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| 3 | <title>EXPGUI -- EXCLEDT</title> |
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| 16 | <? |
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| 17 | include("/var/www/include/navigation.inc"); |
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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="gsas2cif.html">Next page<BR>(CIF export)</A> |
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| 25 | </TH><TH><A Href="liveplot.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 | |
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| 29 | <center><h1> |
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| 30 | <HR noshade width="75%" size="2" align="center"> |
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| 31 | EXPGUI Utilities (2), EXCLEDT |
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| 32 | <HR noshade width="75%" size="2" align="center"> |
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| 33 | </h1></center> |
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| 34 | This page documents the EXCLEDT utility program |
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| 35 | in the EXPGUI package. The purpose of this tool is to select graphically |
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| 36 | regions of data that will not be included in the refinement. |
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| 37 | The EXCLEDT program is called from the Powder/excledt |
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| 38 | menu item or from the "Data Limits/Exclude" button on the Histogram pane. |
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| 39 | <P> |
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| 40 | A common use for this is |
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| 41 | to adjust the lower 2theta/Q limit (maximum d-space/TOF) so that |
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| 42 | data where no reflections occur can be ignored. It |
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| 43 | is also common to start refinements with |
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| 44 | a somewhat limited range of data, raising the upper 2theta/Q limit |
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| 45 | (minimum d-space/TOF) later. (The ideal is to include all data where |
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| 46 | any peaks can be resolved in the final stages of refinement.) |
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| 47 | Note that there is a disadvantage to changing the data range, |
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| 48 | if one is using the Chebyschev polynomial |
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| 49 | (type 1 background function) to fit the background, as this function |
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| 50 | is scaled over the range of data. If the data range is changed, the |
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| 51 | background function will shift and thus must be refit each time the |
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| 52 | data range is changed. |
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| 53 | <P> |
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| 54 | A second purpose of EXCLEDT is to set and change excluded regions within the |
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| 55 | pattern. When a region is set as excluded, the data within that region |
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| 56 | are ignored with respect to the Rietveld refinement. Note that data should |
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| 57 | be removed only where there is a good explanation why the region cannot be |
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| 58 | accurately modeled. This is sometimes needed to deal with |
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| 59 | scattering from a sample |
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| 60 | container (although this can frequently be modeled as an additional |
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| 61 | phase, using Le Bail extraction for that phase when |
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| 62 | the container is badly textured). Excluded regions are also used occasionally |
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| 63 | when an impurity manifests itself with only a few minor peaks, although it is |
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| 64 | usually much better to model the impurity intensity as an additional phase |
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| 65 | (again using Le Bail extraction for that phase when the structure is unknown or |
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| 66 | the material has severe preferred orientation). Excluded regions are sometime |
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| 67 | needed when a section of pattern is affected by stacking faults. Another |
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| 68 | occasional appropriate use is to eliminate spurious intensity that is due |
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| 69 | instrumental malfunctions. |
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| 70 | It is important not to exclude peaks simply because they cannot be indexed. |
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| 71 | Such peaks may indicate a difference in symmetry or unit cell from the |
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| 72 | structural model, or some other error. |
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| 73 | It is also important that excluded regions be documented in the paper |
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| 74 | which describes the study. |
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| 75 | <P> |
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| 76 | <img SRC="exc1.gif" alt="EXCLEDT Screen snapshot"> |
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| 77 | <br clear=all> |
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| 78 | The EXCLEDT program displays the data in a graph, (see the example above) |
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| 79 | with the observed data as data points (black X's by default) |
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| 80 | and the computed values as a line (red by default). Any excluded data points |
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| 81 | are shown in a different color (orange, by default). |
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| 82 | Lines (again orange, by default) at the |
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| 83 | bottom of the plot show the allowed data range as well as any excluded regions. |
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| 84 | Note that if POWPREF has been run more recently then GENLES, the calculated |
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| 85 | values are zero. |
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| 86 | The EXCLEDT program can plot data in the native units (2-theta, TOF, energy), |
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| 87 | converted to d-space units, or in the most ideal unit for |
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| 88 | diffraction analysis, Q (2 pi/d). |
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| 89 | <P> |
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| 90 | <br clear=all> |
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| 91 | |
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| 92 | <H3>Mouse use</H3> |
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| 93 | The mouse can be used in three ways depending on the button pressed |
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| 94 | in the lower portion of the window. |
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| 95 | <P> |
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| 96 | <img SRC="exc2.gif" BORDER=3 align=right alt="EXCLEDT Screen snapshot"> |
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| 97 | In <B>Zoom mode</B>, |
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| 98 | the cursor appears as |
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| 99 | cross hairs, and the mouse is used to select a region to be magnified by |
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| 100 | clicking on diagonal points in the region with the left mouse button |
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| 101 | (see below) or "zoomed out" with the right mouse button. |
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| 102 | Note that is is also possible to set the range manually, |
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| 103 | <a href="#manualzoom">see below.</a> |
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| 104 | <P> |
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| 105 | <a name="AddRegion"></a> |
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| 106 | In <B>Add Region mode</B>, the mouse is used to map out a region which that |
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| 107 | will be excluded from the refinement. When this button is selected, the |
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| 108 | mouse cursor changes to an arrow. After the left mouse is pressed once, |
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| 109 | a yellow background is shown for the excluded region, as is seen below. |
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| 110 | When the left mouse |
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| 111 | button is pressed a second time, the region is selected. |
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| 112 | If the right mouse button is pressed instead, it resets the region selection. |
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| 113 | <br clear=all> |
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| 114 | <img SRC="exc3.gif" alt="EXCLEDT Screen snapshot"> |
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| 115 | <br clear=all> |
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| 116 | <img SRC="exc3a.gif" align=RIGHT alt="EXCLEDT Screen snapshot"> |
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| 117 | Before the region is added to the excluded list, a message is |
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| 118 | displayed to confirm this. This |
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| 119 | confirmation message can optionally be eliminated (See |
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| 120 | <a href="#prompt">Options/Prompt on add/del</a>.) |
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| 121 | <br clear=all> |
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| 122 | <P> |
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| 123 | In <B>Delete Region mode</B>, the mouse is used to select a region to be |
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| 124 | deleted, causing the data in that region to be included in the refinement. |
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| 125 | The cursor appears as a circle in the graph section of the window. After |
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| 126 | a region has been selected to delete, a message is |
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| 127 | displayed to confirm the region to be deleted from the exclusion list. |
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| 128 | This confirmation message can optionally be eliminated (See |
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| 129 | <a href="#prompt">Options/Prompt on add/del</a>.)<br clear=all> |
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| 130 | <P> |
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| 131 | <br clear=all> |
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| 132 | <H3>Keypad Shortcuts</H3> |
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| 133 | <a name="manualzoom"></a> |
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| 134 | <img SRC="mzoom.gif" align=RIGHT alt="EXCLEDT manual zoom"> |
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| 135 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 136 | Zoom settings can also be entered manually by pressing the "Z" key. This |
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| 137 | opens a dialog, as is shown to the right, where the x- or y-axis range |
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| 138 | can be specified. Any value that is not specified is set to the maximum |
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| 139 | or minimum for the entire dataset. It is possible to zoom further in using |
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| 140 | the mouse, but to zoom out beyond the manual zoom limits, the "reset" button |
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| 141 | on the manual zoom menu must be used. |
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| 142 | <P> |
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| 143 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 144 | If more than one histogram is available to plot, it is possible to cycle |
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| 145 | between the histograms by pressing the "n" or "N" (for next) key. |
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| 146 | <P> |
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| 147 | <IMG SRC="new.gif" alt="New!"> |
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| 148 | Tickmarks can be toggled on or off by pressing the |
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| 149 | "1" key for phase 1, "2" for phase 2,... |
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| 150 | <P> |
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| 151 | <br clear=all> |
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| 152 | <P> |
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| 153 | <H3>Excluded Region/Simulation Range Buttons</H3> |
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| 154 | <img SRC="exc4.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot"> |
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| 155 | At the bottom of the window is a set of buttons with the minimum and maximum |
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| 156 | limit on the data as well as a button for every excluded region. Pressing |
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| 157 | a button causes a window to be opened to edit that region by manually entering |
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| 158 | values. |
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| 159 | <P>where the data range can be set |
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| 160 | <br clear=all> |
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| 161 | <img SRC="exc4a.gif" BORDER=3 align=right alt="EXCLEDT excluded regions snapshot"> |
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| 162 | In the case where a dummy histogram will be edited, the information presented |
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| 163 | in this box is formatted slightly differently (as shown to the right). |
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| 164 | Pressing the set button creates a dialog box where the data range can be set, |
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| 165 | see <a href="#editdummy">Editing Dummy Range</a>. |
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| 166 | |
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| 167 | <br clear=all> |
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| 168 | <P> |
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| 169 | <img SRC="exc5.gif" align=right alt="EXCLEDT informational message"> |
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| 170 | If the upper data limit is raised (or d-min is lowered) this message is |
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| 171 | displayed. The reason is that EXCLEDT cannot display data above the |
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| 172 | upper data limit until the changed limit has been processed in POWPREF. |
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| 173 | If you also want to see the computed intensities in this region, |
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| 174 | you will need to run GENLES as well, so this is also offered as an option. |
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| 175 | <br clear=all> |
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| 176 | <P> |
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| 177 | <a name="LimitTooHigh"></a> |
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| 178 | <img SRC="exc7.gif" align=right alt="EXCLEDT informational message"> |
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| 179 | Note that it is possible to set the upper data limit (lower d-min limit) |
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| 180 | well outside the range of data. If this is done, POWPREF will run slower |
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| 181 | because many unneeded reflections are being included in the computation. |
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| 182 | If this occurs and POWPREF is run inside EXCLEDT, a message such as |
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| 183 | that to the right is shown. Unless there is some specific reason |
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| 184 | (I do not know of one) it is probably best to accept this suggestion. |
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| 185 | <br clear=all> |
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| 186 | <P> |
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| 187 | <a name="editdummy"></a> |
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| 188 | <H3>Editing Dummy Range</H3> |
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| 189 | <img SRC="exc8.gif" align=right alt="EXCLEDT informational message"> |
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| 190 | When the data range is edited, a box such as the one to the right will appear |
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| 191 | to set the data limits and step size. Note that these values are always |
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| 192 | displayed in the native units for the histogram (degrees, microseconds or Kev) |
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| 193 | regardless of the setting for the x-axis units, since the step size is constant |
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| 194 | in these native units. The data range is also shown in d-space and Q. |
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| 195 | <P> |
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| 196 | Note that it is not possible to edit the data range for |
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| 197 | histograms with varying steps. At this time, this only affects |
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| 198 | dummy TOF histograms simulated with logarithmic steps. The range can be |
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| 199 | changed in the EXPEDT program. |
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| 200 | <br clear=all> |
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| 201 | <P> |
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| 202 | <H3>Exiting EXCLEDT</H3> |
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| 203 | <img SRC="exc6.gif" align=right alt="EXCLEDT informational message"> |
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| 204 | EXCLEDT can be exited using the File/Exit menu item or by pressing the |
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| 205 | "Save & Exit" button, or by pressing Control-C. If the excluded regions or |
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| 206 | data limits are changed, a message to reminding you to run POWPREF is |
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| 207 | shown. Note that you <I>must</I> run POWPREF before GENLES, if these |
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| 208 | items are changed. |
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| 209 | <br clear=all> |
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| 210 | <P> |
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| 211 | <H3>File Menu Commands</H3> |
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| 212 | <img SRC="excm1.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot"> |
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| 213 | <DL><DL> |
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| 214 | <DT>Tickmarks<DD>Invokes a submenu where tickmarks can be displayed or removed |
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| 215 | for each phase present in the histogram. |
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| 216 | Alternately, tickmarks can be displayed or removed |
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| 217 | <IMG SRC="new.gif" alt="New!">by pressing the |
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| 218 | "1" key for phase 1, "2" for phase 2,... |
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| 219 | See the Options/"Configure Tickmarks"menu item for information |
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| 220 | on tickmarks |
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| 221 | <DT>Histogram |
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| 222 | <DD>This allows a different histogram to be displayed. |
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| 223 | <DT>Set Min/Max Range |
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| 224 | <DD>This opens a window where the usable data range may be changed. |
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| 225 | <DT>Update Plot |
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| 226 | <DD>The causes EXCLEDT to read read the current histogram again from |
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| 227 | the datafile. If excluded region or data range |
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| 228 | changes have been made, POWPREF & GENLES may be run first. |
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| 229 | <DT>Make PostScript |
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| 230 | <DD>Creates a low quality PostScript file containing the LIVEPLOT |
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| 231 | output. See the Options/"Set PS output" button for where the file is created. |
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| 232 | <DT>Exit<DD>Saves any changes to the excluded regions or data range. |
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| 233 | If changes have been made, POWPREF & GENLES may be run. |
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| 234 | </DL></DL> |
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| 235 | |
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| 236 | <br clear=all> |
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| 237 | <img SRC="excm2.gif" BORDER=3 align=right alt="EXCLEDT menu snapshot"> |
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| 238 | <H3>Options Menu</H3> |
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| 239 | <DL><DL> |
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| 240 | <DT>Configure Tickmarks |
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| 241 | <DD>Tickmarks can be placed automatically, similar to their |
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| 242 | placement in POWPLOT or can be drawn one height to another. The default |
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| 243 | is for lines to be draw from "-Inf" to "Inf", which creates lines from the |
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| 244 | 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 |
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| 245 | the vertical placement of the tickmarks can be specified. The "show" flag, |
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| 246 | set in the File/Tickmarks menu can also be changed here. |
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| 247 | <DT>Symbol Type |
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| 248 | <DD>This brings up a menu where the symbol type and size for the |
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| 249 | observed and excluded data points can be selected. |
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| 250 | <DT>Symbol Color |
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| 251 | <DD>The colors for all the displayed lines and symbols can be changed here. |
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| 252 | <DT>X units |
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| 253 | <DD>The x units can be selected here. The choices are |
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| 254 | "as collected" (2Theta/TOF/KeV), d-space (A) or Q (A<sup>-1</sup>) |
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| 255 | <DT>Include Legend |
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| 256 | <DD>The legend is the optional box in the upper left that defines the |
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| 257 | plot entries |
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| 258 | <a name="prompt"></a><DT>Prompt on add/del |
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| 259 | <DD>If this option is set, a prompt will be generated when excluded regions |
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| 260 | are added or deleted. |
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| 261 | <DT>Set PS output |
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| 262 | <DD>For UNIX this allows the file to be sent directly to a printer |
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| 263 | or can be saved in a file. For Windows, a file must be written. |
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| 264 | </DL></DL> |
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| 265 | |
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| 266 | |
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| 267 | <br clear=all> |
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| 268 | |
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| 269 | <hr> |
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| 270 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 271 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 272 | </TH><TH><A Href="gsas2cif.html">Next page<BR>(CIF export)</A> |
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| 274 | </TH></TR></TABLE> |
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| 275 | |
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| 276 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
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| 277 | <font size=-1><? lastmod(); ?> </font> |
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| 278 | <br>$Revision: 764 $ $Date: 2009-12-04 23:11:38 +0000 (Fri, 04 Dec 2009) $ |
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| 279 | </blockquote> |
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