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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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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 Panel</h3> |
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36 | <DL><DL> |
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37 | The phase panel 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 panel. 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 panel, 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 panel 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 Modify Atom</h4> |
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83 | <DL><DL> |
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84 | <img SRC="2a.jpg" align=RIGHT alt="EXPGUI Screen snapshot"> |
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85 | The "Modify Atom" button ("Modify Atoms" when multiple atoms are |
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86 | selected) provides access to additional options that can |
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87 | transform or modify the selected atom(s) from the phase panel |
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88 | <A href="expgui.html#mouseactions">(see Mouse Actions</A> for |
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89 | information on selecting atoms); this opens the menu window shown to |
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90 | the right. |
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91 | Note that changes are made to the coordinates when the buttons on this |
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92 | window (such as |
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93 | "Transform Coordinates", "Set Occupancies",...) are pressed. |
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94 | <P><B>Modify Coordinates:</B> |
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95 | This is used |
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96 | to transform the coordinates coordinates of the selected atoms using a |
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97 | set of transformation relationships. |
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98 | |
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99 | <P><B>Reset Multiplicities:</B> |
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100 | When atom positions are edited in EXPGUI, they may be moved off from |
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101 | or onto special positions in the cell, changing the site |
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102 | multiplicity -- but this will not be reflected in the phase |
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103 | display. When atoms are subsequently refined, GENLES will update the |
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104 | multiplcities. Pressing the "Reset Multiplicities" button cases |
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105 | this to be done right away (I think this may not work if there are no |
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106 | histograms present). |
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107 | |
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108 | <P><B>Xform Origin 1 to Origin 2:</B> This button is only available for those |
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109 | orthorhombic, tetragonal and cubic space groups that are listed in the |
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110 | International Tables with two origin settings. (These space groups have |
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111 | a location in the unit cell that has higher symmetry than a location of |
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112 | a center of symmetry: origin 1 is placed at the highest symmetry location; |
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113 | origin 2 is placed at the computationally reasonable location, the center |
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114 | of symmetry. GSAS only uses the origin 2 settings.) |
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115 | If coordinates have been entered in the origin 1 setting, they may be |
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116 | transformed to the origin 2 setting using this button. It is important |
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117 | to select all atoms in the asymmetric unit before using this button. |
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118 | |
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119 | <P><B>Modify Occupancies:</B> |
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120 | This allows the occupancy to be set for one or more atoms. It is |
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121 | most convenient for when many atoms will have their occupancy |
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122 | changed at one time. |
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123 | |
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124 | <P><B>Modify Displacement Parameters:</B> |
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125 | This allows one to set Uiso (or Uequiv) values for the selected |
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126 | atoms (<B>Set U</B>). To change the flag that determines if the |
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127 | selected atom(s) are represented as Isotropic or Anisotropic, press |
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128 | the <B>Set Isotropic</B> or <B>Set Anisotropic</B> buttons. |
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129 | |
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130 | <P><B>Erase Atoms:</B> |
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131 | The "Erase Atoms" removes the selected atoms from the phase. I |
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132 | usually set the occupancy to 0. instead. |
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133 | |
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134 | <P><B>Fix Atom Coordinates:</B> |
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135 | When an atom is refined in GSAS, only the coordinates that are not |
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136 | defined by site symmetry are refined. However, in some space groups, |
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137 | it is necessary to not refine additional coordinates. The most common |
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138 | example are polar space groups (P1, P2, P2<sub>1</sub>, C2, P4, P4<sub>1</sub>, P |
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139 | 4<sub>2</sub>, P4<sub>3</sub>, I4, I4<sub>1</sub>, P3, P3<sub>1</sub>, P3<sub>2</sub>, R3, P6, P6<sub>1</sub>, P6<sub>5</sub>, P6<sub>2</sub>, P6<sub>4</sub> and |
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140 | P6<sub>3</sub> - from |
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141 | <a href="http://www.ruppweb.org/Xray/comp/space_instr.htm"> Bernard Rupp's |
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142 | web site, http://www.ruppweb.org/Xray/comp/space_instr.htm</A>) where |
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143 | one or more coordinates of the origin are not defined by symmetry. In |
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144 | these space groups an appropriate number of coordinates must be fixed |
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145 | to define the origin. As an example, in P1, one x, one y and one z |
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146 | coordinate must not be refined; in space group P2<sub>1</sub>, the |
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147 | 2<sub>1</sub> screw axis defines the origin at (0,0,z) so one z |
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148 | coordinate cannot be varied. |
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149 | |
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150 | Occasionally, while symmetry may allow |
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151 | atom coordinates to be varied, a crystallographer may choose to |
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152 | simplify or constrain the representation to fix the atom in a |
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153 | particular location and not refine with all allowed degrees of freedom. |
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154 | |
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155 | <IMG SRC="new.gif" alt="New!"> |
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156 | The "Fix Atom Coordinates" buttons allows a flag to be set (or |
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157 | cleared) for an atom |
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158 | to prevent refinement of selected coordinates, even when the X |
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159 | refinement flag is set. Note the addition of an "F" for the x and z |
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160 | coordinates of the first atom as shown in the phase panel, above. This |
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161 | indicates that x & z have been fixed. When the atom position is |
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162 | varied, only y will be optimized. |
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163 | |
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164 | <br clear=all> |
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165 | </DL></DL> |
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166 | <P> |
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167 | <a name="addphase"></a> |
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168 | <h4>A.2.3 Add Phase</h4> |
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169 | <DL><DL> |
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170 | When the "Add Phase" button is pressed, a dialog is created where the |
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171 | space group and unit cell constants can be entered (below). |
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172 | <IMG SRC="note.gif" alt="Note!"> |
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173 | By using the |
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174 | "Import phase from:" button at the lower right, one can read this information, |
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175 | as well as atomic parameters, from a file. |
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176 | The button to the right of the "Import phase from:" button selects |
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177 | the file format to be used. |
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178 | See the <A HREF="expgui.html#import">coordinate import discussion</A> |
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179 | for description of available formats. |
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180 | Note that it is relatively easy to add new routines for |
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181 | importing coordinates; |
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182 | see the <A HREF="expgui_cfg.html#import"> |
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183 | customization information</A> for more details. |
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184 | <BR> |
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185 | <img SRC="2b.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"><P> |
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186 | <img SRC="2c.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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187 | After the "Continue" button is pressed, the spacegroup is checked and the |
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188 | generated symmetry operators are shown. These should be checked carefully, |
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189 | as GSAS will correctly generate a variety of standard and non-standard |
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190 | spacegroups, but it is fussy about spacing: for example "R 3 2" and "R 32" |
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191 | describe different (non-standard) space groups. |
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192 | <br clear=all><P> |
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193 | The EXPTOOL program is then run and the output is |
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194 | optionally displayed (See <a href="expguic.html#exptoolout">Show EXPTOOL output</a>). |
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195 | <P> |
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196 | If atom coordinates have been read from a file, along with the |
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197 | cell and space group, the "add new atoms" dialog is then shown, with the |
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198 | atoms displayed (as below.) |
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199 | If the file contains atoms that should not be included |
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200 | in the .EXP file, the "Use Flag" button to the |
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201 | right of each atom can be deselected to prevent the atom from being used. |
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202 | <img SRC="2d.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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203 | <br clear=all> |
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204 | Atoms will be included in the phase in the order they appear in the table. |
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205 | <IMG SRC="new.gif" alt="New!"> |
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206 | This order can be changed by pressing the buttons in the top row of the |
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207 | table, which sorts the atoms according to the selected column. Note that |
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208 | if the "Use Flag" button is deselected, the atom appears at the bottom |
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209 | of the table. |
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210 | <P> |
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211 | When the "Add Atoms" button is pressed, the table is scanned for errors |
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212 | such as invalid numbers or unknown atom types. If an error is encountered, |
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213 | a message is displayed listing the problem(s). Corrections can then be |
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214 | made to the table before pressing the "Add Atoms" button again. |
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215 | <br clear=all><P> |
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216 | <img SRC="2b1.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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217 | In the case of reading PowderCell .CEL files, the code may |
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218 | have to translate coordinates to shift from an Origin 1 setting |
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219 | to an Origin 2 setting. (GSAS, like many other crystallography programs, |
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220 | assumes that if a center of symmetry is present, it is located at the origin.) |
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221 | If this is done, a message like the one to the left is displayed. |
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222 | |
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223 | <br clear=all><P> |
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224 | </DL></DL> |
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225 | <a name="addatoms"> |
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226 | <h4>A.2.4 Add Atoms</h4> |
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227 | <DL><DL> |
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228 | When the "Add New Atoms" button is pressed, a table is generated, |
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229 | as seen below, to enter atoms. <IMG SRC="note.gif" alt="Note!"> |
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230 | The "Import atoms from:" button can |
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231 | be used to read atoms from a file. |
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232 | The button to the right of the "Import atoms from:" button selects |
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233 | the file format to be used. |
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234 | See the <A HREF="expgui.html#import">coordinate import discussion</A> |
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235 | for description of available formats and |
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236 | the <A HREF="expgui_cfg.html#import"> |
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237 | customization information</A> for more details about adding |
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238 | additional formats. |
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239 | Note that unlike in the |
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240 | <a href="http:#addphase">Add Phase</a> section, the space group |
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241 | and cell parameters in the imported file are ignored. The "Use" button to the |
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242 | right of each atom can be deselected to prevent the atom from being used. |
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243 | <img SRC="2e.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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244 | <br clear=all><P> |
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245 | Atoms will be added to the phase in the order they appear in the table. |
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246 | <IMG SRC="new.gif" alt="New!"> |
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247 | This order can be changed by pressing the buttons in the top row of the |
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248 | table, which sorts the atoms according to the selected column. Note that |
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249 | if the "Use Flag" button is deselected, the atom appears at the bottom |
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250 | of the table. |
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251 | <P> |
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252 | When the "Add Atoms" button is pressed, the table is scanned for errors |
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253 | such as invalid numbers or unknown atom types. If an error is encountered, |
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254 | a message is displayed listing the problem(s). Corrections can then be |
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255 | made to the table before pressing the "Add Atoms" button again. |
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256 | |
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257 | <br clear=all><P> |
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258 | </DL></DL> |
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259 | <a name="replacephase"></a> |
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260 | <h4>A.2.5 Replace Phase</h4> |
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261 | <DL><DL> |
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262 | The "Replace Phase" is used to change the space group and |
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263 | possibly unit cell for a phase. The input dialog, shown below, shows |
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264 | the current space group and unit cell parameters. |
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265 | By using the |
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266 | "Import phase from:" button at the lower right, one can read this information, |
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267 | as well as atomic parameters, from a file. |
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268 | The button to the right of the "Import phase from:" button selects |
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269 | the file format to be used. |
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270 | See the <A HREF="expgui.html#import">coordinate import discussion</A> |
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271 | for description of available formats and |
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272 | the <A HREF="expgui_cfg.html#import"> |
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273 | customization information</A> for more details about adding |
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274 | additional formats. |
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275 | <img SRC="2f.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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276 | <br clear=all><P> |
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277 | |
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278 | Once the |
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279 | "Continue button is pressed, the space group is checked, |
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280 | as is shown in the <a href="http:#addphase">Add Phase</a> section. |
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281 | A table is then generated for input of atoms, very similar to |
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282 | that in the <a href="http:#addphase">Add Phase</a> section. |
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283 | If atom coordinates have been read from a file these atoms |
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284 | are included in the table. |
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285 | It should be noted that when a phase is replaced in EXPGUI, all atoms in |
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286 | that phase are erased. If the current atom positions are to be |
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287 | retained, the "Reenter current atoms" box in the initial |
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288 | "Replace phase" dialog should be checked, these atoms will also |
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289 | be included in the table. |
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290 | <P> |
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291 | Note that no changes are made until after the "Continue" button |
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292 | is pressed on the "Enter Atoms" dialog, so that is is safe to |
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293 | press "Cancel" at any point. |
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294 | |
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295 | <br clear=all> |
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296 | </DL></DL> |
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297 | <hr> |
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298 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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299 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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300 | </TH><TH><A Href="expgui3.html">Next page</A> |
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301 | </TH><TH><A Href="expgui1.html">Previous page</A> |
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302 | </TH></TR></TABLE> |
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303 | |
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304 | </blockquote> |
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305 | </body> |
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306 | </html> |
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