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