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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=4>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="expgui6R.html">Restraints</A></TH>
65<TH><A Href="expgui6A.html">Rigid Bodies</A></TH>
66<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
67</TR>
68<TR>
69<TH><A Href="expguic.html">Menus</A></TH>
70<TH>&nbsp;</TH>
71<TH>&nbsp;</TH>
72</TR>
73<TR><TH BGCOLOR="#F0F0F0" rowspan=3>Utilities:</TH>
74<TH><A Href="liveplot.html">LIVEPLOT</A></TH>
75<TH><A Href="liveplot.html">BKGEDIT</A></TH>
76<TH><A Href="excledt.html">EXCLEDT</A></TH>
77</TR>
78<TR>
79<TH><A Href="#WIDPLT">WIDPLT</A></TH>
80<TH><A Href="#ABSPLT">ABSPLT</A></TH>
81<TH><A Href="#INSTEDIT">INSTEDIT</A></TH>
82</TR>
83<TR>
84<TH><A Href="gsas2cif.html">CIF export</A></TH>
85<TH>&nbsp;</TH>
86<TH>&nbsp;</TH>
87</TR>
88<TR><TH BGCOLOR="#F0F0F0" rowspan=2>Installation Notes:</TH>
89<TH><A Href="expgui_Unix_readme.html">Unix</A></TH>
90<TH><A Href="expgui_Win_readme.html">Windows</A></TH>
91<TH>
92<A Href="osx.html">Mac OS X</A></TH>
93</TR><TR>
94<TH><A Href="expgui_cfg.html">Customization</A></TH>
95<TH>&nbsp;</TH>
96<TH>&nbsp;</TH>
97</TR>
98<TR><TH BGCOLOR="#F0F0F0">Tutorials:</TH>
99<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
100NIST<BR>Neutron data</A></TH>
101<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
102<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
103</TR>
104<TR><TH BGCOLOR="#F0F0F0">Messages:</TH>
105<TH><A Href="expguierr.html#Error">Error</A></TH>
106<TH><A Href="expguierr.html#Warn">Warning</A></TH>
107<TH><A Href="expguierr.html#Info">Informational</A></TH>
108</TR>
109<TR><TH BGCOLOR="#F0F0F0">Other:</TH>
110<TH><A Href="expgui_intro.html">Introduction</A></TH>
111<TH><A Href="wishlist.html">Recent & Planned<BR>Improvements</A></TH>
112<TH><A Href="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
113<I>J. Appl. Cryst.</i><BR>article</A></TH>
114</TR>
115</TABLE><BR CLEAR=ALL>
116<P>
117<B>Citations.</B>
118The appropriate citations to be used for GSAS and EXPGUI are:
119<UL>
120<LI>
121A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
122Los Alamos National Laboratory Report LAUR 86-748 (2000).
123<A
124  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
125[link to PDF copy of manual]
126</A>
127<LI>
128B. H. Toby, <i>EXPGUI</i>, a graphical user interface for <i>GSAS</i>,
129<i>J. Appl. Cryst.</i> <b>34</b>, 210-213 (2001).
130<A HREF="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
131[link to PDF file]
132</A>
133</UL>
134<P>
135<B>Mailing List.</B>
136There is a mailing list for users of EXPGUI for news about about new
137features, bug fixes in EXPGUI, etc.
138<A href="http://www.aps.anl.gov/mailman/listinfo/expgui">Subscription info</A>
139<P>
140<hr>
141
142<h2>A. Experiment file editing</h2>
143<P>
144<DL><DL>
145When an experiment (.EXP) file is read, a copy is made in local
146computer memory. In most cases, values are changed in this
147"in memory" copy of the experiment file
148as this information is changed by the user on the screen.
149<img SRC="rederror.gif" align=LEFT BORDER=3 alt="EXPGUI Screen snapshot">
150<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
151If there is an error in the typed value, (for example if "1..0" is typed, or
152"1.5" is typed where an integer is expected), these values are
153not saved. In this case, the text is turned red, to indicate
154that an error is present, as shown in the figure to the left, where "90.000x"
155has been entered for alpha.
156The edited version of the experiment file is written back out to
157disk when the "File/Save" or "File/Save as"
158<A Href="expguic.html#1">menu bar options</A>
159are used. The File/Save operation is done automatically before any GSAS
160programs, such as GENLES or EXPEDT, are run.
161<P>
162<A name="badexp">
163The GSAS refinement program, GENLES, will sometimes "blow up", where the
164  program changes varied parameters to values very far from their
165  correct values. This occurs when parameters are highly correlated,
166  are refining to values that are not allowed, or some of the refined parameters have
167  very little impact on the quality of the fit. When this happens,
168  invalid values are written to the GSAS experiment file that contain
169  either asterisks (****) or the string "NAN" (not a number). Such
170  files cannot be used for additional GENLES runs.
171  <P>
172  When EXPGUI reads a .EXP file it scans it for evidence of a previous
173  failure of a GENLES refinement and warns if a problem is
174  noted. Please note that this scan is not perfect and occasionally
175  you may be warned in cases where the file is fine (if possible,
176  please send such .EXP file to Brian Toby so this scan can be improved.)
177  When such a "bad" .EXP file is located, one can "revert" to an
178  archived copy of a previous experiment file (with suffix .Oxx). This
179  can be done with the Revert menu item in the File menu. Note that
180clicking on a file in the file selection window causes it to be
181scanned and shows the status of that refinement. Also note that
182usually the last good archived file has settings that will produce the same bad
183refinement, so it is necessary to either revert further back, or to
184change the refinement options before running GENLES.
185<P>
186
187Since the GSAS experiment file is quite complex,
188values are grouped together by function, approximately
189following the outline of the EXPEDT program.
190Each set of values is given a
191"tabbed panel" on a window that has the appearance of a notebook (see below).
192<center><B>
193<br>The notebook panel tabs.
194<br><img SRC="panebar1.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
195</center></B>
196In some cases, where values are
197too numerous or complex to fit onto the notebook panel, one or more buttons
198may be present on a panel that will create a separate window,
199where the associated values can be modified.
200These values are not recorded in the
201"in memory" copy of the experiment file unless the "Save" button on this window
202is pressed. If "Cancel" is pressed, no changes are made.
203Each notebook panel is listed below with a link to the web page documenting
204that panel.
205
206<A Href="expgui1.html">
207<h3>A.1 Least Squares (LS) Controls Panel</h3>
208</A><A Href="expgui2.html">
209<h3>A.2 Phase Panel</h3> 
210</A><A Href="expgui3.html">
211<h3>A.3 Histogram panel</h3> 
212</A><A Href="expgui4.html">
213<h3>A.4 Scaling panel</h3> 
214</A><A Href="expgui5.html">
215<h3>A.5 Profile panel</h3> 
216</A><A Href="expgui6.html">
217<h3>A.6 Constraints panel</h3>
218</A><A Href="expgui7.html">
219<h3>A.7 Preferential Orientation Panel</h3>
220</A>
221<br clear=all>
222</DL></DL>
223<h2>B. Shortcuts</h2></a>
224<a name="multiplehistogram">
225<h3>B.1 Multiple Histogram Selection</h3></a>
226<DL><DL>
227This mode allows parameters to be changed for groups of
228histograms.
229When the "Multiple Histogram Selection" mode is off,
230it is possible to modify parameters
231and refinement flags for only a single histogram, but
232the other settings allow groups of histograms
233to be selected and modified.
234<A href="#mouseactions">(see Mouse Actions)</A>.
235<P>
236It does not make sense, however, to globally modify
237instrument-related parameters and flags for different
238histogram types.
239So global actions can be limited to a single class
240of histogram types (e.g. TOF, CW Neutron,...), which
241allows these parameters to be set for groups of
242similar histograms. Thus, if this mode is set to "All"
243the Histogram and Profile panels are disabled.
244<P>
245The setting for "Multiple Histogram Selection" mode is
246displayed above each histogram selection box and is
247selected using the "Multiple Hist. Selection" item on the
248Options menu to create a submenu or by clicking on the display.
249Note that another option in this "Multiple Hist. Selection"
250submenu is an option "Group Phases Together" that controls how
251EXPGUI treats phases having
252the same profile type that is used when multiple histograms are selected. If
253the "Group Phases Together" option is on, then the refinement flags for
254all phases with the same histogram types are grouped together, when possible.
255If this option is off, phases are treated separately.
256<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
257If the left mouse button is used to click on the selection mode display,
258the mode is cycled between the available modes. If the right mouse
259button is used, the mode is reset, to disable multiple histogram selection.
260<p>
261<a name="mouseactions">
262</DL></DL>
263<h3>B.2 Mouse Actions</h3></a>
264<DL><DL>
265A range of atoms or (in multiple selection mode) histograms may be
266selected by dragging (holding down) the left mouse button. It is also
267possible to select a range by using the Shift key with the left mouse
268button. To select or deselect individual entries, use the Control key
269with the left mouse button. Pressing the right mouse button selects all
270entries in a list.
271</DL></DL>
272
273<h2>C. Menu Commands and Programs</h2>
274<p>
275GSAS programs are invoked either through use of the menu bar
276<center><B>
277<br>The menu bar.
278<br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
279</center></B>
280or by "pressing" a button on the button bar. The button bar
281simply provides an easy way to access commonly used
282actions on the menu bar. Users can
283<A HREF="expgui_cfg.html">
284configure the menu bar</A> to include their own preferred actions and, with
285some knowledge of the program and Tcl/Tk,
286add their own commands to the menu bar or button bar.
287
288<center><B>
289<br>The button bar.
290<br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
291</center></B>
292
293<h3>Invoking of GSAS programs</h3>
294When GSAS programs are invoked, in most cases EXPGUI is suspended while
295the GSAS program is run in a terminal (or DOS) window. When the terminal
296window is closed, EXPGUI is restarted. If desired (see the
297<A Href="expguic.html#Autoicon">
298"Iconify during GSAS"</A>
299option) while this occurs, EXPGUI can be made into an icon
300to save screen space.
301<P>
302<img src="powpref4a.gif" align=left alt="EXPGUI Screen snapshot">
303Once the GSAS program has finished, if the program has modified
304the .EXP file,
305<a Href="expguierr.html#Overwrite">
306"File has been modified..."</a>message box
307similar to the one to the left is displayed (also see the more complete
308discussion on the <a Href="expguierr.html#Overwrite">messages page</A>.
309Note that this message can be avoided if the
310<A Href="expguic.html#Autoupdate">
311"Autoload EXP"</A>
312option is used.
313<BR clear=all>
314<P>
315Note that in both Windows-95 and Windows-NT, a file named <tt>EXPGUI.LCK</tt>
316is created while the GSAS program runs. The presence of this file is used
317to suspend the LIVEPLOT program, since LIVEPLOT has sometimes crashed
318when run at the same time as GENLES (no such problem has been seen in Unix).
319This file is deleted when the GSAS program completes.
320<P>
321<img src="lock.gif" align=left alt="EXPGUI Screen snapshot">
322In Windows-9x, the <a Href="expgui_Win_readme.html#Winexec">Winexec</a>
323package is used to execute a command that creates a DOS window.
324The GSAS programs are then run by a batch file in this DOS window.
325Due to limitations in Tcl/Tk & Windows, the DOS window runs independently
326of EXPGUI, so the lock file (<tt>EXPGUI.LCK</tt>) is also used to suspend
327EXPGUI. While EXPGUI is waiting, the
328<a Href="expguierr.html#lock">
329Please wait...
330</a>
331window shown to the left is displayed. When the GSAS program completes, the
332lock file is deleted, the window automatically disappears and EXPGUI resumes.
333Should a problem arise where the file is not deleted, EXPGUI can be resumed by
334pressing the "Continue" button.
335
336<BR clear=all>
337<h3>GSAS menus</h3>
338
339A description of the EXPGUI menus follows. Use the links to obtain
340more information, including a very
341brief description of the function of each menu option.
342Note that an option may appear under more than one menu.
343
344<DL><DL>
345
346<A Href="expguic.html#1">
347<H3>C.1 File Menu</H3>
348</A>
349<DL><DL>
350The options on the File menu as is the custom contains the commands
351for reading and writing experiment files, as well as starting, 
352ending and controlling the program.
353</DL></DL>
354
355<A Href="expguic.html#2">
356<h3>C.2 Options Menu</h3>
357</A>
358<DL><DL>
359This menu contains options that determine how EXPGUI runs.
360</DL></DL>
361
362<A Href="expguic.html#3">
363<h3>C.3 Powder Menu</h3>
364</A>
365<DL><DL>
366This menu contains links to GSAS programs used for powder diffraction
367analysis.
368</DL></DL>
369
370<A Href="expguic.html#4">
371<h3>C.4 Single Crystal Menu</h3>
372</A>
373<DL><DL>
374This menu contains links to GSAS programs used for
375single-crystal diffraction analysis.
376</DL></DL>
377
378<A Href="expguic.html#5">
379<h3>C.5 Graphics Menu</h3>
380</A>
381<DL><DL>
382This menu contains links to several GSAS and
383non-GSAS programs (such as LIVEPLOT and WIDPLT)
384used for graphical display of data and results.
385</DL></DL>
386
387<A Href="expguic.html#6">
388<h3>C.6 Results Menu</h3>
389</A>
390<DL><DL>
391This menu contains links to several GSAS and
392one non-GSAS (LSTVIEW)
393programs that are used for analysis of results.
394</DL></DL>
395
396<A Href="expguic.html#7">
397<h3>C.7 Calculations Menu</h3>
398</A>
399<DL><DL>
400This menu contains programs for useful crystallographic computations.
401</DL></DL>
402
403<A Href="expguic.html#8">
404<h3>C.8 Import/Export Menu</h3>
405</A>
406<DL><DL>
407This menu contains utilities for importing information into GSAS and
408exporting.
409</DL></DL>
410
411<h2>D. EXPGUI Utility Features</h2></a>
412EXPGUI adds a number of useful functions to the GSAS package. Some,
413but not all, of these features are graphically oriented.
414
415<br clear=all>
416<a name="LSTVIEW"></a>
417<H3>D.1 LSTVIEW</H3>
418
419<DL><DL>
420LSTVIEW is used to browse through the GSAS output listing. It is
421invoked by the "lstview" command in the GUI.
422<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
423to shorten the .LST file by removing older results from the beginning
424of the file.
425<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
426as a function of the cycle number.
427<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
428</DL></DL>
429
430<br clear=all>
431<H3>D.2 LIVEPLOT</H3>
432<DL><DL>
433<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated
434and difference plots for powder
435refinements. The plot is updated as the refinement progresses. The mouse can
436be used to zoom in on sections of the plot.
437LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
438<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
439<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
440LIVEPLOT can now be enhanced to superimpose peak locations for
441input unit cells or peaks from JCPDS/ICDD entries.
442See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
443further documentation, and in particular, the
444See the <A HREF="liveplot.html#customize">
445LIVEPLOT customization information</A>.
446<P>
447</DL></DL>
448<br clear=all>
449<H3>D.3 BKGEDIT</H3>
450<DL><DL>
451<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
452<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to
453fit a GSAS background function to a set of fixed
454background points that are input using the mouse.
455The mouse can also be used to zoom in on sections of the plot.
456BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
457<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
458See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
459further documentation.
460<P>
461</DL></DL>
462<br clear=all>
463<H3>D.4 EXCLEDT</H3>
464<DL><DL>
465<A HREF="excledt.html">EXCLEDT</A> is used to edit the
466range of data used from a histogram. The upper & lower ranges
467can be adjusted to include more data or use less. Also, it is
468possible to remove sections of the data (exclude regions) that
469have known systematic errors that cannot be modeled.
470EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
471<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
472See the <A HREF="excledt.html">EXECLEDT web page</A> for
473further documentation.
474<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
475EXCLEDT can now be used to change the simulation range for dummy histograms.
476<P>
477</DL></DL>
478
479<br clear=all>
480<a name="WIDPLT"></a>
481<a name="ABSPLT"></a>
482<H3>D.5 WIDPLT and ABSPLT</H3>
483<DL><DL>
484WIDPLT is used to plot the peak widths that are generated by a set
485of GSAS profile terms (constant wavelength equations, only).
486The parameters from each phase & histogram will be
487read from the .EXP file. It is also possible to input parameters manually.
488By creating a special file (<A HREF="expgui_cfg.html#import">
489described in the customization information</A>), it
490is possible to define reference curves
491that are loaded automatically for comparison.
492<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
493<P>
494ABSPLT is used to plot the absorption/reflectivity correction for a
495histogram. Values are loaded from the histogram(s), but can be edited manually.
496<P>
497WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
498</DL></DL>
499
500<br clear=all>
501<a name="INSTEDIT"></a>
502<H3>D.6 INSTEDIT</H3>
503<DL><DL>
504
505The INSTEDIT utility is used to edit or create an instrument parameter file.
506The utility can be started from the "Edit File" button in the
507<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
508the "instedit" option in the Powder menu. Alternately, to create a new
509  instrument parameter file, choose Powder menu option "New InstParm
510  file". (It is also possible
511  to create a new file using the standard instedit by selecting
512  "Cancel" when asked for an input file.)
513An example INSTEDIT window appears below.
514<P>
515<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
516<br clear=all>
517<P>
518Note that an instrument parameter file is used for a single type of data,
519as is selected by the menu button at the top of the window.
520However, multiple sets of parameters may be included in a
521file, to be used for example with differing operating modes for the
522instrument. Each set of parameters is called a bank in GSAS terminology.
523The radiobuttons on the top of the window are used to select
524which bank's parameters will be viewed.
525The "Add Bank" button adds an additional bank to the file.
526<P>
527The parameters are described briefly below, but in more depth in the
528GSAS manual (for example, pages 158-166 for profile parameters and
529page 221-223 for the details of the instrument parameter file.)
530<P>
531<H5>Bank Parameters</H5>
532The parameters available for each bank are:
533<DL>
534<DT>Title<DD>This probably has no real use.
535<DT>Instrument Name<DD>This string is used for creation of CIFs. It is
536best if this name is unique for each instrument.
537<DT>Primary Wavelength<DD>Note, this value is set automatically when
538the radiation type is selected
539<DT>Zero Correction<DD>This is the shift to be applied to 2theta
540values in centidegrees (degrees/100). This value should probably be
541near zero for Debye-Scherrer geometry instruments (unless known from
542calibration) and will almost always be fixed at zero
543for Bragg-Brentano geometry.
544<DT>
545</DL>
546<I>X-ray only parameters</I>
547<DL>
548<DT>Radiation type<DD>Used with x-rays. The value set here
549determines the anomolous dispersion (f' and f'' values) used.
550<DT>Monochromatic/Dual<DD>Used with x-rays. Set to dual when Kalpha1, Kalpha2
551radiation is present.
552<DT>Secondary Wavelength<DD>Used in "dual" wavelength mode.
553Note, this value is set automatically when the radiation type is selected
554<DT>Wavelength Ratio<DD>Typically 0.5 for typical K alpha 1,2 instruments,
555<<I>i.e.</I>when K alpha 1 is double the intensity of K alpha 2.
556<DT>Polarization Correction<DD>There are three modes for this, where the
557first two modes work similarly. The first mode ("Diffracted Beam")
558is most common. The third mode ("None") is used when
559Lorentz-polaraization corrections are applied to the data prior to its input
560to GSAS. See page 144-145 in the GSAS manual for more information on these
561corrections.
562<DT>Polarization Ratio<DD>In "Diffracted Beam" mode:
563typically 0.5 for lab instruments without monochromators and higher for
564instruments with a diffracted beam; the value depends on the monochromator
565take-off angle. Typically slightly below unity (0.9-0.98) for synchrotron
566instruments. Ask the instrument scientist for the appropriate value.
567</DL>
568<P>
569Each bank in the instrument parameter file has one or more sets of
570profile parameters associated. Set number 1 is the default loaded
571when a histogram is added. Increase the number of sets
572using the "Add profile" button. Select the optimal profile type
573for use with your data for this set, but for most flexibility, define
574default values for all useful profile types (type 1 is of use only for
575CW neutron work) and set these values from fitting a standard with
576minimal broodening. Note that profiles can be read from a GSAS experiment
577file using the "Import profile", which raises a dialog
578such as the one below.
579<P>
580<img SRC="instedit2.gif" align=RIGHT alt="EXPGUI Screen snapshot">
581<br clear=all>
582
583
584</DL></DL>
585
586<br clear=all>
587<a name="ConvertUnix"></a>
588<a name="ConvertWin"></a>
589<h3>D.7 File Conversions</h3> 
590<DL><DL>
591<P>
592GSAS data, experiment and instrument parameter files are
593expected to have a format with exactly 80 characters per line followed
594by a carriage return and then a linefeed (82 characters total per line).
595Files in this format can be read in "Direct Access" mode.
596Recent versions of GSAS will attempt to detect and repair files that
597are not in this format, but if the file is incorrectly formatted and
598by chance the length of the file is divisible by 82, the problem in the
599file format will not be detected.
600The Convert menu
601in can be used to convert files into the correct format.
602The original version of the
603file is retained and renamed.
604<P>
605</DL></DL>
606
607<br clear=all>
608<a name="Composition"></a>
609<h3>D.8 Compute Composition</h3> 
610<DL><DL>
611The composition box shows the unit cell and asymmetric unit composition
612for all phases in a material. Site multiplicities and occupancies are
613taken into account.
614</DL></DL>
615
616<br clear=all>
617<a name="DeleteHistoryRecords"></a>
618<h3>D.9 Delete History Records</h3> 
619<DL><DL>
620Every time a GSAS program (including EXPGUI) is run, an entry is added to
621the "history records" in the .EXP file. After 999 entries have been written,
622no more can be added to the file. Further, reading large numbers of history
623records can slow the GSAS programs
624(this is less of a problem on faster computers). For these reasons, it may be
625a good idea to prune the older history records from the file.
626The File/EraseHistory command can be used to invoke the this option.
627<P>
628On the dialog the number of history records to be retained is specified.
629Also, after records have been deleted, the remaining records can be renumbered
630starting with 1, so that the 999 record limit is not reached.
631</DL></DL>
632
633<h2>E. Coordinate Export & Import Features</h2></a>
634EXPGUI can be used to read coordinates in formats not
635supported in GSAS. Coordinates can also be exported in a variety of
636formats as well.
637
638<A name="import">
639<h3>E.1 Coordinate Import Formats</h3> 
640Coordinates can be imported using the
641<A HREF="expgui2.html#addphase">"Add Phase"</A>,
642<A HREF="expgui2.html#addatoms">"Add Atoms"</A> or
643<A HREF="expgui2.html#replacephase">"Replace Phase"</A> 
644buttons on the <A HREF="expgui2.html">Phase Panel</A>, by choosing
645the format from the pull-down list to the right of the
646"Import atoms/phase from" button. The formats currently supported
647are listed below.
648Note that it is relatively easy to add new routines for
649importing coordinates;
650see the <A HREF="expgui_cfg.html#import">
651customization information</A> for more details.
652<DL><DL>
653<DT><B>Crystallographic Information File (CIF)</B><DD>
654Coordinates can be read from single block or multiblock CIF files
655using DDL1. If more than one block containing coordinates is found in the
656file, a CIF browser is available to help select the desired block.
657<DT><B>PowderCell .CEL files</B><DD>
658This format is used by the DOS and Windows PowderCell program, a valuable
659program for the transformation and visualization of structures.
660<DT><B>GSAS .EXP files</B><DD>
661This routine is used to copy coordinates, unit cell parameters and space group
662information from other GSAS experiment (.EXP) files.
663<DT><B>MSI .xtl format</B><DD>
664<a HREF="#ExportMSI">see below</a>
665<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
666<a HREF="#ExportSPF">see below</a>
667
668</DL></DL>
669
670<A name="export">
671<h3>E.2 Coordinate Export Formats</h3> 
672Coordinates can be written using the Import/Export=>"Coord Export" menu.
673Note that contents of the submenu will depend on the
674number of export routines found in the EXPGUI directory when the menu
675is first created, thus it is relatively easy to add new routines for
676importing coordinates;
677see the <A HREF="expgui_cfg.html#export">
678customization information</A> for more details.
679<DL><DL>
680<DT><B>Crystallographic Information File (CIF)</B><DD>
681Powder Diffraction Crystallographic Information files (pdCIFs) can
682be created by the GSAS2CIF program. The GSAS2CIF menu item
683invokes this program.
684<a name="ExportMSI"></a>
685<DT><B>MSI .xtl format</B><DD>
686This writes a .xtl file, as is used in Insight-II and
687Cerius2 (Molecular Simulations, Inc.). The routine
688attempts to convert GSAS space group names properly, as well as
689correctly label "Origin 2" setting, however, the naming conversion
690will not work for all valid GSAS space groups. Some effort may be needed
691by the user to get everything worked out correctly.
692<a name="ExportSPF"></a>
693<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
694This writes a .spf file, as used in
695<A HREF="http://www.cryst.chem.uu.nl/platon/">Platon</A> and
696<A HREF="http://www.cryst.chem.uu.nl/platon/">Pluton</A> by A. L. Spek.
697Some attempt is made to get space group naming right, but there is
698no assurance of quality here.
699<a name="ExportSHELX"></a>
700<DT><B>SHELX .ins format</B><DD>
701This writes coordinates and symmetry, as used in the SHELX-97 program, and
702perhaps as used some other programs, such as CrystalMaker. In addition to
703exporing the coordinates and displacement parameters, the fields that
704are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the
705wavelength, included as the first number on the CELL "card", is set to the
706arbitrary value of 1/2.
707</DL></DL>
708
709<A name=tcltk>
710<H2>
711<A Href="http://www.tcl.tk">
712Tcl/Tk</A></H2>
713The
714<A Href="http://www.tcl.tk">
715Tcl/Tk program</A> is a platform-independent scripting language that is
716used to implement most of EXPGUI. This software is available for free
717and must be loaded in order to use EXPGUI. A somewhat out of date
718version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
719more recent versions can be used, but note that the BLT package (see
720below) is needed for all features of EXPGUI.
721While learning Tcl/Tk is a great thing to do, it is not a requirement
722for using or installing EXPGUI.
723
724<A name=blt>
725<H3>
726BLT Package</H3>
727<UL>
728The BLT graphics package is used by the WIDPLT, LIVEPLOT, BKGEDIT & 
729EXCLEDT routines. If the
730package can not be found by these routines, an error message,
731"Error -- Unable to load the BLT package", will be displayed. It is also
732possible for the package to be installed, but not configured properly.
733If this is the case, a message,
734"BLT Setup Error: could not access a Blt_ routine...", will be displayed.
735Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
736</UL>
737
738<A name=La>
739<H3>
740La (Linear Algebra) Package</H3>
741<UL>
742The
743<A HREF="http://www.hume.com">Hume
744</A>
745Linear Algebra Tcl Package,
746<A HREF="http://www.hume.com/la/la.html">
747La</A>,
748is used by the BKGEDIT
749routine to perform least-squares fitting. If the
750package can not be found, the routine cannot run.
751If the package cannot be found, a message,
752"Error -- Unable to load the La package" will be displayed. This
753should not happen, since the package is included with the EXPGUI files.
754So if get this error you probably have an incomplete installation.
755</UL>
756
757<A name=winexec>
758<H3>
759WINEXEC</H3>
760<UL>
761The WINEXEC package was needed under Windows-95 and its offspring
762(-98 and -ME). It was found in older versions of EXPGUI, but is no
763  longer included.
764</UL>
765
766<H2>
767Acknowledgments</H2>
768Praise to Larson and
769Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
770for Tcl/Tk,
771Przemek Klosowski
772for convincing me to learn Tcl/Tk
773and Jonathan Wasserman for helping me get this project started.
774Thanks also to
775Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
776bond-distance restraints module and the (soon to come) rigid body editor;
777Pamela Whitfield of the NRC (Canada) for writing large
778sections of the
779<A Href="expgui7.html">Preferential Orientation Panel</A>
780and the
781<A Href="expgui6.html">Profile Constraints panel</A>
782code and to John Cowgill for the "Export to GRACE" code.
783<P>
784<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
785GSAS</A>
786is written by Allen C. Larson and Robert B. Von Dreele while at
787Los Alamos National Laboratory. Problems, questions
788or kudos concerning GSAS should be sent to Robert B. Von Dreele at
789<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
790EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
791<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
792
793<P><hr><blockquote>
794<P>GSAS is Copyright, 1984-2000, by
795the Regents of the University of California.
796The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
797by the Los Alamos National Laboratory, which is operated by the University
798of California for the U.S. Department of Energy. The U.S. Government is
799licensed to use, reproduce, and distribute this software. Permission is
800granted to the public to copy and use this software without charge, provided
801that this notice and any statement of authorship are reproduced on all
802copies. Neither the Government nor the University makes any warranty, express
803or implied, or assumes any liability or responsibility for the use of this
804software.
805
806<P>EXPGUI was written by a U.S. Government employee, which means that
807EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write
808new sections and make them available to the rest of the world.
809
810<p>Neither the U.S. Government nor any author makes any warranty,
811expressed or implied, or assumes any liability or responsibility
812for the use of this information or the software described
813here.
814</blockquote>
815
816<P><hr WIDTH="100%">
817
818<P>
819<font size=-1><? lastmod(); ?> </font>
820<br>$Revision: 1217 $ $Date: 2012-08-19 18:14:18 +0000 (Sun, 19 Aug 2012) $
821</blockquote>
822</body>
823</html>
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