[Ifeffit] 1. Re xanes feff8 sulfur pyrite

Fri Oct 26 09:05:15 CDT 2007

Hi Josh,

i have made two calculations respectively pyrite. You can see the results
in the postscript file. The first (A) plot is from your pyrite.dat, the
second plot is based on your feff.inp but recalculated on my Computer. The
last (C) plot is based on my own crystallographic data (spacegroup p 2_1
/a -3) and feff.inp (attached as eck-feff.inp) file, maybe the same
crystallographic data you used? With my feff.inp i can approve all of your
atom-positions with the exception of atom 11 in your list respectively
atom Fe3 in my list. But the results in the diagramm are nearly the same.
The third file (feff.inp) is again your feff.inp file you sent to me.

>Hi Josh,
>
>thanks for your help and attached files. I will test your feff.inp files
>and compare the results.
>
>cheers,
>Eckhard
>

> Hi Eckhard,
> Try the attatched feff.inp files (gypsum.inp and pyrite.inp).
> I find that these produce different spectra with edges at
>  	~2468.5 - gypsum
>  	~2469.0 - pyrite
>
> If you use do not get the same results, then there is something wrong
with the code and we will have some debugging to do.
>
> Also, if there are multiple sulfur sites in the material which have
different local structure, you will
> need to do a configurational average by running with each site as the
absorbing atom and averaging the signals.
> Cheers,
> Josh
>
> P.S.
> I am also sending the result (gypsum.dat and pyrite.dat) so that you can
compare.
>
>
> On Tue, 16 Oct 2007, ifeffit-request at millenia.cars.aps.anl.gov wrote:
>
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>> Today's Topics:
>>
>>   1. Re xanes feff8 sulfur (Kelly, Shelly D.)
>>   2. Re: Re xanes feff8 sulfur (s440697 at stud.uni-goettingen.de)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 15 Oct 2007 15:18:14 -0500
>> From: "Kelly, Shelly D." <SKelly at anl.gov>
>> Subject: [Ifeffit] Re xanes feff8 sulfur
>> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Cc: "John J. Rehr" <jjr at leonardo.phys.washington.edu>,	John Katsoudas
>> 	<katsoudas at agni.phys.iit.edu>
>> Message-ID:
>> 	<0BC5625B1BD9494886EBA2F3CF10E957012C1C90 at BIOPOST.bio.anl.gov>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hi Eckard,
>>
>>
>>
>> I realize that you have posted a message every month for about 3 months
in a row without any reply:  Shame on us... I will try to answer some
of your questions and maybe that will help to get some discussion
going. The energy scale in feff8 is NOT defined as you would expect it
to be for determining the absolute energy of an edge.  The energy scale
in FEFF8 is related to the difference between the energy level of the
intersist (potential level inbetween the muffin tins that represent
atoms) and the threshold energy level for the excitation of the
electron.
>>
>>
>>
>> I realize that this doesn't solve your problem, but hopefully it will
spark some discussion.
>>
>>
>>
>> Cheers,
>>
>> Shelly
>>
>>
>>
>>
>> Mon Aug 13 06:00:19 CDT 2007
>> Does anybody know a person, who has experience respective the topics
xanes+feff8 and sulfur K-Edges?
>> I would be very thankful for an answer :-)
>>
>> sincerely yours,
>> Eckhard Bosman
>>
>>
>>
>>
>> Tue Jul 10 10:07:38 CDT 2007
>>
>> Hello,
>>
>> i have problems with feff-xanes calculations related to pyrite. I try
to get the k-edge of sulfur (as absorber) in FeS2. I get the edge at
~2472 eV
>> and i think this is wrong because i get the same energy with gypsum and i
>> think there should be an energyshift related to 2472 eV. My proceeding is
>> as follows:
>>
>> calculate the atomic positions with the asymetric unit from the
http://rruff.geo.arizona.edu/AMS/amcsd.php database (Pyrite spacegroup
Pa3) respectively
>> http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00596.cif
>> with "powdercell 2.4"
>>
>> feffrun with the feff.inp-file like in the attachment
>> (thanks to Josh Kas for his feff-hints)
>>
>> I started the feff-run on the one hand with 12 atoms (unitcell) and on the
>> other hand with 22 atoms (14x Fe and 8x S in the cube)
>>
>> After this i plotted from xmu.dat the absorbtion mu (column 4) as a
function of the energy (column 1). The result is in the attachment too.
>>
>> I don't know why i get everytime the Sulfur-k-edge at the same position
(for pyrite or gypsum) respectively without energyshift related to 2472
eV.
>>
>> many thanks for your help :-)
>> Ciao,
>> Eckhard
>>
>>
>>
>> Fri Jun 15 08:48:21 CDT 2007
>>
>> Hallo @all,
>>
>> (first at all, sorry for my bad english)
>>
>> i'm a student working on my diploma thesis (nexafs/xanes) and my job is to
>> simulate with FEFF 8.4 spectra, for example absorption as a function of
energy (mu_(E)). I'm a newbie in this topic and i tried to get the
k-edge
>> of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2). I'm
>> interested in the XANES-range of the spectra not the EXAFS. I get
everytime my peaks at ~2472 eV for Sulfur as absorber whatever
substance i
>> use (gypsum, pyrite,...). There are no differences with the peak position
>> on the energy-scale or shifts. I'm really confused :-( I think, there
should be differences in the spectra... I send you two feff.inp files
from
>> my feff-runs. My source is the mineralogy database
>> (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for the
>> unitcell. Then i put the data in the XtalDraw program to get the positions
>> of the Atoms in Angstrom, by the way i get i nice 3D-View of the unitcell
>> :-). Then i put the values of the positions into feff...
>> I simulated pyrite with 12 atoms and gypsum with 48.
>> I'm appreciative for every help :-)
>>
>> ciao,
>> Eckhard
>>
>>
>>
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 16 Oct 2007 11:17:11 +0200 (CEST)
>> From: s440697 at stud.uni-goettingen.de
>> Subject: Re: [Ifeffit] Re xanes feff8 sulfur
>> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Message-ID:
>> 	<45622.134.76.41.165.1192526231.squirrel at webmail.stud.uni-goettingen.de>
>>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> Hi Shelly,
>>
>> this is no problem with the late answer. Thanks for your hint. I will talk
>> about this with my boss for further proceeding.
>>
>> cheers,
>> Eckhard
>>
>>
>>> Hi Eckard,
>>>
>>>
>>>
>>> I realize that you have posted a message every month for about 3
months in a row without any reply:  Shame on us... I will try to
answer some of
>>> your questions and maybe that will help to get some discussion going.
The energy scale in feff8 is NOT defined as you would expect it to be
for determining the absolute energy of an edge.  The energy scale in
FEFF8 is related to the difference between the energy level of the
intersist (potential level inbetween the muffin tins that represent
atoms) and the threshold energy level for the excitation of the
electron.
>>>
>>>
>>>
>>> I realize that this doesn't solve your problem, but hopefully it will
spark some discussion.
>>>
>>>
>>>
>>> Cheers,
>>>
>>> Shelly
>>>
>>>
>>>
>>>
>>> Mon Aug 13 06:00:19 CDT 2007
>>> Does anybody know a person, who has experience respective the topics
xanes+feff8 and sulfur K-Edges?
>>> I would be very thankful for an answer :-)
>>>
>>> sincerely yours,
>>> Eckhard Bosman
>>>
>>>
>>>
>>>
>>> Tue Jul 10 10:07:38 CDT 2007
>>>
>>> Hello,
>>>
>>> i have problems with feff-xanes calculations related to pyrite. I try to
>>> get the k-edge of sulfur (as absorber) in FeS2. I get the edge at
~2472 eV
>>> and i think this is wrong because i get the same energy with gypsum and i
>>> think there should be an energyshift related to 2472 eV. My proceeding is
>>> as follows:
>>>
>>> calculate the atomic positions with the asymetric unit from the
http://rruff.geo.arizona.edu/AMS/amcsd.php database (Pyrite spacegroup
Pa3) respectively
>>> http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00596.cif
>>> with "powdercell 2.4"
>>>
>>> feffrun with the feff.inp-file like in the attachment
>>> (thanks to Josh Kas for his feff-hints)
>>>
>>> I started the feff-run on the one hand with 12 atoms (unitcell) and on
the
>>> other hand with 22 atoms (14x Fe and 8x S in the cube)
>>>
>>> After this i plotted from xmu.dat the absorbtion mu (column 4) as a
function of the energy (column 1). The result is in the attachment
too.
>>>
>>> I don't know why i get everytime the Sulfur-k-edge at the same
position (for pyrite or gypsum) respectively without energyshift
related to 2472 eV.
>>>
>>> many thanks for your help :-)
>>> Ciao,
>>> Eckhard
>>>
>>>
>>>
>>> Fri Jun 15 08:48:21 CDT 2007
>>>
>>> Hallo @all,
>>>
>>> (first at all, sorry for my bad english)
>>>
>>> i'm a student working on my diploma thesis (nexafs/xanes) and my job
is to
>>> simulate with FEFF 8.4 spectra, for example absorption as a function
of energy (mu_(E)). I'm a newbie in this topic and i tried to get the
k-edge
>>> of Sulfur for the substance gypsum (CaSO4 * 2(H2O)) and pyrite (FeS2).
I'm
>>> interested in the XANES-range of the spectra not the EXAFS. I get
everytime my peaks at ~2472 eV for Sulfur as absorber whatever
substance
>>> i
>>> use (gypsum, pyrite,...). There are no differences with the peak position
>>> on the energy-scale or shifts. I'm really confused :-( I think, there
should be differences in the spectra... I send you two feff.inp files
from
>>> my feff-runs. My source is the mineralogy database
>>> (http://rruff.geo.arizona.edu/AMS/amcsd.php) where i get the data for the
>>> unitcell. Then i put the data in the XtalDraw program to get the
positions
>>> of the Atoms in Angstrom, by the way i get i nice 3D-View of the unitcell
>>> :-). Then i put the values of the positions into feff...
>>> I simulated pyrite with 12 atoms and gypsum with 48.
>>> I'm appreciative for every help :-)
>>>
>>> ciao,
>>> Eckhard
>>>
>>>
>>>
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>
>>
>>
>> ---------------------------------
>> Eckhard Bosman
>> e.bosman at stud.uni-goettingen.de
>> +49 (0)551-39-14441
>> Raum: E0.104
>> Institut f?r R?ntgenphysik
>> Friedrich-Hund-Platz 1
>> 37077 G?ttingen
>> Germany
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
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>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
>> End of Ifeffit Digest, Vol 56, Issue 11
>> ***************************************
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---------------------------------
Eckhard Bosman
e.bosman at stud.uni-goettingen.de
+49 (0)551-39-14441
Raum: E0.104
Institut für Röntgenphysik
Friedrich-Hund-Platz 1
37077 Göttingen
Germany

---------------------------------
Eckhard Bosman
e.bosman at stud.uni-goettingen.de
+49 (0)551-39-14441
Raum: E0.104
Institut für Röntgenphysik
Friedrich-Hund-Platz 1
37077 Göttingen
Germany
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