[24] | 1 | <html> |
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| 2 | <head> |
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[148] | 3 | <META NAME="Author" CONTENT="Brian H. Toby"> |
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| 4 | <title>EXPGUI</title> |
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[24] | 5 | </head> |
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[148] | 6 | <BODY BGCOLOR="#FFFFFF"> |
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[24] | 7 | |
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[148] | 8 | <A HREF=http://www.ncnr.nist.gov> |
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| 9 | <IMG SRC="http://www.ncnr.nist.gov/images/ncnrtrans.gif" |
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| 10 | alt="Link to NIST Center for Neutron Research home page" |
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| 11 | ALIGN=RIGHT></A> |
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| 12 | <A HREF=http://www.nist.gov> |
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| 13 | <IMG SRC="http://www.ncnr.nist.gov/images/webidblue_2lineright.gif" |
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| 14 | alt="Link to National Institute of Standards & Technology home page" |
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| 15 | ALIGN=LEFT></A> |
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| 16 | <CENTER> |
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| 17 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html"> |
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| 18 | <IMG SRC="tcltklogo100.gif" |
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| 19 | alt="Link to Tcl/Tk information"> |
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| 20 | </CENTER></A> |
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| 21 | <hr> |
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[24] | 22 | |
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[148] | 23 | <center><h1> |
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| 24 | EXPGUI<BR> |
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| 25 | A Graphical User Interface for |
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| 26 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html"> |
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| 27 | GSAS</A> |
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| 28 | </h1></center> |
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| 29 | <P><P> |
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| 30 | EXPGUI is a graphical interface for the |
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| 31 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html"> |
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| 32 | GSAS</A> package. |
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| 33 | It allows two types of actions: |
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[202] | 34 | it can be used to directly modify the GSAS |
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| 35 | experiment file with a graphical user interface (GUI) and |
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| 36 | it can be used to invoke the programs inside the |
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| 37 | GSAS package such as EXPEDT, GENLES, FOURIER... |
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| 38 | These programs can be run from a menu or in many cases by pressing buttons. |
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[96] | 39 | |
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[202] | 40 | <P> |
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| 41 | This documentation describes the different actions that |
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| 42 | can be accomplished with the different panes and the |
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| 43 | contents of the menus. Other documents about EXPGUI are: |
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| 44 | <a name="installation"></A> |
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| 45 | <A HREF="expgui_Win_readme.html"> |
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| 46 | Installation notes for Windows</A>, |
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| 47 | <A HREF="expgui_Unix_readme.html"> |
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| 48 | Installation notes for UNIX</A>, |
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[148] | 49 | <A HREF="expgui_cfg.html"> |
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[202] | 50 | Customization notes</A> and two example tutorials: for |
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| 51 | <A HREF="tutorial1/index.html"> |
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| 52 | TOF</A> |
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| 53 | and |
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| 54 | <A HREF="tutorial2/index.html"> |
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| 55 | constant-wavelength neutron</A>. |
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| 56 | Note that screen images in this document are not updated as frequently as the |
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| 57 | text. |
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| 58 | <hr> |
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[24] | 59 | |
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[202] | 60 | <h2>A. Experiment file editing</h2> |
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[24] | 61 | <P> |
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| 62 | Different sections of the .EXP file can be edited by selecting different |
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[202] | 63 | panes ("pages" or "panels") from the tabbed list. |
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[24] | 64 | <center><B> |
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[202] | 65 | <br>The notebook pane tabs. |
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[24] | 66 | <br><img SRC="panebar1.gif" BORDER=3 > |
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| 67 | </center></B> |
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[202] | 68 | |
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[24] | 69 | <P> |
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[202] | 70 | <h3>A.1 Least Squares (LS) Controls Pane</h3> |
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[24] | 71 | <DL><DL> |
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[202] | 72 | <p>The LS Controls pane shows information about the |
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[24] | 73 | current experiment, typically found in the EXPEDT "Least |
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| 74 | Squares Controls" options. |
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| 75 | <P> |
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| 76 | Note that the order that histograms appear in this |
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[202] | 77 | pane is determined by the |
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| 78 | <a href="http:#sorthist">"Sort histograms by"</a> option in |
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[24] | 79 | the Options Menu. |
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| 80 | <img SRC="1.gif" align=TEXTTOP> |
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| 81 | </DL></DL> |
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[202] | 82 | |
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[24] | 83 | <P> |
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[202] | 84 | <h3>A.2 Phase Pane</h3> |
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[24] | 85 | <DL><DL> |
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[202] | 86 | The phase pane is used to edit information |
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| 87 | about the structural model(s) found in the experiment |
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| 88 | file. The flags for refining the unit cell and atomic parameters, |
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| 89 | as well as ther damping values, |
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| 90 | can be set on this pane. Note that if a |
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[24] | 91 | single atom is selected using the mouse, the information |
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| 92 | for that atom can be edited. If a group of atoms is |
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| 93 | selected |
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| 94 | <A href="#mouseactions">(see Mouse Actions)</A> |
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| 95 | the damping and refinement flags |
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[202] | 96 | for all the selected atoms are changed. |
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[24] | 97 | <P> |
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[96] | 98 | If the EXPTOOL program |
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| 99 | <A href="#installation">(see the installation instructions)</A> |
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| 100 | is installed, buttons for adding phases and atoms will |
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[202] | 101 | appear on this pane, as seen below. If the |
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[96] | 102 | program is not properly installed, no errors occur, but the buttons |
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| 103 | do not appear. |
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| 104 | <P> |
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[202] | 105 | Note that the order that atoms appear in this pane is |
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| 106 | determined by the |
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| 107 | <a href="http:#sortatoms">"Sort Atoms by"</a> option in the Options Menu. |
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[24] | 108 | <img SRC="2.gif" align=TEXTTOP> |
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| 109 | </DL></DL> |
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| 110 | |
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[202] | 111 | <h3>A.3 Histogram pane</h3> |
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[24] | 112 | <DL><DL> |
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[202] | 113 | The histogram pane is used to edit background |
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[24] | 114 | and diffractometer constants for a histogram, as well as |
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| 115 | set damping and refinement flags for these parameters. |
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| 116 | <P> |
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| 117 | If |
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| 118 | <A href="#multiplehistogram"> |
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| 119 | "Multiple Histogram Selection" mode</A> is set to "All", |
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[202] | 120 | this pane is disabled. For other settings of this mode, |
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[24] | 121 | groups of histograms can be selected and modified |
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| 122 | collectively. |
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| 123 | <P> |
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[96] | 124 | If the EXPTOOL program |
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| 125 | <A href="#installation">(see the installation instructions)</A> |
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| 126 | is installed, a button for adding histograms will |
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[202] | 127 | appear on the bottom right on this pane, as seen below. If the |
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[96] | 128 | program is not properly installed, no errors occur, but the button |
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| 129 | does not appear. |
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| 130 | <P> |
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[24] | 131 | Note that the order that histograms appear in this |
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[202] | 132 | pane is determined by the <a href="http:#sorthist">"Sort histograms by"</a> option in |
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[24] | 133 | the Options Menu. |
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| 134 | <img SRC="3.gif" align=TEXTTOP> |
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| 135 | </DL></DL> |
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| 136 | |
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[202] | 137 | <h3>A.4 Scaling pane</h3> |
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[24] | 138 | <DL><DL> |
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[202] | 139 | The Scaling pane is used to edit the scale factor for a |
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[24] | 140 | histogram as well as the phase fractions for each phase |
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| 141 | present in that histogram. Damping and refinement flags |
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[202] | 142 | for the scaling terms can also be set here. |
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[24] | 143 | <P> |
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| 144 | If |
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| 145 | <A href="#multiplehistogram"> |
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| 146 | "Multiple Histogram Selection" mode</A> is set to |
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| 147 | any value other than "Off," |
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| 148 | groups of histograms can be selected and modified |
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| 149 | collectively. |
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| 150 | <P> |
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| 151 | Note that the order that histograms appear in this |
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[202] | 152 | pane is determined by the <a href="http:#sorthist">"Sort histograms by"</a> option in |
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[24] | 153 | the Options Menu. |
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| 154 | <img SRC="4.gif" align=TEXTTOP> |
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| 155 | </DL></DL> |
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| 156 | |
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[202] | 157 | <h3>A.5 Profile pane</h3> |
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[24] | 158 | <DL><DL> |
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[202] | 159 | The Profile pane is used to edit the profile values for |
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[24] | 160 | each phase present in a histogram as well as set |
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| 161 | the refinement flags and a damping value for each phase. |
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| 162 | <P> |
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| 163 | If |
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| 164 | <A href="#multiplehistogram"> |
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| 165 | "Multiple Histogram Selection" mode</A> is set to "All", |
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[202] | 166 | this pane is disabled. For other settings of this mode, |
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[24] | 167 | profile values and settings can be collectively |
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| 168 | modified for groups of histograms. |
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| 169 | <P> |
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| 170 | Note that the order that histograms appear in this |
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[202] | 171 | pane is determined by the |
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| 172 | <a href="http:#sorthist">"Sort histograms by"</a> option in |
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[24] | 173 | the Options Menu. |
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| 174 | <img SRC="5.gif" align=TEXTTOP> |
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| 175 | </DL></DL> |
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| 176 | |
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[202] | 177 | <h3>A.6 Constraints pane</h3> |
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[148] | 178 | <DL><DL> |
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| 179 | GSAS offers two types of restraints that can be included in a model. |
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| 180 | So called "soft constraints" or "restraints" penalize the fit if |
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| 181 | aspects of a model (for example, bond lengths) differ from selected values. |
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| 182 | So called "hard constraints" reduce the actual number of |
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| 183 | parameters in a model, |
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| 184 | by grouping parameters so that a single shift (possibly scaled) is |
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| 185 | applied to each parameter in the group. |
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[202] | 186 | The constraints pane is used to set these "hard constraints." |
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[148] | 187 | At this time the only constraints that can be set in EXPGUI are on atomic |
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| 188 | parameters (others can be set in EXPEDT). |
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| 189 | <P> |
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[202] | 190 | Note that these constraints are only applied to shifts but not to the |
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| 191 | actual values. This means that, for example, |
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| 192 | if two atoms |
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[148] | 193 | are constrained so that the shift on their occupancy is the same, but |
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[202] | 194 | the initial occupancies differ, the in occupancy difference will not change |
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| 195 | as the values refine. |
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[148] | 196 | <P> |
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[202] | 197 | <H4>Atom Constraints</H4> |
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| 198 | The atom constraints editing pane appears below. Note that constraints can |
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[148] | 199 | be listed sorted by constraint number, phase number, lowest atom number or |
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[202] | 200 | variable by clicking on the buttons at the top of the pane. |
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[148] | 201 | <P> |
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| 202 | To delete one or more constraints, click on the appropriate checkbuttons in the <B>Delete</B> column and the press the Delete button, below. |
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| 203 | <img SRC="mc.gif" align=TEXTTOP> |
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| 204 | Due to the way GSAS implements these constraints, a parameter can be included |
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| 205 | in only one constraint. Should one or more parameters be constrained twice, |
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| 206 | an error message is shown as shown below. |
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| 207 | Note that the constraint number is displayed as red, for constraints that |
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[202] | 208 | have conflicts in the constraints editing pane (see above.) |
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[148] | 209 | <img SRC="mcerr.gif" align=TEXTTOP> |
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| 210 | <P> |
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| 211 | <img SRC="mcedit.gif" align=LEFT> |
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| 212 | <img SRC="mcvar.gif" align=RIGHT> |
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| 213 | When the edit button for a constraint is pressed, the constraint is |
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| 214 | opened for editing. Controls are available to select the phase, variable, |
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| 215 | multiplier and atom(s). Note that for atom selection, use of the control key |
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| 216 | and the left mouse button allow individual atoms to be selected or deselected. |
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| 217 | Shift and the left mouse button allow ranges of atoms to be selected and the |
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| 218 | right mouse button selects all atoms |
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| 219 | <A href="#mouseactions">(see Mouse Actions)</A>. |
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| 220 | <P> |
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| 221 | Note that it is inappropriate |
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| 222 | to constrain different types of parameters together, for example X and Uiso. |
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| 223 | The left-most variable button is the "master" which |
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| 224 | determines what variable are allowed in the |
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| 225 | other variable buttons. |
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| 226 | <P> |
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| 227 | When the "New Constraint" button is pressed, a blank constraint editing |
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| 228 | window is opened. Note that any variable to the right may then be selected, |
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| 229 | including two special codes, Uxx and XYZU. XYZU creates four constraints, |
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| 230 | requiring the shifts on x, y, z and Uiso to be the same for all the selected |
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| 231 | atoms. Uxx does the same for the six anisotropic displacement parameters. |
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| 232 | These special codes are valuable for atoms that share a site. |
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| 233 | <P> |
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| 234 | Note that only 100 parameters may be included in a constraint, |
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| 235 | with one exception. When shifts for Uiso for all atoms in a phase |
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| 236 | are constrained, this counts as a single parameter. If more than 100 |
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| 237 | parameters are entered for a constraint, an error message is shown. |
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| 238 | Up to 2000 atomic constraints may be entered. |
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| 239 | EXPGUI does not warn if you exceed this limit. |
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| 240 | </DL></DL> |
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| 241 | |
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[202] | 242 | <P> |
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| 243 | <h3>A.7 Preferential Orientation Pane</h3></a> |
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| 244 | The Preferential Orientation Pane is used to control parameters related |
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| 245 | to fitting parameters using the March-Dollase formulation |
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| 246 | for preferred orientation. In this model one or more axes are designated |
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| 247 | as directions [designated by (<i>hkl</i>)] where crystallites are over |
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| 248 | (Ratio > 1) or underrepresented (Ratio < 1). |
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| 249 | The checkbox to the right of the Ratio value determines if it will |
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| 250 | be refined. |
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| 251 | <img SRC="po1.gif" align=TEXTTOP> |
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| 252 | If more than one axis is present, one must define the relative fraction |
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| 253 | of preferred orientation for each direction. These fractions are normalized, |
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| 254 | so do not vary the fractions for all directions in a phase. |
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| 255 | <img SRC="po2.gif" align=TEXTTOP> |
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| 256 | If |
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| 257 | <A href="#multiplehistogram"> |
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| 258 | "Multiple Histogram Selection" mode</A> is set to any value other than |
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| 259 | "Off", all terms are displayed for all selected histograms. |
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| 260 | No attempt is made to group terms or flags. |
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| 261 | <P> |
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| 262 | Note that the other model for treating preferred orientation -- the orientation |
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| 263 | distribution function (spherical harmonics) is not yet implemented |
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| 264 | in EXPGUI and must be accessed from EXPEDT. |
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| 265 | |
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| 266 | <P> |
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| 267 | <h2>B. Shortcuts</h2></a> |
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[24] | 268 | <a name="multiplehistogram"> |
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[202] | 269 | <h3>B.1 Multiple Histogram Selection</h3></a> |
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[24] | 270 | <DL><DL> |
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| 271 | This mode allows parameters to be changed for groups of |
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| 272 | histograms. |
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| 273 | When the "Multiple Histogram Selection" mode is off, |
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| 274 | it is possible to modify parameters |
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| 275 | and refinement flags for only a single histogram, but |
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| 276 | the other settings allow groups of histograms |
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| 277 | to be selected and modified. |
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| 278 | <A href="#mouseactions">(see Mouse Actions)</A>. |
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| 279 | |
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| 280 | It does not make sense, however, to globally modify |
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| 281 | instrument-related parameters and flags for different |
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| 282 | histogram types. |
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| 283 | So global actions can be limited to a single class |
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| 284 | of histogram types (e.g. TOF, CW Neutron,...), which |
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| 285 | allows these parameters to be set for groups of |
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| 286 | similar histograms. Thus, if this mode is set to "All" |
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[202] | 287 | the Histogram and Profile panes are disabled. |
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[24] | 288 | <P> |
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| 289 | The setting for "Multiple Histogram Selection" mode is |
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| 290 | selected using the "Multiple Hist. Selection" item on the |
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[115] | 291 | Options menu to create a submenu. Also on this submenu is an option |
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| 292 | "Group Phases Together" that controls how EXPGUI treats phases having |
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| 293 | the same profile type when multiple histograms are selected. If |
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| 294 | the "Group Phases Together" option is on, then the refinement flags for |
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| 295 | all phases with the same histogram types are grouped together, when possible. |
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| 296 | If this option is off, phases are treated separately. |
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[24] | 297 | <p> |
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| 298 | <a name="mouseactions"> |
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| 299 | </DL></DL> |
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[202] | 300 | <h3>B.2 Mouse Actions</h3></a> |
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[24] | 301 | <DL><DL> |
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| 302 | A range of atoms or (in multiple selection mode) histograms may be |
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| 303 | selected by dragging (holding down) the left mouse button. It is also |
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| 304 | possible to select a range by using the Shift key with the left mouse |
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| 305 | button. To select or deselect individual entries, use the Control key |
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[96] | 306 | with the left mouse button. Pressing the right mouse button selects all |
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| 307 | entries in a list. |
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[24] | 308 | </DL></DL> |
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| 309 | |
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[202] | 310 | <h2>C. Menu Commands and Programs</h2> |
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| 311 | <p> |
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| 312 | GSAS programs are invoked either through use of the menu bar |
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| 313 | <center><B> |
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| 314 | <br>The menu bar. |
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| 315 | <br><img SRC="menubar.gif" BORDER=3 > |
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| 316 | </center></B> |
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| 317 | or by "pressing" a button on the button bar. The button bar |
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| 318 | simply provides an easy way to access commonly used |
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| 319 | actions on the menu bar. Users can |
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| 320 | <A HREF="expgui_cfg.html"> |
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| 321 | configure the menu bar</A> to include their own preferred actions and, with |
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| 322 | some knowledge of the program and Tcl/Tk, |
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| 323 | add their own commands to the menu bar or button bar. |
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| 324 | |
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| 325 | <center><B> |
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| 326 | <br>The button bar. |
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| 327 | <br><img SRC="buttonbar.gif" BORDER=3 > |
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| 328 | </center></B> |
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| 329 | |
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[24] | 330 | A description of the EXPGUI menus follows along with a very |
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| 331 | brief description of the function of each menu option. |
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| 332 | Note that an option may appear under more than one menu. |
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[202] | 333 | <H3>C.1 File Menu</H3> |
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[24] | 334 | <DL><DL> |
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| 335 | The options on the File menu as is the custom contains the commands |
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| 336 | for reading and writing experiment files, as well as starting |
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| 337 | and ending the program. |
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| 338 | <DL> |
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[37] | 339 | <DT>expnam<DD> |
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[148] | 340 | Select an existing GSAS experiment to be used. If a name is entered |
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| 341 | that does not exists, it is possible to create a new |
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[37] | 342 | experiment file from scratch. |
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[148] | 343 | <DT>Save<DD>Saves modifications to the current experiment file to disk (shortcut Alt-S). |
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[24] | 344 | <DT>Save As<DD>Saves modifications to the current experiment file to disk |
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| 345 | under a new file name |
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| 346 | <DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk. |
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[148] | 347 | <DT>EraseHistory<DD>Deletes old history records to speed reading of the .EXP file. |
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[24] | 348 | <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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[148] | 349 | <DT>exit<DD>Exit EXPGUI (shortcut Alt-X or ^C) |
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[24] | 350 | </DL> |
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| 351 | <img SRC="m1.gif" BORDER=3 > |
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| 352 | </DL></DL> |
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| 353 | |
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[202] | 354 | <h3>C.2 Options Menu</h3> |
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[24] | 355 | <DL><DL> |
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| 356 | This menu contains options that determine how EXPGUI runs. |
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| 357 | <DL> |
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| 358 | <DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are |
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| 359 | saved prior to each save or run of expedt in a file named |
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| 360 | [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX) |
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| 361 | or in a file named [expnam].ZIP or [expnam].xxx (Windows) |
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[148] | 362 | <DT>Use DISAGL Window<DD>When this option is set, results from DISAGL are |
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| 363 | shown in a separate window. When it is not set, the results are |
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| 364 | written in the .LST file. |
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[202] | 365 | <a name="sortatoms"></a><DT>Sort atoms by<DD> Determines the order that atoms are displayed on the "Phase" pane |
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[24] | 366 | Atoms may be displayed sorted by atom number, atom type, |
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| 367 | or by x, y or z |
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| 368 | |
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[202] | 369 | <a name="sorthist"></a><DT>Sort histograms by<DD>Determines the order that histograms are displayed on the |
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| 370 | Histogram, Scaling and Profile panes |
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[24] | 371 | |
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| 372 | Histograms may be sorted by histogram number, histogram type, |
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| 373 | original bank number, or diffraction angle/wavelength |
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[115] | 374 | <DT><A href="#multiplehistogram">Multiple hist. selection</A><DD> |
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| 375 | When this mode is off, it is possible to modify parameters |
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[24] | 376 | and refinement flags for only a single histogram. For other settings, |
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| 377 | it is possible to modify parameters and flags for groups of |
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| 378 | histograms (see help for Mouse actions). |
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| 379 | |
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| 380 | It does not make sense, however, to globally modify |
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| 381 | instrument-related parameters and flags for different histogram types. |
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| 382 | So global actions can be limited to a single class of histogram types |
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| 383 | (e.g. TOF, CW Neutron,...), which allows these parameters to be set |
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| 384 | for groups of similar histograms. Thus, if this mode is set to "All" |
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[202] | 385 | the Histogram and Profile panes are disabled. |
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[24] | 386 | <DT>Override backspace<DD>This option is available in UNIX only, as there are different |
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| 387 | ways that backspace can be implemented. When option is set |
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| 388 | as "On," the backspace key is overridden to send a "delete" |
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| 389 | character. If backspace does not work in a program such as |
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| 390 | EXPEDT, change try the other setting for this option. |
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[96] | 391 | <DT>Autoupdate EXP<DD>Normally EXPGUI prompts before rereading the EXP |
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| 392 | file when GENLES, POWPREF,... are run (this is so that one can change |
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| 393 | the experiment file and rerun with the current input). If this option is |
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[148] | 394 | set, the new file is automatically read without a prompt. |
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| 395 | This option is not available in Windows. |
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[96] | 396 | |
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[35] | 397 | <DT>SaveOptions<DD>Save the current values for "Override backspace", |
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[202] | 398 | <a href="http:#sortatoms">"Sort atoms by"</a>, |
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| 399 | <a href="http:#sorthist">"Sort histograms by"</a> and "archive EXP" |
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[35] | 400 | in file ~/.gsas_config (c:\.gsas_config on Windows). |
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[24] | 401 | <DT>liveplot_options<DD>Used to set options for liveplot, |
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| 402 | for example, the histogram to be plotted |
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| 403 | </DL> |
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[37] | 404 | <img SRC="m2.gif" BORDER=3> |
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[24] | 405 | </DL></DL> |
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| 406 | |
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[202] | 407 | <h3>C.3 Powder Menu</h3> |
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[24] | 408 | <DL><DL> |
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| 409 | This menu contains links to GSAS programs used for powder diffraction |
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| 410 | analysis. |
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| 411 | <DL> |
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[148] | 412 | <DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E) |
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| 413 | <DT>powpref<DD>Powder data preparation (shortcut Alt-P) |
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| 414 | <DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G) |
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[24] | 415 | <DT>powplot<DD>Display powder patterns |
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| 416 | <DT>rawplot<DD>Plot powder data |
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| 417 | <DT>fitspec<DD>Fit a TOF vanadium scattering spectrum |
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| 418 | <DT>tofnorm<DD>Normalize a TOF spectrum |
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| 419 | </DL> |
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[37] | 420 | <img SRC="m3.gif" BORDER=3> |
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[24] | 421 | </DL></DL> |
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| 422 | |
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[202] | 423 | <h3>C.4 Single Crystal Menu</h3> |
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[24] | 424 | <DL><DL> |
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| 425 | This menu contains links to GSAS programs used for |
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| 426 | single-rystal diffraction analysis. |
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| 427 | <DL> |
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[148] | 428 | <DT>expedt<DD>Run GSAS experiment editor (shortcut Alt-E) |
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| 429 | <DT>genles<DD>Run GSAS experiment editor (shortcut Alt-G) |
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[24] | 430 | <DT>scabs<DD>Single crystal absorption |
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| 431 | <DT>scmerge<DD>Sort and merge single crystal data |
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| 432 | <DT>sxtldata<DD>Prepare generic single crystal data |
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| 433 | </DL> |
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[37] | 434 | <img SRC="m4.gif" BORDER=3> |
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[24] | 435 | </DL></DL> |
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| 436 | |
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[202] | 437 | <h3>C.5 Graphics Menu</h3> |
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[24] | 438 | <DL><DL> |
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| 439 | This menu contains links to several GSAS and |
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| 440 | two non-GSAS (liveplot and widplt) |
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| 441 | programs used for graphical display of data and results. |
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| 442 | <DL> |
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| 443 | <DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT |
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| 444 | and then compute with FOURIER |
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| 445 | <DT>polfplot<DD>Display polefigures |
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| 446 | <DT>powplot<DD>Display powder patterns |
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| 447 | <DT>ortep<DD>Draw crystal structure |
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| 448 | <DT>rawplot<DD>Plot powder data |
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| 449 | <DT>fourier<DD>Generate Fourier map |
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| 450 | <DT>forsrh<DD>Search Fourier map for peaks |
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| 451 | <DT>liveplot<DD>Create a plot of powder data |
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| 452 | with zooming, automatic update and other nice features. |
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[96] | 453 | <DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software |
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[24] | 454 | <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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| 455 | </DL> |
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[37] | 456 | <img SRC="m5.gif" BORDER=3> |
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[24] | 457 | </DL></DL> |
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| 458 | |
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[202] | 459 | <h3>C.6 Results Menu</h3> |
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[24] | 460 | <DL><DL> |
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| 461 | This menu contains links to several GSAS and |
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| 462 | one non-GSAS (lstview) |
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| 463 | programs used for analysis of results. |
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| 464 | <DL> |
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| 465 | <DT>bijcalc<DD>Thermal parameter analysis |
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| 466 | <DT>disagl<DD>Distance/angle calculations |
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| 467 | <DT>reflist<DD>List reflection data |
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| 468 | <DT>geometry<DD>Molecular geometry calculations |
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| 469 | <DT>hstdmp<DD>List powder histogram data |
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| 470 | <DT>istats<DD>HKL Intensity statistics |
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| 471 | <DT>rcalc<DD>Compute reflection resuduals |
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[96] | 472 | <DT>composition<DD>Computes the chemical composition of a unit cell |
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| 473 | accounting for site multiplicies and occupancies |
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[24] | 474 | <DT>lstview<DD>Create a box with scrollbars containing the current .LST file |
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| 475 | </DL> |
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[37] | 476 | <img SRC="m6.gif" BORDER=3> |
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[24] | 477 | </DL></DL> |
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| 478 | |
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[202] | 479 | <h3>C.7 Calculations Menu</h3> |
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[24] | 480 | <DL><DL> |
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| 481 | This menu contains programs for useful crystallographic computations. |
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| 482 | <DL> |
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| 483 | <DT>cllchg<DD>Transform unit cell |
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| 484 | <DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths |
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| 485 | <DT>rducll<DD>Unit cell reduction |
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| 486 | <DT>spcgroup<DD>Space group symbol interpreter |
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| 487 | <DT>unimol<DD>Unique molecule assembler |
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| 488 | </DL> |
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[37] | 489 | <img SRC="m7.gif" BORDER=3> |
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[24] | 490 | </DL></DL> |
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| 491 | |
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[202] | 492 | <h3>C.8 Import/Export Menu</h3> |
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[24] | 493 | <DL><DL> |
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| 494 | This menu contains utilities for importing information into GSAS and |
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| 495 | exporting. |
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| 496 | <DL> |
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[96] | 497 | <DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This |
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| 498 | file is used in MSI software such as Cerius and InsightII. |
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[24] | 499 | <DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file |
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| 500 | <DT>hklsort<DD>Prepare HKL tables |
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| 501 | <DT>pubtable<DD>Prepare atom parameter tables |
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| 502 | <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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| 503 | <DT>cad4rd<DD>Prepare CAD4 single crystal data |
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| 504 | <DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format |
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| 505 | <DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b |
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| 506 | <DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data |
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| 507 | <DT>sxtldata<DD>Prepare generic single crystal data |
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| 508 | </DL> |
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[37] | 509 | <img SRC="m8.gif" BORDER=3> |
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[24] | 510 | </DL></DL> |
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[26] | 511 | |
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[202] | 512 | <h2>D. EXPGUI Utility Programs</h2></a> |
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[26] | 513 | <DL><DL> |
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| 514 | <P><B>LSTVIEW</B> |
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| 515 | |
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| 516 | <P>lstview is used to browse through the GSAS output listing. It is |
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| 517 | invoked by the "lstview" command in the GUI. |
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[96] | 518 | <CENTER><IMG SRC="textview.gif"></CENTER> |
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[26] | 519 | |
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| 520 | |
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| 521 | <P><B>LIVEPLOT</B> |
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| 522 | |
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| 523 | <P>liveplot shows the observed, calculated and difference plots for powder |
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| 524 | refinements. The plot is updated as the refinement progresses. The mouse can |
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| 525 | be used to zoom in on sections of the plot. |
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[148] | 526 | Liveplot uses the <A href="#blt">BLT</A> graphics package. |
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[96] | 527 | <CENTER><IMG SRC="liveplot.gif"></CENTER> |
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[26] | 528 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36> |
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| 529 | LIVEPLOT can now be enhanced to superimpose peak locations for |
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| 530 | input unit cells or peaks from JCPDS/ICDD entries. |
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[96] | 531 | See the <A HREF="expgui_cfg.html#liveplot"> |
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[26] | 532 | LIVEPLOT customization information</A> |
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[37] | 533 | or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory. |
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[66] | 534 | <P> |
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| 535 | LIVEPLOT gets the current diffraction information by running the TCLDUMP program, if installed, or |
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| 536 | HSTDUMP otherwise. The TCLDUMP program has been optimized for use with LIVEPLOT and offers a number of extra |
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| 537 | options that are not available when HSTDUMP is used: plots can be displayed in the native units (2Theta/TOF/KeV), or |
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[154] | 538 | in d-space or Q; fixed plus fitted background curves are shown in green; if reflection tickmarks are displayed, <IMG SRC="new.gif" HEIGHT=13 WIDTH=36> |
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| 539 | reflection tickmarks can be displayed by pressing "H" or "h" while the |
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| 540 | mouse is near a reflection (holding the shift key while |
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| 541 | pressing the left mouse button also works). |
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[66] | 542 | See the installation instructions for installing TCLDUMP. |
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[26] | 543 | <P><B>WIDPLT</B> |
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| 544 | |
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[148] | 545 | <P>WIDPLT can be used to plot the actual peak widths generated by the profile |
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| 546 | parameters used in GSAS. |
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| 547 | It is possible to define reference curves |
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| 548 | that are loaded automatically. |
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| 549 | WIDPLT uses the <A href="#blt">BLT</A> graphics package. |
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[96] | 550 | <CENTER><IMG SRC="widplt.gif"></CENTER> |
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[26] | 551 | <BR> |
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| 552 | </DL></DL> |
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| 553 | |
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[148] | 554 | <A name=blt> |
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[26] | 555 | <H2> |
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[148] | 556 | BLT</H2> |
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| 557 | The BLT graphics package is used by the WIDPLT and LIVEPLOT routines. If the |
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| 558 | package can not be loaded these routines, an error message, |
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| 559 | "Error -- Unable to load the BLT package", will be displayed. A frequent |
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| 560 | problem is the package is installed, but not configured so that common |
---|
| 561 | support routines are loaded automatically. If this is the case, |
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| 562 | a message, "BLT Setup Error: could not access a Blt_ routine...", |
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| 563 | will be displayed. |
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| 564 | Please see |
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| 565 | <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html"> |
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| 566 | http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html |
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| 567 | </A> for more information on installation of BLT. |
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| 568 | |
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| 569 | <H2> |
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[26] | 570 | Acknowledgements</H2> |
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[66] | 571 | Praise to Larson and |
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[103] | 572 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm"> |
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| 573 | Von Dreele</A> for GSAS, <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.scriptics.com/">Ousterhout</A> |
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[37] | 574 | for Tcl/Tk, |
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[103] | 575 | Przemek Klosowski</A> |
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[37] | 576 | for convincing me to learn Tcl/Tk |
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[202] | 577 | and Jonathan Wasserman for helping get this project started. |
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| 578 | Large sections of the Preferred Orientation GUI were written by |
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| 579 | Pamela Whitfield of the NRC (Canada). |
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| 580 | <P> |
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[148] | 581 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html"> |
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| 582 | GSAS</A> |
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| 583 | is written by Allen C. Larson and <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm"> |
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[66] | 584 | Robert B. Von Dreele</A>, MS-H805, |
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[26] | 585 | Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions |
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| 586 | or kudos concerning GSAS should be sent to Robert B. Von Dreele at |
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| 587 | <A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A> |
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[202] | 588 | EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research, |
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| 589 | <A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> |
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| 590 | with help from Jonathan Wasserman. |
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| 591 | |
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| 592 | <P>GSAS is Copyright, 1984-2000, by |
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| 593 | the Regents of the University of California. |
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[26] | 594 | The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36) |
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| 595 | by the Los Alamos National Laboratory, which is operated by the University |
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| 596 | of California for the U.S. Department of Energy. The U.S. Government is |
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| 597 | licensed to use, reproduce, and distribute this software. Permission is |
---|
| 598 | granted to the public to copy and use this software without charge, provided |
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| 599 | that this notice and any statement of authorship are reproduced on all |
---|
| 600 | copies. Neither the Government nor the University makes any warranty, express |
---|
| 601 | or implied, or assumes any liability or responsibility for the use of this |
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| 602 | software. |
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| 603 | |
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[202] | 604 | <P>EXPGUI is not subject to copyright. Have fun with it. Modify it. Write |
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| 605 | new sections and make them available to the reset of the world. |
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[26] | 606 | |
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| 607 | <p>Neither the U.S. Government nor any author makes any warranty, |
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[24] | 608 | expressed or implied, or assumes any liability or responsibility |
---|
| 609 | for the use of this information or the software described |
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| 610 | here. Brand names cited here are used for |
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| 611 | identification purposes and do not consitute an endorsement by NIST. |
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[26] | 612 | |
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[103] | 613 | <p><a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>) |
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[24] | 614 | <br> |
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| 615 | $Revision: 202 $ $Date: 2009-12-04 23:02:06 +0000 (Fri, 04 Dec 2009) $ |
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| 616 | </body> |
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| 617 | </html> |
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