Changeset 520


Ignore:
Timestamp:
Dec 4, 2009 5:07:32 PM (11 years ago)
Author:
toby
Message:

# on 2002/01/22 21:02:55, toby did:
l-s in BKGEDT & support for functions 1-6
export to grace
cycle with "N"

File:
1 edited

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  • trunk/doc/liveplot.html

    • Property rcs:date changed from 2001/12/19 18:55:42 to 2002/01/22 21:02:55
    • Property rcs:lines changed from +26 -24 to +115 -38
    • Property rcs:rev changed from 1.7 to 1.8
    r518 r520  
    7979<H3>BKGEDIT</H3>
    8080<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
    81 For most refinements, it is possible to simply select a background
     81BKGEDIT is used to fit a background function to a set of points
     82selected by the user.
     83For most refinements, this is not needed,
     84as it is possible to simply select a background
    8285function (I find that the type 1 function,
    83 shifted Chebyschev polynomials, work well)
     86shifted Chebyschev polynomials, works well)
    8487and then refine, adding terms until a good fit is obtained.
    8588On occasion, poor initial fits are obtained in this manner. This is
     
    99102is good enough for the initial stages of refinement and that can be
    100103refined once the model is adequate for the task.
     104<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     105BKGEDIT can be used to fit GSAS background functions 1-6 (though
     106for most purposes only type 1 is needed.)
    101107<P>
    102108<IMG SRC="b1.gif" align=TEXTOP alt="BKGEDIT screen image">
     
    125131<DL><DL>
    126132Note that it is advisable to place many background points in areas where
    127 the background varies greatly.
     133the background is changing rapidly (where the background is most bumpy).
    128134</DL></DL>
    129135As background points are entered, they are saved in a file named
     
    138144"Background points" area.
    139145<LI>After enough background points have been entered, the
    140 "Start Fit" button turns from gray to black. When pressed, the Chebyschev
    141 polynomial is fitted and the resulting curve is shown as a blue dashed line.
    142 <DL><DL>
    143 It is suggested that you start with relatively few
     146"Fit" button turns from gray to black. When pressed, the selected
     147background function is fitted
     148and the resulting curve is shown as a blue dashed line.
     149<DL><DL>
     150<LI>It is suggested that you start with relatively few
    144151terms and add terms and background points as needed.
    145 Note that the maximum number of Chebyschev terms increases as
     152Note that the maximum number of increases as
    146153more background points are entered.
    147 </DL></DL>
    148 The "Improve Fit" button is black when the fit did not
    149 converge or the number of terms has been changed. "Improve Fit" causes the
    150 fit to be refined starting from the previous values.
    151 <LI>Editing the Chebyschev terms is possible. The curve is reevaluated as
     154<LI>Editing the terms manually is possible. The curve is reevaluated as
    152155changes are made.
     156<LI>For the type 3 background function (radial distribution function),
     157the R terms are listed separately from the other
     158background terms. These R (radii) values must be entered manually and
     159are not refined.
     160</DL></DL>
    153161<LI>Once a good background function is determined, it can be saved in the
    154162experiment file by pressing the "Save in EXP file & Exit" button. This will
    155 set the background type to 1, and save the Chebyschev terms.
     163set the background type, and save the terms.
    156164It will also turn off
    157165the background refinement flag for the appropriate histogram so that the
     
    203211from the correct values of 0.042 and 3.0, respectively, to misleading
    204212values of 0.036 and 0.8,
    205 respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045;
    206 FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036.]
     213respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045
     214with the different fixed background errors;
     215FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036,
     216so I would consider the refined background to be better.]
    207217<P>
    208218If the background is so truly irregular that only use of fixed background
     
    211221The file used by BKGEDIT to save these points,
    212222<I>EXPNAM</I><tt>.bkg</tt><I>N</I>,
    213 can be read into EXPEDT by typing "@R" at the initial prompt
    214 in EXPEDT:
     223will define the background points if read directly into EXPEDT
     224by typing "@R" at the initial prompt in EXPEDT:
    215225<PRE>
    216226   Is this the file you wish to use? (<?>,D,K,Q,R,Y) ><u>@r</u>
     
    220230   Enter the name of your macro file: <u>GARNET.bkg1</u>
    221231</PRE>
    222 And this will enter the background points entered into BKGEDIT as GSAS
    223 fixed background points. If you do this you do not want to fit and enter
    224 Note that you are allowed to use both fixed and a refined background together,
    225 though this is seldom done.
     232Doing this will cause the background points you entered into BKGEDIT to
     233be used in GSAS
     234fixed background points. If you do this you do not want to save the
     235fitted background function as well, as this would effectively subtract
     236double the desired background.
     237Note that GSAS allows simultaneous use of
     238both fixed and a refined background;
     239this is seldom done.
    226240
    227241<hr><h2>LIVEPLOT/BKGEDIT Features</h2>
     242<B>Plot contents:</B>
     243Reflection markers can be placed using the File/Tickmarks menu item
     244<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">or by pressing the
     245"1" key for phase 1, "2" for phase 2,... Note that many attributes
     246for reflection markers can be edited using
     247Options/<a href="#configTick">Configure Tickmarks</a>
     248
     249<P>
     250<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     251If more than one histogram is available to plot, it is possible to cycle
     252between the histograms by pressing the "n" or "N" (for next) key.
     253<P>
    228254<a name="zoom"></a>
    229 <B>Plot zooming</B>
     255<B>Plot zooming:</B>
    230256When the left (usual) mouse button is pressed, this defines one corner
    231257of a region to be magnified, as is shown to the right.
     
    248274the mouse, but to zoom out beyond the manual zoom limits, the "reset" button
    249275on the manual zoom menu must be used.
    250 <P>
    251 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
    252 If more than one histogram is available to plot, it is possible to cycle
    253 between the histograms by pressing the "n" or "N" (for next) key.
    254276<P>
    255277<br clear=all>
     
    292314
    293315<img SRC="lind1.gif" align=LEFT alt="LIVEPLOT Screen snapshot">
    294 <P>
     316
    295317<br clear=all>
     318<P>
     319<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     320<B>Export plot to Grace</B>
     321The plot can be exported to
     322<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
     323that produces publication-quality graphics. Many UNIX users know
     324this program under a previous name, xmgr.
     325The export is implemented
     326by producing an ASCII file with instructions that
     327creates a plot with similar formatting to what appears on the
     328screen in LIVEPLOT/BKGEDIT. However, the output quality from
     329Grace is much higher quality. Further, Grace
     330can be used to enhanced and annotate the plot further.
    296331
    297332<hr><h2>LIVEPLOT/BKGEDIT Menu Contents</h2>
     
    302337<DT>Tickmarks
    303338<DD>Checkbuttons are provided for each phase to determine if tick marks
    304 are shown. See the Options/"Configure Tickmarks"menu item for information
    305 on tickmarks
     339will be shown.
     340<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">Tickmarks can also be
     341toggled by pressing the
     342"1" key for phase 1, "2" for phase 2,...
     343Also see the Options/<a href="#configTick">Configure Tickmarks</a>
     344menu item for information
     345on tickmarks.
    306346<DT>Histogram
    307347<DD>This allows a histogram to be selected to be loaded
     
    314354<DD>The causes LIVEPLOT to read read the current histogram again from
    315355the datafile
    316 <DT>Make PostScript
    317 <DD>Creates a low quality PostScript file containing the LIVEPLOT
     356<DT>Export Plot
     357<DD>This offers options for exporting the plot in multiple formats.
     358I am hoping to add more export formats eventually.
     359<DL><DL>
     360<DT>to PostScript
     361<DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT
    318362output. See the Options/"Set PS output" button for where the file is created.
     363Most unix systems are capable or printing PostScript files.
     364On Windows, a program such ghostview may be needed to translate the
     365PostScript to a format that can be viewed or printed.
     366<A name="grace">
     367<DT>to Grace
     368<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
     369<DD>Plots can be exported to
     370<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
     371that produces publication-quality graphics.
     372After the plot is exported, it can be further
     373enhanced and annotated in grace.
     374</DL></DL>
    319375<DT>Quit
    320376<DD>Exits BKGEDIT/LIVEPLOT.
     
    324380<H3>Options Menu</H3>
    325381<DL><DL>
    326 <DT>Configure Tickmarks
    327 <DD>Tickmarks can be placed automatically, similar to their
    328  placement in POWPLOT or can be drawn one height to another. The default
     382<a name="configTick"></a>
     383<DT>Configure Tickmarks<DD>
     384This submenu provides options that controls how tickmarks are displayed.
     385<DL><DL>
     386<DT>Auto locate<DD>
     387When this option is selected, tickmarks are placed in different positions
     388for each phase, automatically, similar to how tickmarks are shown in POWPLOT.
     389<DT>Manual Placement<DD>
     390Tickmarks are drawn at specific heights that can be set for each phase
     391(see below). The default
    329392is for lines to be draw from "-Inf" to "Inf", which creates lines from the
    330 bottom to the top of the plot. The options for each phase allow the line to be changed between solid and dashed, color of the line can be specified and
    331 the vertical placement of the tickmarks can be specified. The "show" flag,
    332 set in the File/Tickmarks menu can also be changed here.
     393bottom to the top of the plot.
     394<DT>Label by name
     395<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
     396<DD>
     397By default, a label "Phase1",... is displayed in the legend when tickmarks
     398for that phase are displayed. When this button is pressed, the first
     39920 characters of each phase name (phase title) are used instead. This
     400label can be edited, as described in the next paragraph.
     401<DT>Phase <I>n</I> opts<DD>
     402The options for each phase allow the line to be changed between
     403solid and dashed, color of the line can be specified and
     404the vertical placement of the tickmarks can be specified. The
     405"Show Reflections" flag,
     406set in the File/Tickmarks menu,
     407as well as the label used for the phase can also be changed here.
     408
     409</DL></DL>
    333410<DT>Obs Symbol (Symbol Type)
    334411<DD>This brings up a menu where the symbol type and size for the
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