Re: [Ifeffit] S02 selection from reviewer

2021-10-03 Thread Peng Liu
Dear IFEFFIT members,

Thanks for all your suggestions, we got the idea to revise our manuscript
without just comparing the CNs. We are also planning to provide more
discussion for the selection of S02 and factors thay may affect it.

Thanks for your in depth discussion.

On Sun, Oct 3, 2021 at 12:08 PM John J Rehr  wrote:

>
> 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
>>> ___
>>> Ifeffit mailing list
>>> Ifeffit@millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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-- 
Best Regards,

Peng Liu
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Re: [Ifeffit] S02 selection from reviewer

2021-10-02 Thread 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
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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Re: [Ifeffit] S02 selection from reviewer

2021-10-02 Thread Anatoly Frenkel
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
> ___
> Ifeffit mailing list
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> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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Re: [Ifeffit] S02 selection from reviewer

2021-10-02 Thread Jeff Catalano

Peng,

I think what everyone has said is quite useful, but there is likely 
another aspect to consider as you make revisions. Based on the reviewer 
comments, it sounds like you are trying to interpret your fitted N 
values as being statistically distinct. My guess is that is not correct, 
as Matt suggested, and the fact that the N is lower in fluorescence 
suggests that overabsorption is attenuating the EXAFS amplitude, as 
Matthew suggested.


If you really want to make the claim of differences in coordination 
environment then you should also look at R. A lower coordination number 
should be accompanied by a decrease in R. How R shifts will be impacted 
by the resolution of the data, determined by your k-range, but I think 
if fitting a single Sb-O path then in most cases you should see R change 
if N is truly going down. It can get more complicated, clearly, and the 
S02 you are using may not be a perfect value, as Shelly's paper 
indicates, but if N is truly going down in one sample then R definitely 
should be changing.


I do not think about Sb very often, so if the only way for coordination 
to change is from a change in redox state then you should see a shift in 
the XANES spectrum. However, be cautious here because overabsorption 
will increase the intensity of a XANES spectrum for normalized 
absorbances below 1 and decrease the intensity above 1. If the XANES 
fine structure features of all samples are the same (in position) but 
you see what I describe in the overall absorbance, then your 
fluorescence samples is likely just suffering from overabsorption 
effects and your N will appear smaller. This gives a lower apparent S02, 
which is likely what the reviewer is getting at.


My sense is that what the reviewer is really criticizing is your 
interpretations based on differences in fitted N values, which may not 
be valid.


Jeff



On 10/2/2021 9:48 AM, Kelly, Shelly D. wrote:

Hi Peng:

It might be helpful to understanding some of Matt's points regarding S02 
transferability, Ei and energy resolution by looking at this paper.

Comparison of EXAFS foil spectra from around the world
DOI: 10.1088/1742-6596/190/1/012032

Kind regards,
Shelly

-Original Message-
From: Ifeffit  On Behalf Of Matthew 
Marcus
Sent: Saturday, October 2, 2021 9:04 AM
To:ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] S02 selection from reviewer

Since S02 is a parameter in the description of EXAFS and not of the experiment, 
it's independent of technique.  Overabsorption (misnamed
'self-absorption') can reduce the *measured* amplitude, an effect which can be 
fudged in analysis by reducing S02.  If the sample is truly homogeneous (on the 
scale of the absorption length), then you can calculate the amount of 
overabsorption to see if it's significant.
However, many kinds of samples, such as concentrated powders mixed with a 
diluent such as BN, this condition is not met.  If the particles are large 
enough for each to have significant absorption edge jumps, then diluting them 
in BN doesn't fix the problem.
mam

On 10/2/2021 12:49 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] S02 selection from reviewer

2021-10-02 Thread Kelly, Shelly D.
Hi Peng:

It might be helpful to understanding some of Matt's points regarding S02 
transferability, Ei and energy resolution by looking at this paper. 

Comparison of EXAFS foil spectra from around the world 
DOI: 10.1088/1742-6596/190/1/012032 

Kind regards,
Shelly

-Original Message-
From: Ifeffit  On Behalf Of Matthew 
Marcus
Sent: Saturday, October 2, 2021 9:04 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] S02 selection from reviewer

Since S02 is a parameter in the description of EXAFS and not of the experiment, 
it's independent of technique.  Overabsorption (misnamed
'self-absorption') can reduce the *measured* amplitude, an effect which can be 
fudged in analysis by reducing S02.  If the sample is truly homogeneous (on the 
scale of the absorption length), then you can calculate the amount of 
overabsorption to see if it's significant. 
However, many kinds of samples, such as concentrated powders mixed with a 
diluent such as BN, this condition is not met.  If the particles are large 
enough for each to have significant absorption edge jumps, then diluting them 
in BN doesn't fix the problem.
mam

On 10/2/2021 12:49 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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> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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Re: [Ifeffit] S02 selection from reviewer

2021-10-02 Thread Matthew Marcus
Since S02 is a parameter in the description of EXAFS and not of the 
experiment, it's independent of technique.  Overabsorption (misnamed 
'self-absorption') can reduce the *measured* amplitude, an effect which 
can be fudged in analysis by reducing S02.  If the sample is truly 
homogeneous (on the scale of the absorption length), then you can 
calculate the amount of overabsorption to see if it's significant. 
However, many kinds of samples, such as concentrated powders mixed with 
a diluent such as BN, this condition is not met.  If the particles are 
large enough for each to have significant absorption edge jumps, then 
diluting them in BN doesn't fix the problem.

mam

On 10/2/2021 12:49 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] S02 selection from reviewer

2021-10-02 Thread Matt Newville
Hi Peng,

On Sat, Oct 2, 2021 at 2:50 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.
>


It is always challenging to know what to do when a reviewer insists on
being wrong.   Well, I guess it is even more challenging when they turn out
to be right. ;).

Many different sample preparation and measurement effects can suppress the
overall XAFS amplitude.  There are "theoretical/calculational" terms:
 a) the relaxation of passive electrons to the core-hole that gives S02.
 b) the photo-electron mean-free-path.

that are expected to be "atomic only" and so will not vary with measurement
mode or sample-to-sample (mean-free path might be affected by samples
smaller than a few mean-free path lengths, but the evidence for this is
incomplete).  But, the calculations for these (at least from "easily run
XAFS calculations'') terms are imperfect and may need adjusting to
completely match experimental spectra.  For simplicity, we tend to adjust
S02 but not the mean-free-path.

There is also an amplitude term that may vary beamline-to-beamline (or even
between beam runs) but not between samples or measurement mode:
c) the actual energy resolution of the beamline.

This could be compensated by adjusting either the mean-free-path term or
S02.  Again, we typically just adjust S02.  In my experience, adjusting the
mean-free-path ("Ei" in ifeffit/Artemis/Larch) is not any better than
folding this into S02.   I'll also say that for the very common situation
of "Si(111) monochromator at a beamline intended for XAFS" especially in
the common 5 to 20 keV range, that spectral resolutions tend to be pretty
close to one another.

And there are terms that can reduce the amplitude that can vary from
sample-to-sample, and some of these are different depending on the
measurement mode.
   d) pinhole effects, important for transmission mode.
   e) over-absorption for fluorescence mode.
   f) detector saturation effects for fluorescence mode measured with
pulse-counting, energy-dispersive detectors.
   g) edge step from normalization, where slowly varying backgrounds can be
different for collection mode.

That is, if you have avoided or corrected for "d", "e", "f", and "g", then
S02 will be transferable between samples, at least those measured with the
same beamtime to account for "c".

All that said, I would expect the reviewer may be correct when saying "I am
confident that CN values 5.6, 7.1 and 6.9 correspond to CN(Sb-O)=6.",
especially if that is a main conclusion of the work.   It appears to me
that the reviewer may not be convinced that effects "e" and "f" were
completely avoided or compensated.

That is, claiming that the uncertainty in coordination number is less than
1 (and claiming that CN of 7 and 6 are significantly different) would
require special attention and confidence that the sample-dependent factors
were carefully addressed.   For example, if two transmission measurements
give CN of 7.1 and 6.9 (say with fitting uncertainty of 1) and a sample
measured in fluorescence measurement gives CN of 5.6 +/- 1, I think it
would be fair to suspect that the effects "e", "f", and "g" could be
influencing that difference.  If those effects are large, then you may need
to convince the gentle reader and the not-so-gentle reviewer that
corrections are done appropriately.

Hope that helps,

--Matt
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[Ifeffit] S02 selection from reviewer

2021-10-02 Thread Peng Liu
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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