[Ifeffit] LCF on Larch - EXAFS Region

Matt Newville newville at cars.uchicago.edu
Tue Aug 14 12:33:35 CDT 2018

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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--Matt Newville <newville at cars.uchicago.edu> 630-252-0431
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