[Ifeffit] Postdoctoral position at Yeshiva University

2011-08-03 Thread Frenkel, Anatoly
Dear IFEFFIT subscribers: Please find here the info about the job opening: Postdoctoral position at Yeshiva University Physics Department of Yeshiva University in New York City has immediate opening for a postdoctoral research associate position. The postdoc will investigate thermal,

Re: [Ifeffit] Athena (Question about LC fitting)

2011-05-15 Thread Frenkel, Anatoly
I meant fit the standards to the unknown, and I also noticed that Bruce had already replied to the same question below. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly Sent: Sun 5/15/2011 2:34 PM To: XAFS Analysis using

Re: [Ifeffit] What does FEFF stand for?

2011-05-10 Thread Frenkel, Anatoly
You are both mistaken, but do not check what FEFF is on Urban Dictionary, as it is inappropriate. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Ravel, Bruce Sent: Tue 5/10/2011 3:16 PM To: XAFS Analysis using Ifeffit Subject: Re:

Re: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS fromMD simulations

2011-04-11 Thread Frenkel, Anatoly
The answer depends, really, on what you want to accomplish. There are several approaches: 1. Full atom-by-atom calculations of EXAFS following an MD trajectory: Riscioni, et al, PRB 83, 115409 (2011). This is required if you have disordered clusters, for example, and your electronic

Re: [Ifeffit] Fe in glassy ceramics

2011-02-16 Thread Frenkel, Anatoly
Diffraction anomalous fine structure seems to the most appropriate method here. Anatoly Frenkel Sent from my mobile phone, please forgive typos. -Original message- From: Andrei Shiryaev a_shiry...@mail.ru To: ifeffit@millenia.cars.aps.anl.gov Sent: Wed, Feb 16, 2011 12:52:38

Re: [Ifeffit] Distortion of transmission spectra due to particlesize

2010-11-24 Thread Frenkel, Anatoly
Jeremy: In your simulation, (c) 1/2 original, 1/2 nothing (a large pinhole) it appears that chi(k) is half intensity of the original spectrum. Does it mean that when the pinhole is present, EXAFS wiggles are half of the original ones in amplitude but the edge step remains the same? Or,

Re: [Ifeffit] Distortion of transmission spectra due to particlesize

2010-11-24 Thread Frenkel, Anatoly
You are right about the amplitude factor: it should change. The ln(1+x/2) is not the full story, since x is the exponent: x= exp(-mu*t) and when mu*t is small (thin samples), x is not, and vice versa. More accurate expansion of ln(1+x/2) in the limit of thick and thin samples shows that

Re: [Ifeffit] Transmission EXAFS sample

2010-11-19 Thread Frenkel, Anatoly
That's probably how they discovered graphene, by trying to make exafs sample. Anatoly Sent from my mobile phone, please forgive typos. -Original message- From: Scott Calvin dr.scott.cal...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Fri, Nov 19,

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-24 Thread Frenkel, Anatoly
Scott, It is a strange result. Suppose you fit a bulk metal foil and vary the 1nn coordination number. You will not get 12 +/- 1000. You will get about 12 +/- 0.3 depending on the data quality and the k range, and on the amplitude factor you fix constant. Then, suppose you take your formula for

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-22 Thread Frenkel, Anatoly
On a related subject, now I understand why we use the concept of chemical transferability of amplitudes and phases by recycling the same FEFF path for different systems. The true reason is historic: back then it took one hour for one FEFF calculation Anatoly

Re: [Ifeffit] Asymmetric error bars in IFeffit

2010-10-22 Thread Frenkel, Anatoly
, for instance trying to change Al for Au or an oxide for a metal. Brings back memories, not all of them fond :-) mam - Original Message - From: Frenkel, Anatoly mailto:fren...@bnl.gov To: ifeffit@millenia.cars.aps.anl.gov Sent: Friday, October 22, 2010 2:38 PM

Re: [Ifeffit] Multiple scattering paths in fitting

2010-10-07 Thread Frenkel, Anatoly
For bond angles, this google search would be helpful: buckling angle multiple scattering xafs Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Abhijeet Gaur Sent: Thu 10/7/2010 3:21 AM To: ifeffit Subject: [Ifeffit] Multiple scattering

Re: [Ifeffit] Multiple scattering paths in fitting

2010-10-07 Thread Frenkel, Anatoly
For relationships between sigma2 for MS and SS paths, some are listed in the Appendix to this article: P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). Anatoly winmail.dat___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28

2010-09-30 Thread Frenkel, Anatoly
It is because you made delta E0=0, but the fit gave you delta E0=8. Since the fit agrees with the data in k-space at low wavenumbers (I assume), then the signal with delta E0=0 should not, and vice versa. Anatoly From:

Re: [Ifeffit] debye function

2010-08-24 Thread Frenkel, Anatoly
Just to add: These procedures, described in that article, can be easily implemented in Mathematica. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Ravel, Bruce Sent: Tue 8/24/2010 1:23 PM To: XAFS Analysis using Ifeffit Subject: Re:

Re: [Ifeffit] Haha

2010-08-15 Thread Frenkel, Anatoly
And for the red curve, someone forgot the sample... Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Heinz-Eberhard Mahnke Sent: Sun 8/15/2010 12:04 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Haha Hi, nice spectrum. Why is

Re: [Ifeffit] fitting

2010-05-13 Thread Frenkel, Anatoly
There is a large number of articles explaining how to fit CeO2 including discussions why multi-electron excitatoins complicate the fit, and some of those authors (e.g., A. Soldatov, but also M. Benfatto) propose first principle methods that account for those. Some papers even show that ignoring

Re: [Ifeffit] fitting

2010-05-13 Thread Frenkel, Anatoly
, but...for me there is something wrong since the Athena fitting, because there are too many peaks below the main one, and specially below 1 A. Am I right or not? Maria Elena 2010/5/13 Frenkel, Anatoly fren...@bnl.gov There is a large number of articles explaining how to fit CeO2

Re: [Ifeffit] Debye model on Artemis

2010-05-12 Thread Frenkel, Anatoly
Kleber, Correlated Debye Model (CDM) was proposed by Sevillano, Meuth and Rehr in 1979 in a Phys Rev B artcile. It also shows how to find sigma2(T) from the CDM- and also from Einsten model, by the way. In the former case, you take phonon density of states in Debye approximation (where it is

Re: [Ifeffit] Differences between fluorescence and transmission of thesame sample

2010-05-05 Thread Frenkel, Anatoly
What can be done in this case, is not to use either flourescence or transmission data, - because both are bad by the reasons Bruce explained - but use corrections, if you cannot change your experimental geometry (different concentration of the sample or different thickness or different reactor

Re: [Ifeffit] energy resolution

2010-05-05 Thread Frenkel, Anatoly
This is a quote from Joseph Dvorak' report on energy resolution measurements at the NSLS beamlines: The energy resolution was measured as follows. A Si 220 crystal was used as an analyzer crystal. This was placed in the hutch in near back reflection condition (87 deg inc). The reflected

Re: [Ifeffit] Logicused in Artemis to do the error minimization

2010-03-08 Thread Frenkel, Anatoly
Bruce, Some time ago I was trying to find a reference (and failed) explaining the relationship between the error bar reported by the fitting algorithm of ifeffit and one standard deviation in the fitting parameter. From your reply below it appears that they are the same (error bars reported

Re: [Ifeffit] Logicused in Artemis to do the error minimization

2010-03-08 Thread Frenkel, Anatoly
I meant that error bars are related to standard deviations of the mean, not standard deviations... Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly Sent: Mon 3/8/2010 9:25 AM To: XAFS Analysis using Ifeffit Subject: Re

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Frenkel, Anatoly
I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but the method can be used with Artemis, of course. A. I. Frenkel, M. Vairavamurthy, and M. Newville, A study of the coordination environment in aqueous cadmium-thiol

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Frenkel, Anatoly
and phase. You feed it amp and phases which come from the FT program, also available at the website. The amp and phase files are simple 2-column ASCII, thus readable anywhere. mam - Original Message - From: Frenkel, Anatoly fren...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit

Re: [Ifeffit] Fitting using Experimental standard

2010-01-04 Thread Frenkel, Anatoly
- From: Frenkel, Anatoly mailto:fren...@bnl.gov To: ifeffit@millenia.cars.aps.anl.gov Sent: Monday, January 04, 2010 7:43 PM Subject: Re: [Ifeffit] Fitting using Experimental standard Thank you, Matthew. As they say in Russia, everything new

Re: [Ifeffit] Lattice parameters: EXAFS vs. XRD

2009-12-30 Thread Frenkel, Anatoly
A correction to Matt's email: In random alloys, smaller size atoms and larger size atoms are at different average distances (measured by EXAFS and other local-structure-sensitive techniques, e.g., XRD/PDF) that are, respectively, smaller and larger than the distance between the average lattice

Re: [Ifeffit] Lattice parameters: EXAFS vs. XRD

2009-12-25 Thread Frenkel, Anatoly
Big deal... We have final exams on Christmas... Anatoly Frenkel Yeshiva University From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Scott Calvin Sent: Fri 12/25/2009 1:04 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Lattice parameters:

Re: [Ifeffit] Path degeneracy modification in feffNNN.dat

2009-11-20 Thread Frenkel, Anatoly
It takes it from N. Anatoly - Original Message - From: ifeffit-boun...@millenia.cars.aps.anl.gov ifeffit-boun...@millenia.cars.aps.anl.gov To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Fri Nov 20 18:57:29 2009 Subject: Re: [Ifeffit] Path degeneracy

Re: [Ifeffit] Bug in Athena?

2009-11-19 Thread Frenkel, Anatoly
Yay! Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Matt Newville Sent: Thu 11/19/2009 2:59 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Bug in Athena? Hi Scott On Thu, Nov 19, 2009 at 9:50 AM, Scott

Re: [Ifeffit] modeling anti-site disorder

2009-11-08 Thread Frenkel, Anatoly
I would make a feff.inp file corresponding to the Co as a central atom in CoGa in its original CsCl structure. Then, I would substitute all Ga atoms by Co (the two sites are crystallographically equivalent in the bcc lattice, and there is no need to do it separately for Cs and Cl sites). That

Re: [Ifeffit] modeling anti-site disorder

2009-11-08 Thread Frenkel, Anatoly
another contraint, e.g., a known value of site occupancy of Ga (i.e., y = 0.2). Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly Sent: Sun 11/8/2009 12:15 PM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] modeling anti

Re: [Ifeffit] new release of my software

2009-07-01 Thread Frenkel, Anatoly
It is when you take a bug from a pot and then put it back in the pot. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Julie Olmsted Cross Sent: Wed 7/1/2009 4:47 PM To: Ravel, Bruce; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] new

Re: [Ifeffit] problem with E0 (enot) parameters

2009-06-19 Thread Frenkel, Anatoly
Just a comment, to add some sanity in this discussion: FEFF6 is overestimating delta E0 for Pt and a few other metals. I forgot the reason but it could be the cause of a problem. I think FEFF8 is doing a better job. Fortunately - and it was checked - no other problems occur, just E0 values

Re: [Ifeffit] Multiple data set fit

2009-04-17 Thread Frenkel, Anatoly
I don't think there is much published on that, so it is worth trying and see what you get. Anatoly -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov]on Behalf Of Debora Meira Sent: Friday, April 17, 2009 10:23 AM To:

Re: [Ifeffit] huge S02 value ??

2009-04-05 Thread Frenkel, Anatoly
Hi Mengqiang, I have done fits of aqueous solution of NiSO4 before and obtained S02 of 0.8 for the octahedrally coordinated Ni-O shell. You did not send the mu(E) data, just chi(k), so I was not able to compare my and your raw data fully, just in k-space. Here is what I found: my data is in

Re: [Ifeffit] Mixed Multiple scattering shell

2009-04-01 Thread Frenkel, Anatoly
Could be helpful: RbBr, KBr, RbCl, AgBr(x)Cl(1-x) etc.l: A. Frenkel, E. A. Stern, M. Qian, and M. Newville, Multiple - scattering x-ray-absorption fine-structure analysis and thermal expansion of alkali halides, Phys. Rev. B 48 , 12449 (1993). A. Frenkel, E. A. Stern, A. Voronel, M. Qian,

Re: [Ifeffit] (no subject)

2009-03-11 Thread Frenkel, Anatoly
I would like to be proven wrong but my feeling is, without even knowing anything about this particular system, that one cannot observe Fe-Fe pair at that distance in such complex case. However, to approach it more rigorously, the first step would be to examine the relative importance factors

Re: [Ifeffit] Lost second shell

2009-02-01 Thread Frenkel, Anatoly
Eugenio, The possibilities depend on the actual data at hand. Not seeing second shell is a relative term. Do you mean that you do not see it above noise? Then, technically, you cannot say that you do not have a second shell. Er may substitute for Zn and you will still have Er-Zn

Re: [Ifeffit] small-screen version of Athena document

2009-01-26 Thread Frenkel, Anatoly
Bruce and Matt: When Athena and Artemis are completely moved to BlackBerry and iPhone, there will be a number of really nice options out there. For example, ringtones for a really bad fit should be made very unpleasant, and even more so, when Delta E0 is out of bounds, or r-factor is greater

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Frenkel, Anatoly
Hi Scott, Third cumulant in your example will not be zero because this arrangement is symmetric only on the average. Locally, the interatomic pair potential (and the cumulants are the measures of the effective pair potential) which is the sum of the two potentials - between the interestitial

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Frenkel, Anatoly
a histogram approach in the Ifeffit world, and modeled somewhat after The GNXAS Approach) has been used successfully a number of times. --Matt On Jan 21, 2009, at 10:12 AM, Frenkel, Anatoly wrote: Hi Scott, Third cumulant in your example will not be zero because this arrangement

Re: [Ifeffit] Cumulant expansion fittings

2009-01-21 Thread Frenkel, Anatoly
that the fourth cumulant alone is not enough. --Scott Calvin Sarah Lawrence College On Jan 21, 2009, at 10:11 PM, Frenkel, Anatoly wrote: Thus, I am pretty much convinced, unless there is some mistake in my reasoning, that no case exists in 3D with a zero third cumulant

Re: [Ifeffit] difference between Zn-Zn/Fe and Zn-Fe paths

2009-01-16 Thread Frenkel, Anatoly
Hashem, it is not very clear, give mode details for each fitting scheme. Anatoly -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov]on Behalf Of Hashem Stietiya Sent: Friday, January 16, 2009 12:13 PM To:

Re: [Ifeffit] How to identify N and O atoms in the first coordinate

2008-12-19 Thread Frenkel, Anatoly
Dear Mengqiang, To the best of my knowledge, in most cases Nitrogen cannot be discerned from Oxygen as a nearest neighbor since their scattering properties are similar. Thus, if you want to solve an inverse problem (Which type of neighbors do I have) you cannot do it. However, if you believe

Re: [Ifeffit] Normalization of XANES spectra

2008-10-29 Thread Frenkel, Anatoly
Jens: This example may help you understand your problem: if compound a) has a small fraction of metal Cu mixed with a large fraction of oxidized Cu, while a compound b) has it the other way around, then the main (1s - 4p) absorption peak in compound a) will be smaller than in b) after edge

Re: [Ifeffit] Fit XANES spectra using Athena

2008-10-26 Thread Frenkel, Anatoly
PCA works only if there are series of spectra with change in the makeup of S species, not for a single spectrum. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Sun Oct 26 13:05:32

Re: [Ifeffit] Comparison of amp between Feff8.40 and feff6 - Curved waves or Plane waves?

2008-08-29 Thread Frenkel, Anatoly
By looking at the FEFF.inp file it appears that the path in question is a Ti-O-Ti where the angle of this linkage is very close to 180 degree (had it been 180 degree, the total length would be not 3.9317 but either 3.90500 or 4.15600. In a perovskite with Ti on center such angle would be 180

Re: [Ifeffit] questions concerning paper

2008-05-22 Thread Frenkel, Anatoly
We should ask John Rehr to rename FEFF to Odysseus. It makes both physical and mythological sense. Anatoly - Original Message - From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: Ravel, Bruce; XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Sent: Thu May 22 14:30:38 2008

Re: [Ifeffit] Using the amplitude reduction factor as a linearcombination fitting parameter

2008-04-29 Thread Frenkel, Anatoly
There are a few points in your description that puzzle me. Have you collected not one but a series of spectra where some external condition (e.g., temperature, concentration, time, pH etc) were varied? If not, PCA cannot be used if only one spectrum was collected containing a mixture of two

Re: [Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter

2008-04-29 Thread Frenkel, Anatoly
An option could be, if you collected just one spectrum, to construct 1st shell EXAFS data for each compound using FEFF and use a linear combination option of Athena to see if there is any value of the mixing fraction of these two theoretical compounds that resemble good fit. You will still need

Re: [Ifeffit] cofe2o4 chi data

2008-01-14 Thread Frenkel, Anatoly
I have it. Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Tai-Yen Chen Sent: Monday, January 14, 2008 12:27 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] cofe2o4 chi data Dear all Does anyone have cofe2o4 chi data by anychance or know

Re: [Ifeffit] Log-Ratio

2007-12-05 Thread Frenkel, Anatoly
It adds (or subtracts) 2pi to the phase difference between the unkown and the standard as some times it does not eztrapolate to zero as 2k*delta r term should. Anatoly -Original Message- From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov

Re: [Ifeffit] Exafs distance resolution

2007-11-27 Thread Frenkel, Anatoly
Yes and a very important one - see Ed Stern's talk at the 2001 EXAFS workshop advanced methods and tricks etc. His talk is online. Anatoly -Original Message- From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: ifeffit@millenia.cars.aps.anl.gov ifeffit@millenia.cars.aps.anl.gov Sent: Tue

Re: [Ifeffit] [howto] configurational average in EXAFS with FEFF

2007-03-27 Thread Frenkel, Anatoly
Mauro, If I do understand your question correctly, you may be asking how to handle a multiple of inequivalent sites in atomic clusters with N atoms, where each atom generates a unique sequence of single- and multiple-scattering paths. A possible solution is given in this article: D.

Re: [Ifeffit] E0 for bulk crystals and nanoparticles

2007-02-25 Thread Frenkel, Anatoly
That's true - if there are no shift-like changes in XANES, E0 may be constrained. Anatoly From: [EMAIL PROTECTED] on behalf of Scott Calvin Sent: Sun 2/25/2007 10:20 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] E0 for bulk crystals and

RE: [Ifeffit] Alloy EXAFS data fitting

2006-08-31 Thread Frenkel, Anatoly
Hey Xianqin, If it is a (bulk) alloy system, and if A-A and A-B are 1NN pairs, then, unless there is a phase transition or other perturbations that can involve chemical changes either within the sample of heterogeneous (say, nanophase formation of different composition) or homogeneous (say,

RE: [Ifeffit] Right way of choosing E0 in Athena

2006-07-02 Thread Frenkel, Anatoly
Vadim, The ss2 of multiple-scattering (ms) paths and single-scattering (ss) paths are not simply related unless the legs in the ms paths are collinear. In that case, as published in Frenkel, Stern, Qian, Newville, Phys. Rev. B, 48, 12449 (1993), if the intervening atom is a first nearest