Re: [Ifeffit] inp file - artemis crashing when running feff calc on manually generated inp file
The dartemis output log file -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
Stephen, When you attach one of Demeter's log files to a bug report, you have to attach the one that is written immediately after the problem you are reporting. You clearly launched Artemis again, overwriting the log file, thus overwriting the information useful for the bug report. It is true that I do not explain that clearly enough in the link I sent you to earlier -- I will clarify that on the web page. It turns out that you are seeing the same problem as http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-October/012145.html That is, your input structure has distances that are too unphysical for the atom species in your structure. In your case, I suspect that the near neighbor distance is simply too long, although I will make the same caveat to you that I made to that fellow: I don't understand that part of Feff well enough to know why a those particular distances are causing a problem with the calculation of muffin tin radii. Although I don't know the details of Feff well enough to know why this happening, I am unsurprised. 2.91 A is a very long distance for the bond between a 3d metal like Ga and a first row element like carbon. Are you really sure that your EXAFS data are telling you that that's the first neighbor distance? Simply shortening the distance, even by 1% via "RMULTIPLIER 0.99" allows Feff to run to completion. But I would encourage you to take a careful look at your whole strategy. I just find it very hard to believe that your starting structure is representative of your actual material. I also find it hard to believe that your starting structure will yield physically reasonable muffin tin radii. B PS: Just in case you are interested... you said in your first email, "The feff.run error log file contains nothing obvious." That is because the feff.run file only captures messages written to STDOUT. The useful bit in this case is the thing that feff writes to STDERR, which Demeter captures in the dartemis.log file. In practice, the feff.run file is just not all that useful. On 11/03/2014 12:11 PM, stephen.parry@diamond.ac.uk wrote:
The dartemis output log file
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-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
On 11/03/2014 01:51 PM, Bruce Ravel wrote:
Simply shortening the distance, even by 1% via "RMULTIPLIER 0.99" allows Feff to run to completion.
Except that Artemis does not seem to process the RMULTIPLIER parameter correctly. Drat! Using the RMULTIPLIER works when running Feff6L from the command line, but not when running it from within Artemis. Another thing for the to do list! In any case, my comment remains the same -- your distances appear to be unphysically large. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
The next release of Demeter will interpret RMULTIPLIER sensibly. It will also fail in this situation (and many others where Feff fails to run to completion) in a more graceful way. It is, however, somewhat difficult to capture feff's error messages in a way that I know will work on all the platforms. Still, a more graceful failure and a useful message to the Feff console should go a long way towards making the original problem more understandable. Stephen: thanks for the bug report. B On 11/03/2014 01:55 PM, Bruce Ravel wrote:
On 11/03/2014 01:51 PM, Bruce Ravel wrote:
Simply shortening the distance, even by 1% via "RMULTIPLIER 0.99" allows Feff to run to completion.
Except that Artemis does not seem to process the RMULTIPLIER parameter correctly. Drat!
Using the RMULTIPLIER works when running Feff6L from the command line, but not when running it from within Artemis. Another thing for the to do list!
In any case, my comment remains the same -- your distances appear to be unphysically large.
B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
participants (2)
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Bruce Ravel
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stephen.parry@diamond.ac.uk