and Robert B. Von Dreele while at
783Los Alamos National Laboratory. Problems, questions
784or kudos concerning GSAS should be sent to Robert B. Von Dreele at
785<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
786EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
787<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
788
789<P><hr><blockquote>
790<P>GSAS is Copyright, 1984-2000, by
791the Regents of the University of California.
792The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
793by the Los Alamos National Laboratory, which is operated by the University
794of California for the U.S. Department of Energy. The U.S. Government is
795licensed to use, reproduce, and distribute this software. Permission is
796granted to the public to copy and use this software without charge, provided
797that this notice and any statement of authorship are reproduced on all
798copies. Neither the Government nor the University makes any warranty, express
799or implied, or assumes any liability or responsibility for the use of this
800software.
801
802<P>EXPGUI was written by a U.S. Government employee, which means that
803EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write
804new sections and make them available to the rest of the world.
805
806<p>Neither the U.S. Government nor any author makes any warranty,
807expressed or implied, or assumes any liability or responsibility
808for the use of this information or the software described
809here.
810</blockquote>
811
812<P><hr WIDTH="100%">
813
814<P>
815<font size=-1><? lastmod(); ?> </font>
816<br>$Revision: 1157 $ $Date: 2011-07-26 17:47:57 +0000 (Tue, 26 Jul 2011) $
817</blockquote>
818</body>
819</html>
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