Changeset 401
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 Dec 4, 2009 5:05:33 PM (11 years ago)
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trunk/doc/expgui1.html
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r331 r401 43 43 <img SRC="1.gif" align=TEXTTOP alt="EXPGUI Screen snapshot"> 44 44 </DL> 45 45 <DL><DL> 46 The entries on the upper part of this pane are overall options for the 47 entire experiment. 48 <P> 49 <DT><B>Last History</B><DD> 50 This shows the last history record written into 51 the experiment file, showing the last program that modified the file 52 and when it was run. 53 <DT><B>Title</B><DD> 54 This is a title for the refinement. users can specify any information 55 they want saved in the experiment file. 56 <DT><B>Number of Cycles</B><DD> 57 This is the number of refinement cycles to be performed in GENLES. 58 If this number is zero when GENLES is run, 59 powder diffraction intensities are computed and, when requested 60 (<a href="#extract">see below</a>) reflection intensities are estimated 61 but parameters are not refined. Note that when a 62 <a href="#lebail">LeBail extraction</a> is performed 63 with the cycles set at zero, reflection 64 intensities are optimized even when though no cycles of refinement are 65 performed. 66 <DT><B>Print Options</B><DD> 67 <img SRC="1a.gif" align=right alt="EXPGUI Screen snapshot"> 68 This allows you to control what types of output GENLES provides. The menu of 69 options is shown to the right. I recommend including the summary of shifts and 70 in most cases the correlation matrix in the output. 71 <DT><B>Convergence Criterion</B><DD> 72 GENLES stops refinements when the sum of the squares of each 73 parameter shifts divided by its standard uncertainty is less than 74 this "Convergence Criterion." Since this quantity is the <I>total</I> 75 sum of squares, it is reasonable to raise this value for refinements 76 where large numbers of parameters will be refined. 77 <DT><B>Marquardt Damping</B><DD> 78 Marquardt damping increases the weighting of the diagonal elements 79 in the Hessian matrix, reducing the impact of parameter correlation 80 on the refinement. It increases refinement stability at the cost 81 of requiring additional cycles of refinement. A Marquardt term of 1.0 82 corresponds to a standard leastsquares refinement with no Marquardt 83 damping. The value 1.2 has been recommended to me by Lachlan Cranswick as 84 a good choice. 85 <P> 86 </DL> 87 <br clear=all> 88 <DL> 89 The lower section, labeled "Reflection Intensity Extraction" has options 90 for each histogram that determine if reflection intensities will be estimated, 91 and if so, how. 92 <P> 93 <DT><B>Extract Fobs</B><DD> 94 When the Extract Fobs option is on, reflection intensities are computed 95 using the method developed by Hugo Rietveld. In this method 96 the intensity for each reflection is determined by summing the 97 appropriate data points, weighed by the ratio of the computed intensity 98 from that reflection to the total computed intensity at that point. This means 99 that in the case of severely overlapped reflections, "observed" 100 intensities are apportioned according to the relative computed reflection 101 intensities. This is clearly biased since it invokes the crystallographic 102 model, but is about the best that can be done. Turning this option off 103 saves a very small amount of computer time. 104 <a name="extract"> 105 </a><DT><B>Intensity Extraction Methods</B><DD> 106 There are two approaches to reflection intensity determination. In the 107 conventional <B>Rietveld</B> approach, if the "Extract Fobs" flag is on, 108 reflection intensities are determined 109 as part of the Rietveld refinement, reflection Rfactors are 110 computed, and the reflection intensities 111 are saved on disk file for use in Fourier or other computations. 112 <P> 113 In the extraction method developed by Armel <B>LeBail</B>, 114 reflection intensities are "optimized" by treating the setting the F<sub>calc</sub> value 115 for each reflection to the F<sub>obs</sub> value extracted 116 during the previous cycle. 117 By iterating, the F<sub>calc</sub> values slowly converge to a 118 set of reflection 119 intensities that yields a best fit to the pattern. 120 The F<sub>obs</sub> values are determined every time GENLES is run, 121 or a least squares 122 refinement cycle is run. This it is possible to improve the LeBail fit, by 123 running GENLES with the "Number of Cycles" set to zero. 124 <P> 125 Note that due to reflection 126 overlap, there are usually many different ways to apportion intensities with 127 fits of comparable quality, depending on what starting values are used for 128 F<sub>obs</sub>. Any time POWPREF is run, the reflection list 129 is regenerated and the first time that GENLES is run, the 130 starting F<sub>calc</sub> values are set one of two ways: 131 <P><DL> 132 <a name="lebail"> 133 <DT><B>F(calc) weighted</B><DD> 134 In a "F(calc) weighted" LeBail extraction the initial F<sub>calc</sub> values are computed 135 from the crystal structure model. If the model is fairly close to being 136 correct, it will likely apportion intensity for overlapping reflections in 137 a manner that is fairly close to correct. Thus, the F<sub>calc</sub> values obtained 138 from a "F(calc) weighted" LeBail extraction are about as good as can be 139 done for the case where the structure is pretty close to correct. 140 <DT><B>Equally weighted</B><DD> 141 On the other hand, if one has no good structural model, but would like to 142 use LeBail extraction as a way to obtain F<sub>obs</sub> values for use in structure 143 solution, for example, by direct methods, then it is best to assume that all 144 reflections are equally likely to contain intensity. In the "Equally weighted" 145 mode, all reflections are given an identical F<sub>obs</sub> starting value. Thus, if 146 two reflections are completely overlapped, in this methods, they will 147 be assigned equal F<sub>obs</sub> values through the LeBail fit. 148 </DL> 149 <P> 150 It is possible to refine unit cell, background, profile and other 151 nonstructural parameters at the same time as a LeBail extraction is 152 performed. I often do this, for two reasons. One is that the final LeBail 153 R<sub>wp</sub> and Chi<sup>2</sup> provides a better measure of the 154 best possible fit 155 than the statistical values, particularly if the material has nonideal 156 peak shapes or other factors that cannot modeled. The second reason is the 157 LeBail fit provides excellent starting values for the unit cell, background 158 and profile parameters, so these terms need not be refined again 159 until all structural terms have been fit well. 160 <P> 161 These LeBail refinements, alas, are prone to diverge 162 if the the extracted intensities are changing rapidly and 163 other parameters, such as unit cell parameters are compensating. It is 164 a good practice to run GENLES several times with 165 the "Number of Cycles" set to zero each time POWPREF is run  to allow the 166 reflection intensities to converge before refining parameters. 167 <P> 168 Note that extraction different methods can be used for different phases 169 in a histogram. 170 It can be convenient to use LeBail extraction for an impurity phase, 171 in the case where the impurity has preferred orientation or has a known 172 unit cell, but an unknown structure. I have also used LeBail fits to 173 obtain precise lattice constants via profile fits of materials where the 174 exact structure is not known, so a Rietveld refinement cannot be performed. 175 <DT><B>LeBail Damping</B><DD> 176 The shifts to the reflection intensities can damped. This is useful when 177 refining lattice constants or other terms that might otherwise cause the 178 reflection intensities to shift dramatically and in turn cause the refinement 179 to diverge. 180 </DL></DL> 46 181 <hr> 47 182 <TABLE BORDER BGCOLOR="#FFFF40" ALIGN=RIGHT>
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