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, 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)

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Message: 1 Date: Thu, 12 Jun 2014 15:42:22 -0400 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Scattering paths in XANES calculations Message-ID: <539A029E.4050609@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-scat...

B

-- Bruce Ravel ------------------------------------ bravel@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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Message: 2 Date: Thu, 12 Jun 2014 15:49:56 -0400 From: Bruce Ravel To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Crystallographic input for a structure having screw axis and co-ordinates shifted by certain amount Message-ID: <539A0464.1090102@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

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-- Bruce Ravel ------------------------------------ bravel@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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