[Ifeffit] Problems with potential overlap for small molecule
joshua jason kas
hebhop at u.washington.edu
Tue Jun 2 13:18:25 CDT 2009
In order to solve the overlap problem, I tried some of the standard
methods of fixing these problems, i.e. using
the FOLP cards and such with no luck. This will take some time to debug,
but we are looking into it.
As for the negative density problem, this is something that we have worked
on, and know how to fix, but will also take some time.
> Dear FEFF users,
> I have a FEFF8.4-related question concerning the abortion of the potential
> module in a XANES calculation for a small molecule in solution. It might not
> be totally appropriate for the ifeffit mailing list, but the FEFFusers
> mailing list doesn?t seem to be used very often. I have looked through the
> archive, but I haven?t found an entry with this specific problem.
> I am trying to simulate the L3-edge XANES spectrum for the linear I3-
> molecule (I-I-I) embedded in a solvent with O-H groups. In order to simulate
> the scattering from the solvent, I have put two O-H groups at either end of
> the molecule with the H-atoms pointing towards the I-atoms (expected charge
> transfer from I3- towards solvent). The I-H and I-O distances are taken from
> ab initio calculations in the literature, the O-H distance is well-known and
> amounts to 0.96 A. It is also known from the literature on similar ions in
> solution that the H-atoms contribute to the XANES and should therefore be
> I pasted my feff.inp file below.
> Running this file results in abortion at the beginning of the potential
> Number of processors = 12
> Calculating potentials ...
> free atom potential and density for atom type 0
> Abnormal termination on processor 8
> [n7:09539] MPI_ABORT invoked on rank 8 in communicator MPI_COMM_WORLD with
> errorcode 512
> It seems to occur when it is trying to overlap the potentials (MOVRLP-1). I
> tried including the FOLP 2 0.8 card as suggested for H-atoms in the manual,
> but this does not help.
> It seems like the O-H bond <1 A is too small: moving the O atoms further
> away such that the O-H bond is 1.05 A ?solves? the problem, although this is
> not what I want. But: moving the H atom closer to the I atom while keeping
> the O positions fixed, which increases the O-H bond as well, does not help!
> Also, to make things even more complicated, excluding the H-atoms fully,
> i.e. putting only two O-atoms at 3.5 A from the iodines, results in the
> WARNING during the SCF loop that the interstitial potential level lies
> higher than the Fermi energy (moving the O atom closer to ca. 2 A removes
> this message). In addition, certain combinations of H- and O- positions give
> the output ?negative dens? during the SCF loop, for which I checked that
> FOLP 2 0.8 did not help...
> It is obvious that FEFF has problems with generating the MT potentials for a
> small and ?open? system such as the one here. Did somebody encounter similar
> problems (abortion, Ei>Ef, negative dens) for systems like this? Is there
> something wrong with my input cards?
> I?d appreciate any help.
> Best regards,
> Renske van der Veen
> P.s. I am running the parallel version of FEFF8.4 on Linux
> TITLE I3- XANES spectrum
> * I L3 edge energy = 4557.0 eV
> EDGE L3
> S02 1.0
> CONTROL 1 1 1 1 1 1
> SIG2 0.01
> PRINT 1 0 0 0 0 0
> EXCHANGE 0 0.0 0.0 0
> SCF 10 1 30 0.2 1
> LDOS -30 60 -1
> XANES 6
> FMS 10 1
> 0 53 I 3 4
> 1 53 I 3 4
> 2 1 H
> 3 8 O 2 3
> *FOLP 2 0.8
> 0.0000 0.0000 0.0000 0
> -2.91 0.0000 0.0000 1
> 2.91 0.0000 0.0000 1
> -5.45 0.0000 0.0000 2
> 5.45 0.0000 0.0000 2
> -6.41 0.0000 0.0000 3
> 6.41 0.0000 0.0000 3
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