Hi Victor,
It should be restraint_sum = restraint1 + restraint2 + restraint3 + ...
That is, a restraint should be a value that you'd like to me made as small as possible, but can take either sign. The restraints are simply appended to the "vector to be minimized" in the least squares sense.
I'm not sure that will fully solve the issue of having different results between 10+ individual restraints and fewer summed restraints. But I'm interested to hear and see more....
--Matt
Given that individual restraints might be of either sign, you might consider adding them in quadrature and using the square root of that as the restraint. As Matt said, the details matter, but I think that would be a serviceable work around for more than 10 restraints.
B
I am confused. I thought I did exactly what Bruce said. I added them in quadrature and used square root of that as the restraint in artemis: After summing in quadrature: restraint_sum = sqrt((restraint1)^2 + (restraint2)^2 + (restraint3)^2...) I asked artemis "to build restraint from "restraint_sum"" and artemis added line: res_restraint_sum=penalty(restraint_sum,n1,n2)*scale This way of summing them seems closer to the way of adding them individually squared to the "vector to be minimized", provided artemis/ifeffit squares them before appending to the "vector" (you don't need to square them before). I guess the questions is what artemis does when asked to "build restraint from ..."? Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov@csiro.au
Hi All Does anyone know a good place to buy metal foil XAS standards? Sorry for the pedestrian question. And thanks in advance... Best Wishes Matt =================================== Matthew T Kieber-Emmons Riordan Group, 302-831-4518 Rm 222 Lammont DuPont Laboratory Department of Chemistry and Biochemistry University of Delaware, Newark, DE 19716 ===================================
The XAS foil standards the we use are from : EXAFS Materials 871 El Cerro Blvd Danville CA 94526 Their old phone number was 510-838-7162. Unfortunately, the phone number was scratched off on our most recent box, although the new area code is 925. It is possible the area code only that has changed. Jeff On Apr 14, 2007, at 10:21 AM, Matthew Kieber-Emmons wrote:
Hi All
Does anyone know a good place to buy metal foil XAS standards? Sorry for the pedestrian question. And thanks in advance...
Best Wishes
Matt
=================================== Matthew T Kieber-Emmons Riordan Group, 302-831-4518 Rm 222 Lammont DuPont Laboratory Department of Chemistry and Biochemistry University of Delaware, Newark, DE 19716 ===================================
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Matthew, Jeff,
EXAFS Materials 871 El Cerro Blvd Danville CA 94526
Their old phone number was 510-838-7162.
You might also search for Joe Wong in the IXS "community archive". Or, contact the EXAFS Company at http://www.exafsco.com/products.html If you're looking for one or two metal foils, you can usually get an appropriate thickness from Goodfellow (www.goodfellow.com) and sometimes even Alfa Aesar. Goodfellow prices tend to be a bit steeper, but the selection is very good. --Matt
Hi Victor,
I am confused.
I think Bruce had the same idea as you: Because each restraint is appended to the vector to be minimized in the least square sense, the important quantity is Sum_restraints ( restraint_i)^2 and so you could just do that ahead of time, and then say that sqrt(Sum_restraints[restraint_i^2]) is a good substitute for the set of restraints. It does have the appealing feature that it separates there interdependence compared to a simple addition (where you could easily get competition between restraints). I think adding in quadrature is not quite right, as not only is the minimum of chi-square important, but also the ability to find the minimum and explore the parameter space. By adding in quadrature, you prevent the restraints from being negative. Well, the sign *is* arbitrary (is it data-model or model-data??), but the ability to switch signs is important. I am not sure whether adding in quadrature is worse than a simple addition, but neither is ideal. For sure, having enough individual restraints is the best approach. --Matt
On Friday 13 April 2007 19:08, Victor.Streltsov@csiro.au wrote:
I am confused. I thought I did exactly what Bruce said. I added them in quadrature and used square root of that as the restraint in artemis: After summing in quadrature: restraint_sum = sqrt((restraint1)^2 + (restraint2)^2 + (restraint3)^2...)
I asked artemis "to build restraint from "restraint_sum"" and
artemis added line: res_restraint_sum=penalty(restraint_sum,n1,n2)*scale
This way of summing them seems closer to the way of adding them individually squared to the "vector to be minimized", provided artemis/ifeffit squares them before appending to the "vector" (you don't need to square them before). I guess the questions is what artemis does when asked to "build restraint from ..."?
"penalty" is just a normal ifeffit function. It is useful for making restraints, but has no special relationship to restraints. Use the sum in quadrature as *the* restraint, not as an argument of the penalty function. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
participants (5)
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Bruce Ravel -
Jeff Terry -
Matt Newville -
Matthew Kieber-Emmons -
Victor.Streltsov＠csiro.au