one more thing about atoms error
Bruce: One more thing I noticed. If I try FEFF7 there is an error at the same spot, however, FEFF8 and FEFF8-exafs do work. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
Hey Carlo, Upon further investigation, the root of the problem is in TkAtoms. More specifically, it is when you have TkAtoms save an atoms.inp file. When you do, it sets all of the occupancies to 0 *and* puts itself into a state where you cannot change the occupancies. This, in turn, leads to the problem computing the corrections. This is quite strange in that I don't remember changing anything in TkAtoms that would have lead to this behavior. The simplest solution seems to be not to use TkAtoms. Artemis isn't broken in the same way. Saving the input file via "Theory->Write special output->atoms" causes no such problem. You can re-import that atoms.inp file and have no problem. Or, you could edit the atoms.inp file remove all the 0's for occupancy. Or, you could edit the atoms.atp file to not write out the occupancy. Many work-arounds! So, the bugs that I need to fix: 1. Whatever is causing the problem in TkAtoms (see P.S. below) 2. Do some better error handling in the part of the code that computes corrections so that it does not choke on the occupancy problem 3. I discovered a problem in the order of paths that are searched for atp files 4. The atoms page in Artemis is very unhappy if you forget to select a central atom when entering data by hand As I said, that's a pretty decent list for a single bug report! B P.S. I can't remember if I mentioned this before, but I plan to discontinue support for TkAtoms eventually. I suspect that some might complain about this, but I have my reasons. I mention this so that no one is surprised when the day come that I stop fixing bugs when they crop up in TkAtoms. That day ain't today, but it will be soon. P.P.S. In private email, you mentioned that you would rebuild your debs with the modified feff.atp file. That's your prerogative, but the file isn't broken. In my opinion, the best move would be to edit your atoms.inp file, remove the occupancy column, and carry on. The second best move would be to edit the atoms.atp file to not write out the occupancies since they are not used for anything in Artemis. Editing the feff.atp file is, I think, a distant third best option. -- Bruce Ravel ----------------------------------- ravel@phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Bruce: On Thu, 29 Jul 2004, Bruce Ravel wrote:
P.P.S. In private email, you mentioned that you would rebuild your debs with the modified feff.atp file. That's your prerogative, but the file isn't broken. In my opinion, the best move would be to edit your atoms.inp file, remove the occupancy column, and carry on. The second best move would be to edit the atoms.atp file to not write out the occupancies since they are not used for anything in Artemis. Editing the feff.atp file is, I think, a distant third best option.
Now that you have explained the source of the problem. I will definitely NOT change the package. It is clearly a problem with an old file that I wrote out with tkAtoms. Writing out the file within the artemis framework is far better anyway, I just had not completely familiarized myself with the new atoms interface. As for dropping support of tkAtoms, there are reasons that I continue to use it when I just want to generate an xyz file outside of artemis. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre@iit.edu http://www.iit.edu/~segre
participants (2)
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Bruce Ravel
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Carlo U. Segre