[Ifeffit] feff doesn't like cluster
Juraj Majzlan
juraj.majzlan at minpet.uni-freiburg.de
Thu Jul 21 10:13:42 CDT 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 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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