| 1 | <!-- add lstview liveplot and widplt sections (see tkGSAS.html) --!> |
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| 2 | <html> |
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| 3 | <head> |
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| 4 | <title>EXPGUI</title> |
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| 5 | </head> |
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| 6 | <body> |
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| 7 | |
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| 8 | <center> |
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| 9 | <h1> |
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| 10 | Using EXPGUI</h1></center> |
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| 11 | |
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| 12 | <h2>Introduction</h2> |
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| 13 | EXPGUI allows two types of actions: |
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| 14 | it allows the different |
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| 15 | GSAS programs such as EXPEDT, GENLES, FOURIER,... |
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| 16 | to be run, |
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| 17 | and it can be used to directly modify the GSAS |
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| 18 | experiment file without using EXPEDT. |
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| 19 | Programs are invoked either through use of the menu bar |
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| 20 | <center><B> |
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| 21 | <br>The menu bar. |
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| 22 | <br><img SRC="menubar.gif" BORDER=3 > |
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| 23 | </center></B> |
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| 24 | or by "pressing" a button on the button bar. The button bar |
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| 25 | simply provides an easy way to access commonly used |
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| 26 | actions on the menu bar. Users can configure the menu |
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| 27 | bar to include their own preferred actions and, with |
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| 28 | some knowledge of the program and Tcl/Tk, |
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| 29 | add their own commands to the menu bar or button bar. |
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| 30 | |
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| 31 | <center><B> |
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| 32 | <br>The button bar. |
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| 33 | <br><img SRC="buttonbar.gif" BORDER=3 > |
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| 34 | </center></B> |
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| 35 | |
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| 36 | <P> |
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| 37 | Different sections of the .EXP file can be edited by selecting different |
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| 38 | panels or pages from the tabbed list. These tabs will have slightly different |
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| 39 | appearance depending on the packages |
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| 40 | available with your local version of Tcl/Tk. |
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| 41 | <center><B> |
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| 42 | <br>The panel tabs using the Tix package. |
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| 43 | <br><img SRC="panebar1.gif" BORDER=3 > |
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| 44 | </center></B> |
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| 45 | <center><B> |
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| 46 | <br>The panel tabs without the Tix package. |
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| 47 | <br><img SRC="panebar2.gif" BORDER=3 > |
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| 48 | </center></B> |
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| 49 | If the Tix package is loaded on your machine, it will be |
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| 50 | used, but if it is not, EXPGUI will run fine without it. |
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| 51 | <P> |
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| 52 | This documentation will describe the different actions that |
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| 53 | can be accomplished with the different panels and the |
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| 54 | contents of the menus. |
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| 55 | <hr> |
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| 56 | |
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| 57 | <h2>1. LS Controls panel</h2> |
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| 58 | <DL><DL> |
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| 59 | <p>The LS Controls panel shows information about the |
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| 60 | current experiment, typically found in the EXPEDT "Least |
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| 61 | Squares Controls" options. |
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| 62 | <P> |
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| 63 | Note that the order that histograms appear in this |
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| 64 | panel is determined by the "Sort histograms by" option in |
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| 65 | the Options Menu. |
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| 66 | <img SRC="1.gif" align=TEXTTOP> |
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| 67 | </DL></DL> |
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| 68 | <P> |
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| 69 | <h2>2. Phase panel</h2> |
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| 70 | <DL><DL> |
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| 71 | The phase panel is used to edit information |
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| 72 | about the phase or phases found in the experiment |
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| 73 | file. The cell and atomic damping and refinement |
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| 74 | flags can be changed here. Note that if a |
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| 75 | single atom is selected using the mouse, the information |
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| 76 | for that atom can be edited. If a group of atoms is |
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| 77 | selected |
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| 78 | <A href="#mouseactions">(see Mouse Actions)</A> |
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| 79 | the damping and refinement flags |
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| 80 | for all the selected atom can be changed at one time. |
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| 81 | <P> |
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| 82 | Note that the order that atoms appear in this panel is |
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| 83 | determined by the "Sort Atoms by" option in the Options |
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| 84 | Menu. |
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| 85 | <img SRC="2.gif" align=TEXTTOP> |
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| 86 | </DL></DL> |
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| 87 | |
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| 88 | <h2>3. Histogram panel</h2> |
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| 89 | <DL><DL> |
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| 90 | The histogram panel is used to edit background |
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| 91 | and diffractometer constants for a histogram, as well as |
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| 92 | set damping and refinement flags for these parameters. |
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| 93 | <P> |
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| 94 | If |
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| 95 | <A href="#multiplehistogram"> |
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| 96 | "Multiple Histogram Selection" mode</A> is set to "All", |
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| 97 | this panel is disabled. For other settings of this mode, |
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| 98 | groups of histograms can be selected and modified |
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| 99 | collectively. |
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| 100 | <P> |
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| 101 | Note that the order that histograms appear in this |
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| 102 | panel is determined by the "Sort histograms by" option in |
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| 103 | the Options Menu. |
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| 104 | <img SRC="3.gif" align=TEXTTOP> |
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| 105 | </DL></DL> |
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| 106 | |
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| 107 | <h2>4. Scaling panel</h2> |
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| 108 | <DL><DL> |
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| 109 | The Scaling panel is used to edit the scale factor for a |
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| 110 | histogram as well as the phase fractions for each phase |
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| 111 | present in that histogram. Damping and refinement flags |
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| 112 | can also be set here. |
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| 113 | <P> |
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| 114 | If |
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| 115 | <A href="#multiplehistogram"> |
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| 116 | "Multiple Histogram Selection" mode</A> is set to |
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| 117 | any value other than "Off," |
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| 118 | groups of histograms can be selected and modified |
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| 119 | collectively. |
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| 120 | <P> |
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| 121 | Note that the order that histograms appear in this |
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| 122 | panel is determined by the "Sort histograms by" option in |
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| 123 | the Options Menu. |
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| 124 | <img SRC="4.gif" align=TEXTTOP> |
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| 125 | </DL></DL> |
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| 126 | |
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| 127 | <h2>5. Profile panel</h2> |
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| 128 | <DL><DL> |
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| 129 | The Profile panel is used to edit the profile values for |
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| 130 | each phase present in a histogram as well as set |
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| 131 | the refinement flags and a damping value for each phase. |
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| 132 | <P> |
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| 133 | If |
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| 134 | <A href="#multiplehistogram"> |
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| 135 | "Multiple Histogram Selection" mode</A> is set to "All", |
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| 136 | this panel is disabled. For other settings of this mode, |
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| 137 | profile values and settings can be collectively |
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| 138 | modified for groups of histograms. |
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| 139 | <P> |
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| 140 | Note that the order that histograms appear in this |
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| 141 | panel is determined by the "Sort histograms by" option in |
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| 142 | the Options Menu. |
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| 143 | <img SRC="5.gif" align=TEXTTOP> |
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| 144 | </DL></DL> |
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| 145 | |
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| 146 | <a name="multiplehistogram"> |
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| 147 | <h2>6. Multiple Histogram Selection</h2></a> |
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| 148 | <DL><DL> |
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| 149 | This mode allows parameters to be changed for groups of |
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| 150 | histograms. |
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| 151 | When the "Multiple Histogram Selection" mode is off, |
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| 152 | it is possible to modify parameters |
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| 153 | and refinement flags for only a single histogram, but |
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| 154 | the other settings allow groups of histograms |
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| 155 | to be selected and modified. |
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| 156 | <A href="#mouseactions">(see Mouse Actions)</A>. |
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| 157 | |
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| 158 | It does not make sense, however, to globally modify |
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| 159 | instrument-related parameters and flags for different |
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| 160 | histogram types. |
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| 161 | So global actions can be limited to a single class |
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| 162 | of histogram types (e.g. TOF, CW Neutron,...), which |
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| 163 | allows these parameters to be set for groups of |
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| 164 | similar histograms. Thus, if this mode is set to "All" |
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| 165 | the Histogram and Profile panels are disabled. |
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| 166 | <P> |
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| 167 | The setting for "Multiple Histogram Selection" mode is |
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| 168 | selected using the "Multiple Hist. Selection" item on the |
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| 169 | Options menu. |
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| 170 | <p> |
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| 171 | <a name="mouseactions"> |
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| 172 | </DL></DL> |
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| 173 | <h2>7. Mouse Actions</h2></a> |
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| 174 | <DL><DL> |
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| 175 | A range of atoms or (in multiple selection mode) histograms may be |
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| 176 | selected by dragging (holding down) the left mouse button. It is also |
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| 177 | possible to select a range by using the Shift key with the left mouse |
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| 178 | button. To select or deselect individual entries, use the Control key |
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| 179 | with the left mouse button. The right mouse button selects all |
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| 180 | entries. |
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| 181 | </DL></DL> |
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| 182 | |
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| 183 | <h2>8. Menus</h2> |
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| 184 | A description of the EXPGUI menus follows along with a very |
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| 185 | brief description of the function of each menu option. |
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| 186 | Note that an option may appear under more than one menu. |
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| 187 | <H3>8.1 File Menu</H3> |
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| 188 | <DL><DL> |
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| 189 | The options on the File menu as is the custom contains the commands |
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| 190 | for reading and writing experiment files, as well as starting |
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| 191 | and ending the program. |
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| 192 | <DL> |
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| 193 | <DT> |
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| 194 | expnam |
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| 195 | <DD> |
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| 196 | Select an existing GSAS experiment to be used |
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| 197 | <DT>Save<DD>Saves modifications to the current experiment file to disk |
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| 198 | <DT>Save As<DD>Saves modifications to the current experiment file to disk |
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| 199 | under a new file name |
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| 200 | <DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk. |
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| 201 | <DT>New_expnam<DD>Create a new GSAS experiment from scratch |
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| 202 | <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse) |
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| 203 | <DT>exit<DD>Exit EXPGUI |
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| 204 | </DL> |
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| 205 | <img SRC="m1.gif" BORDER=3 > |
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| 206 | </DL></DL> |
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| 207 | |
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| 208 | <h3>8.2 Options Menu</h3> |
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| 209 | <DL><DL> |
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| 210 | This menu contains options that determine how EXPGUI runs. |
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| 211 | <DL> |
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| 212 | <DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are |
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| 213 | saved prior to each save or run of expedt in a file named |
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| 214 | [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX) |
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| 215 | or in a file named [expnam].ZIP or [expnam].xxx (Windows) |
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| 216 | <DT>Sort atoms by<DD> Determines the order that atoms are displayed on the "Phase" page |
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| 217 | Atoms may be displayed sorted by atom number, atom type, |
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| 218 | or by x, y or z |
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| 219 | |
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| 220 | <DT>Sort histograms by<DD>Determines the order that histograms are displayed on the |
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| 221 | Histogram, Scaling and Profile pages |
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| 222 | |
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| 223 | Histograms may be sorted by histogram number, histogram type, |
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| 224 | original bank number, or diffraction angle/wavelength |
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| 225 | <DT>Multiple hist. selection<DD>When this mode is off, it is possible to modify parameters |
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| 226 | and refinement flags for only a single histogram. For other settings, |
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| 227 | it is possible to modify parameters and flags for groups of |
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| 228 | histograms (see help for Mouse actions). |
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| 229 | |
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| 230 | It does not make sense, however, to globally modify |
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| 231 | instrument-related parameters and flags for different histogram types. |
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| 232 | So global actions can be limited to a single class of histogram types |
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| 233 | (e.g. TOF, CW Neutron,...), which allows these parameters to be set |
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| 234 | for groups of similar histograms. Thus, if this mode is set to "All" |
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| 235 | the Histogram and Profile pages are disabled. |
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| 236 | <DT>Override backspace<DD>This option is available in UNIX only, as there are different |
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| 237 | ways that backspace can be implemented. When option is set |
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| 238 | as "On," the backspace key is overridden to send a "delete" |
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| 239 | character. If backspace does not work in a program such as |
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| 240 | EXPEDT, change try the other setting for this option. |
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| 241 | <DT>SaveOptions<DD>Save the current values for "Override backspace", |
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| 242 | "Sort atoms by", "Sort histograms by" and "archive EXP" |
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| 243 | in file ~/.gsas_config (c:\.gsas_config on Windows). |
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| 244 | <DT>liveplot_options<DD>Used to set options for liveplot, |
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| 245 | for example, the histogram to be plotted |
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| 246 | </DL> |
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| 247 | <img SRC="m2.gif" align=TEXTTOP> |
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| 248 | </DL></DL> |
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| 249 | |
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| 250 | <h3>8.3 Powder Menu</h3> |
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| 251 | <DL><DL> |
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| 252 | This menu contains links to GSAS programs used for powder diffraction |
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| 253 | analysis. |
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| 254 | <DL> |
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| 255 | <DT>expedt<DD>Run GSAS experiment editor |
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| 256 | <DT>powpref<DD>Powder data preparation |
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| 257 | <DT>genles<DD>Run GSAS experiment editor |
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| 258 | <DT>powplot<DD>Display powder patterns |
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| 259 | <DT>rawplot<DD>Plot powder data |
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| 260 | <DT>fitspec<DD>Fit a TOF vanadium scattering spectrum |
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| 261 | <DT>tofnorm<DD>Normalize a TOF spectrum |
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| 262 | </DL> |
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| 263 | <img SRC="m3.gif" align=TEXTTOP> |
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| 264 | </DL></DL> |
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| 265 | |
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| 266 | <h3>8.4 Single Crystal Menu</h3> |
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| 267 | <DL><DL> |
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| 268 | This menu contains links to GSAS programs used for |
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| 269 | single-rystal diffraction analysis. |
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| 270 | <DL> |
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| 271 | <DT>expedt<DD>Run GSAS experiment editor |
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| 272 | <DT>powpref<DD>Powder data preparation |
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| 273 | <DT>scabs<DD>Single crystal absorption |
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| 274 | <DT>scmerge<DD>Sort and merge single crystal data |
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| 275 | <DT>sxtldata<DD>Prepare generic single crystal data |
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| 276 | </DL> |
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| 277 | <img SRC="m4.gif" align=TEXTTOP> |
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| 278 | </DL></DL> |
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| 279 | |
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| 280 | <h3>8.5 Graphics Menu</h3> |
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| 281 | <DL><DL> |
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| 282 | This menu contains links to several GSAS and |
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| 283 | two non-GSAS (liveplot and widplt) |
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| 284 | programs used for graphical display of data and results. |
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| 285 | <DL> |
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| 286 | <DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT |
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| 287 | and then compute with FOURIER |
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| 288 | <DT>polfplot<DD>Display polefigures |
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| 289 | <DT>powplot<DD>Display powder patterns |
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| 290 | <DT>ortep<DD>Draw crystal structure |
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| 291 | <DT>rawplot<DD>Plot powder data |
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| 292 | <DT>fourier<DD>Generate Fourier map |
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| 293 | <DT>forsrh<DD>Search Fourier map for peaks |
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| 294 | <DT>liveplot<DD>Create a plot of powder data |
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| 295 | with zooming, automatic update and other nice features. |
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| 296 | <DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file |
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| 297 | </DL> |
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| 298 | <img SRC="m5.gif" align=TEXTTOP |
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| 299 | </DL></DL> |
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| 300 | |
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| 301 | <h3>8.6 Results Menu</h3> |
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| 302 | <DL><DL> |
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| 303 | This menu contains links to several GSAS and |
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| 304 | one non-GSAS (lstview) |
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| 305 | programs used for analysis of results. |
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| 306 | <DL> |
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| 307 | <DT>bijcalc<DD>Thermal parameter analysis |
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| 308 | <DT>disagl<DD>Distance/angle calculations |
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| 309 | <DT>reflist<DD>List reflection data |
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| 310 | <DT>geometry<DD>Molecular geometry calculations |
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| 311 | <DT>hstdmp<DD>List powder histogram data |
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| 312 | <DT>istats<DD>HKL Intensity statistics |
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| 313 | <DT>rcalc<DD>Compute reflection resuduals |
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| 314 | <DT>lstview<DD>Create a box with scrollbars containing the current .LST file |
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| 315 | </DL> |
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| 316 | <img SRC="m6.gif" align=TEXTTOP> |
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| 317 | </DL></DL> |
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| 318 | |
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| 319 | <h3>8.7 Calculations Menu</h3> |
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| 320 | <DL><DL> |
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| 321 | This menu contains programs for useful crystallographic computations. |
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| 322 | <DL> |
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| 323 | <DT>cllchg<DD>Transform unit cell |
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| 324 | <DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths |
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| 325 | <DT>rducll<DD>Unit cell reduction |
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| 326 | <DT>spcgroup<DD>Space group symbol interpreter |
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| 327 | <DT>unimol<DD>Unique molecule assembler |
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| 328 | </DL> |
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| 329 | <img SRC="m7.gif" align=TEXTTOP> |
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| 330 | </DL></DL> |
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| 331 | |
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| 332 | <h3>8.8 Import/Export Menu</h3> |
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| 333 | <DL><DL> |
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| 334 | This menu contains utilities for importing information into GSAS and |
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| 335 | exporting. |
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| 336 | <DL> |
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| 337 | <DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file |
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| 338 | <DT>hklsort<DD>Prepare HKL tables |
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| 339 | <DT>pubtable<DD>Prepare atom parameter tables |
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| 340 | <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse) |
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| 341 | <DT>cad4rd<DD>Prepare CAD4 single crystal data |
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| 342 | <DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format |
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| 343 | <DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b |
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| 344 | <DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data |
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| 345 | <DT>sxtldata<DD>Prepare generic single crystal data |
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| 346 | </DL> |
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| 347 | <img SRC="m8.gif" align=TEXTTOP> |
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| 348 | </DL></DL> |
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| 349 | |
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| 350 | <h2>9. EXPGUI Utility Programs</h2></a> |
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| 351 | <DL><DL> |
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| 352 | <P><B>LSTVIEW</B> |
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| 353 | |
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| 354 | <P>lstview is used to browse through the GSAS output listing. It is |
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| 355 | invoked by the "lstview" command in the GUI. |
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| 356 | <CENTER><IMG SRC="http://rrdjazz.nist.gov/~toby/textview.gif"></CENTER> |
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| 357 | |
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| 358 | |
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| 359 | <P><B>LIVEPLOT</B> |
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| 360 | |
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| 361 | <P>liveplot shows the observed, calculated and difference plots for powder |
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| 362 | refinements. The plot is updated as the refinement progresses. The mouse can |
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| 363 | be used to zoom in on sections of the plot. |
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| 364 | <CENTER><IMG SRC="http://rrdjazz.nist.gov/~toby/liveplot.gif"></CENTER> |
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| 365 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36> |
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| 366 | LIVEPLOT can now be enhanced to superimpose peak locations for |
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| 367 | input unit cells or peaks from JCPDS/ICDD entries. |
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| 368 | See the <A HREF="http://rrdjazz.nist.gov/~toby/tkGSAS_cfg.html#liveplot"> |
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| 369 | LIVEPLOT customization information</A> |
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| 370 | or read file <tt>tkGSAS_cfg.html</tt> in the gsas/tcl directory. |
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| 371 | |
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| 372 | <P><B>WIDPLT</B> |
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| 373 | |
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| 374 | <P>widplt can be used to plot the actual peak widths generated by the profile |
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| 375 | parameters used in GSAS. It is possible to define reference curves |
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| 376 | that are loaded automatically. |
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| 377 | <CENTER><IMG SRC="http://rrdjazz.nist.gov/~toby/widplt.gif"></CENTER> |
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| 378 | <BR> |
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| 379 | </DL></DL> |
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| 380 | |
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| 381 | <H2> |
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| 382 | Acknowledgements</H2> |
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| 383 | Praise to Larson and <A HREF="http://strider.lansce.lanl.gov/mlnsc/scientists/vondreele.html">Von |
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| 384 | Dreele</A> for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A> |
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| 385 | for Tcl/Tk and <A HREF="http://rrdjazz.nist.gov/przemek.html">Przemek Klosowski</A> |
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| 386 | for convincing me to learn Tcl/Tk. |
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| 387 | <hr> |
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| 388 | GSAS is written by Allen C. Larson and Robert B. Von Dreele, MS-H805, |
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| 389 | Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions |
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| 390 | or kudos concerning GSAS should be sent to Robert B. Von Dreele at |
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| 391 | <A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A> |
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| 392 | <P>GSAS is Copyright, 1984-1997, The Regents of the University of California. |
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| 393 | The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36) |
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| 394 | by the Los Alamos National Laboratory, which is operated by the University |
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| 395 | of California for the U.S. Department of Energy. The U.S. Government is |
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| 396 | licensed to use, reproduce, and distribute this software. Permission is |
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| 397 | granted to the public to copy and use this software without charge, provided |
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| 398 | that this notice and any statement of authorship are reproduced on all |
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| 399 | copies. Neither the Government nor the University makes any warranty, express |
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| 400 | or implied, or assumes any liability or responsibility for the use of this |
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| 401 | software. |
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| 402 | <P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research, |
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| 403 | <A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> |
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| 404 | with help from Jonathan Wasserman. |
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| 405 | |
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| 406 | <P>EXPGUI is not subject to copyright. Have fun with it. |
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| 407 | |
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| 408 | <p>Neither the U.S. Government nor any author makes any warranty, |
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| 409 | expressed or implied, or assumes any liability or responsibility |
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| 410 | for the use of this information or the software described |
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| 411 | here. Brand names cited here are used for |
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| 412 | identification purposes and do not consitute an endorsement by NIST. |
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| 413 | |
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| 414 | <p><a href="http://rrdjazz.nist.gov/~toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>) |
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| 415 | <br> |
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| 416 | $Revision: 35 $ $Date: 2009-12-04 22:59:17 +0000 (Fri, 04 Dec 2009) $ |
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| 417 | </body> |
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| 418 | </html> |
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