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scan .EXP files for GENLES blowups; update web pages

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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</A></TH>
62</TR>
63<TR>
64<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
65<TH><A Href="expguic.html">Menus</A></TH>
66<TH>&nbsp;</TH>
67</TR>
68<TR><TH BGCOLOR="#F0F0F0" rowspan=3>Utilities:</TH>
69<TH><A Href="liveplot.html">LIVEPLOT</A></TH>
70<TH><A Href="liveplot.html">BKGEDIT</A></TH>
71<TH><A Href="excledt.html">EXCLEDT</A></TH>
72</TR>
73<TR>
74<TH><A Href="#WIDPLT">WIDPLT</A></TH>
75<TH><A Href="#ABSPLT">ABSPLT</A></TH>
76<TH><A Href="#INSTEDIT">INSTEDIT</A></TH>
77</TR>
78<TR>
79<TH><A Href="gsas2cif.html">CIF export</A></TH>
80<TH>&nbsp;</TH>
81<TH>&nbsp;</TH>
82</TR>
83<TR><TH BGCOLOR="#F0F0F0" rowspan=2>Installation Notes:</TH>
84<TH><A Href="expgui_Unix_readme.html">Unix</A></TH>
85<TH><A Href="expgui_Win_readme.html">Windows</A></TH>
86<TH>
87<A Href="osx.html">Mac OS X</A></TH>
88</TR><TR>
89<TH><A Href="expgui_cfg.html">Customization</A></TH>
90<TH>&nbsp;</TH>
91<TH>&nbsp;</TH>
92</TR>
93<TR><TH BGCOLOR="#F0F0F0">Tutorials:</TH>
94<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
95NIST<BR>Neutron data</A></TH>
96<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
97<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
98</TR>
99<TR><TH BGCOLOR="#F0F0F0">Messages:</TH>
100<TH><A Href="expguierr.html#Error">Error</A></TH>
101<TH><A Href="expguierr.html#Warn">Warning</A></TH>
102<TH><A Href="expguierr.html#Info">Informational</A></TH>
103</TR>
104<TR><TH BGCOLOR="#F0F0F0">Other:</TH>
105<TH><A Href="expgui_intro.html">Introduction</A></TH>
106<TH><A Href="wishlist.html">Recent & Planned<BR>Improvements</A></TH>
107<TH><A Href="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
108<I>J. Appl. Cryst.</i><BR>article</A></TH>
109</TR>
110</TABLE><BR CLEAR=ALL>
111<P>
112<B>Citations.</B>
113The appropriate citations to be used for GSAS and EXPGUI are:
114<UL>
115<LI>
116A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
117Los Alamos National Laboratory Report LAUR 86-748 (2000).
118<A
119  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
120[link to PDF copy of manual]
121</A>
122<LI>
123B. H. Toby, <i>EXPGUI</i>, a graphical user interface for <i>GSAS</i>,
124<i>J. Appl. Cryst.</i> <b>34</b>, 210-213 (2001).
125<A HREF="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
126[link to PDF file]
127</A>
128</UL>
129<P>
130<B>Mailing List.</B>
131There is a mailing list for users of EXPGUI for news about about new
132features, bug fixes in EXPGUI, etc.
133<A href="http://www.aps.anl.gov/mailman/listinfo/expgui">Subscription info</A>
134<P>
135<hr>
136
137<h2>A. Experiment file editing</h2>
138<P>
139<DL><DL>
140When an experiment (.EXP) file is read, a copy is made in local
141computer memory. In most cases, values are changed in this
142"in memory" copy of the experiment file
143as this information is changed by the user on the screen.
144<img SRC="rederror.gif" align=LEFT BORDER=3 alt="EXPGUI Screen snapshot">
145<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
146If there is an error in the typed value, (for example if "1..0" is typed, or
147"1.5" is typed where an integer is expected), these values are
148not saved. In this case, the text is turned red, to indicate
149that an error is present, as shown in the figure to the left, where "90.000x"
150has been entered for alpha.
151The edited version of the experiment file is written back out to
152disk when the "File/Save" or "File/Save as"
153<A Href="expguic.html#1">menu bar options</A>
154are used. The File/Save operation is done automatically before any GSAS
155programs, such as GENLES or EXPEDT, are run.
156<P>
157<A name="badexp">
158The GSAS refinement program, GENLES, will sometimes "blow up", where the
159  program changes varied parameters to values very far from their
160  correct values. This occurs when parameters are highly correlated,
161  are refining to values that are not allowed, or some of the refined parameters have
162  very little impact on the quality of the fit. When this happens,
163  invalid values are written to the GSAS experiment file that contain
164  either asterisks (****) or the string "NAN" (not a number). Such
165  files cannot be used for additional GENLES runs.
166  <P>
167  When EXPGUI reads a .EXP file it scans it for evidence of a previous
168  failure of a GENLES refinement and warns if a problem is
169  noted. Please note that this scan is not perfect and occasionally
170  you may be warned in cases where the file is fine (if possible,
171  please send such .EXP file to Brian Toby so this scan can be improved.)
172  When such a "bad" .EXP file is located, one can "revert" to an
173  archived copy of a previous experiment file (with suffix .Oxx). This
174  can be done with the Revert menu item in the File menu. Note that
175clicking on a file in the file selection window causes it to be
176scanned and shows the status of that refinement. Also note that
177usually the last good archived file has settings that will produce the same bad
178refinement, so it is necessary to either revert further back, or to
179change the refinement options before running GENLES.
180<P>
181
182Since the GSAS experiment file is quite complex,
183values are grouped together by function, approximately
184following the outline of the EXPEDT program.
185Each set of values is given a
186"tabbed panel" on a window that has the appearance of a notebook (see below).
187<center><B>
188<br>The notebook panel tabs.
189<br><img SRC="panebar1.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
190</center></B>
191In some cases, where values are
192too numerous or complex to fit onto the notebook panel, one or more buttons
193may be present on a panel that will create a separate window,
194where the associated values can be modified.
195These values are not recorded in the
196"in memory" copy of the experiment file unless the "Save" button on this window
197is pressed. If "Cancel" is pressed, no changes are made.
198Each notebook panel is listed below with a link to the web page documenting
199that panel.
200
201<A Href="expgui1.html">
202<h3>A.1 Least Squares (LS) Controls Panel</h3>
203</A><A Href="expgui2.html">
204<h3>A.2 Phase Panel</h3> 
205</A><A Href="expgui3.html">
206<h3>A.3 Histogram panel</h3> 
207</A><A Href="expgui4.html">
208<h3>A.4 Scaling panel</h3> 
209</A><A Href="expgui5.html">
210<h3>A.5 Profile panel</h3> 
211</A><A Href="expgui6.html">
212<h3>A.6 Constraints panel</h3>
213</A><A Href="expgui7.html">
214<h3>A.7 Preferential Orientation Panel</h3>
215</A>
216<br clear=all>
217</DL></DL>
218<h2>B. Shortcuts</h2></a>
219<a name="multiplehistogram">
220<h3>B.1 Multiple Histogram Selection</h3></a>
221<DL><DL>
222This mode allows parameters to be changed for groups of
223histograms.
224When the "Multiple Histogram Selection" mode is off,
225it is possible to modify parameters
226and refinement flags for only a single histogram, but
227the other settings allow groups of histograms
228to be selected and modified.
229<A href="#mouseactions">(see Mouse Actions)</A>.
230<P>
231It does not make sense, however, to globally modify
232instrument-related parameters and flags for different
233histogram types.
234So global actions can be limited to a single class
235of histogram types (e.g. TOF, CW Neutron,...), which
236allows these parameters to be set for groups of
237similar histograms. Thus, if this mode is set to "All"
238the Histogram and Profile panels are disabled.
239<P>
240The setting for "Multiple Histogram Selection" mode is
241displayed above each histogram selection box and is
242selected using the "Multiple Hist. Selection" item on the
243Options menu to create a submenu or by clicking on the display.
244Note that another option in this "Multiple Hist. Selection"
245submenu is an option "Group Phases Together" that controls how
246EXPGUI treats phases having
247the same profile type that is used when multiple histograms are selected. If
248the "Group Phases Together" option is on, then the refinement flags for
249all phases with the same histogram types are grouped together, when possible.
250If this option is off, phases are treated separately.
251<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
252If the left mouse button is used to click on the selection mode display,
253the mode is cycled between the available modes. If the right mouse
254button is used, the mode is reset, to disable multiple histogram selection.
255<p>
256<a name="mouseactions">
257</DL></DL>
258<h3>B.2 Mouse Actions</h3></a>
259<DL><DL>
260A range of atoms or (in multiple selection mode) histograms may be
261selected by dragging (holding down) the left mouse button. It is also
262possible to select a range by using the Shift key with the left mouse
263button. To select or deselect individual entries, use the Control key
264with the left mouse button. Pressing the right mouse button selects all
265entries in a list.
266</DL></DL>
267
268<h2>C. Menu Commands and Programs</h2>
269<p>
270GSAS programs are invoked either through use of the menu bar
271<center><B>
272<br>The menu bar.
273<br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
274</center></B>
275or by "pressing" a button on the button bar. The button bar
276simply provides an easy way to access commonly used
277actions on the menu bar. Users can
278<A HREF="expgui_cfg.html">
279configure the menu bar</A> to include their own preferred actions and, with
280some knowledge of the program and Tcl/Tk,
281add their own commands to the menu bar or button bar.
282
283<center><B>
284<br>The button bar.
285<br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
286</center></B>
287
288<h3>Invoking of GSAS programs</h3>
289When GSAS programs are invoked, in most cases EXPGUI is suspended while
290the GSAS program is run in a terminal (or DOS) window. When the terminal
291window is closed, EXPGUI is restarted. If desired (see the
292<A Href="expguic.html#Autoicon">
293"Iconify during GSAS"</A>
294option) while this occurs, EXPGUI can be made into an icon
295to save screen space.
296<P>
297<img src="powpref4a.gif" align=left alt="EXPGUI Screen snapshot">
298Once the GSAS program has finished, if the program has modified
299the .EXP file,
300<a Href="expguierr.html#Overwrite">
301"File has been modified..."</a>message box
302similar to the one to the left is displayed (also see the more complete
303discussion on the <a Href="expguierr.html#Overwrite">messages page</A>.
304Note that this message can be avoided if the
305<A Href="expguic.html#Autoupdate">
306"Autoload EXP"</A>
307option is used.
308<BR clear=all>
309<P>
310Note that in both Windows-95 and Windows-NT, a file named <tt>EXPGUI.LCK</tt>
311is created while the GSAS program runs. The presence of this file is used
312to suspend the LIVEPLOT program, since LIVEPLOT has sometimes crashed
313when run at the same time as GENLES (no such problem has been seen in Unix).
314This file is deleted when the GSAS program completes.
315<P>
316<img src="lock.gif" align=left alt="EXPGUI Screen snapshot">
317In Windows-9x, the <a Href="expgui_Win_readme.html#Winexec">Winexec</a>
318package is used to execute a command that creates a DOS window.
319The GSAS programs are then run by a batch file in this DOS window.
320Due to limitations in Tcl/Tk & Windows, the DOS window runs independently
321of EXPGUI, so the lock file (<tt>EXPGUI.LCK</tt>) is also used to suspend
322EXPGUI. While EXPGUI is waiting, the
323<a Href="expguierr.html#lock">
324Please wait...
325</a>
326window shown to the left is displayed. When the GSAS program completes, the
327lock file is deleted, the window automatically disappears and EXPGUI resumes.
328Should a problem arise where the file is not deleted, EXPGUI can be resumed by
329pressing the "Continue" button.
330
331<BR clear=all>
332<h3>GSAS menus</h3>
333
334A description of the EXPGUI menus follows. Use the links to obtain
335more information, including a very
336brief description of the function of each menu option.
337Note that an option may appear under more than one menu.
338
339<DL><DL>
340
341<A Href="expguic.html#1">
342<H3>C.1 File Menu</H3>
343</A>
344<DL><DL>
345The options on the File menu as is the custom contains the commands
346for reading and writing experiment files, as well as starting, 
347ending and controlling the program.
348</DL></DL>
349
350<A Href="expguic.html#2">
351<h3>C.2 Options Menu</h3>
352</A>
353<DL><DL>
354This menu contains options that determine how EXPGUI runs.
355</DL></DL>
356
357<A Href="expguic.html#3">
358<h3>C.3 Powder Menu</h3>
359</A>
360<DL><DL>
361This menu contains links to GSAS programs used for powder diffraction
362analysis.
363</DL></DL>
364
365<A Href="expguic.html#4">
366<h3>C.4 Single Crystal Menu</h3>
367</A>
368<DL><DL>
369This menu contains links to GSAS programs used for
370single-crystal diffraction analysis.
371</DL></DL>
372
373<A Href="expguic.html#5">
374<h3>C.5 Graphics Menu</h3>
375</A>
376<DL><DL>
377This menu contains links to several GSAS and
378non-GSAS programs (such as LIVEPLOT and WIDPLT)
379used for graphical display of data and results.
380</DL></DL>
381
382<A Href="expguic.html#6">
383<h3>C.6 Results Menu</h3>
384</A>
385<DL><DL>
386This menu contains links to several GSAS and
387one non-GSAS (LSTVIEW)
388programs that are used for analysis of results.
389</DL></DL>
390
391<A Href="expguic.html#7">
392<h3>C.7 Calculations Menu</h3>
393</A>
394<DL><DL>
395This menu contains programs for useful crystallographic computations.
396</DL></DL>
397
398<A Href="expguic.html#8">
399<h3>C.8 Import/Export Menu</h3>
400</A>
401<DL><DL>
402This menu contains utilities for importing information into GSAS and
403exporting.
404</DL></DL>
405
406<h2>D. EXPGUI Utility Features</h2></a>
407EXPGUI adds a number of useful functions to the GSAS package. Some,
408but not all, of these features are graphically oriented.
409
410<br clear=all>
411<a name="LSTVIEW"></a>
412<H3>D.1 LSTVIEW</H3>
413
414<DL><DL>
415LSTVIEW is used to browse through the GSAS output listing. It is
416invoked by the "lstview" command in the GUI.
417<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
418to shorten the .LST file by removing older results from the beginning
419of the file.
420<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
421as a function of the cycle number.
422<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
423</DL></DL>
424
425<br clear=all>
426<H3>D.2 LIVEPLOT</H3>
427<DL><DL>
428<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated
429and difference plots for powder
430refinements. The plot is updated as the refinement progresses. The mouse can
431be used to zoom in on sections of the plot.
432LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
433<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
434<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
435LIVEPLOT can now be enhanced to superimpose peak locations for
436input unit cells or peaks from JCPDS/ICDD entries.
437See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
438further documentation, and in particular, the
439See the <A HREF="liveplot.html#customize">
440LIVEPLOT customization information</A>.
441<P>
442</DL></DL>
443<br clear=all>
444<H3>D.3 BKGEDIT</H3>
445<DL><DL>
446<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
447<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to
448fit a GSAS background function to a set of fixed
449background points that are input using the mouse.
450The mouse can also be used to zoom in on sections of the plot.
451BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
452<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
453See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
454further documentation.
455<P>
456</DL></DL>
457<br clear=all>
458<H3>D.4 EXCLEDT</H3>
459<DL><DL>
460<A HREF="excledt.html">EXCLEDT</A> is used to edit the
461range of data used from a histogram. The upper & lower ranges
462can be adjusted to include more data or use less. Also, it is
463possible to remove sections of the data (exclude regions) that
464have known systematic errors that cannot be modeled.
465EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
466<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
467See the <A HREF="excledt.html">EXECLEDT web page</A> for
468further documentation.
469<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
470EXCLEDT can now be used to change the simulation range for dummy histograms.
471<P>
472</DL></DL>
473
474<br clear=all>
475<a name="WIDPLT"></a>
476<a name="ABSPLT"></a>
477<H3>D.5 WIDPLT and ABSPLT</H3>
478<DL><DL>
479WIDPLT is used to plot the peak widths that are generated by a set
480of GSAS profile terms (constant wavelength equations, only).
481The parameters from each phase & histogram will be
482read from the .EXP file. It is also possible to input parameters manually.
483By creating a special file (<A HREF="expgui_cfg.html#import">
484described in the customization information</A>), it
485is possible to define reference curves
486that are loaded automatically for comparison.
487<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
488<P>
489ABSPLT is used to plot the absorption/reflectivity correction for a
490histogram. Values are loaded from the histogram(s), but can be edited manually.
491<P>
492WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
493</DL></DL>
494
495<br clear=all>
496<a name="INSTEDIT"></a>
497<H3>D.6 INSTEDIT</H3>
498<DL><DL>
499
500The INSTEDIT utility is used to edit or create an instrument parameter file.
501At this time it can only be used to edit files for
502constant-wavelength data. The utility can be started from the "Edit File"
503button in the
504<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
505the "instedit" option in the Powder menu. In the latter case, the user
506is given the chance to select an input file. If no file is selected,
507a new, empty, file is created. An example INSTEDIT window appears below.
508<P>
509<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
510<br clear=all>
511<P>
512Note that an instrument parameter file is used for a single type of data,
513as is selected by the menu button at the top of the window.
514However, multiple sets of parameters may be included in a
515file, to be used for example with differing operating modes for the
516instrument. Each set of parameters is called a bank in GSAS terminology.
517The radiobuttons on the top of the window are used to select
518which bank's parameters will be viewed.
519The "Add Bank" button adds an additional bank to the file.
520<P>
521The parameters are described briefly below, but in more depth in the
522GSAS manual (for example, pages 158-166 for profile parameters and
523page 221-223 for the details of the instrument parameter file.)
524<P>
525<H5>Bank Parameters</H5>
526The parameters available for each bank are:
527<DL>
528<DT>Title<DD>This probably has no real use.
529<DT>Instrument Name<DD>This string is used for creation of CIFs. It is
530best if this name is unique for each instrument.
531<DT>Primary Wavelength<DD>Note, this value is set automatically when
532the radiation type is selected
533<DT>Zero Correction<DD>This is the shift to be applied to 2theta
534values in centidegrees (degrees/100). This value should probably be
535near zero for Debye-Scherrer geometry instruments (unless known from
536calibration) and will almost always be fixed at zero
537for Bragg-Brentano geometry.
538<DT>
539</DL>
540<I>X-ray only parameters</I>
541<DL>
542<DT>Radiation type<DD>Used with x-rays. The value set here
543determines the anomolous dispersion (f' and f'' values) used.
544<DT>Monochromatic/Dual<DD>Used with x-rays. Set to dual when Kalpha1, Kalpha2
545radiation is present.
546<DT>Secondary Wavelength<DD>Used in "dual" wavelength mode.
547Note, this value is set automatically when the radiation type is selected
548<DT>Wavelength Ratio<DD>Typically 0.5 for typical K alpha 1,2 instruments,
549<<I>i.e.</I>when K alpha 1 is double the intensity of K alpha 2.
550<DT>Polarization Correction<DD>There are three modes for this, where the
551first two modes work similarly. The first mode ("Diffracted Beam")
552is most common. The third mode ("None") is used when
553Lorentz-polaraization corrections are applied to the data prior to its input
554to GSAS. See page 144-145 in the GSAS manual for more information on these
555corrections.
556<DT>Polarization Ratio<DD>In "Diffracted Beam" mode:
557typically 0.5 for lab instruments without monochromators and higher for
558instruments with a diffracted beam; the value depends on the monochromator
559take-off angle. Typically slightly below unity (0.9-0.98) for synchrotron
560instruments. Ask the instrument scientist for the appropriate value.
561</DL>
562<P>
563Each bank in the instrument parameter file has one or more sets of
564profile parameters associated. Set number 1 is the default loaded
565when a histogram is added. Increase the number of sets
566using the "Add profile" button. Select the optimal profile type
567for use with your data for this set, but for most flexibility, define
568default values for all useful profile types (type 1 is of use only for
569CW neutron work) and set these values from fitting a standard with
570minimal broodening. Note that profiles can be read from a GSAS experiment
571file using the "Import profile", which raises a dialog
572such as the one below.
573<P>
574<img SRC="instedit2.gif" align=RIGHT alt="EXPGUI Screen snapshot">
575<br clear=all>
576
577
578</DL></DL>
579
580<br clear=all>
581<a name="ConvertUnix"></a>
582<a name="ConvertWin"></a>
583<h3>D.7 File Conversions</h3> 
584<DL><DL>
585<P>
586GSAS data, experiment and instrument parameter files are
587expected to have a format with exactly 80 characters per line followed
588by a carriage return and then a linefeed (82 characters total per line).
589Files in this format can be read in "Direct Access" mode.
590Recent versions of GSAS will attempt to detect and repair files that
591are not in this format, but if the file is incorrectly formatted and
592by chance the length of the file is divisible by 82, the problem in the
593file format will not be detected.
594The Convert menu
595in can be used to convert files into the correct format.
596The original version of the
597file is retained and renamed.
598<P>
599</DL></DL>
600
601<br clear=all>
602<a name="Composition"></a>
603<h3>D.8 Compute Composition</h3> 
604<DL><DL>
605The composition box shows the unit cell and asymmetric unit composition
606for all phases in a material. Site multiplicities and occupancies are
607taken into account.
608</DL></DL>
609
610<br clear=all>
611<a name="DeleteHistoryRecords"></a>
612<h3>D.9 Delete History Records</h3> 
613<DL><DL>
614Every time a GSAS program (including EXPGUI) is run, an entry is added to
615the "history records" in the .EXP file. After 999 entries have been written,
616no more can be added to the file. Further, reading large numbers of history
617records can slow the GSAS programs
618(this is less of a problem on faster computers). For these reasons, it may be
619a good idea to prune the older history records from the file. If more than 100
620history records are found in an experiment file, EXPGUI suggests that the
621older history entries be deleted. Alternately the File/EraseHistory command
622can 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: 1115 $ $Date: 2011-02-27 03:47:37 +0000 (Sun, 27 Feb 2011) $
817</blockquote>
818</body>
819</html>
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