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3 | <title>EXPGUI</title> |
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5 | GSAS, EXPGUI"> |
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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="expgui6R.html">Next page</A> |
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25 | </TH><TH><A Href="expgui5.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 6 |
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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 | <h3>A.6 Constraints panel</h3> |
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35 | <DL><DL> |
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36 | GSAS offers two ways to limit changes to parameters that are based rules |
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37 | created by a crystallographer to create what is felt to be the most |
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38 | reasonable model. |
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39 | So called "soft constraints", which are better described as "restraints" |
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40 | penalize the fit if |
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41 | aspects of a model (for example, bond lengths) differ from selected |
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42 | values. They are now located on the on the <A Href="expgui6R.html">Restraints panel</A>. |
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43 | Actual constraints, which are sometimes called "hard constraints", are |
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44 | on panel described here. They reduce the actual number of |
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45 | parameters in a model, |
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46 | by grouping parameters so that a single shift (possibly scaled) is |
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47 | applied to each parameter in the group. |
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48 | At this time the only constraints that can be set in EXPGUI are on |
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49 | <a href="#AtomConstraints"><B>Atom Constraints</B></A> for normal phases, |
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50 | <a href="#MMConstraints"><B>Macromolecular Atom Constraints</B></A> |
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51 | when a macromolecular phase is present, or |
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52 | <a href="#ProfileConstraints"><B>Peak Profile Constraints</B></A>. |
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53 | GSAS offers many other types of restraints, but these must be |
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54 | accessed in EXPEDT. |
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55 | <P> |
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56 | Note that in GSAS these constraints are only applied to shifts, but not to the |
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57 | actual values. This means that, for example, |
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58 | if two atoms |
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59 | are constrained so that the shift on their occupancy is the same, but |
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60 | the initial occupancies differ, the difference in their occupancies |
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61 | will not change as the values are refined. |
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62 | <P> |
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63 | Due to the way GSAS implements constraints, a parameter can be included |
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64 | in only one constraint. Should one or more parameters be constrained twice, |
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65 | the refinement results are unpredictable, so EXPGUI will not allow |
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66 | this (EXPEDT will). One can sometimes bypass |
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67 | this problem by defining redundant parameters. For example to |
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68 | constrain the occupancy of site A to B and site A to C, one can |
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69 | create two atom A sites: A<sub>1</sub> & A<sub>2</sub>. Then one can create two |
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70 | constraints, for site A<sub>1</sub> to B and site A<sub>2</sub> to C. The actual occupancy |
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71 | of site A is then that of A<sub>1</sub> plus A<sub>2</sub> |
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72 | |
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73 | </DL></DL> |
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74 | <a name="AtomConstraints"></a> |
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75 | <H4>A.6.1 Atom Constraints</H4> |
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76 | <DL><DL> |
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77 | The atom constraints editing panel appears below. Note that constraints can |
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78 | be listed sorted by constraint number, phase number, lowest atom number or |
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79 | variable by clicking on the buttons at the top of the panel. |
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80 | <P> |
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81 | To delete one or more constraints, click on the appropriate |
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82 | checkbuttons |
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83 | in the <B>Delete</B> column and the press the Delete button, below. |
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84 | </DL></DL> |
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85 | <img SRC="mc.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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86 | <DL><DL> |
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87 | <a name="AtomConstraintsError"></a> |
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88 | Should parameters be included in more than one constraint, |
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89 | an error message is displayed, as shown below. |
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90 | Note that the constraint number is displayed as red on the main |
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91 | atomic constraints window (see above), if the |
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92 | constraint contains a parameter referenced elsewhere. |
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93 | Negative contraint values are highlighted with a beige background |
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94 | to make them more visible. |
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95 | |
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96 | </DL></DL> |
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97 | <img SRC="mcerr.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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98 | <DL><DL> |
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99 | <a name="EditAtomConstraints"></a> |
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100 | <P> |
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101 | <img SRC="mcedit.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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102 | <img SRC="mcvar.gif" align=RIGHT alt="EXPGUI Screen snapshot"> |
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103 | When the edit button for a constraint is pressed, the constraint is |
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104 | opened for editing. Controls are available to select the phase, variable, |
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105 | multiplier and atom(s). Note that for atom selection, use of the control key |
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106 | and the left mouse button allow individual atoms to be selected or deselected. |
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107 | Shift and the left mouse button allow ranges of atoms to be selected and the |
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108 | right mouse button selects all atoms |
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109 | <A href="expgui.html#mouseactions">(see Mouse Actions)</A>. |
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110 | <P> |
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111 | Note that it is inappropriate |
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112 | to constrain different types of parameters together, for example X and Uiso. |
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113 | The left-most variable button is the "master" which |
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114 | determines what variable are allowed in the |
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115 | other variable buttons. |
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116 | <P> |
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117 | When the "New Constraint" button is pressed, a blank constraint editing |
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118 | window is opened. Note that any variable to the right may then be selected, |
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119 | including three special codes, Uxx, XYZU and XYZU+-F. |
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120 | <UL><LI> |
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121 | XYZU creates |
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122 | four constraints, |
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123 | requiring the shifts on x, y, z and Uiso to be the same for all the selected |
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124 | atoms. |
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125 | <LI> |
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126 | Uxx does the same for the six anisotropic displacement parameters. |
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127 | <LI> |
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128 | <a name="XYZUF"></a>XYZU+-F is used for pairs of atoms where |
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129 | the shifts on x, y, z and Uiso are required to be equal, but the shifts |
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130 | on Frac are opposite. |
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131 | </UL> |
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132 | These special codes are valuable for atoms that share a site or are |
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133 | otherwise grouped together. |
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134 | <P> |
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135 | <a name="AtomConstraintsMax"></a> |
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136 | Note that only 100 parameters may be included in a single atomic constraint, |
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137 | with one exception. When shifts for Uiso |
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138 | are constrained to the same value for all atoms in a phase, |
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139 | this counts as a single parameter. If more than 500 |
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140 | parameters are entered for a constraint, an error message is shown. |
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141 | Up to 2000 total atomic constraints may be entered. |
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142 | EXPGUI does not warn if you exceed this limit. |
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143 | </DL></DL> |
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144 | |
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145 | <a name="MMConstraints"></a> |
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146 | <H4>A.6.2 Macromolecular Constraints</H4> |
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147 | <DL><DL> |
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148 | Constraints for a macromolecular phase can be entered on a |
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149 | panel similar to the Atomic Constraints, except that the phase number |
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150 | does not appear anywhere (since the macromolecular phase must |
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151 | be phase #1). The variables that can be constrained for |
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152 | a macromolecular phase are the coordinates, x, y, & z as well as |
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153 | the occupancy, FRA and the atomic displacement parameter, UIS. |
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154 | The special constraint, XYZU, is used to constrain all coordinates |
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155 | and the displacement parameter. |
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156 | </DL></DL> |
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157 | |
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158 | <a name="ProfileConstraints"></a> |
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159 | <H4>A.6.3 Profile Constraints</H4> |
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160 | <DL><DL> |
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161 | The profile constraints editing panel appears below. Profile constraints |
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162 | are used to relate the shifts applied to profile terms for different |
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163 | phase/histogram combinations. Profile terms are identified by number, |
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164 | so while EXPEDT allows one to constrain the first profile term for |
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165 | a TOF histogram to a the first term in a CW histogram, EXPGUI attempts to |
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166 | make this impossible. |
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167 | <P> |
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168 | To delete one or more constraints, click on the appropriate checkbuttons |
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169 | in the <B>Delete</B> column and the press the Delete button, below. |
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170 | </DL></DL> |
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171 | <img SRC="pc.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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172 | <DL><DL> |
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173 | |
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174 | <a name="ProfileConstraintErr"></a> |
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175 | <img SRC="pcerr.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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176 | Should parameters be included in more than one constraint, |
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177 | an error message is displayed, as shown below. |
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178 | Note that the constraint number is displayed as red on the main |
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179 | profile constraints window (see above), if the |
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180 | constraint contains a parameter referenced elsewhere. |
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181 | |
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182 | <BR CLEAR=LEFT> |
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183 | <P> |
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184 | <a name="EditProfileConstraints"></a> |
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185 | When the edit button for a constraint is pressed, the constraint is |
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186 | opened for editing, as shown below. |
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187 | Listboxes contain the available phases and histograms. |
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188 | Only the histograms of the same data type (TOF, CW or ED) are included, |
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189 | but no check is made to ensure that the |
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190 | selected phase/histogram combinations |
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191 | all have the same profile type. |
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192 | Note that for phase and histogram selection, use of the control key |
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193 | and the left mouse button allow individual items to be selected or deselected. |
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194 | Shift and the left mouse button allow ranges of items to be selected and the |
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195 | right mouse button selects all phases or histograms. |
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196 | <A href="expgui.html#mouseactions">(see Mouse Actions)</A>. |
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197 | <P> |
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198 | <img SRC="pcedit.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> |
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199 | <P> |
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200 | </DL></DL> |
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201 | <a name="NewProfileConstraints"></a> |
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202 | <img SRC="pcnew1.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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203 | When the "New Constraint" button is pressed, a window is opened to select |
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204 | the histogram and profile function type to be constrained. Note that |
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205 | only for profile function #4, where the number of terms depends on the |
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206 | phase symmetry, does it matter what phase you select. The available profile |
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207 | terms are displayed on the bottom of the window and more than |
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208 | one can be selected. |
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209 | <BR CLEAR=LEFT> |
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210 | <P> |
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211 | <DL><DL> |
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212 | <img SRC="pcnew2.gif" align=LEFT alt="EXPGUI Screen snapshot"> |
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213 | |
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214 | After the "Continue" button is pressed, a constraint |
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215 | edit window is opened, as shown to the left. |
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216 | Listboxes contain the available phases and histograms and |
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217 | only the histograms of the selected data type are included, as before. |
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218 | Also, for phase and histogram selection, use of the control or shift key |
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219 | and the left mouse button allow individual items to be selected or deselected |
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220 | and the right mouse button selects all phases or histograms. |
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221 | Note that if more than one profile term was selected on the previous window, |
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222 | the same set of constraints are for each term. |
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223 | <BR CLEAR=LEFT> |
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224 | <P> |
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225 | <a name="ProfileConstraintsMax"></a> |
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226 | Note that only 27 terms can be included in a single profile constraint. |
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227 | Also, only like profile terms can be constrained. While GSAS does allow |
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228 | different types of profile terms to be constrained together, this does not |
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229 | usually make sense and EXPGUI does not allow it. |
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230 | </DL></DL> |
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231 | <hr> |
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232 | <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT> |
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233 | <TR><TH><A Href="expgui.html">EXPGUI top</A> |
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234 | </TH><TH><A Href="expgui6R.html">Next page</A> |
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235 | </TH><TH><A Href="expgui5.html">Previous page</A> |
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236 | </TH></TR></TABLE> |
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237 | |
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238 | </blockquote> |
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239 | </body> |
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240 | </html> |
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