Re: [Ifeffit] Fortran runtime error when running feff on Hydrotalcite cif
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 wrote: > 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.v...@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 630-327-7411 Test1.cif Description: Binary data ___ 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
Re: [Ifeffit] Fortran runtime error when running feff on Hydrotalcite cif
At a guess, I would say the atom list in the cif file is not suitable: Mg 0.0 0.0 0.0 0.7 Al 0.0 0.0 0.0 0.3 O1 0.0 0.0 0.37710 1.0 H1 0.0 0.0 0.41440 1.0 C 0.0 0.0 0.16700 0.08333 O2 0.09200 -0.09200 0.5 0.08333 Wat 0.09200 -0.09200 0.5 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 1.0, 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 wrote: > 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.v...@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 > ___ 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
[Ifeffit] 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.v...@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
