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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"
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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="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
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
36Los Alamos
37<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
38GSAS</A> package.
39EXPGUI does two things:
40it can be used to directly modify the GSAS
41experiment file with a graphical user interface (GUI) and
42it can be used to invoke the programs inside the
43GSAS package such as EXPEDT, GENLES, FOURIER...
44These programs can be run from a menu or in many cases by pressing buttons.
45EXPGUI is written using the
46<A href="#tcltk">Tcl/Tk</A> scripting language.
47<P>
48This web page describes the different actions that
49can be accomplished with the different panels and the
50contents of the menus. The table below contains links to the other
51web accessible documentation.
52<P>
53<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=CENTER>
54<TR><TH BGCOLOR="#F0F0F0" rowspan=3>GUI Sections</TH>
55<TH><A Href="expgui1.html">Least Squares</A></TH>
56<TH><A Href="expgui2.html">Phase info</A></TH>
57<TH><A Href="expgui3.html">Histogram info</A></TH>
58</TR>
59<TR>
60<TH><A Href="expgui4.html">Scaling info</A></TH>
61<TH><A Href="expgui5.html">Profile terms</A></TH>
62<TH><A Href="expgui6.html">Constraints</A></TH>
63</TR>
64<TR>
65<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
66<TH><A Href="expguic.html">Menus</A></TH>
67<TH>&nbsp;</TH>
68</TR>
69<TR><TH BGCOLOR="#F0F0F0" rowspan=3>Utilities:</TH>
70<TH><A Href="liveplot.html">LIVEPLOT</A></TH>
71<TH><A Href="liveplot.html">BKGEDIT</A></TH>
72<TH><A Href="excledt.html">EXCLEDT</A></TH>
73</TR>
74<TR>
75<TH><A Href="#WIDPLT">WIDPLT</A></TH>
76<TH><A Href="#ABSPLT">ABSPLT</A></TH>
77<TH><A Href="#INSTEDIT">INSTEDIT</A></TH>
78</TR>
79<TR>
80<TH><A Href="gsas2cif.html">CIF export</A></TH>
81<TH>&nbsp;</TH>
82<TH>&nbsp;</TH>
83</TR>
84<TR><TH BGCOLOR="#F0F0F0" rowspan=2>Installation Notes:</TH>
85<TH><A Href="expgui_Unix_readme.html">Unix</A></TH>
86<TH><A Href="expgui_Win_readme.html">Windows</A></TH>
87<TH>
88<A Href="osx.html">Mac OS X</A></TH>
89</TR><TR>
90<TH><A Href="expgui_cfg.html">Customization</A></TH>
91<TH>&nbsp;</TH>
92<TH>&nbsp;</TH>
93</TR>
94<TR><TH BGCOLOR="#F0F0F0">Tutorials:</TH>
95<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
96NIST<BR>Neutron data</A></TH>
97<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
98<TH><A Href="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
99</TR>
100<TR><TH BGCOLOR="#F0F0F0">Messages:</TH>
101<TH><A Href="expguierr.html#Error">Error</A></TH>
102<TH><A Href="expguierr.html#Warn">Warning</A></TH>
103<TH><A Href="expguierr.html#Info">Informational</A></TH>
104</TR>
105<TR><TH BGCOLOR="#F0F0F0">Other:</TH>
106<TH><A Href="expgui_intro.html">Introduction</A></TH>
107<TH><A Href="wishlist.html">Recent & Planned<BR>Improvements</A></TH>
108<TH><A Href="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
109<I>J. Appl. Cryst.</i><BR>article</A></TH>
110</TR>
111</TABLE><BR CLEAR=ALL>
112<P>
113<B>Citations.</B>
114The appropriate citations to be used for GSAS and EXPGUI are:
115<UL>
116<LI>
117A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
118Los Alamos National Laboratory Report LAUR 86-748 (2000).
119<A HREF="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.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
158Since the GSAS experiment file is quite complex,
159values are grouped together by function, approximately
160following the outline of the EXPEDT program.
161Each set of values is given a
162"tabbed panel" on a window that has the appearance of a notebook (see below).
163<center><B>
164<br>The notebook panel tabs.
165<br><img SRC="panebar1.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
166</center></B>
167In some cases, where values are
168too numerous or complex to fit onto the notebook panel, one or more buttons
169may be present on a panel that will create a separate window,
170where the associated values can be modified.
171These values are not recorded in the
172"in memory" copy of the experiment file unless the "Save" button on this window
173is pressed. If "Cancel" is pressed, no changes are made.
174Each notebook panel is listed below with a link to the web page documenting
175that panel.
176
177<A Href="expgui1.html">
178<h3>A.1 Least Squares (LS) Controls Panel</h3>
179</A><A Href="expgui2.html">
180<h3>A.2 Phase Panel</h3> 
181</A><A Href="expgui3.html">
182<h3>A.3 Histogram panel</h3> 
183</A><A Href="expgui4.html">
184<h3>A.4 Scaling panel</h3> 
185</A><A Href="expgui5.html">
186<h3>A.5 Profile panel</h3> 
187</A><A Href="expgui6.html">
188<h3>A.6 Constraints panel</h3>
189</A><A Href="expgui7.html">
190<h3>A.7 Preferential Orientation Panel</h3>
191</A>
192<br clear=all>
193</DL></DL>
194<h2>B. Shortcuts</h2></a>
195<a name="multiplehistogram">
196<h3>B.1 Multiple Histogram Selection</h3></a>
197<DL><DL>
198This mode allows parameters to be changed for groups of
199histograms.
200When the "Multiple Histogram Selection" mode is off,
201it is possible to modify parameters
202and refinement flags for only a single histogram, but
203the other settings allow groups of histograms
204to be selected and modified.
205<A href="#mouseactions">(see Mouse Actions)</A>.
206<P>
207It does not make sense, however, to globally modify
208instrument-related parameters and flags for different
209histogram types.
210So global actions can be limited to a single class
211of histogram types (e.g. TOF, CW Neutron,...), which
212allows these parameters to be set for groups of
213similar histograms. Thus, if this mode is set to "All"
214the Histogram and Profile panels are disabled.
215<P>
216The setting for "Multiple Histogram Selection" mode is
217displayed above each histogram selection box and is
218selected using the "Multiple Hist. Selection" item on the
219Options menu to create a submenu or by clicking on the display.
220Note that another option in this "Multiple Hist. Selection"
221submenu is an option "Group Phases Together" that controls how
222EXPGUI treats phases having
223the same profile type that is used when multiple histograms are selected. If
224the "Group Phases Together" option is on, then the refinement flags for
225all phases with the same histogram types are grouped together, when possible.
226If this option is off, phases are treated separately.
227<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
228If the left mouse button is used to click on the selection mode display,
229the mode is cycled between the available modes. If the right mouse
230button is used, the mode is reset, to disable multiple histogram selection.
231<p>
232<a name="mouseactions">
233</DL></DL>
234<h3>B.2 Mouse Actions</h3></a>
235<DL><DL>
236A range of atoms or (in multiple selection mode) histograms may be
237selected by dragging (holding down) the left mouse button. It is also
238possible to select a range by using the Shift key with the left mouse
239button. To select or deselect individual entries, use the Control key
240with the left mouse button. Pressing the right mouse button selects all
241entries in a list.
242</DL></DL>
243
244<h2>C. Menu Commands and Programs</h2>
245<p>
246GSAS programs are invoked either through use of the menu bar
247<center><B>
248<br>The menu bar.
249<br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
250</center></B>
251or by "pressing" a button on the button bar. The button bar
252simply provides an easy way to access commonly used
253actions on the menu bar. Users can
254<A HREF="expgui_cfg.html">
255configure the menu bar</A> to include their own preferred actions and, with
256some knowledge of the program and Tcl/Tk,
257add their own commands to the menu bar or button bar.
258
259<center><B>
260<br>The button bar.
261<br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
262</center></B>
263
264<h3>Invoking of GSAS programs</h3>
265When GSAS programs are invoked, in most cases EXPGUI is suspended while
266the GSAS program is run in a terminal (or DOS) window. When the terminal
267window is closed, EXPGUI is restarted. If desired (see the
268<A Href="expguic.html#Autoicon">
269"Iconify during GSAS"</A>
270option) while this occurs, EXPGUI can be made into an icon
271to save screen space.
272<P>
273<img src="powpref4a.gif" align=left alt="EXPGUI Screen snapshot">
274Once the GSAS program has finished, if the program has modified
275the .EXP file,
276<a Href="expguierr.html#Overwrite">
277"File has been modified..."</a>message box
278similar to the one to the left is displayed (also see the more complete
279discussion on the <a Href="expguierr.html#Overwrite">messages page</A>.
280Note that this message can be avoided if the
281<A Href="expguic.html#Autoupdate">
282"Autoload EXP"</A>
283option is used.
284<BR clear=all>
285<P>
286Note that in both Windows-95 and Windows-NT, a file named <tt>EXPGUI.LCK</tt>
287is created while the GSAS program runs. The presence of this file is used
288to suspend the LIVEPLOT program, since LIVEPLOT has sometimes crashed
289when run at the same time as GENLES (no such problem has been seen in Unix).
290This file is deleted when the GSAS program completes.
291<P>
292<img src="lock.gif" align=left alt="EXPGUI Screen snapshot">
293In Windows-9x, the <a Href="expgui_Win_readme.html#Winexec">Winexec</a>
294package is used to execute a command that creates a DOS window.
295The GSAS programs are then run by a batch file in this DOS window.
296Due to limitations in Tcl/Tk & Windows, the DOS window runs independently
297of EXPGUI, so the lock file (<tt>EXPGUI.LCK</tt>) is also used to suspend
298EXPGUI. While EXPGUI is waiting, the
299<a Href="expguierr.html#lock">
300Please wait...
301</a>
302window shown to the left is displayed. When the GSAS program completes, the
303lock file is deleted, the window automatically disappears and EXPGUI resumes.
304Should a problem arise where the file is not deleted, EXPGUI can be resumed by
305pressing the "Continue" button.
306
307<BR clear=all>
308<h3>GSAS menus</h3>
309
310A description of the EXPGUI menus follows. Use the links to obtain
311more information, including a very
312brief description of the function of each menu option.
313Note that an option may appear under more than one menu.
314
315<DL><DL>
316
317<A Href="expguic.html#1">
318<H3>C.1 File Menu</H3>
319</A>
320<DL><DL>
321The options on the File menu as is the custom contains the commands
322for reading and writing experiment files, as well as starting, 
323ending and controlling the program.
324</DL></DL>
325
326<A Href="expguic.html#2">
327<h3>C.2 Options Menu</h3>
328</A>
329<DL><DL>
330This menu contains options that determine how EXPGUI runs.
331</DL></DL>
332
333<A Href="expguic.html#3">
334<h3>C.3 Powder Menu</h3>
335</A>
336<DL><DL>
337This menu contains links to GSAS programs used for powder diffraction
338analysis.
339</DL></DL>
340
341<A Href="expguic.html#4">
342<h3>C.4 Single Crystal Menu</h3>
343</A>
344<DL><DL>
345This menu contains links to GSAS programs used for
346single-crystal diffraction analysis.
347</DL></DL>
348
349<A Href="expguic.html#5">
350<h3>C.5 Graphics Menu</h3>
351</A>
352<DL><DL>
353This menu contains links to several GSAS and
354non-GSAS programs (such as LIVEPLOT and WIDPLT)
355used for graphical display of data and results.
356</DL></DL>
357
358<A Href="expguic.html#6">
359<h3>C.6 Results Menu</h3>
360</A>
361<DL><DL>
362This menu contains links to several GSAS and
363one non-GSAS (LSTVIEW)
364programs that are used for analysis of results.
365</DL></DL>
366
367<A Href="expguic.html#7">
368<h3>C.7 Calculations Menu</h3>
369</A>
370<DL><DL>
371This menu contains programs for useful crystallographic computations.
372</DL></DL>
373
374<A Href="expguic.html#8">
375<h3>C.8 Import/Export Menu</h3>
376</A>
377<DL><DL>
378This menu contains utilities for importing information into GSAS and
379exporting.
380</DL></DL>
381
382<h2>D. EXPGUI Utility Features</h2></a>
383EXPGUI adds a number of useful functions to the GSAS package. Some,
384but not all, of these features are graphically oriented.
385
386<br clear=all>
387<a name="LSTVIEW"></a>
388<H3>D.1 LSTVIEW</H3>
389
390<DL><DL>
391LSTVIEW is used to browse through the GSAS output listing. It is
392invoked by the "lstview" command in the GUI.
393<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
394to shorten the .LST file by removing older results from the beginning
395of the file.
396<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
397as a function of the cycle number.
398<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
399</DL></DL>
400
401<br clear=all>
402<H3>D.2 LIVEPLOT</H3>
403<DL><DL>
404<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated
405and difference plots for powder
406refinements. The plot is updated as the refinement progresses. The mouse can
407be used to zoom in on sections of the plot.
408LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
409<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
410<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
411LIVEPLOT can now be enhanced to superimpose peak locations for
412input unit cells or peaks from JCPDS/ICDD entries.
413See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
414further documentation, and in particular, the
415See the <A HREF="liveplot.html#customize">
416LIVEPLOT customization information</A>.
417<P>
418</DL></DL>
419<br clear=all>
420<H3>D.3 BKGEDIT</H3>
421<DL><DL>
422<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
423<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to
424fit a GSAS background function to a set of fixed
425background points that are input using the mouse.
426The mouse can also be used to zoom in on sections of the plot.
427BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
428<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
429See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
430further documentation.
431<P>
432</DL></DL>
433<br clear=all>
434<H3>D.4 EXCLEDT</H3>
435<DL><DL>
436<A HREF="excledt.html">EXCLEDT</A> is used to edit the
437range of data used from a histogram. The upper & lower ranges
438can be adjusted to include more data or use less. Also, it is
439possible to remove sections of the data (exclude regions) that
440have known systematic errors that cannot be modeled.
441EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
442<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
443See the <A HREF="excledt.html">EXECLEDT web page</A> for
444further documentation.
445<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
446EXCLEDT can now be used to change the simulation range for dummy histograms.
447<P>
448</DL></DL>
449
450<br clear=all>
451<a name="WIDPLT"></a>
452<a name="ABSPLT"></a>
453<H3>D.5 WIDPLT and ABSPLT</H3>
454<DL><DL>
455WIDPLT is used to plot the peak widths that are generated by a set
456of GSAS profile terms (constant wavelength equations, only).
457The parameters from each phase & histogram will be
458read from the .EXP file. It is also possible to input parameters manually.
459By creating a special file (<A HREF="expgui_cfg.html#import">
460described in the customization information</A>), it
461is possible to define reference curves
462that are loaded automatically for comparison.
463<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
464<P>
465ABSPLT is used to plot the absorption/reflectivity correction for a
466histogram. Values are loaded from the histogram(s), but can be edited manually.
467<P>
468WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
469</DL></DL>
470
471<br clear=all>
472<a name="INSTEDIT"></a>
473<H3>D.6 INSTEDIT</H3>
474<DL><DL>
475
476The INSTEDIT utility is used to edit or create an instrument parameter file.
477At this time it can only be used to edit files for
478constant-wavelength data. The utility can be started from the "Edit File"
479button in the
480<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
481the "instedit" option in the Powder menu. In the latter case, the user
482is given the chance to select an input file. If no file is selected,
483a new, empty, file is created. An example INSTEDIT window appears below.
484<P>
485<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
486<br clear=all>
487<P>
488Note that an instrument parameter file is used for a single type of data,
489as is selected by the menu button at the top of the window.
490However, multiple sets of parameters may be included in a
491file, to be used for example with differing operating modes for the
492instrument. Each set of parameters is called a bank in GSAS terminology.
493The radiobuttons on the top of the window are used to select
494which bank's parameters will be viewed.
495The "Add Bank" button adds an additional bank to the file.
496<P>
497The parameters are described briefly below, but in more depth in the
498GSAS manual (for example, pages 158-166 for profile parameters and
499page 221-223 for the details of the instrument parameter file.)
500<P>
501<H5>Bank Parameters</H5>
502The parameters available for each bank are:
503<DL>
504<DT>Title<DD>This probably has no real use.
505<DT>Instrument Name<DD>This string is used for creation of CIFs. It is
506best if this name is unique for each instrument.
507<DT>Primary Wavelength<DD>Note, this value is set automatically when
508the radiation type is selected
509<DT>Zero Correction<DD>This is the shift to be applied to 2theta
510values in centidegrees (degrees/100). This value should probably be
511near zero for Debye-Scherrer geometry instruments (unless known from
512calibration) and will almost always be fixed at zero
513for Bragg-Brentano geometry.
514<DT>
515</DL>
516<I>X-ray only parameters</I>
517<DL>
518<DT>Radiation type<DD>Used with x-rays. The value set here
519determines the anomolous dispersion (f' and f'' values) used.
520<DT>Monochromatic/Dual<DD>Used with x-rays. Set to dual when Kalpha1, Kalpha2
521radiation is present.
522<DT>Secondary Wavelength<DD>Used in "dual" wavelength mode.
523Note, this value is set automatically when the radiation type is selected
524<DT>Wavelength Ratio<DD>Typically 0.5 for typical K alpha 1,2 instruments,
525<<I>i.e.</I>when K alpha 1 is double the intensity of K alpha 2.
526<DT>Polarization Correction<DD>There are three modes for this, where the
527first two modes work similarly. The first mode ("Diffracted Beam")
528is most common. The third mode ("None") is used when
529Lorentz-polaraization corrections are applied to the data prior to its input
530to GSAS. See page 144-145 in the GSAS manual for more information on these
531corrections.
532<DT>Polarization Ratio<DD>In "Diffracted Beam" mode:
533typically 0.5 for lab instruments without monochromators and higher for
534instruments with a diffracted beam; the value depends on the monochromator
535take-off angle. Typically slightly below unity (0.9-0.98) for synchrotron
536instruments. Ask the instrument scientist for the appropriate value.
537</DL>
538<P>
539Each bank in the instrument parameter file has one or more sets of
540profile parameters associated. Set number 1 is the default loaded
541when a histogram is added. Increase the number of sets
542using the "Add profile" button. Select the optimal profile type
543for use with your data for this set, but for most flexibility, define
544default values for all useful profile types (type 1 is of use only for
545CW neutron work) and set these values from fitting a standard with
546minimal broodening. Note that profiles can be read from a GSAS experiment
547file using the "Import profile", which raises a dialog
548such as the one below.
549<P>
550<img SRC="instedit2.gif" align=RIGHT alt="EXPGUI Screen snapshot">
551<br clear=all>
552
553
554</DL></DL>
555
556<br clear=all>
557<a name="ConvertUnix"></a>
558<a name="ConvertWin"></a>
559<h3>D.7 File Conversions</h3> 
560<DL><DL>
561<P>
562GSAS data, experiment and instrument parameter files are
563expected to have a format with exactly 80 characters per line followed
564by a carriage return and then a linefeed (82 characters total per line).
565Files in this format can be read in "Direct Access" mode.
566Recent versions of GSAS will attempt to detect and repair files that
567are not in this format, but if the file is incorrectly formatted and
568by chance the length of the file is divisible by 82, the problem in the
569file format will not be detected.
570The Convert menu
571in can be used to convert files into the correct format.
572The original version of the
573file is retained and renamed.
574<P>
575</DL></DL>
576
577<br clear=all>
578<a name="Composition"></a>
579<h3>D.8 Compute Composition</h3> 
580<DL><DL>
581The composition box shows the unit cell and asymmetric unit composition
582for all phases in a material. Site multiplicities and occupancies are
583taken into account.
584</DL></DL>
585
586<br clear=all>
587<a name="DeleteHistoryRecords"></a>
588<h3>D.9 Delete History Records</h3> 
589<DL><DL>
590Every time a GSAS program (including EXPGUI) is run, an entry is added to
591the "history records" in the .EXP file. After 999 entries have been written,
592no more can be added to the file. Further, reading large numbers of history
593records can slow the GSAS programs
594(this is less of a problem on faster computers). For these reasons, it may be
595a good idea to prune the older history records from the file. If more than 100
596history records are found in an experiment file, EXPGUI suggests that the
597older history entries be deleted. Alternately the File/EraseHistory command
598can be used to invoke the this option.
599<P>
600On the dialog the number of history records to be retained is specified.
601Also, after records have been deleted, the remaining records can be renumbered
602starting with 1, so that the 999 record limit is not reached.
603</DL></DL>
604
605<h2>E. Coordinate Export & Import Features</h2></a>
606EXPGUI can be used to read coordinates in formats not
607supported in GSAS. Coordinates can also be exported in a variety of
608formats as well.
609
610<A name="import">
611<h3>E.1 Coordinate Import Formats</h3> 
612Coordinates can be imported using the
613<A HREF="expgui2.html#addphase">"Add Phase"</A>,
614<A HREF="expgui2.html#addatoms">"Add Atoms"</A> or
615<A HREF="expgui2.html#replacephase">"Replace Phase"</A> 
616buttons on the <A HREF="expgui2.html">Phase Panel</A>, by choosing
617the format from the pull-down list to the right of the
618"Import atoms/phase from" button. The formats currently supported
619are listed below.
620Note that it is relatively easy to add new routines for
621importing coordinates;
622see the <A HREF="expgui_cfg.html#import">
623customization information</A> for more details.
624<DL><DL>
625<DT><B>Crystallographic Information File (CIF)</B><DD>
626Coordinates can be read from single block or multiblock CIF files
627using DDL1. If more than one block containing coordinates is found in the
628file, a CIF browser is available to help select the desired block.
629<DT><B>PowderCell .CEL files</B><DD>
630This format is used by the DOS and Windows PowderCell program, a valuable
631program for the transformation and visualization of structures.
632<DT><B>GSAS .EXP files</B><DD>
633This routine is used to copy coordinates, unit cell parameters and space group
634information from other GSAS experiment (.EXP) files.
635<DT><B>MSI .xtl format</B><DD>
636<a HREF="#ExportMSI">see below</a>
637<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
638<a HREF="#ExportSPF">see below</a>
639
640</DL></DL>
641
642<A name="export">
643<h3>E.2 Coordinate Export Formats</h3> 
644Coordinates can be written using the Import/Export=>"Coord Export" menu.
645Note that contents of the submenu will depend on the
646number of export routines found in the EXPGUI directory when the menu
647is first created, thus it is relatively easy to add new routines for
648importing coordinates;
649see the <A HREF="expgui_cfg.html#export">
650customization information</A> for more details.
651<DL><DL>
652<DT><B>Crystallographic Information File (CIF)</B><DD>
653Powder Diffraction Crystallographic Information files (pdCIFs) can
654be created by the GSAS2CIF program. The GSAS2CIF menu item
655invokes this program.
656<a name="ExportMSI"></a>
657<DT><B>MSI .xtl format</B><DD>
658This writes a .xtl file, as is used in Insight-II and
659Cerius2 (Molecular Simulations, Inc.). The routine
660attempts to convert GSAS space group names properly, as well as
661correctly label "Origin 2" setting, however, the naming conversion
662will not work for all valid GSAS space groups. Some effort may be needed
663by the user to get everything worked out correctly.
664<a name="ExportSPF"></a>
665<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
666This writes a .spf file, as used in
667<A HREF="http://www.cryst.chem.uu.nl/platon/">Platon</A> and
668<A HREF="http://www.cryst.chem.uu.nl/platon/">Pluton</A> by A. L. Spek.
669Some attempt is made to get space group naming right, but there is
670no assurance of quality here.
671<a name="ExportSHELX"></a>
672<DT><B>SHELX .ins format</B><DD>
673This writes coordinates and symmetry, as used in the SHELX-97 program, and
674perhaps as used some other programs, such as CrystalMaker. In addition to
675exporing the coordinates and displacement parameters, the fields that
676are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the
677wavelength, included as the first number on the CELL "card", is set to the
678arbitrary value of 1/2.
679</DL></DL>
680
681<A name=tcltk>
682<H2>
683<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
684Tcl/Tk</A></H2>
685The
686<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
687Tcl/Tk program</A> is a platform-independent scripting language that is
688used to implement most of EXPGUI. This software is available for free
689and must be loaded in order to use EXPGUI. See the
690installation notes for
691<A HREF="expgui_Win_readme.html">Windows</A>,
692and for
693<A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this.
694While learning Tcl/Tk is a great thing to do, it is not a requirement
695for using or installing EXPGUI.
696
697<A name=winexec>
698<H3>
699WINEXEC</H3>
700<UL>
701The WINEXEC package is needed under Windows-95 and its offspring
702(-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation
703notes</A> for more details.
704</UL>
705
706<A name=blt>
707<H3>
708BLT Package</H3>
709<UL>
710The BLT graphics package is used by the WIDPLT, LIVEPLOT, BKGEDIT & 
711EXCLEDT routines. If the
712package can not be found by these routines, an error message,
713"Error -- Unable to load the BLT package", will be displayed. It is also
714possible for the package to be installed, but not configured properly.
715If this is the case, a message,
716"BLT Setup Error: could not access a Blt_ routine...", will be displayed.
717This is most common in UNIX and is discussed further in the
718<A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see
719<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
720http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
721</A> for more information on installation of BLT.
722</UL>
723
724<A name=La>
725<H3>
726La (Linear Algebra) Package</H3>
727<UL>
728The
729<A HREF="www.hume.com">Hume
730</A>
731Linear Algebra Tcl Package,
732<A HREF="www.hume.com">
733La</A>,
734is used by the BKGEDIT
735routine to perform least-squares fitting. If the
736package can not be found, the routine cannot run.
737If the package cannot be found, a message,
738"Error -- Unable to load the La package" will be displayed. This
739should not happen, since the package is included with the EXPGUI files.
740So if get this error you probably have an incomplete installation.
741Note that the La package requires Tcl/Tk version 8.1 or higher, so that if
742you are using an older version of Tcl/Tk, you will need to upgrade.
743See the installation instructions for
744<A HREF="expgui_Win_readme.html">Windows</A>,
745and for
746<A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk.
747</UL>
748
749<H2>
750Acknowledgments</H2>
751Praise to Larson and
752Von Dreele for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
753for Tcl/Tk,
754Przemek Klosowski</A>
755for convincing me to learn Tcl/Tk
756and Jonathan Wasserman for helping get this project started.
757Thanks also to
758Pamela Whitfield of the NRC (Canada) for writing large
759sections of the
760<A Href="expgui7.html">Preferential Orientation Panel</A>
761and the
762<A Href="expgui6.html">Profile Constraints panel</A>
763code and to John Cowgill for the "Export to GRACE" code.
764<P>
765<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
766GSAS</A>
767is written by Allen C. Larson and Robert B. Von Dreele while at
768Los Alamos National Laboratory. Problems, questions
769or kudos concerning GSAS should be sent to Robert B. Von Dreele at
770<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
771EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
772<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A> 
773with help from Jonathan Wasserman.
774
775<P><hr><blockquote>
776<P>GSAS is Copyright, 1984-2000, by
777the Regents of the University of California.
778The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
779by the Los Alamos National Laboratory, which is operated by the University
780of California for the U.S. Department of Energy. The U.S. Government is
781licensed to use, reproduce, and distribute this software. Permission is
782granted to the public to copy and use this software without charge, provided
783that this notice and any statement of authorship are reproduced on all
784copies. Neither the Government nor the University makes any warranty, express
785or implied, or assumes any liability or responsibility for the use of this
786software.
787
788<P>The author of EXPGUI is a U.S. Government employee which means that
789EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write
790new sections and make them available to the rest of the world.
791
792<p>Neither the U.S. Government nor any author makes any warranty,
793expressed or implied, or assumes any liability or responsibility
794for the use of this information or the software described
795here. Brand names cited herein are used for
796identification purposes and do not constitute an endorsement by NIST.
797</blockquote>
798
799<P><hr WIDTH="100%">
800
801<P>
802<font size=-1><? lastmod(); ?> </font>
803<br>$Revision: 973 $ $Date: 2010-03-28 17:19:55 +0000 (Sun, 28 Mar 2010) $
804</blockquote>
805</body>
806</html>
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