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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.xray.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.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows">
27Windows</A>,
28<A HREF="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/InstallOSX">
29Mac (OS X)</A>, or
30<A HREF="https://subversion.xray.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.xray.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" rowspan=2>Tutorials:</TH>
99<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
100NIST<BR>Neutron data</A></TH>
101<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
102<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
103</TR>
104<TR>
105<TH><A Href="https://subversion.xray.aps.anl.gov/EXPGUI/tutorials/tutorial4/FapatitleExample.htm">
106Lab x-ray data<BR>(Fluoroapatite)</A></TH>
107<TH>&nbsp;</TH>
108<TH>&nbsp;</TH>
109</TR>
110<TR><TH BGCOLOR="#F0F0F0">Messages:</TH>
111<TH><A Href="expguierr.html#Error">Error</A></TH>
112<TH><A Href="expguierr.html#Warn">Warning</A></TH>
113<TH><A Href="expguierr.html#Info">Informational</A></TH>
114</TR>
115<TR><TH BGCOLOR="#F0F0F0">Other:</TH>
116<TH><A Href="expgui_intro.html">Introduction</A></TH>
117<TH><A Href="wishlist.html">Recent & Planned<BR>Improvements</A></TH>
118<TH><A Href="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
119<I>J. Appl. Cryst.</i><BR>article</A></TH>
120</TR>
121</TABLE><BR CLEAR=ALL>
122<P>
123<B>Citations.</B>
124The appropriate citations to be used for GSAS and EXPGUI are:
125<UL>
126<LI>
127A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
128Los Alamos National Laboratory Report LAUR 86-748 (2000).
129<A
130  HREF="https://subversion.xray.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
131[link to PDF copy of manual]
132</A>
133<LI>
134B. H. Toby, <i>EXPGUI</i>, a graphical user interface for <i>GSAS</i>,
135<i>J. Appl. Cryst.</i> <b>34</b>, 210-213 (2001).
136<A HREF="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
137[link to PDF file]
138</A>
139</UL>
140<P>
141<B>Mailing List.</B>
142There is a mailing list for users of EXPGUI for news about about new
143features, bug fixes in EXPGUI, etc.
144<A href="http://www.aps.anl.gov/mailman/listinfo/expgui">Subscription info</A>
145<P>
146<hr>
147
148<h2>A. Experiment file editing</h2>
149<P>
150<DL><DL>
151When an experiment (.EXP) file is read, a copy is made in local
152computer memory. In most cases, values are changed in this
153"in memory" copy of the experiment file
154as this information is changed by the user on the screen.
155<img SRC="rederror.gif" align=LEFT BORDER=3 alt="EXPGUI Screen snapshot">
156<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
157If there is an error in the typed value, (for example if "1..0" is typed, or
158"1.5" is typed where an integer is expected), these values are
159not saved. In this case, the text is turned red, to indicate
160that an error is present, as shown in the figure to the left, where "90.000x"
161has been entered for alpha.
162The edited version of the experiment file is written back out to
163disk when the "File/Save" or "File/Save as"
164<A Href="expguic.html#1">menu bar options</A>
165are used. The File/Save operation is done automatically before any GSAS
166programs, such as GENLES or EXPEDT, are run.
167<P>
168<A name="badexp">
169The GSAS refinement program, GENLES, will sometimes "blow up", where the
170  program changes varied parameters to values very far from their
171  correct values. This occurs when parameters are highly correlated,
172  are refining to values that are not allowed, or some of the refined parameters have
173  very little impact on the quality of the fit. When this happens,
174  invalid values are written to the GSAS experiment file that contain
175  either asterisks (****) or the string "NAN" (not a number). Such
176  files cannot be used for additional GENLES runs.
177  <P>
178  When EXPGUI reads a .EXP file it scans it for evidence of a previous
179  failure of a GENLES refinement and warns if a problem is
180  noted. Please note that this scan is not perfect and occasionally
181  you may be warned in cases where the file is fine (if possible,
182  please send such .EXP file to Brian Toby so this scan can be improved.)
183  When such a "bad" .EXP file is located, one can "revert" to an
184  archived copy of a previous experiment file (with suffix .Oxx). This
185  can be done with the Revert menu item in the File menu. Note that
186clicking on a file in the file selection window causes it to be
187scanned and shows the status of that refinement. Also note that
188usually the last good archived file has settings that will produce the same bad
189refinement, so it is necessary to either revert further back, or to
190change the refinement options before running GENLES.
191<P>
192
193Since the GSAS experiment file is quite complex,
194values are grouped together by function, approximately
195following the outline of the EXPEDT program.
196Each set of values is given a
197"tabbed panel" on a window that has the appearance of a notebook (see below).
198<center><B>
199<br>The notebook panel tabs.
200<br><img SRC="panebar1.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
201</center></B>
202In some cases, where values are
203too numerous or complex to fit onto the notebook panel, one or more buttons
204may be present on a panel that will create a separate window,
205where the associated values can be modified.
206These values are not recorded in the
207"in memory" copy of the experiment file unless the "Save" button on this window
208is pressed. If "Cancel" is pressed, no changes are made.
209Each notebook panel is listed below with a link to the web page documenting
210that panel.
211
212<A Href="expgui1.html">
213<h3>A.1 Least Squares (LS) Controls Panel</h3>
214</A><A Href="expgui2.html">
215<h3>A.2 Phase Panel</h3> 
216</A><A Href="expgui3.html">
217<h3>A.3 Histogram panel</h3> 
218</A><A Href="expgui4.html">
219<h3>A.4 Scaling panel</h3> 
220</A><A Href="expgui5.html">
221<h3>A.5 Profile panel</h3> 
222</A><A Href="expgui6.html">
223<h3>A.6 Constraints panel</h3>
224</A><A Href="expgui7.html">
225<h3>A.7 Preferential Orientation Panel</h3>
226</A>
227<br clear=all>
228</DL></DL>
229<h2>B. Shortcuts</h2></a>
230<a name="multiplehistogram">
231<h3>B.1 Multiple Histogram Selection</h3></a>
232<DL><DL>
233This mode allows parameters to be changed for groups of
234histograms.
235When the "Multiple Histogram Selection" mode is off,
236it is possible to modify parameters
237and refinement flags for only a single histogram, but
238the other settings allow groups of histograms
239to be selected and modified.
240<A href="#mouseactions">(see Mouse Actions)</A>.
241<P>
242It does not make sense, however, to globally modify
243instrument-related parameters and flags for different
244histogram types.
245So global actions can be limited to a single class
246of histogram types (e.g. TOF, CW Neutron,...), which
247allows these parameters to be set for groups of
248similar histograms. Thus, if this mode is set to "All"
249the Histogram and Profile panels are disabled.
250<P>
251The setting for "Multiple Histogram Selection" mode is
252displayed above each histogram selection box and is
253selected using the "Multiple Hist. Selection" item on the
254Options menu to create a submenu or by clicking on the display.
255Note that another option in this "Multiple Hist. Selection"
256submenu is an option "Group Phases Together" that controls how
257EXPGUI treats phases having
258the same profile type that is used when multiple histograms are selected. If
259the "Group Phases Together" option is on, then the refinement flags for
260all phases with the same histogram types are grouped together, when possible.
261If this option is off, phases are treated separately.
262<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
263If the left mouse button is used to click on the selection mode display,
264the mode is cycled between the available modes. If the right mouse
265button is used, the mode is reset, to disable multiple histogram selection.
266<p>
267<a name="mouseactions">
268</DL></DL>
269<h3>B.2 Mouse Actions</h3></a>
270<DL><DL>
271A range of atoms or (in multiple selection mode) histograms may be
272selected by dragging (holding down) the left mouse button. It is also
273possible to select a range by using the Shift key with the left mouse
274button. To select or deselect individual entries, use the Control key
275with the left mouse button. Pressing the right mouse button selects all
276entries in a list.
277</DL></DL>
278
279<h2>C. Menu Commands and Programs</h2>
280<p>
281GSAS programs are invoked either through use of the menu bar
282<center><B>
283<br>The menu bar.
284<br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
285</center></B>
286or by "pressing" a button on the button bar. The button bar
287simply provides an easy way to access commonly used
288actions on the menu bar. Users can
289<A HREF="expgui_cfg.html">
290configure the menu bar</A> to include their own preferred actions and, with
291some knowledge of the program and Tcl/Tk,
292add their own commands to the menu bar or button bar.
293
294<center><B>
295<br>The button bar.
296<br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
297</center></B>
298
299<h3>Invoking of GSAS programs</h3>
300When GSAS programs are invoked, in most cases EXPGUI is suspended while
301the GSAS program is run in a terminal (or DOS) window. When the terminal
302window is closed, EXPGUI is restarted. If desired (see the
303<A Href="expguic.html#Autoicon">
304"Iconify during GSAS"</A>
305option) while this occurs, EXPGUI can be made into an icon
306to save screen space.
307<P>
308<img src="powpref4a.gif" align=left alt="EXPGUI Screen snapshot">
309Once the GSAS program has finished, if the program has modified
310the .EXP file,
311<a Href="expguierr.html#Overwrite">
312"File has been modified..."</a>message box
313similar to the one to the left is displayed (also see the more complete
314discussion on the <a Href="expguierr.html#Overwrite">messages page</A>.
315Note that this message can be avoided if the
316<A Href="expguic.html#Autoupdate">
317"Autoload EXP"</A>
318option is used.
319<BR clear=all>
320<P>
321Note that in both Windows-95 and Windows-NT, a file named <tt>EXPGUI.LCK</tt>
322is created while the GSAS program runs. The presence of this file is used
323to suspend the LIVEPLOT program, since LIVEPLOT has sometimes crashed
324when run at the same time as GENLES (no such problem has been seen in Unix).
325This file is deleted when the GSAS program completes.
326<P>
327<img src="lock.gif" align=left alt="EXPGUI Screen snapshot">
328In Windows-9x, the <a Href="expgui_Win_readme.html#Winexec">Winexec</a>
329package is used to execute a command that creates a DOS window.
330The GSAS programs are then run by a batch file in this DOS window.
331Due to limitations in Tcl/Tk & Windows, the DOS window runs independently
332of EXPGUI, so the lock file (<tt>EXPGUI.LCK</tt>) is also used to suspend
333EXPGUI. While EXPGUI is waiting, the
334<a Href="expguierr.html#lock">
335Please wait...
336</a>
337window shown to the left is displayed. When the GSAS program completes, the
338lock file is deleted, the window automatically disappears and EXPGUI resumes.
339Should a problem arise where the file is not deleted, EXPGUI can be resumed by
340pressing the "Continue" button.
341
342<BR clear=all>
343<h3>GSAS menus</h3>
344
345A description of the EXPGUI menus follows. Use the links to obtain
346more information, including a very
347brief description of the function of each menu option.
348Note that an option may appear under more than one menu.
349
350<DL><DL>
351
352<A Href="expguic.html#1">
353<H3>C.1 File Menu</H3>
354</A>
355<DL><DL>
356The options on the File menu as is the custom contains the commands
357for reading and writing experiment files, as well as starting, 
358ending and controlling the program.
359</DL></DL>
360
361<A Href="expguic.html#2">
362<h3>C.2 Options Menu</h3>
363</A>
364<DL><DL>
365This menu contains options that determine how EXPGUI runs.
366</DL></DL>
367
368<A Href="expguic.html#3">
369<h3>C.3 Powder Menu</h3>
370</A>
371<DL><DL>
372This menu contains links to GSAS programs used for powder diffraction
373analysis.
374</DL></DL>
375
376<A Href="expguic.html#4">
377<h3>C.4 Single Crystal Menu</h3>
378</A>
379<DL><DL>
380This menu contains links to GSAS programs used for
381single-crystal diffraction analysis.
382</DL></DL>
383
384<A Href="expguic.html#5">
385<h3>C.5 Graphics Menu</h3>
386</A>
387<DL><DL>
388This menu contains links to several GSAS and
389non-GSAS programs (such as LIVEPLOT and WIDPLT)
390used for graphical display of data and results.
391</DL></DL>
392
393<A Href="expguic.html#6">
394<h3>C.6 Results Menu</h3>
395</A>
396<DL><DL>
397This menu contains links to several GSAS and
398one non-GSAS (LSTVIEW)
399programs that are used for analysis of results.
400</DL></DL>
401
402<A Href="expguic.html#7">
403<h3>C.7 Calculations Menu</h3>
404</A>
405<DL><DL>
406This menu contains programs for useful crystallographic computations.
407</DL></DL>
408
409<A Href="expguic.html#8">
410<h3>C.8 Import/Export Menu</h3>
411</A>
412<DL><DL>
413This menu contains utilities for importing information into GSAS and
414exporting.
415</DL></DL>
416
417<h2>D. EXPGUI Utility Features</h2></a>
418EXPGUI adds a number of useful functions to the GSAS package. Some,
419but not all, of these features are graphically oriented.
420
421<br clear=all>
422<a name="LSTVIEW"></a>
423<H3>D.1 LSTVIEW</H3>
424
425<DL><DL>
426LSTVIEW is used to browse through the GSAS output listing. It is
427invoked by the "lstview" command in the GUI.
428<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
429to shorten the .LST file by removing older results from the beginning
430of the file.
431<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
432as a function of the cycle number.
433<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
434</DL></DL>
435
436<br clear=all>
437<H3>D.2 LIVEPLOT</H3>
438<DL><DL>
439<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated
440and difference plots for powder
441refinements. The plot is updated as the refinement progresses. The mouse can
442be used to zoom in on sections of the plot.
443LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
444<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
445<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
446LIVEPLOT can now be enhanced to superimpose peak locations for
447input unit cells or peaks from JCPDS/ICDD entries.
448See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
449further documentation, and in particular, the
450See the <A HREF="liveplot.html#customize">
451LIVEPLOT customization information</A>.
452<P>
453</DL></DL>
454<br clear=all>
455<H3>D.3 BKGEDIT</H3>
456<DL><DL>
457<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
458<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to
459fit a GSAS background function to a set of fixed
460background points that are input using the mouse.
461The mouse can also be used to zoom in on sections of the plot.
462BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
463<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
464See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
465further documentation.
466<P>
467</DL></DL>
468<br clear=all>
469<H3>D.4 EXCLEDT</H3>
470<DL><DL>
471<A HREF="excledt.html">EXCLEDT</A> is used to edit the
472range of data used from a histogram. The upper & lower ranges
473can be adjusted to include more data or use less. Also, it is
474possible to remove sections of the data (exclude regions) that
475have known systematic errors that cannot be modeled.
476EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
477<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
478See the <A HREF="excledt.html">EXECLEDT web page</A> for
479further documentation.
480<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
481EXCLEDT can now be used to change the simulation range for dummy histograms.
482<P>
483</DL></DL>
484
485<br clear=all>
486<a name="WIDPLT"></a>
487<a name="ABSPLT"></a>
488<H3>D.5 WIDPLT and ABSPLT</H3>
489<DL><DL>
490WIDPLT is used to plot the peak widths that are generated by a set
491of GSAS profile terms (constant wavelength equations, only).
492The parameters from each phase & histogram will be
493read from the .EXP file. It is also possible to input parameters manually.
494By creating a special file (<A HREF="expgui_cfg.html#import">
495described in the customization information</A>), it
496is possible to define reference curves
497that are loaded automatically for comparison.
498<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
499<P>
500ABSPLT is used to plot the absorption/reflectivity correction for a
501histogram. Values are loaded from the histogram(s), but can be edited manually.
502<P>
503WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
504</DL></DL>
505
506<br clear=all>
507<a name="INSTEDIT"></a>
508<H3>D.6 INSTEDIT</H3>
509<DL><DL>
510
511The INSTEDIT utility is used to edit or create an instrument parameter file.
512The utility can be started from the "Edit File" button in the
513<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
514the "instedit" option in the Powder menu. Alternately, to create a new
515  instrument parameter file, choose Powder menu option "New InstParm
516  file". (It is also possible
517  to create a new file using the standard instedit by selecting
518  "Cancel" when asked for an input file.)
519An example INSTEDIT window appears below.
520<P>
521<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
522<br clear=all>
523<P>
524Note that an instrument parameter file is used for a single type of data,
525as is selected by the menu button at the top of the window.
526However, multiple sets of parameters may be included in a
527file, to be used for example with differing operating modes for the
528instrument. Each set of parameters is called a bank in GSAS terminology.
529The radiobuttons on the top of the window are used to select
530which bank's parameters will be viewed.
531The "Add Bank" button adds an additional bank to the file.
532<P>
533The parameters are described briefly below, but in more depth in the
534GSAS manual (for example, pages 158-166 for profile parameters and
535page 221-223 for the details of the instrument parameter file.)
536<P>
537<H5>Bank Parameters</H5>
538The parameters available for each bank are:
539<DL>
540<DT>Title<DD>This probably has no real use.
541<DT>Instrument Name<DD>This string is used for creation of CIFs. It is
542best if this name is unique for each instrument.
543<DT>Primary Wavelength<DD>Note, this value is set automatically when
544the radiation type is selected
545<DT>Zero Correction<DD>This is the shift to be applied to 2theta
546values in centidegrees (degrees/100). This value should probably be
547near zero for Debye-Scherrer geometry instruments (unless known from
548calibration) and will almost always be fixed at zero
549for Bragg-Brentano geometry.
550<DT>
551</DL>
552<I>X-ray only parameters</I>
553<DL>
554<DT>Radiation type<DD>Used with x-rays. The value set here
555determines the anomolous dispersion (f' and f'' values) used.
556<DT>Monochromatic/Dual<DD>Used with x-rays. Set to dual when Kalpha1, Kalpha2
557radiation is present.
558<DT>Secondary Wavelength<DD>Used in "dual" wavelength mode.
559Note, this value is set automatically when the radiation type is selected
560<DT>Wavelength Ratio<DD>Typically 0.5 for typical K alpha 1,2 instruments,
561<<I>i.e.</I>when K alpha 1 is double the intensity of K alpha 2.
562<DT>Polarization Correction<DD>There are three modes for this, where the
563first two modes work similarly. The first mode ("Diffracted Beam")
564is most common. The third mode ("None") is used when
565Lorentz-polaraization corrections are applied to the data prior to its input
566to GSAS. See page 144-145 in the GSAS manual for more information on these
567corrections.
568<DT>Polarization Ratio<DD>In "Diffracted Beam" mode:
569typically 0.5 for lab instruments without monochromators and higher for
570instruments with a diffracted beam; the value depends on the monochromator
571take-off angle. Typically slightly below unity (0.9-0.98) for synchrotron
572instruments. Ask the instrument scientist for the appropriate value.
573</DL>
574<P>
575Each bank in the instrument parameter file has one or more sets of
576profile parameters associated. Set number 1 is the default loaded
577when a histogram is added. Increase the number of sets
578using the "Add profile" button. Select the optimal profile type
579for use with your data for this set, but for most flexibility, define
580default values for all useful profile types (type 1 is of use only for
581CW neutron work) and set these values from fitting a standard with
582minimal broodening. Note that profiles can be read from a GSAS experiment
583file using the "Import profile", which raises a dialog
584such as the one below.
585<P>
586<img SRC="instedit2.gif" align=RIGHT alt="EXPGUI Screen snapshot">
587<br clear=all>
588
589
590</DL></DL>
591
592<br clear=all>
593<a name="ConvertUnix"></a>
594<a name="ConvertWin"></a>
595<h3>D.7 File Conversions</h3> 
596<DL><DL>
597<P>
598GSAS data, experiment and instrument parameter files are
599expected to have a format with exactly 80 characters per line followed
600by a carriage return and then a linefeed (82 characters total per line).
601Files in this format can be read in "Direct Access" mode.
602Recent versions of GSAS will attempt to detect and repair files that
603are not in this format, but if the file is incorrectly formatted and
604by chance the length of the file is divisible by 82, the problem in the
605file format will not be detected.
606The Convert menu
607in can be used to convert files into the correct format.
608The original version of the
609file is retained and renamed.
610<P>
611</DL></DL>
612
613<br clear=all>
614<a name="Composition"></a>
615<h3>D.8 Compute Composition</h3> 
616<DL><DL>
617The composition box shows the unit cell and asymmetric unit composition
618for all phases in a material. Site multiplicities and occupancies are
619taken into account.
620</DL></DL>
621
622<br clear=all>
623<a name="DeleteHistoryRecords"></a>
624<h3>D.9 Delete History Records</h3> 
625<DL><DL>
626Every time a GSAS program (including EXPGUI) is run, an entry is added to
627the "history records" in the .EXP file. After 999 entries have been written,
628no more can be added to the file. Further, reading large numbers of history
629records can slow the GSAS programs
630(this is less of a problem on faster computers). For these reasons, it may be
631a good idea to prune the older history records from the file.
632The File/EraseHistory command can be used to invoke the this option.
633<P>
634On the dialog the number of history records to be retained is specified.
635Also, after records have been deleted, the remaining records can be renumbered
636starting with 1, so that the 999 record limit is not reached.
637</DL></DL>
638
639<h2>E. Coordinate Export & Import Features</h2></a>
640EXPGUI can be used to read coordinates in formats not
641supported in GSAS. Coordinates can also be exported in a variety of
642formats as well.
643
644<A name="import">
645<h3>E.1 Coordinate Import Formats</h3> 
646Coordinates can be imported using the
647<A HREF="expgui2.html#addphase">"Add Phase"</A>,
648<A HREF="expgui2.html#addatoms">"Add Atoms"</A> or
649<A HREF="expgui2.html#replacephase">"Replace Phase"</A> 
650buttons on the <A HREF="expgui2.html">Phase Panel</A>, by choosing
651the format from the pull-down list to the right of the
652"Import atoms/phase from" button. The formats currently supported
653are listed below.
654Note that it is relatively easy to add new routines for
655importing coordinates;
656see the <A HREF="expgui_cfg.html#import">
657customization information</A> for more details.
658<DL><DL>
659<DT><B>Crystallographic Information File (CIF)</B><DD>
660Coordinates can be read from single block or multiblock CIF files
661using DDL1. If more than one block containing coordinates is found in the
662file, a CIF browser is available to help select the desired block.
663<DT><B>PowderCell .CEL files</B><DD>
664This format is used by the DOS and Windows PowderCell program, a valuable
665program for the transformation and visualization of structures.
666<DT><B>GSAS .EXP files</B><DD>
667This routine is used to copy coordinates, unit cell parameters and space group
668information from other GSAS experiment (.EXP) files.
669<DT><B>MSI .xtl format</B><DD>
670<a HREF="#ExportMSI">see below</a>
671<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
672<a HREF="#ExportSPF">see below</a>
673
674</DL></DL>
675
676<A name="export">
677<h3>E.2 Coordinate Export Formats</h3> 
678Coordinates can be written using the Import/Export=>"Coord Export" menu.
679Note that contents of the submenu will depend on the
680number of export routines found in the EXPGUI directory when the menu
681is first created, thus it is relatively easy to add new routines for
682importing coordinates;
683see the <A HREF="expgui_cfg.html#export">
684customization information</A> for more details.
685<DL><DL>
686<DT><B>Crystallographic Information File (CIF)</B><DD>
687Powder Diffraction Crystallographic Information files (pdCIFs) can
688be created by the GSAS2CIF program. The GSAS2CIF menu item
689invokes this program.
690<a name="ExportMSI"></a>
691<DT><B>MSI .xtl format</B><DD>
692This writes a .xtl file, as is used in Insight-II and
693Cerius2 (Molecular Simulations, Inc.). The routine
694attempts to convert GSAS space group names properly, as well as
695correctly label "Origin 2" setting, however, the naming conversion
696will not work for all valid GSAS space groups. Some effort may be needed
697by the user to get everything worked out correctly.
698<a name="ExportSPF"></a>
699<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
700This writes a .spf file, as used in
701<A HREF="http://www.cryst.chem.uu.nl/platon/">Platon</A> and
702<A HREF="http://www.cryst.chem.uu.nl/platon/">Pluton</A> by A. L. Spek.
703Some attempt is made to get space group naming right, but there is
704no assurance of quality here.
705<a name="ExportSHELX"></a>
706<DT><B>SHELX .ins format</B><DD>
707This writes coordinates and symmetry, as used in the SHELX-97 program, and
708perhaps as used some other programs, such as CrystalMaker. In addition to
709exporing the coordinates and displacement parameters, the fields that
710are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the
711wavelength, included as the first number on the CELL "card", is set to the
712arbitrary value of 1/2.
713</DL></DL>
714
715<A name=tcltk>
716<H2>
717<A Href="http://www.tcl.tk">
718Tcl/Tk</A></H2>
719The
720<A Href="http://www.tcl.tk">
721Tcl/Tk program</A> is a platform-independent scripting language that is
722used to implement most of EXPGUI. This software is available for free
723and must be loaded in order to use EXPGUI. A somewhat out of date
724version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
725more recent versions can be used, but note that the BLT package (see
726below) is needed for all features of EXPGUI.
727While learning Tcl/Tk is a great thing to do, it is not a requirement
728for using or installing EXPGUI.
729
730<A name=blt>
731<H3>
732BLT Package</H3>
733<UL>
734The BLT graphics package is used by the WIDPLT, LIVEPLOT, BKGEDIT & 
735EXCLEDT routines. If the
736package can not be found by these routines, an error message,
737"Error -- Unable to load the BLT package", will be displayed. It is also
738possible for the package to be installed, but not configured properly.
739If this is the case, a message,
740"BLT Setup Error: could not access a Blt_ routine...", will be displayed.
741Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
742</UL>
743
744<A name=La>
745<H3>
746La (Linear Algebra) Package</H3>
747<UL>
748The
749<A HREF="http://www.hume.com">Hume
750</A>
751Linear Algebra Tcl Package,
752<A HREF="http://www.hume.com/la/la.html">
753La</A>,
754is used by the BKGEDIT
755routine to perform least-squares fitting. If the
756package can not be found, the routine cannot run.
757If the package cannot be found, a message,
758"Error -- Unable to load the La package" will be displayed. This
759should not happen, since the package is included with the EXPGUI files.
760So if get this error you probably have an incomplete installation.
761</UL>
762
763<A name=winexec>
764<H3>
765WINEXEC</H3>
766<UL>
767The WINEXEC package was needed under Windows-95 and its offspring
768(-98 and -ME). It was found in older versions of EXPGUI, but is no
769  longer included.
770</UL>
771
772<H2>
773Acknowledgments</H2>
774Praise to Larson and
775Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
776for Tcl/Tk,
777Przemek Klosowski
778for convincing me to learn Tcl/Tk
779and Jonathan Wasserman for helping me get this project started.
780Thanks also to
781Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
782bond-distance restraints module and the (soon to come) rigid body editor;
783Pamela Whitfield of the NRC (Canada) for writing large
784sections of the
785<A Href="expgui7.html">Preferential Orientation Panel</A>
786and the
787<A Href="expgui6.html">Profile Constraints panel</A>
788code and to John Cowgill for the "Export to GRACE" code.
789<P>
790<A Href="https://subversion.xray.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
791GSAS</A>
792is written by Allen C. Larson and Robert B. Von Dreele while at
793Los Alamos National Laboratory. Problems, questions
794or kudos concerning GSAS should be sent to Robert B. Von Dreele at
795<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
796EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
797<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
798
799<P><hr><blockquote>
800<P>GSAS is Copyright, 1984-2000, by
801the Regents of the University of California.
802The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
803by the Los Alamos National Laboratory, which is operated by the University
804of California for the U.S. Department of Energy. The U.S. Government is
805licensed to use, reproduce, and distribute this software. Permission is
806granted to the public to copy and use this software without charge, provided
807that this notice and any statement of authorship are reproduced on all
808copies. Neither the Government nor the University makes any warranty, express
809or implied, or assumes any liability or responsibility for the use of this
810software.
811
812<P>EXPGUI was written by a U.S. Government employee, which means that
813EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write
814new sections and make them available to the rest of the world.
815
816<p>Neither the U.S. Government nor any author makes any warranty,
817expressed or implied, or assumes any liability or responsibility
818for the use of this information or the software described
819here.
820</blockquote>
821
822<P><hr WIDTH="100%">
823
824<P>
825<font size=-1><? lastmod(); ?> </font>
826<br>$Revision: 1225 $ $Date: 2012-11-08 19:42:25 +0000 (Thu, 08 Nov 2012) $
827</blockquote>
828</body>
829</html>
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