Re: [Ifeffit] request for comments on XDI and NeXuS data formatting

[John J Rehr]

Hi Matt et al.

  The improved NeXuS format for XAS data looks fine  to me. Good idea.  But
it makes me wonder whether
a similar formatting  for theoretical XAS data would be useful, especially
for analysis purposes.

  Cheers,
  John

  Cheers,
  John

On Sun, Aug 6, 2023 at 11:45 PM Matt Newville 
wrote:

> Hi Folks,
>
> As some of you are aware, there is a Q2XAFS meeting in a few weeks. I will
> be presenting some work on using NeXuS and HDF5 to store and distribute XAS
> data.  This builds on and closely follows the XDI format from Bruce Ravel.
>
>
> While XDI is a great way to represent a single XAS spectrum, it is not
> able to contain multiple spectra.  It also is not very specific about how
> to deal with data files with a large number (say, > 20) columns as might be
> found coming from many beamlines with multi-element detectors.   I think
> that many of us are starting to see the need to regularly provide "raw" or
> "nearly raw" data as supplementary data for published articles or as part
> of datasets made available under FAIR data principles.   While XDI could be
> one way to do that, I think it is also reasonable to reconsider formats
> other than plaintext files holding one spectrum.
>
> As I am preparing to present this, I've put together something like a blog
> post on a proof-of-concept for a NeXuS file format based on XDI at
> https://millenia.cars.aps.anl.gov/nxxas/
> .
> There are a few example data files using the proposed layout at
> https://millenia.cars.aps.anl.gov/nxxas/nexus_xas.html
> .
> There is also a Pull Request in with the NeXuS developers for this.
>
> If you are interested and have time over the next week or two, please read
> the pages above and let me know your thoughts on this.  I know that not
> everyone is interested in this, but I also know that some who might be
> interested are not able to attend Q2XAFS.  I think the discussion on this
> topic should be as wide as possible, which is why I am posting this here
> and before the meeting.
>
> Thanks,
>
> --Matt Newville  
> >
>
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Re: [Ifeffit] FEFF10 simulation of Pt alloy

[John J Rehr]

Hi Harry,

  If you're calculating HERFD with FEFF, you have  to suppress the
core-hole broadening, which will reduce the white line intensity.
This can be done by using  a negative value of  vi0 in the EXCHANGE card.
You can find the default value of the width in the header
files to xmu.dat.

  If you have problems doing that, please send us your feff.inp and a
comparison  with the expt data and we can troubleshoot.

  With best wishes,
   John

On Mon, Jan 16, 2023 at 3:45 AM Andy Zhang  wrote:

> Dear all, I tried to use FEFF10 to simulate the XANES of Pt alloy (Pt L3
> edge), and the simulation results fit the XANES collected using TFY mode.
> However, the white line intensity of the simulated XANES is much lower than
> the experiential spectra
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> Dear all,
>
> I tried to use FEFF10 to simulate the XANES of Pt alloy (Pt L3 edge), and
> the simulation results fit the XANES collected using TFY mode. However, the
> white line intensity of the simulated XANES is much lower than the
> experiential spectra collected using HERFD mode.
>
> I wonder if there is way to fit the HERFD XANES results through simulation
> (in other words, to increase the white line intensity of the simulated
> XANES).
>
> Thanks a lot in advance!
>
> Best,
> Harry
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Re: [Ifeffit] S02 selection from reviewer

[John J Rehr]

Hi everyone

I wonder how much effect on the expt value of S02 comes from background
subtraction including previous edges, the energy dependence of the atomic
background, and the range of the EXAFS. Theoretically S02 is nut a constant
but a spectral average. I’d like to see a careful study with a well defined
algorithm that could be compared with theoretical estimates. Thanks.

John

On Sat, Oct 2, 2021 at 8:47 AM Anatoly Frenkel <
anatoly.fren...@stonybrook.edu> wrote:

> I think that the variability of S02 between different samples, detection
> methods etc. may or may not be a big concern for you if 1) the error bars
> in the CNs (that you are not reporting) are larger than the difference in
> their mean values (that you are reporting), and/or 2) larger than the
> difference between their mean values and the CN=6 that the reviewer is
> asking about. If yes to either 1) or 2), then the variability in the S02
> values for differently prepared samples may cause smaller variation in your
> best fit values of CN than the error bars reported by your fitting program,
> and your choice of fixing your S02 to be constant (0.85) may be justified.
> You need to have a really bad non-uniformity or concentration problem so
> that your effective S02 changed from the expected 0.85 (assuming it is what
> a correctly performed measurement would give) to, say, 0.5 or 0.6 is my
> thought.
>
>
> Anatoly
>
>
>
> On Sat, Oct 2, 2021 at 3:50 AM Peng Liu  wrote:
>
>> Dear IFEFFIT members,
>>
>> I am sorry to bother you again. I asked about S02 selection for the first
>> major revision. I just received the second revision. The reviewer is not
>> satisfied with one S02 value for all our samples.
>> "
>>
>> 1. I am still not satisfied with selected SO2 value (it is set to 0.85).
>> SO2 is not transferable between different samples and detection methods. It
>> is not possible to use a value obtained from different compound using
>> transmission measurement mode to completely different other compound
>> measured using fluorescence mode. One method to fix SO2 value is to measure
>> diluted solution (to avoid self-absorption) of reference material in
>> fluorescence mode. Other is to use multiple spectra fitting for all samples
>> of interest (e.g. with Sb(V)) measured using fluorescence mode where SO2
>> parameter is the same for all samples.
>>
>> At the same time I am confident that CN values 5.6, 7.1 and 6.9
>> correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for
>> measurements in fluorescence mode.
>> "
>>
>> We do get the S02 from a similar reference material measured in
>> transmission mode, and our samples were all measured in fluorescence mode.
>> It is not possible to measure the diluted reference material in
>> fluorescence mode in one or two months. If you could give me some
>> suggestions, that would be great.
>>
>>
>> --
>> Best Regards,
>>
>> Peng Liu
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Re: [Ifeffit] How Artemis handle crystal structure data with partial occupancy in vorlanite (cubic CaUO4)

[John J Rehr]

Just a comment: typically the A and B atoms cluster with a given NN
distribution function to help set the
structure. In our experience the results from FEFF are often not very
sensitive to the distribution but you
can try a couple of sample distributions to check this.\

John



On Tue, Apr 28, 2020 at 9:29 AM Matt Newville 
wrote:

> Hi Dien,
>
> Yes, basically Artemis / Atoms cannot handle partial occupancy for
> crystallographic sites because partial occupancy is not readily translated
> to a cluster of atoms.  So, what you have to do is start with a CIF without
> fractional occupancy, say that has only Ca or only U in that site, and
> generate a cluster of atoms from it.  Then, you can (and here, have to)
> edit that cluster of atoms to replace some of the Ca/U with U/Ca.  Which
> ones, and how many, is up to you.
>
> --Matt
>
>
>
>
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Re: [Ifeffit] XANES convolution method in FEFF9

[John J Rehr]

Dear Ying,

Actually FEFF does not transform the LDOS into the final XAS spectrum.
Although both the LDOS and the XAS are obtained
from matrix elements of a one-particle Green's function, they  are obtained
in FEFF  from two different calculations: the
XAS is calculated in the presence of a core-hole, and the LDOS is obtained
from the ground state without a core-hole..
This is explained in detail, for example, in  Ankudinov, et al., Phys Rev.
B 58, 7565 (1998) as summarized in their Eq. (1):

 [image: image.png]
 As a consequence the  LDOS and the XAS are not directly related.
Indeed, as pointed out in the above reference:

[image: image.png]

  I hope this answers your question.
  With best regards,
   John

On Fri, Feb 15, 2019 at 8:48 AM Ying Liu  wrote:

> Dear all.
>
> I am currently running FEFF9 on XANES calculation. However I could not
> figure out how FEFF transformed LDOS to the final xmu.dat. What function
> did LDOS data convoluted with to achieve xmu.dat?
>
> Looking forward to hearing any answer.
>
> Thank you.
>
> Ying
>
> Queen Mary University of London
>
>
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Re: [Ifeffit] Question about statistics

[John J Rehr]

Dear Olga,

 Thanks for your interest in the Bayesian analysis codes.  I'm glad to
hear that your are interested in developing the method. Although some
prototype Bayes-Turchin based codes were developed by Josh Kas as part
of his  thesis research, the project was never fully integrated into the
IFEFFIT
package and progress stalled for lack of funding.  But there has also been
a
parallel effort to develop a Bayes-Turchin code by Elizabeta Holub-Krappe
and her colleagues in Chiba, Japan. and I would suggest that you ask her
for a copy of their BT code and documentation.   I think this topic will
also be discussed at the XAFS16 conf in Karlsruhe in Aug 2015 - will you be
there ?

 With very best regards,
 John

cc E. Holub-Krappe


On Fri, Mar 6, 2015 at 12:39 PM, Olga Kashurnikova ok...@mail.ru wrote:

 Hello, Dr Matt Newville,

 Thank you very much for the answer.

 There is a message with some corrections in the next thread – the numbers
 of my hand try to check am I right about chi_square and error calculation
 in IFEFFIT, were not right in the first time. I will try to attach the
 calculation files later, it is not clear for me how they will be shown here.

 I will write the main question and then about Bayesian analysis for thread
 splitting if you don’t mind. These things are interconnected that’s why I
 didn’t split them.

 The main question was about how IFEFFIT calculates chi_square and to what
 minimization function it adds restraints, in case of k_space. What is the
 normalization? I thought it should be
 (N_idp/N_data)sum[(dat-model)^2/eps^2], and in k space only the real part
 of data compared with imaginary part of model, but my hand calculation for
 check this gave the different result. It is necessary for the choice of
 optimal restraint (it is chi^2 without normalization that I need to
 compare) and for normalization of errors for them to be covariance matrix
 of this chi^2, as of Krappe and Rossner. Restraint will change errors, of
 course, because covariance matrix is (Q+A)^(-1) where A is regularizer in
 restraint and Q is what should be without restraint. If Q is not invertible
 (in case of some parametra don’t influence spectrum) it is critical, and
 optimal A can be found to strictly divide the ‘parametra space’ and verify
 models. That’s why I need to rescale them well, because for bayes it should
 be chi^2=sum[(dat-model)^2/eps^2]+A*sum(x-x0)**2  (A is connected with a
 priori ranges of parametra, it should be not one number, but algorithm of
 finding optimal diagonal A matrix is harder and I think not with
 IFEFFIT/Larch help). It is the same as your (paramA-A_0)/eps_A restraint, I
 understood what formula should be for a restraint, but don’t understand how
 to weight data and restraint part. It were Krappe and Rossner who mentioned
 Tikhonov regularization if I remember right, and it is very close, if I
 understood the paper about this regularization. That’s what I mean in
 ‘doesn’t fit’: 4 coordination spheres (Gd-O, Gd-Gd,Gd-Hf, next Gd-O for
 instance, and only first is in separate peak) may be in the N_idp range,
 but are so correlated that without constraints or other structure model the
 fit give bad results – some parametra will leave the acceptable range etc,
 and I’m not sure that without a Bayesian analysis I can define the better
 model of constraints, and the sphere splitting is even more difficult to
 define.

 So, the main question is ‘how IFEFFIT calculates this, what is the
 formula’, because FEFFIT manual doesn’t give the k-space case, and the
 check was wrong. I can append calculation files in a while if needed (I
 need to convert from a program to iff file), though I wrote formulae and
 they may be can be verified without numerical values.

 Chi_square in your method is close to what should be minimized and for
 what the covariance matrix should be found in Bayesian analysis, with the
 right normalization, that’s why I ask if I could use IFEFFIT to calculate
 this with renormalization of the results. If I put the right normalization
 to restraint, I need only rescale chi_square and errors and then calculate
 what I need. It is not that I think IFEFFIT use Bayesian statistics, I
 understand there are different approaches.



 Thankful for your assistance,

 Olga Kashurnikova, MEPhI, Moscow



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Re: [Ifeffit] feff6l licence

[John J. Rehr]

Hi Carmelo et al.,

 Short answer: FEFF6L may be freely distributed; there is no special
agreement restricting the code to IFEFFIT or other codes. Let me know
if you have other questions about this.

 Sincerely,
 J. Rehr
 PI FEFF Project

 From the FEFF6L license header:

c///
c Distribution:  FEFF6L
c Copyright (c) [2002] University of Washington
c
c This software was prepared in part with US Government Funding under
c DOE contract DE-FG03-97ER45623.

c Redistribution and use of this Distribution in source and binary
c formats, with or without modification is permitted, provided the
c following conditions are met:
c
c Redistributions must retain the above notices and the following list
c of conditions and disclaimer;
c
c Modified versions carry the marking
c Based on or developed using Distribution: FEFF6L
c  Copyright (c) [2002] University of Washington
c
c Recipient acknowledges the right of the University of Washington to
c prepare uses of this Distribution and its modifications that may be
c substantially similar or functionally equivalent to
c Recipient-prepared modifications.
c Recipient and anyone obtaining access to the Distribution through
c recipient's actions accept all risk associated with possession and
c use of the Distribution.
c
c THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED
c WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
c MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
c IN NO EVENT SHALL THE UNIVERSITY OF WASHINGTON OR CONTRIBUTORS TO THE
c DISTRIBUTION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
c EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
c PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
c REVENUE; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
c LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
c NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
c SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
c///





On Wed, 16 Nov 2011, Carmelo Prestipino wrote:


Hi to everybody
I'm currently working to an another GUI to Ifeffit,  aimed to large
dataset , it is still in beta version and full of bug but some
collaborators start to use it .
In the installer that I send to them is present  the feff6l.exe
file,  to generates phase and amplitudes , but now I have a doubt.
Does the feff6l licence allows a generic redistribution? , or  have
the Horae and the Sixpack packages  a special agreement?
Thanks in advance
Carmelo

--
Carmelo Prestipino
Sciences Chimiques de Rennes UMR 6226
Campus de Beaulieu, B?t 10B
F-35042 RENNES
France
Tel: (+33) 22323 6531
FAX: (+33) 22323 5959

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Re: [Ifeffit] What does FEFF stand for?

[John J. Rehr]

  Everyone is at least partially right.  In our PR B34,4350(86) paper
(which was rejected by PRL) we noted that the exact single scattering
XAFS eq. could be recast in the same form as that of Sayers Stern 
Lytle (PRL 27,1204(71) by replacing the backscattering amplitude
f(pi) with the exact curved wave expression given by ~f  (see our
Eq. 9). For single scattering this ~f is equivalent to the Z factor in
Lee and Pendry and a similar quantity in Schaich.  We replaced ~f with
f_eff (i.e., the effective scattering amplitude)in our PRB 44, 4146 (91),
which also describes the single-scattering FEFF code.  This code started
in pieces at Los Alamos in 1984, but the integrated version with a reliable
overlapped atom potential became FEFF3 some years later.  The name FEFF
originated during a meeting with Jose Mustre de Leon, Steve Zabinsky
and others (?) when we were looking for a catchy name for the code. Although
it was not an acronym, I thought FEFF seemed quite appropriate.
Interestingly, we found that one can also define an exact effective scattering
amplitude for multiple-scattering paths, e.g. as in PRL 69, 3397 (92).
The beauty of this representation is that permits an interpretation of both
single- and multiple-scattering contributions using the standard EXAFS
equation. Thus in subsequent papers and code developments we simply used
f_eff to describe all SS and MS paths. Thus the name FEFF was also
retained for subsequent versions of the code.

 J. Rehr

On Tue, 10 May 2011, Francisco Garcia wrote:


Dear all,

I wish to ask a somewhat novice question: What does the acronym FEFF stand for?

Thank you.
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Re: [Ifeffit] how to reduce the core-hole lifetime broadening in feff8.2

[John J. Rehr]

Hi Tony,

  Following Bruce's suggestion, you can reduce the core-hole broadening
by making Vi negative. When you do this, note that the amount of reduction
is limited by the core-hole broadening (i.e.,  the variable Gam_ch which
is printed out in the header to xmu.dat or  chi.dat).  Thus for a typical
case (Al) where Gam_ch=3.763E-01, you can set Vi= -0.018 in the EXCHANGE
or CORRECTIONS cardds.

  J. Rehr



On Thu, 11 Jun 2009, tony vitova wrote:


Dear?all,
?
Could somebody give me a hint how to reduce the core-hole lifetime broadening 
in feff8.2? Do I?need to change the source code? I have partial fluorescence 
yield XANES spectrum whose White Line is narrow than the one in the calculation.
?
Thanks for any help
?
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Re: [Ifeffit] Hard tests failed in fovrg

[John J. Rehr]

Hi Everyone,

 If you ever encounter problems like this, please attach a feff.inp
so we and others can duplicate and troubleshoot the problem. Thanks.

 Cheers,
 John


known (hopefully correct). The default feff6l in Artemis reports an error
?Hard tests failed in fovrg. Muffin-tin radius may be too large;
coordination number too small???. When I run feff8.2, this error exchanges
with the following message ???The phase shift correction is accurate to
k=19???. I guess that this is not a problem, because my data is until k equal
12 A^-1. However, the fit of the first shell (9O/9N) gives Eo equal to 13,
which is unrealistic. This fit with paths calculated with feff6l gives
reasonable Eo value. But the phase shifts seem to be calculated
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Re: [Ifeffit] Fe_L2L3

[John J. Rehr]

Subject: Re: [Ifeffit] Fe_L2L3

Dear Guvenc,

  It's pretty easy, but you have to do the calculation edge by edge and
then add, i.e., two calculations, one with

EDGE L3

and one with

EDGE L2

The FEFF project has scripts for adding FEFF results for two edges - send
email to [EMAIL PROTECTED] for details.

  J. Rehr









On Wed, 29 Oct 2008, Guvenc Akgul (gakgul) wrote:

 dear all,
 
 I have to calculate L3 and L2 absorption edges for pure Fe as theorical .how 
 can I do this using FEFF?
 
 thanks
 
 guven
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Re: [Ifeffit] feff82 issue with perovskites

[John J. Rehr]

Ciao Francesco,

 Thanks for the comment.

 As you've seen Ba has a sharp edge resonance which confuses the defaults
for calculating phase shifts in FEFF. To tame it, add a little broadening
and a finer grid:

EXCHANGE  0 0 1.0
RGRID 0.01

and the problem seems to goes away.  Also, the problem does not appear
to be visible with FEFF8.4. Fortunately (I think) this is an unusual case.

 Cheers,
 J. Rehr


On Mon, 3 Mar 2008, Francesco Giannici wrote:


Hi all,

 when calculating paths around Ba (K-edge) in the cubic perovskite BaZrO3, the 
third path (Ba-Ba) is totally screwed up in the 2.6 - 3.8 ang^-1 range, with 
amplitude going up to 1000. You can find the input file at 
http://giannici.altervista.org/feff.inp

Actually, this is also the case of Gd:BaCeO3, substituting one Gd for one Ce, 
and calculating paths for the Gd K-edge: the Gd-Ba path shows the same issue. 
This applies to Feff8.2 on Debian, Fedora, and MacOSX 10.4.11. I found that 
playing around with FOLPs seems to help, but I?m not very confident with that, 
and I?d like to hear your opinion on what the cause could be. (Yeah, just 
throwing away all those low-k data would also be a solution).

On the other hand, Zr and In K-edge in Ba(In,Zr)O3 work just fine, as do Ce, 
Ba, Y and In K-edges in Ba(Y/In,Ce)O3. Also Gd K-edge in Gd2O3 works fine.

Cheers from Stuttgart,
--
Francesco Giannici
Dip. di Chimica Inorganica e Analitica
Universit? di Palermo / ISMN-CNR
[EMAIL PROTECTED]


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Re: [Ifeffit] FEFF and XANES

[John J. Rehr]

Hi Jakob,

As you have noted the fine structure in the projected DOS and the XAS
is the same, so  the relation between them is:

  XAS =  gamma(E) LDOS, where   gamma(E) = mu_0(E)/rho_0(E),

where gamma(E) is a smoothly varying atomic-like quantity which
is essentially a ratio of embedded atomic matrix elements.  In systems with
a white line $mu_0$ and hence, gamma(E) will likely be peaked at threshold.
As a result the XAS is smoothly related to the LDOS with appropriate
selection rules.  This discussion assumes core-hole effects are small,
and final state broadening is applied both the the LDOS and XAS.

  J. Rehr

On Mon, 11 Dec 2006, Frommer  Jakob wrote:



Dear all,
I have a FEFF related question (I know that this is an IFEFFIT list, but I 
guess the subjects are closely related). I try to model some of my Cr XANES 
data with FEFF (following the procedure outlined in an excellent publication in 
Chem Phys 300 (2004) 13-22 ? the authors have shown that it is possible to 
explain the Cr XANES spectra at least qualitatively by the means of FEFF 
calculations). I have however still some trouble to understand the difference 
(or the relation) between the XANES results given in the xmu.dat file and the 
l-projected density of states results (ldosXX.dat). Due to 
rho(E)=rho_0(E)[1+chi(E)] I would expect them to conincide (if the rho is 
calculated for the correct l ? i.e. if the matrix element is non-zero). However 
I observed that the ldos and the xmu do not always coincide ? is this possible? 
Furthermore at the white line position (from what I know, the white line is 
commonly interpreted as being due to the transition into unoccupied but bound 
states)!
the xmu shows strong intensity whereas the ldos do not (maybe one comment: I 
assume that the e-scales in the ldos-file and in the xmu-file are the same).
I am using FEFF8.2 with the SCF, DOS, XANES and FMS card.
I would be obliged for your help.
Thanks
Jakob

P.s.: for hydroxide structures FEFF is always returning ?bad counts? if I 
include the protons into the FEFF calculation ? however this might be also due 
to bad input structures.


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Jakob Frommer
Soil Chemistry Group
Institute of Biogeochemistry and Pollutant Dynamics, ETH Z?rich
Universit?tstrasse 16, CHN F19
CH - 8092 Z?rich
Tel: +41 44 632 87 58
Fax: +41 44 633 11 18
Email: [EMAIL PROTECTED]
http://www.ito.ethz.ch/SoilChem/


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RE: [Ifeffit] Phase corrected Fourier transforms

[John J. Rehr]

 Anatoly is correct that the phase correction cannot work for all shells
in inhomogeneous systems. However, it's *always* possible to remove the
central atom phase shift 2 delta_c which often dominates the phase
correction. Second, if one corrects by the 1st nn phase, delta_1, the dominant
near neighbor shell will appear at the correct distance. The correction
is not right for subsequent shells but the error is given by a phase
difference
delta R = (1/2)(d/dk) [delta_n-delta_1]
This correction is typically order 0.1 Ang and usually smaller than the
typical shift of about 0.3 - 0.4 Ang in uncorrected FT peaks.

 The upshot is that the phase corrected FT can be correct for the first shell
which often dominates the FT and generally better than uncorrected FTs.

 Corrective lenses for vision aren't perfect either at all distances,
but it's hard to argue that it's preferable not to use them for that
reason.

 J. Rehr


On Sat, 23 Sep 2006, Anatoly Frenkel wrote:


My 0.533 Rouble: In my experience with some Mn oxides, the Mn-O FT magnitude
peak's position is 0.5 A lower its corresponding 1NN bond length, while the
Mn-Mn are 0.3 A lower than their bond lenghts. Thus, it would be misleading
for this and other similar compounds to apply theoretical phase correction
of the 1NN to the entire data, as it will shift only one peak correctly.

Anatoly

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Matthew
Marcus
Sent: Saturday, September 23, 2006 4:14 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Phase corrected Fourier transforms


OK, I have to put in my US$0.02/e0.02.  The phase correction can't mean much
if the scattering atoms are different, which is usually
the case.  If the scattering atoms are very heavy, then the phase correction
has a kink in it which could cause strange shapes if applied
to light-atom shells.  I've played with this phase correction and amplitude
correction, while I was at it, and not been very impressed.
One place where it might be useful is in the aforementioned case of heavy
and light scatterers.  If you use the correction for one of
these, then the corresponding shells sharpen and the other ones blur out, so
you can get a rough idea of who's who.  I suspect
this works better if you do the amplitude as well.

A related technique is to use model compounds+FEFF to get 'semi-empirical'
amps and phases which include all the artifacts
of the experiment.  Suppose, for instance, that you're looking at Cu in a
matrix of Fe, and you have data for Cu metal but
not for any known Cu-Fe scattering pair.  You can synthesize a
'semi-empirical' Cu-Fe phase and amp like this:

phi(Cu-Fe) = phi_exp(Cu-Cu)+(phi_theor(Cu-Fe)-phi_theor(Cu-Cu))
amp(Cu-Fe) = amp_exp(Cu-Cu)*amp_theor(Cu-Fe)/amp_theor(Cu-Cu)

If you don't want to do this for modeling, you can use this method for
comparing two spectra which you think might
be alike except for the central atom, by correcting one spectrum with the
difference to make it comparable to the other.

Another aspect to this whole thing is that people are very used to
uncorrected FT's and are aware that you have to add 0.3-0.4A
to the distances.  If you show only corrected FT's, I wonder if that will be
satisfying to the audience.
   mam

- Original Message -
From: John J. Rehr [EMAIL PROTECTED]
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Cc: John J. Rehr [EMAIL PROTECTED]
Sent: Saturday, September 23, 2006 7:18 AM
Subject: Re: [Ifeffit] Phase corrected Fourier transforms



Dear Juan Antonio,

 I personally feel that adding phase correction to the XAFS FT is
highly desirable, and I encouraged its implementation in Athena.
The reasons are the following:

1) Peaks in  non-phase corrected FT are substantially in error.
2) The non-linearity of the phase shifts in high-Z materials leads
to multiple-peaks, thus blurring the FT.
3) Theoretical phase shifts are good enough that adding phase correction
tends to correct the peak positions and the problems due to non-linearities.
4) Adding phase correction does no-harm to the fits. That is, one gets
the same results whether or not phase correction is included.
5) Adding phase correction gives a FT which can be more easily
interpreted by eye, that is the peaks have a more physical interpretation.
On the contrary, non-phase corrected FTs can be mis-interpreted.

Overall, my view is that the phase correction is like a prescription
lens which gives a sharper image. While the image may not be perfect,
at least it's generally much superior to the non-phase corrected FT.

 J. Rehr

On Fri, 22 Sep 2006, Juan Antonio [iso-8859-1] Maci? Agull? wrote:




Hi all,

I have read Phase corrected Fourier transforms in Athena manual and now
I have a big doubt, ?phase correction or not in a publication?

I have read also that this correction is different (more complete) in
Artemis and I am not sure if I should correct also in Artemis and which
path should I use