[Ifeffit] Ifeffit Digest, Vol 136, Issue 11
madhusmita sahoo
krushna.chem at gmail.com
Wed Jun 18 06:52:44 CDT 2014
Contd- Crystallographic input for a structure having screw axis and
co-ordinates shifted by certain amount
Dear sir,
herewith I am attaching two input files. The first one with the name
wyckoff .inp generates The first co-ordination sphere at 1.9465 angstrom
with degenracy of 6.
According to crystal structure data anatase structure should have 4 oxygens
at 1.9339 angstrom and 2 oxygens at 1.9796 angstrom.
So, I tried with the crystal input from the latest PDF-4+2013
database(attaching the PDF as word file for your ref.
That ( inp file - attached)eventually generates the required co-ordination
sphere with 4 oxygen at 1.3964( as against the XRD data of 1.9339) and 2
oxygen at 1.8925(aginst the XRD data from PDf-4+2013 of 1.9796 angstrom)
Regards
Madhusmita Sahoo,
SO/C,TFCS/SND/MSG(22171)
Indira Gandhi Centre for Atomic Research,
Kalpakkam, Tamilnadu
On 13 June 2014 22:30, <ifeffit-request at millenia.cars.aps.anl.gov> wrote:
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> Today's Topics:
>
> 1. Re: Scattering paths in XANES calculations (Bruce Ravel)
> 2. Re: Crystallographic input for a structure having screw axis
> and co-ordinates shifted by certain amount (Bruce Ravel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Jun 2014 15:42:22 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Scattering paths in XANES calculations
> Message-ID: <539A029E.4050609 at bnl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 06/12/2014 10:07 AM, Stefanie Roese wrote:
> > But now I fail at getting the plots with the Energy at the x-axis and
> > the normailzed mu at the y-axis likle Bruce did it in his talk. Which
> > program was used there? Athena? And how can I get the
> > energy/mu-information out of my feffnnn.dat files to compare to the
> > total spectrum? I think I am quite close to the solution, but it does
> > not work.
>
> Stefanie,
>
> The R-space figures were made using Artemis. I fit the Fe foil data
> using the version of Feff6 that comes with Artemis, then plotted the
> data and the path relevant to each slide.
>
> The energy plots were made using Athena back in the early days of Feff8
> (which were also the early days of Athena!). The plots show Fe foil
> data and (if I remember correctly) column 4 of the xmu.dat file that was
> one of the output files from Feff of that vintage. I imported the data
> and the xmu.dat file into Athena to make those plots. The calculation
> is offset downwards a bit using the y-axis offset in Athena.
>
> To answer Matthew's question: interesting? Not sure I'd go that far...!
> Here's the link:
>
>
>
> https://speakerdeck.com/bruceravel/a-practical-introduction-to-multiple-scattering-theory
>
> B
>
>
>
> --
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
>
> Homepage: http://xafs.org/BruceRavel
> Software: https://github.com/bruceravel
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 12 Jun 2014 15:49:56 -0400
> From: Bruce Ravel <bravel at bnl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Crystallographic input for a structure having
> screw axis and co-ordinates shifted by certain amount
> Message-ID: <539A0464.1090102 at bnl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Madhusmita,
>
> Regarding the first question, I am not clear what the problem is. I
> grabbed the crystal data for anatase from Matt's website:
>
> http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp
>
> and imported it into Artemis. I certainly don't know what the
> interatomic distances for anatase should be off the top of my head, but
> what Atoms produced from that input data certainly seems reasonable. If
> you think there is a problem, you are going to need to explain it in a
> way that I can reproduce easily on my own computer.
>
> Regarding the second question, the vector specified in the box labeled
> "Shift vector" will be added to each site *before* any calculation is made.
>
> B
>
> On 06/12/2014 01:45 AM, madhusmita sahoo wrote:
> > Dear Members,
> >
> > I would like to know,
> >
> > *Q1)* If there is a screw axis in the system, like the anatase phase of
> > TiO2, whose space group is I41/amd, how should I enter that in the
> > atoms for feff calculation. Kindly tell me which is the correct way.
> >
> > When I entered 141(the space group number) and I41/amd, both generated
> > separate set of atomic positions.
> >
> > The older version of artemis, now the new one(latest version), both
> > generates different set of atomic position with the same
> > crystallographic input, i.e if I enter 141(or I41/amd) in place of space
> > group and run atoms, it generates two different set of co-ordinates in
> > Artemis 0.8.012 and in Demeter 0.9.18. Ideally this should be same.
> >
> > *Q2)* And when co-ordinates is shifted by certain amount, do we have to
> > enter that in the shift vector as well as while defining the (x y z)
> > of a particular site. Or I should just enter the shift vector and
> > define the co-ordinates at its usual position ( I feel this one is
> > correct).
> >
> > For example in anatase crystal structure the co-ordinates are shifted
> > by (0,0.25,-0.125).
> >
> > So, the inputs can be
> >
> > For shift vector 0,0.25,-0.125 and in place of sites Ti(core) x=0, y=0,
> > z= 0 and O (scatterer) x= 0, y=0, z=0.20806
> >
> > (Or) shift vector 0,0,0 and in place of sites Ti(core) x=0, y=0.25, z=
> > -0.125 and O (scatterer) x= 0, y=0.25, z=0.08160 Ideally
> >
> > both should give the same result. But it gives different set of atomic
> > positions.
> >
> > Even the same input in different version of artemis is yielding
> > different results(in Artemis 0.8.012 and in Demeter 0.9.18) .
> >
> > I am confused about how atoms work in artemis. I request you to
> > elucidate the correct method.
> >
> > Warm wishes
> >
> > Madhusmita
> >
> > India
> >
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
>
>
> --
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
> Building 535A
> Upton NY, 11973
>
> Homepage: http://xafs.org/BruceRavel
> Software: https://github.com/bruceravel
>
>
> ------------------------------
>
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>
> End of Ifeffit Digest, Vol 136, Issue 11
> ****************************************
>
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