| 1 | <html> |
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| 2 | <head> |
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| 3 | <title>EXPGUI</title> |
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| 4 | <meta name="keywords" content="crystallography, Rietveld, diffraction, |
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| 5 | GSAS, EXPGUI"> |
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| 6 | </HEAD> |
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| 7 | <style> |
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| 8 | A:link {text-decoration:none} |
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| 9 | A:vlink {text-decoration:none} |
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| 10 | </style> |
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| 11 | |
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| 12 | <BODY BGCOLOR="#FFFFFF" |
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| 13 | topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" |
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| 14 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
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| 15 | |
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| 16 | <? |
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| 17 | include("/var/www/include/navigation.inc"); |
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| 18 | include("/var/www/include/utility.inc"); |
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| 19 | ?> |
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| 20 | <blockquote><font face="arial, helvetica, sans-serif"> |
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| 21 | |
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| 22 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 23 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 24 | </TH><TH><A Href="expgui3.html">Next page</A> |
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| 25 | </TH><TH><A Href="expgui1.html">Previous page</A> |
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| 26 | </TH></TR></TABLE><BR CLEAR=ALL> |
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| 27 | |
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| 28 | <center><h1> |
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| 29 | <HR noshade width="75%" size="2" align="center"> |
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| 30 | EXPGUI, part 2 |
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| 31 | <HR noshade width="75%" size="2" align="center"> |
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| 32 | </h1></center> |
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| 33 | |
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| 34 | |
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| 35 | <h3>A.2 Phase Pane</h3> |
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| 36 | <DL><DL> |
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| 37 | The phase pane is used to edit information |
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| 38 | about the structural model(s) found in the experiment |
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| 39 | file. The flags for refining the unit cell and atomic parameters, |
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| 40 | as well as ther damping values, |
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| 41 | can be set on this pane. Note that if a |
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| 42 | single atom is selected using the mouse, the information |
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| 43 | for that atom can be edited. If a group of atoms is |
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| 44 | selected |
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| 45 | <A href="expgui.html#mouseactions">(see Mouse Actions)</A> |
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| 46 | the damping and refinement flags |
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| 47 | for all the selected atoms are changed. |
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| 48 | <P> |
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| 49 | If the EXPTOOL program |
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| 50 | <A href="expgui.html#installation">(see the installation instructions)</A> |
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| 51 | is installed, buttons for adding phases and atoms will |
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| 52 | appear on this pane, as seen below. If the |
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| 53 | program is not properly installed, no errors occur, but the buttons |
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| 54 | do not appear. |
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| 55 | <P> |
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| 56 | Note that the order that atoms appear in this pane is |
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| 57 | determined by the |
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| 58 | <a href="expguic.html#sortatoms">"Sort Atoms by"</a> option |
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| 59 | in the Options Menu. <IMG SRC="note.gif" alt="Note!"> |
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| 60 | The parameter used for sorting is designated |
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| 61 | with a "*" on the title line above the atoms. |
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| 62 | <IMG SRC="note.gif" alt="Note!"> |
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| 63 | Clicking on this title line rotates through the sorting modes. |
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| 64 | </DL></DL> |
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| 65 | <img SRC="2.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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| 66 | <P> |
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| 67 | <P> |
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| 68 | <a name="addphase"></a> |
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| 69 | <h4>A.2.1 Modify Unit Cell Parameters |
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| 70 | <IMG SRC="new.gif" alt="New!"> |
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| 71 | </h4> |
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| 72 | <DL><DL> |
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| 73 | <img SRC="2g.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
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| 74 | If the "Edit Cell" button is pressed, the unit cell parameters can be |
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| 75 | changed, as shown to the right. Note that only the parameters allowed |
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| 76 | by symmetry can be changed. |
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| 77 | |
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| 78 | <br clear=all> |
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| 79 | </DL></DL> |
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| 80 | <P> |
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| 81 | <a name="xform"></a> |
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| 82 | <h4>A.2.2 Transform Coordinates</h4> |
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| 83 | <DL><DL> |
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| 84 | <img SRC="2a.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
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| 85 | If one or more atoms have been selected |
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| 86 | <A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible |
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| 87 | to transform the atom coordinates, globally set occupancy or Uiso (Uequiv) |
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| 88 | values for the selected atoms, or erase the selected atoms, by pressing the |
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| 89 | "Xform atom(s)" button. It is also possible to transform the selected atoms |
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| 90 | from isotropic to anisotropic, or the reverse. |
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| 91 | <P> |
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| 92 | Note that no changes are actually made, until the |
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| 93 | "Transform Coordinates", "Set Occupancies",... buttons are pressed. |
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| 94 | |
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| 95 | <br clear=all> |
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| 96 | </DL></DL> |
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| 97 | <P> |
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| 98 | <a name="addphase"></a> |
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| 99 | <h4>A.2.3 Add Phase</h4> |
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| 100 | <DL><DL> |
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| 101 | When the "Add Phase" button is pressed, a dialog is created where the |
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| 102 | space group and unit cell constants can be entered (below). |
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| 103 | <IMG SRC="note.gif" alt="Note!"> |
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| 104 | By using the |
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| 105 | "Import phase from:" button at the lower right, one can read this information, |
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| 106 | as well as atomic parameters, from a file. |
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| 107 | The button to the right of the "Import phase from:" button selects |
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| 108 | the file format to be used. |
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| 109 | See the <A HREF="expgui.html#import">coordinate import discussion</A> |
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| 110 | for description of available formats. |
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| 111 | Note that it is relatively easy to add new routines for |
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| 112 | importing coordinates; |
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| 113 | see the <A HREF="expgui_cfg.html#import"> |
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| 114 | customization information</A> for more details. |
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| 115 | <BR> |
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| 116 | <img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P> |
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| 117 | <img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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| 118 | After the "Continue" button is pressed, the spacegroup is checked and the |
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| 119 | generated symmetry operators are shown. These should be checked carefully, |
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| 120 | as GSAS will correctly generate a variety of standard and non-standard |
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| 121 | spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32" |
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| 122 | describe different (non-standard) space groups. |
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| 123 | <br clear=all><P> |
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| 124 | The EXPTOOL program is then run and the output is |
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| 125 | optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>). |
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| 126 | <P> |
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| 127 | If atom coordinates have been read from a file, along with the |
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| 128 | cell and space group, the "add new atoms" dialog is then shown, with the |
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| 129 | atoms displayed (as below.) |
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| 130 | If the file contains atoms that should not be included |
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| 131 | in the .EXP file, the "Use Flag" button to the |
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| 132 | right of each atom can be deselected to prevent the atom from being used. |
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| 133 | <img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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| 134 | <br clear=all> |
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| 135 | Atoms will be included in the phase in the order they appear in the table. |
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| 136 | <IMG SRC="new.gif" alt="New!"> |
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| 137 | This order can be changed by pressing the buttons in the top row of the |
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| 138 | table, which sorts the atoms according to the selected column. Note that |
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| 139 | if the "Use Flag" button is deselected, the atom appears at the bottom |
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| 140 | of the table. |
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| 141 | <P> |
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| 142 | When the "Add Atoms" button is pressed, the table is scanned for errors |
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| 143 | such as invalid numbers or unknown atom types. If an error is encountered, |
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| 144 | a message is displayed listing the problem(s). Corrections can then be |
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| 145 | made to the table before pressing the "Add Atoms" button again. |
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| 146 | <br clear=all><P> |
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| 147 | <img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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| 148 | In the case of reading PowderCell .CEL files, the code may |
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| 149 | have to translate coordinates to shift from an Origin 1 setting |
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| 150 | to an Origin 2 setting. (GSAS, like many other crystallography programs, |
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| 151 | assumes that if a center of symmetry is present, it is located at the origin.) |
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| 152 | If this is done, a message like the one to the left is displayed. |
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| 153 | |
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| 154 | <br clear=all><P> |
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| 155 | </DL></DL> |
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| 156 | <a name="addatoms"> |
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| 157 | <h4>A.2.4 Add Atoms</h4> |
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| 158 | <DL><DL> |
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| 159 | When the "Add New Atoms" button is pressed, a table is generated, |
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| 160 | as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!"> |
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| 161 | The "Import atoms from:" button can |
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| 162 | be used to read atoms from a file. |
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| 163 | The button to the right of the "Import atoms from:" button selects |
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| 164 | the file format to be used. |
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| 165 | See the <A HREF="expgui.html#import">coordinate import discussion</A> |
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| 166 | for description of available formats and |
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| 167 | the <A HREF="expgui_cfg.html#import"> |
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| 168 | customization information</A> for more details about adding |
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| 169 | additional formats. |
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| 170 | Note that unlike in the |
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| 171 | <a href="http:#addphase">Add Phase</a> section, the space group |
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| 172 | and cell parameters in the imported file are ignored. The "Use" button to the |
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| 173 | right of each atom can be deselected to prevent the atom from being used. |
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| 174 | <img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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| 175 | <br clear=all><P> |
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| 176 | Atoms will be added to the phase in the order they appear in the table. |
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| 177 | <IMG SRC="new.gif" alt="New!"> |
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| 178 | This order can be changed by pressing the buttons in the top row of the |
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| 179 | table, which sorts the atoms according to the selected column. Note that |
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| 180 | if the "Use Flag" button is deselected, the atom appears at the bottom |
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| 181 | of the table. |
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| 182 | <P> |
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| 183 | When the "Add Atoms" button is pressed, the table is scanned for errors |
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| 184 | such as invalid numbers or unknown atom types. If an error is encountered, |
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| 185 | a message is displayed listing the problem(s). Corrections can then be |
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| 186 | made to the table before pressing the "Add Atoms" button again. |
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| 187 | |
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| 188 | <br clear=all><P> |
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| 189 | </DL></DL> |
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| 190 | <a name="replacephase"></a> |
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| 191 | <h4>A.2.5 Replace Phase</h4> |
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| 192 | <DL><DL> |
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| 193 | The "Replace Phase" is used to change the space group and |
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| 194 | possibly unit cell for a phase. The input dialog, shown below, shows |
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| 195 | the current space group and unit cell parameters. |
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| 196 | By using the |
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| 197 | "Import phase from:" button at the lower right, one can read this information, |
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| 198 | as well as atomic parameters, from a file. |
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| 199 | The button to the right of the "Import phase from:" button selects |
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| 200 | the file format to be used. |
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| 201 | See the <A HREF="expgui.html#import">coordinate import discussion</A> |
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| 202 | for description of available formats and |
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| 203 | the <A HREF="expgui_cfg.html#import"> |
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| 204 | customization information</A> for more details about adding |
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| 205 | additional formats. |
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| 206 | <img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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| 207 | <br clear=all><P> |
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| 208 | |
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| 209 | Once the |
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| 210 | "Continue button is pressed, the space group is checked, |
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| 211 | as is shown in the <a href="http:#addphase">Add Phase</a> section. |
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| 212 | A table is then generated for input of atoms, very similar to |
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| 213 | that in the <a href="http:#addphase">Add Phase</a> section. |
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| 214 | If atom coordinates have been read from a file these atoms |
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| 215 | are included in the table. |
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| 216 | It should be noted that when a phase is replaced in EXPGUI, all atoms in |
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| 217 | that phase are erased. If the current atom positions are to be |
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| 218 | retained, the "Reenter current atoms" box in the initial |
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| 219 | "Replace phase" dialog should be checked, these atoms will also |
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| 220 | be included in the table. |
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| 221 | <P> |
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| 222 | Note that no changes are made until after the "Continue" button |
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| 223 | is pressed on the "Enter Atoms" dialog, so that is is safe to |
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| 224 | press "Cancel" at any point. |
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| 225 | |
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| 226 | <br clear=all> |
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| 227 | </DL></DL> |
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| 228 | <hr> |
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| 229 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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| 230 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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| 231 | </TH><TH><A Href="expgui3.html">Next page</A> |
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| 232 | </TH><TH><A Href="expgui1.html">Previous page</A> |
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| 233 | </TH></TR></TABLE> |
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| 234 | |
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| 235 | <P><font size=-1><A HREF="MAILTO:crystal@NIST.gov?subject=WWW page <?=$PHP_SELF?>">Comments, corrections or questions: crystal@NIST.gov</A></font><BR> |
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| 236 | <font size=-1><? lastmod(); ?> </font> |
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| 237 | <br>$Revision: 678 $ $Date: 2009-12-04 23:10:11 +0000 (Fri, 04 Dec 2009) $ |
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| 238 | </blockquote> |
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| 239 | </body> |
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| 240 | </html> |
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