Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

[Mike Massey]

Hi Chris,


Thanks for the suggestion, I'll give it a try on the morrow. 

Interestingly enough, I loaded up the non-truncated version of this spectrum 
for comparison purposes, and...The extended background is pretty flat but not 
really increasing. If I use it for normalization, the edge jump computed by 
Athena is negative.

I'm going to try using Athena for normalization, and another program for LCF, 
and see how that goes.

In the majority of cases, Athena seems to work just fine...But a few points of 
the particular datasets I've been working with recently have a pesky 
negatively-sloping pre-edge. Looks fine when I line up the normalized plots, 
but the fitting doesn't seem to work out.

Thanks to all for your input, I've been working at the low-Z XAS for 4-5 years 
now and it feels like I learn new ways to screw it up (and new solutions!) 
every day. If you have any thoughts, don't hesitate to reach out.



Mike





> On Jan 15, 2019, at 7:42 PM, Christopher Patridge  
> wrote:
> 
> Hi Mike,
> 
> I would suggest that, as Carlo mentions, that because you cut off at 2200 eV, 
> the post edge background function in purple might be skewed a bit.  I might 
> be use values ~2190 eV and 2164 eV?  Though it appears to be a “flat” region 
> where you place the points, it may actually not be all that flat if data was 
> collected further out.  Even if you were to collected new data, if this short 
> range is used and the same approach to normalization is used, I don’t know if 
> LCF would improve.
> 
> Chris
> 
> 
>> On Jan 15, 2019, at 8:23 PM, Mike Massey  wrote:
>> 
>> Hi Scott,
>> 
>> 
>> I collect up to 2240 eV often, because that's about where the mirror stops, 
>> but end up truncating it at 2200 eV before fitting because sometimes I end 
>> up with all sorts of non-systematic background things at higher energies, 
>> depending on the sample.
>> 
>> I still collect the data because it helps me to troubleshoot, but I chop it 
>> before fitting because 2200 eV is the limit of what I normally consider 
>> consistently "good data." I end up with spectra that, to my eye anyway, are 
>> comparable. For dilute samples, I don't usually trust it beyond that. For 
>> concentrated samples, I don't have a problem.
>> 
>> 
>> Thanks,
>> 
>> 
>> 
>> Mike
>> 
>> 
>> 
>>> On Jan 15, 2019, at 5:12 PM, Scott Calvin  wrote:
>>> 
>>> Hi Mike,
>>> 
>>> Is there a reason the data stops at 2200 eV—e.g., is there another edge 
>>> just above that?
>>> 
>>> —Scott
>>> 
 On Jan 15, 2019, at 8:02 PM, Mike Massey  wrote:
 
 Thanks Riti and Carlo.
 
 Riti: will give it a go, thanks! I think the data are salvageable, it's 
 just a question of how...
 
 Carlo: Interesting point. In terms of how I'm fitting it, I just use the 
 LCF window to do a two-component fit. Nothing super fancy.
 
 But what you're suggesting is that maybe I have a misunderstanding in the 
 way I'm normalizing my data. That's entirely possible. I generally try to 
 get a nice flat background by following the "flat part" of the spectra but 
 in cases like this the pre- and post-edge lines end up not parallel. I can 
 force it to be parallel, and that helps the fit to behave better, but ends 
 up creating other normalization issues.
 
 
 Much obliged for the responses so far.
 
 
 
 Mike
 
 
 
 
> On Jan 15, 2019, at 4:42 PM, Carlo Segre  wrote:
> 
> 
> Hi Mike:
> 
> How are you trying to fit it?  It looks to me like the post edge line is 
> not in the right place.  You need to tune it by hand when you have such a 
> short energy range after the edge since the normalization is critically 
> dependent on how you set this line.
> 
> carlo
> 
>> On Tue, 15 Jan 2019, Mike Massey wrote:
>> 
>> Hi All,
>> 
>> 
>> Does anyone have advice for LCF of spectra with a small edge step?
>> 
>> I've recently found myself with more and more issues fitting spectra 
>> like the one shown in the attached photo, where the spectrum is of good 
>> quality, but the fits end up not working out due to normalization (as 
>> far as I can tell).
>> 
>> Sadly, I have so far ended up just throwing these fits out, but I'm 
>> hoping there is a better solution out there that someone might be able 
>> to recommend.
>> 
>> One solution is "get more of the element of interest," as a beamline 
>> scientist recently told me. I'm just reluctant to really load it up in 
>> the data collection, because at 2 keV I get nervous about artifacts like 
>> self-absorption.
>> 
>> Is there a better way? What am I missing?
>> 
>> Thanks for your thoughts,
>> 
>> 
>> 
>> Mike
> 
> -- 
> Carlo U. Segre -- Duchossois Leadership Professor of Physics
> Interim Chair, Department of Chemistry
> Director, Center for Synchrotron 

Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

[Christopher Patridge]

Hi Mike,

I would suggest that, as Carlo mentions, that because you cut off at 2200 eV, 
the post edge background function in purple might be skewed a bit.  I might be 
use values ~2190 eV and 2164 eV?  Though it appears to be a “flat” region where 
you place the points, it may actually not be all that flat if data was 
collected further out.  Even if you were to collected new data, if this short 
range is used and the same approach to normalization is used, I don’t know if 
LCF would improve.

Chris


> On Jan 15, 2019, at 8:23 PM, Mike Massey  wrote:
> 
> Hi Scott,
> 
> 
> I collect up to 2240 eV often, because that's about where the mirror stops, 
> but end up truncating it at 2200 eV before fitting because sometimes I end up 
> with all sorts of non-systematic background things at higher energies, 
> depending on the sample.
> 
> I still collect the data because it helps me to troubleshoot, but I chop it 
> before fitting because 2200 eV is the limit of what I normally consider 
> consistently "good data." I end up with spectra that, to my eye anyway, are 
> comparable. For dilute samples, I don't usually trust it beyond that. For 
> concentrated samples, I don't have a problem.
> 
> 
> Thanks,
> 
> 
> 
> Mike
> 
> 
> 
>> On Jan 15, 2019, at 5:12 PM, Scott Calvin  wrote:
>> 
>> Hi Mike,
>> 
>> Is there a reason the data stops at 2200 eV—e.g., is there another edge just 
>> above that?
>> 
>> —Scott
>> 
>>> On Jan 15, 2019, at 8:02 PM, Mike Massey  wrote:
>>> 
>>> Thanks Riti and Carlo.
>>> 
>>> Riti: will give it a go, thanks! I think the data are salvageable, it's 
>>> just a question of how...
>>> 
>>> Carlo: Interesting point. In terms of how I'm fitting it, I just use the 
>>> LCF window to do a two-component fit. Nothing super fancy.
>>> 
>>> But what you're suggesting is that maybe I have a misunderstanding in the 
>>> way I'm normalizing my data. That's entirely possible. I generally try to 
>>> get a nice flat background by following the "flat part" of the spectra but 
>>> in cases like this the pre- and post-edge lines end up not parallel. I can 
>>> force it to be parallel, and that helps the fit to behave better, but ends 
>>> up creating other normalization issues.
>>> 
>>> 
>>> Much obliged for the responses so far.
>>> 
>>> 
>>> 
>>> Mike
>>> 
>>> 
>>> 
>>> 
 On Jan 15, 2019, at 4:42 PM, Carlo Segre  wrote:
 
 
 Hi Mike:
 
 How are you trying to fit it?  It looks to me like the post edge line is 
 not in the right place.  You need to tune it by hand when you have such a 
 short energy range after the edge since the normalization is critically 
 dependent on how you set this line.
 
 carlo
 
> On Tue, 15 Jan 2019, Mike Massey wrote:
> 
> Hi All,
> 
> 
> Does anyone have advice for LCF of spectra with a small edge step?
> 
> I've recently found myself with more and more issues fitting spectra like 
> the one shown in the attached photo, where the spectrum is of good 
> quality, but the fits end up not working out due to normalization (as far 
> as I can tell).
> 
> Sadly, I have so far ended up just throwing these fits out, but I'm 
> hoping there is a better solution out there that someone might be able to 
> recommend.
> 
> One solution is "get more of the element of interest," as a beamline 
> scientist recently told me. I'm just reluctant to really load it up in 
> the data collection, because at 2 keV I get nervous about artifacts like 
> self-absorption.
> 
> Is there a better way? What am I missing?
> 
> Thanks for your thoughts,
> 
> 
> 
> Mike
 
 -- 
 Carlo U. Segre -- Duchossois Leadership Professor of Physics
 Interim Chair, Department of Chemistry
 Director, Center for Synchrotron Radiation Research and Instrumentation
 Illinois Institute of Technology
 Voice: 312.567.3498Fax: 312.567.3494
 se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
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Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

[Mike Massey]

Hi Scott,


I collect up to 2240 eV often, because that's about where the mirror stops, but 
end up truncating it at 2200 eV before fitting because sometimes I end up with 
all sorts of non-systematic background things at higher energies, depending on 
the sample.

I still collect the data because it helps me to troubleshoot, but I chop it 
before fitting because 2200 eV is the limit of what I normally consider 
consistently "good data." I end up with spectra that, to my eye anyway, are 
comparable. For dilute samples, I don't usually trust it beyond that. For 
concentrated samples, I don't have a problem.


Thanks,



Mike



> On Jan 15, 2019, at 5:12 PM, Scott Calvin  wrote:
> 
> Hi Mike,
> 
> Is there a reason the data stops at 2200 eV—e.g., is there another edge just 
> above that?
> 
> —Scott
> 
>> On Jan 15, 2019, at 8:02 PM, Mike Massey  wrote:
>> 
>> Thanks Riti and Carlo.
>> 
>> Riti: will give it a go, thanks! I think the data are salvageable, it's just 
>> a question of how...
>> 
>> Carlo: Interesting point. In terms of how I'm fitting it, I just use the LCF 
>> window to do a two-component fit. Nothing super fancy.
>> 
>> But what you're suggesting is that maybe I have a misunderstanding in the 
>> way I'm normalizing my data. That's entirely possible. I generally try to 
>> get a nice flat background by following the "flat part" of the spectra but 
>> in cases like this the pre- and post-edge lines end up not parallel. I can 
>> force it to be parallel, and that helps the fit to behave better, but ends 
>> up creating other normalization issues.
>> 
>> 
>> Much obliged for the responses so far.
>> 
>> 
>> 
>> Mike
>> 
>> 
>> 
>> 
>>> On Jan 15, 2019, at 4:42 PM, Carlo Segre  wrote:
>>> 
>>> 
>>> Hi Mike:
>>> 
>>> How are you trying to fit it?  It looks to me like the post edge line is 
>>> not in the right place.  You need to tune it by hand when you have such a 
>>> short energy range after the edge since the normalization is critically 
>>> dependent on how you set this line.
>>> 
>>> carlo
>>> 
 On Tue, 15 Jan 2019, Mike Massey wrote:
 
 Hi All,
 
 
 Does anyone have advice for LCF of spectra with a small edge step?
 
 I've recently found myself with more and more issues fitting spectra like 
 the one shown in the attached photo, where the spectrum is of good 
 quality, but the fits end up not working out due to normalization (as far 
 as I can tell).
 
 Sadly, I have so far ended up just throwing these fits out, but I'm hoping 
 there is a better solution out there that someone might be able to 
 recommend.
 
 One solution is "get more of the element of interest," as a beamline 
 scientist recently told me. I'm just reluctant to really load it up in the 
 data collection, because at 2 keV I get nervous about artifacts like 
 self-absorption.
 
 Is there a better way? What am I missing?
 
 Thanks for your thoughts,
 
 
 
 Mike
>>> 
>>> -- 
>>> Carlo U. Segre -- Duchossois Leadership Professor of Physics
>>> Interim Chair, Department of Chemistry
>>> Director, Center for Synchrotron Radiation Research and Instrumentation
>>> Illinois Institute of Technology
>>> Voice: 312.567.3498Fax: 312.567.3494
>>> se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
>>> ___
>>> 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] Advice on using Athena for XANES LCF on spectra with a small edge step?

[Scott Calvin]

Hi Mike,

Is there a reason the data stops at 2200 eV—e.g., is there another edge just 
above that?

—Scott

> On Jan 15, 2019, at 8:02 PM, Mike Massey  wrote:
> 
> Thanks Riti and Carlo.
> 
> Riti: will give it a go, thanks! I think the data are salvageable, it's just 
> a question of how...
> 
> Carlo: Interesting point. In terms of how I'm fitting it, I just use the LCF 
> window to do a two-component fit. Nothing super fancy.
> 
> But what you're suggesting is that maybe I have a misunderstanding in the way 
> I'm normalizing my data. That's entirely possible. I generally try to get a 
> nice flat background by following the "flat part" of the spectra but in cases 
> like this the pre- and post-edge lines end up not parallel. I can force it to 
> be parallel, and that helps the fit to behave better, but ends up creating 
> other normalization issues.
> 
> 
> Much obliged for the responses so far.
> 
> 
> 
> Mike
> 
> 
> 
> 
>> On Jan 15, 2019, at 4:42 PM, Carlo Segre  wrote:
>> 
>> 
>> Hi Mike:
>> 
>> How are you trying to fit it?  It looks to me like the post edge line is not 
>> in the right place.  You need to tune it by hand when you have such a short 
>> energy range after the edge since the normalization is critically dependent 
>> on how you set this line.
>> 
>> carlo
>> 
>>> On Tue, 15 Jan 2019, Mike Massey wrote:
>>> 
>>> Hi All,
>>> 
>>> 
>>> Does anyone have advice for LCF of spectra with a small edge step?
>>> 
>>> I've recently found myself with more and more issues fitting spectra like 
>>> the one shown in the attached photo, where the spectrum is of good quality, 
>>> but the fits end up not working out due to normalization (as far as I can 
>>> tell).
>>> 
>>> Sadly, I have so far ended up just throwing these fits out, but I'm hoping 
>>> there is a better solution out there that someone might be able to 
>>> recommend.
>>> 
>>> One solution is "get more of the element of interest," as a beamline 
>>> scientist recently told me. I'm just reluctant to really load it up in the 
>>> data collection, because at 2 keV I get nervous about artifacts like 
>>> self-absorption.
>>> 
>>> Is there a better way? What am I missing?
>>> 
>>> Thanks for your thoughts,
>>> 
>>> 
>>> 
>>> Mike
>> 
>> -- 
>> Carlo U. Segre -- Duchossois Leadership Professor of Physics
>> Interim Chair, Department of Chemistry
>> Director, Center for Synchrotron Radiation Research and Instrumentation
>> Illinois Institute of Technology
>> Voice: 312.567.3498Fax: 312.567.3494
>> se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
>> ___
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Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

[Mike Massey]

Thanks Riti and Carlo.

Riti: will give it a go, thanks! I think the data are salvageable, it's just a 
question of how...

Carlo: Interesting point. In terms of how I'm fitting it, I just use the LCF 
window to do a two-component fit. Nothing super fancy.

But what you're suggesting is that maybe I have a misunderstanding in the way 
I'm normalizing my data. That's entirely possible. I generally try to get a 
nice flat background by following the "flat part" of the spectra but in cases 
like this the pre- and post-edge lines end up not parallel. I can force it to 
be parallel, and that helps the fit to behave better, but ends up creating 
other normalization issues.


Much obliged for the responses so far.



Mike




> On Jan 15, 2019, at 4:42 PM, Carlo Segre  wrote:
> 
> 
> Hi Mike:
> 
> How are you trying to fit it?  It looks to me like the post edge line is not 
> in the right place.  You need to tune it by hand when you have such a short 
> energy range after the edge since the normalization is critically dependent 
> on how you set this line.
> 
> carlo
> 
>> On Tue, 15 Jan 2019, Mike Massey wrote:
>> 
>> Hi All,
>> 
>> 
>> Does anyone have advice for LCF of spectra with a small edge step?
>> 
>> I've recently found myself with more and more issues fitting spectra like 
>> the one shown in the attached photo, where the spectrum is of good quality, 
>> but the fits end up not working out due to normalization (as far as I can 
>> tell).
>> 
>> Sadly, I have so far ended up just throwing these fits out, but I'm hoping 
>> there is a better solution out there that someone might be able to recommend.
>> 
>> One solution is "get more of the element of interest," as a beamline 
>> scientist recently told me. I'm just reluctant to really load it up in the 
>> data collection, because at 2 keV I get nervous about artifacts like 
>> self-absorption.
>> 
>> Is there a better way? What am I missing?
>> 
>> Thanks for your thoughts,
>> 
>> 
>> 
>> Mike
> 
> -- 
> Carlo U. Segre -- Duchossois Leadership Professor of Physics
> Interim Chair, Department of Chemistry
> Director, Center for Synchrotron Radiation Research and Instrumentation
> Illinois Institute of Technology
> Voice: 312.567.3498Fax: 312.567.3494
> se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
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Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

[Carlo Segre]

Hi Mike:

How are you trying to fit it?  It looks to me like the post edge line is 
not in the right place.  You need to tune it by hand when you have such a 
short energy range after the edge since the normalization is critically 
dependent on how you set this line.


carlo

On Tue, 15 Jan 2019, Mike Massey wrote:


Hi All,


Does anyone have advice for LCF of spectra with a small edge step?

I've recently found myself with more and more issues fitting spectra like the 
one shown in the attached photo, where the spectrum is of good quality, but the 
fits end up not working out due to normalization (as far as I can tell).

Sadly, I have so far ended up just throwing these fits out, but I'm hoping 
there is a better solution out there that someone might be able to recommend.

One solution is "get more of the element of interest," as a beamline scientist 
recently told me. I'm just reluctant to really load it up in the data collection, because 
at 2 keV I get nervous about artifacts like self-absorption.

Is there a better way? What am I missing?

Thanks for your thoughts,



Mike




--
Carlo U. Segre -- Duchossois Leadership Professor of Physics
Interim Chair, Department of Chemistry
Director, Center for Synchrotron Radiation Research and Instrumentation
Illinois Institute of Technology
Voice: 312.567.3498Fax: 312.567.3494
se...@iit.edu   http://phys.iit.edu/~segre   se...@debian.org
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Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

[Mike Massey]

Thanks for the response!

I should clarify, the data are collected in fluorescence, concentration is 
perhaps in the hundreds of ppm to tenths-of-percent range in this case.

Personally I haven't had great luck with self-absorption correction in the past 
(actually I've had basically no luck), so for concentrated samples I generally 
follow Scott Calvin's "cut twice, measure once" rule and that has been helpful. 
When the concentrations get _too low_ though, it seems that I run into this 
problem...


Cheers,


Mike








> On Jan 15, 2019, at 4:31 PM, "daltonabd...@gmail.com" 
>  wrote:
> 
> Hello, Mike et al., 
> 
> you can correct for self-absorption using the "self-absorption correction 
> tool" in Athena, as long as the chemical composition of your sample is known.
> 
> In case it's not possible to determine the chemical composition of you 
> sample, and your sample is conductive, then running your experiment in total 
> electron yield (TEY) mode would be an alternative.
> 
> If you're sample isn't suitable for TEY, and the only choice you have left is 
> to run it in fluorescence mode, then you should dilute your sample to a total 
> concentration of P of ~ 0.1 - 0.15% to avoid self-absorption.
> 
> It's very important to think through your experiment/samples before you get 
> to the beamline as it avoids you running into such issues, saving you a lot 
> of time. 
> 
> Hope it helps ;)
> 
> 
>  - Dalton Abdala
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Re: [Ifeffit] Advice on using Athena for XANES LCF on spectra with a small edge step?

[daltonabd...@gmail.com]

Hello, Mike et al.,

you can correct for self-absorption using the "self-absorption correction
tool" in Athena, as long as the chemical composition of your sample is
known.

In case it's not possible to determine the chemical composition of you
sample, and your sample is conductive, then running your experiment in
total electron yield (TEY) mode would be an alternative.

If you're sample isn't suitable for TEY, and the only choice you have left
is to run it in fluorescence mode, then you should dilute your sample to a
total concentration of P of ~ 0.1 - 0.15% to avoid self-absorption.

It's very important to think through your experiment/samples before you get
to the beamline as it avoids you running into such issues, saving you a lot
of time.

Hope it helps ;)


 - Dalton Abdala
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[Ifeffit] Nickel Chloride XAS data at RT and 320C

[Gill, Simerjeet]

Hi,

I am working with a molten salt system with Nickel Chloride as one of the 
components. If you have measured XAS data on anhydrous and hydrated Nickel 
Chloride at RT and 320C, I would really appreciate if you could share the raw 
data with me.

Thanks in advance for your help!

Simer

Simerjeet K Gill,
Materials Scientist,
Nuclear Science and Technology Department,
Brookhaven National Lab,
Upton, NY 11973

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Subject: Ifeffit Digest, Vol 191, Issue 7

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Today's Topics:

   1. Re: Standard deviation of R value (Matt Newville)
   2. Re: Standard deviation of R value (Anatoly Frenkel)
   3. Re: Standard deviation of R value (Erin Finley)


--

Message: 1
Date: Fri, 11 Jan 2019 10:04:49 -0600
From: Matt Newville 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Standard deviation of R value
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Hi Erin,

On Fri, Jan 11, 2019 at 8:19 AM Erin Finley  wrote:

> Hello, I see in many publications the R value reported with a standard 
> deviation. However, when I look at my resulting data from a fit I 
> don't see one listed. I am still new to EXAFS research and so I am 
> wondering where I can get this information. I am assuming I need to 
> calculate it from another parameter I am just not sure which one.
>
>
The uncertainties in R are typically in the fit report.  But also, we typically 
refine a "delR" parameter that is R - Reff, where Reff is the distance (half 
path-lengh) for the scattering path.  So, if you don't see an uncertainty 
reported for R but do see an uncertainty for delR (or whatever parameter name 
you used), use that.  The uncertainty in R will
(normally) be the uncertainty in delR.

If I'm misunderstanding the question, pleas give more details about what you 
are doing.

--Matt






Thanks for your help!
> Cheers,
>
> --
> Erin Finley
> PhD Candidate
> Brgoch Research Group
> Department of Chemistry
> University of Houston
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--Matt Newville  630-252-0431
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Message: 2
Date: Fri, 11 Jan 2019 11:18:03 -0500
From: Anatoly Frenkel 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Standard deviation of R value
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As an additional comment, it is a murky issue whether the reported thing 
together with R is the standard deviation. It is not easy to find it in the 
literature but there are some papers dating back to the 1990s that state that 
the uncertainties reported in the EXAFS fitting results correspond to the 95% 
confidence level which means 2 standard deviations for an approximately normal 
data set. I don't think it is correct. Regardless whether the distribution of 
some or all fitting variables are treated by the Levenburg-Marquartd method as 
normal or not, the reported error is really not a standard deviation but a 
square root of the element in a covariance matrix. What is the relationship of 
that and the standard deviation of the fitting variable is one of the few 
remaining unsolved mysteries in EXAFS analysis.

Anatoly


On Fri, Jan 11, 2019 at 11:05 AM Matt Newville 
wrote:

> Hi Erin,
>
> On Fri, Jan 11, 2019 at 8:19 AM Erin Finley  wrote:
>
>> Hello, I see in many publications the R value reported with a 
>> standard deviation. However, when I look at my resulting data from a 
>> fit I don't see one listed. I am still new to EXAFS research and so I 
>> am wondering where I can get this information. I am assuming I need 
>> to calculate it from another parameter I am just not sure which one.
>>
>>
> The uncertainties in R are typically in the fit report.  But also, we 
> typically refine a "delR" parameter that is R - Reff, where Reff is 
> the distance (half path-lengh) for the scattering path.  So, if you 
> don't see an uncertainty