Fortran runtime error when running feff on Hydrotalcite cif
Dear all, I'm trying to run feff on the Hydrotalcite cif file as can be found in the Larch Am Min CIF browser and I get the following error: *At line 125 of file ff2chi.f (unit = 1, file = 'list.dat')Fortran runtime error: Bad real number in item 2 of list input* I've been able to gather that this means there is some unreadable input in the file that is been used, but I don't know what file this is so I don't know what the actual bad input is and what has caused it. Any help is greatly appreciated! Kind regards, -- *Siebe van der Veer* | *PhD student* Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: s.van.der.veer@rug.nl |
At a guess, I would say the atom list in the cif file is not suitable:
Mg 0.00000 0.00000 0.00000 0.66667
Al 0.00000 0.00000 0.00000 0.33333
O1 0.00000 0.00000 0.37710 1.00000
H1 0.00000 0.00000 0.41440 1.00000
C 0.00000 0.00000 0.16700 0.08333
O2 0.09200 -0.09200 0.50000 0.08333
Wat 0.09200 -0.09200 0.50000 0.08333
Wat is not a recognized element and occupies the same position as O2.
Partial occupancies are also not supported in atoms.
If I change occupancies to 1.00000, and delete the Mg and Wat lines, the
file reads in to
and runs in atoms without issue. One would then have to manually modify the
feff input to
have the partial occupancies.
-R.
On Thu, Mar 30, 2023 at 4:51 AM van der Veer, Siebe
Dear all,
I'm trying to run feff on the Hydrotalcite cif file as can be found in the Larch Am Min CIF browser and I get the following error:
*At line 125 of file ff2chi.f (unit = 1, file = 'list.dat')Fortran runtime error: Bad real number in item 2 of list input*
I've been able to gather that this means there is some unreadable input in the file that is been used, but I don't know what file this is so I don't know what the actual bad input is and what has caused it.
Any help is greatly appreciated!
Kind regards,
-- *Siebe van der Veer* | *PhD student* Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: s.van.der.veer@rug.nl | _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Hi Siebe,
Sorry for the trouble. I agree with Robert's suggestion to check whether
"Wat" might be causing the problem.
The CIF Browser and Feff runner in XAS Viewer does actually support
fractional occupancies, by randomly assigning atoms to match the partial
occupancy (but of course, not with great precision -- each X, Y, Z position
has exactly one actual atom of a determinant Z). That allows a lot CIF
files to "just work" that would otherwise need manual intervention. At the
moment (and possibly for the foreseeable future), the CIF Browser does not
support editing the CIF directly, but does support editing the result
Feff.inp file, but one can export a CIF, edit that elsewhere, and then
import it.
What I see trying to run a calculation from that CIF file is that there are
many oxygen atoms that are too close together. Like Robert suggested, I
suspected these come from the "Wat", but when I removed those and the H
atoms, the prolem still happened. As Robert listed the atomic positions
for this structure, I think it might actually be the "C", "O2", as well as
the "Wat" with the low occupancy of "0.0833" that might be the problem.
If I remove CO groups and Waters, these to generate the attached CIF (I
changed the ID number) that seems to run, though I don't know if it is then
the structure you actually are trying to model ;).
--Matt
On Thu, Mar 30, 2023 at 6:51 AM van der Veer, Siebe
Dear all,
I'm trying to run feff on the Hydrotalcite cif file as can be found in the Larch Am Min CIF browser and I get the following error:
*At line 125 of file ff2chi.f (unit = 1, file = 'list.dat')Fortran runtime error: Bad real number in item 2 of list input*
I've been able to gather that this means there is some unreadable input in the file that is been used, but I don't know what file this is so I don't know what the actual bad input is and what has caused it.
Any help is greatly appreciated!
Kind regards,
-- *Siebe van der Veer* | *PhD student* Nanostructures of Functional Oxides | Zernike Institute for Advanced Materials University of Groningen | Nijenborgh 4, 9747 AG Groningen | The Netherlands Email: s.van.der.veer@rug.nl | _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
-- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411
participants (3)
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Matt Newville -
Robert Gordon -
van der Veer, Siebe