RE: [Ifeffit] feff doesn't like cluster

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@millenia.cars.aps.anl.gov [mailto:ifeffit- bounces@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:

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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:

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Juraj,

Please post the feff.inp file. You might also send the atoms.inp file.

-Matt

On Thu, 21 Jul 2005, Juraj Majzlan wrote:

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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 _______________________________________________ Ifeffit mailing list Ifeffit@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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