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1<html>
2<head>
3   <title>EXPGUI -- LIVEPLOT/BKGEDIT</title>
4   <meta name="keywords" content="crystallography, Rietveld, diffraction,
5   GSAS, EXPGUI">
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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<TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
23<TR><TH><A  Href="expgui.html">EXPGUI top</A> 
24</TH><TH><A Href="excledt.html">Next page<BR>(EXCLEDT)</A>
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27
28<center><h1>
29<HR noshade width="75%" size="2" align="center">
30EXPGUI Utilities (1),<BR>LIVEPLOT and BKGEDIT
31<HR noshade width="75%" size="2" align="center">
32</h1></center>
33This page documents the LIVEPLOT and BKGEDIT utility programs
34in the EXPGUI package.
35LIVEPLOT and BKGEDIT are actually the same program, but perform
36different functions, depending on how they are invoked.
37LIVEPLOT is used to display the quality of the diffraction fit, while
38BKGEDIT is used to fit a background function to fixed background points
39that have been input by the user.
40<P>
41Both LIVEPLOT and BKGEDIT get the current diffraction information
42by running the TCLDUMP program, if installed, or
43HSTDUMP otherwise. The TCLDUMP program has been optimized for use
44with LIVEPLOT and offers a number of extra
45options that are not available when HSTDUMP is used. Since TCLDUMP has been
46included in GSAS since April of 2000, it is assumed that this is now the case.
47
48<a name="liveplot"></a>
49<H3>LIVEPLOT</H3>
50LIVEPLOT is started by pressing the LIVEPLOT button on the toolbar
51or via the Graphs/liveplot menu item.
52<P>
53Some of the features available in LIVEPLOT are:
54<UL>
55<LI>The plot is updated automatically after each refinement run
56<LI>The plot can be zoomed, by clicking on the corners of the
57area to be magnified.
58<LI>
59The units used for plotting histograms can be selected. Choices are:
60native units (2Theta/TOF/KeV); d-space (A) or Q (A<sup>-1</sup>)
61<LI>
62The background (fixed plus fitted) can be plotted or can be subtracted.
63<LI>
64Reflection tickmarks can be displayed in a variety of formats
65<LI>
66LIVEPLOT can be coupled to the LOGIC or CMPR programs, so that
67peak positions from an ICDD entry or for an arbitrary unit cell and
68spacegroup can be shown superimposed on the "Rietveld plot."
69<LI>
70<IMG SRC="note.gif" alt="Note!">
71Reflection indices (<I>hkl</I> values) can be shown for tickmarks
72<LI>
73<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
74The cumulative chi<sup>2</sup> function can be plotted.
75<LI>
76<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
77The cursor position can be displayed
78</UL>
79
80<a name="bkgedit"></a>
81<H3>BKGEDIT</H3>
82<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
83BKGEDIT is used to fit a background function to a set of points
84selected by the user.
85For most refinements, this is not needed,
86as it is possible to simply select a background
87function (I find that the type 1 function,
88shifted Chebyschev polynomials, works well)
89and then refine, adding terms until a good fit is obtained.
90On occasion, poor initial fits are obtained in this manner. This is
91most common in cases where large numbers of peaks are poorly fit. Since
92significant sections of the data are not well fit, the refinement results in
93an unreasonable background function, because this yields better agreement
94with the observed data.
95In these cases,
96it may be best to fix the background to follow a "reasonable" curve in the
97initial stages and then refine the background in the final stages of
98refinement, when a good model has been obtained.
99<P>
100The BKGEDIT program, as shown below, is used to input a set a background
101points via the mouse. The points are then used to determine a type 1
102(Chebyschev) background function that fits the input background points. These
103terms can then be saved in the experiment file creating a background that
104is good enough for the initial stages of refinement and that can be
105refined once the model is adequate for the task.
106<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
107BKGEDIT can be used to fit GSAS background functions 1-6 (though
108for most purposes only type 1 is needed.)
109<P>
110<IMG SRC="b1.gif" align=TEXTOP alt="BKGEDIT screen image">
111<H4>Steps in fitting a background function</H4>
112The BKGEDIT program is started from
113via the Powder/bkgedit menu item or by pressing the
114"Fit Background Graphically" button on the
115<A href="expgui3.html#EditBackground">"Edit Background"</A>
116dialog box (invoked from the "Edit Background" button on the
117<A href="expgui3.html">Histogram pane</A>.)
118toolbar
119or
120<OL>
121<LI><a href="#zoom">Zoom in</a> on the lower intensity section of the
122plot, so that the background is clearly discernible. In some cases, the
123data will need to be handled in sections.
124<LI>Press the "Add" button to add background points.
125Note the cursor changes from cross-hairs to an arrow,
126when the "Add" button is pressed.
127<LI>Move the mouse to the first location
128where a background point will be added and click with the left
129mouse button. A magenta triangle will appear at the location.
130Points can be added in any order. It is best to make sure that the fixed points
131are placed over the entire range of the data, e.g. near the maximum and minimum
132data points in TOF, 2theta, etc.
133<DL><DL>
134Note that it is advisable to place many background points in areas where
135the background is changing rapidly (where the background is most bumpy).
136</DL></DL>
137As background points are entered, they are saved in a file named
138<I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>, where
139<I>EXPNAM</I> is the experiment name and <I>N</I> is the histogram number.
140If BKGEDIT is restarted at some later time, these points are reread.
141<LI>If any points are placed in incorrect positions, they can be deleted by
142pressing the "Delete" button. The mouse cursor changes to a circle. When
143the mouse left clicked, the fixed background point closest to the mouse
144position (which may be outside the zoom range) is deleted.
145<LI>Background points can also be edited by entering numbers into the
146"Background points" area.
147<LI>After enough background points have been entered, the
148"Fit" button turns from gray to black. When pressed, the selected
149background function is fitted
150and the resulting curve is shown as a blue dashed line.
151<DL><DL>
152<LI>It is suggested that you start with relatively few
153terms and add terms and background points as needed.
154Note that the maximum number of increases as
155more background points are entered.
156<LI>Editing the terms manually is possible. The curve is reevaluated as
157changes are made.
158<LI>For the type 3 background function (radial distribution function),
159the R terms are listed separately from the other
160background terms. These R (radii) values must be entered manually and
161are not refined.
162</DL></DL>
163<LI>Once a good background function is determined, it can be saved in the
164experiment file by pressing the "Save in EXP file & Exit" button. This will
165set the background type, and save the terms.
166It will also turn off
167the background refinement flag for the appropriate histogram so that the
168terms are not refined inadvertently.
169</OL>
170
171<P>
172Note that POWPREF must be run at least once before BKGEDIT can be used,
173however, use of
174GENLES before BKGEDIT is optional. If the data range is changed, for example
175by excluding a section of the data at the lower end, or changing tmax (dmin),
176the Chebyschev polynomial terms must change to generate the same
177background values, so both POWPREF and BKGEDIT should be rerun to
178regenerate the Chebyschev terms.
179
180<H4>Why not use fixed background points?</H4>
181I personally feel that
182a refined background function is preferrable to use of a fixed model,
183if at all possible.
184One reason for this is that Rietveld refinements usually achieve better fits
185when the background is optimized. A second reason refining the background
186provides a
187feel for the interaction between background values and displacement
188(thermal) parameters.
189Usually, background and displacement parameters are fairly independent, but
190for some materials, where the high Q (high 2theta) portion of the pattern
191has many completely overlapped peaks, it is impossible to uniquely
192determine where the
193background should be placed, either by refinement or by manual placement.
194Under these circumstances, the background should be refined with the
195displacement parameters fixed at an appropriate value for the material. The
196background should then be fixed for all future refinements
197and the displacement parameters can then be refined. <I>Of course this
198means you have predjudiced the refinement to result in the expected
199average displacement parameter and this </I><B>must</B><I> be noted
200any publication. However, if this is necessary, the data simply do not
201contain sufficient information to independently determine
202background and displacement parameters. Use of fixed background points
203would not demonstrate this and would lead the researcher to a false
204sense of security (or fear, if the values are unreasonable)
205that the displacement parameters actually mean something.</I>
206<P>
207If you still want to use fixed background points, despite this tirade,
208be sure to set the estimated
209error on those points to be 0.0. Use of non-zero estimated errors, can
210result in artificially lowered R-factors and chi-squared values.
211In one test, I was able to lower the R<sub>wp</sub> and
212reduced chi<sup>2</sup> values,
213from the correct values of 0.042 and 3.0, respectively, to misleading
214values of 0.036 and 0.8,
215respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045
216with the different fixed background errors;
217FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036,
218so I would consider the refined background to be better.]
219<P>
220If the background is so truly irregular that only use of fixed background
221points will do,
222BKGEDIT can be used to generate these fixed background points.
223The file used by BKGEDIT to save these points,
224<I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>,
225will define the background points if read directly into EXPEDT
226by typing "@R" at the initial prompt in EXPEDT:
227<FONT FACE="COURIER"><PRE>
228   Is this the file you wish to use? (?,D,K,Q,R,Y) ><u>@r</u>
229</PRE></FONT>
230prompt and then supplying the name of the file, in response to the next prompt:
231<FONT FACE="COURIER"><PRE>
232   Enter the name of your macro file: <u>GARNET.bkg1</u>
233</PRE></FONT>
234Doing this will cause the background points you entered into BKGEDIT to
235be used in GSAS
236fixed background points. If you do this you do not want to save the
237fitted background function as well, as this would effectively subtract
238double the desired background.
239Note that GSAS allows simultaneous use of
240both fixed and a refined background;
241this is seldom done.
242
243<hr><h2>LIVEPLOT/BKGEDIT Features</h2>
244<B>Plot contents:</B>
245Reflection markers can be placed using the File/Tickmarks menu item
246<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">or by pressing the
247"1" key for phase 1, "2" for phase 2,... Note that many attributes
248for reflection markers can be edited using
249Options/<a href="#configTick">Configure Tickmarks</a>
250
251<P>
252<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
253If more than one histogram is available to plot, it is possible to cycle
254between the histograms by pressing the "n" or "N" (for next) key.
255<P>
256<a name="zoom"></a>
257<B>Plot zooming:</B>
258When the left (usual) mouse button is pressed, this defines one corner
259of a region to be magnified, as is shown to the right.
260If the mouse is then moved, the diagonal
261corner of this magnification region is defined. When the left mouse button
262is pressed a second time, the selected section of the plot is magnified to
263fill the entire plot.
264<P>
265<img SRC="mzoom.gif" align=RIGHT alt="LIVEPLOT manual zoom">
266Zoom settings are saved.
267If the right mouse button is pressed, the previous zoom setting is used,
268so that the left mouse button is used to "zoom in" and the right mouse
269button is used to "zoom out."
270<P>
271<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
272Zoom settings can also be entered manually by pressing the "Z" key. This
273opens a dialog, as is shown to the right, where the x- or y-axis range
274can be specified. Any value that is not specified is set to the maximum
275or minimum for the entire dataset. It is possible to zoom further in using
276the mouse, but to zoom out beyond the manual zoom limits, the "reset" button
277on the manual zoom menu must be used.
278<P>
279<a name="LiveCursor"></a>
280<img SRC="cursor.gif" align=RIGHT alt="LIVEPLOT live cursor">
281<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
282<B>Cursor Display:</B>
283Pressing the "L" (or "l") key, or using the Option/Show Cursor Position
284menu button causes the position of the cursor (mouse position)
285in plot to be shown. The coordinates are listing in a small area below
286the plot. The position display is updated as the mouse is moved. The
287same key, menu button, or the button labeled "Close cursor display" can be
288used to remove the display.
289<P>
290<br clear=all>
291<h2>Features in LIVEPLOT only</h2>
292<img SRC="lz.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot">
293<a name="Cchi2"></a>
294<B>The cumulative chi<sup>2</sup></B>
295function was first suggested by
296Bill David as a way to see which reflections have the greatest influence on
297chi<sup>2</sup> [W.I.F. David, <I>Accuracy in Powder Diffraction-III</I>, 2001].
298It is defined for point j as
299<IMG SRC="cchi2.gif" alt="equation for cumulative chi2 function" ALIGN=TOP>
300where y<sub>obs,i</sub> and y<sub>calc,i</sub> are the observed and computed
301data points and sigma<sub>i</sub> is the expected error. Thus, the statistically
302expected value for
303[(y<sub>obs,i</sub>-y<sub>calc,i</sub>)/sigma<sub>i</sub>]<sup>2</sup> is 1
304and this function should rise in a smooth line if all points are fitted as
305statistically expected.
306<P>
307In the plot to the right, the cumulative chi<sup>2</sup> function is shown in
308purple. Note that first peak is not well fit, but the low angle "shoulder" is
309as important as the peak misfitting, with respect to the chi<sup>2</sup>.
310<br clear=all>
311<P>
312<img SRC="lind.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot">
313<B>Reflection indices</B>
314are be displayed by pressing "H" or "h" while the
315mouse is near a reflection (holding the shift key while
316pressing the left mouse button also works, but sometimes interferes with the
317zoom feature).
318Pressing "A" or "a" shows all reflections in the displayed region.
319The indices are shown
320on the screen for phases with tickmarks (as shown to the right).
321Indices are listed in the "Separate window for <I>hkl</I> labels"
322(as seen below) for all phases, regardless of the tickmark settings.
323Displayed indices will remain on the screen for a preset time and
324then will be deleted; alternately, pressing "D" or "d" deletes the hkl labels.
325Several aspects of reflection labeling can be customized,
326see the <a href="#hklOpts">HKL labeling options</a> for further information.
327
328<img SRC="lind1.gif" align=LEFT alt="LIVEPLOT Screen snapshot">
329
330<br clear=all>
331<P>
332<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
333<B>Export plot to Grace</B>
334The plot can be exported to
335<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
336that produces publication-quality graphics. Many UNIX users know
337this program under a previous name, xmgr.
338The export is implemented
339by producing an ASCII file with instructions that
340creates a plot with similar formatting to what appears on the
341screen in LIVEPLOT/BKGEDIT. However, the output quality from
342Grace is much higher quality. Further, Grace
343can be used to enhanced and annotate the plot further.
344
345<hr><h2>LIVEPLOT/BKGEDIT Menu Contents</h2>
346A few of these options are omitted from BKGEDIT.
347<img SRC="lm1.gif" align=RIGHT alt="LIVEPLOT Menu">
348<H3>File Menu</H3>
349<DL><DL>
350<DT>Tickmarks
351<DD>Checkbuttons are provided for each phase to determine if tick marks
352will be shown.
353<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">Tickmarks can also be
354toggled by pressing the
355"1" key for phase 1, "2" for phase 2,...
356Also see the Options/<a href="#configTick">Configure Tickmarks</a>
357menu item for information
358on tickmarks.
359<DT>Histogram
360<DD>This allows a histogram to be selected to be loaded
361<DL><DL>
362<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
363It is also possible to advance
364between the histograms by pressing the "n" or "N" (for next) key.
365</DL></DL>
366<DT>Update Plot
367<DD>The causes LIVEPLOT to read read the current histogram again from
368the datafile
369<DT>Export Plot
370<DD>This offers options for exporting the plot in multiple formats.
371I am hoping to add more export formats eventually.
372<DL><DL>
373<DT>to PostScript
374<DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT
375output. See the Options/"Set PS output" button for where the file is created.
376Most unix systems are capable or printing PostScript files.
377On Windows, a program such ghostview may be needed to translate the
378PostScript to a format that can be viewed or printed.
379<A name="grace">
380<DT>to Grace
381<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
382<DD>Plots can be exported to
383<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
384that produces publication-quality graphics.
385After the plot is exported, it can be further
386enhanced and annotated in grace.
387</DL></DL>
388<DT>Quit
389<DD>Exits BKGEDIT/LIVEPLOT.
390</DL></DL>
391<br clear=all>
392<img SRC="lm2.gif" align=RIGHT alt="LIVEPLOT Menu">
393<H3>Options Menu</H3>
394<DL><DL>
395<a name="configTick"></a>
396<DT>Configure Tickmarks<DD>
397This submenu provides options that controls how tickmarks are displayed.
398<DL><DL>
399<DT>Auto locate<DD>
400When this option is selected, tickmarks are placed in different positions
401for each phase, automatically, similar to how tickmarks are shown in POWPLOT.
402<DT>Manual Placement<DD>
403Tickmarks are drawn at specific heights that can be set for each phase
404(see below). The default
405is for lines to be draw from "-Inf" to "Inf", which creates lines from the
406bottom to the top of the plot.
407<DT>Label by name
408<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
409<DD>
410By default, a label "Phase1",... is displayed in the legend when tickmarks
411for that phase are displayed. When this button is pressed, the first
41220 characters of each phase name (phase title) are used instead. This
413label can be edited, as described in the next paragraph.
414<DT>Phase <I>n</I> opts<DD>
415The options for each phase allow the line to be changed between
416solid and dashed, color of the line can be specified and
417the vertical placement of the tickmarks can be specified. The
418"Show Reflections" flag,
419set in the File/Tickmarks menu,
420as well as the label used for the phase can also be changed here.
421
422</DL></DL>
423<DT>Obs Symbol (Symbol Type)
424<DD>This brings up a menu where the symbol type and size for the
425observed data points (and for BKGEDIT, the fixed background points)
426can be selected.
427<DT>Symbol Color
428<DD>The colors for all the displayed lines and symbols can be changed here.
429<DT>X units
430<DD>The x units can be selected here. The choices are
431"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
432<DT>Y units
433<DD>The intensity values can be normalized by the incident spectrum
434(for energy dispersive methods).
435</DL></DL>
436<br clear=all>
437<img SRC="lm3.gif" align=RIGHT alt="LIVEPLOT menu">
438<a name="hklOpts"></a>
439<DL><DL>
440<DT>HKL labeling
441<DD>This brings up a menu that selects
442<UL><LI>Erase time:
443how long in seconds that <I>hkl</I> values are shown
444before they are erased (0 means that they are not erased),
445<LI>Label size: the size of the
446labels in pixels,
447<LI>Search Region: only reflections within this number of pixels of the mouse,
448when the "h" key is pressed (if any) are labeled,
449<LI>Separate window: when this
450option is selected, reflection labels are shown in a text window
451</UL>
452<DT>Subtract background
453<DD>The background is always shown, even when subtracted
454<DT>Include legend
455<DD>The legend is the optional box in the upper left that defines the
456plot entries
457<DT>Show [Hide] Cursor Position
458<DD>This turns <a href="#LiveCursor">Cursor position display</a> on and off.
459<DT>Set PS output
460<DD>For UNIX this allows the file to be sent directly to a printer
461or can be saved in a file. For Windows, a file must be written.
462<DT>Set screen font
463<DD>This option is used to control the font used for menus, graphics and
464other aspects of windows.
465<DT>Raise on update
466<DD>This causes the plot to be placed on top of other windows, if partially
467obscured, when the plot is updated. At this time, this option does not
468work in Windows-NT and -2000.
469<DT>Cumulative Chi2
470<DD>The causes the Cumulative chi<sup>2</sup> function to be displayed
471(as <a href="#Cchi2">presented above</a>).
472<DT>Save Options
473<DD>Causes many of the options set in this menu to be saved in the <FONT FACE="COURIER">.gsas_config</FONT> file.
474</DL></DL>
475<br clear=all>
476
477<P>
478<hr><H2>Customization of LIVEPLOT & BKGEDIT</H2><A NAME="customize"></A>
479The <FONT FACE="COURIER">localconfig</FONT> and <FONT FACE="COURIER">.gsas_config</FONT> files are read, if present.
480The following variables control how LIVEPLOT, and in most cases BKGEDIT,
481function and can be
482customized by changing their values in the
483<FONT FACE="COURIER">localconfig</FONT> and <FONT FACE="COURIER">.gsas_config</FONT> files.
484Note that some of these options are relevant only if the tcldump program is
485present.
486<DL><DL>
487<DT><FONT FACE="COURIER">peakinfo(flag<i>n</i>)</FONT><DD>
488These variables define if peak positions will be shown
489for reflections in phase "<i>n</i>". Reflections will be shown if
490the value is non-zero.
491
492<DT><FONT FACE="COURIER">peakinfo(color<i>n</i>)</FONT><DD>
493These variables define the default colors for
494reflections in phase "<i>n</i>"
495
496<DT><FONT FACE="COURIER">peakinfo(dashes<i>n</i>)</FONT><DD>
497These variables define if peaks will be dashed for
498reflections in phase "<i>n</i>" (UNIX only). Lines will be dashed if
499the value is non-zero.
500
501<DT><FONT FACE="COURIER">peakinfo(min<i>n</i>) and peakinfo(max<i>n</i>)</FONT><DD>
502These variables dictate the placement vertical position for reflection
503markers, when manually placed (see expgui(autotick), below). To draw
504to the edge of the screen, use -Inf and Inf.
505</DL></DL>
506
507The following variables are written to <font face="courier">.gsas_config</font> when
508"Save Options" is used. These variables are all set from the GUI and therefore
509do not need to be edited manually.
510
511<DL><DL>
512<DT><FONT FACE="COURIER">graph(printout)</FONT><DD>
513This is set to 1 if PostScript files
514will be printed and 0 if they will be written to disk (for Windows all
515files should be written to disk).
516
517<DT><FONT FACE="COURIER">graph(outname)</FONT><DD>
518This is the default for the file name used
519when PostScript files will be written to disk.
520
521<DT><FONT FACE="COURIER">graph(outcmd)</FONT><DD>
522This is the default for the command used
523to print PostScript files (Unix only).
524
525<DT><FONT FACE="COURIER">graph(legend)</FONT><DD>
526Sets the default value for display of the legend in LIVEPLOT and WIDPLT.
527
528<DT><FONT FACE="COURIER">graph(autoraise)</FONT><DD>
529This option shows up in the options menu item as "Raise on update."
530When set to non-zero, the LIVEPLOT window is raised
531(placed on top of any other overlapping) windows
532each time it is updated.
533This option does not seem to work in Windows-NT, but this may depend on
534the version of Tcl/Tk.
535
536<DT><FONT FACE="COURIER">peakinfo(obssym)</FONT><DD>
537Symbol for observed data points. Valid choices are square, circle, diamond,
538plus, cross, splus and scross.
539
540<DT><FONT FACE="COURIER">peakinfo(obssize)</FONT><DD>
541Size for the symbol for observed data points. A value of 1 corresponds to about 1/8 inch
542(about 3 mm).
543
544<DT><FONT FACE="COURIER">expgui(pixelregion)</FONT><DD>
545When hkl values are loaded (using tcldump) and reflections are labeled, reflections
546can be labeled using a Shift-Left-Mouse click. All labeled reflections within expgui(pixelregion)
547pixels of the mouse position are assumed to be overlapped and are labeled.
548
549<DT><FONT FACE="COURIER">expgui(fadetime)</FONT><DD>
550The time in seconds before reflection labels are removed. A value of zero means that reflections
551must be deleted manually (Shift-Right-Mouse).
552
553<DT><FONT FACE="COURIER">expgui(lblfontsize)</FONT><DD>
554A size for reflections labels in pixels.
555
556<DT><FONT FACE="COURIER">expgui(hklbox)</FONT><DD>
557If this variable is non-zero, reflection indices are shown in a box.
558
559<DT><FONT FACE="COURIER">expgui(autotick)</FONT><DD>
560If this variable is non-zero, reflection markers positions are
561set automatically.
562</DL></DL>
563<P>
564<hr><H2>Installation details/External Programs</H2>
565<B>Using TCLDUMP with LIVEPLOT.</B>
566LIVEPLOT works with the standard GSAS program HSTDMP, but it works faster and is more
567powerful when used with the TCLDUMP program.
568Note that as of the April 2000 releases, GSAS is now distributed with TCLDUMP
569included. For older versions of GSAS, note the
570instructions for downloading this file can in the installation notes for
571<A HREF="expgui_Win_readme.html">
572Windows</A> and
573<A HREF="expgui_Unix_readme.html">
574UNIX</A>.
575<P>
576
577<B>Combining CMPR and LIVEPLOT.</B>
578If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">CMPR</A>
579installed on your computer, you can use superimpose on the GSAS results
580the peaks for an arbitrary unit cell. If desired, space group extinctions
581can even be shown.
582This is pretty neat! To enable this feature, you must have a version
583of CMPR downloaded after 4 May 1998
584<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">
585(see link for CMPR installation instructions.)</A>
586<UL><LI>
587For UNIX, create a link from in the EXPGUI
588directory to file cellgen.tcl in the CMPR directory. For example:
589<FONT FACE="COURIER"><PRE>
590   ln -s /usr/local/cmpr/cellgen.tcl /usr/local/gsas/expgui/cellgen.tcl
591</PRE></FONT>
592<LI>For Windows, copy all the .tcl and .exe files from the CMPR directory
593into the EXPGUI directory.
594</UL>
595<P>
596
597<B>Combining LOGIC and LIVEPLOT.</B>
598If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">LOGIC</A>
599installed on your computer, you can superimpose peaks
600for a entry from the ICDD/JCPDS database on a pattern in LIVEPLOT.
601This is also pretty neat!
602To enable this feature, you must have
603a version of LOGIC downloaded after 4 May 1998
604<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">
605(see the LOGIC installation instructions.)</A>
606<UL><LI>
607For UNIX, create a link from in the GSAS GUI
608directory to file icddcmd.tcl in the LOGIC directory. For example:
609<FONT FACE="COURIER"><PRE>
610   ln -s /usr/local/powdersuite/icddcmd.tcl /usr/local/gsas/expgui/icddcmd.tcl
611</PRE></FONT>
612<LI>For Windows, copy all the LOGIC files into the EXPGUI directory.
613</UL>
614<hr>
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620
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624$Revision: 580 $ $Date: 2009-12-04 23:08:33 +0000 (Fri, 04 Dec 2009) $
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