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| 3 | <title>EXPGUI</title> |
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| 4 | <meta name="keywords" content="crystallography, Rietveld, diffraction, |
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| 5 | GSAS, EXPGUI"> |
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| 8 | A:link {text-decoration:none} |
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| 14 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
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| 16 | <? |
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| 17 | include("/var/www/include/navigation.inc"); |
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| 18 | include("/var/www/include/utility.inc"); |
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| 19 | ?> |
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| 20 | <blockquote><font face="arial, helvetica, sans-serif"> |
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| 21 | |
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| 22 | <center><h1> |
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| 23 | <HR noshade width="75%" size="2" align="center"> |
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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 | <HR noshade width="75%" size="2" align="center"> |
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| 29 | </h1></center> |
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| 30 | <P><P> |
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| 31 | <I><B> |
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| 32 | <blockquote> |
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| 33 | For the impatient: |
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| 34 | <A HREF="../downloads.html"> |
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| 35 | Download links</A> |
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| 36 | </blockquote> |
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| 37 | </I></B> |
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| 38 | <P><P> |
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| 39 | EXPGUI is a graphical interface for the |
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| 40 | Los Alamos |
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| 41 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html"> |
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| 42 | GSAS</A> package. |
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| 43 | EXPGUI does two things: |
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| 44 | it can be used to directly modify the GSAS |
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| 45 | experiment file with a graphical user interface (GUI) and |
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| 46 | it can be used to invoke the programs inside the |
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| 47 | GSAS package such as EXPEDT, GENLES, FOURIER... |
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| 48 | These programs can be run from a menu or in many cases by pressing buttons. |
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| 49 | EXPGUI is written using the |
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| 50 | <A href="#tcltk">Tcl/Tk</A> scripting language. |
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| 51 | <P> |
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| 52 | This web page describes 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. The table below contains links to the other |
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| 55 | web accessible documentation. |
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| 56 | <P> |
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| 57 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=CENTER> |
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| 58 | <TR><TH BGCOLOR="#F0F0F0" rowspan=3>GUI Sections</TH> |
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| 59 | <TH><A Href="expgui1.html">Least Squares</A></TH> |
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| 60 | <TH><A Href="expgui2.html">Phase info</A></TH> |
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| 61 | <TH><A Href="expgui3.html">Histogram info</A></TH> |
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| 62 | </TR> |
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| 63 | <TR> |
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| 64 | <TH><A Href="expgui4.html">Scaling info</A></TH> |
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| 65 | <TH><A Href="expgui5.html">Profile terms</A></TH> |
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| 66 | <TH><A Href="expgui6.html">Constraints</A></TH> |
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| 67 | </TR> |
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| 68 | <TR> |
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| 69 | <TH><A Href="expgui7.html">Preferred Orientation</A></TH> |
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| 70 | <TH><A Href="expguic.html">Menus</A></TH> |
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| 71 | <TH> </TH> |
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| 72 | </TR> |
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| 73 | <TR><TH BGCOLOR="#F0F0F0" rowspan=3>Utilities:</TH> |
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| 74 | <TH><A Href="liveplot.html">LIVEPLOT</A></TH> |
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| 75 | <TH><A Href="liveplot.html">BKGEDIT</A></TH> |
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| 76 | <TH><A Href="excledt.html">EXCLEDT</A></TH> |
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| 77 | </TR> |
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| 78 | <TR> |
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| 79 | <TH><A Href="#WIDPLT">WIDPLT</A></TH> |
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| 80 | <TH><A Href="#ABSPLT">ABSPLT</A></TH> |
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| 81 | <TH><A Href="#INSTEDIT">INSTEDIT</A></TH> |
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| 82 | </TR> |
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| 83 | <TR> |
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| 84 | <TH><A Href="gsas2cif.html">CIF export</A></TH> |
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| 85 | <TH> </TH> |
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| 86 | <TH> </TH> |
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| 87 | </TR> |
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| 88 | <TR><TH BGCOLOR="#F0F0F0" rowspan=2>Installation Notes:</TH> |
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| 89 | <TH><A Href="expgui_Unix_readme.html">Unix</A></TH> |
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| 90 | <TH><A Href="expgui_Win_readme.html">Windows</A></TH> |
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| 91 | <TH> |
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| 92 | <A Href="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial3"> |
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| 93 | <A Href="osx.html">Mac OS X</A></TH> |
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| 94 | </TR><TR> |
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| 95 | <TH><A Href="expgui_cfg.html">Customization</A></TH> |
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| 96 | <TH> </TH> |
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| 97 | <TH> </TH> |
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| 98 | </TR> |
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| 99 | <TR><TH BGCOLOR="#F0F0F0">Tutorials:</TH> |
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| 100 | <TH><A Href="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial3"> |
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| 101 | NIST<BR>Neutron data</A></TH> |
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| 102 | <TH><A Href="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial1/index.html">GSAS Manual<BR>Example #1 (TOF)</A></TH> |
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| 103 | <TH><A Href="http://www.ncnr.nist.gov/xtal/software/expgui/tutorial2/index.html">GSAS Manual<BR>Example #2 (Garnet)</A></TH> |
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| 104 | </TR> |
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| 105 | <TR><TH BGCOLOR="#F0F0F0">Messages:</TH> |
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| 106 | <TH><A Href="expguierr.html#Error">Error</A></TH> |
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| 107 | <TH><A Href="expguierr.html#Warn">Warning</A></TH> |
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| 108 | <TH><A Href="expguierr.html#Info">Informational</A></TH> |
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| 109 | </TR> |
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| 110 | <TR><TH BGCOLOR="#F0F0F0">Other:</TH> |
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| 111 | <TH><A Href="expgui_intro.html">Introduction</A></TH> |
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| 112 | <TH><A Href="wishlist.html">Recent & Planned<BR>Improvements</A></TH> |
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| 113 | <TH><A Href="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf"> |
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| 114 | <I>J. Appl. Cryst.</i><BR>article</A></TH> |
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| 115 | </TR> |
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| 116 | </TABLE><BR CLEAR=ALL> |
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| 117 | <P> |
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| 118 | <B>Citations.</B> |
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| 119 | The appropriate citations to be used for GSAS and EXPGUI are: |
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| 120 | <UL> |
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| 121 | <LI> |
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| 122 | A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)", |
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| 123 | Los Alamos National Laboratory Report LAUR 86-748 (2000). |
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| 124 | <A HREF="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.pdf"> |
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| 125 | [link to PDF copy of manual] |
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| 126 | </A> |
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| 127 | <LI> |
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| 128 | B. H. Toby, <i>EXPGUI</i>, a graphical user interface for <i>GSAS</i>, |
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| 129 | <i>J. Appl. Cryst.</i> <b>34</b>, 210-213 (2001). |
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| 130 | <A HREF="http://www.ncnr.nist.gov/xtal/software/EXPGUI_reprint.pdf"> |
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| 131 | [link to PDF file] |
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| 132 | </A> |
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| 133 | </UL> |
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| 134 | <P> |
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| 135 | <B>Mailing List.</B> |
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| 136 | There is a mailing list for users of EXPGUI for news about about new |
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| 137 | features, bug fixes in EXPGUI, etc. |
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| 138 | <A href="http://www.aps.anl.gov/mailman/listinfo/expgui">Subscription info</A> |
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| 139 | <P> |
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| 140 | <hr> |
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| 141 | |
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| 142 | <h2>A. Experiment file editing</h2> |
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| 143 | <P> |
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| 144 | <DL><DL> |
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| 145 | When an experiment (.EXP) file is read, a copy is made in local |
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| 146 | computer memory. In most cases, values are changed in this |
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| 147 | "in memory" copy of the experiment file |
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| 148 | as this information is changed by the user on the screen. |
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| 149 | <img SRC="rederror.gif" align=LEFT BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 150 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 151 | If there is an error in the typed value, (for example if "1..0" is typed, or |
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| 152 | "1.5" is typed where an integer is expected), these values are |
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| 153 | not saved. In this case, the text is turned red, to indicate |
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| 154 | that an error is present, as shown in the figure to the left, where "90.000x" |
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| 155 | has been entered for alpha. |
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| 156 | The edited version of the experiment file is written back out to |
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| 157 | disk when the "File/Save" or "File/Save as" |
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| 158 | <A Href="expguic.html#1">menu bar options</A> |
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| 159 | are used. The File/Save operation is done automatically before any GSAS |
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| 160 | programs, such as GENLES or EXPEDT, are run. |
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| 161 | <P> |
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| 162 | |
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| 163 | Since the GSAS experiment file is quite complex, |
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| 164 | values are grouped together by function, approximately |
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| 165 | following the outline of the EXPEDT program. |
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| 166 | Each set of values is given a |
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| 167 | "tabbed panel" on a window that has the appearance of a notebook (see below). |
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| 168 | <center><B> |
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| 169 | <br>The notebook panel tabs. |
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| 170 | <br><img SRC="panebar1.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 171 | </center></B> |
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| 172 | In some cases, where values are |
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| 173 | too numerous or complex to fit onto the notebook panel, one or more buttons |
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| 174 | may be present on a panel that will create a separate window, |
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| 175 | where the associated values can be modified. |
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| 176 | These values are not recorded in the |
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| 177 | "in memory" copy of the experiment file unless the "Save" button on this window |
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| 178 | is pressed. If "Cancel" is pressed, no changes are made. |
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| 179 | Each notebook panel is listed below with a link to the web page documenting |
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| 180 | that panel. |
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| 181 | |
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| 182 | <A Href="expgui1.html"> |
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| 183 | <h3>A.1 Least Squares (LS) Controls Panel</h3> |
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| 184 | </A><A Href="expgui2.html"> |
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| 185 | <h3>A.2 Phase Panel</h3> |
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| 186 | </A><A Href="expgui3.html"> |
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| 187 | <h3>A.3 Histogram panel</h3> |
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| 188 | </A><A Href="expgui4.html"> |
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| 189 | <h3>A.4 Scaling panel</h3> |
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| 190 | </A><A Href="expgui5.html"> |
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| 191 | <h3>A.5 Profile panel</h3> |
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| 192 | </A><A Href="expgui6.html"> |
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| 193 | <h3>A.6 Constraints panel</h3> |
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| 194 | </A><A Href="expgui7.html"> |
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| 195 | <h3>A.7 Preferential Orientation Panel</h3> |
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| 196 | </A> |
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| 197 | <br clear=all> |
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| 198 | </DL></DL> |
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| 199 | <h2>B. Shortcuts</h2></a> |
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| 200 | <a name="multiplehistogram"> |
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| 201 | <h3>B.1 Multiple Histogram Selection</h3></a> |
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| 202 | <DL><DL> |
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| 203 | This mode allows parameters to be changed for groups of |
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| 204 | histograms. |
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| 205 | When the "Multiple Histogram Selection" mode is off, |
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| 206 | it is possible to modify parameters |
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| 207 | and refinement flags for only a single histogram, but |
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| 208 | the other settings allow groups of histograms |
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| 209 | to be selected and modified. |
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| 210 | <A href="#mouseactions">(see Mouse Actions)</A>. |
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| 211 | <P> |
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| 212 | It does not make sense, however, to globally modify |
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| 213 | instrument-related parameters and flags for different |
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| 214 | histogram types. |
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| 215 | So global actions can be limited to a single class |
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| 216 | of histogram types (e.g. TOF, CW Neutron,...), which |
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| 217 | allows these parameters to be set for groups of |
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| 218 | similar histograms. Thus, if this mode is set to "All" |
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| 219 | the Histogram and Profile panels are disabled. |
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| 220 | <P> |
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| 221 | The setting for "Multiple Histogram Selection" mode is |
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| 222 | displayed above each histogram selection box and is |
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| 223 | selected using the "Multiple Hist. Selection" item on the |
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| 224 | Options menu to create a submenu or by clicking on the display. |
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| 225 | Note that another option in this "Multiple Hist. Selection" |
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| 226 | submenu is an option "Group Phases Together" that controls how |
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| 227 | EXPGUI treats phases having |
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| 228 | the same profile type that is used when multiple histograms are selected. If |
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| 229 | the "Group Phases Together" option is on, then the refinement flags for |
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| 230 | all phases with the same histogram types are grouped together, when possible. |
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| 231 | If this option is off, phases are treated separately. |
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| 232 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
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| 233 | If the left mouse button is used to click on the selection mode display, |
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| 234 | the mode is cycled between the available modes. If the right mouse |
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| 235 | button is used, the mode is reset, to disable multiple histogram selection. |
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| 236 | <p> |
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| 237 | <a name="mouseactions"> |
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| 238 | </DL></DL> |
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| 239 | <h3>B.2 Mouse Actions</h3></a> |
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| 240 | <DL><DL> |
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| 241 | A range of atoms or (in multiple selection mode) histograms may be |
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| 242 | selected by dragging (holding down) the left mouse button. It is also |
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| 243 | possible to select a range by using the Shift key with the left mouse |
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| 244 | button. To select or deselect individual entries, use the Control key |
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| 245 | with the left mouse button. Pressing the right mouse button selects all |
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| 246 | entries in a list. |
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| 247 | </DL></DL> |
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| 248 | |
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| 249 | <h2>C. Menu Commands and Programs</h2> |
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| 250 | <p> |
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| 251 | GSAS programs are invoked either through use of the menu bar |
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| 252 | <center><B> |
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| 253 | <br>The menu bar. |
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| 254 | <br><img SRC="menubar.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 255 | </center></B> |
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| 256 | or by "pressing" a button on the button bar. The button bar |
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| 257 | simply provides an easy way to access commonly used |
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| 258 | actions on the menu bar. Users can |
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| 259 | <A HREF="expgui_cfg.html"> |
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| 260 | configure the menu bar</A> to include their own preferred actions and, with |
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| 261 | some knowledge of the program and Tcl/Tk, |
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| 262 | add their own commands to the menu bar or button bar. |
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| 263 | |
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| 264 | <center><B> |
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| 265 | <br>The button bar. |
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| 266 | <br><img SRC="buttonbar.gif" BORDER=3 alt="EXPGUI Screen snapshot"> |
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| 267 | </center></B> |
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| 268 | |
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| 269 | <h3>Invoking of GSAS programs</h3> |
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| 270 | When GSAS programs are invoked, in most cases EXPGUI is suspended while |
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| 271 | the GSAS program is run in a terminal (or DOS) window. When the terminal |
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| 272 | window is closed, EXPGUI is restarted. If desired (see the |
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| 273 | <A Href="expguic.html#Autoicon"> |
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| 274 | "Iconify during GSAS"</A> |
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| 275 | option) while this occurs, EXPGUI can be made into an icon |
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| 276 | to save screen space. |
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| 277 | <P> |
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| 278 | <img src="powpref4a.gif" align=left alt="EXPGUI Screen snapshot"> |
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| 279 | Once the GSAS program has finished, if the program has modified |
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| 280 | the .EXP file, |
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| 281 | <a Href="expguierr.html#Overwrite"> |
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| 282 | "File has been modified..."</a>message box |
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| 283 | similar to the one to the left is displayed (also see the more complete |
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| 284 | discussion on the <a Href="expguierr.html#Overwrite">messages page</A>. |
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| 285 | Note that this message can be avoided if the |
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| 286 | <A Href="expguic.html#Autoupdate"> |
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| 287 | "Autoload EXP"</A> |
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| 288 | option is used. |
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| 289 | <BR clear=all> |
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| 290 | <P> |
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| 291 | Note that in both Windows-95 and Windows-NT, a file named <tt>EXPGUI.LCK</tt> |
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| 292 | is created while the GSAS program runs. The presence of this file is used |
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| 293 | to suspend the LIVEPLOT program, since LIVEPLOT has sometimes crashed |
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| 294 | when run at the same time as GENLES (no such problem has been seen in Unix). |
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| 295 | This file is deleted when the GSAS program completes. |
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| 296 | <P> |
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| 297 | <img src="lock.gif" align=left alt="EXPGUI Screen snapshot"> |
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| 298 | In Windows-9x, the <a Href="expgui_Win_readme.html#Winexec">Winexec</a> |
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| 299 | package is used to execute a command that creates a DOS window. |
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| 300 | The GSAS programs are then run by a batch file in this DOS window. |
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| 301 | Due to limitations in Tcl/Tk & Windows, the DOS window runs independently |
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| 302 | of EXPGUI, so the lock file (<tt>EXPGUI.LCK</tt>) is also used to suspend |
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| 303 | EXPGUI. While EXPGUI is waiting, the |
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| 304 | <a Href="expguierr.html#lock"> |
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| 305 | Please wait... |
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| 306 | </a> |
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| 307 | window shown to the left is displayed. When the GSAS program completes, the |
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| 308 | lock file is deleted, the window automatically disappears and EXPGUI resumes. |
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| 309 | Should a problem arise where the file is not deleted, EXPGUI can be resumed by |
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| 310 | pressing the "Continue" button. |
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| 311 | |
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| 312 | <BR clear=all> |
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| 313 | <h3>GSAS menus</h3> |
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| 314 | |
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| 315 | A description of the EXPGUI menus follows. Use the links to obtain |
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| 316 | more information, including a very |
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| 317 | brief description of the function of each menu option. |
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| 318 | Note that an option may appear under more than one menu. |
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| 319 | |
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| 320 | <DL><DL> |
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| 321 | |
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| 322 | <A Href="expguic.html#1"> |
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| 323 | <H3>C.1 File Menu</H3> |
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| 324 | </A> |
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| 325 | <DL><DL> |
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| 326 | The options on the File menu as is the custom contains the commands |
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| 327 | for reading and writing experiment files, as well as starting, |
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| 328 | ending and controlling the program. |
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| 329 | </DL></DL> |
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| 330 | |
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| 331 | <A Href="expguic.html#2"> |
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| 332 | <h3>C.2 Options Menu</h3> |
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| 333 | </A> |
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| 334 | <DL><DL> |
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| 335 | This menu contains options that determine how EXPGUI runs. |
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| 336 | </DL></DL> |
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| 337 | |
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| 338 | <A Href="expguic.html#3"> |
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| 339 | <h3>C.3 Powder Menu</h3> |
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| 340 | </A> |
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| 341 | <DL><DL> |
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| 342 | This menu contains links to GSAS programs used for powder diffraction |
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| 343 | analysis. |
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| 344 | </DL></DL> |
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| 345 | |
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| 346 | <A Href="expguic.html#4"> |
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| 347 | <h3>C.4 Single Crystal Menu</h3> |
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| 348 | </A> |
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| 349 | <DL><DL> |
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| 350 | This menu contains links to GSAS programs used for |
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| 351 | single-crystal diffraction analysis. |
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| 352 | </DL></DL> |
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| 353 | |
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| 354 | <A Href="expguic.html#5"> |
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| 355 | <h3>C.5 Graphics Menu</h3> |
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| 356 | </A> |
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| 357 | <DL><DL> |
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| 358 | This menu contains links to several GSAS and |
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| 359 | non-GSAS programs (such as LIVEPLOT and WIDPLT) |
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| 360 | used for graphical display of data and results. |
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| 361 | </DL></DL> |
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| 362 | |
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| 363 | <A Href="expguic.html#6"> |
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| 364 | <h3>C.6 Results Menu</h3> |
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| 365 | </A> |
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| 366 | <DL><DL> |
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| 367 | This menu contains links to several GSAS and |
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| 368 | one non-GSAS (LSTVIEW) |
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| 369 | programs that are used for analysis of results. |
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| 370 | </DL></DL> |
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| 371 | |
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| 372 | <A Href="expguic.html#7"> |
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| 373 | <h3>C.7 Calculations Menu</h3> |
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| 374 | </A> |
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| 375 | <DL><DL> |
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| 376 | This menu contains programs for useful crystallographic computations. |
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| 377 | </DL></DL> |
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| 378 | |
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| 379 | <A Href="expguic.html#8"> |
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| 380 | <h3>C.8 Import/Export Menu</h3> |
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| 381 | </A> |
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| 382 | <DL><DL> |
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| 383 | This menu contains utilities for importing information into GSAS and |
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| 384 | exporting. |
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| 385 | </DL></DL> |
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| 386 | |
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| 387 | <h2>D. EXPGUI Utility Features</h2></a> |
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| 388 | EXPGUI adds a number of useful functions to the GSAS package. Some, |
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| 389 | but not all, of these features are graphically oriented. |
|---|
| 390 | |
|---|
| 391 | <br clear=all> |
|---|
| 392 | <a name="LSTVIEW"></a> |
|---|
| 393 | <H3>D.1 LSTVIEW</H3> |
|---|
| 394 | |
|---|
| 395 | <DL><DL> |
|---|
| 396 | LSTVIEW is used to browse through the GSAS output listing. It is |
|---|
| 397 | invoked by the "lstview" command in the GUI. |
|---|
| 398 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used |
|---|
| 399 | to shorten the .LST file by removing older results from the beginning |
|---|
| 400 | of the file. |
|---|
| 401 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">LSTVIEW can also be used to plot R-factors and parameter shifts |
|---|
| 402 | as a function of the cycle number. |
|---|
| 403 | <CENTER><IMG SRC="textview.gif" alt="EXPGUI Screen snapshot"></CENTER> |
|---|
| 404 | </DL></DL> |
|---|
| 405 | |
|---|
| 406 | <br clear=all> |
|---|
| 407 | <H3>D.2 LIVEPLOT</H3> |
|---|
| 408 | <DL><DL> |
|---|
| 409 | <A HREF="liveplot.html">LIVEPLOT</A> shows the observed, calculated |
|---|
| 410 | and difference plots for powder |
|---|
| 411 | refinements. The plot is updated as the refinement progresses. The mouse can |
|---|
| 412 | be used to zoom in on sections of the plot. |
|---|
| 413 | LIVEPLOT uses the <A href="#blt">BLT</A> graphics package. |
|---|
| 414 | <CENTER><IMG SRC="liveplot.gif" alt="LIVEPLOT Screen snapshot"></CENTER> |
|---|
| 415 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 416 | LIVEPLOT can now be enhanced to superimpose peak locations for |
|---|
| 417 | input unit cells or peaks from JCPDS/ICDD entries. |
|---|
| 418 | See the <A HREF="liveplot.html">LIVEPLOT web page</A> for |
|---|
| 419 | further documentation, and in particular, the |
|---|
| 420 | See the <A HREF="liveplot.html#customize"> |
|---|
| 421 | LIVEPLOT customization information</A>. |
|---|
| 422 | <P> |
|---|
| 423 | </DL></DL> |
|---|
| 424 | <br clear=all> |
|---|
| 425 | <H3>D.3 BKGEDIT</H3> |
|---|
| 426 | <DL><DL> |
|---|
| 427 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 428 | <A HREF="liveplot.html#bkgedit">BKGEDIT</A> is used to |
|---|
| 429 | fit a GSAS background function to a set of fixed |
|---|
| 430 | background points that are input using the mouse. |
|---|
| 431 | The mouse can also be used to zoom in on sections of the plot. |
|---|
| 432 | BKGEDIT uses the <A href="#blt">BLT</A> graphics package. |
|---|
| 433 | <CENTER><IMG SRC="b2.gif" alt="BKGEDIT Screen snapshot"></CENTER> |
|---|
| 434 | See the <A HREF="liveplot.html#bkgedit">BKGEDIT web page</A> for |
|---|
| 435 | further documentation. |
|---|
| 436 | <P> |
|---|
| 437 | </DL></DL> |
|---|
| 438 | <br clear=all> |
|---|
| 439 | <H3>D.4 EXCLEDT</H3> |
|---|
| 440 | <DL><DL> |
|---|
| 441 | <A HREF="excledt.html">EXCLEDT</A> is used to edit the |
|---|
| 442 | range of data used from a histogram. The upper & lower ranges |
|---|
| 443 | can be adjusted to include more data or use less. Also, it is |
|---|
| 444 | possible to remove sections of the data (exclude regions) that |
|---|
| 445 | have known systematic errors that cannot be modeled. |
|---|
| 446 | EXCLEDT uses the <A href="#blt">BLT</A> graphics package. |
|---|
| 447 | <CENTER><IMG SRC="exc1a.gif" alt="EXCLEDT Screen snapshot"></CENTER> |
|---|
| 448 | See the <A HREF="excledt.html">EXECLEDT web page</A> for |
|---|
| 449 | further documentation. |
|---|
| 450 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!"> |
|---|
| 451 | EXCLEDT can now be used to change the simulation range for dummy histograms. |
|---|
| 452 | <P> |
|---|
| 453 | </DL></DL> |
|---|
| 454 | |
|---|
| 455 | <br clear=all> |
|---|
| 456 | <a name="WIDPLT"></a> |
|---|
| 457 | <a name="ABSPLT"></a> |
|---|
| 458 | <H3>D.5 WIDPLT and ABSPLT</H3> |
|---|
| 459 | <DL><DL> |
|---|
| 460 | WIDPLT is used to plot the peak widths that are generated by a set |
|---|
| 461 | of GSAS profile terms (constant wavelength equations, only). |
|---|
| 462 | The parameters from each phase & histogram will be |
|---|
| 463 | read from the .EXP file. It is also possible to input parameters manually. |
|---|
| 464 | By creating a special file (<A HREF="expgui_cfg.html#import"> |
|---|
| 465 | described in the customization information</A>), it |
|---|
| 466 | is possible to define reference curves |
|---|
| 467 | that are loaded automatically for comparison. |
|---|
| 468 | <CENTER><IMG SRC="widplt.gif" alt="EXPGUI Screen snapshot"></CENTER> |
|---|
| 469 | <P> |
|---|
| 470 | ABSPLT is used to plot the absorption/reflectivity correction for a |
|---|
| 471 | histogram. Values are loaded from the histogram(s), but can be edited manually. |
|---|
| 472 | <P> |
|---|
| 473 | WIDPLT and ABSPLT both use the <A href="#blt">BLT</A> graphics package. |
|---|
| 474 | </DL></DL> |
|---|
| 475 | |
|---|
| 476 | <br clear=all> |
|---|
| 477 | <a name="INSTEDIT"></a> |
|---|
| 478 | <H3>D.6 INSTEDIT</H3> |
|---|
| 479 | <DL><DL> |
|---|
| 480 | |
|---|
| 481 | The INSTEDIT utility is used to edit or create an instrument parameter file. |
|---|
| 482 | At this time it can only be used to edit files for |
|---|
| 483 | constant-wavelength data. The utility can be started from the "Edit File" |
|---|
| 484 | button in the |
|---|
| 485 | <A HREF="expgui3.html#AddHist">"Add New Histogram"</A> dialog, or from the |
|---|
| 486 | the "instedit" option in the Powder menu. In the latter case, the user |
|---|
| 487 | is given the chance to select an input file. If no file is selected, |
|---|
| 488 | a new, empty, file is created. An example INSTEDIT window appears below. |
|---|
| 489 | <P> |
|---|
| 490 | <img SRC="instedit1.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
|---|
| 491 | <br clear=all> |
|---|
| 492 | <P> |
|---|
| 493 | Note that an instrument parameter file is used for a single type of data, |
|---|
| 494 | as is selected by the menu button at the top of the window. |
|---|
| 495 | However, multiple sets of parameters may be included in a |
|---|
| 496 | file, to be used for example with differing operating modes for the |
|---|
| 497 | instrument. Each set of parameters is called a bank in GSAS terminology. |
|---|
| 498 | The radiobuttons on the top of the window are used to select |
|---|
| 499 | which bank's parameters will be viewed. |
|---|
| 500 | The "Add Bank" button adds an additional bank to the file. |
|---|
| 501 | <P> |
|---|
| 502 | The parameters are described briefly below, but in more depth in the |
|---|
| 503 | GSAS manual (for example, pages 158-166 for profile parameters and |
|---|
| 504 | page 221-223 for the details of the instrument parameter file.) |
|---|
| 505 | <P> |
|---|
| 506 | <H5>Bank Parameters</H5> |
|---|
| 507 | The parameters available for each bank are: |
|---|
| 508 | <DL> |
|---|
| 509 | <DT>Title<DD>This probably has no real use. |
|---|
| 510 | <DT>Instrument Name<DD>This string is used for creation of CIFs. It is |
|---|
| 511 | best if this name is unique for each instrument. |
|---|
| 512 | <DT>Primary Wavelength<DD>Note, this value is set automatically when |
|---|
| 513 | the radiation type is selected |
|---|
| 514 | <DT>Zero Correction<DD>This is the shift to be applied to 2theta |
|---|
| 515 | values in centidegrees (degrees/100). This value should probably be |
|---|
| 516 | near zero for Debye-Scherrer geometry instruments (unless known from |
|---|
| 517 | calibration) and will almost always be fixed at zero |
|---|
| 518 | for Bragg-Brentano geometry. |
|---|
| 519 | <DT> |
|---|
| 520 | </DL> |
|---|
| 521 | <I>X-ray only parameters</I> |
|---|
| 522 | <DL> |
|---|
| 523 | <DT>Radiation type<DD>Used with x-rays. The value set here |
|---|
| 524 | determines the anomolous dispersion (f' and f'' values) used. |
|---|
| 525 | <DT>Monochromatic/Dual<DD>Used with x-rays. Set to dual when Kalpha1, Kalpha2 |
|---|
| 526 | radiation is present. |
|---|
| 527 | <DT>Secondary Wavelength<DD>Used in "dual" wavelength mode. |
|---|
| 528 | Note, this value is set automatically when the radiation type is selected |
|---|
| 529 | <DT>Wavelength Ratio<DD>Typically 0.5 for typical K alpha 1,2 instruments, |
|---|
| 530 | <<I>i.e.</I>when K alpha 1 is double the intensity of K alpha 2. |
|---|
| 531 | <DT>Polarization Correction<DD>There are three modes for this, where the |
|---|
| 532 | first two modes work similarly. The first mode ("Diffracted Beam") |
|---|
| 533 | is most common. The third mode ("None") is used when |
|---|
| 534 | Lorentz-polaraization corrections are applied to the data prior to its input |
|---|
| 535 | to GSAS. See page 144-145 in the GSAS manual for more information on these |
|---|
| 536 | corrections. |
|---|
| 537 | <DT>Polarization Ratio<DD>In "Diffracted Beam" mode: |
|---|
| 538 | typically 0.5 for lab instruments without monochromators and higher for |
|---|
| 539 | instruments with a diffracted beam; the value depends on the monochromator |
|---|
| 540 | take-off angle. Typically slightly below unity (0.9-0.98) for synchrotron |
|---|
| 541 | instruments. Ask the instrument scientist for the appropriate value. |
|---|
| 542 | </DL> |
|---|
| 543 | <P> |
|---|
| 544 | Each bank in the instrument parameter file has one or more sets of |
|---|
| 545 | profile parameters associated. Set number 1 is the default loaded |
|---|
| 546 | when a histogram is added. Increase the number of sets |
|---|
| 547 | using the "Add profile" button. Select the optimal profile type |
|---|
| 548 | for use with your data for this set, but for most flexibility, define |
|---|
| 549 | default values for all useful profile types (type 1 is of use only for |
|---|
| 550 | CW neutron work) and set these values from fitting a standard with |
|---|
| 551 | minimal broodening. Note that profiles can be read from a GSAS experiment |
|---|
| 552 | file using the "Import profile", which raises a dialog |
|---|
| 553 | such as the one below. |
|---|
| 554 | <P> |
|---|
| 555 | <img SRC="instedit2.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
|---|
| 556 | <br clear=all> |
|---|
| 557 | |
|---|
| 558 | |
|---|
| 559 | </DL></DL> |
|---|
| 560 | |
|---|
| 561 | <br clear=all> |
|---|
| 562 | <a name="ConvertUnix"></a> |
|---|
| 563 | <a name="ConvertWin"></a> |
|---|
| 564 | <h3>D.7 File Conversions</h3> |
|---|
| 565 | <DL><DL> |
|---|
| 566 | <P> |
|---|
| 567 | GSAS data, experiment and instrument parameter files are |
|---|
| 568 | expected to have a format with exactly 80 characters per line followed |
|---|
| 569 | by a carriage return and then a linefeed (82 characters total per line). |
|---|
| 570 | Files in this format can be read in "Direct Access" mode. |
|---|
| 571 | Recent versions of GSAS will attempt to detect and repair files that |
|---|
| 572 | are not in this format, but if the file is incorrectly formatted and |
|---|
| 573 | by chance the length of the file is divisible by 82, the problem in the |
|---|
| 574 | file format will not be detected. |
|---|
| 575 | The Convert menu |
|---|
| 576 | in can be used to convert files into the correct format. |
|---|
| 577 | The original version of the |
|---|
| 578 | file is retained and renamed. |
|---|
| 579 | <P> |
|---|
| 580 | </DL></DL> |
|---|
| 581 | |
|---|
| 582 | <br clear=all> |
|---|
| 583 | <a name="Composition"></a> |
|---|
| 584 | <h3>D.8 Compute Composition</h3> |
|---|
| 585 | <DL><DL> |
|---|
| 586 | The composition box shows the unit cell and asymmetric unit composition |
|---|
| 587 | for all phases in a material. Site multiplicities and occupancies are |
|---|
| 588 | taken into account. |
|---|
| 589 | </DL></DL> |
|---|
| 590 | |
|---|
| 591 | <br clear=all> |
|---|
| 592 | <a name="DeleteHistoryRecords"></a> |
|---|
| 593 | <h3>D.9 Delete History Records</h3> |
|---|
| 594 | <DL><DL> |
|---|
| 595 | Every time a GSAS program (including EXPGUI) is run, an entry is added to |
|---|
| 596 | the "history records" in the .EXP file. After 999 entries have been written, |
|---|
| 597 | no more can be added to the file. Further, reading large numbers of history |
|---|
| 598 | records can slow the GSAS programs |
|---|
| 599 | (this is less of a problem on faster computers). For these reasons, it may be |
|---|
| 600 | a good idea to prune the older history records from the file. If more than 100 |
|---|
| 601 | history records are found in an experiment file, EXPGUI suggests that the |
|---|
| 602 | older history entries be deleted. Alternately the File/EraseHistory command |
|---|
| 603 | can be used to invoke the this option. |
|---|
| 604 | <P> |
|---|
| 605 | On the dialog the number of history records to be retained is specified. |
|---|
| 606 | Also, after records have been deleted, the remaining records can be renumbered |
|---|
| 607 | starting with 1, so that the 999 record limit is not reached. |
|---|
| 608 | </DL></DL> |
|---|
| 609 | |
|---|
| 610 | <h2>E. Coordinate Export & Import Features</h2></a> |
|---|
| 611 | EXPGUI can be used to read coordinates in formats not |
|---|
| 612 | supported in GSAS. Coordinates can also be exported in a variety of |
|---|
| 613 | formats as well. |
|---|
| 614 | |
|---|
| 615 | <A name="import"> |
|---|
| 616 | <h3>E.1 Coordinate Import Formats</h3> |
|---|
| 617 | Coordinates can be imported using the |
|---|
| 618 | <A HREF="expgui2.html#addphase">"Add Phase"</A>, |
|---|
| 619 | <A HREF="expgui2.html#addatoms">"Add Atoms"</A> or |
|---|
| 620 | <A HREF="expgui2.html#replacephase">"Replace Phase"</A> |
|---|
| 621 | buttons on the <A HREF="expgui2.html">Phase Panel</A>, by choosing |
|---|
| 622 | the format from the pull-down list to the right of the |
|---|
| 623 | "Import atoms/phase from" button. The formats currently supported |
|---|
| 624 | are listed below. |
|---|
| 625 | Note that it is relatively easy to add new routines for |
|---|
| 626 | importing coordinates; |
|---|
| 627 | see the <A HREF="expgui_cfg.html#import"> |
|---|
| 628 | customization information</A> for more details. |
|---|
| 629 | <DL><DL> |
|---|
| 630 | <DT><B>Crystallographic Information File (CIF)</B><DD> |
|---|
| 631 | Coordinates can be read from single block or multiblock CIF files |
|---|
| 632 | using DDL1. If more than one block containing coordinates is found in the |
|---|
| 633 | file, a CIF browser is available to help select the desired block. |
|---|
| 634 | <DT><B>PowderCell .CEL files</B><DD> |
|---|
| 635 | This format is used by the DOS and Windows PowderCell program, a valuable |
|---|
| 636 | program for the transformation and visualization of structures. |
|---|
| 637 | <DT><B>GSAS .EXP files</B><DD> |
|---|
| 638 | This routine is used to copy coordinates, unit cell parameters and space group |
|---|
| 639 | information from other GSAS experiment (.EXP) files. |
|---|
| 640 | <DT><B>MSI .xtl format</B><DD> |
|---|
| 641 | <a HREF="#ExportMSI">see below</a> |
|---|
| 642 | <DT><B>PLATON .spf (Standard Parameter File) format</B><DD> |
|---|
| 643 | <a HREF="#ExportSPF">see below</a> |
|---|
| 644 | |
|---|
| 645 | </DL></DL> |
|---|
| 646 | |
|---|
| 647 | <A name="export"> |
|---|
| 648 | <h3>E.2 Coordinate Export Formats</h3> |
|---|
| 649 | Coordinates can be written using the Import/Export=>"Coord Export" menu. |
|---|
| 650 | Note that contents of the submenu will depend on the |
|---|
| 651 | number of export routines found in the EXPGUI directory when the menu |
|---|
| 652 | is first created, thus it is relatively easy to add new routines for |
|---|
| 653 | importing coordinates; |
|---|
| 654 | see the <A HREF="expgui_cfg.html#export"> |
|---|
| 655 | customization information</A> for more details. |
|---|
| 656 | <DL><DL> |
|---|
| 657 | <DT><B>Crystallographic Information File (CIF)</B><DD> |
|---|
| 658 | Powder Diffraction Crystallographic Information files (pdCIFs) can |
|---|
| 659 | be created by the GSAS2CIF program. The GSAS2CIF menu item |
|---|
| 660 | invokes this program. |
|---|
| 661 | <a name="ExportMSI"></a> |
|---|
| 662 | <DT><B>MSI .xtl format</B><DD> |
|---|
| 663 | This writes a .xtl file, as is used in Insight-II and |
|---|
| 664 | Cerius2 (Molecular Simulations, Inc.). The routine |
|---|
| 665 | attempts to convert GSAS space group names properly, as well as |
|---|
| 666 | correctly label "Origin 2" setting, however, the naming conversion |
|---|
| 667 | will not work for all valid GSAS space groups. Some effort may be needed |
|---|
| 668 | by the user to get everything worked out correctly. |
|---|
| 669 | <a name="ExportSPF"></a> |
|---|
| 670 | <DT><B>PLATON .spf (Standard Parameter File) format</B><DD> |
|---|
| 671 | This writes a .spf file, as used in |
|---|
| 672 | <A HREF="http://www.cryst.chem.uu.nl/platon/">Platon</A> and |
|---|
| 673 | <A HREF="http://www.cryst.chem.uu.nl/platon/">Pluton</A> by A. L. Spek. |
|---|
| 674 | Some attempt is made to get space group naming right, but there is |
|---|
| 675 | no assurance of quality here. |
|---|
| 676 | <a name="ExportSHELX"></a> |
|---|
| 677 | <DT><B>SHELX .ins format</B><DD> |
|---|
| 678 | This writes coordinates and symmetry, as used in the SHELX-97 program, and |
|---|
| 679 | perhaps as used some other programs, such as CrystalMaker. In addition to |
|---|
| 680 | exporing the coordinates and displacement parameters, the fields that |
|---|
| 681 | are generated are TITL, CELL, LATT, SYMM and SFAC. Note that the |
|---|
| 682 | wavelength, included as the first number on the CELL "card", is set to the |
|---|
| 683 | arbitrary value of 1/2. |
|---|
| 684 | </DL></DL> |
|---|
| 685 | |
|---|
| 686 | <A name=tcltk> |
|---|
| 687 | <H2> |
|---|
| 688 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html"> |
|---|
| 689 | Tcl/Tk</A></H2> |
|---|
| 690 | The |
|---|
| 691 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html"> |
|---|
| 692 | Tcl/Tk program</A> is a platform-independent scripting language that is |
|---|
| 693 | used to implement most of EXPGUI. This software is available for free |
|---|
| 694 | and must be loaded in order to use EXPGUI. See the |
|---|
| 695 | installation notes for |
|---|
| 696 | <A HREF="expgui_Win_readme.html">Windows</A>, |
|---|
| 697 | and for |
|---|
| 698 | <A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this. |
|---|
| 699 | While learning Tcl/Tk is a great thing to do, it is not a requirement |
|---|
| 700 | for using or installing EXPGUI. |
|---|
| 701 | |
|---|
| 702 | <A name=winexec> |
|---|
| 703 | <H3> |
|---|
| 704 | WINEXEC</H3> |
|---|
| 705 | <UL> |
|---|
| 706 | The WINEXEC package is needed under Windows-95 and its offspring |
|---|
| 707 | (-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation |
|---|
| 708 | notes</A> for more details. |
|---|
| 709 | </UL> |
|---|
| 710 | |
|---|
| 711 | <A name=blt> |
|---|
| 712 | <H3> |
|---|
| 713 | BLT Package</H3> |
|---|
| 714 | <UL> |
|---|
| 715 | The BLT graphics package is used by the WIDPLT, LIVEPLOT, BKGEDIT & |
|---|
| 716 | EXCLEDT routines. If the |
|---|
| 717 | package can not be found by these routines, an error message, |
|---|
| 718 | "Error -- Unable to load the BLT package", will be displayed. It is also |
|---|
| 719 | possible for the package to be installed, but not configured properly. |
|---|
| 720 | If this is the case, a message, |
|---|
| 721 | "BLT Setup Error: could not access a Blt_ routine...", will be displayed. |
|---|
| 722 | This is most common in UNIX and is discussed further in the |
|---|
| 723 | <A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see |
|---|
| 724 | <A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html"> |
|---|
| 725 | http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html |
|---|
| 726 | </A> for more information on installation of BLT. |
|---|
| 727 | </UL> |
|---|
| 728 | |
|---|
| 729 | <A name=La> |
|---|
| 730 | <H3> |
|---|
| 731 | La (Linear Algebra) Package</H3> |
|---|
| 732 | <UL> |
|---|
| 733 | The |
|---|
| 734 | <A HREF="www.hume.com">Hume |
|---|
| 735 | </A> |
|---|
| 736 | Linear Algebra Tcl Package, |
|---|
| 737 | <A HREF="www.hume.com"> |
|---|
| 738 | La</A>, |
|---|
| 739 | is used by the BKGEDIT |
|---|
| 740 | routine to perform least-squares fitting. If the |
|---|
| 741 | package can not be found, the routine cannot run. |
|---|
| 742 | If the package cannot be found, a message, |
|---|
| 743 | "Error -- Unable to load the La package" will be displayed. This |
|---|
| 744 | should not happen, since the package is included with the EXPGUI files. |
|---|
| 745 | So if get this error you probably have an incomplete installation. |
|---|
| 746 | Note that the La package requires Tcl/Tk version 8.1 or higher, so that if |
|---|
| 747 | you are using an older version of Tcl/Tk, you will need to upgrade. |
|---|
| 748 | See the installation instructions for |
|---|
| 749 | <A HREF="expgui_Win_readme.html">Windows</A>, |
|---|
| 750 | and for |
|---|
| 751 | <A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk. |
|---|
| 752 | </UL> |
|---|
| 753 | |
|---|
| 754 | <H2> |
|---|
| 755 | Acknowledgments</H2> |
|---|
| 756 | Praise to Larson and |
|---|
| 757 | Von Dreele for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A> |
|---|
| 758 | for Tcl/Tk, |
|---|
| 759 | Przemek Klosowski</A> |
|---|
| 760 | for convincing me to learn Tcl/Tk |
|---|
| 761 | and Jonathan Wasserman for helping get this project started. |
|---|
| 762 | Thanks also to |
|---|
| 763 | Pamela Whitfield of the NRC (Canada) for writing large |
|---|
| 764 | sections of the |
|---|
| 765 | <A Href="expgui7.html">Preferential Orientation Panel</A> |
|---|
| 766 | and the |
|---|
| 767 | <A Href="expgui6.html">Profile Constraints panel</A> |
|---|
| 768 | code and to John Cowgill for the "Export to GRACE" code. |
|---|
| 769 | <P> |
|---|
| 770 | <A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html"> |
|---|
| 771 | GSAS</A> |
|---|
| 772 | is written by Allen C. Larson and Robert B. Von Dreele while at |
|---|
| 773 | Los Alamos National Laboratory. Problems, questions |
|---|
| 774 | or kudos concerning GSAS should be sent to Robert B. Von Dreele at |
|---|
| 775 | <A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A> |
|---|
| 776 | EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research, |
|---|
| 777 | <A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A> |
|---|
| 778 | with help from Jonathan Wasserman. |
|---|
| 779 | |
|---|
| 780 | <P><hr><blockquote> |
|---|
| 781 | <P>GSAS is Copyright, 1984-2000, by |
|---|
| 782 | the Regents of the University of California. |
|---|
| 783 | The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36) |
|---|
| 784 | by the Los Alamos National Laboratory, which is operated by the University |
|---|
| 785 | of California for the U.S. Department of Energy. The U.S. Government is |
|---|
| 786 | licensed to use, reproduce, and distribute this software. Permission is |
|---|
| 787 | granted to the public to copy and use this software without charge, provided |
|---|
| 788 | that this notice and any statement of authorship are reproduced on all |
|---|
| 789 | copies. Neither the Government nor the University makes any warranty, express |
|---|
| 790 | or implied, or assumes any liability or responsibility for the use of this |
|---|
| 791 | software. |
|---|
| 792 | |
|---|
| 793 | <P>The author of EXPGUI is a U.S. Government employee which means that |
|---|
| 794 | EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write |
|---|
| 795 | new sections and make them available to the rest of the world. |
|---|
| 796 | |
|---|
| 797 | <p>Neither the U.S. Government nor any author makes any warranty, |
|---|
| 798 | expressed or implied, or assumes any liability or responsibility |
|---|
| 799 | for the use of this information or the software described |
|---|
| 800 | here. Brand names cited herein are used for |
|---|
| 801 | identification purposes and do not constitute an endorsement by NIST. |
|---|
| 802 | </blockquote> |
|---|
| 803 | |
|---|
| 804 | <P><hr WIDTH="100%"> |
|---|
| 805 | |
|---|
| 806 | <P> |
|---|
| 807 | <font size=-1><? lastmod(); ?> </font> |
|---|
| 808 | <br>$Revision: 971 $ $Date: 2010-03-28 14:19:30 +0000 (Sun, 28 Mar 2010) $ |
|---|
| 809 | </blockquote> |
|---|
| 810 | </body> |
|---|
| 811 | </html> |
|---|
