source: trunk/doc/liveplot.html @ 710

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change to GSAS.CONFIG for Windows

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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">
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" 
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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>
25</TH><TH><A Href="expguic.html">Previous page</A>
26</TH></TR></TABLE><BR CLEAR=ALL>
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<LI>
79<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
80Plots can be <a href="#export">exported to obtain publication-quality
81graphics.</a>
82</UL>
83
84<a name="bkgedit"></a>
85<H3>BKGEDIT</H3>
86<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
87BKGEDIT is used to fit a background function to a set of points
88selected by the user.
89For most refinements, this is not needed,
90as it is possible to simply select a background
91function (I find that the type 1 function,
92shifted Chebyschev polynomials, works well)
93and then refine, adding terms until a good fit is obtained.
94On occasion, poor initial fits are obtained in this manner. This is
95most common in cases where large numbers of peaks are poorly fit. Since
96significant sections of the data are not well fit, the refinement results in
97an unreasonable background function, because this yields better agreement
98with the observed data.
99In these cases,
100it may be best to fix the background to follow a "reasonable" curve in the
101initial stages and then refine the background in the final stages of
102refinement, when a good model has been obtained.
103<P>
104The BKGEDIT program, as shown below, is used to input a set a background
105points via the mouse. The points are then used to determine a type 1
106(Chebyschev) background function that fits the input background points. These
107terms can then be saved in the experiment file creating a background that
108is good enough for the initial stages of refinement and that can be
109refined once the model is adequate for the task.
110<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
111BKGEDIT can be used to fit GSAS background functions 1-6 (though
112for most purposes only type 1 is needed.)
113<P>
114<IMG SRC="b1.gif" align=TEXTOP alt="BKGEDIT screen image">
115<H4>Steps in fitting a background function</H4>
116The BKGEDIT program is started from
117via the Powder/bkgedit menu item or by pressing the
118"Fit Background Graphically" button on the
119<A href="expgui3.html#EditBackground">"Edit Background"</A>
120dialog box (invoked from the "Edit Background" button on the
121<A href="expgui3.html">Histogram pane</A>.)
122toolbar
123or
124<OL>
125<LI><a href="#zoom">Zoom in</a> on the lower intensity section of the
126plot, so that the background is clearly discernible. In some cases, the
127data will need to be handled in sections.
128<LI>Press the "Add" button to add background points.
129Note the cursor changes from cross-hairs to an arrow,
130when the "Add" button is pressed.
131<LI>Move the mouse to the first location
132where a background point will be added and click with the left
133mouse button. A magenta triangle will appear at the location.
134Points can be added in any order. It is best to make sure that the fixed points
135are placed over the entire range of the data, e.g. near the maximum and minimum
136data points in TOF, 2theta, etc.
137<DL><DL>
138Note that it is advisable to place many background points in areas where
139the background is changing rapidly (where the background is most bumpy).
140</DL></DL>
141As background points are entered, they are saved in a file named
142<I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>, where
143<I>EXPNAM</I> is the experiment name and <I>N</I> is the histogram number.
144If BKGEDIT is restarted at some later time, these points are reread.
145<LI>If any points are placed in incorrect positions, they can be deleted by
146pressing the "Delete" button. The mouse cursor changes to a circle. When
147the mouse left clicked, the fixed background point closest to the mouse
148position (which may be outside the zoom range) is deleted.
149<LI>Background points can also be edited by entering numbers into the
150"Background points" area.
151<LI>After enough background points have been entered, the
152"Fit" button turns from gray to black. When pressed, the selected
153background function is fitted
154and the resulting curve is shown as a blue dashed line.
155<DL><DL>
156<LI>It is suggested that you start with relatively few
157terms and add terms and background points as needed.
158Note that the maximum number of increases as
159more background points are entered.
160<LI>Editing the terms manually is possible. The curve is reevaluated as
161changes are made.
162<LI>For the type 3 background function (radial distribution function),
163the R terms are listed separately from the other
164background terms. These R (radii) values must be entered manually and
165are not refined.
166</DL></DL>
167<LI>Once a good background function is determined, it can be saved in the
168experiment file by pressing the "Save in EXP file & Exit" button. This will
169set the background type, and save the terms.
170It will also turn off
171the background refinement flag for the appropriate histogram so that the
172terms are not refined inadvertently.
173</OL>
174
175<P>
176Note that POWPREF must be run at least once before BKGEDIT can be used,
177however, use of
178GENLES before BKGEDIT is optional. If the data range is changed, for example
179by excluding a section of the data at the lower end, or changing tmax (dmin),
180the Chebyschev polynomial terms must change to generate the same
181background values, so both POWPREF and BKGEDIT should be rerun to
182regenerate the Chebyschev terms.
183
184<H4>Why not use fixed background points?</H4>
185I personally feel that
186a refined background function is preferrable to use of a fixed model,
187if at all possible.
188One reason for this is that Rietveld refinements usually achieve better fits
189when the background is optimized. A second reason refining the background
190provides a
191feel for the interaction between background values and displacement
192(thermal) parameters.
193Usually, background and displacement parameters are fairly independent, but
194for some materials, where the high Q (high 2theta) portion of the pattern
195has many completely overlapped peaks, it is impossible to uniquely
196determine where the
197background should be placed, either by refinement or by manual placement.
198Under these circumstances, the background should be refined with the
199displacement parameters fixed at an appropriate value for the material. The
200background should then be fixed for all future refinements
201and the displacement parameters can then be refined. <I>Of course this
202means you have predjudiced the refinement to result in the expected
203average displacement parameter and this </I><B>must</B><I> be noted
204any publication. However, if this is necessary, the data simply do not
205contain sufficient information to independently determine
206background and displacement parameters. Use of fixed background points
207would not demonstrate this and would lead the researcher to a false
208sense of security (or fear, if the values are unreasonable)
209that the displacement parameters actually mean something.</I>
210<P>
211If you still want to use fixed background points, despite this tirade,
212be sure to set the estimated
213error on those points to be 0.0. Use of non-zero estimated errors, can
214result in artificially lowered R-factors and chi-squared values.
215In one test, I was able to lower the R<sub>wp</sub> and
216reduced chi<sup>2</sup> values,
217from the correct values of 0.042 and 3.0, respectively, to misleading
218values of 0.036 and 0.8,
219respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045
220with the different fixed background errors;
221FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036,
222so I would consider the refined background to be better.]
223<P>
224If the background is so truly irregular that only use of fixed background
225points will do,
226BKGEDIT can be used to generate these fixed background points.
227The file used by BKGEDIT to save these points,
228<I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>,
229will define the background points if read directly into EXPEDT
230by typing "@R" at the initial prompt in EXPEDT:
231<FONT FACE="COURIER"><PRE>
232   Is this the file you wish to use? (?,D,K,Q,R,Y) ><u>@r</u>
233</PRE></FONT>
234prompt and then supplying the name of the file, in response to the next prompt:
235<FONT FACE="COURIER"><PRE>
236   Enter the name of your macro file: <u>GARNET.bkg1</u>
237</PRE></FONT>
238Doing this will cause the background points you entered into BKGEDIT to
239be used in GSAS
240fixed background points. If you do this you do not want to save the
241fitted background function as well, as this would effectively subtract
242double the desired background.
243Note that GSAS allows simultaneous use of
244both fixed and a refined background;
245this is seldom done.
246
247<hr><h2>LIVEPLOT/BKGEDIT Features</h2>
248<B>Plot contents:</B>
249Reflection markers can be placed using the File/Tickmarks menu item
250<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">or by pressing the
251"1" key for phase 1, "2" for phase 2,... Note that many attributes
252for reflection markers can be edited using
253Options/<a href="#configTick">Configure Tickmarks</a>
254
255<P>
256<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
257If more than one histogram is available to plot, it is possible to cycle
258between the histograms by pressing the "n" or "N" (for next) key.
259<P>
260<a name="zoom"></a>
261<B>Plot zooming:</B>
262When the left (usual) mouse button is pressed, this defines one corner
263of a region to be magnified, as is shown to the right.
264If the mouse is then moved, the diagonal
265corner of this magnification region is defined. When the left mouse button
266is pressed a second time, the selected section of the plot is magnified to
267fill the entire plot.
268<P>
269<img SRC="mzoom.gif" align=RIGHT alt="LIVEPLOT manual zoom">
270Zoom settings are saved.
271If the right mouse button is pressed, the previous zoom setting is used,
272so that the left mouse button is used to "zoom in" and the right mouse
273button is used to "zoom out."
274<P>
275<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
276Zoom settings can also be entered manually by pressing the "Z" key. This
277opens a dialog, as is shown to the right, where the x- or y-axis range
278can be specified. Any value that is not specified is set to the maximum
279or minimum for the entire dataset. It is possible to zoom further in using
280the mouse, but to zoom out beyond the manual zoom limits, the "reset" button
281on the manual zoom menu must be used.
282<P>
283<a name="LiveCursor"></a>
284<img SRC="cursor.gif" align=RIGHT alt="LIVEPLOT live cursor">
285<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
286<B>Cursor Display:</B>
287Pressing the "L" (or "l") key, or using the Option/Show Cursor Position
288menu button causes the position of the cursor (mouse position)
289in plot to be shown. The coordinates are listing in a small area below
290the plot. The position display is updated as the mouse is moved. The
291same key, menu button, or the button labeled "Close cursor display" can be
292used to remove the display.
293<P>
294<br clear=all>
295<h2>Features in LIVEPLOT only</h2>
296<img SRC="lz.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot">
297<a name="Cchi2"></a>
298<B>The cumulative chi<sup>2</sup></B>
299function was first suggested by
300Bill David as a way to see which reflections have the greatest influence on
301chi<sup>2</sup> [W.I.F. David, <I>Accuracy in Powder Diffraction-III</I>, 2001].
302It is defined for point j as
303<IMG SRC="cchi2.gif" alt="equation for cumulative chi2 function" ALIGN=TOP>
304where y<sub>obs,i</sub> and y<sub>calc,i</sub> are the observed and computed
305data points and sigma<sub>i</sub> is the expected error. Thus, the statistically
306expected value for
307[(y<sub>obs,i</sub>-y<sub>calc,i</sub>)/sigma<sub>i</sub>]<sup>2</sup> is 1
308and this function should rise in a smooth line if all points are fitted as
309statistically expected.
310<P>
311In the plot to the right, the cumulative chi<sup>2</sup> function is shown in
312purple. Note that first peak is not well fit, but the low angle "shoulder" is
313as important as the peak misfitting, with respect to the chi<sup>2</sup>.
314<br clear=all>
315<P>
316<img SRC="lind.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot">
317<B>Reflection indices</B>
318are be displayed by pressing "H" or "h" while the
319mouse is near a reflection (holding the shift key while
320pressing the left mouse button also works, but sometimes interferes with the
321zoom feature).
322Pressing "A" or "a" shows all reflections in the displayed region.
323The indices are shown
324on the screen for phases with tickmarks (as shown to the right).
325Indices are listed in the "Separate window for <I>hkl</I> labels"
326(as seen below) for all phases, regardless of the tickmark settings.
327Displayed indices will remain on the screen for a preset time and
328then will be deleted; alternately, pressing "D" or "d" deletes the hkl labels.
329Several aspects of reflection labeling can be customized,
330see the <a href="#hklOpts">HKL labeling options</a> for further information.
331
332<img SRC="lind1.gif" align=LEFT alt="LIVEPLOT Screen snapshot">
333
334<br clear=all>
335<P>
336<a name="export"></a>
337<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
338<B>Export plot options</B>
339<UL><LI>
340The plot can be exported to
341<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
342that produces publication-quality graphics. Many UNIX users know
343this program under a previous name, xmgr.
344The export is implemented
345by producing an ASCII file with instructions that
346creates a plot with similar formatting to what appears on the
347screen in LIVEPLOT/BKGEDIT. However, the output quality from
348Grace is much higher quality. Further, Grace
349can be used to enhanced and annotate the plot further.
350<LI>
351For use in many other graphics programs, LIVEPLOT will produce a
352"comma separated variable" data file with the data displayed on the screen.
353The user will need to read this in,
354set line styles and scaling, etc., but this does provide an option for
355generating high-quality graphics for presentations and publications.
356<LI>LIVEPLOT will produce PostScript versions of the plot on the screen,
357but the quality is rather low (this is a limitation of the BLT graphics
358package).
359</UL>
360
361<hr><h2>LIVEPLOT/BKGEDIT Menu Contents</h2>
362A few of these options are omitted from BKGEDIT.
363<img SRC="lm1.gif" align=RIGHT alt="LIVEPLOT Menu">
364<H3>File Menu</H3>
365<DL><DL>
366<DT>Tickmarks
367<DD>Checkbuttons are provided for each phase to determine if tick marks
368will be shown.
369<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">Tickmarks can also be
370toggled by pressing the
371"1" key for phase 1, "2" for phase 2,...
372Also see the Options/<a href="#configTick">Configure Tickmarks</a>
373menu item for information
374on tickmarks.
375<DT>Histogram
376<DD>This allows a histogram to be selected to be loaded
377<DL><DL>
378<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
379It is also possible to advance
380between the histograms by pressing the "n" or "N" (for next) key.
381</DL></DL>
382<DT>Update Plot
383<DD>The causes LIVEPLOT to read read the current histogram again from
384the datafile
385<DT>Export Plot
386<DD>This offers options for exporting the plot in multiple formats.
387I am hoping to add more export formats eventually.
388<DL><DL>
389<DT>to PostScript
390<DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT
391output. See the Options/"Set PS output" button for where the file is created.
392Most unix systems are capable or printing PostScript files.
393On Windows, a program such ghostview may be needed to translate the
394PostScript to a format that can be viewed or printed.
395<A name="grace">
396<DT>to Grace
397<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
398<DD>Plots can be exported to
399<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
400that produces publication-quality graphics.
401After the plot is exported, it can be further
402enhanced and annotated in grace.
403</DL></DL>
404<DT>Quit
405<DD>Exits BKGEDIT/LIVEPLOT.
406</DL></DL>
407<br clear=all>
408<img SRC="lm2.gif" align=RIGHT alt="LIVEPLOT Menu">
409<H3>Options Menu</H3>
410<DL><DL>
411<a name="configTick"></a>
412<DT>Configure Tickmarks<DD>
413This submenu provides options that controls how tickmarks are displayed.
414<DL><DL>
415<DT>Auto locate<DD>
416When this option is selected, tickmarks are placed in different positions
417for each phase, automatically, similar to how tickmarks are shown in POWPLOT.
418<DT>Manual Placement<DD>
419Tickmarks are drawn at specific heights that can be set for each phase
420(see below). The default
421is for lines to be draw from "-Inf" to "Inf", which creates lines from the
422bottom to the top of the plot.
423<DT>Label by name
424<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
425<DD>
426By default, a label "Phase1",... is displayed in the legend when tickmarks
427for that phase are displayed. When this button is pressed, the first
42820 characters of each phase name (phase title) are used instead. This
429label can be edited, as described in the next paragraph.
430<DT>Phase <I>n</I> opts<DD>
431The options for each phase allow the line to be changed between
432solid and dashed, color of the line can be specified and
433the vertical placement of the tickmarks can be specified. The
434"Show Reflections" flag,
435set in the File/Tickmarks menu,
436as well as the label used for the phase can also be changed here.
437
438</DL></DL>
439<DT>Obs Symbol (Symbol Type)
440<DD>This brings up a menu where the symbol type and size for the
441observed data points (and for BKGEDIT, the fixed background points)
442can be selected.
443<DT>Symbol Color
444<DD>The colors for all the displayed lines and symbols can be changed here.
445<DT>X units
446<DD>The x units can be selected here. The choices are
447"as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>)
448<DT>Y units
449<DD>The intensity values can be normalized by the incident spectrum
450(for energy dispersive methods).
451</DL></DL>
452<br clear=all>
453<img SRC="lm3.gif" align=RIGHT alt="LIVEPLOT menu">
454<a name="hklOpts"></a>
455<DL><DL>
456<DT>HKL labeling
457<DD>This brings up a menu that selects
458<UL><LI>Erase time:
459how long in seconds that <I>hkl</I> values are shown
460before they are erased (0 means that they are not erased),
461<LI>Label size: the size of the
462labels in pixels,
463<LI>Search Region: only reflections within this number of pixels of the mouse,
464when the "h" key is pressed (if any) are labeled,
465<LI>Separate window: when this
466option is selected, reflection labels are shown in a text window
467</UL>
468<DT>Subtract background
469<DD>The background is always shown, even when subtracted
470<DT>Include legend
471<DD>The legend is the optional box in the upper left that defines the
472plot entries
473<DT>Show [Hide] Cursor Position
474<DD>This turns <a href="#LiveCursor">Cursor position display</a> on and off.
475<DT>Set PS output
476<DD>For UNIX this allows the file to be sent directly to a printer
477or can be saved in a file. For Windows, a file must be written.
478<DT>Set screen font
479<DD>This option is used to control the font used for menus, graphics and
480other aspects of windows.
481<DT>Raise on update
482<DD>This causes the plot to be placed on top of other windows, if partially
483obscured, when the plot is updated. At this time, this option does not
484work in Windows-NT and -2000.
485<DT>Cumulative Chi2
486<DD>The causes the Cumulative chi<sup>2</sup> function to be displayed
487(as <a href="#Cchi2">presented above</a>).
488<DT>Save Options
489<DD>Causes many of the options set in this menu to be saved in the
490<FONT FACE="COURIER">.gsas_config</FONT> 
491(or <FONT FACE="COURIER">c:\gsas.config</FONT>) file.
492</DL></DL>
493<br clear=all>
494
495<P>
496<hr><H2>Customization of LIVEPLOT & BKGEDIT</H2><A NAME="customize"></A>
497The <FONT FACE="COURIER">localconfig</FONT> and
498<FONT FACE="COURIER">.gsas_config</FONT> 
499(or <FONT FACE="COURIER">c:\gsas.config</FONT>)
500files are read, if present.
501The following variables control how LIVEPLOT, and in most cases BKGEDIT,
502function and can be
503customized by changing their values in the
504<FONT FACE="COURIER">localconfig</FONT> and
505<FONT FACE="COURIER">.gsas_config</FONT> 
506(or <FONT FACE="COURIER">c:\gsas.config</FONT>)
507files.
508Note that some of these options are relevant only if the tcldump program is
509present.
510<DL><DL>
511<DT><FONT FACE="COURIER">peakinfo(flag<i>n</i>)</FONT><DD>
512These variables define if peak positions will be shown
513for reflections in phase "<i>n</i>". Reflections will be shown if
514the value is non-zero.
515
516<DT><FONT FACE="COURIER">peakinfo(color<i>n</i>)</FONT><DD>
517These variables define the default colors for
518reflections in phase "<i>n</i>"
519
520<DT><FONT FACE="COURIER">peakinfo(dashes<i>n</i>)</FONT><DD>
521These variables define if peaks will be dashed for
522reflections in phase "<i>n</i>" (UNIX only). Lines will be dashed if
523the value is non-zero.
524
525<DT><FONT FACE="COURIER">peakinfo(min<i>n</i>) and peakinfo(max<i>n</i>)</FONT><DD>
526These variables dictate the placement vertical position for reflection
527markers, when manually placed (see expgui(autotick), below). To draw
528to the edge of the screen, use -Inf and Inf.
529</DL></DL>
530
531The following variables are written to
532<font face="courier">.gsas_config</font> 
533(or <FONT FACE="COURIER">c:\gsas.config</FONT>)
534when
535"Save Options" is used. These variables are all set from the GUI and therefore
536do not need to be edited manually.
537
538<DL><DL>
539<DT><FONT FACE="COURIER">graph(printout)</FONT><DD>
540This is set to 1 if PostScript files
541will be printed and 0 if they will be written to disk (for Windows all
542files should be written to disk).
543
544<DT><FONT FACE="COURIER">graph(outname)</FONT><DD>
545This is the default for the file name used
546when PostScript files will be written to disk.
547
548<DT><FONT FACE="COURIER">graph(outcmd)</FONT><DD>
549This is the default for the command used
550to print PostScript files (Unix only).
551
552<DT><FONT FACE="COURIER">graph(legend)</FONT><DD>
553Sets the default value for display of the legend in LIVEPLOT and WIDPLT.
554
555<DT><FONT FACE="COURIER">graph(autoraise)</FONT><DD>
556This option shows up in the options menu item as "Raise on update."
557When set to non-zero, the LIVEPLOT window is raised
558(placed on top of any other overlapping) windows
559each time it is updated.
560This option does not seem to work in Windows-NT, but this may depend on
561the version of Tcl/Tk.
562
563<DT><FONT FACE="COURIER">peakinfo(obssym)</FONT><DD>
564Symbol for observed data points. Valid choices are square, circle, diamond,
565plus, cross, splus and scross.
566
567<DT><FONT FACE="COURIER">peakinfo(obssize)</FONT><DD>
568Size for the symbol for observed data points. A value of 1 corresponds to about 1/8 inch
569(about 3 mm).
570
571<DT><FONT FACE="COURIER">expgui(pixelregion)</FONT><DD>
572When hkl values are loaded (using tcldump) and reflections are labeled, reflections
573can be labeled using a Shift-Left-Mouse click. All labeled reflections within expgui(pixelregion)
574pixels of the mouse position are assumed to be overlapped and are labeled.
575
576<DT><FONT FACE="COURIER">expgui(fadetime)</FONT><DD>
577The time in seconds before reflection labels are removed. A value of zero means that reflections
578must be deleted manually (Shift-Right-Mouse).
579
580<DT><FONT FACE="COURIER">expgui(lblfontsize)</FONT><DD>
581A size for reflections labels in pixels.
582
583<DT><FONT FACE="COURIER">expgui(hklbox)</FONT><DD>
584If this variable is non-zero, reflection indices are shown in a box.
585
586<DT><FONT FACE="COURIER">expgui(autotick)</FONT><DD>
587If this variable is non-zero, reflection markers positions are
588set automatically.
589</DL></DL>
590<P>
591<hr><H2>Installation details/External Programs</H2>
592<B>Using TCLDUMP with LIVEPLOT.</B>
593LIVEPLOT works with the standard GSAS program HSTDMP, but it works faster and is more
594powerful when used with the TCLDUMP program.
595Note that as of the April 2000 releases, GSAS is now distributed with TCLDUMP
596included. For older versions of GSAS, note the
597instructions for downloading this file can in the installation notes for
598<A HREF="expgui_Win_readme.html">
599Windows</A> and
600<A HREF="expgui_Unix_readme.html">
601UNIX</A>.
602<P>
603
604<B>Combining CMPR and LIVEPLOT.</B>
605If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">CMPR</A>
606installed on your computer, you can use superimpose on the GSAS results
607the peaks for an arbitrary unit cell. If desired, space group extinctions
608can even be shown.
609This is pretty neat! To enable this feature, you must have a version
610of CMPR downloaded after 4 May 1998
611<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">
612(see link for CMPR installation instructions.)</A>
613<UL><LI>
614For UNIX, create a link from in the EXPGUI
615directory to file cellgen.tcl in the CMPR directory. For example:
616<FONT FACE="COURIER"><PRE>
617   ln -s /usr/local/cmpr/cellgen.tcl /usr/local/gsas/expgui/cellgen.tcl
618</PRE></FONT>
619<LI>For Windows, copy all the .tcl and .exe files from the CMPR directory
620into the EXPGUI directory.
621</UL>
622<P>
623
624<B>Combining LOGIC and LIVEPLOT.</B>
625If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">LOGIC</A>
626installed on your computer, you can superimpose peaks
627for a entry from the ICDD/JCPDS database on a pattern in LIVEPLOT.
628This is also pretty neat!
629To enable this feature, you must have
630a version of LOGIC downloaded after 4 May 1998
631<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">
632(see the LOGIC installation instructions.)</A>
633<UL><LI>
634For UNIX, create a link from in the GSAS GUI
635directory to file icddcmd.tcl in the LOGIC directory. For example:
636<FONT FACE="COURIER"><PRE>
637   ln -s /usr/local/powdersuite/icddcmd.tcl /usr/local/gsas/expgui/icddcmd.tcl
638</PRE></FONT>
639<LI>For Windows, copy all the LOGIC files into the EXPGUI directory.
640</UL>
641<hr>
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651$Revision: 710 $ $Date: 2009-12-04 23:10:43 +0000 (Fri, 04 Dec 2009) $
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