[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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