Structures with multiple crystallographic sites
Do a Feff calculation with each unique Co site as the absorbing atom, then use paths from each calculation, weighted by the fractional site occupancy. Cheers, --Matt
Thanks, Matt! Yes, that's exactly what I tried doing. It's a simple cubic lattice with 20 atoms per unit cell, 8 of one type (Co1) and 12 of the other (Co2). So I did two FEFF runs in the same Artemis project, with Co1 and Co2 as the core atom, and multiplied their respective amplitudes by 0.4 and 0.6. Then I noticed that if I calculate a sum of all included paths I get a different FT spectrum than if the sums are calculated separately for the two FEFF runs and averaged (with correct weighting) outside of Artemis. Of course, it is a bit late here and I could be missing some obvious mistake. On the other hand, I am trying for 1.6-5.5 angstrom fitting range, which involves 70+ paths for Co1 core and ~120 for Co2. Is it possible that Artemis does not like to deal with too many paths and/or variables? I better go check the manual... :o) Regards. Vadim.
Hi Vadim,
Thanks, Matt! Yes, that's exactly what I tried doing. It's a simple cubic lattice with 20 atoms per unit cell, 8 of one type (Co1) and 12 of the other (Co2). So I did two FEFF runs in the same Artemis project, with Co1 and Co2 as the core atom, and multiplied their respective amplitudes by 0.4 and 0.6. Then I noticed that if I calculate a sum of all included paths I get a different FT spectrum than if the sums are calculated separately for the two FEFF runs and averaged (with correct weighting) outside of Artemis. Of course, it is a bit late here and I could be missing some obvious mistake. On the other hand, I am trying for 1.6-5.5 angstrom fitting range, which involves 70+ paths for Co1 core and ~120 for Co2. Is it possible that Artemis does not like to deal with too many paths and/or variables? I better go check the manual... :o) Regards.
The "if the sums are calculated .... outside of Artemis" might be the issues: When the sums are done inside Artemis, the set of Path Parameters is applied to each path during the sum That is, E0, delR, S02*N, and sigma2 will be applied. In addition, Artemis probably has helped you pick a subset of the paths to include in the sum. Depending on how you do the sums outside of Artemis, the Path Parameters may or may not be applied, and the set of paths used might be different. If, for example, you're using the chi.dat file from a Feff calculation done by Artemis, then it almost certainly has S02*N=1 and sigma2=0, delR=0, and E0=0 for all paths. Hope that helps, --Matt PS: There is a limit on the number of paths you can use (1024 paths), but you're not hitting it.
Thanks, Matt! Yes, that's exactly what I tried doing. It's a simple cubic lattice with 20 atoms per unit cell, 8 of one type (Co1) and 12 of the other (Co2). So I did two FEFF runs in the same Artemis project, with Co1 and Co2 as the core atom, and multiplied their respective amplitudes by 0.4 and 0.6. Then I noticed that if I calculate a sum of all included paths I get a different FT spectrum than if the sums are calculated separately for the two FEFF runs and averaged (with correct weighting) outside of Artemis.
I usually do something like: guess amp = 0.9 then for a path in the first feff calculation: s02 = 0.4 * amp and for a path in the second feff calculation: s02 = 0.6 * amp
Of course, it is a bit late here and I could be missing some obvious mistake. On the other hand, I am trying for 1.6-5.5 angstrom fitting range, which involves 70+ paths for Co1 core and ~120 for Co2. Is it possible that Artemis does not like to deal with too many paths and/or variables? I better go check the manual... :o) Regards. Vadim.
Getting the math expressions right for 190 paths is tedious and error prone, but there artemis and ifeffit should deal with that many paths without a problem. There is the caveat that you might start pushing ifeffit's built-in memory lmitations, so you should save your project often. ;-) B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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 (3)
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Bruce Ravel -
Matt Newville -
Vadim G Palshin