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Timestamp:
Dec 4, 2009 5:11:24 PM (11 years ago)
Author:
toby
Message:

# on 2003/11/13 17:31:03, toby did:
revise to remove info about TCLDUMP (now standard in GSAS)
revise CMPR/LOGIC references

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  • trunk/doc/liveplot.html

    • Property rcs:date changed from 2003/05/22 22:07:46 to 2003/11/13 17:31:03
    • Property rcs:lines changed from +16 -5 to +85 -71
    • Property rcs:rev changed from 1.12 to 1.13
    r710 r751  
    4040<P>
    4141Both LIVEPLOT and BKGEDIT get the current diffraction information
    42 by running the TCLDUMP program, if installed, or
    43 HSTDUMP otherwise. The TCLDUMP program has been optimized for use
    44 with LIVEPLOT and offers a number of extra
     42by running the GSAS TCLDUMP program, if installed, or
     43the GSAS HSTDUMP otherwise. The TCLDUMP program has been optimized for use
     44with LIVEPLOT and allows LIVEPLOT to offer a number of extra
    4545options that are not available when HSTDUMP is used. Since TCLDUMP has been
    46 included in GSAS since April of 2000, it is assumed that this is now the case.
     46included in GSAS since April of 2000, the following documentation assumes
     47that TCLDUMP is installed.
    4748
    4849<a name="liveplot"></a>
     
    5455<UL>
    5556<LI>The plot is updated automatically after each refinement run
    56 <LI>The plot can be zoomed, by clicking on the corners of the
    57 area to be magnified.
     57<LI>The plot can be "zoomed-in", by clicking on the corners of the
     58area to be magnified and "zoomed-out" using the
     59right mouse button (Mac: Apple+click)
    5860<LI>
    5961The units used for plotting histograms can be selected. Choices are:
     
    7173Reflection indices (<I>hkl</I> values) can be shown for tickmarks
    7274<LI>
    73 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     75<IMG SRC="note.gif" alt="Note!">
    7476The cumulative chi<sup>2</sup> function can be plotted.
    7577<LI>
    76 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     78<IMG SRC="note.gif" alt="Note!">
    7779The cursor position can be displayed
    7880<LI>
    79 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     81<IMG SRC="note.gif" alt="Note!">
    8082Plots can be <a href="#export">exported to obtain publication-quality
    8183graphics.</a>
     
    8486<a name="bkgedit"></a>
    8587<H3>BKGEDIT</H3>
    86 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     88<IMG SRC="note.gif" alt="Note!">
    8789BKGEDIT is used to fit a background function to a set of points
    8890selected by the user.
     
    108110is good enough for the initial stages of refinement and that can be
    109111refined once the model is adequate for the task.
    110 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     112<IMG SRC="note.gif" alt="Note!">
    111113BKGEDIT can be used to fit GSAS background functions 1-6 (though
    112114for most purposes only type 1 is needed.)
     
    248250<B>Plot contents:</B>
    249251Reflection 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
     252<IMG SRC="note.gif" alt="Note!">or by pressing the
    251253"1" key for phase 1, "2" for phase 2,... Note that many attributes
    252254for reflection markers can be edited using
     
    254256
    255257<P>
    256 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     258<IMG SRC="note.gif" alt="Note!">
    257259If more than one histogram is available to plot, it is possible to cycle
    258260between the histograms by pressing the "n" or "N" (for next) key.
     
    271273If the right mouse button is pressed, the previous zoom setting is used,
    272274so that the left mouse button is used to "zoom in" and the right mouse
    273 button is used to "zoom out."
    274 <P>
    275 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     275button is used to "zoom out." Note, on the Macintosh, hold down the
     276Apple button while using the [only] mouse button to simulate a right-click.
     277
     278<P>
     279<IMG SRC="note.gif" alt="Note!">
    276280Zoom settings can also be entered manually by pressing the "Z" key. This
    277281opens a dialog, as is shown to the right, where the x- or y-axis range
     
    283287<a name="LiveCursor"></a>
    284288<img SRC="cursor.gif" align=RIGHT alt="LIVEPLOT live cursor">
    285 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     289<IMG SRC="note.gif" alt="Note!">
    286290<B>Cursor Display:</B>
    287291Pressing the "L" (or "l") key, or using the Option/Show Cursor Position
     
    335339<P>
    336340<a name="export"></a>
    337 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     341<IMG SRC="note.gif" alt="Note!">
    338342<B>Export plot options</B>
    339343<UL><LI>
     
    367371<DD>Checkbuttons are provided for each phase to determine if tick marks
    368372will be shown.
    369 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">Tickmarks can also be
     373<IMG SRC="note.gif" alt="Note!">
     374Tickmarks can also be
    370375toggled by pressing the
    371376"1" key for phase 1, "2" for phase 2,...
     
    376381<DD>This allows a histogram to be selected to be loaded
    377382<DL><DL>
    378 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     383<IMG SRC="note.gif" alt="Note!">
    379384It is also possible to advance
    380385between the histograms by pressing the "n" or "N" (for next) key.
     
    395400<A name="grace">
    396401<DT>to Grace
    397 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     402<IMG SRC="note.gif" alt="Note!">
    398403<DD>Plots can be exported to
    399404<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
     
    422427bottom to the top of the plot.
    423428<DT>Label by name
    424 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     429<IMG SRC="note.gif" alt="Note!">
    425430<DD>
    426431By default, a label "Phase1",... is displayed in the legend when tickmarks
     
    506511(or <FONT FACE="COURIER">c:\gsas.config</FONT>)
    507512files.
    508 Note that some of these options are relevant only if the tcldump program is
    509 present.
    510513<DL><DL>
    511514<DT><FONT FACE="COURIER">peakinfo(flag<i>n</i>)</FONT><DD>
     
    577580The time in seconds before reflection labels are removed. A value of zero means that reflections
    578581must be deleted manually (Shift-Right-Mouse).
    579 
     582(Mac: Shift+Apple+click)
    580583<DT><FONT FACE="COURIER">expgui(lblfontsize)</FONT><DD>
    581584A size for reflections labels in pixels.
     
    589592</DL></DL>
    590593<P>
    591 <hr><H2>Installation details/External Programs</H2>
    592 <B>Using TCLDUMP with LIVEPLOT.</B>
    593 LIVEPLOT works with the standard GSAS program HSTDMP, but it works faster and is more
    594 powerful when used with the TCLDUMP program.
    595 Note that as of the April 2000 releases, GSAS is now distributed with TCLDUMP
    596 included. For older versions of GSAS, note the
    597 instructions for downloading this file can in the installation notes for
    598 <A HREF="expgui_Win_readme.html">
    599 Windows</A> and
    600 <A HREF="expgui_Unix_readme.html">
    601 UNIX</A>.
    602 <P>
    603 
    604 <B>Combining CMPR and LIVEPLOT.</B>
    605 If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">CMPR</A>
    606 installed on your computer, you can use superimpose on the GSAS results
    607 the peaks for an arbitrary unit cell. If desired, space group extinctions
    608 can even be shown.
    609 This is pretty neat! To enable this feature, you must have a version
    610 of CMPR downloaded after 4 May 1998
     594<hr><H2>Interfacing External Programs</H2>
     595<IMG SRC="new.gif" alt="New!">
     596<B>Combining LIVEPLOT with CMPR & LOGIC</B>
     597If you have the
    611598<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr">
    612 (see link for CMPR installation instructions.)</A>
    613 <UL><LI>
    614 For UNIX, create a link from in the EXPGUI
    615 directory 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
    620 into the EXPGUI directory.
    621 </UL>
    622 <P>
    623 
    624 <B>Combining LOGIC and LIVEPLOT.</B>
    625 If you have <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/logic.html">LOGIC</A>
    626 installed on your computer, you can superimpose peaks
    627 for a entry from the ICDD/JCPDS database on a pattern in LIVEPLOT.
    628 This is also pretty neat!
    629 To enable this feature, you must have
    630 a 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>
    634 For UNIX, create a link from in the GSAS GUI
    635 directory 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.
     599CMPR/LOGIC</A>
     600programs installed on your computer, you can use superimpose on the
     601GSAS results the peaks for an arbitrary unit cell.
     602If you have the
     603<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.icdd.com/products/overview.htm">
     604ICDD-JCPDS PDF-2 powder diffraction database</a>,
     605you can also superimpose entries from this database on the
     606GSAS results displayed in LIVEPLOT.
     607<P>
     608When the CMPR/LOGIC program is installed in the same location
     609as the GSAS package (<i>e.g.</i>
     610<font face="courier">/home/gsas</font> &
     611<font face="courier">/home/cmpr</font>
     612or <font face="courier">C:\DIFRC\GSAS</font> &
     613<font face="courier">C:\DIFRC\CMPR</font>) or if
     614the CMPR/LOGIC programs are loaded into standard locations
     615(<font face="courier">/usr/local/cmpr</font> or
     616<font face="courier">~/cmpr</font> for Unix and Mac OSX or
     617<font face="courier">c:\cmpr</font> or
     618<font face="courier">c:\Program files\cmpr</font> for Windows),
     619the LIVEPLOT program will locate both programs and add an extra menu labeled
     620"Peak Gen" to the menu bar. If the CMPR program is not located automatically,
     621you may customize this location by specifying a value for
     622Tcl/Tk variable cmprdid by including a line such as this:
     623<PRE>
     624          set cmprdir C:/ncnrpkg/cmpr
     625</PRE>
     626 in the <FONT FACE="COURIER">localconfig</FONT>,
     627<FONT FACE="COURIER">.gsas_config</FONT>
     628or <FONT FACE="COURIER">c:\gsas.config</FONT> files
     629[note that forward slashes ("/") should be used here, even for windows.]
     630
     631<P>
     632The "Peak Gen" menu will have either or both of two entries
     633"Display a cell" and "Plot ICDD Entry", depending on what
     634software is located. The
     635"Display a cell" option produces a window similar to the
     636<A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">
     637Edit Cell feature in CMPR</A>
     638where allowed reflection positions are displayed for a set of unit cell
     639parameters and optionally a space group or extinction conditions.
     640The "Plot ICDD Entry" provides a window similar to the
     641<A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell">
     642LOGIC interface in CMPR</A>
     643where ICDD searches may be conducted. From the resulting list of matches,
     644selected entries may be displayed.
     645<P>
     646Note that these routines display peak positions in units of 2Theta, Q or
     647d-space. If you are using TOF or EDS data, you must select Q or d-space
     648display in LIVEPLOT. If you are using 2Theta, you must supply the correct
     649wavelength.
     650<P>
     651Note that a version of both EXPGUI and CMPR/LOGIC from November 2003 or later
     652must be used for these features to work.
     653
    640654</UL>
    641655<hr>
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