source: trunk/doc/expgui.html @ 770

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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<style>
8A:link {text-decoration:none}
9A:vlink {text-decoration:none}
10</style>
11
12<BODY BGCOLOR="#FFFFFF"
13      topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" 
14      text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff">
15
16<?
17   include("/var/www/include/navigation.inc");
18   include("/var/www/include/utility.inc");
19?>
20<blockquote><font face="arial, helvetica, sans-serif">
21
22<center><h1>
23<HR noshade width="75%" size="2" align="center">
24EXPGUI<BR>
25A Graphical User Interface for
26<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
27GSAS</A>
28<HR noshade width="75%" size="2" align="center">
29</h1></center>
30<P><P>
31<I><B>
32<blockquote>
33Note that the current EXPGUI release is intended to work with the
34current GSAS release. [EXPGUI v1.47 or later requires GSAS from Oct 2001
35(or later) for all features to work as described].
36</blockquote>
37</I></B>
38<P><P>
39EXPGUI is a graphical interface for the
40Los Alamos
41<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
42GSAS</A> package.
43EXPGUI does two things:
44it can be used to directly modify the GSAS
45experiment file with a graphical user interface (GUI) and
46it can be used to invoke the programs inside the
47GSAS package such as EXPEDT, GENLES, FOURIER...
48These programs can be run from a menu or in many cases by pressing buttons.
49EXPGUI is written using the
50<A href="#tcltk">Tcl/Tk</A> scripting language.
51<P>
52This web page describes the different actions that
53can be accomplished with the different panes and the
54contents of the menus. The table below contains links to the other
55web accessible documentation.
56<P>
57<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=CENTER>
58<TR><TH BGCOLOR="#F0F0F0" rowspan=3>GUI Sections</TH>
59<TH><A Href="expgui1.html">Least Squares</A></TH>
60<TH><A Href="expgui2.html">Phase info</A></TH>
61<TH><A Href="expgui3.html">Histogram info</A></TH>
62</TR>
63<TR>
64<TH><A Href="expgui4.html">Scaling info</A></TH>
65<TH><A Href="expgui5.html">Profile terms</A></TH>
66<TH><A Href="expgui6.html">Constraints</A></TH>
67</TR>
68<TR>
69<TH><A Href="expgui7.html">Preferred Orientation</A></TH>
70<TH><A Href="expguic.html">Menus</A></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="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial3">
93<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
94<A Href="osx.html">Mac OS X</A></TH>
95</TR><TR>
96<TH><A Href="expgui_cfg.html">Customization</A></TH>
97<TH>&nbsp;</TH>
98<TH>&nbsp;</TH>
99</TR>
100<TR><TH BGCOLOR="#F0F0F0">Tutorials:</TH>
101<TH><A Href="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial3">
102<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
103NIST<BR>Neutron data</A></TH>
104<TH><A Href="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH>
105<TH><A Href="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH>
106</TR>
107<TR><TH BGCOLOR="#F0F0F0">Messages:</TH>
108<TH><A Href="expguierr.html#Error">Error</A></TH>
109<TH><A Href="expguierr.html#Warn">Warning</A></TH>
110<TH><A Href="expguierr.html#Info">Informational</A></TH>
111</TR>
112<TR><TH BGCOLOR="#F0F0F0">Other:</TH>
113<TH><A Href="expgui_intro.html">Introduction</A></TH>
114<TH><A Href="wishlist.html">Recent & Planned<BR>Improvements</A></TH>
115<TH><A Href="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
116<I>J. Appl. Cryst.</i><BR>article</A></TH>
117</TR>
118</TABLE><BR CLEAR=ALL>
119<P>
120<B>Citations.</B>
121The appropriate citations to be used for GSAS and EXPGUI are:
122<UL>
123<LI>
124A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)",
125Los Alamos National Laboratory Report LAUR 86-748 (2000).
126<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.pdf">
127[link to PDF copy of manual]
128</A>
129<LI>
130B. H. Toby, <i>EXPGUI</i>, a graphical user interface for <i>GSAS</i>,
131<i>J. Appl. Cryst.</i> <b>34</b>, 210-213 (2001).
132<A HREF="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf">
133[link to PDF file]
134</A>
135</UL>
136<P>
137<B>Mailing List.</B>
138If you would like to get news about about new features
139& bug fixes in EXPGUI and also support
140the project by demonstrating how many people use it,
141please send e-mail to
142<a href="mailto:brian.toby@nist.gov?subject=EXPGUI Mailing List">Brian.Toby@NIST.GOV</a>.
143<P>
144<hr>
145
146<h2>A. Experiment file editing</h2>
147<P>
148<DL><DL>
149When an experiment (.EXP) file is read, a copy is made in local
150computer memory. In most cases, values are changed in this
151"in memory" copy of the experiment file
152as this information is changed by the user on the screen.
153<img SRC="rederror.gif" align=LEFT BORDER=3 alt="EXPGUI Screen snapshot">
154<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
155If there is an error in the typed value, (for example if "1..0" is typed, or
156"1.5" is typed where an integer is expected), these values are
157not saved. In this case, the text is turned red, to indicate
158that an error is present, as shown in the figure to the left, where "90.000x"
159has been entered for alpha.
160The edited version of the experiment file is written back out to
161disk when the "File/Save" or "File/Save as"
162<A Href="expguic.html#1">menu bar options</A>
163are used. The File/Save operation is done automatically before any GSAS
164programs, such as GENLES or EXPEDT, are run.
165<P>
166
167Since the GSAS experiment file is quite complex,
168values are grouped together by function, approximately
169following the outline of the EXPEDT program.
170Each set of values is given a
171"tabbed pane" on a window that has the appearance of a notebook (see below).
172<center><B>
173<br>The notebook pane tabs.
174<br><img SRC="panebar1.gif"  BORDER=3 alt="EXPGUI Screen snapshot">
175</center></B>
176In some cases, where values are
177too numerous or complex to fit onto the notebook pane, one or more buttons
178may be present on a pane that will create a separate window,
179where the associated values can be modified.
180These values are not recorded in the
181"in memory" copy of the experiment file unless the "Save" button on this window
182is pressed. If "Cancel" is pressed, no changes are made.
183Each notebook pane is listed below with a link to the web page documenting
184that pane.
185
186<A Href="expgui1.html">
187<h3>A.1 Least Squares (LS) Controls Pane</h3>
188</A><A Href="expgui2.html">
189<h3>A.2 Phase Pane</h3> 
190</A><A Href="expgui3.html">
191<h3>A.3 Histogram pane</h3> 
192</A><A Href="expgui4.html">
193<h3>A.4 Scaling pane</h3> 
194</A><A Href="expgui5.html">
195<h3>A.5 Profile pane</h3> 
196</A><A Href="expgui6.html">
197<h3>A.6 Constraints pane</h3>
198</A><A Href="expgui7.html">
199<h3>A.7 Preferential Orientation Pane</h3>
200</A>
201<br clear=all>
202</DL></DL>
203<h2>B. Shortcuts</h2></a>
204<a name="multiplehistogram">
205<h3>B.1 Multiple Histogram Selection</h3></a>
206<DL><DL>
207This mode allows parameters to be changed for groups of
208histograms.
209When the "Multiple Histogram Selection" mode is off,
210it is possible to modify parameters
211and refinement flags for only a single histogram, but
212the other settings allow groups of histograms
213to be selected and modified.
214<A href="#mouseactions">(see Mouse Actions)</A>.
215<P>
216It does not make sense, however, to globally modify
217instrument-related parameters and flags for different
218histogram types.
219So global actions can be limited to a single class
220of histogram types (e.g. TOF, CW Neutron,...), which
221allows these parameters to be set for groups of
222similar histograms. Thus, if this mode is set to "All"
223the Histogram and Profile panes are disabled.
224<P>
225The setting for "Multiple Histogram Selection" mode is
226displayed above each histogram selection box and is
227selected using the "Multiple Hist. Selection" item on the
228Options menu to create a submenu or by clicking on the display.
229Note that another option in this "Multiple Hist. Selection"
230submenu is an option "Group Phases Together" that controls how
231EXPGUI treats phases having
232the same profile type that is used when multiple histograms are selected. If
233the "Group Phases Together" option is on, then the refinement flags for
234all phases with the same histogram types are grouped together, when possible.
235If this option is off, phases are treated separately.
236<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
237If the left mouse button is used to click on the selection mode display,
238the mode is cycled between the available modes. If the right mouse
239button is used, the mode is reset, to disable multiple histogram selection.
240<p>
241<a name="mouseactions">
242</DL></DL>
243<h3>B.2 Mouse Actions</h3></a>
244<DL><DL>
245A range of atoms or (in multiple selection mode) histograms may be
246selected by dragging (holding down) the left mouse button. It is also
247possible to select a range by using the Shift key with the left mouse
248button. To select or deselect individual entries, use the Control key
249with the left mouse button. Pressing the right mouse button selects all
250entries in a list.
251</DL></DL>
252
253<h2>C. Menu Commands and Programs</h2>
254<p>
255GSAS programs are invoked either through use of the menu bar
256<center><B>
257<br>The menu bar.
258<br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
259</center></B>
260or by "pressing" a button on the button bar. The button bar
261simply provides an easy way to access commonly used
262actions on the menu bar. Users can
263<A HREF="expgui_cfg.html">
264configure the menu bar</A> to include their own preferred actions and, with
265some knowledge of the program and Tcl/Tk,
266add their own commands to the menu bar or button bar.
267
268<center><B>
269<br>The button bar.
270<br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot">
271</center></B>
272
273<h3>Invoking of GSAS programs</h3>
274When GSAS programs are invoked, in most cases EXPGUI is suspended while
275the GSAS program is run in a terminal (or DOS) window. When the terminal
276window is closed, EXPGUI is restarted. If desired (see the
277<A Href="expguic.html#Autoicon">
278"Iconify during GSAS"</A>
279option) while this occurs, EXPGUI can be made into an icon
280to save screen space.
281<P>
282<img src="powpref4a.gif" align=left alt="EXPGUI Screen snapshot">
283Once the GSAS program has finished, if the program has modified
284the .EXP file,
285<a Href="expguierr.html#Overwrite">
286"File has been modified..."</a>message box
287similar to the one to the left is displayed (also see the more complete
288discussion on the <a Href="expguierr.html#Overwrite">messages page</A>.
289Note that this message can be avoided if the
290<A Href="expguic.html#Autoupdate">
291"Autoload EXP"</A>
292option is used.
293<BR clear=all>
294<P>
295Note that in both Windows-95 and Windows-NT, a file named <tt>EXPGUI.LCK</tt>
296is created while the GSAS program runs. The presence of this file is used
297to suspend the LIVEPLOT program, since LIVEPLOT has sometimes crashed
298when run at the same time as GENLES (no such problem has been seen in Unix).
299This file is deleted when the GSAS program completes.
300<P>
301<img src="lock.gif" align=left alt="EXPGUI Screen snapshot">
302In Windows-9x, the <a Href="expgui_Win_readme.html#Winexec">Winexec</a>
303package is used to execute a command that creates a DOS window.
304The GSAS programs are then run by a batch file in this DOS window.
305Due to limitations in Tcl/Tk & Windows, the DOS window runs independently
306of EXPGUI, so the lock file (<tt>EXPGUI.LCK</tt>) is also used to suspend
307EXPGUI. While EXPGUI is waiting, the
308<a Href="expguierr.html#lock">
309Please wait...
310</a>
311window shown to the left is displayed. When the GSAS program completes, the
312lock file is deleted, the window automatically disappears and EXPGUI resumes.
313Should a problem arise where the file is not deleted, EXPGUI can be resumed by
314pressing the "Continue" button.
315
316<BR clear=all>
317<h3>GSAS menus</h3>
318
319A description of the EXPGUI menus follows. Use the links to obtain
320more information, including a very
321brief description of the function of each menu option.
322Note that an option may appear under more than one menu.
323
324<DL><DL>
325
326<A Href="expguic.html#1">
327<H3>C.1 File Menu</H3>
328</A>
329<DL><DL>
330The options on the File menu as is the custom contains the commands
331for reading and writing experiment files, as well as starting
332and ending the program.
333</DL></DL>
334
335<A Href="expguic.html#2">
336<h3>C.2 Options Menu</h3>
337</A>
338<DL><DL>
339This menu contains options that determine how EXPGUI runs.
340</DL></DL>
341
342<A Href="expguic.html#3">
343<h3>C.3 Powder Menu</h3>
344</A>
345<DL><DL>
346This menu contains links to GSAS programs used for powder diffraction
347analysis.
348</DL></DL>
349
350<A Href="expguic.html#4">
351<h3>C.4 Single Crystal Menu</h3>
352</A>
353<DL><DL>
354This menu contains links to GSAS programs used for
355single-crystal diffraction analysis.
356</DL></DL>
357
358<A Href="expguic.html#5">
359<h3>C.5 Graphics Menu</h3>
360</A>
361<DL><DL>
362This menu contains links to several GSAS and
363non-GSAS programs (such as LIVEPLOT and WIDPLT)
364used for graphical display of data and results.
365</DL></DL>
366
367<A Href="expguic.html#6">
368<h3>C.6 Results Menu</h3>
369</A>
370<DL><DL>
371This menu contains links to several GSAS and
372one non-GSAS (LSTVIEW)
373programs that are used for analysis of results.
374</DL></DL>
375
376<A Href="expguic.html#7">
377<h3>C.7 Calculations Menu</h3>
378</A>
379<DL><DL>
380This menu contains programs for useful crystallographic computations.
381</DL></DL>
382
383<A Href="expguic.html#8">
384<h3>C.8 Import/Export Menu</h3>
385</A>
386<DL><DL>
387This menu contains utilities for importing information into GSAS and
388exporting.
389</DL></DL>
390
391<h2>D. EXPGUI Utility Features</h2></a>
392EXPGUI adds a number of useful functions to the GSAS package. Some,
393but not all, of these features are graphically oriented.
394
395<br clear=all>
396<H3>D.1 LSTVIEW</H3>
397
398<DL><DL>
399LSTVIEW is used to browse through the GSAS output listing. It is
400invoked by the "lstview" command in the GUI.
401<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used
402to shorten the .LST file by removing older results from the beginning
403of the file.
404<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts
405as a function of the cycle number.
406<CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER>
407</DL></DL>
408
409<br clear=all>
410<H3>D.2 LIVEPLOT</H3>
411<DL><DL>
412<A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated
413and difference plots for powder
414refinements. The plot is updated as the refinement progresses. The mouse can
415be used to zoom in on sections of the plot.
416LIVEPLOT uses the <A href="#blt">BLT</A> graphics package.
417<CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER>
418<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
419LIVEPLOT can now be enhanced to superimpose peak locations for
420input unit cells or peaks from JCPDS/ICDD entries.
421See the <A HREF="liveplot.html">LIVEPLOT web page</A> for
422further documentation, and in particular, the
423See the <A HREF="liveplot.html#customize">
424LIVEPLOT customization information</A>.
425<P>
426</DL></DL>
427<br clear=all>
428<H3>D.3 BKGEDIT</H3>
429<DL><DL>
430<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
431<A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to
432fit a GSAS background function to a set of fixed
433background points that are input using the mouse.
434The mouse can also be used to zoom in on sections of the plot.
435BKGEDIT uses the <A href="#blt">BLT</A> graphics package.
436<CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER>
437See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for
438further documentation.
439<P>
440</DL></DL>
441<br clear=all>
442<H3>D.4 EXCLEDT</H3>
443<DL><DL>
444<A HREF="excledt.html">EXCLEDT</A> is used to edit the
445range of data used from a histogram. The upper & lower ranges
446can be adjusted to include more data or use less. Also, it is
447possible to remove sections of the data (exclude regions) that
448have known systematic errors that cannot be modeled.
449EXCLEDT uses the <A href="#blt">BLT</A> graphics package.
450<CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER>
451See the <A HREF="excledt.html">EXECLEDT web page</A> for
452further documentation.
453<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
454EXCLEDT can now be used to change the simulation range for dummy histograms.
455<P>
456</DL></DL>
457
458<br clear=all>
459<a name="WIDPLT"></a>
460<a name="ABSPLT"></a>
461<H3>D.5 WIDPLT and ABSPLT</H3>
462<DL><DL>
463WIDPLT is used to plot the peak widths that are generated by a set
464of GSAS profile terms (constant wavelength equations, only).
465The parameters from each phase & histogram will be
466read from the .EXP file. It is also possible to input parameters manually.
467By creating a special file (<A HREF="expgui_cfg.html#import">
468described in the customization information</A>), it
469is possible to define reference curves
470that are loaded automatically for comparison.
471<CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER>
472<P>
473ABSPLT is used to plot the absorption/reflectivity correction for a
474histogram. Values are loaded from the histogram(s), but can be edited manually.
475<P>
476WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package.
477</DL></DL>
478
479<br clear=all>
480<a name="INSTEDIT"></a>
481<H3>D.6 INSTEDIT</H3>
482<DL><DL>
483
484The INSTEDIT utility is used to edit or create an instrument parameter file.
485At this time it can only be used to edit files for
486constant-wavelength data. The utility can be started from the "Edit File"
487button in the
488<A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the
489the "instedit" option in the Powder menu. In the latter case, the user
490is given the chance to select an input file. If no file is selected,
491a new, empty, file is created. An example INSTEDIT window appears below.
492<P>
493<img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot">
494<br clear=all>
495<P>
496Note that an instrument parameter file is used for a single type of data,
497as is selected by the menu button at the top of the window.
498However, multiple sets of parameters may be included in a
499file, to be used for example with differing operating modes for the
500instrument. Each set of parameters is called a bank in GSAS terminology.
501The radiobuttons on the top of the window are used to select
502which bank's parameters will be viewed.
503The "Add Bank" button adds an additional bank to the file.
504<P>
505The parameters are described briefly below, but in more depth in the
506GSAS manual (for example, pages 158-166 for profile parameters and
507page 221-223 for the details of the instrument parameter file.)
508<P>
509<H5>Bank Parameters</H5>
510The parameters available for each bank are:
511<DL>
512<DT>Title<DD>This probably has no real use.
513<DT>Instrument Name<DD>This string is used for creation of CIFs. It is
514best if this name is unique for each instrument.
515<DT>Primary Wavelength<DD>Note, this value is set automatically when
516the radiation type is selected
517<DT>Zero Correction<DD>This is the shift to be applied to 2theta
518values in centidegrees (degrees/100). This value should probably be
519near zero for Debye-Scherrer geometry instruments (unless known from
520calibration) and will almost always be fixed at zero
521for Bragg-Brentano geometry.
522<DT>
523</DL>
524<I>X-ray only parameters</I>
525<DL>
526<DT>Radiation type<DD>Used with x-rays. The value set here
527determines the anomolous dispersion (f' and f'' values) used.
528<DT>Monochromatic/Dual<DD>Used with x-rays. Set to dual when Kalpha1, Kalpha2
529radiation is present.
530<DT>Secondary Wavelength<DD>Used in "dual" wavelength mode.
531Note, this value is set automatically when the radiation type is selected
532<DT>Wavelength Ratio<DD>Typically 0.5 for typical K alpha 1,2 instruments,
533<<I>i.e.</I>when K alpha 1 is double the intensity of K alpha 2.
534<DT>Polarization Correction<DD>There are three modes for this, where the
535first two modes work similarly. The first mode ("Diffracted Beam")
536is most common. The third mode ("None") is used when
537Lorentz-polaraization corrections are applied to the data prior to its input
538to GSAS. See page 144-145 in the GSAS manual for more information on these
539corrections.
540<DT>Polarization Ratio<DD>In "Diffracted Beam" mode:
541typically 0.5 for lab instruments without monochromators and higher for
542instruments with a diffracted beam; the value depends on the monochromator
543take-off angle. Typically slightly below unity (0.9-0.98) for synchrotron
544instruments. Ask the instrument scientist for the appropriate value.
545</DL>
546<P>
547Each bank in the instrument parameter file has one or more sets of
548profile parameters associated. Set number 1 is the default loaded
549when a histogram is added. Increase the number of sets
550using the "Add profile" button. Select the optimal profile type
551for use with your data for this set, but for most flexibility, define
552default values for all useful profile types (type 1 is of use only for
553CW neutron work) and set these values from fitting a standard with
554minimal broodening. Note that profiles can be read from a GSAS experiment
555file using the "Import profile", which raises a dialog
556such as the one below.
557<P>
558<img SRC="instedit2.gif" align=RIGHT alt="EXPGUI Screen snapshot">
559<br clear=all>
560
561
562</DL></DL>
563
564<br clear=all>
565<a name="ConvertUnix"></a>
566<a name="ConvertWin"></a>
567<h3>D.7 File Conversions</h3> 
568<DL><DL>
569<P>
570GSAS data, experiment and instrument parameter files are
571expected to have a format with exactly 80 characters per line followed
572by a carriage return and then a linefeed (82 characters total per line).
573Files in this format can be read in "Direct Access" mode.
574Recent versions of GSAS will attempt to detect and repair files that
575are not in this format, but if the file is incorrectly formatted and
576by chance the length of the file is divisible by 82, the problem in the
577file format will not be detected.
578The Convert menu
579in can be used to convert files into the correct format.
580The original version of the
581file is retained and renamed.
582<P>
583</DL></DL>
584
585<br clear=all>
586<a name="Composition"></a>
587<h3>D.8 Compute Composition</h3> 
588<DL><DL>
589The composition box shows the unit cell and asymmetric unit composition
590for all phases in a material. Site multiplicities and occupancies are
591taken into account.
592</DL></DL>
593
594<br clear=all>
595<a name="DeleteHistoryRecords"></a>
596<h3>D.9 Delete History Records</h3> 
597<DL><DL>
598Every time a GSAS program (including EXPGUI) is run, an entry is added to
599the "history records" in the .EXP file. After 999 entries have been written,
600no more can be added to the file. Further, reading large numbers of history
601records can slow the GSAS programs
602(this is less of a problem on faster computers). For these reasons, it may be
603a good idea to prune the older history records from the file. If more than 100
604history records are found in an experiment file, EXPGUI suggests that the
605older history entries be deleted. Alternately the File/EraseHistory command
606can be used to invoke the this option.
607<P>
608On the dialog the number of history records to be retained is specified.
609Also, after records have been deleted, the remaining records can be renumbered
610starting with 1, so that the 999 record limit is not reached.
611</DL></DL>
612
613<h2>E. Coordinate Export & Import Features</h2></a>
614EXPGUI can be used to read coordinates in formats not
615supported in GSAS. Coordinates can also be exported in a variety of
616formats as well.
617
618<A name="import">
619<h3>E.1 Coordinate Import Formats</h3> 
620Coordinates can be imported using the
621<A HREF="expgui2.html#addphase">"Add Phase"</A>,
622<A HREF="expgui2.html#addatoms">"Add Atoms"</A> or
623<A HREF="expgui2.html#replacephase">"Replace Phase"</A> 
624buttons on the <A HREF="expgui2.html">Phase Pane</A>, by choosing
625the format from the pull-down list to the right of the
626"Import atoms/phase from" button. The formats currently supported
627are listed below.
628Note that it is relatively easy to add new routines for
629importing coordinates;
630see the <A HREF="expgui_cfg.html#import">
631customization information</A> for more details.
632<DL><DL>
633<DT><B>Crystallographic Information File (CIF)</B><DD>
634Coordinates can be read from single block or multiblock CIF files
635using DDL1. If more than one block containing coordinates is found in the
636file, a CIF browser is available to help select the desired block.
637<DT><B>PowderCell .CEL files</B><DD>
638This format is used by the DOS and Windows PowderCell program, a valuable
639program for the transformation and visualization of structures.
640<DT><B>GSAS .EXP files</B><DD>
641This routine is used to copy coordinates, unit cell parameters and space group
642information from other GSAS experiment (.EXP) files.
643<DT><B>MSI .xtl format</B><DD>
644<a HREF="#ExportMSI">see below</a>
645<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
646<a HREF="#ExportSPF">see below</a>
647
648</DL></DL>
649
650<A name="export">
651<h3>E.2 Coordinate Export Formats</h3> 
652Coordinates can be written using the Import/Export=>"Coord Export" menu.
653Note that contents of the submenu will depend on the
654number of export routines found in the EXPGUI directory when the menu
655is first created, thus it is relatively easy to add new routines for
656importing coordinates;
657see the <A HREF="expgui_cfg.html#export">
658customization information</A> for more details.
659<DL><DL>
660<DT><B>Crystallographic Information File (CIF)</B><DD>
661Powder Diffraction Crystallographic Information files (pdCIFs) can
662be created by the GSAS2CIF program. The GSAS2CIF menu item
663invokes this program.
664<a name="ExportMSI"></a>
665<DT><B>MSI .xtl format</B><DD>
666This writes a .xtl file, as is used in Insight-II and
667Cerius2 (Molecular Simulations, Inc.). The routine
668attempts to convert GSAS space group names properly, as well as
669correctly label "Origin 2" setting, however, the naming conversion
670will not work for all valid GSAS space groups. Some effort may be needed
671by the user to get everything worked out correctly.
672<a name="ExportSPF"></a>
673<DT><B>PLATON .spf (Standard Parameter File) format</B><DD>
674This writes a .spf file, as used in
675<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.cryst.chem.uu.nl/platon/">Platon</A> and
676<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.cryst.chem.uu.nl/platon/">Pluton</A> by A. L. Spek.
677Some attempt is made to get space group naming right, but there is
678no assurance of quality here.
679<a name="ExportSHELX"></a>
680<DT><B>SHELX .ins format</B><DD>
681This writes coordinates and symmetry, as used in the SHELX-97 program, and
682perhaps as used some other programs, such as CrystalMaker. In addition to
683exporing the coordinates and displacement parameters, the fields that
684are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the
685wavelength, included as the first number on the CELL "card", is set to the
686arbitrary value of 1/2.
687</DL></DL>
688
689<A name=tcltk>
690<H2>
691<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
692Tcl/Tk</A></H2>
693The
694<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
695Tcl/Tk program</A> is a platform-independent scripting language that is
696used to implement most of EXPGUI. This software is available for free
697and must be loaded in order to use EXPGUI. See the
698installation notes for
699<A HREF="expgui_Win_readme.html">Windows</A>,
700and for
701<A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this.
702While learning Tcl/Tk is a great thing to do, it is not a requirement
703for using or installing EXPGUI.
704
705<A name=winexec>
706<H3>
707WINEXEC</H3>
708<UL>
709The WINEXEC package is needed under Windows-95 and its offspring
710(-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation
711notes</A> for more details.
712</UL>
713
714<A name=blt>
715<H3>
716BLT Package</H3>
717<UL>
718The BLT graphics package is used by the WIDPLT, LIVEPLOT, BKGEDIT & 
719EXCLEDT routines. If the
720package can not be found by these routines, an error message,
721"Error -- Unable to load the BLT package", will be displayed. It is also
722possible for the package to be installed, but not configured properly.
723If this is the case, a message,
724"BLT Setup Error: could not access a Blt_ routine...", will be displayed.
725This is most common in UNIX and is discussed further in the
726<A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see
727<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
728http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
729</A> for more information on installation of BLT.
730</UL>
731
732<A name=La>
733<H3>
734La (Linear Algebra) Package</H3>
735<UL>
736The
737<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=www.hume.com">Hume
738</A>
739Linear Algebra Tcl Package,
740<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=www.hume.com">
741La</A>,
742is used by the BKGEDIT
743routine to perform least-squares fitting. If the
744package can not be found, the routine cannot run.
745If the package cannot be found, a message,
746"Error -- Unable to load the La package" will be displayed. This
747should not happen, since the package is included with the EXPGUI files.
748So if get this error you probably have an incomplete installation.
749Note that the La package requires Tcl/Tk version 8.1 or higher, so that if
750you are using an older version of Tcl/Tk, you will need to upgrade.
751See the installation instructions for
752<A HREF="expgui_Win_readme.html">Windows</A>,
753and for
754<A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk.
755</UL>
756
757<H2>
758Acknowledgments</H2>
759Praise to Larson and
760<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
761Von Dreele</A> for GSAS, <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.scriptics.com/">Ousterhout</A>
762for Tcl/Tk,
763Przemek Klosowski</A>
764for convincing me to learn Tcl/Tk
765and Jonathan Wasserman for helping get this project started.
766Thanks also to
767Pamela Whitfield of the NRC (Canada) for writing large
768sections of the
769<A Href="expgui7.html">Preferential Orientation Pane</A>
770and the
771<A Href="expgui6.html">Profile Constraints pane</A>
772code and to John Cowgill for the "Export to GRACE" code.
773<P>
774<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
775GSAS</A>
776is written by Allen C. Larson and <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm">
777Robert B. Von Dreele</A>, MS-H805,
778Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions
779or kudos concerning GSAS should be sent to Robert B. Von Dreele at
780<A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
781EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research,
782<A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> 
783with help from Jonathan Wasserman.
784
785<P><hr><blockquote>
786<P>GSAS is Copyright, 1984-2000, by
787the Regents of the University of California.
788The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36)
789by the Los Alamos National Laboratory, which is operated by the University
790of California for the U.S. Department of Energy. The U.S. Government is
791licensed to use, reproduce, and distribute this software. Permission is
792granted to the public to copy and use this software without charge, provided
793that this notice and any statement of authorship are reproduced on all
794copies. Neither the Government nor the University makes any warranty, express
795or implied, or assumes any liability or responsibility for the use of this
796software.
797
798<P>The author of EXPGUI is a U.S. Government employee which means that
799EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write
800new sections and make them available to the rest of the world.
801
802<p>Neither the U.S. Government nor any author makes any warranty,
803expressed or implied, or assumes any liability or responsibility
804for the use of this information or the software described
805here. Brand names cited herein are used for
806identification purposes and do not constitute an endorsement by NIST.
807</blockquote>
808
809<P><hr WIDTH="100%">
810
811<P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR>
812<font size=-1><? lastmod(); ?> </font>
813<br>$Revision: 766 $ $Date: 2009-12-04 23:11:40 +0000 (Fri, 04 Dec 2009) $
814</blockquote>
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816</html>
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