[Ifeffit] Fwd: Feff calc

Gemma Guilera gguilera at cells.es
Thu Jun 12 04:19:44 CDT 2008


Hi Josh,

Thanks a lot for your answer and help!

Yes, indeed these last 3 atoms should not be there; they were created
automatically by symmetry when I ran atoms and forgot to take them out

Now it does work nicely!

Thanks again.

Cheers,
Gemma 

-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of joshua jason
kas
Sent: Wednesday, June 11, 2008 10:10 PM
To: John J. Rehr
Cc: ifeffit at millenia.cars.aps.anl.gov; Gemma Guilera
Subject: Re: [Ifeffit] Fwd: Feff calc

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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> Ifeffit at millenia.cars.aps.anl.gov
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>
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