[Ifeffit] Fwd: Feff calc
joshua jason kas
hebhop at u.washington.edu
Wed Jun 11 15:10:20 CDT 2008
Hi Gemma,
This error basically comes from the fact that you have two very different
types of oxygen atoms in your system, but only one potential.
In this case the oxygen potential and muffin tin radius is being defined
by the oxygen that is bonded directly to the Rh atom. This gives a
relatively large muffin tin radius which, when used at the other oxygen
sites, overlaps too much with the carbon muffin tins.
The way to fix this is to give the two types of oxygens different
potentials, i.e.
POTENTIALS
* ipot Z element
0 45 Rh
1 17 Cl
2 6 C
3 8 O
4 8 O
ATOMS
0.000000 0.000000 0.000000 0 Rh1 0.000000 1
0.066250 -1.715140 -0.175300 2 C1_1 1.725348 2
1.699390 0.099230 -0.398490 2 C2_1 1.748304 3
-0.109490 2.041000 0.145210 3 O3_1 2.049086 4
-2.233040 -0.277590 0.571930 1 Cl1_1 2.321773 5
0.063490 -2.904610 -0.348340 4 O1_1 2.926112 6
2.880780 0.195790 -0.586340 4 O2_1 2.946357 7
-3.609490 2.682000 -4.216430 3 O3_2 6.164400 8
-6.320060 0.195790 1.175470 3 O2_2 6.431425 9
-1.485940 5.000590 -4.643160 1 Cl1_2 6.983756 10
END
The above input file runs, but I would be a bit concerned about the last
three atoms in the list, since they so far away from everything else. Are
they really supposed to be there?
Cheers,
Josh Kas
On Sat, 7 Jun 2008, John J. Rehr wrote:
> Hi Josh,
>
> Are you familiar with this error msg? If not, could you check it
> out? It comes up fairly often.
>
> Thanks.
> J.
>
> ---------- Forwarded message ----------
> Date: Thu, 5 Jun 2008 09:33:40 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis Using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>,
> Gemma Guilera <gguilera at cells.es>
> Subject: [Ifeffit] Fwd: Feff calc
>
>
> Hi Gemma,
>
> I don't know what that error message from Feff means either, so I am
> forwarding this along to the Ifeffit mailing list in hopes that
> someone else -- maybe someone from John's group -- can explain.
>
> If I had to guess, I would say that there was a problem constructing
> the muffin tins either because the atom list is so short or because
> the atoms are too far apart. The muffin tin algorithm does presume
> that the atoms will not be separated by unphysically large distances,
> as the last three atoms in your list are.
>
> It would seem that you are using some version of Feff8 -- is that
> correct? It woul have been helpful had you identified the version of
> Feff you are using and had you captured the screen output from Feff to
> a file. It usually helps you receive the answer you are looking for
> if you provide as much context as possible.
>
> B
>
>
>
> ---------- Forwarded Message ----------
>
> Subject: Feff calc
> Date: Thursday 05 June 2008
> From: "Gemma Guilera" <gguilera at cells.es>
> To: bravel at anl.gov
>
> Dear Bruce,
>
>
> I was trying to run a FEFF calculation (herein attached) and I got a message
> telling me to ask you to INCREASE NOVP.
>
> To be honest, I don't know what is this and why it could not run (maybe
> there is something wrong on the feff.inp file or maybe it is correct that I
> need to increase such 'NOVP'), but here I am.
>
> I would be really grateful if you could give me a hand so I can continue
> with my calculations.
>
>
>
> Thanks a lot and have a nice day,
>
> Gemma
>
>
>
>
> * This feff6 input file was generated by Atoms 3.0.1
> * Atoms written by and copyright (c) Bruce Ravel, 1998-2001
>
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
> * total mu*x=1: 500.60 microns, unit edge step: 622.91 microns
> * specific gravity = 0.620
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
> * Normalization correction: 0.00020 ang^2
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
>
> * -----------------------------------------------------------------
> * The following crystallographic data were used:
> *
> * title [Rh(CO)2ClO]
> * space = P 21/c
> * a = 9.3680 b = 13.410 c = 18.2710
> * alpha = 90.0 beta = 100.840 gamma = 90.0
> * core = Rh1 edge = K
> * atoms
> * ! elem x y z tag occ
> * Cl -0.04060 0.19680 0.13880 Cl1 1.00000
> * C 0.20930 0.30400 0.12200 C1 1.00000
> * C 0.38680 0.16870 0.12690 C2 1.00000
> * O 0.20900 0.39270 0.11250 O1 1.00000
> * O 0.51520 0.16150 0.12900 O2 1.00000
> * O 0.19020 0.02390 0.13770 O3 1.00000
> * Rh 0.20210 0.17610 0.13090 Rh1 1.00000
> * -----------------------------------------------------------------
>
>
> TITLE [Rh(CO)2ClO]
>
> * Rh K edge (23220.0 eV), second number is S0^2
> EDGE K
> S02 1.0
>
> * pot xsph fms paths genfmt ff2chi
> CONTROL 1 1 1 1 1 1
> PRINT 1 0 0 0 0 3
>
> *** ixc=0 means to use Hedin-Lundqvist
> * ixc [ Vr Vi ]
> EXCHANGE 0
>
> * r_scf [ l_scf n_scf ca ]
> SCF 4.0 1
>
>
> RMAX 7.0
> EXAFS
>
>
> POTENTIALS
> * ipot Z element
> 0 45 Rh
> 1 17 Cl
> 2 6 C
> 3 8 O
>
>
> ATOMS * this list contains 10 atoms
> * x y z ipot tag distance
> 0.00000 0.00000 0.00000 0 Rh1 0.00000
> 0.06625 -1.71514 -0.17530 2 C1_1 1.72535
> 1.69939 0.09923 -0.39849 2 C2_1 1.74830
> -0.10949 2.04100 0.14521 3 O3_1 2.04909
> -2.23304 -0.27759 0.57193 1 Cl1_1 2.32177
> 0.06349 -2.90461 -0.34834 3 O1_1 2.92611
> 2.88078 0.19579 -0.58634 3 O2_1 2.94636
> -3.60949 2.68200 -4.21643 3 O3_2 6.16440
> -6.32006 0.19579 1.17547 3 O2_2 6.43142
> -1.48594 5.00059 -4.64316 1 Cl1_2 6.98376
> END
>
>
>
>
> -------------------------------------------------------
>
> --
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
>
> My homepage: http://xafs.org/BruceRavel
> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
>
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