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

how to manage Demeter with a newer FEFF version ?
by M. Janeth LOZANO RODRIGUEZ 08 Jun '15

08 Jun '15

Dear XAFS community, I wondering about the availability to use a newer FEFF version in Demeter. Since my knowledge only I can run FEFF6. In my case I found different discrepancies using FEFF6 and FEFF9 in the determination of bond length distances for instance. In terms of review of papers, reviewers ask to use a newer version instead FEFF6. These points strongly suggest me coming back to the obsolete Athena/Artemis version. On this obsolete version, you can download the paths generated by FEFF8, FEFF9. This issue is really useful when we have access to FEFF 9, for example. Is there any option to implement this nice feature in Demeter? Does anyone have an idea how to do it? Kind regards Janeth Lozano

1 0

Re: [Ifeffit] Mn3O4 EXAFS fitting
by 이국승 02 Jun '15

02 Jun '15

3 2

Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 6
by Nidhi Tiwari 02 Jun '15

02 Jun '15

congratulations :) Give your Best *Nidhi Tiwari*, Junior Research Fellow, Atomic and Molecular Physics Division, Bhabha Atomic Research Center, Mumbai- 400085 On Mon, Jun 1, 2015 at 10:30 PM, <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: Create Atoms input with just coordinates (M Ferrier) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Jun 2015 18:04:40 +0200 > From: M Ferrier <mferrier(a)hotmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Create Atoms input with just coordinates > Message-ID: <DUB118-W1424A6BB66DA7BFA91C7C2DFB60(a)phx.gbl> > Content-Type: text/plain; charset="windows-1252" > > Thank you very much. It worked except that the feff calculation created > ipot 0 and 1 for the same atom (core atom) I just had to change the ipot > values in the text before running feff. But once done it did calculation > correctly I think. > > Maryline > > From: scalvin(a)sarahlawrence.edu > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Mon, 1 Jun 2015 10:53:36 -0400 > Subject: Re: [Ifeffit] Create Atoms input with just coordinates > > Hi Maryline, > Use a = b = c = 10, with alpha = beta = gamma = 90. Now enter the > coordinates from your simulation in units of angstroms/10 (which happens to > be nm). > ?Scott CalvinSarah Lawrence College > On Jun 1, 2015, at 10:43 AM, M Ferrier <mferrier(a)hotmail.com> wrote:Hi, > > I am trying to create an Atoms input file for actinium. Since not a lot is > known about this element we run some DT calculations. One molecule of Ac > acetate in a box surrounded by water. > I have the coordinate of each elements. I was told the symmetry was P1 (I > guess for the box) but unfortunately their is no symmetry in liquid and > thus we cannot input the cell parameters (distances a, b, c and angles > alpha, beta, gamma). I was wondering if their were a way to make Atoms run > to obtain the Feff calculations. Or we should use a different model with a > known solid? > > Thank you for your help > > Maryline Ferrier _______________________________________________Ifeffit > mailing listIfeffit@millenia.cars.aps.anl.govhttp:// > millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

1 0

Create Atoms input with just coordinates
by M Ferrier 01 Jun '15

01 Jun '15

Hi, I am trying to create an Atoms input file for actinium. Since not a lot is known about this element we run some DT calculations. One molecule of Ac acetate in a box surrounded by water. I have the coordinate of each elements. I was told the symmetry was P1 (I guess for the box) but unfortunately their is no symmetry in liquid and thus we cannot input the cell parameters (distances a, b, c and angles alpha, beta, gamma). I was wondering if their were a way to make Atoms run to obtain the Feff calculations. Or we should use a different model with a known solid? Thank you for your help Maryline Ferrier

4 5

low and negative ss2 and bug in the log file of fit history
by Raj kumar 01 Jun '15

01 Jun '15

Dear All, I am trying to fit the first shell FT of bulk YbVO4 (measured in dispersive EXAFS) with the reference YbVO4. The resultant SS2 value for the first shell is found to be low for wide k-range selection, whereas approaching negative for the relatively short k-range window. While approaching negative value (of ss2), i have tried to constraint the ss2 value using expression abs(ss). In that case, ss2 value is found to take value 0. Please help me to figure out the problem. Further i have found a small bug in the fit history window. After each fit, earlier data set in the log file of fit history is found to overwritten with the latest fitting parameters (like k range, dk, etc..). Here in my log file window, all fit data set contain the same data set value as like the last fit (fit9). Regards, Raj

2 1

Re: [Ifeffit] Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

1 0

Re: [Ifeffit] Mn3O4 EXAFS fitting
by fred.mosselmans＠diamond.ac.uk 01 Jun '15

01 Jun '15

Dear Kug-Seung Your main initial problem is you didn't understand the structure of Mn3O4. It is a spinel with two Mn sites one octahedral and one tetrahedral. You need to consider both sites to have a chance of fitting, and set multiplication factors on the relative amps in the ratio. It has 1/3 tetrahedral sites and 2/3 octahedral. You need to do the feff calculation twice with each site as the core atom. In the attached project I have done this. You then end up with a lot of paths so to try to restrict the no of variables I have made several of sigma squared to be the same. I am sure this model could be improved upon but I wanted to show you how to get going in fitting the structure. In theory as the Mn tetrahedral site and octahedral sites are different oxidations states they might (should) have different E0s as well but with a limited data range this gets hard to test properly. Best wishes Fred Mosselmans Message: 1 Date: Mon, 01 Jun 2015 15:59:40 +0900 From: ??? <lks3006(a)postech.ac.kr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Mn3O4 EXAFS fitting Message-ID: <1433141980110.23146.postech(a)postech.ac.kr> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150601/4ec…>

2 1

Re: [Ifeffit] _Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

1 0

Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 147, Issue 20
by Raj kumar 29 May '15

29 May '15

Hi Bruce, The comments are very helpful to assure my data processing and for future experiments. Yes, all measurements were obtained in Dispersive EXAFS mode. As for i know (at least until my preparation time) the bulk sample (first one) doesn't contain the Hf impurities. However, i will double check that point. Regards, Raj On Fri, May 29, 2015 at 7:00 PM, <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: Peak at short distance in FT - YbVO4 nanoparticles > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 29 May 2015 12:52:38 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Peak at short distance in FT - YbVO4 > nanoparticles > Message-ID: <55689956.8040302(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 05/29/2015 11:54 AM, Raj kumar wrote: > > Recently, i have performed EXAFS for YbVO4 bulk (prepared through > > sintering process) and nanoparticles (at room temperature). > > Nanoparticles were synthesized by co-precipitation technique and their > > EXAFS was measured by passing the prepared solution using peristaltic > > pump. After all subtraction (background and solvent), nanoparticles XAS > > data were recovered and processed for the fitting. After Fourier > > transform, it was observed that both nanoparticles posses an additional > > short peak (or shoulder) at about 1.2 A from bulk. Since the peak > > appears much closer to 1 A, i suspect this may due to artifact or bad > > background subtraction. Hence, i would like to know the way to eliminate > > this peak at short distance. > > Hi Raj, > > A few comments: > > 1. Your bulk sample (the first one in the list) may have a bit of Hf > in it it. It's hard to tell, but the mu(E) seems to be trending > upward right at the end of the data, which is the approximate edge > energy of Hf L3. I got a slightly better background removal by > changing the end of the spline range to 600. But this a minor > detail. The real story seems to be that .... > > 2. You data are pretty noisy. If you plot chi(R) out to 10 Angstroms > (which is, presumably, well beyond where you should expect to see > good signal in your data), you get a sense of how the level of > noise manifests itself in chi(R). To my eye, the peak/shoulder at > about 1.2 that you are asking about is of about the same size as > the level of noise in your data. > > You are asking how to get rid of a feature in the data that is > aesthetically unpleasing. I don't think that's the right question. > > Your data are what they are. Your data are noisy and measured over a > rather short energy range. That doesn't give you a lot of choices > about how aesthetically appealing you can make the Fourier transform > be. > > You seem to be operating Athena correctly and there aren't any magic > buttons that will make your short, noisy data longer or less noisy. I > don't see anything obviously wrong in how you are processing your data > and -- short of using PhotoShop ;) -- I don't see any defensible way of > making the feature at 1.2 go away. > > > > Am I correct in thinking that these data are measured in the > dispersive geometry? If so, my suggestion is to reconsider how you > make your samples. This kind of experiment is VERY sensitive to the > homogeneity of the sample. You have to take extraordinary care to make > your samples as homogeneous as possible. I suspect most of the > glitchy little points in your data are indicative of sample > inhomogeneity. > > You also should worry about purity of your source material. Granted, > it canbe very difficult to obtain rare earth metal samples that are > elementally pure. But if your data range is short because of other > edges, then you need samples that are more pure. > > HTH, > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 147, Issue 20 > **************************************** >

1 0