| 1 | <html> |
|---|
| 2 | <head> |
|---|
| 3 | <META NAME="Author" CONTENT="Brian H. Toby"> |
|---|
| 4 | <title>EXPGUI</title> |
|---|
| 5 | <meta name="keywords" content="crystallography, Rietveld, diffraction, |
|---|
| 6 | GSAS, EXPGUI"> |
|---|
| 7 | </HEAD> |
|---|
| 8 | <style> |
|---|
| 9 | A:link {text-decoration:none} |
|---|
| 10 | A:vlink {text-decoration:none} |
|---|
| 11 | </style> |
|---|
| 12 | |
|---|
| 13 | <BODY BGCOLOR="#FFFFFF" |
|---|
| 14 | topmargin="0" leftmargin="0" marginwidth="0" marginheight="0" |
|---|
| 15 | text="#000000" link="#0033ff" vlink="#0033ff" alink="#0033ff"> |
|---|
| 16 | |
|---|
| 17 | <? |
|---|
| 18 | include("/var/www/include/navigation.inc"); |
|---|
| 19 | include("/var/www/include/utility.inc"); |
|---|
| 20 | ?> |
|---|
| 21 | <blockquote><font face="arial, helvetica, sans-serif"> |
|---|
| 22 | |
|---|
| 23 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 24 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 25 | </TH><TH><A Href="expgui3.html">Next page</A> |
|---|
| 26 | </TH><TH><A Href="expgui1.html">Previous page</A> |
|---|
| 27 | </TH></TR></TABLE><BR CLEAR=ALL> |
|---|
| 28 | |
|---|
| 29 | <center><h1> |
|---|
| 30 | <HR noshade width="75%" size="2" align="center"> |
|---|
| 31 | EXPGUI, part 2 |
|---|
| 32 | <HR noshade width="75%" size="2" align="center"> |
|---|
| 33 | </h1></center> |
|---|
| 34 | |
|---|
| 35 | |
|---|
| 36 | <h3>A.2 Phase Pane</h3> |
|---|
| 37 | <DL><DL> |
|---|
| 38 | The phase pane is used to edit information |
|---|
| 39 | about the structural model(s) found in the experiment |
|---|
| 40 | file. The flags for refining the unit cell and atomic parameters, |
|---|
| 41 | as well as ther damping values, |
|---|
| 42 | can be set on this pane. Note that if a |
|---|
| 43 | single atom is selected using the mouse, the information |
|---|
| 44 | for that atom can be edited. If a group of atoms is |
|---|
| 45 | selected |
|---|
| 46 | <A href="expgui.html#mouseactions">(see Mouse Actions)</A> |
|---|
| 47 | the damping and refinement flags |
|---|
| 48 | for all the selected atoms are changed. |
|---|
| 49 | <P> |
|---|
| 50 | If the EXPTOOL program |
|---|
| 51 | <A href="expgui.html#installation">(see the installation instructions)</A> |
|---|
| 52 | is installed, buttons for adding phases and atoms will |
|---|
| 53 | appear on this pane, as seen below. If the |
|---|
| 54 | program is not properly installed, no errors occur, but the buttons |
|---|
| 55 | do not appear. |
|---|
| 56 | <P> |
|---|
| 57 | Note that the order that atoms appear in this pane is |
|---|
| 58 | determined by the |
|---|
| 59 | <a href="expguic.html#sortatoms">"Sort Atoms by"</a> option |
|---|
| 60 | in the Options Menu. <IMG SRC="note.gif" alt="Note!"> |
|---|
| 61 | The parameter used for sorting is designated |
|---|
| 62 | with a "*" on the title line above the atoms. |
|---|
| 63 | <IMG SRC="note.gif" alt="Note!"> |
|---|
| 64 | Clicking on this title line rotates through the sorting modes. |
|---|
| 65 | </DL></DL> |
|---|
| 66 | <img SRC="2.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
|---|
| 67 | <P> |
|---|
| 68 | <a name="xform"></a> |
|---|
| 69 | <img SRC="2a.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
|---|
| 70 | <IMG SRC="note.gif" alt="Note!"> |
|---|
| 71 | If one or more atoms have been selected |
|---|
| 72 | <A href="expgui.html#mouseactions">(see Mouse Actions)</A>, it is possible |
|---|
| 73 | to transform the atom coordinates, globally set occupancy or Uiso (Uequiv) |
|---|
| 74 | values for the selected atoms, or erase the selected atoms, by pressing the |
|---|
| 75 | "Xform atom(s)" button. It is also possible to transform the selected atoms |
|---|
| 76 | from isotropic to anisotropic, or the reverse. |
|---|
| 77 | <P> |
|---|
| 78 | Note that no changes are actually made, until the |
|---|
| 79 | "Transform Coordinates", "Set Occupancies",... buttons are pressed. |
|---|
| 80 | <br clear=all> |
|---|
| 81 | <P> |
|---|
| 82 | <a name="addphase"> |
|---|
| 83 | </a><h4>A.2.1 Add Phase</h4> |
|---|
| 84 | <DL><DL> |
|---|
| 85 | When the "Add Phase" button is pressed, a dialog is created where the |
|---|
| 86 | space group and unit cell constants can be entered (below). |
|---|
| 87 | <IMG SRC="note.gif" alt="Note!"> |
|---|
| 88 | By using the |
|---|
| 89 | "Import phase from:" button at the lower right, one can read this information, |
|---|
| 90 | as well as atomic parameters, from a file. |
|---|
| 91 | The button to the right of the "Import phase from:" button selects |
|---|
| 92 | the file format to be used. |
|---|
| 93 | Currently three formats are supported, |
|---|
| 94 | the Crystallographic Information File (CIF), |
|---|
| 95 | .CEL files from PowderCell and importing coordinates from other |
|---|
| 96 | GSAS .EXP files. |
|---|
| 97 | Note that it is relatively easy to add new routines for |
|---|
| 98 | importing coordinates; |
|---|
| 99 | see the <A HREF="expgui_cfg.html#import"> |
|---|
| 100 | customization information</A> for more details. |
|---|
| 101 | <BR> |
|---|
| 102 | <img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P> |
|---|
| 103 | <img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
|---|
| 104 | After the "Continue" button is pressed, the spacegroup is checked and the |
|---|
| 105 | generated symmetry operators are shown. These should be checked carefully, |
|---|
| 106 | as GSAS will correctly generate a variety of standard and non-standard |
|---|
| 107 | spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32" |
|---|
| 108 | describe different (non-standard) space groups. |
|---|
| 109 | <br clear=all><P> |
|---|
| 110 | The EXPTOOL program is then run and the output is |
|---|
| 111 | optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>). |
|---|
| 112 | <P> |
|---|
| 113 | If atom coordinates have been read from a file, along with the |
|---|
| 114 | cell and space group, the "add new atoms" dialog is then shown, with the |
|---|
| 115 | atoms displayed (as below.) |
|---|
| 116 | If the file contains atoms that should not be included |
|---|
| 117 | in the .EXP file, the "Use Flag" button to the |
|---|
| 118 | right of each atom can be deselected to prevent the atom from being used. |
|---|
| 119 | <img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
|---|
| 120 | <br clear=all> |
|---|
| 121 | Atoms will be included in the phase in the order they appear in the table. |
|---|
| 122 | <IMG SRC="new.gif" alt="New!"> |
|---|
| 123 | This order can be changed by pressing the buttons in the top row of the |
|---|
| 124 | table, which sorts the atoms according to the selected column. Note that |
|---|
| 125 | if the "Use Flag" button is deselected, the atom appears at the bottom |
|---|
| 126 | of the table. |
|---|
| 127 | <P> |
|---|
| 128 | When the "Add Atoms" button is pressed, the table is scanned for errors |
|---|
| 129 | such as invalid numbers or unknown atom types. If an error is encountered, |
|---|
| 130 | a message is displayed listing the problem(s). Corrections can then be |
|---|
| 131 | made to the table before pressing the "Add Atoms" button again. |
|---|
| 132 | <br clear=all><P> |
|---|
| 133 | <img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
|---|
| 134 | In the case of reading PowderCell .CEL files, the code may |
|---|
| 135 | have to translate coordinates to shift from an Origin 1 setting |
|---|
| 136 | to an Origin 2 setting. (GSAS, like many other crystallography programs, |
|---|
| 137 | assumes that if a center of symmetry is present, it is located at the origin.) |
|---|
| 138 | If this is done, a message like the one to the left is displayed. |
|---|
| 139 | |
|---|
| 140 | <br clear=all><P> |
|---|
| 141 | </DL></DL> |
|---|
| 142 | <a name="addatoms"> |
|---|
| 143 | <h4>A.2.2 Add Atoms</h4> |
|---|
| 144 | <DL><DL> |
|---|
| 145 | When the "Add New Atoms" button is pressed, a table is generated, |
|---|
| 146 | as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!"> |
|---|
| 147 | The "Import atoms from:" button can |
|---|
| 148 | be used to read atoms from a file. |
|---|
| 149 | The button to the right of the "Import atoms from:" button selects |
|---|
| 150 | the file format to be used. |
|---|
| 151 | Currently two formats are supported, the Crystallographic Information File (CIF) |
|---|
| 152 | and .CEL files from PowderCell. |
|---|
| 153 | See the <A HREF="expgui_cfg.html#import"> |
|---|
| 154 | customization information</A> for more details about importing coordinates. |
|---|
| 155 | Note that unlike in the |
|---|
| 156 | <a href="http:#addphase">Add Phase</a> section, the space group |
|---|
| 157 | and cell parameters in the file are ignored. The "Use" button to the |
|---|
| 158 | right of each atom can be deselected to prevent the atom from being used. |
|---|
| 159 | <img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
|---|
| 160 | <br clear=all><P> |
|---|
| 161 | Atoms will be added to the phase in the order they appear in the table. |
|---|
| 162 | <IMG SRC="new.gif" alt="New!"> |
|---|
| 163 | This order can be changed by pressing the buttons in the top row of the |
|---|
| 164 | table, which sorts the atoms according to the selected column. Note that |
|---|
| 165 | if the "Use Flag" button is deselected, the atom appears at the bottom |
|---|
| 166 | of the table. |
|---|
| 167 | <P> |
|---|
| 168 | When the "Add Atoms" button is pressed, the table is scanned for errors |
|---|
| 169 | such as invalid numbers or unknown atom types. If an error is encountered, |
|---|
| 170 | a message is displayed listing the problem(s). Corrections can then be |
|---|
| 171 | made to the table before pressing the "Add Atoms" button again. |
|---|
| 172 | |
|---|
| 173 | <br clear=all><P> |
|---|
| 174 | </DL></DL> |
|---|
| 175 | <a name="replacephase"></a><h4> |
|---|
| 176 | A.2.3 Replace Phase |
|---|
| 177 | <IMG SRC="note.gif" alt="Note!"> |
|---|
| 178 | </h4> |
|---|
| 179 | <DL><DL> |
|---|
| 180 | The "Replace Phase" is used to change the space group and |
|---|
| 181 | possibly unit cell for a phase. The input dialog, shown below, shows |
|---|
| 182 | the current space group and unit cell parameters. |
|---|
| 183 | By using the |
|---|
| 184 | "Import phase from:" button at the lower right, one can read this information, |
|---|
| 185 | as well as atomic parameters, from a file. |
|---|
| 186 | The button to the right of the "Import phase from:" button selects |
|---|
| 187 | the file format to be used. |
|---|
| 188 | Currently two formats are supported, the Crystallographic Information File (CIF) |
|---|
| 189 | and .CEL files from PowderCell. |
|---|
| 190 | See the <A HREF="expgui_cfg.html#import"> |
|---|
| 191 | customization information</A> for more details about importing coordinates. |
|---|
| 192 | <img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
|---|
| 193 | <br clear=all><P> |
|---|
| 194 | |
|---|
| 195 | Once the |
|---|
| 196 | "Continue button is pressed, the space group is checked, |
|---|
| 197 | as is shown in the <a href="http:#addphase">Add Phase</a> section. |
|---|
| 198 | A table is then generated for input of atoms, very similar to |
|---|
| 199 | that in the <a href="http:#addphase">Add Phase</a> section. |
|---|
| 200 | If atom coordinates have been read from a file these atoms |
|---|
| 201 | are included in the table. |
|---|
| 202 | It should be noted that when a phase is replaced in EXPGUI, all atoms in |
|---|
| 203 | that phase are erased. If the current atom positions are to be |
|---|
| 204 | retained, the "Reenter current atoms" box in the initial |
|---|
| 205 | "Replace phase" dialog should be checked, these atoms will also |
|---|
| 206 | be included in the table. |
|---|
| 207 | <P> |
|---|
| 208 | Note that no changes are made until after the "Continue" button |
|---|
| 209 | is pressed on the "Enter Atoms" dialog, so that is is safe to |
|---|
| 210 | press "Cancel" at any point. |
|---|
| 211 | |
|---|
| 212 | <br clear=all> |
|---|
| 213 | </DL></DL> |
|---|
| 214 | <hr> |
|---|
| 215 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
|---|
| 216 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
|---|
| 217 | </TH><TH><A Href="expgui3.html">Next page</A> |
|---|
| 218 | </TH><TH><A Href="expgui1.html">Previous page</A> |
|---|
| 219 | </TH></TR></TABLE> |
|---|
| 220 | |
|---|
| 221 | <a href="http://www.ncnr.nist.gov/staff/toby/">Brian Toby</a> (<a href="mailto:brian.toby@nist.gov">Brian.Toby@NIST.GOV</a>) |
|---|
| 222 | <br> |
|---|
| 223 | $Revision: 506 $ $Date: 2009-12-04 23:07:18 +0000 (Fri, 04 Dec 2009) $ |
|---|
| 224 | </blockquote> |
|---|
| 225 | </body> |
|---|
| 226 | </html> |
|---|
