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| 2 | <head> |
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| 3 | <title>EXPGUI</title> |
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| 4 | <meta name="keywords" content="crystallography, Rietveld, diffraction, |
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| 5 | GSAS, EXPGUI"> |
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| 6 | </HEAD> |
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| 7 | <style> |
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| 8 | A:link {text-decoration:none} |
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| 10 | </style> |
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| 11 | |
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| 12 | <BODY BGCOLOR="#FFFFFF" |
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| 13 | topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" |
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| 14 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
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| 15 | |
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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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| 19 | ?> |
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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="expgui4.html">Next page</A> |
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| 25 | </TH><TH><A Href="expgui2.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, part 3 |
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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 | <h3>A.3 Histogram pane</h3> |
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| 34 | <DL><DL> |
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| 35 | The histogram pane is used to edit background |
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| 36 | and diffractometer constants for a histogram, as well as |
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| 37 | set damping and refinement flags for these parameters. |
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| 38 | <P> |
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| 39 | If |
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| 40 | <A href="expgui.html#multiplehistogram"> |
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| 41 | "Multiple Histogram Selection" mode</A> is set to "All", |
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| 42 | this pane is disabled. For other settings of this mode, |
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| 43 | groups of histograms can be selected and modified |
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| 44 | collectively. |
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| 45 | <P> |
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| 46 | If the EXPTOOL program |
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| 47 | <A href="expgui.html#installation">(see the installation instructions)</A> |
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| 48 | is installed, a button for adding histograms will |
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| 49 | appear on the bottom right on this pane, as seen below. If the |
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| 50 | program is not properly installed, no errors occur, but the button |
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| 51 | does not appear. |
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| 52 | <P> |
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| 53 | Note that the order that histograms appear in this |
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| 54 | pane is determined by the <a href="expguic.html#sorthist">"Sort histograms by"</a> option in |
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| 55 | the Options Menu. |
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| 56 | </DL></DL> |
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| 57 | </blockquote> |
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| 58 | <img SRC="3.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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| 59 | <blockquote> |
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| 60 | <br clear=all> |
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| 61 | |
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| 62 | <a name="EditBackground"></a> |
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| 63 | <h3>A.3.1 Editing background</h3> |
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| 64 | <DL><DL> |
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| 65 | <img SRC="3b1.gif" align=TEXTOP alt="EXPGUI Screen snapshot"> |
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| 66 | When the button labeled "Edit Background", (or "Globally Edit Background" |
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| 67 | or in the case where <A href="expgui.html#multiplehistogram"> |
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| 68 | "Multiple Histogram Selection" mode</A> is set to a single histogram type) |
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| 69 | is pressed, a window such as the one |
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| 70 | to the left is displayed. In the case where background coefficients |
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| 71 | are being edited for more than one histogram |
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| 72 | (<A href="expgui.html#multiplehistogram"> |
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| 73 | "Multiple Histogram Selection" mode</A> must be |
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| 74 | set to a single histogram type) the entry boxes will appear blank |
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| 75 | and only those terms that are filled in will be changed when the "Set" |
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| 76 | button is pressed. |
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| 77 | This option is mostly useful when changing the background function or the |
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| 78 | number of terms for several histograms at a single time. |
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| 79 | Note that no changes are made until the "Set" |
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| 80 | button is pressed. |
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| 81 | <P> |
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| 82 | |
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| 83 | The "Fit Background Graphically" button is displayed only when a single |
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| 84 | histogram is selected for background editing. When this button is |
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| 85 | pressed, the <A HREF="liveplot.html#bkgedit">BKGEDIT</A> program is |
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| 86 | called to fit a background function to user-input fixed background points. |
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| 87 | See the <A HREF="liveplot.html#bkgedit">BKGEDIT documentation</A> for more |
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| 88 | information. |
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| 89 | </DL></DL> |
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| 90 | <br clear=all> |
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| 91 | |
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| 92 | <a name="EditAbsorption"></a> |
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| 93 | <h3>A.3.2 Editing absorption/reflectivity</h3> |
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| 94 | <DL><DL> |
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| 95 | <img SRC="3h.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
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| 96 | The refinement flag and damping factor for correction for absorption |
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| 97 | effects (or for flat-plate samples, reflectivity corrections) can be |
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| 98 | seen in a box near the bottom of the pane. |
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| 99 | The terms and the type of correction used |
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| 100 | are set using the "Edit Abs./Refl." button in this box. Pressing this |
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| 101 | button creates a window, shown to the right. A message is shown in the |
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| 102 | bottom of the window summarizing information about the selected correction. |
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| 103 | <P> |
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| 104 | <a name="AbsorptionSanity"></a> |
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| 105 | Please note, each correction is only appropriate for certain types of data |
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| 106 | and frequently the correction must be fixed rather than refined. It is |
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| 107 | wise to read the "Powder absorption factor" section of the GSAS manual |
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| 108 | (p 138-140 in 1/19/01 edition) before using this correction. |
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| 109 | Since some combinations of data types and correction types are unlikely -- |
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| 110 | but not impossible |
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| 111 | (for example, a cylindical absorption correction and K-alpha1,2 radiation) |
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| 112 | EXPGUI will generate a warning message, such as the one below, |
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| 113 | but not all inappropriate actions can be prevented. |
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| 114 | The user must ultimately understand the role of the correction |
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| 115 | and the nature of the experiment to decide what is appropriate. |
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| 116 | <br clear=all> |
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| 117 | <img SRC="3h1.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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| 118 | <br clear=all> |
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| 119 | </DL></DL> |
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| 120 | <br clear=all> |
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| 121 | |
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| 122 | <a name="EditParm"></a> |
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| 123 | <h3>A.3.3 Global Editing of Parameters</h3> |
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| 124 | <DL><DL> |
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| 125 | It is possible to access parameters and settings for more than one histogram |
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| 126 | at a time when a multiple selection of a specific histogram type |
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| 127 | is allowed |
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| 128 | (see |
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| 129 | <A href="expgui.html#multiplehistogram"> |
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| 130 | "Multiple Histogram Selection" mode</A>). |
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| 131 | In this mode, the histogram pane |
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| 132 | appears slightly differently, as is shown below. |
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| 133 | </DL></DL> |
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| 134 | </blockquote> |
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| 135 | <img SRC="3c.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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| 136 | <blockquote> |
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| 137 | <br clear=all> |
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| 138 | <DL><DL> |
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| 139 | <img SRC="3d.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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| 140 | Pressing a refinement flag checkbox will set all |
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| 141 | selected histogram refinement flags either off or on. |
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| 142 | Pressing a "Globally Edit..." button, will allow a parameter to be set. |
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| 143 | For example, the window to the left shows how |
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| 144 | a diffractometer constant can be |
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| 145 | edited for more than one histogram |
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| 146 | <P> |
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| 147 | A similar window is also used to globally set the |
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| 148 | <A href="expgui4.html">Phase Fraction</A> in |
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| 149 | <A href="expgui.html#multiplehistogram"> |
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| 150 | "Multiple Histogram Selection"</A> mode. |
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| 151 | <br clear=all> |
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| 152 | |
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| 153 | </DL></DL> |
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| 154 | |
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| 155 | <a name="AddHist"></a> |
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| 156 | <h3>A.3.4 Entering New Diffractograms</h3> |
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| 157 | <DL><DL> |
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| 158 | Pressing the "Add New Histogram" button creates the dialog |
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| 159 | shown below. This dialog can be used to enter diffraction data to be used |
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| 160 | in the refinement, or can be used to define parameters for pattern |
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| 161 | simulation, through use of the "dummy histogram" option |
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| 162 | <a href="#Dummy">(see below)</a>. |
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| 163 | <img SRC="3e.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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| 164 | <br clear=all> |
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| 165 | In the case where diffraction data will be input, |
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| 166 | a data file and an instrument parameter file must be |
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| 167 | selected using the "Select File" buttons. The limit for reflection |
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| 168 | generation (maximum energy or two-theta, or minimum d-space or TOF) |
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| 169 | must be entered, as well as the units. |
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| 170 | If more than one bank is defined, either in the data file or in the |
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| 171 | instrument parameter file, the bank must be selected as well. |
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| 172 | Note that the data range can be edited at a later time using the |
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| 173 | <a href="excledt.html">EXCLEDT</a> utility. |
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| 174 | <P> |
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| 175 | <img SRC="3e3.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
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| 176 | |
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| 177 | <h4> |
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| 178 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 179 | Plotting Diffraction Patterns</H4> |
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| 180 | |
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| 181 | To view a plot of a data file, so that the range of the data |
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| 182 | may be viewed, the RAWPLOT program may be invoked using the "Run RAWPLOT" |
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| 183 | button. Note that EXPGUI cannot communicate the names |
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| 184 | of the data and instrument parameter files to RAWPLOT, so they must be |
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| 185 | reentered. The window to the right is shown to aid doing this. |
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| 186 | When files have been selected in the "add histogram" menu, the "put name in |
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| 187 | clipboard" button can be used to place the file name into the |
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| 188 | clipboard. The appropriate paste function (for example the Paste button |
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| 189 | for the DOS window) can be used to avoid typing in the file name. |
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| 190 | <P> |
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| 191 | |
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| 192 | <h4> |
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| 193 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 194 | Editing Instrument Parameter Files</H4> |
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| 195 | |
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| 196 | Instrument parameter files can be edited using the "Edit File" |
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| 197 | button to call the <a href="expgui.html#INSTEDIT">INSTEDIT</a> utility. |
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| 198 | Alternately, to create a new instrument parameter file, you can |
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| 199 | call the same utility using the "instedit" option in the Powder menu. |
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| 200 | Refer to the documentation on |
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| 201 | <a href="expgui.html#INSTEDIT">INSTEDIT</a> to see how this utility functions. |
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| 202 | |
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| 203 | <P><h4> |
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| 204 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 205 | Adding Multiple Diffraction Patterns</H4> |
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| 206 | |
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| 207 | For working with instruments with large numbers of detectors, |
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| 208 | when the number of datasets in the data file matches the number of |
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| 209 | instrument parameters, the button "Add multiple banks" becomes available. |
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| 210 | When this button is pressed, a new window is created that shows a |
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| 211 | checkbutton and a two-theta max (or E-max/TOF-min) for each bank. Banks |
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| 212 | may be selected and pressing a button causes all selected banks to be loaded. |
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| 213 | |
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| 214 | <P> |
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| 215 | <br clear=all> |
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| 216 | <img SRC="3e1.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
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| 217 | <a name="Dummy"></a><h4>Simulating Diffraction Patterns</H4> |
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| 218 | When the dummy histogram option is selected, diffraction data can |
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| 219 | be simulated based a set of experimental constants |
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| 220 | described in an instrument parameter file. |
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| 221 | Note that most of these instrumental parameters, |
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| 222 | such as wavelength or DIFC can be edited on this pane or |
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| 223 | on the <A HREF="expgui5.html">profile</A> pane |
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| 224 | (the simulated pattern is also affected by constants on the |
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| 225 | <A HREF="expgui4.html">scaling</A> pane.) |
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| 226 | The 2-theta/energy/TOF |
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| 227 | range to be used for the computation, as well as the step size, |
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| 228 | must be entered before pressing the "Add" button. |
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| 229 | Note that once the histogram is added, this range and step size |
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| 230 | cannot be edited within EXPGUI at present. However, |
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| 231 | EXPEDT can be used to change these values. |
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| 232 | <br clear=all> |
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| 233 | <P> |
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| 234 | <a name="AddHistErr"></a> |
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| 235 | <img SRC="3e2.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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| 236 | If errors are detected in the input, an error message is displayed |
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| 237 | detailing where the errors are found. Otherwise, the EXPTOOL program is run |
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| 238 | and the output is optionally displayed |
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| 239 | (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>). |
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| 240 | </DL></DL> |
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| 241 | <br clear=all> |
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| 242 | <P> |
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| 243 | <h3>A.3.5 Editing the Data Range & Excluded Regions</h3> |
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| 244 | <DL><DL> |
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| 245 | The button at the bottom of the pane, labeled |
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| 246 | "Set Data Limits & Excluded Regions" invokes |
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| 247 | the <a href="excledt.html">EXCLEDT</a> utility, which is used to |
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| 248 | modify the lower and upper data limits and can be used to add or delete |
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| 249 | excluded regions. |
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| 250 | </DL></DL> |
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| 251 | |
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| 252 | <h3>A.3.6 Setting Histogram Flags</h3> |
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| 253 | <DL><DL> |
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| 254 | <img SRC="3f.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
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| 255 | The button at the bottom of the pane, labeled "Set Histogram Use Flags" invokes |
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| 256 | a menu where the "Use"/"Do not use" flag for powder histogram can be set. |
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| 257 | When this flag is turned off, the histogram is ignored for |
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| 258 | subsequent computations, effectively removing from the experiment. |
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| 259 | <P> |
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| 260 | When these "Use" flags are changed, it is necessary to run POWPREF, |
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| 261 | to propogate the changes. After the "Save" button is pressed, a prompt such |
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| 262 | as the example below, is generated to run POWPREF. Note that GENLES may |
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| 263 | fail if POWPREF is not run after changing these flags. |
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| 264 | <br clear=all> |
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| 265 | <P> |
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| 266 | <img SRC="3g.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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| 267 | <br clear=all> |
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| 268 | </DL></DL> |
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| 269 | |
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| 270 | <h3>A.3.7 Setting Phase Flags</h3> |
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| 271 | <DL><DL> |
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| 272 | If there is more than one phase present in the refinement, |
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| 273 | an extra box appears at the top of the pane to allow phase flags |
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| 274 | to be selected. This allows a phase to be used in some histograms |
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| 275 | but not in others. It also offers a simple way to effectively "delete" a |
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| 276 | phase by removing it from all histograms. Be sure to rerun POWPREF after |
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| 277 | changing the phase flags. |
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| 278 | </DL></DL> |
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| 279 | </blockquote> |
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| 280 | <img SRC="3a.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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| 281 | <blockquote> |
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| 282 | <br clear=all> |
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| 283 | <hr> |
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| 284 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 285 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 286 | </TH><TH><A Href="expgui4.html">Next page</A> |
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| 287 | </TH><TH><A Href="expgui2.html">Previous page</A> |
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| 288 | </TH></TR></TABLE> |
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| 289 | |
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| 290 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
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| 291 | <font size=-1><? lastmod(); ?> </font> |
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| 292 | <br>$Revision: 737 $ $Date: 2009-12-04 23:11:10 +0000 (Fri, 04 Dec 2009) $ |
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| 293 | </blockquote> |
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| 294 | </body> |
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| 295 | </html> |
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