- Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 17
by madhusmita sahoo 22 Jun '14

22 Jun '14

Respected Dr. Bruce, I am looking forward to the updated version with the correction. Regards Madhusmita Regards Madhusmita Sahoo, SO/C,TFCS/SND/MSG(22171) Indira Gandhi Centre for Atomic Research, Kalpakkam, Tamilnadu On 21 June 2014 22:30, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: Ifeffit Digest, Vol 136, Issue 11 (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 20 Jun 2014 17:47:31 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 11 > Message-ID: <53A4ABF3.4070901(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Well, not only was the shift vector not working, it seems I had somehow > neglected to even implement it in Demeter! It's amazing what can go > unnoticed and for how long. > > This will be fixed in the next release. Thank you, Madhusmita, for > bringing this to my attention. > > B > > > On 06/18/2014 09:38 AM, Bruce Ravel wrote: > > On 06/18/2014 07:52 AM, madhusmita sahoo wrote: > >> 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) > > > > You seem to be asking about Atoms' use of the shift vector. > > Specifically, you seem to be asking whether the shift vector is > > working correctly. > > > > If so, that appears to be a legitimate question and the answer appears > > to be /no/. Sigh.... I will look into it and try to have that fixed > > in time for the next release. > > > > Cheers, > > B > > > > > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 136, Issue 17 > **************************************** >

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Re: [Ifeffit] Ifeffit Digest, Vol 136, Issue 11
by madhusmita sahoo 20 Jun '14

20 Jun '14

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(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: 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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Scattering paths in XANES calculations > Message-ID: <539A029E.4050609(a)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-sca… > > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)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(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)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(a)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(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 136, Issue 11 > **************************************** >

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Postdoctoral position in Yeshiva University and Brookhaven National Laboratory
by Anatoly I Frenkel 20 Jun '14

20 Jun '14

Dear subscribers, Please pass along this information to anyone who may be interested in this opportunity. Physics Department of Yeshiva University in New York City will have an opening for a postdoctoral research associate position, beginning September 2014. The project title is: "Characterization of structure, diffusion mechanism and optoelectronic properties of doped colloidal semiconductor nanocrystals." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II for X-ray spectroscopy and Center for Functional Nanomaterials for electron microscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods and their applications to nanomaterials, and experience with in situ characterization methods. Working knowledge of Raman spectroscopy is a plus. The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to Prof. Frenkel at anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

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Use of the 3rd and 4th Parameter
by Michael Kömm 16 Jun '14

16 Jun '14

Hello, I'm trying to make an EXAFS analysis on the Structure of Tb in a borogermanate glass System. The reference is an .cif of Terbium-Gallium-Garnet (TGG). I expect some disorder caused to working in glass. Therefore I would like to use the 3rd and/or the 4th parameter. I tried to set a guess parameter to evaluate those parameters. Could you tell me a reasonable value for these parameters? The 3rd only varies a little bit around its guessed value (+- 0.01) and if I try to do the same with the 4th parameter no fit at all takes place. The errors in the GDS-window are exactly 0.00000 with no fit taking place (enot = 0, amp = 0 (guess amp = 1) delr = 0 and ss = 0.003) and the R-factor of the fit is way over the top (>10^20). I've chosen a value of 0.5 for the 3rd and the 4th parameter just to see if they're working and I was only doing a quick first shell fit with the surrounding oxygen-shell. Please can somebody tell me how to deal with this problems. Thanks a lot for your time and efford. Sincerly yours, Michael Kömm

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Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Ah okay. I think now I get it. Is it correct that in the mu(E) spectrum you plot the total spectrum in blue and in red you chose different fms-radii like 2.5, 3.0, 4.1 to get the XANES spectrum for different shells? Or are the red curves another varied FEFF parameter? Thanks so much for your support! Stefanie

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Re: [Ifeffit] Scattering paths in XANES calculations
by Stefanie Roese 16 Jun '14

16 Jun '14

Dear Bruce, thanks for your answer! My problem is how to get the E/mu information for each single scattering path. If I get it right, the xmu.dat contains the sum of all scattering paths. This is the blue curve in your talk. But there are also the spetra for the first,s econd, third,... path at page 11 in red. I think the information comes from the feff0001.dat. feff0002.dat and so on. But these files do not contain mu! Or do I understand it wrong? I have no data to fit, just the FEFF calculations. Is there any possibility to get the XANES spectrum of all paths and the XANES spectrum of every single path to compare how the single paths influence the complete spectrum? Thanks! Stefanie

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Crystallographic input for a structure having screw axis and co-ordinates shifted by certain amount
by madhusmita sahoo 12 Jun '14

12 Jun '14

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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Scattering paths in XANES calculations
by Stefanie Roese 12 Jun '14

12 Jun '14

Dear all, I am performing XANES calculations for silver clusters with FEFF. Aditional to my XANES results, I would like to get information about the participating scattering paths and how they influence my spectra. In detail I want to get the same pictures that Bruce ravel used in his talk "a practical introduction to multiple scattering theory" from page 11. I have performed calculations for XANES using the rpath algorithm to obtain the feffnnnn.dat files. I already checked, that the course of the rpath spectra agrees to the fms calculations in ordner to make sure that the algorithm converged. 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. Thanks in advance for every help! Steffi

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Demeter on Mac OS X
by Juliana Fonseca de Lima 06 Jun '14

06 Jun '14

Hi all, I have used Athena on my Mac since last month, but from last week I have had the below problem to open the software. Could you help me to solve that? perl5.16(423,0x7fff75854310) malloc: *** mach_vm_map(size=18446744071562072064) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Out of memory! PS: I have 8 GB of physical memory. Cheers, Juliana

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Demeter-devel port added in Macports for OS X
by Schima, Frank 06 Jun '14

06 Jun '14

OS X Users, I have created a new port in Macports for demeter-devel based on the 0.9.20 version which is still in development. This has important fixes for the black window problem in Artemis. To install it, simply run the following commands in Terminal: sudo port selfupdate sudo port uninstall demeter sudo port install demeter-devel Feedback appreciated. I have only tested it on OS X 10.9.3 so far. Just keep in mind that the “devel” part means that this is not a release version and problems may exist. Cheers! Frank

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