[Ifeffit] feff doesn't like cluster

Kelly, Shelly D. SKelly at anl.gov
Thu Jul 21 10:22:21 CDT 2005


Oh well,  I guess that could be fixed.  Atoms assumes that the absorbing
atom will also be a scattering atom, hence ipot 0 and ipot 1 are always
defined with the same atom type.

SK

> -----Original Message-----
> From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-
> bounces at millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan
> Sent: Thursday, July 21, 2005 10:14 AM
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] feff doesn't like cluster
> 
> Shelly,
> 
> but why did ATOMS generate an ipot that doesn't exist?
> 
> Juro
> 
> On Jul 21, 2005, at 4:59 PM, Kelly, Shelly D. wrote:
> 
> >
> > Hi Juro,
> >
> > Feff is old fasioned.  It requires that all ipot numbers are in
order
> > and that they exist, otherwise it just quits.  In your example below
> > ipot number 1 was not defined.
> >
> > Shelly
> >
> >> -----Original Message-----
> >> From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:ifeffit-
> >> bounces at millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan
> >> Sent: Thursday, July 21, 2005 9:51 AM
> >> To: XAFS Analysis using Ifeffit
> >> Subject: Re: [Ifeffit] feff doesn't like cluster
> >>
> >> Hello,
> >>
> >> thank you for the fast response. According to Norbert's
> >> suggestion, I looked in the feff file. The problem seems to
> >> be with the potential 1, assigned to As. Removing this line
> >> and rewriting all potentials in the list makes feff like
> >> the input. However, I don't understand why ATOMS has
> >> generated these ipot values. The atoms.inp is below.
> >>
> >> Juro
> >>
> >> ----------------------------------part of feff.inp
> >>  POTENTIALS
> >>  *    ipot   Z  element
> >>         0   33   As
> >>         1   33   As
> >>         2    8   O
> >>         3   26   Fe
> >>
> >>  ATOMS                          * this list contains 24
> >> atoms
> >>  *   x          y          z      ipot  tag
> >>              distance
> >>     0.00000    0.00000    0.00000  0    As
> >>               0.00000
> >>    -1.40201    0.76410   -0.53997  2    O3_1
> >>             1.68554
> >>     0.00000   -1.59002   -0.56202  2    O4_1
> >>             1.68643
> >>     0.00000   -0.00003    1.68705  2    O1_1
> >>             1.68705
> >>     1.37801    0.79495   -0.56207  2    O2_1
> >>             1.68724
> >>    -2.86303   -0.03582   -1.71095  3    Fe2_1
> >>            3.33550
> >>    -1.39501   -2.50095   -1.71100  3    Fe3_1
> >>            3.33591
> >>    -1.46101   -0.86989   -2.91804  2    O13_1
> >>            3.37731
> >>    -2.86203   -1.70487   -0.55592  2    O12_1
> >>            3.37740
> >>     0.00000   -0.69408    3.59511  3    Fe1_1
> >>            3.66150
> >>     0.00000   -2.60210    2.90109  2    O7_1
> >>             3.89708
> >>     2.03002   -0.69418    3.59504  2    O9_1
> >>             4.18655
> >>    -2.03002   -0.69397    3.59518  2    O8_1
> >>             4.18663
> >>    -2.86503    1.63323   -2.86599  2    O11_1
> >>            4.36918
> >>     0.07200   -3.29702   -2.86609  2    O15_1
> >>            4.36921
> >>    -4.26604    0.79825   -0.50387  2    O10_1
> >>            4.36923
> >>    -1.32901   -4.13200   -0.50397  2    O14_1
> >>            4.36963
> >>     0.00000    1.21295    4.28913  2    O6_1
> >>             4.45734
> >>     0.00000   -1.38895   -4.49813  2    O5_1
> >>             4.70769
> >>    -2.79603   -3.41087   -2.86399  2    O17_1
> >>            5.25873
> >>    -4.33104   -0.83474   -2.86393  2    O16_1
> >>            5.25897
> >>     0.00000   -1.38912    5.50217  2    O5_2
> >>             5.67482
> >>     5.73406    0.79772   -0.50422  2    O10_2
> >>            5.81120
> >>     0.00000    1.21312   -5.71117  2    O6_2
> >>             5.83859
> >>  END
> >>
> >>
> >> ----------------------------------atoms.inp
> >> title model6
> >> space  P 1
> >> rmax=6.0  a=10.0001  b=10.0002  c=10.0003  alpha=90.001
> >>  beta=90.002  gamma=90.003
> >> core=As
> >> atom
> >> !  At.type   x         y         z      tag
> >>     As     0.00000   0.00000   0.00000  As
> >>     Fe     0.00000  -0.06940   0.35950  Fe1
> >>     Fe    -0.28630  -0.00360  -0.17110  Fe2
> >>     Fe    -0.13950  -0.25010  -0.17110  Fe3
> >>     O      0.00000   0.00000   0.16870  O1
> >>     O      0.13780   0.07950  -0.05620  O2
> >>     O     -0.14020   0.07640  -0.05400  O3
> >>     O      0.00000  -0.15900  -0.05620  O4
> >>     O      0.00000  -0.13890   0.55020  O5
> >>     O      0.00000   0.12130   0.42890  O6
> >>     O      0.00000  -0.26020   0.29010  O7
> >>     O     -0.20300  -0.06940   0.35950  O8
> >>     O      0.20300  -0.06940   0.35950  O9
> >>     O     -0.42660   0.07980  -0.05040  O10
> >>     O     -0.28650   0.16330  -0.28660  O11
> >>     O     -0.28620  -0.17050  -0.05560  O12
> >>     O     -0.14610  -0.08700  -0.29180  O13
> >>     O     -0.13290  -0.41320  -0.05040  O14
> >>     O      0.00720  -0.32970  -0.28660  O15
> >>     O     -0.43310  -0.08350  -0.28640  O16
> >>     O     -0.27960  -0.34110  -0.28640  O17
> >>
> >>
> >> On Thu, 21 Jul 2005 08:53:27 -0500 (CDT)
> >>  Matt Newville <newville at cars.uchicago.edu> wrote:
> >>> Juraj,
> >>>
> >>> Please post the feff.inp file.  You might also
> >>> send the atoms.inp file.
> >>>
> >>> -Matt
> >>>
> >>> On Thu, 21 Jul 2005, Juraj Majzlan wrote:
> >>>
> >>>> Hello,
> >>>>
> >>>> I collected As K EXAFS data and created a cluster which
> >>>> could represent the "probable geometry". I have an
> >>> ATOMS
> >>>> file with coordinates of the atoms in a triclinic unit
> >>>> cell. ATOMS did its thing but FEFF refused to process
> >>> the
> >>>> data and generated an error:
> >>>>  Feff 6L.02
> >>>>    No atoms or overlap cards for unique pot     1
> >>>>   Cannot calculate potentials, etc.
> >>>>  Fatal Error: at RDINP
> >>>>
> >>>> Then I filled the empty space around the cluster with
> >>>> hydrogen atoms on a grid, hoping that FEFF would like
> >>> it
> >>>> more, but the same error came.
> >>>>
> >>>> Short of creating a complete structure (of some sort)
> >>> with
> >>>> the cluster embedded in it, what can I do to make this
> >>>> work?
> >>>
> >>>
> >>> _______________________________________________
> >>> Ifeffit mailing list
> >>> Ifeffit at millenia.cars.aps.anl.gov
> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >>
> >>
> >>
> >> ----------------------------------
> >> Juraj Majzlan
> >> Institute of Mineralogy and Petrology
> >> Albert-Ludwig-University of Freiburg
> >> Albertstrasse 23b
> >> Freiburg, D-79104, Germany
> >> telephone +49-761-203-6416
> >> fax +49-761-203-6407
> >> http://www.minpet.uni-freiburg.de
> >> _______________________________________________
> >> Ifeffit mailing list
> >> Ifeffit at millenia.cars.aps.anl.gov
> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
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> >
> 
> ----------------------------------------------------------------------
> Juraj Majzlan
> Institute of Mineralogy and Geochemistry
> Albert-Ludwig-University of Freiburg
> Albertstrasse 23b
> D-79104 Germany
> telephone +49-761-203-6416
> fax +49-761-203-6407
> http://www.minpet.uni-freiburg.de/Majzlan.html
> 
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