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| 3 | <title>EXPGUI -- LIVEPLOT/BKGEDIT</title> |
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| 18 | include("/var/www/include/utility.inc"); |
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| 20 | <blockquote><font face="arial, helvetica, sans-serif"> |
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| 21 | |
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| 22 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 23 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 24 | </TH><TH><A Href="excledt.html">Next page<BR>(EXCLEDT)</A> |
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| 25 | </TH><TH><A Href="expguic.html">Previous page</A> |
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| 26 | </TH></TR></TABLE><BR CLEAR=ALL> |
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| 27 | |
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| 28 | <center><h1> |
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| 29 | <HR noshade width="75%" size="2" align="center"> |
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| 30 | EXPGUI Utilities (1),<BR>LIVEPLOT and BKGEDIT |
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| 31 | <HR noshade width="75%" size="2" align="center"> |
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| 32 | </h1></center> |
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| 33 | This page documents the LIVEPLOT and BKGEDIT utility programs |
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| 34 | in the EXPGUI package. |
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| 35 | LIVEPLOT and BKGEDIT are actually the same program, but perform |
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| 36 | different functions, depending on how they are invoked. |
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| 37 | LIVEPLOT is used to display the quality of the diffraction fit, while |
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| 38 | BKGEDIT is used to fit a background function to fixed background points |
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| 39 | that have been input by the user. |
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| 40 | <P> |
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| 41 | Both LIVEPLOT and BKGEDIT get the current diffraction information |
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| 42 | by running the GSAS TCLDUMP program, if installed, or |
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| 43 | the GSAS HSTDUMP otherwise. The TCLDUMP program has been optimized for use |
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| 44 | with LIVEPLOT and allows LIVEPLOT to offer a number of extra |
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| 45 | options that are not available when HSTDUMP is used. Since TCLDUMP has been |
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| 46 | included in GSAS since April of 2000, the following documentation assumes |
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| 47 | that TCLDUMP is installed. |
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| 48 | |
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| 49 | <a name="liveplot"></a> |
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| 50 | <H3>LIVEPLOT</H3> |
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| 51 | LIVEPLOT is started by pressing the LIVEPLOT button on the toolbar |
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| 52 | or via the Graphs/liveplot menu item. |
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| 53 | <P> |
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| 54 | Some of the features available in LIVEPLOT are: |
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| 55 | <UL> |
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| 56 | <LI>The plot is updated automatically after each refinement run |
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| 57 | <LI>The plot can be "zoomed-in", by clicking on the corners of the |
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| 58 | area to be magnified and "zoomed-out" using the |
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| 59 | right mouse button (Mac: Apple+click) |
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| 60 | <LI> |
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| 61 | The units used for plotting histograms can be selected. Choices are: |
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| 62 | native units (2Theta/TOF/KeV); d-space (A) or Q (A<sup>-1</sup>) |
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| 63 | <LI> |
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| 64 | The background (fixed plus fitted) can be plotted or can be subtracted. |
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| 65 | <LI> |
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| 66 | Reflection tickmarks can be displayed in a variety of formats |
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| 67 | <LI> |
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| 68 | LIVEPLOT can be coupled to the LOGIC or CMPR programs, so that |
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| 69 | peak positions from an ICDD entry or for an arbitrary unit cell and |
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| 70 | spacegroup can be shown superimposed on the "Rietveld plot." |
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| 71 | <LI> |
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| 72 | <IMG SRC="note.gif" alt="Note!"> |
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| 73 | Reflection indices (<I>hkl</I> values) can be shown for tickmarks |
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| 74 | <LI> |
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| 75 | <IMG SRC="note.gif" alt="Note!"> |
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| 76 | The cumulative chi<sup>2</sup> function can be plotted. |
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| 77 | <LI> |
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| 78 | <IMG SRC="note.gif" alt="Note!"> |
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| 79 | The cursor position can be displayed |
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| 80 | <LI> |
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| 81 | <IMG SRC="note.gif" alt="Note!"> |
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| 82 | Plots can be <a href="#export">exported to obtain publication-quality |
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| 83 | graphics.</a> |
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| 84 | </UL> |
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| 85 | |
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| 86 | <a name="bkgedit"></a> |
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| 87 | <H3>BKGEDIT</H3> |
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| 88 | <IMG SRC="note.gif" alt="Note!"> |
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| 89 | BKGEDIT is used to fit a background function to a set of points |
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| 90 | selected by the user. |
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| 91 | For most refinements, this is not needed, |
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| 92 | as it is possible to simply select a background |
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| 93 | function (I find that the type 1 function, |
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| 94 | shifted Chebyschev polynomials, works well) |
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| 95 | and then refine, adding terms until a good fit is obtained. |
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| 96 | On occasion, poor initial fits are obtained in this manner. This is |
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| 97 | most common in cases where large numbers of peaks are poorly fit. Since |
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| 98 | significant sections of the data are not well fit, the refinement results in |
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| 99 | an unreasonable background function, because this yields better agreement |
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| 100 | with the observed data. |
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| 101 | In these cases, |
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| 102 | it may be best to fix the background to follow a "reasonable" curve in the |
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| 103 | initial stages and then refine the background in the final stages of |
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| 104 | refinement, when a good model has been obtained. |
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| 105 | <P> |
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| 106 | The BKGEDIT program, as shown below, is used to input a set a background |
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| 107 | points via the mouse. The points are then used to determine a type 1 |
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| 108 | (Chebyschev) background function that fits the input background points. These |
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| 109 | terms can then be saved in the experiment file creating a background that |
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| 110 | is good enough for the initial stages of refinement and that can be |
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| 111 | refined once the model is adequate for the task. |
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| 112 | <IMG SRC="note.gif" alt="Note!"> |
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| 113 | BKGEDIT can be used to fit GSAS background functions 1-6 (though |
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| 114 | for most purposes only type 1 is needed.) |
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| 115 | <P> |
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| 116 | <IMG SRC="b1.gif" align=TEXTOP alt="BKGEDIT screen image"> |
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| 117 | <H4>Steps in fitting a background function</H4> |
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| 118 | The BKGEDIT program is started from |
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| 119 | via the Powder/bkgedit menu item or by pressing the |
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| 120 | "Fit Background Graphically" button on the |
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| 121 | <A href="expgui3.html#EditBackground">"Edit Background"</A> |
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| 122 | dialog box (invoked from the "Edit Background" button on the |
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| 123 | <A href="expgui3.html">Histogram pane</A>.) |
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| 124 | toolbar |
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| 125 | or |
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| 126 | <OL> |
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| 127 | <LI><a href="#zoom">Zoom in</a> on the lower intensity section of the |
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| 128 | plot, so that the background is clearly discernible. In some cases, the |
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| 129 | data will need to be handled in sections. |
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| 130 | <LI>Press the "Add" button to add background points. |
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| 131 | Note the cursor changes from cross-hairs to an arrow, |
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| 132 | when the "Add" button is pressed. |
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| 133 | <LI>Move the mouse to the first location |
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| 134 | where a background point will be added and click with the left |
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| 135 | mouse button. A magenta triangle will appear at the location. |
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| 136 | Points can be added in any order. It is best to make sure that the fixed points |
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| 137 | are placed over the entire range of the data, e.g. near the maximum and minimum |
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| 138 | data points in TOF, 2theta, etc. |
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| 139 | <DL><DL> |
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| 140 | Note that it is advisable to place many background points in areas where |
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| 141 | the background is changing rapidly (where the background is most bumpy). |
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| 142 | </DL></DL> |
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| 143 | As background points are entered, they are saved in a file named |
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| 144 | <I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>, where |
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| 145 | <I>EXPNAM</I> is the experiment name and <I>N</I> is the histogram number. |
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| 146 | If BKGEDIT is restarted at some later time, these points are reread. |
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| 147 | <LI>If any points are placed in incorrect positions, they can be deleted by |
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| 148 | pressing the "Delete" button. The mouse cursor changes to a circle. When |
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| 149 | the mouse left clicked, the fixed background point closest to the mouse |
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| 150 | position (which may be outside the zoom range) is deleted. |
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| 151 | <LI>Background points can also be edited by entering numbers into the |
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| 152 | "Background points" area. |
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| 153 | <LI>After enough background points have been entered, the |
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| 154 | "Fit" button turns from gray to black. When pressed, the selected |
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| 155 | background function is fitted |
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| 156 | and the resulting curve is shown as a blue dashed line. |
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| 157 | <DL><DL> |
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| 158 | <LI>It is suggested that you start with relatively few |
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| 159 | terms and add terms and background points as needed. |
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| 160 | Note that the maximum number of increases as |
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| 161 | more background points are entered. |
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| 162 | <LI>Editing the terms manually is possible. The curve is reevaluated as |
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| 163 | changes are made. |
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| 164 | <LI>For the type 3 background function (radial distribution function), |
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| 165 | the R terms are listed separately from the other |
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| 166 | background terms. These R (radii) values must be entered manually and |
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| 167 | are not refined. |
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| 168 | </DL></DL> |
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| 169 | <LI>Once a good background function is determined, it can be saved in the |
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| 170 | experiment file by pressing the "Save in EXP file & Exit" button. This will |
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| 171 | set the background type, and save the terms. |
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| 172 | It will also turn off |
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| 173 | the background refinement flag for the appropriate histogram so that the |
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| 174 | terms are not refined inadvertently. |
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| 175 | </OL> |
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| 176 | |
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| 177 | <P> |
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| 178 | Note that POWPREF must be run at least once before BKGEDIT can be used, |
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| 179 | however, use of |
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| 180 | GENLES before BKGEDIT is optional. If the data range is changed, for example |
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| 181 | by excluding a section of the data at the lower end, or changing tmax (dmin), |
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| 182 | the Chebyschev polynomial terms must change to generate the same |
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| 183 | background values, so both POWPREF and BKGEDIT should be rerun to |
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| 184 | regenerate the Chebyschev terms. |
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| 185 | |
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| 186 | <H4>Why not use fixed background points?</H4> |
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| 187 | I personally feel that |
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| 188 | a refined background function is preferrable to use of a fixed model, |
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| 189 | if at all possible. |
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| 190 | One reason for this is that Rietveld refinements usually achieve better fits |
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| 191 | when the background is optimized. A second reason refining the background |
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| 192 | provides a |
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| 193 | feel for the interaction between background values and displacement |
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| 194 | (thermal) parameters. |
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| 195 | Usually, background and displacement parameters are fairly independent, but |
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| 196 | for some materials, where the high Q (high 2theta) portion of the pattern |
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| 197 | has many completely overlapped peaks, it is impossible to uniquely |
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| 198 | determine where the |
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| 199 | background should be placed, either by refinement or by manual placement. |
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| 200 | Under these circumstances, the background should be refined with the |
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| 201 | displacement parameters fixed at an appropriate value for the material. The |
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| 202 | background should then be fixed for all future refinements |
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| 203 | and the displacement parameters can then be refined. <I>Of course this |
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| 204 | means you have predjudiced the refinement to result in the expected |
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| 205 | average displacement parameter and this </I><B>must</B><I> be noted |
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| 206 | any publication. However, if this is necessary, the data simply do not |
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| 207 | contain sufficient information to independently determine |
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| 208 | background and displacement parameters. Use of fixed background points |
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| 209 | would not demonstrate this and would lead the researcher to a false |
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| 210 | sense of security (or fear, if the values are unreasonable) |
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| 211 | that the displacement parameters actually mean something.</I> |
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| 212 | <P> |
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| 213 | If you still want to use fixed background points, despite this tirade, |
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| 214 | be sure to set the estimated |
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| 215 | error on those points to be 0.0. Use of non-zero estimated errors, can |
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| 216 | result in artificially lowered R-factors and chi-squared values. |
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| 217 | In one test, I was able to lower the R<sub>wp</sub> and |
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| 218 | reduced chi<sup>2</sup> values, |
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| 219 | from the correct values of 0.042 and 3.0, respectively, to misleading |
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| 220 | values of 0.036 and 0.8, |
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| 221 | respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045 |
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| 222 | with the different fixed background errors; |
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| 223 | FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036, |
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| 224 | so I would consider the refined background to be better.] |
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| 225 | <P> |
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| 226 | If the background is so truly irregular that only use of fixed background |
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| 227 | points will do, |
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| 228 | BKGEDIT can be used to generate these fixed background points. |
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| 229 | The file used by BKGEDIT to save these points, |
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| 230 | <I>EXPNAM</I><font face="courier">.bkg</font><I>N</I>, |
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| 231 | will define the background points if read directly into EXPEDT |
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| 232 | by typing "@R" at the initial prompt in EXPEDT: |
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| 233 | <FONT FACE="COURIER"><PRE> |
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| 234 | Is this the file you wish to use? (?,D,K,Q,R,Y) ><u>@r</u> |
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| 235 | </PRE></FONT> |
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| 236 | prompt and then supplying the name of the file, in response to the next prompt: |
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| 237 | <FONT FACE="COURIER"><PRE> |
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| 238 | Enter the name of your macro file: <u>GARNET.bkg1</u> |
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| 239 | </PRE></FONT> |
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| 240 | Doing this will cause the background points you entered into BKGEDIT to |
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| 241 | be used in GSAS |
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| 242 | fixed background points. If you do this you do not want to save the |
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| 243 | fitted background function as well, as this would effectively subtract |
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| 244 | double the desired background. |
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| 245 | Note that GSAS allows simultaneous use of |
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| 246 | both fixed and a refined background; |
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| 247 | this is seldom done. |
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| 248 | |
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| 249 | <hr><h2>LIVEPLOT/BKGEDIT Features</h2> |
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| 250 | <B>Plot contents:</B> |
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| 251 | Reflection markers can be placed using the File/Tickmarks menu item |
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| 252 | <IMG SRC="note.gif" alt="Note!">or by pressing the |
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| 253 | "1" key for phase 1, "2" for phase 2,... Note that many attributes |
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| 254 | for reflection markers can be edited using |
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| 255 | Options/<a href="#configTick">Configure Tickmarks</a> |
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| 256 | |
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| 257 | <P> |
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| 258 | <IMG SRC="note.gif" alt="Note!"> |
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| 259 | If more than one histogram is available to plot, it is possible to cycle |
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| 260 | between the histograms by pressing the "n" or "N" (for next) key. |
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| 261 | <P> |
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| 262 | <a name="zoom"></a> |
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| 263 | <B>Plot zooming:</B> |
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| 264 | When the left (usual) mouse button is pressed, this defines one corner |
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| 265 | of a region to be magnified, as is shown to the right. |
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| 266 | If the mouse is then moved, the diagonal |
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| 267 | corner of this magnification region is defined. When the left mouse button |
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| 268 | is pressed a second time, the selected section of the plot is magnified to |
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| 269 | fill the entire plot. |
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| 270 | <P> |
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| 271 | <img SRC="mzoom.gif" align=RIGHT alt="LIVEPLOT manual zoom"> |
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| 272 | Zoom settings are saved. |
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| 273 | If the right mouse button is pressed, the previous zoom setting is used, |
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| 274 | so that the left mouse button is used to "zoom in" and the right mouse |
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| 275 | button is used to "zoom out." Note, on the Macintosh, hold down the |
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| 276 | Apple button while using the [only] mouse button to simulate a right-click. |
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| 277 | |
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| 278 | <P> |
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| 279 | <IMG SRC="note.gif" alt="Note!"> |
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| 280 | Zoom settings can also be entered manually by pressing the "Z" key. This |
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| 281 | opens a dialog, as is shown to the right, where the x- or y-axis range |
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| 282 | can be specified. Any value that is not specified is set to the maximum |
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| 283 | or minimum for the entire dataset. It is possible to zoom further in using |
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| 284 | the mouse, but to zoom out beyond the manual zoom limits, the "reset" button |
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| 285 | on the manual zoom menu must be used. |
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| 286 | <P> |
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| 287 | <IMG SRC="new.gif" alt="New!"> |
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| 288 | To shift the zoom region around, |
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| 289 | the right and left arrow keys can be used to shift the |
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| 290 | region 10 % to the left or right. |
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| 291 | Likewise, |
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| 292 | the up and down arrow keys can be used to shift the region up or down by 10 %. |
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| 293 | Holding down the control key down while pressing these keys increases |
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| 294 | the amount of the shift to 100 %. |
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| 295 | <P> |
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| 296 | <a name="LiveCursor"></a> |
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| 297 | <img SRC="cursor.gif" align=RIGHT alt="LIVEPLOT live cursor"> |
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| 298 | <IMG SRC="note.gif" alt="Note!"> |
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| 299 | <B>Cursor Display:</B> |
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| 300 | Pressing the "L" (or "l") key, or using the Option/Show Cursor Position |
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| 301 | menu button causes the position of the cursor (mouse position) |
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| 302 | in plot to be shown. The coordinates are listing in a small area below |
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| 303 | the plot. The position display is updated as the mouse is moved. The |
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| 304 | same key, menu button, or the button labeled "Close cursor display" can be |
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| 305 | used to remove the display. |
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| 306 | <P> |
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| 307 | <br clear=all> |
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| 308 | <h2>Features in LIVEPLOT only</h2> |
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| 309 | <img SRC="lz.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot"> |
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| 310 | <a name="Cchi2"></a> |
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| 311 | <B>The cumulative chi<sup>2</sup></B> |
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| 312 | function was first suggested by |
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| 313 | Bill David as a way to see which reflections have the greatest influence on |
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| 314 | chi<sup>2</sup> [W.I.F. David, <I>Accuracy in Powder Diffraction-III</I>, 2001]. |
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| 315 | It is defined for point j as |
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| 316 | <IMG SRC="cchi2.gif" alt="equation for cumulative chi2 function" ALIGN=TOP> |
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| 317 | where y<sub>obs,i</sub> and y<sub>calc,i</sub> are the observed and computed |
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| 318 | data points and sigma<sub>i</sub> is the expected error. Thus, the statistically |
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| 319 | expected value for |
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| 320 | [(y<sub>obs,i</sub>-y<sub>calc,i</sub>)/sigma<sub>i</sub>]<sup>2</sup> is 1 |
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| 321 | and this function should rise in a smooth line if all points are fitted as |
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| 322 | statistically expected. |
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| 323 | <P> |
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| 324 | In the plot to the right, the cumulative chi<sup>2</sup> function is shown in |
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| 325 | purple. Note that first peak is not well fit, but the low angle "shoulder" is |
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| 326 | as important as the peak misfitting, with respect to the chi<sup>2</sup>. |
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| 327 | <br clear=all> |
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| 328 | <P> |
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| 329 | <img SRC="lind.gif" BORDER=3 align=RIGHT alt="LIVEPLOT Screen snapshot"> |
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| 330 | <B>Reflection indices</B> |
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| 331 | are be displayed by pressing "H" or "h" while the |
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| 332 | mouse is near a reflection (holding the shift key while |
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| 333 | pressing the left mouse button also works, but sometimes interferes with the |
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| 334 | zoom feature). |
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| 335 | Pressing "A" or "a" shows all reflections in the displayed region. |
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| 336 | The indices are shown |
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| 337 | on the screen for phases with tickmarks (as shown to the right). |
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| 338 | Indices are listed in the "Separate window for <I>hkl</I> labels" |
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| 339 | (as seen below) for all phases, regardless of the tickmark settings. |
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| 340 | Displayed indices will remain on the screen for a preset time and |
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| 341 | then will be deleted; alternately, pressing "D" or "d" deletes the hkl labels. |
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| 342 | Several aspects of reflection labeling can be customized, |
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| 343 | see the <a href="#hklOpts">HKL labeling options</a> for further information. |
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| 344 | |
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| 345 | <img SRC="lind1.gif" align=LEFT alt="LIVEPLOT Screen snapshot"> |
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| 346 | |
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| 347 | <br clear=all> |
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| 348 | <P> |
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| 349 | <a name="export"></a> |
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| 350 | <IMG SRC="note.gif" alt="Note!"> |
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| 351 | <B>Export plot options</B> |
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| 352 | <UL><LI> |
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| 353 | The plot can be exported to |
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| 354 | <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 |
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| 355 | that produces publication-quality graphics. Many UNIX users know |
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| 356 | this program under a previous name, xmgr. |
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| 357 | The export is implemented |
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| 358 | by producing an ASCII file with instructions that |
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| 359 | creates a plot with similar formatting to what appears on the |
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| 360 | screen in LIVEPLOT/BKGEDIT. However, the output quality from |
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| 361 | Grace is much higher quality. Further, Grace |
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| 362 | can be used to enhanced and annotate the plot further. |
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| 363 | <LI> |
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| 364 | For use in many other graphics programs, LIVEPLOT will produce a |
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| 365 | "comma separated variable" data file with the data displayed on the screen. |
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| 366 | The user will need to read this in, |
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| 367 | set line styles and scaling, etc., but this does provide an option for |
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| 368 | generating high-quality graphics for presentations and publications. |
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| 369 | <LI>LIVEPLOT will produce PostScript versions of the plot on the screen, |
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| 370 | but the quality is rather low (this is a limitation of the BLT graphics |
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| 371 | package). |
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| 372 | </UL> |
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| 373 | |
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| 374 | <hr><h2>LIVEPLOT/BKGEDIT Menu Contents</h2> |
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| 375 | A few of these options are omitted from BKGEDIT. |
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| 376 | <img SRC="lm1.gif" align=RIGHT alt="LIVEPLOT Menu"> |
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| 377 | <H3>File Menu</H3> |
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| 378 | <DL><DL> |
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| 379 | <DT>Tickmarks |
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| 380 | <DD>Checkbuttons are provided for each phase to determine if tick marks |
|---|
| 381 | will be shown. |
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| 382 | <IMG SRC="note.gif" alt="Note!"> |
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| 383 | Tickmarks can also be |
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| 384 | toggled by pressing the |
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| 385 | "1" key for phase 1, "2" for phase 2,... |
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| 386 | Also see the Options/<a href="#configTick">Configure Tickmarks</a> |
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| 387 | menu item for information |
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| 388 | on tickmarks. |
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| 389 | <DT>Histogram |
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| 390 | <DD>This allows a histogram to be selected to be loaded |
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| 391 | <DL><DL> |
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| 392 | <IMG SRC="note.gif" alt="Note!"> |
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| 393 | It is also possible to advance |
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| 394 | between the histograms by pressing the "n" or "N" (for next) key. |
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| 395 | </DL></DL> |
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| 396 | <DT>Update Plot |
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| 397 | <DD>The causes LIVEPLOT to read read the current histogram again from |
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| 398 | the datafile |
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| 399 | <DT>Export Plot |
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| 400 | <DD>This offers options for exporting the plot in multiple formats. |
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| 401 | I am hoping to add more export formats eventually. |
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| 402 | <DL><DL> |
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| 403 | <DT>to PostScript |
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| 404 | <DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT |
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| 405 | output. See the Options/"Set PS output" button for where the file is created. |
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| 406 | Most unix systems are capable or printing PostScript files. |
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| 407 | On Windows, a program such ghostview may be needed to translate the |
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| 408 | PostScript to a format that can be viewed or printed. |
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| 409 | <A name="grace"> |
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| 410 | <DT>to Grace |
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| 411 | <IMG SRC="note.gif" alt="Note!"> |
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| 412 | <DD>Plots can be exported to |
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| 413 | <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 |
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| 414 | that produces publication-quality graphics. |
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| 415 | After the plot is exported, it can be further |
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| 416 | enhanced and annotated in grace. |
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| 417 | </DL></DL> |
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| 418 | <DT>Quit |
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| 419 | <DD>Exits BKGEDIT/LIVEPLOT. |
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| 420 | </DL></DL> |
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| 421 | <br clear=all> |
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| 422 | <img SRC="lm2.gif" align=RIGHT alt="LIVEPLOT Menu"> |
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| 423 | <H3>Options Menu</H3> |
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| 424 | <DL><DL> |
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| 425 | <a name="configTick"></a> |
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| 426 | <DT>Configure Tickmarks<DD> |
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| 427 | This submenu provides options that controls how tickmarks are displayed. |
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| 428 | <DL><DL> |
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| 429 | <DT>Auto locate<DD> |
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| 430 | When this option is selected, tickmarks are placed in different positions |
|---|
| 431 | for each phase, automatically, similar to how tickmarks are shown in POWPLOT. |
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| 432 | <DT>Manual Placement<DD> |
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| 433 | Tickmarks are drawn at specific heights that can be set for each phase |
|---|
| 434 | (see below). The default |
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| 435 | is for lines to be draw from "-Inf" to "Inf", which creates lines from the |
|---|
| 436 | bottom to the top of the plot. |
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| 437 | <DT>Label by name |
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| 438 | <IMG SRC="note.gif" alt="Note!"> |
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| 439 | <DD> |
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| 440 | By default, a label "Phase1",... is displayed in the legend when tickmarks |
|---|
| 441 | for that phase are displayed. When this button is pressed, the first |
|---|
| 442 | 20 characters of each phase name (phase title) are used instead. This |
|---|
| 443 | label can be edited, as described in the next paragraph. |
|---|
| 444 | <DT>Phase <I>n</I> opts<DD> |
|---|
| 445 | The options for each phase allow the line to be changed between |
|---|
| 446 | solid and dashed, color of the line can be specified and |
|---|
| 447 | the vertical placement of the tickmarks can be specified. The |
|---|
| 448 | "Show Reflections" flag, |
|---|
| 449 | set in the File/Tickmarks menu, |
|---|
| 450 | as well as the label used for the phase can also be changed here. |
|---|
| 451 | |
|---|
| 452 | </DL></DL> |
|---|
| 453 | <DT>Obs Symbol (Symbol Type) |
|---|
| 454 | <DD>This brings up a menu where the symbol type and size for the |
|---|
| 455 | observed data points (and for BKGEDIT, the fixed background points) |
|---|
| 456 | can be selected. |
|---|
| 457 | <DT>Symbol Color |
|---|
| 458 | <DD>The colors for all the displayed lines and symbols can be changed here. |
|---|
| 459 | <DT>X units |
|---|
| 460 | <DD>The x units can be selected here. The choices are |
|---|
| 461 | "as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>) |
|---|
| 462 | <DT>Y units |
|---|
| 463 | <DD>The intensity values can be normalized by the incident spectrum |
|---|
| 464 | (for energy dispersive methods). |
|---|
| 465 | </DL></DL> |
|---|
| 466 | <br clear=all> |
|---|
| 467 | <img SRC="lm3.gif" align=RIGHT alt="LIVEPLOT menu"> |
|---|
| 468 | <a name="hklOpts"></a> |
|---|
| 469 | <DL><DL> |
|---|
| 470 | <DT>HKL labeling |
|---|
| 471 | <DD>This brings up a menu that selects |
|---|
| 472 | <UL><LI>Erase time: |
|---|
| 473 | how long in seconds that <I>hkl</I> values are shown |
|---|
| 474 | before they are erased (0 means that they are not erased), |
|---|
| 475 | <LI>Label size: the size of the |
|---|
| 476 | labels in pixels, |
|---|
| 477 | <LI>Search Region: only reflections within this number of pixels of the mouse, |
|---|
| 478 | when the "h" key is pressed (if any) are labeled, |
|---|
| 479 | <LI>Separate window: when this |
|---|
| 480 | option is selected, reflection labels are shown in a text window |
|---|
| 481 | </UL> |
|---|
| 482 | <DT>Subtract background |
|---|
| 483 | <DD>The background is always shown, even when subtracted |
|---|
| 484 | <DT>Include legend |
|---|
| 485 | <DD>The legend is the optional box in the upper left that defines the |
|---|
| 486 | plot entries |
|---|
| 487 | <DT>Show [Hide] Cursor Position |
|---|
| 488 | <DD>This turns <a href="#LiveCursor">Cursor position display</a> on and off. |
|---|
| 489 | <DT>Set PS output |
|---|
| 490 | <DD>For UNIX this allows the file to be sent directly to a printer |
|---|
| 491 | or can be saved in a file. For Windows, a file must be written. |
|---|
| 492 | <DT>Set screen font |
|---|
| 493 | <DD>This option is used to control the font used for menus, graphics and |
|---|
| 494 | other aspects of windows. |
|---|
| 495 | <DT>Raise on update |
|---|
| 496 | <DD>This causes the plot to be placed on top of other windows, if partially |
|---|
| 497 | obscured, when the plot is updated. At this time, this option does not |
|---|
| 498 | work in Windows-NT and -2000. |
|---|
| 499 | <DT>Cumulative Chi2 |
|---|
| 500 | <DD>The causes the Cumulative chi<sup>2</sup> function to be displayed |
|---|
| 501 | (as <a href="#Cchi2">presented above</a>). |
|---|
| 502 | <DT>Save Options |
|---|
| 503 | <DD>Causes many of the options set in this menu to be saved in the |
|---|
| 504 | <FONT FACE="COURIER">.gsas_config</FONT> |
|---|
| 505 | (or <FONT FACE="COURIER">c:\gsas.config</FONT>) file. |
|---|
| 506 | </DL></DL> |
|---|
| 507 | <br clear=all> |
|---|
| 508 | |
|---|
| 509 | <P> |
|---|
| 510 | <hr><H2>Customization of LIVEPLOT & BKGEDIT</H2><A NAME="customize"></A> |
|---|
| 511 | The <FONT FACE="COURIER">localconfig</FONT> and |
|---|
| 512 | <FONT FACE="COURIER">.gsas_config</FONT> |
|---|
| 513 | (or <FONT FACE="COURIER">c:\gsas.config</FONT>) |
|---|
| 514 | files are read, if present. |
|---|
| 515 | The following variables control how LIVEPLOT, and in most cases BKGEDIT, |
|---|
| 516 | function and can be |
|---|
| 517 | customized by changing their values in the |
|---|
| 518 | <FONT FACE="COURIER">localconfig</FONT> and |
|---|
| 519 | <FONT FACE="COURIER">.gsas_config</FONT> |
|---|
| 520 | (or <FONT FACE="COURIER">c:\gsas.config</FONT>) |
|---|
| 521 | files. |
|---|
| 522 | <DL><DL> |
|---|
| 523 | <DT><FONT FACE="COURIER">peakinfo(flag<i>n</i>)</FONT><DD> |
|---|
| 524 | These variables define if peak positions will be shown |
|---|
| 525 | for reflections in phase "<i>n</i>". Reflections will be shown if |
|---|
| 526 | the value is non-zero. |
|---|
| 527 | |
|---|
| 528 | <DT><FONT FACE="COURIER">peakinfo(color<i>n</i>)</FONT><DD> |
|---|
| 529 | These variables define the default colors for |
|---|
| 530 | reflections in phase "<i>n</i>" |
|---|
| 531 | |
|---|
| 532 | <DT><FONT FACE="COURIER">peakinfo(dashes<i>n</i>)</FONT><DD> |
|---|
| 533 | These variables define if peaks will be dashed for |
|---|
| 534 | reflections in phase "<i>n</i>" (UNIX only). Lines will be dashed if |
|---|
| 535 | the value is non-zero. |
|---|
| 536 | |
|---|
| 537 | <DT><FONT FACE="COURIER">peakinfo(min<i>n</i>) and peakinfo(max<i>n</i>)</FONT><DD> |
|---|
| 538 | These variables dictate the placement vertical position for reflection |
|---|
| 539 | markers, when manually placed (see expgui(autotick), below). To draw |
|---|
| 540 | to the edge of the screen, use -Inf and Inf. |
|---|
| 541 | </DL></DL> |
|---|
| 542 | |
|---|
| 543 | The following variables are written to |
|---|
| 544 | <font face="courier">.gsas_config</font> |
|---|
| 545 | (or <FONT FACE="COURIER">c:\gsas.config</FONT>) |
|---|
| 546 | when |
|---|
| 547 | "Save Options" is used. These variables are all set from the GUI and therefore |
|---|
| 548 | do not need to be edited manually. |
|---|
| 549 | |
|---|
| 550 | <DL><DL> |
|---|
| 551 | <DT><FONT FACE="COURIER">graph(printout)</FONT><DD> |
|---|
| 552 | This is set to 1 if PostScript files |
|---|
| 553 | will be printed and 0 if they will be written to disk (for Windows all |
|---|
| 554 | files should be written to disk). |
|---|
| 555 | |
|---|
| 556 | <DT><FONT FACE="COURIER">graph(outname)</FONT><DD> |
|---|
| 557 | This is the default for the file name used |
|---|
| 558 | when PostScript files will be written to disk. |
|---|
| 559 | |
|---|
| 560 | <DT><FONT FACE="COURIER">graph(outcmd)</FONT><DD> |
|---|
| 561 | This is the default for the command used |
|---|
| 562 | to print PostScript files (Unix only). |
|---|
| 563 | |
|---|
| 564 | <DT><FONT FACE="COURIER">graph(legend)</FONT><DD> |
|---|
| 565 | Sets the default value for display of the legend in LIVEPLOT and WIDPLT. |
|---|
| 566 | |
|---|
| 567 | <DT><FONT FACE="COURIER">graph(autoraise)</FONT><DD> |
|---|
| 568 | This option shows up in the options menu item as "Raise on update." |
|---|
| 569 | When set to non-zero, the LIVEPLOT window is raised |
|---|
| 570 | (placed on top of any other overlapping) windows |
|---|
| 571 | each time it is updated. |
|---|
| 572 | This option does not seem to work in Windows-NT, but this may depend on |
|---|
| 573 | the version of Tcl/Tk. |
|---|
| 574 | |
|---|
| 575 | <DT><FONT FACE="COURIER">peakinfo(obssym)</FONT><DD> |
|---|
| 576 | Symbol for observed data points. Valid choices are square, circle, diamond, |
|---|
| 577 | plus, cross, splus and scross. |
|---|
| 578 | |
|---|
| 579 | <DT><FONT FACE="COURIER">peakinfo(obssize)</FONT><DD> |
|---|
| 580 | Size for the symbol for observed data points. A value of 1 corresponds to about 1/8 inch |
|---|
| 581 | (about 3 mm). |
|---|
| 582 | |
|---|
| 583 | <DT><FONT FACE="COURIER">expgui(pixelregion)</FONT><DD> |
|---|
| 584 | When hkl values are loaded (using tcldump) and reflections are labeled, reflections |
|---|
| 585 | can be labeled using a Shift-Left-Mouse click. All labeled reflections within expgui(pixelregion) |
|---|
| 586 | pixels of the mouse position are assumed to be overlapped and are labeled. |
|---|
| 587 | |
|---|
| 588 | <DT><FONT FACE="COURIER">expgui(fadetime)</FONT><DD> |
|---|
| 589 | The time in seconds before reflection labels are removed. A value of zero means that reflections |
|---|
| 590 | must be deleted manually (Shift-Right-Mouse). |
|---|
| 591 | (Mac: Shift+Apple+click) |
|---|
| 592 | <DT><FONT FACE="COURIER">expgui(lblfontsize)</FONT><DD> |
|---|
| 593 | A size for reflections labels in pixels. |
|---|
| 594 | |
|---|
| 595 | <DT><FONT FACE="COURIER">expgui(hklbox)</FONT><DD> |
|---|
| 596 | If this variable is non-zero, reflection indices are shown in a box. |
|---|
| 597 | |
|---|
| 598 | <DT><FONT FACE="COURIER">expgui(autotick)</FONT><DD> |
|---|
| 599 | If this variable is non-zero, reflection markers positions are |
|---|
| 600 | set automatically. |
|---|
| 601 | </DL></DL> |
|---|
| 602 | <P> |
|---|
| 603 | <hr><H2>Interfacing External Programs</H2> |
|---|
| 604 | <IMG SRC="new.gif" alt="New!"> |
|---|
| 605 | <B>Combining LIVEPLOT with CMPR & LOGIC</B> |
|---|
| 606 | If you have the |
|---|
| 607 | <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/cmpr"> |
|---|
| 608 | CMPR/LOGIC</A> |
|---|
| 609 | programs installed on your computer, you can use superimpose on the |
|---|
| 610 | GSAS results the peaks for an arbitrary unit cell. |
|---|
| 611 | If you have the |
|---|
| 612 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.icdd.com/products/overview.htm"> |
|---|
| 613 | ICDD-JCPDS PDF-2 powder diffraction database</a>, |
|---|
| 614 | you can also superimpose entries from this database on the |
|---|
| 615 | GSAS results displayed in LIVEPLOT. |
|---|
| 616 | <P> |
|---|
| 617 | When the CMPR/LOGIC program is installed in the same location |
|---|
| 618 | as the GSAS package (<i>e.g.</i> |
|---|
| 619 | <font face="courier">/home/gsas</font> & |
|---|
| 620 | <font face="courier">/home/cmpr</font> |
|---|
| 621 | or <font face="courier">C:\DIFRC\GSAS</font> & |
|---|
| 622 | <font face="courier">C:\DIFRC\CMPR</font>) or if |
|---|
| 623 | the CMPR/LOGIC programs are loaded into standard locations |
|---|
| 624 | (<font face="courier">/usr/local/cmpr</font> or |
|---|
| 625 | <font face="courier">~/cmpr</font> for Unix and Mac OSX or |
|---|
| 626 | <font face="courier">c:\cmpr</font> or |
|---|
| 627 | <font face="courier">c:\Program files\cmpr</font> for Windows), |
|---|
| 628 | the LIVEPLOT program will locate both programs and add an extra menu labeled |
|---|
| 629 | "Peak Gen" to the menu bar. If the CMPR program is not located automatically, |
|---|
| 630 | you may customize this location by specifying a value for |
|---|
| 631 | Tcl/Tk variable cmprdir by including a line such as this: |
|---|
| 632 | <PRE> |
|---|
| 633 | set cmprdir C:/ncnrpkg/cmpr |
|---|
| 634 | </PRE> |
|---|
| 635 | in the <FONT FACE="COURIER">localconfig</FONT>, |
|---|
| 636 | <FONT FACE="COURIER">.gsas_config</FONT> |
|---|
| 637 | or <FONT FACE="COURIER">c:\gsas.config</FONT> files |
|---|
| 638 | [note that forward slashes ("/") should be used here, even for windows.] |
|---|
| 639 | |
|---|
| 640 | <P> |
|---|
| 641 | The "Peak Gen" menu will have either or both of two entries |
|---|
| 642 | "Display a cell" and "Plot ICDD Entry", depending on what |
|---|
| 643 | software is located. The |
|---|
| 644 | "Display a cell" option produces a window similar to the |
|---|
| 645 | <A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell"> |
|---|
| 646 | Edit Cell feature in CMPR</A> |
|---|
| 647 | where allowed reflection positions are displayed for a set of unit cell |
|---|
| 648 | parameters and optionally a space group or extinction conditions. |
|---|
| 649 | The "Plot ICDD Entry" provides a window similar to the |
|---|
| 650 | <A href="http://www.ncnr.nist.gov/xtal/software/cmpr/doc/cmprdoc.html#editcell"> |
|---|
| 651 | LOGIC interface in CMPR</A> |
|---|
| 652 | where ICDD searches may be conducted. From the resulting list of matches, |
|---|
| 653 | selected entries may be displayed. |
|---|
| 654 | <P> |
|---|
| 655 | Note that these routines display peak positions in units of 2Theta, Q or |
|---|
| 656 | d-space. If you are using TOF or EDS data, you must select Q or d-space |
|---|
| 657 | display in LIVEPLOT. If you are using 2Theta, you must supply the correct |
|---|
| 658 | wavelength. |
|---|
| 659 | <P> |
|---|
| 660 | Note that a version of both EXPGUI and CMPR/LOGIC from November 2003 or later |
|---|
| 661 | must be used for these features to work. |
|---|
| 662 | |
|---|
| 663 | </UL> |
|---|
| 664 | <hr> |
|---|
| 665 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 666 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 667 | </TH><TH><A Href="excledt.html">Next page<BR>(EXCLEDT)</A> |
|---|
| 668 | </TH><TH><A Href="expguic.html">Previous page</A> |
|---|
| 669 | </TH></TR></TABLE> |
|---|
| 670 | |
|---|
| 671 | <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> |
|---|
| 672 | <font size=-1><? lastmod(); ?> </font> |
|---|
| 673 | <br> |
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| 674 | $Revision: 785 $ $Date: 2009-12-04 23:11:59 +0000 (Fri, 04 Dec 2009) $ |
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| 675 | </blockquote> |
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| 676 | </body> |
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| 677 | </html> |
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