1 | <html> |
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2 | <head> |
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3 | <title>EXPGUI</title> |
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4 | </head> |
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5 | <body> |
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6 | |
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7 | <center> |
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8 | <h1> |
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9 | Using EXPGUI</h1></center> |
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10 | |
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11 | <h2>Introduction</h2> |
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12 | EXPGUI allows two types of actions: |
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13 | it allows the different |
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14 | GSAS programs such as EXPEDT, GENLES, FOURIER,... |
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15 | to be run, |
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16 | and it can be used to directly modify the GSAS |
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17 | experiment file without using EXPEDT. |
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18 | |
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19 | <P> |
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20 | Note that pictures on this page are somewhat out-of-date with respect to the |
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21 | current software version so they may differ from what is |
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22 | described in the text. |
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23 | |
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24 | <p> |
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25 | Programs are invoked either through use of the menu bar |
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26 | <center><B> |
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27 | <br>The menu bar. |
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28 | <br><img SRC="menubar.gif" BORDER=3 > |
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29 | </center></B> |
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30 | or by "pressing" a button on the button bar. The button bar |
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31 | simply provides an easy way to access commonly used |
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32 | actions on the menu bar. Users can configure the menu |
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33 | bar to include their own preferred actions and, with |
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34 | some knowledge of the program and Tcl/Tk, |
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35 | add their own commands to the menu bar or button bar. |
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36 | |
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37 | <center><B> |
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38 | <br>The button bar. |
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39 | <br><img SRC="buttonbar.gif" BORDER=3 > |
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40 | </center></B> |
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41 | |
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42 | <P> |
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43 | Different sections of the .EXP file can be edited by selecting different |
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44 | panels or pages from the tabbed list. These tabs will have slightly different |
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45 | appearance depending on the packages |
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46 | available with your local version of Tcl/Tk. |
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47 | <center><B> |
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48 | <br>The panel tabs using the Tix package. |
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49 | <br><img SRC="panebar1.gif" BORDER=3 > |
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50 | </center></B> |
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51 | <center><B> |
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52 | <br>The panel tabs without the Tix package. |
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53 | <br><img SRC="panebar2.gif" BORDER=3 > |
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54 | </center></B> |
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55 | If the Tix package is loaded on your machine, it will be |
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56 | used, but if it is not, EXPGUI will run fine without it. |
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57 | <P> |
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58 | This documentation will describe the different actions that |
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59 | can be accomplished with the different panels and the |
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60 | contents of the menus. Other documents contain: |
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61 | <a name="installation"></A> |
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62 | <A HREF="expgui_Win_readme.html"> |
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63 | Installation notes for Windows</A>, |
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64 | <A HREF="expgui_Unix_readme.html"> |
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65 | Installation notes for UNIX</A> and |
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66 | <A HREF="expgui_cfg.html"> |
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67 | Customization notes</A>. |
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68 | <hr> |
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69 | |
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70 | <h2>1. LS Controls panel</h2> |
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71 | <DL><DL> |
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72 | <p>The LS Controls panel shows information about the |
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73 | current experiment, typically found in the EXPEDT "Least |
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74 | Squares Controls" options. |
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75 | <P> |
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76 | Note that the order that histograms appear in this |
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77 | panel is determined by the "Sort histograms by" option in |
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78 | the Options Menu. |
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79 | <img SRC="1.gif" align=TEXTTOP> |
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80 | </DL></DL> |
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81 | <P> |
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82 | <h2>2. Phase panel</h2> |
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83 | <DL><DL> |
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84 | The phase panel is used to edit information |
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85 | about the phase or phases found in the experiment |
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86 | file. The cell and atomic damping and refinement |
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87 | flags can be changed here. Note that if a |
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88 | single atom is selected using the mouse, the information |
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89 | for that atom can be edited. If a group of atoms is |
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90 | selected |
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91 | <A href="#mouseactions">(see Mouse Actions)</A> |
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92 | the damping and refinement flags |
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93 | for all the selected atom can be changed at one time. |
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94 | <P> |
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95 | If the EXPTOOL program |
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96 | <A href="#installation">(see the installation instructions)</A> |
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97 | is installed, buttons for adding phases and atoms will |
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98 | appear on this panel, as seen below. If the |
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99 | program is not properly installed, no errors occur, but the buttons |
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100 | do not appear. |
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101 | <P> |
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102 | Note that the order that atoms appear in this panel is |
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103 | determined by the "Sort Atoms by" option in the Options |
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104 | Menu. |
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105 | <img SRC="2.gif" align=TEXTTOP> |
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106 | </DL></DL> |
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107 | |
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108 | <h2>3. Histogram panel</h2> |
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109 | <DL><DL> |
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110 | The histogram panel is used to edit background |
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111 | and diffractometer constants for a histogram, as well as |
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112 | set damping and refinement flags for these parameters. |
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113 | <P> |
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114 | If |
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115 | <A href="#multiplehistogram"> |
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116 | "Multiple Histogram Selection" mode</A> is set to "All", |
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117 | this panel is disabled. For other settings of this mode, |
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118 | groups of histograms can be selected and modified |
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119 | collectively. |
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120 | <P> |
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121 | If the EXPTOOL program |
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122 | <A href="#installation">(see the installation instructions)</A> |
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123 | is installed, a button for adding histograms will |
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124 | appear on the bottom right on this panel, as seen below. If the |
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125 | program is not properly installed, no errors occur, but the button |
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126 | does not appear. |
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127 | <P> |
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128 | Note that the order that histograms appear in this |
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129 | panel is determined by the "Sort histograms by" option in |
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130 | the Options Menu. |
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131 | <img SRC="3.gif" align=TEXTTOP> |
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132 | </DL></DL> |
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133 | |
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134 | <h2>4. Scaling panel</h2> |
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135 | <DL><DL> |
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136 | The Scaling panel is used to edit the scale factor for a |
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137 | histogram as well as the phase fractions for each phase |
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138 | present in that histogram. Damping and refinement flags |
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139 | can also be set here. |
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140 | <P> |
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141 | If |
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142 | <A href="#multiplehistogram"> |
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143 | "Multiple Histogram Selection" mode</A> is set to |
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144 | any value other than "Off," |
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145 | groups of histograms can be selected and modified |
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146 | collectively. |
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147 | <P> |
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148 | Note that the order that histograms appear in this |
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149 | panel is determined by the "Sort histograms by" option in |
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150 | the Options Menu. |
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151 | <img SRC="4.gif" align=TEXTTOP> |
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152 | </DL></DL> |
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153 | |
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154 | <h2>5. Profile panel</h2> |
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155 | <DL><DL> |
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156 | The Profile panel is used to edit the profile values for |
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157 | each phase present in a histogram as well as set |
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158 | the refinement flags and a damping value for each phase. |
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159 | <P> |
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160 | If |
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161 | <A href="#multiplehistogram"> |
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162 | "Multiple Histogram Selection" mode</A> is set to "All", |
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163 | this panel is disabled. For other settings of this mode, |
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164 | profile values and settings can be collectively |
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165 | modified for groups of histograms. |
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166 | <P> |
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167 | Note that the order that histograms appear in this |
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168 | panel is determined by the "Sort histograms by" option in |
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169 | the Options Menu. |
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170 | <img SRC="5.gif" align=TEXTTOP> |
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171 | </DL></DL> |
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172 | |
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173 | <a name="multiplehistogram"> |
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174 | <h2>6. Multiple Histogram Selection</h2></a> |
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175 | <DL><DL> |
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176 | This mode allows parameters to be changed for groups of |
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177 | histograms. |
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178 | When the "Multiple Histogram Selection" mode is off, |
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179 | it is possible to modify parameters |
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180 | and refinement flags for only a single histogram, but |
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181 | the other settings allow groups of histograms |
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182 | to be selected and modified. |
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183 | <A href="#mouseactions">(see Mouse Actions)</A>. |
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184 | |
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185 | It does not make sense, however, to globally modify |
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186 | instrument-related parameters and flags for different |
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187 | histogram types. |
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188 | So global actions can be limited to a single class |
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189 | of histogram types (e.g. TOF, CW Neutron,...), which |
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190 | allows these parameters to be set for groups of |
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191 | similar histograms. Thus, if this mode is set to "All" |
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192 | the Histogram and Profile panels are disabled. |
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193 | <P> |
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194 | The setting for "Multiple Histogram Selection" mode is |
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195 | selected using the "Multiple Hist. Selection" item on the |
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196 | Options menu. |
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197 | <p> |
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198 | <a name="mouseactions"> |
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199 | </DL></DL> |
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200 | <h2>7. Mouse Actions</h2></a> |
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201 | <DL><DL> |
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202 | A range of atoms or (in multiple selection mode) histograms may be |
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203 | selected by dragging (holding down) the left mouse button. It is also |
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204 | possible to select a range by using the Shift key with the left mouse |
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205 | button. To select or deselect individual entries, use the Control key |
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206 | with the left mouse button. Pressing the right mouse button selects all |
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207 | entries in a list. |
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208 | </DL></DL> |
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209 | |
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210 | <h2>8. Menus</h2> |
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211 | A description of the EXPGUI menus follows along with a very |
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212 | brief description of the function of each menu option. |
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213 | Note that an option may appear under more than one menu. |
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214 | <H3>8.1 File Menu</H3> |
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215 | <DL><DL> |
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216 | The options on the File menu as is the custom contains the commands |
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217 | for reading and writing experiment files, as well as starting |
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218 | and ending the program. |
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219 | <DL> |
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220 | <DT>expnam<DD> |
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221 | Select an existing GSAS experiment to be used or create a new |
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222 | experiment file from scratch. |
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223 | <DT>Save<DD>Saves modifications to the current experiment file to disk |
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224 | <DT>Save As<DD>Saves modifications to the current experiment file to disk |
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225 | under a new file name |
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226 | <DT>Reread .EXP file<DD>Reread the last saved version of the experiment file from disk. |
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227 | <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse) |
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228 | <DT>exit<DD>Exit EXPGUI |
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229 | </DL> |
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230 | <img SRC="m1.gif" BORDER=3 > |
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231 | </DL></DL> |
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232 | |
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233 | <h3>8.2 Options Menu</h3> |
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234 | <DL><DL> |
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235 | This menu contains options that determine how EXPGUI runs. |
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236 | <DL> |
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237 | <DT>archive EXP<DD>Toggles archiving of .EXP files. When on, files are |
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238 | saved prior to each save or run of expedt in a file named |
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239 | [expnam].EXP.xxx.gz where xxx = 000, 001 (UNIX) |
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240 | or in a file named [expnam].ZIP or [expnam].xxx (Windows) |
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241 | <DT>Sort atoms by<DD> Determines the order that atoms are displayed on the "Phase" page |
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242 | Atoms may be displayed sorted by atom number, atom type, |
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243 | or by x, y or z |
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244 | |
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245 | <DT>Sort histograms by<DD>Determines the order that histograms are displayed on the |
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246 | Histogram, Scaling and Profile pages |
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247 | |
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248 | Histograms may be sorted by histogram number, histogram type, |
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249 | original bank number, or diffraction angle/wavelength |
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250 | <DT>Multiple hist. selection<DD>When this mode is off, it is possible to modify parameters |
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251 | and refinement flags for only a single histogram. For other settings, |
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252 | it is possible to modify parameters and flags for groups of |
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253 | histograms (see help for Mouse actions). |
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254 | |
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255 | It does not make sense, however, to globally modify |
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256 | instrument-related parameters and flags for different histogram types. |
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257 | So global actions can be limited to a single class of histogram types |
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258 | (e.g. TOF, CW Neutron,...), which allows these parameters to be set |
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259 | for groups of similar histograms. Thus, if this mode is set to "All" |
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260 | the Histogram and Profile pages are disabled. |
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261 | <DT>Override backspace<DD>This option is available in UNIX only, as there are different |
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262 | ways that backspace can be implemented. When option is set |
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263 | as "On," the backspace key is overridden to send a "delete" |
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264 | character. If backspace does not work in a program such as |
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265 | EXPEDT, change try the other setting for this option. |
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266 | <DT>Autoupdate EXP<DD>Normally EXPGUI prompts before rereading the EXP |
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267 | file when GENLES, POWPREF,... are run (this is so that one can change |
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268 | the experiment file and rerun with the current input). If this option is |
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269 | set, the new file is automatically read without a prompt. |
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270 | |
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271 | <DT>SaveOptions<DD>Save the current values for "Override backspace", |
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272 | "Sort atoms by", "Sort histograms by" and "archive EXP" |
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273 | in file ~/.gsas_config (c:\.gsas_config on Windows). |
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274 | <DT>liveplot_options<DD>Used to set options for liveplot, |
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275 | for example, the histogram to be plotted |
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276 | </DL> |
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277 | <img SRC="m2.gif" BORDER=3> |
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278 | </DL></DL> |
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279 | |
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280 | <h3>8.3 Powder Menu</h3> |
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281 | <DL><DL> |
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282 | This menu contains links to GSAS programs used for powder diffraction |
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283 | analysis. |
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284 | <DL> |
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285 | <DT>expedt<DD>Run GSAS experiment editor |
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286 | <DT>powpref<DD>Powder data preparation |
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287 | <DT>genles<DD>Run GSAS experiment editor |
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288 | <DT>powplot<DD>Display powder patterns |
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289 | <DT>rawplot<DD>Plot powder data |
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290 | <DT>fitspec<DD>Fit a TOF vanadium scattering spectrum |
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291 | <DT>tofnorm<DD>Normalize a TOF spectrum |
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292 | </DL> |
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293 | <img SRC="m3.gif" BORDER=3> |
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294 | </DL></DL> |
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295 | |
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296 | <h3>8.4 Single Crystal Menu</h3> |
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297 | <DL><DL> |
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298 | This menu contains links to GSAS programs used for |
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299 | single-rystal diffraction analysis. |
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300 | <DL> |
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301 | <DT>expedt<DD>Run GSAS experiment editor |
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302 | <DT>powpref<DD>Powder data preparation |
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303 | <DT>scabs<DD>Single crystal absorption |
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304 | <DT>scmerge<DD>Sort and merge single crystal data |
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305 | <DT>sxtldata<DD>Prepare generic single crystal data |
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306 | </DL> |
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307 | <img SRC="m4.gif" BORDER=3> |
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308 | </DL></DL> |
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309 | |
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310 | <h3>8.5 Graphics Menu</h3> |
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311 | <DL><DL> |
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312 | This menu contains links to several GSAS and |
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313 | two non-GSAS (liveplot and widplt) |
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314 | programs used for graphical display of data and results. |
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315 | <DL> |
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316 | <DT>forplot<DD>Display Fourier maps (set Fourier options in EXPEDT |
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317 | and then compute with FOURIER |
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318 | <DT>polfplot<DD>Display polefigures |
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319 | <DT>powplot<DD>Display powder patterns |
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320 | <DT>ortep<DD>Draw crystal structure |
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321 | <DT>rawplot<DD>Plot powder data |
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322 | <DT>fourier<DD>Generate Fourier map |
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323 | <DT>forsrh<DD>Search Fourier map for peaks |
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324 | <DT>liveplot<DD>Create a plot of powder data |
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325 | with zooming, automatic update and other nice features. |
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326 | <DT>vrstplot<DD>Create a VRML 3-D file for viewing with 3rd party software |
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327 | <DT>widplt<DD>Displays the FWHM as a function of Q, 2Theta,... for UVWXY values input or read from an EXP file |
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328 | </DL> |
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329 | <img SRC="m5.gif" BORDER=3> |
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330 | </DL></DL> |
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331 | |
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332 | <h3>8.6 Results Menu</h3> |
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333 | <DL><DL> |
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334 | This menu contains links to several GSAS and |
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335 | one non-GSAS (lstview) |
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336 | programs used for analysis of results. |
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337 | <DL> |
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338 | <DT>bijcalc<DD>Thermal parameter analysis |
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339 | <DT>disagl<DD>Distance/angle calculations |
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340 | <DT>reflist<DD>List reflection data |
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341 | <DT>geometry<DD>Molecular geometry calculations |
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342 | <DT>hstdmp<DD>List powder histogram data |
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343 | <DT>istats<DD>HKL Intensity statistics |
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344 | <DT>rcalc<DD>Compute reflection resuduals |
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345 | <DT>composition<DD>Computes the chemical composition of a unit cell |
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346 | accounting for site multiplicies and occupancies |
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347 | <DT>lstview<DD>Create a box with scrollbars containing the current .LST file |
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348 | </DL> |
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349 | <img SRC="m6.gif" BORDER=3> |
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350 | </DL></DL> |
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351 | |
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352 | <h3>8.7 Calculations Menu</h3> |
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353 | <DL><DL> |
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354 | This menu contains programs for useful crystallographic computations. |
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355 | <DL> |
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356 | <DT>cllchg<DD>Transform unit cell |
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357 | <DT>fprime<DD>Compute f, f', f'' and mu/rho for an element for a range of x-ray wavelengths |
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358 | <DT>rducll<DD>Unit cell reduction |
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359 | <DT>spcgroup<DD>Space group symbol interpreter |
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360 | <DT>unimol<DD>Unique molecule assembler |
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361 | </DL> |
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362 | <img SRC="m7.gif" BORDER=3> |
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363 | </DL></DL> |
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364 | |
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365 | <h3>8.8 Import/Export Menu</h3> |
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366 | <DL><DL> |
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367 | This menu contains utilities for importing information into GSAS and |
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368 | exporting. |
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369 | <DL> |
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370 | <DT>exp2xtl<DD>Prepare a .XTL format file of atomic positions. This |
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371 | file is used in MSI software such as Cerius and InsightII. |
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372 | <DT>gsas2cif<DD>Prepare IUCr crystallographic information (CIF) file |
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373 | <DT>hklsort<DD>Prepare HKL tables |
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374 | <DT>pubtable<DD>Prepare atom parameter tables |
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375 | <DT>convert<DD>Convert a standard ASCII file to the direct access format used by GSAS (and for UNIX, the reverse) |
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376 | <DT>cad4rd<DD>Prepare CAD4 single crystal data |
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377 | <DT>dbwscnv<DD>Convert a powder diffraction data file from DBWS format |
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378 | <DT>x17bcnv<DD>Convert an energy dispersive diffractogram data file from NSLS X17b |
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379 | <DT>p3r3data<DD>Prepare Siemens/Brucker P3R3 single crystal data |
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380 | <DT>sxtldata<DD>Prepare generic single crystal data |
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381 | </DL> |
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382 | <img SRC="m8.gif" BORDER=3> |
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383 | </DL></DL> |
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384 | |
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385 | <h2>9. EXPGUI Utility Programs</h2></a> |
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386 | <DL><DL> |
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387 | <P><B>LSTVIEW</B> |
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388 | |
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389 | <P>lstview is used to browse through the GSAS output listing. It is |
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390 | invoked by the "lstview" command in the GUI. |
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391 | <CENTER><IMG SRC="textview.gif"></CENTER> |
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392 | |
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393 | |
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394 | <P><B>LIVEPLOT</B> |
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395 | |
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396 | <P>liveplot shows the observed, calculated and difference plots for powder |
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397 | refinements. The plot is updated as the refinement progresses. The mouse can |
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398 | be used to zoom in on sections of the plot. |
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399 | <CENTER><IMG SRC="liveplot.gif"></CENTER> |
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400 | <IMG SRC="new.gif" HEIGHT=13 WIDTH=36> |
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401 | LIVEPLOT can now be enhanced to superimpose peak locations for |
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402 | input unit cells or peaks from JCPDS/ICDD entries. |
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403 | See the <A HREF="expgui_cfg.html#liveplot"> |
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404 | LIVEPLOT customization information</A> |
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405 | or read file <tt>expgui_cfg.html</tt> in the <tt>gsas/tcl/doc</tt> directory. |
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406 | <P> |
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407 | LIVEPLOT gets the current diffraction information by running the TCLDUMP program, if installed, or |
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408 | HSTDUMP otherwise. The TCLDUMP program has been optimized for use with LIVEPLOT and offers a number of extra |
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409 | options that are not available when HSTDUMP is used: plots can be displayed in the native units (2Theta/TOF/KeV), or |
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410 | in d-space or Q; fixed plus fitted background curves are shown in green; if reflection tickmarks are displayed, |
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411 | reflection tickmarks can be displayed by holding the shift key while pressing the left mouse button. |
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412 | See the installation instructions for installing TCLDUMP. |
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413 | |
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414 | <P><B>WIDPLT</B> |
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415 | |
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416 | <P>widplt can be used to plot the actual peak widths generated by the profile |
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417 | parameters used in GSAS. It is possible to define reference curves |
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418 | that are loaded automatically. |
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419 | <CENTER><IMG SRC="widplt.gif"></CENTER> |
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420 | <BR> |
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421 | </DL></DL> |
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422 | |
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423 | <H2> |
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424 | Acknowledgements</H2> |
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425 | Praise to Larson and |
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426 | <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm"> |
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427 | Von Dreele</A> for GSAS, <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.scriptics.com/">Ousterhout</A> |
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428 | for Tcl/Tk, |
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429 | Przemek Klosowski</A> |
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430 | for convincing me to learn Tcl/Tk |
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431 | and Jonathan Wasserman for starting this project. |
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432 | |
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433 | <hr> |
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434 | GSAS is written by Allen C. Larson and <A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://lansce.lanl.gov/lujan/staff12/vondreele.htm"> |
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435 | Robert B. Von Dreele</A>, MS-H805, |
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436 | Los Alamos National Laboratory, Los Alamos, NM 87545. Problems, questions |
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437 | or kudos concerning GSAS should be sent to Robert B. Von Dreele at |
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438 | <A HREF="MAILTO:vondreele@lanl.gov">vondreele@lanl.gov</A> |
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439 | <P>GSAS is Copyright, 1984-1997, The Regents of the University of California. |
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440 | The GSAS software was produced under a U.S. Government contract (W-7405-ENG-36) |
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441 | by the Los Alamos National Laboratory, which is operated by the University |
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442 | of California for the U.S. Department of Energy. The U.S. Government is |
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443 | licensed to use, reproduce, and distribute this software. Permission is |
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444 | granted to the public to copy and use this software without charge, provided |
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445 | that this notice and any statement of authorship are reproduced on all |
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446 | copies. Neither the Government nor the University makes any warranty, express |
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447 | or implied, or assumes any liability or responsibility for the use of this |
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448 | software. |
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449 | <P>EXPGUI is written by Brian H. Toby of the NIST Center for Neutron Research, |
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450 | <A HREF="MAILTO:Brian.Toby@NIST.GOV">Brian.Toby@NIST.GOV</A> |
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451 | with help from Jonathan Wasserman. |
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452 | |
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453 | <P>EXPGUI is not subject to copyright. Have fun with it. |
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454 | |
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455 | <p>Neither the U.S. Government nor any author makes any warranty, |
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456 | expressed or implied, or assumes any liability or responsibility |
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457 | for the use of this information or the software described |
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458 | here. Brand names cited here are used for |
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459 | identification purposes and do not consitute an endorsement by NIST. |
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460 | |
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461 | <p><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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462 | <br> |
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463 | $Revision: 108 $ $Date: 2009-12-04 23:00:32 +0000 (Fri, 04 Dec 2009) $ |
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464 | </body> |
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465 | </html> |
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