[Ifeffit] Ifeff calculation

Bruce Ravel bravel at bnl.gov
Wed Aug 15 09:34:07 CDT 2018


Rmax is not the problem here.  This is a CIF file that the software is 
not interpreting correctly for some reason.  I am quite sure that the 
Re-O near neighbor distance in NaReO4 is NOT 1.1191 AA.  That -- not the 
error message -- should have been the thing you asked about!

The CIF file is calling for I 41/a (group 88) origin choice #2.  I would 
guess that Demeter is not interpreting the origin correctly.  I'll put 
this on my to do list, but I have not been able to spend much time on 
Demeter in recent months.

You might need to use something that is smarter about crystallography 
data than my software -- Crystal Maker or whatnot -- and make a feff.inp 
file by hand.

B


On 08/15/2018 09:42 AM, Dien.Li at srnl.doe.gov wrote:
> Hi, Carlo and Matt or others
> 
> Attached please find the cif crystal structure data file for NaReO4 that was downloaded from Crystallography Open database. As I added it into Artemis for calculation, it gave error message saying that it has more than 500 atoms that exceeds the limit. Could you help to troubleshooting?? Thanks a lot.
> 
> 
> Dien Li
> 
> -----Original Message-----
> From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request at millenia.cars.aps.anl.gov
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> Subject: Ifeffit Digest, Vol 186, Issue 13
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> Today's Topics:
> 
>     1. Re: LCF on Larch - EXAFS Region (Matt Newville)
>     2. Re: wavelet transforms for EXAFS (Matt Newville)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 14 Aug 2018 12:33:35 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] LCF on Larch - EXAFS Region
> Message-ID:
> 	<CA+7ESbr8s-gQOeLOo302hTdtT+XLS8g55goXvYm6hqJFiLCkaQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Martin and Mike,
> 
> Thanks -- I'll take a closer look at your paper on this!   I think we all
> basically agree that linear analysis of EXAFS can work, but also that
> compared to linear analysis of XANES, linear analysis of EXAFS has a few
> more caveats and issues that need to be addressed for each case.
> 
> On Mon, Aug 13, 2018 at 8:26 PM Martin McBriarty <memcbr at gmail.com> wrote:
> 
>> Matt,
>>
>> Glad to read your impressions of EXAFS LCF. I've had reasonable success
>> with LCF using EXAFS spectra generated by ab initio molecular dynamics
>> (AIMD) to figure out the local structure of dopants whose preferred
>> coordination is symmetrically dissimilar from the crystals they inhabit,
>> i.e. for which there are no good experimental standards. This can be pretty
>> tough to do accurately with shell-by-shell fitting.
>>
>> As you point out, disorder is a huge hurdle (in both LCF and
>> shell-by-shell EXAFS analysis). We assume that a good AIMD model will
>> simulate thermal disorder pretty well, but there are likely differences in
>> configurational disorder between a periodic infinite structure and the real
>> material due to defects. Fortunately, defects can be explicitly accounted
>> for in a simulation, assuming you have the computational capability to
>> screen a set of defect configurations.
>>
>> Background subtraction should ideally be done using the same procedure for
>> all data. Theoretical data could be used to refine a background subtraction
>> procedure; spline fit parameters such as Rbkg or clamping may be tweaked to
>> improve agreement between a simulated chi(k) and a measured standard over a
>> reasonable k-range.
>>
>> Simulating spectra with a range of binding energy offsets can explicitly
>> address the problem of E0 choice, but it can also be used as a fudge factor
>> for strain. In my LCFs, dE0 is the only parameter besides the fractions of
>> the chosen phases.
>>
>> To address the above problems, benchmarking is key. Quantitative agreement
>> should be sought between simulated spectra and experimental standards to
>> ensure the theory is sound and the chi(k) extraction is reasonable.
>> However, there are probably still systematic sources of error which are
>> larger than the uncertainties Athena's LCF tool will report; I agree with
>> Mike's practical estimate of 10% or so.
>>
>> I discuss these issues in somewhat greater detail in my recent (open
>> access!) article that demonstrates how LCF using AIMD-simulated spectra
>> yields answers that shell-by-shell fitting struggles with due to multiple
>> overlapping components: https://pubs.acs.org/doi/10.1021/acs.est.8b00297
>>
>> Martin
>>
>>
>> On Sun, Aug 12, 2018 at 10:19 PM, Matt Newville <
>> newville at cars.uchicago.edu> wrote:
>>
>>> Hi Mike,
>>>
>>> On Thu, Aug 9, 2018 at 10:04 PM Mike Massey <mmassey at gmail.com> wrote:
>>>
>>>> This is interesting. Could you say more about your skepticism of the
>>>> robustness of EXAFS LCF, Matt?
>>>>
>>>> To be fair, it suffers from many of the same drawbacks of XANES LCF,
>>>> plus others. But I'm curious about your thoughts on it since yours seems to
>>>> be what amounts to a "strong opinion" on the subject.
>>>>
>>>
>>>
>>> I would not say that no one should ever do linear combination fitting for
>>> EXAFS.  For sure, linear analysis of XANES is quite robust and verified
>>> many times to give good results, at least at level of a few percent.
>>> Linear analysis of EXAFS suffers more data processing challenges and
>>> conceptual problems that limit its robustness.  For sure, there are cases
>>> for which it can work well.
>>>
>>> Longer answer:
>>> Any linear analysis (LCF, PCA, MCR-ALS, etc) of XANES works reasonably
>>> well (typically to a few percent) because:
>>>     a) the processing needed is minimal.  Data need to have a common
>>> energy calibration better than the intrinsic energy resolution -- typically
>>> energy calibration of 0.25 eV or better will be OK.  Data need to have a
>>> consistent normalization of mu(E), typically to a few percent.   Variations
>>> in these processing steps will have a direct and negative effect on the
>>> results.
>>>
>>>     b) conceptually, the assumption is that there exists a nearly 1 to 1
>>> correspondence between "local chemical configuration" and "measured XANES",
>>> and that the "local chemical configurations" that are being investigated
>>> are discrete and well-defined (ie "iron carbonate") and not continuous.
>>>   That is, if you determine that your Fe XANES spectra is "50% iron
>>> carbonate and 50% iron sulfate" then implicit conclusion is that 50% of the
>>> iron atoms are iron carbonate and 50 percent are iron sulfate, not that all
>>> irons are 50% carbonate and 50% sulfate.
>>>
>>> To be clear, linear analysis of XANES does not work well to ppm levels,
>>> partly due to the poor experimental contrast (that is, mu(E) tend to all
>>> look alike and features are intrinsically broadened to the ~eV level), but
>>> also conceptually, because at the ppm level, local chemical configurations
>>> are not always limited to 3 to 10 discrete states.
>>>
>>> Linear Combination EXAFS is more challenging from both the processing and
>>> conceptual point of view.
>>>
>>> For Processing, EXAFS requires more data processing than XANES.  The
>>> selection of E0 and the background mu0(E) will have an effect on linear
>>> analysis of EXAFS if not done consistently.  It is not really obvious how
>>> E0 or mu0(E) can be selected consistently for very different spectra.
>>>
>>> Conceptually, EXAFS is much more sensitive to disorder and subtle
>>> variations in the bond lengths (thermal or static disorder) and can have
>>> significant variation in its sensitivity to second and further neighbors.
>>>   In that sense, EXAFS is much less discrete and much more continuous in its
>>> variability across different kinds of local structures.
>>>
>>> Again, this is not to say that linear analysis of EXAFS cannot ever work,
>>> just that is probably more limited in applicability and absolute accuracy
>>> than linear analysis of XANES.  Of course, for EXAFS you can also do an
>>> actual fit of structural parameters.  The information content is somewhat
>>> limited so that refining multiple overlapping components may not always be
>>> possible, and linear combinations of end-member spectra may look
>>> attractive....
>>>
>>> Hopefully, anyone who has other insights or experiences will be able to
>>> correct any of my misunderstandings.
>>>
>>> --Matt
>>>
>>>
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-- 
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 06BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Beamline:    https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/


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