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| 2 | <head> |
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| 3 | <title>EXPGUI Tutorial #6</title> |
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| 11 | <BODY BGCOLOR="#FFFFFF" |
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| 13 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
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| 14 | |
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| 15 | <? |
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| 16 | include("/var/www/include/navigation.inc"); |
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| 17 | include("/var/www/include/utility.inc"); |
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| 18 | ?> |
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| 19 | <blockquote> |
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| 20 | |
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| 21 | <CENTER> |
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| 22 | <H1>GSAS Nickel example using EXPGUI (part 6)</H1> |
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| 23 | </CENTER> |
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| 24 | <H1> |
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| 25 | 6. Plot data using POWPLOT or LIVEPLOT |
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| 26 | </H1> |
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| 27 | At this point in the GSAS tutorial |
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| 28 | program POWPLOT is used to plot the diffraction data. This |
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| 29 | is done in EXPGUI by pressing POWPLOT button in the button bar, or |
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| 30 | by pressing the POWPLOT menu item in either the Powder menu |
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| 31 | or the Graphs menu. The input supplied to POWPLOT and the |
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| 32 | results are the same as what is shown in the menu, so this will |
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| 33 | not be repeated here. |
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| 34 | <P> |
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| 35 | EXPGUI does offer another way to display diffraction data, LIVEPLOT. |
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| 36 | Similar to the way POWPREF was run in the previous step, |
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| 37 | LIVEPLOT can be started by pressing LIVEPLOT button in the button bar, |
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| 38 | or by pressing the LIVEPLOT menu item in the Graphs menu. |
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| 39 | <P> |
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| 40 | <img src="liveplot1.gif" align=left> |
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| 41 | Since no cycles of refinement have been run, |
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| 42 | after LIVEPLOT has generated a blank window, it must be |
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| 43 | triggered to read the POWPREF output by pressing the "Update Plot" |
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| 44 | item in the File menu. |
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| 45 | A plot similar to the one to the left is then displayed. |
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| 46 | <P> |
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| 47 | The contents of the LIVEPLOT window are discussed more fully |
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| 48 | <A HREF="#liveplot"> |
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| 49 | below</A>, but |
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| 50 | note that the calculated diffraction intensities are all |
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| 51 | zero at this point, since GENLES |
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| 52 | has not yet been to run to simulate the pattern. |
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| 53 | Likewise the background values have not yet been fit so |
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| 54 | this curve is a poor fit. |
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| 55 | The blue line shows the values of |
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| 56 | obs-calc (diff), offset negatively. The sum of the fixed background |
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| 57 | values plus the fitted background function is shown |
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| 58 | difference |
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| 59 | pattern is |
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| 60 | <BR clear=left><P> |
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| 61 | <img src="liveplot2.gif" align=left> |
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| 62 | Note that the region plotted can be changed by clicking with the left |
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| 63 | mouse button, to outline the region to be shown, as seen to the left. |
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| 64 | When the left mouse button is pressed a second time, the graph is "zoomed in," |
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| 65 | as is shown below. |
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| 66 | To "zoom out" to the previous region, press the right mouse button. |
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| 67 | <BR clear=left><P> |
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| 68 | <img src="liveplot3.gif"> |
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| 69 | <P> |
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| 70 | <img src="liveplot4.gif" align=left> |
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| 71 | Reflection positions can be marked, using the File/Tickmarks menu. |
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| 72 | <BR clear=left><P> |
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| 73 | <img src="liveplot5.gif" align=left> |
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| 74 | Reflection indices can be displayed by pressing the "h" (or "H") key in the |
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| 75 | position of the reflection to be labeled. The size and time before |
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| 76 | the reflection labels are removed is determined by values in the Options/HKL labeling menu. |
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| 77 | <BR clear=left><P> |
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| 78 | <I>Do not exit LIVEPLOT at this time as it will be used again in part 8 of this |
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| 79 | tutorial.</I> |
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| 80 | <a name="liveplot"> |
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| 81 | <H4>LIVEPLOT Contents and Options</H1> |
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| 82 | </a> |
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| 83 | Note that the observed data points (obs) are marked with "x" symbols in |
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| 84 | LIVEPLOT. |
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| 85 | This can be changed in the Options/Obs symbol menu. The simulated |
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| 86 | diffraction data based on the crystallographic model (calc) is shown as |
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| 87 | a red line. The lower blue line shows the values of |
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| 88 | obs-calc (diff), offset negatively to avoid overlapping with the previous |
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| 89 | curves. The green line (mostly obscured in this figure) shows the background |
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| 90 | function (bckg). This is the sum of the fixed background |
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| 91 | values (if any) plus the fitted background function (if used). |
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| 92 | The dashed magenta vertical lines denote reflection positions. The color |
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| 93 | and lengths of these lines can be customized using the |
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| 94 | options/Configure Tickmarks menu item, for example, auto placement mode |
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| 95 | creates the more customary short tickmarks placed below the pattern, |
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| 96 | at different heights when more than one phase is present. |
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| 97 | <P> |
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| 98 | There are many other options available in LIVEPLOT in the Options menu. The |
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| 99 | Appearance and location of the tickmarks can be set. The symbol and symbol size |
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| 100 | used for observed data can be selected. |
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| 101 | The X and Y units can be changed to Q or d-space values. Background |
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| 102 | can be subtracted. The legend can be removed from the plot. |
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| 103 | |
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| 104 | <BR clear=left><HR> |
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| 105 | Previous step: <A HREF="nickel5.html"> |
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| 106 | Run POWPREF</A> |
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| 107 | <BR> |
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| 108 | Next step: <A HREF="nickel7.html"> |
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| 109 | Setup for Least-Squares Refinement</A> |
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| 110 | |
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| 111 | <HR> |
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| 112 | </blockquote> |
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| 113 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
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| 114 | <font size=-1><? lastmod(); ?> </font> |
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| 115 | <BR>$Revision: 588 $ $Date: 2009-12-04 23:08:41 +0000 (Fri, 04 Dec 2009) $ |
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| 116 | </body> |
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| 117 | </html> |
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