problem with Demeter- Artemis/Atoms
I was attempting to import a .cif file into Artemis to use for a FEFF calculation and I am getting the following error message: "Atoms is currently unable to use crystal data which has sites of partial occupancy. Sorry." These .cif files work fine with the old version of Artemis/Atoms. Is there currently a way around this problem, or is this something that will be addresses in later version. Thank you for your help. Sincerely, Matt Frith
Attaching the CIF would make it much easier to help.
Is the CIF supposed to have partial occupancy? (In which case the old
version would only work if it ignored one all but one partial occupancy
site.)
-Jason
On Wed, May 23, 2012 at 6:33 PM, Matt Frith
I was attempting to import a .cif file into Artemis to use for a FEFF calculation and I am getting the following error message:
"Atoms is currently unable to use crystal data which has sites of partial occupancy. Sorry."
These .cif files work fine with the old version of Artemis/Atoms. Is there currently a way around this problem, or is this something that will be addresses in later version.
Thank you for your help.
Sincerely,
Matt Frith
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Matt, Question 15 at http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling is relevant. That said, your are not wrong that the error message that I have posted is a bit of a cop-out. I could have all the data imported from the CIF and trust you to delete all but one of the atoms that partially occupy a site. So, the reasonable request is that such a CIF file be imported and that the situation be recognized and communicated to the user. Of course, what I wrote above suggests a fairly straight forward work-around. A CIF file is a plain text file. It can be opened in any text editor. You, then, could delete all but one lines of atoms that partially occupy a site, save the CIF file, and import that into Artemis. That's perhaps a bit inconvenient, but not exactly rocket science. B PS: And to reiterate Jason's point about attaching the file about which you are asking: http://bruceravel.github.com/demeter/pods/bugs.pod.html On Wednesday, May 23, 2012 06:33:22 PM Matt Frith wrote:
I was attempting to import a .cif file into Artemis to use for a FEFF calculation and I am getting the following error message:
"Atoms is currently unable to use crystal data which has sites of partial occupancy. Sorry."
These .cif files work fine with the old version of Artemis/Atoms. Is there currently a way around this problem, or is this something that will be addresses in later version.
Thank you for your help.
Sincerely,
Matt Frith
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
participants (3)
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Bruce Ravel
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Jason Gaudet
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Matt Frith