[Ifeffit] 1. Re xanes feff8 sulfur

Sun Oct 21 13:59:19 CDT 2007

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:
>
>> Send Ifeffit mailing list submissions to
>> 	ifeffit at millenia.cars.aps.anl.gov
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> or, via email, send a message with subject or body 'help' to
>> 	ifeffit-request at millenia.cars.aps.anl.gov
>>
>> You can reach the person managing the list at
>> 	ifeffit-owner at millenia.cars.aps.anl.gov
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Ifeffit digest..."
>>
>>
>> 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 --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20071015/d1d34403/attachment-0001.html
>>
>> ------------------------------
>>
>> 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
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
>> End of Ifeffit Digest, Vol 56, Issue 11
>> ***************************************
>>_______________________________________________
> 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 für Röntgenphysik
Friedrich-Hund-Platz 1
37077 Göttingen
Germany