Re: [Ifeffit] feff doesn't like cluster

21 Jul 2005

      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@millenia.cars.aps.anl.gov [mailto:ifeffit-
bounces@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  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?
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----------------------------------
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
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_______________________________________________
Ifeffit mailing list
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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