Re: [Ifeffit] P K-edge EXAFS

[Mike Massey]

The other difficulty I have experienced with P EXAFS is that a lot of the 
second-shell backscatterers are fairly weak, so picking that signal out is 
pretty difficult.

I have some spectra of minerals and that's where I've wanted to start with P 
EXAFS (since the structures are well-constrained). But as has been mentioned, 
low-frequency oscillations and background subtraction have massive impacts on 
the P K-edge EXAFS function (tested this by taking spectra of the same sample 
during different runs and getting different EXAFS due to slightly different 
background).

I don't think it's necessarily impossible, I just personally put it in the 
not-right-now basket.





> On Sep 14, 2023, at 07:42, Mike Massey  wrote:
> 
> 
> In my experience the main difficulties with EXAFS on P (phosphate) come from 
> two factors (not signal to noise, it's not hard to get a nice smooth line, 
> but):
> 
> 1) You've got 4 O atoms, guaranteed, so any other signal will be small and on 
> top of that very strong signal generated from the first-neighbor O
> 
> Unfortunately,
> 
> 2) You have very limited data range, either due to instrumental limitations, 
> or due to interference from sulfur
> 
> Don't get me wrong I still have some data sitting around and I'd love to try 
> P EXAFS analysis on it just to try and grasp that brass ring but...It's not 
> the easiest task ever.
> 
> If you want good data quality "scan longer" is always an option. Some might 
> think it's crazy but I do think I have some P XAS data where I took 30 or 60 
> scans, maybe overnight or something. The scans are so short that repeats are 
> easy.
> 
> 
> Hope this commentary is helpful.
> 
> 
> 
> Mike
> 
> 
> 
> 
>>> On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves  wrote:
>>> 
>> 
>> Hi there,
>> 
>> I begin by examining phosphorus adsorption by goethite, hematite, and 
>> gibbsite.
>> 
>> Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K 
>> edge that can be properly used, i.e., spectra with a high signal-to-noise 
>> ratio, especially for dilute samples?
>> 
>> Would it be possible to use arsenic as a phosphorus proxy to get conclusions 
>> from As K-edge EXAFS data that could be extended to P?
>> 
>> Thank you.
>> 
>> 
>> 
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Re: [Ifeffit] P K-edge EXAFS

[Mike Massey]

In my experience the main difficulties with EXAFS on P (phosphate) come from 
two factors (not signal to noise, it's not hard to get a nice smooth line, but):

1) You've got 4 O atoms, guaranteed, so any other signal will be small and on 
top of that very strong signal generated from the first-neighbor O

Unfortunately,

2) You have very limited data range, either due to instrumental limitations, or 
due to interference from sulfur

Don't get me wrong I still have some data sitting around and I'd love to try P 
EXAFS analysis on it just to try and grasp that brass ring but...It's not the 
easiest task ever.

If you want good data quality "scan longer" is always an option. Some might 
think it's crazy but I do think I have some P XAS data where I took 30 or 60 
scans, maybe overnight or something. The scans are so short that repeats are 
easy.


Hope this commentary is helpful.



Mike




> On Sep 14, 2023, at 07:04, Marcelo Eduardo Alves  wrote:
> 
> 
> Hi there,
> 
> I begin by examining phosphorus adsorption by goethite, hematite, and 
> gibbsite.
> 
> Why is it difficult, if not impossible, to obtain EXAFS spectra at the P-K 
> edge that can be properly used, i.e., spectra with a high signal-to-noise 
> ratio, especially for dilute samples?
> 
> Would it be possible to use arsenic as a phosphorus proxy to get conclusions 
> from As K-edge EXAFS data that could be extended to P?
> 
> Thank you.
> 
> 
> 
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Re: [Ifeffit] Brain teaser

[Mike Massey]

A question because I'm not really super clear on how harmonics work: (I'll get to the question in a moment...) I note that I0 starts to go non-linear around 12200-12400 eV and stays that way. So an increase (proportional?) in the amount of signal in It might be happening at around the same point.Could Pd fluorescence into It be impacting the signal in It? I realize that the Pd emission lines are very low in energy but they are around 3k eV.I'm not super familiar with alloy systems but I did have an issue once upon a time with back fluorescence into an ion chamber and things went a bit wonky. This wouldn't exactly be "back" fluorescence, but if the system is mostly Pd with a little bit of Au, I guess...? And it might be easy enough to test, just put a high-pass filter in front of It?I got nothin' but it's kinda fun to take a shot. Cheers,MikeOn Jun 16, 2023, at 03:26, Matt Newville  wrote:Hi Anatoly, I think Robert or Matthew made this point, but if set up for Pd, the mirror angle may have been chosen to reject ~70 keV, but possibly not 36 keV -- the harmonic at the Au edge.  Do you know what the mirror angle was?    The Ar-filled I0 would be very efficient at absorbing 12 keV, and only pretty efficient at absorbing 36 keV.   That would leave a more harmonic-rich beam exiting I0 and hitting the sample than entering I0.  The good news is that the dense Pd/Au sample would be efficient at absorbing 36 keV too (but it was ~1 absorption length at 24 keV?) too.Mono reflectivity of 36 keV vs 12 keV might also factor in.  If you were not deliberately detuning but the crystals were slightly misaligned,  the harmonic content may change significantly over the scan range.   I would not guess that to dominate, but maybe it factors in.On Thu, Jun 15, 2023 at 9:54 AM Anatoly Frenkel  wrote:Thank you, Matt. Ion chambers were filled with 90% Ar, and Pt coating was used, because we were measuring Pd K edge for the project, but we decided to look at the Au edge for testing purposes. AnatolyOn Jun 15, 2023, at 10:45 AM, Matt Newville  wrote:I'm not sure why the intensity would go up unless the ion chamber was poorly set up.   But, as others have pointed out, the mirror reflectivity for a Pt mirror should not change significantly over this energy range - the energy range is not that close to the Pt L3 or L2 edges.    Depending on where it was located, fluorescence from the Pt mirror might pollute the signal in the I0 ion chamber, but that would also likely be a fairly constant background. But, why would you fill the I0 ion chamber with Argon?  A 10-cm ion chamber filled with Ar would absorb about 50% of the beam at 12 keV.   Even at 24 keV, that would absorb 8% of the beam - not necessarily a problem but also probably generating at least a micro-Amp, so way more signal than you would need.For mirror reflectivity curves, allow me to humbly remind everyone of   https://xraydb.xrayabsorption.org/reflectivity/Pt/21.45/2.5/10/s/1000/51000/50/platinum/linearwhich is both interactive and works with X-ray energies above 30 keV.On Wed, Jun 14, 2023 at 7:28 PM Anatoly Frenkel  wrote:Hello, all. It is a low- to medium- level brain teaser.Pt-coated collimating mirror was in place for Pd K-edge measurement, but Au L3-edge of Pd-Au alloy was measured (for testing purposes). I0 and It detectors were both Ar filled ionization chambers. Because of the energy dependence of reflectivity of the Pt mirror, I0 intensity was strongly nonlinear (blue curve). However, the transmission intensity in the It detector was almost linear (red curve). Why? Anatoly
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Re: [Ifeffit] Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra

[Mike Massey]

Hi Patricia,


When you say "worse than the initial one," what do you mean?

If it's a "worse" match than nonsensical fit results, but makes some physical 
and chemical sense, I'd personally argue it's a much better fit ;)

What you are doing seems reasonable to me, but I would further recommend 
keeping your fit component selection as simple as possible.

I'm a big proponent of two-component fits, maybe three if there's a really good 
reason. I feel like a lot of people do multicomponent (3-4 fitting spectra, 
maybe even more) LCF with the argument that the inclusion of additional 
components improves the fit statistics...But to me that gives a false sense of 
certainty that the technique doesn't really allow (at least for the systems I 
work with).

For reporting qualitative trends, it seems like you're on the right track. 
Perhaps unless it's a qualitative trend of a minor component that might not 
even be there at all and you're basing your entire argument on it definitely 
being there, which uhh. Seems to happen a lot.


Cheers,



Mike



> On Mar 11, 2021, at 1:42 AM, Patricia Poths  
> wrote:
> 
> 
> Hi,
> 
> I am a theoretical chemistry PhD student working on fitting experimental 
> spectra with computed spectra in order to get a better understanding of the 
> composition. In the LCF process with athena, I have found that when I allow 
> "sum coefficients to 1", I get an unphysical negative coefficient of the last 
> standard- after reading through the mailing list I understood why, and so no 
> longer use that. The sum of my coefficients during the fitting now is close 
> to 1- generally within the range of 0.95-1.1 at the absolute extremes, but 
> more often around ~0.98- ~1.05. 
> 
> In order to compare these coefficients, I renormalize them to 1, so they can 
> represent the fractions of each component present. However, to test this I 
> took the new normalized coefficients and summed up the standards with their 
> respective weights to create this normalized "fit", and found that it is 
> worse than the initial one. Is this something I should be concerned about 
> when reporting the qualitative trends in how the composition changes? And if 
> so, is there a better way to do the fits in a more normalized way?
> 
> Many thanks,
> Patricia
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[Ifeffit] Wyartite XAS spectrum?

[Mike Massey]

Hi All,


And now for something not-phosphorus...

Does anyone happen to have a wyartite U L3-edge XAS spectrum laying around?
If you do, and happened to be willing to talk with me about it, I would be
most grateful.


Kind Regards,



Mike
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Re: [Ifeffit] P K-edge XANES spectrum question (Mangold, Stefan (IPS))

[Mike Massey]

Yes I was wondering about this as well. Technically P(III) exists, and maybe 
one could find it in an AMBR? But I don't think anyone has a clue about what 
the K-edge XANES spectrum looks like.

Has anyone ever collected a phosphite spectrum? That would be pretty cool. I 
would totally do it but I'm not in a position to collect new synchrotron data 
anymore...



Mike



> On Oct 17, 2020, at 10:59 AM, Ganga Hettiarachchi  wrote:
> 
> 
> Stefan,
> Thanks for sharing your thoughts. Please share if you do have spectra for any 
> other P (i.e., not +5).
>  
> Best regards,
>  
> Ganga
>  
> 
>  
> Ganga M. Hettiarachchi, Ph.D.
> Professor of Soil and Environmental Chemistry
> Department of Agronomy
> 2107 Throckmorton Plant Sciences Center
> 1712 Claflin Road
> Kansas State University
> Manhattan, KS 66506 USA
>  
> 785-532-7209 (office)
> 785-532-6094 (FAX)
>  
> http://www.agronomy.k-state.edu/research/soil-and-environment/soil-environment-chem/
> http://www.agronomy.k-state.edu/people/faculty/hettiarachchi-ganga/index.html
>  
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Re: [Ifeffit] P K-edge XANES spectrum question

[Mike Massey]

I recommend diluting this sample by a lot (20x maybe, or more) and collecting 
another spectrum. I've had instances of strange features in P spectra that 
ended up being weird self-absorption type artifacts.

I will dig through the spectra I have from similar samples, this one reminds me 
of a spectrum I saw once, perhaps in a similar system...It would be interesting 
if we inadvertently got similar results. Thanks for sharing!



Mike





> On Oct 16, 2020, at 10:22 PM, Dean Hesterberg  
> wrote:
> 
> 
> Hello Ganga,
> 
> That is a very interesting spectrum. Given what you said about the system, 
> the lower energy feature at ~ 2146 eV should be Fe(III)-bonded phosphate and 
> the feature at ~2149 eV should be Al(III)-bonded phosphate. Both produce 
> pre-white line absorption peaks, but the Al-bonded phosphate peak is closer 
> to the white line and less distinct in spectra of Al-phosphates like 
> variscite and non-crystalline Al-phosphate, for example (see Khare et al. 
> 2007. Geochimica et Cosmochimica Acta 71:4405, Fig. 5C). A significant 
> proportion of the phosphate in your system apparently precipitated with Al-13 
> polymer structures in the aluminum chlorohydrate.
> 
> Dean 
> 
>> On Fri, Oct 16, 2020 at 1:26 AM Ganga Hettiarachchi  wrote:
>> All,
>> 
>> Can anyone provide some insight into the pre-edge “features” in this P XANES 
>> spectrum?
>> 
>> This is the P XANES spectrum we got for a recovered P-product (rich in Fe 
>> and Al) from wastewater using the AnMBR technology. During the coagulation 
>> process, our collaborators (environmental engineers) used stock solutions of 
>> aluminum chlorohydrate (ACH) and FeCl3.
>> 
>>  
>> 
>> Thanks very much.
>> 
>>  
>> 
>> Best regards,
>> 
>>  
>> 
>> Ganga
>> 
>>  
>> 
>> 
>> 
>>  
>> 
>> Ganga M. Hettiarachchi, Ph.D.
>> 
>> Professor of Soil and Environmental Chemistry
>> 
>> Department of Agronomy
>> 
>> 2107 Throckmorton Plant Sciences Center
>> 
>> 1712 Claflin Road
>> 
>> Kansas State University
>> 
>> Manhattan, KS 66506 USA
>> 
>>  
>> 
>> 785-532-7209 (office)
>> 
>> 785-532-6094 (FAX)
>> 
>>  
>> 
>> http://www.agronomy.k-state.edu/research/soil-and-environment/soil-environment-chem/
>> http://www.agronomy.k-state.edu/people/faculty/hettiarachchi-ganga/index.html
>> 
>>  
>> 
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> 
> 
> -- 
> DEAN HESTERBERG
> William Neal Reynolds Distinguished Professor of Soil Chemistry
> Dept. of Crop and Soil Sciences
> NC State University
> 
> email: dean_hesterb...@ncsu.edu
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Re: [Ifeffit] Requesting guidance in understanding results from Athena

[Mike Massey]

It sounds to me like you are understanding things well. The short, short 
version is that the purpose of the rbkg parameter is to filter out the 
low-frequency oscillations (arising from any of numerous sources) in the 
spectrum, that correspond to interatomic distances that make no physical sense.

Or maybe I don't get it either ;)

Scott Calvin's book has a nice discussion of these points, I recommend it.


Kind Regards,


 Mike




> On Sep 14, 2020, at 9:18 AM, Deepak Varanasi  wrote:
> 
> 
> Good afternoon
>  
> The problem lies with understanding the meaning behind signals occurring 
> below the 1-angstrom mark. The location of the peaks and the physical meaning 
> thereof are making no sense to me. Kindly provide me with your guidance in 
> facilitating my understanding.
>  
> Yours Sincerely
> Deepak Varanasi
>  
> Sent from Mail for Windows 10
>  
> From: Anatoly Frenkel
> Sent: Sunday, September 13, 2020 12:58
> To: XAFS Analysis using Ifeffit
> Subject: Re: [Ifeffit] Requesting guidance in understanding results from 
> Athena
>  
> Where is the conundrum? You make rbkg smaller and you see more low frequency 
> features in EXAFS, as expected.
> Anatoly
>  
>  
>  
> On Sun, Sep 13, 2020 at 1:47 PM Deepak Varanasi  wrote:
> Good afternoon
>  
> I hope that you are doing well and are healthy. My name is Deepak
> Varanasi and ii am an undergraduate student at Middle Tennessee State 
> University In need of your guidance for my thesis project. I am having  
> trouble interpreting results for my EXAFS analysis done on Athena – 
> specifically, the emergence of a signal in R-space, below the 1 – angstrom 
> mark,  after suppressing it via its rbkg parameter (signified by the black 
> arrows). I have checked my back ground reduction and normalization multiple 
> time sand have failed to isolate the reason behind my results or maybe it is 
> the due to the gaps in my knowledge that prohibit my understanding of the 
> results. At the risk of sounding armature, may I request your guidance in 
> resolving my conundrum please? I would be honored to have your council in 
> solving, understanding and comprehending the physical and chemical 
> implications of my results. For your convenience, I have also appended a 
> picture of my results to illustrate my query. Kindly contact me at your 
> earliest convenience and please stay safe and healthy.
>  
> Yours Sincerely
> Deepak Varanasi
>  
> P.S.: For your convenience, I have also appended a picture of my results to 
> illustrate my query.
>  
> <57BA12E4C0E6403EA1E7F05BCB60610D.png>
>  
> 
>  
>  
> Resulting R – space graphs: -
>  
> <13111BEC5BCF46A8A8E5CDAE32782D44.png>
>  
>  
> 
>  
> <4A7FE6C9D4EC4E0F83E8B43E23D5ED48.png>
>  
> Resulting R – space graphs: -
>  
>  
> <83E495E5D37B431AB31567B6ED982716.png>
>  
>  
>  
>  
>  
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Re: [Ifeffit] Reported W L3-edge and L2-edge energy

[Mike Massey]

I agree Matthew, I also tend to use the primary K-edge peak for P calibration, 
but one issue to be wary of is attenuation/flattening of the primary peak (if 
one is using a concentrated sample).

Gypsum sounds like a good material to use for S, since it is commonly available 
and probably not too variable. My material of choice for P (lazulite) might 
fail on both counts, so it might be a poor choice.



Mike





> On May 8, 2020, at 10:19 AM, Matthew Marcus  wrote:
> 
> For elements like P and S, people often use the energies of peaks. These are 
> more immune to noise, energy-resolution effects and overabsorption than 
> inflection points are.  For instance, on ALS 10.3.2, I used the sulfate peak 
> of gypsum set at 2482.74eV.  I forget where I got that number.  Going down to 
> soft X-rays, a common convention for the carbon edge is to use a pair of 
> sharp peaks in CO2 gas at 292.74 and 294.96eV.
>mam
> 
>> On 5/7/2020 3:09 PM, Mike Massey wrote:
>> Hi Matt,
>> Indeed, in my experience (which is limited to one beamline at one 
>> synchrotron facility for P XAS), once it is calibrated, the energy selection 
>> tends to be quite stable, so I think you're on-target there.
>> The trouble I still run into, though, is comparability of data between 
>> studies. The difficulty is magnified by the fact that people tend to 
>> identify certain near-edge features by the energy range at which they occur. 
>> I do the same, of course, but I also try to carefully document the material 
>> and energy I used to calibrate the monochromator.
>> For the P K-edge, it doesn't really seem like people have settled on a 
>> convention for calibrating the monochromator, unlike in the case of iron, 
>> for example (where one just uses a foil and sets some feature of that 
>> spectrum to their preferred value). If everyone was using the same thing all 
>> would be happy, but most people use different materials and different 
>> values. So datasets for P at the K-edge really aren't too comparable just 
>> yet.
>> Sorry to hijack the conversation, it's just an issue I've been mulling over 
>> for a few years. The discussion of energy calibration values made me think 
>> of it again.
>> Best,
>> Mike
>>>> On May 8, 2020, at 8:51 AM, Matt Newville  
>>>> wrote:
>>> 
>>> 
>>> Hi Mike,
>>> 
>>> 
>>>> On Tue, May 5, 2020 at 10:56 PM Mike Massey >>> <mailto:mmas...@gmail.com>> wrote:
>>> 
>>>On a tangentially related topic, I find that phosphorus K-edge XAS
>>>energy calibration conventions are still in a bit of a "Wild West"
>>>state, with a wide variety of materials and values in use for
>>>energy calibration. As an extreme example, one or two frequently
>>>cited papers in my field from the 2000s don't even report the
>>>material or value used for energy calibration, and only show
>>>portions of the spectra on an energy axis with values relative to
>>>an unknown E0.
>>> 
>>> 
>>> I have never measured a P K edge, or indeed any edge lower in energy than 
>>> the S K edge (ignoring some X-ray raman work).  But if one is using a 
>>> Si(111) double-crystal monochromator where P or S is approximately the 
>>> low-energy (high-angle) limit, then it really should be that the 
>>> calibration does not drift much and cannot be too wrong at low energies.
>>> 
>>> That is, a mono calibration is controlled by a d-spacing and angular 
>>> offset. Normally (or perhaps, in my experience), "re-calibrating" is done 
>>> by changing the angular offset, leaving the d-spacing alone.  That is, the 
>>> d-spacing is presumably known, at least to within some thermal drift.
>>> If that is the case that the d-spacing really is not changing and what 
>>> needs to be refined is the angular offset, then setting the offset at 
>>> relatively high energy edges will be much more sensitive, and changing the 
>>> angular offset to that a high-energy edge is correct should move lower 
>>> energy edges by a smaller amount.   The corollary is that you have to move 
>>> the offset a lot to move the P  K edge around, and that would have a larger 
>>> (and ever-increasing) impact on higher energy edges such as Ca, Fe, Cu or 
>>> Mo.
>>> 
>>> The counter-argument is also true:  d-spacing has a bigger effect on the 
>>> high-angle / low-energy edges.
>>> 
>>> So, if you believe the mono d-spacing (or you believe the beamline 
>>> scientist

Re: [Ifeffit] Reported W L3-edge and L2-edge energy

[Mike Massey]

Hi Matt,


Indeed, in my experience (which is limited to one beamline at one synchrotron 
facility for P XAS), once it is calibrated, the energy selection tends to be 
quite stable, so I think you're on-target there.

The trouble I still run into, though, is comparability of data between studies. 
The difficulty is magnified by the fact that people tend to identify certain 
near-edge features by the energy range at which they occur. I do the same, of 
course, but I also try to carefully document the material and energy I used to 
calibrate the monochromator.

For the P K-edge, it doesn't really seem like people have settled on a 
convention for calibrating the monochromator, unlike in the case of iron, for 
example (where one just uses a foil and sets some feature of that spectrum to 
their preferred value). If everyone was using the same thing all would be 
happy, but most people use different materials and different values. So 
datasets for P at the K-edge really aren't too comparable just yet.

Sorry to hijack the conversation, it's just an issue I've been mulling over for 
a few years. The discussion of energy calibration values made me think of it 
again.


Best,



Mike




> On May 8, 2020, at 8:51 AM, Matt Newville  wrote:
> 
> 
> Hi Mike, 
> 
> 
>> On Tue, May 5, 2020 at 10:56 PM Mike Massey  wrote:
>> On a tangentially related topic, I find that phosphorus K-edge XAS energy 
>> calibration conventions are still in a bit of a "Wild West" state, with a 
>> wide variety of materials and values in use for energy calibration. As an 
>> extreme example, one or two frequently cited papers in my field from the 
>> 2000s don't even report the material or value used for energy calibration, 
>> and only show portions of the spectra on an energy axis with values relative 
>> to an unknown E0.
>> 
> 
> I have never measured a P K edge, or indeed any edge lower in energy than the 
> S K edge (ignoring some X-ray raman work).  But if one is using a Si(111) 
> double-crystal monochromator where P or S is approximately the low-energy 
> (high-angle) limit, then it really should be that the calibration does not 
> drift much and cannot be too wrong at low energies.  
> 
> That is, a mono calibration is controlled by a d-spacing and angular offset. 
> Normally (or perhaps, in my experience), "re-calibrating" is done by changing 
> the angular offset, leaving the d-spacing alone.  That is, the d-spacing is 
> presumably known, at least to within some thermal drift. 
> If that is the case that the d-spacing really is not changing and what needs 
> to be refined is the angular offset, then setting the offset at relatively 
> high energy edges will be much more sensitive, and changing the angular 
> offset to that a high-energy edge is correct should move lower energy edges 
> by a smaller amount.   The corollary is that you have to move the offset a 
> lot to move the P  K edge around, and that would have a larger (and 
> ever-increasing) impact on higher energy edges such as Ca, Fe, Cu or Mo.  
> 
> The counter-argument is also true:  d-spacing has a bigger effect on the 
> high-angle / low-energy edges. 
> 
> So, if you believe the mono d-spacing (or you believe the beamline scientist 
> who believes it ;)) then calibrate at the highest energy you can.   The Kraft 
> values don't go very low in energy.  
> 
> All that said, if using a different mono crystal such as InSb or more exotic 
> crystals, I have no idea how stable those are.
> 
> 
>> I too have picked my own material and value, and will be the first to 
>> acknowledge that I did so out of necessity and ease of comparison to other 
>> available data, rather than because I thought it was correct.
>> 
>> The issue of calibration conventions and values definitely seems to be one 
>> that merits continued discussion. It has been interesting to watch things 
>> evolve over time in the case of iron, for example (it's good to know that 
>> 7110.75 is a candidate calibration value...) I appreciate Matt's detailed 
>> thoughts, and the data that he's been working with. Thanks Matt!
>> 
> 
>> Cheers,
>> 
>> 
>> 
>> Mike
>> 
>> 
>> 
>> 
>> 
>>>> On May 6, 2020, at 3:32 PM, Matt Newville  
>>>> wrote:
>>>> 
>>> 
>>> Hi Simon,
>>> 
>>> This is definitely a timely discussion for me, as I've been spending part 
>>> of the quartine working on collating data and expanding datasets for an 
>>> XAFS spectral database.  I'm hoping to have something ready for public 
>>> comment and to start asking for contributions of data in a few weeks, but 
>>> I'll be happy to h

Re: [Ifeffit] Reported W L3-edge and L2-edge energy

[Mike Massey]

On a tangentially related topic, I find that phosphorus K-edge XAS energy 
calibration conventions are still in a bit of a "Wild West" state, with a wide 
variety of materials and values in use for energy calibration. As an extreme 
example, one or two frequently cited papers in my field from the 2000s don't 
even report the material or value used for energy calibration, and only show 
portions of the spectra on an energy axis with values relative to an unknown E0.

I too have picked my own material and value, and will be the first to 
acknowledge that I did so out of necessity and ease of comparison to other 
available data, rather than because I thought it was correct.

The issue of calibration conventions and values definitely seems to be one that 
merits continued discussion. It has been interesting to watch things evolve 
over time in the case of iron, for example (it's good to know that 7110.75 is a 
candidate calibration value...) I appreciate Matt's detailed thoughts, and the 
data that he's been working with. Thanks Matt!

Cheers,



Mike





> On May 6, 2020, at 3:32 PM, Matt Newville  wrote:
> 
> 
> Hi Simon,
> 
> This is definitely a timely discussion for me, as I've been spending part of 
> the quartine working on collating data and expanding datasets for an XAFS 
> spectral database.  I'm hoping to have something ready for public comment and 
> to start asking for contributions of data in a few weeks, but I'll be happy 
> to have more discussion about that sooner too. 
> 
> I generally believe that the monochromator I use at GSECARS is both 
> well-calibrated and reasonably accurate.  That is, with 2 angular encoders 
> with a resolution of >130,000 lines per degree and an air-bearing, I believe 
> the angular accuracy and repeatability are very good.  I believe there are 
> equally good moons in existence.   As Matthew Marcus pointed to the Kraft 
> paper (which used an older source but 4-bounce mono to improve resolution), 
> we find that Fe foil is definitely better defined as 7110.75 and Cu foil is 
> between 8980.0 and 8980.5 eV.  That is, we've measured multiple foils, found 
> their first derivatives, and refined the d-spacing and angular offset.  We do 
> this about once per run, and the offsets tend to be very consistent.   For 
> sure, there is some question about whether the Kraft numbers are perfect.   
> For sure, putting Fe foil at 7110.75 +/- 0.25 eV appears to be "most right" 
> to us.
> 
> I also believe that we should probably re-measure these metal foils (and 
> other compounds) with a single calibration set for both Si(111) and Si(311).  
> We will probably have time to do that this summer in the time between 
> "beamline staff can get back to the beamline" and "open for outside users".
> 
> What I can tell you now is:  I have some data on W metal, WO2, and WO3 
> measured all at the same time on our bending magnet line, with Si(111).  An 
> Athena project for this is attached (W.prj).   I cannot vouch for the 
> absolute calibration. 
> 
> I also attach a set of foils (V, Fe, Cu, Mo) measured with the same 
> calibration (and Si(111) on our ID line), after adjusting d-space and offset 
> to be close to the Kraft values (CalibratedFoils2013.prj). 
> 
> I also attach a set of foils (Fe, Cu, Au L3, Au L2, Au L1, Pb L3, Pb L2, Pb 
> L1 edges) measured in 2016 (again, using Si(111) on our ID line), also with 
> the same calibration values (FeCu_Au_Pb.prj).  I'm pretty certain these use 
> the same d-spacing as the 2013 Foils to at least 5 digits.   For 
> completeness, all of the raw data files are also under 
> https://github.com/XraySpectroscopy/XASDataLibrary/tree/master/data
> 
> In my experience, the Pb L3 edge value has the biggest variation in the 
> literature, with values ranging from 13035 to 13055 eV (possibly a typo 
> somewhere along the line).  Fortunately, the Kraft-based calibration splits 
> the difference and puts the value at 13040 eV.
> 
> For W in particular, I will look if I have measured this recently on our ID 
> line.  I can tell you that I use CdWO4 as a phosphor and use that to focus 
> our X-ray beam.   I use this trick all the time: any tail from the beam 
> penetrating the phosphor is shortest at the peak of the white-line and for 
> CdWO4 that is always between 10210 and 10215 eV.
> 
> I hope that helps.  I am interested in trying to get all these values as 
> accurately as possible, so any comments or suggestions would be most welcome.
> 
> --Matt
> 
> 
> 
> 
> 
> 
> 
> 
> 
>> On Tue, May 5, 2020 at 5:14 PM Bare, Simon R  
>> wrote:
>> All:
>> 
>>  
>> 
>> We are wondering if others agree that the reported values for the W L3 and W 
>> L2 edges are incorrect. We recently noticed the following:
>> 
>>  
>> 
>> The “Edge” – defined by the inflection point of the absorption edge step
>> 
>>  
>> 
>> When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and 
>> L2-edges are 10203.4 eV and 11542.4 eV, respectively.  
>> 
>>  
>> 
>> 

Re: [Ifeffit] smoothing XAS data

[Mike Massey]

At this juncture, I'd like to bring up a "rule" I've made for myself regarding 
data quality and smoothing: I'd rather walk away from a beam run with one good 
spectrum than a hundred poor ones.

Meaning, for me anyway, if the data aren't smooth enough on their own, I'd 
rather spend more precious time counting than move on. I'd count for three days 
on a sample if I had to (I've never had to).

While it has been proven that, contrary to the popular saying, one _can_ polish 
a turd, I'd personally rather not try.

I realize this approach was more difficult when I was a grad student and 
everyone in the research group was clamoring for data, but even in that 
situation, good data > not-good data.

Apologies for the tangent, but I hope someone out there might find it useful.


Cheers,



Mike





> On Jan 22, 2020, at 5:44 PM, Carlo Segre  wrote:
> 
> 
> Hi Daria:
> 
> I smooth (or boxcar average) the data which it is oversampled, such as in a 
> continuous scan where the data in the exafs region is spaced closer than the 
> usual delta k of 0.05.
> 
> I generally don't like to smooth XANES data since smoothing does tend to 
> attenuate sharp features such as the ones which exist near the absorption 
> edge.
> 
> Carlo
> 
>> On Wed, 22 Jan 2020, Daria Boglaienko wrote:
>> 
>> Hello,
>> 
>> In what case smoothing of the data is OK? My data have a lot of noise and
>> smoothing really helps (visually). I compared fit done in Artemis for
>> smoothed and non-smoothed data sets and the result is very similar, however
>> when I searched about it online, it looks like it is not recommended.
>> What is a good way to justify it?
>> 
>> Thank you!
>> 
>> -Daria
>> 
> 
> -- 
> Carlo U. Segre -- Duchossois Leadership Professor of Physics
> Directory, 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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[Ifeffit] X-ray analysis books available if you want them

[Mike Massey]

Hi all,


I have a small selection of x-ray books I'm happy to give you if you want them. 
Please contact me privately if you do. I'd rather give them away to a good home 
than send them to book heaven.

Koningsberger and Prins, X-Ray Absorption
Attwood, Soft X-rays and Extreme Ultraviolet Radiation
Stohr, NEXAFS Spectroscopy
Stock, MicroComputed Tomography
RIMG vol 18, Spectroscopic Methods in Mineralogy and Geology

...And maybe one or two more.


Kind Regards,



Mike
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Re: [Ifeffit] XAS fitting

[Mike Massey]

The short, short version, in my estimation, is "pick two paths as a reasonable 
starting point and let the fitting parameters do the rest." You could even use 
two clones of the same path, which will end up getting different CNs, delr, and 
ss in the fit.

There's no law that says you have to use Feff paths that correspond to paths in 
your structural model (if an analogous path even exists). As long as it's 
close-ish to start (the program will throw a warning if it's not close enough), 
the fitting parameters can be used to handle small differences arising from 
e.g., octahedral vs tetrahedral coordination.





> On Oct 12, 2019, at 12:39 PM, Chris Patridge  wrote:
> 
> You can run two calculations and import the paths and scale the contributions 
> from each site. There are a lot of examples and this has been discussed 
> before on the mailing list if you search. 
> 
> Hope that helps,
> 
> Chris
> 
> *
> Dr. Chris Patridge
> Assistant Professor
> Department of Chemistry 
> SASE 315
> D’Youville College 
> 320 Porter Ave
> Buffalo, NY 14201
> 716-829-8096
> patri...@dyc.edu
> 
> 
>> On Oct 11, 2019, at 6:34 PM, Wang, Maoyu  wrote:
>> 
>> Hi
>> 
>> I am running an EXAFS fitting for spinel Co3O4. As we know, the Co3O4 will 
>> have two different two local coordinations. One is 6 Co-O coordinated 
>> octahedral site, and another one is 4 Co-O coordinated tetrahedral site. 
>> When we run the Feff calculation, we can only use one Co site to do the 
>> calculation once, and we can only get one site coordination by one 
>> calculation. However, the EXAFS will tell us the average local structure. 
>> How could we use these two different calculation paths to do the fitting?
>>  
>> Sincerely,
>> 
>> Maoyu Wang
>> Chemical Engineering 
>> Oregon State University
>> wan...@oregonstate.edu
>> 541-602-1707
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Re: [Ifeffit] Two analysts, one spectrum, similar outcome?

[Mike Massey]

This is a great example, Scott! Thanks for sharing your experience. Hopefully 
ours will be similarly positive and the results will be in the ballpark of each 
other. It's at least comforting to know there's a chance.



Mike





> On Aug 13, 2019, at 8:18 PM, Scott Calvin  wrote:
> 
> Yes, I did.
> 
> I set up a double-blind experiment with mixtures of various iron standards 
> and an “unknown” iron-containing compound. This was years ago, so I may have 
> a few details wrong, but it will get the gist:
> 
>  I used undergraduates to make the mixtures with random amounts of random 
> selections of the standards. An undergraduate also ordered the “unknown” 
> compound. 
> 
> We then measured the spectra, along with the spectra of the pure standards 
> (but not the pure “unknown”). The spectra were measured at somewhat different 
> temperatures so that simple linear combination analysis would be of limited 
> use. Three of us then attempted analysis independently: myself, one of my 
> most advanced undergraduates (who did not participate in the preparation of 
> the samples), and a high school student with roughly two weeks training in 
> analysis. We attempted to find what compounds were present, how much of each, 
> and, in the case of the unknown compound, as much as we could suss out 
> structurally.
> 
> The results were that we all did OK, but my analyses were the most accurate, 
> the advanced undergraduate less so, and the high school student the least 
> (but still generally in the ballpark).
> 
> It was satisfying to know that different analysts could find similar results, 
> that those results reflected reality, and that those with greater expertise 
> did achieve more accurate results.
> 
> If I recall correctly, I didn’t publish because the undergraduate who 
> prepared the pure standards did a lousy job (pinholes, etc.), which distorted 
> our measurement of the standards enough to make it more difficult to evaluate 
> our analyses. Still, it showed things work in principle.
> 
> The data, including a remeasured set of standards, is still available as the 
> EXAFS Divination Set.
> 
> Best,
> 
> Scott Calvin
> Lehman College of the City University of New York
> 
>> On Tue, Aug 13, 2019 at 9:41 PM Mike Massey  wrote:
>> Hi Everyone,
>> 
>> 
>> I'm curious, has anyone ever tried turning two analysts loose on the same 
>> unknown EXAFS spectrum to see if their fits come out with similar 
>> conclusions? If you have tried it, how did it work out? Were the conclusions 
>> indeed similar? If not, why not, and what did you end up doing about it?
>> 
>> I was talking with a colleague today about our plans for data analysis, and 
>> we settled on this approach (since there are two interested parties willing 
>> to try to fit a series of unknown EXAFS datasets).
>> 
>> The hope is, of course, that the two analysts will independently reach 
>> similar conclusions with similar fits and structural models, but to my mind 
>> that outcome is by no means guaranteed. Given the (presumably) wide 
>> variation in fitting customs and procedures, I can envision a scenario in 
>> which there are major differences.
>> 
>> This got me wondering, "Has anyone tried this?" So I thought I'd ask.
>> 
>> 
>> Your thoughts and experiences would be welcome. Thanks!
>> 
>> 
>> 
>> Mike Massey
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Re: [Ifeffit] Two analysts, one spectrum, similar outcome?

[Mike Massey]

It is true that we both have background information regarding the samples, and 
similar goals in terms of the questions we are looking to answer.

"You also need to think about what question you are trying to answer.  If you 
have a specific goal in mind, then you may choose a different model than the 
individual who is seeking the answer to a different question."

This is, somewhat, the issue we are grappling with. A reasonable EXAFS fit is 
one interpretation of the data, but we are trying to find a way to deal with 
the problem of seeing what one wants to see in EXAFS data. To me, it's a bit of 
a problem, anyway. A version of "confirmation bias," I suppose.

The hope is that, if two of us independently reach a similar conclusion, we can 
have more confidence in the findings, perhaps?






> On Aug 13, 2019, at 7:59 PM, Carlo Segre  wrote:
> 
> 
> The answer you get will depend somewhat on the assumptions you make.  if you 
> are truly provided with data and no other information about the sample, then 
> the job is challenging.  If you know something about the sample that can help 
> you start in a particular direction then the two analyses have a better 
> chance of converging but it still depends on how you decide to approach the 
> structural model.
> 
> You also need to think about what question you are trying to answer.  If you 
> have a specific goal in mind, then you may choose a different model than the 
> individual who is seeking the answer to a different question.
> 
> The most likely way to approach this problem is to both have the same 
> background information about the sample(s) and to mutually determine what 
> question you are trying to answer.
> 
> Cheers,
> 
> Carlo
> 
> 
>> On Tue, 13 Aug 2019, Mike Massey wrote:
>> 
>> I'm the dumb one. But it's an interesting question, and gets perhaps to the 
>> heart of the issue: to what extent does the smartness of the analyst, or 
>> their experience, or the fitting procedures used, or a butterfly flapping 
>> its wings in Micronesia, impact the results?
>> 
>> For the sake of argument, can two equally smart and experienced analysts 
>> working on fitting the same EXAFS spectra be expected to reach similar 
>> conclusions? I guess we'll find out.
>> 
>> Another colleague once said something like, "EXAFS is great: you publish a 
>> paper, then later you publish another paper re-analyzing the same data." Of 
>> course, he's a strictly computational guy, so I'm not sure he necessarily 
>> has standing to criticize...(Good-natured sarcasm font...)
>> 
>> 
>> 
>>> On Aug 13, 2019, at 6:43 PM, Anatoly Frenkel 
>>>  wrote:
>>> 
>>> Are they equally smart?
>>> 
>>> Anatoly
>>> 
>>>> On Aug 13, 2019, at 9:39 PM, Mike Massey  wrote:
>>>> 
>>>> Hi Everyone,
>>>> 
>>>> 
>>>> I'm curious, has anyone ever tried turning two analysts loose on the same 
>>>> unknown EXAFS spectrum to see if their fits come out with similar 
>>>> conclusions? If you have tried it, how did it work out? Were the 
>>>> conclusions indeed similar? If not, why not, and what did you end up doing 
>>>> about it?
>>>> 
>>>> I was talking with a colleague today about our plans for data analysis, 
>>>> and we settled on this approach (since there are two interested parties 
>>>> willing to try to fit a series of unknown EXAFS datasets).
>>>> 
>>>> The hope is, of course, that the two analysts will independently reach 
>>>> similar conclusions with similar fits and structural models, but to my 
>>>> mind that outcome is by no means guaranteed. Given the (presumably) wide 
>>>> variation in fitting customs and procedures, I can envision a scenario in 
>>>> which there are major differences.
>>>> 
>>>> This got me wondering, "Has anyone tried this?" So I thought I'd ask.
>>>> 
>>>> 
>>>> Your thoughts and experiences would be welcome. Thanks!
>>>> 
>>>> 
>>>> 
>>>> Mike Massey
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Re: [Ifeffit] Two analysts, one spectrum, similar outcome?

[Mike Massey]

I'm the dumb one. But it's an interesting question, and gets perhaps to the 
heart of the issue: to what extent does the smartness of the analyst, or their 
experience, or the fitting procedures used, or a butterfly flapping its wings 
in Micronesia, impact the results?

For the sake of argument, can two equally smart and experienced analysts 
working on fitting the same EXAFS spectra be expected to reach similar 
conclusions? I guess we'll find out.

Another colleague once said something like, "EXAFS is great: you publish a 
paper, then later you publish another paper re-analyzing the same data." Of 
course, he's a strictly computational guy, so I'm not sure he necessarily has 
standing to criticize...(Good-natured sarcasm font...)



> On Aug 13, 2019, at 6:43 PM, Anatoly Frenkel  
> wrote:
> 
> Are they equally smart?
> 
> Anatoly
> 
>> On Aug 13, 2019, at 9:39 PM, Mike Massey  wrote:
>> 
>> Hi Everyone,
>> 
>> 
>> I'm curious, has anyone ever tried turning two analysts loose on the same 
>> unknown EXAFS spectrum to see if their fits come out with similar 
>> conclusions? If you have tried it, how did it work out? Were the conclusions 
>> indeed similar? If not, why not, and what did you end up doing about it?
>> 
>> I was talking with a colleague today about our plans for data analysis, and 
>> we settled on this approach (since there are two interested parties willing 
>> to try to fit a series of unknown EXAFS datasets).
>> 
>> The hope is, of course, that the two analysts will independently reach 
>> similar conclusions with similar fits and structural models, but to my mind 
>> that outcome is by no means guaranteed. Given the (presumably) wide 
>> variation in fitting customs and procedures, I can envision a scenario in 
>> which there are major differences.
>> 
>> This got me wondering, "Has anyone tried this?" So I thought I'd ask.
>> 
>> 
>> Your thoughts and experiences would be welcome. Thanks!
>> 
>> 
>> 
>> Mike Massey
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[Ifeffit] Two analysts, one spectrum, similar outcome?

[Mike Massey]

Hi Everyone,


I'm curious, has anyone ever tried turning two analysts loose on the same 
unknown EXAFS spectrum to see if their fits come out with similar conclusions? 
If you have tried it, how did it work out? Were the conclusions indeed similar? 
If not, why not, and what did you end up doing about it?

I was talking with a colleague today about our plans for data analysis, and we 
settled on this approach (since there are two interested parties willing to try 
to fit a series of unknown EXAFS datasets).

The hope is, of course, that the two analysts will independently reach similar 
conclusions with similar fits and structural models, but to my mind that 
outcome is by no means guaranteed. Given the (presumably) wide variation in 
fitting customs and procedures, I can envision a scenario in which there are 
major differences.

This got me wondering, "Has anyone tried this?" So I thought I'd ask.


Your thoughts and experiences would be welcome. Thanks!



Mike Massey
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Re: [Ifeffit] Multiple species with Artemis

[Mike Massey]

Hi Vineetha,


I am aware of some people doing (or at least attempting) multi-species 
shell-by-shell fits, but it's a pretty daunting task, depending on your system.

Another approach that some people have had success with (check papers by Martin 
McBriarty and colleagues) is a combination of LCF and structural and spectral 
modeling. The situation I am familiar with in that case is the use of a 
spectrum from an adsorbed species and the simulation of EXAFS from AIMD 
structural models to tease out the contribution of each species to the overall 
mixed spectrum. Martin is a big advocate of this approach, and it does seem to 
make otherwise intractable problems more tractable.

Personally, although multi-species shell-by-shell fitting would be perfect for 
the types of systems I like to work on and the types of questions I like to 
answer, I feel like there's already enough uncertainty in interpreting the 
EXAFS spectra in those systems. A multi-species fit just makes the 
interpretation even murkier.

On the other hand, the coupled AIMD approach actually seems less uncertain, 
since you can explicitly account for factors such as thermal vs static disorder 
(rather than lumping the two together). It seems to improve the quality of 
conclusions one can draw from complicated spectra.


Sorry I can't be more helpful,



Mike





> On Jun 17, 2019, at 8:20 AM, Mukundan, Vineetha  
> wrote:
> 
> Hi All,
> A couple of questions. I was searching the previous threads to check if 
> someone here had posted/explained an example with mixing parameters to find 
> the % content of different constituents present in a sample with Artemis. 
> This is for shell-by-shell fitting. Can Artemis fit multiple chemical 
> species/phases to the experimental spectra simultaneously?
>  
> OR fit the samples spectra measured at 2 different edges with one or two 
> phase simultaneously?
> Don’t know if I searched far enough.  Apology if it has been discussed. In 
> that case, could anyone please direct me to those threads.
> Thanks you,
> Vineetha
>  
>  
>  
>  
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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 s

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
>>> ___
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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?

[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] 32ビット版アプリケーションの申請

[Mike Massey]

Just in case this might help...

"Dear Maintainers of Ifeffit,

I would like to use the 32-bit version of the application. Would you mind 
posting a 32-bit version of the installation application?

Thank you very much."






> On Aug 22, 2018, at 9:25 PM, 天田雄大  wrote:
> 
> Ifeffit管理者様
> 
> 32ビット版アプリケーションを使用したいので、
> 32ビット版 のインストールアプリを添付していただけませんか？
> 
> よろしくお願いします。
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Re: [Ifeffit] LCF on Larch - EXAFS Region

[Mike Massey]

Hi Matt,


Thanks for your thoughts. In general, I agree with all of your points, but my 
typical uncertainty estimate for both XANES and EXAFS LCF is much greater than 
a few percent. Typically I quote 10-15% uncertainty, depending on the analysis.

I particularly agree with your point regarding disorder. In my limited 
experience, anyway, if one attempts an EXAFS LCF of a nanoscale material with a 
spectrum from a nice, well-ordered bulk crystal, for example, the results are 
unworkable. Even if it's the right material and the oscillations happen to be 
in the right places, the amplitudes are all wrong and the fit will be useless. 
So the EXAFS LCF is probably even more sensitive to choice of fitting 
components than XANES.

As usual, care is warranted, grains of salt and whatnot.

Thanks again,



Mike



> On Aug 12, 2018, at 10:19 PM, Matt Newville  
> wrote:
> 
> Hi Mike, 
> 
>> On Thu, Aug 9, 2018 at 10:04 PM Mike Massey  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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Re: [Ifeffit] LCF on Larch - EXAFS Region

[Mike Massey]

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.






> On Aug 9, 2018, at 12:56 PM, Matt Newville  wrote:
> 
> Hi Garret,
> 
>> On Thu, Aug 9, 2018 at 12:27 PM Garret Bland  wrote:
>> Hello!
>> 
>> I've recently been trying to use Larch instead of Athena for EXAFS analysis, 
>> and I mainly do linear combination fitting for my samples. It seems that the 
>> XANES fitting is doing just fine requesting a specified region to fit (-25 
>> to +75 eV). When I try to fit in the k-space however, Larch does not request 
>> a specific region in k space. I try to input the eV values corresponding to 
>> the k value I want to fit, but it is still plotting in mu rather than k . Is 
>> there anyway I can change this and/or do it manually on the larch GUI? Any 
>> help would be appreciated!
> 
> You're right that linear combinations in k-space are not really working in 
> Larch's XAS Viewer, including that the range can only be set in energy.  Much 
> of XAS Viewer is fairly new -- I think it is fairly complete, but there are a 
> few missing parts.  I don't ever do linear combinations of chi(k) myself and 
> am slightly skeptical that they are robust, so they've haven't surfaced to 
> the top of the ToDo list yet.  Any help would be greatly appreciated.
> 
> --Matt
> 
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Re: [Ifeffit] iron carbide fitting with Artemis

[Mike Massey]

The way I usually do it is to just pick one of the FEFF paths (instead of both) 
corresponding to the distance you care about. I actually haven't used the 
latest version of Artemis to do any fitting recently, but I assume it is still 
similar.

In your list of FEFF paths, pick C1.1, right-click and "include C1.1 in the 
fit." Then you define your fitting parameters for that atom at that distance, 
one of which should be the coordination number of the atom (I typically might 
define amplitude as S02*CN and put path degeneracy at 1, but there are probably 
other, better ways to do this ― I hope someone more knowledgeable might correct 
me if this is a poor approach).

So then your amplitude fitting parameter, "amp_C1," basically becomes a proxy 
for the coordination number of that atom at that distance, and "ss_C1" is your 
measure of disorder. So instead of trying to fit two C at 1.94 and 1.99 
Angstroms individually, you model that with a single path of C at around 1.97 
Angstroms (or whatever FEFF's R plus your fit's delr is) with disorder ss_C1, 
and you either set the coordination number to 2, or you guess it in the fit and 
hope it comes out to around 2, since it probably should.

There are probably a lot of ways to approach this, every person seems to have 
their preferred method. You might consider setting up a screen-sharing 
videoconference with someone and get them to walk you through their process for 
fitting. It seems to be something that is effectively learned through 
apprenticeship. Another possibility is attending an EXAFS fitting workshop, if 
any are coming up.

I recommend getting a really good handle on single-phase fitting before even 
attempting multi-phase fits. If appropriate, you can even just do LCF for the 
multi-phase system.


Just my two cents, hope my thoughts are helpful and not grossly wrong (if 
wrong, hopefully someone will correct me ― thanks in advance).

Cheers,


Mike





> On Oct 26, 2017, at 2:06 PM, Yunyun Zhou <yyzhouz...@gmail.com> wrote:
> 
> Hello Mike,
> 
> Thank you very much for your help. I have a question about combining 
> different atoms in a shell. For example, in the Fe5C2 model,
>  ATOMS  * this list contains 221 atoms
>  *   x  y  z ipot tag   distance
> 0.00.00.0  0  Fe1   0.0
>-0.193851.76888   -0.78107  4  C1.1  1.94335
>-0.19385   -0.945521.72493  4  C1.2  1.97661
> 
> If I am going to combine C1.1 and C1.2, shall I set them the cartisian 
> coordinate as in FEFF file?
> 
>  ATOMS  * this list contains 221 atoms
>  *   x  y  z ipot tag   distance
> 0.00.00.0  0  Fe1   0.0
>0.0 0.01.94335  4  C1.11.94335
> 
> Thanks a lot for your help again!
> 
> Best,
> 
> Yunyun
>  
> 
>> On Thu, Oct 26, 2017 at 4:40 PM, Mike Massey <mmas...@gmail.com> wrote:
>> I definitely recommend combining multiple atoms of similar distances into 
>> the same path. That's what you end up with anyway if you use multiple paths, 
>> with a lot more potential problems in the software.
>> 
>> Sometimes it is beneficial to split a shell of of atoms into two, to capture 
>> some physical behavior (for example, 2 atoms at 3 Angstroms and 4 atoms at 
>> 3.3 Angstroms, instead of one very disordered shell of 6 atoms at 3.2 
>> Angstroms).
>> 
>> Depending on your data quality, I recommend building a fitting model with 
>> maybe 2-8 total "shells" of atoms at different distances.
>> 
>> 
>> 
>> Mike
>> 
>> 
>> > On Oct 26, 2017, at 12:52 PM, Yunyun Zhou <yyzhouz...@gmail.com> wrote:
>> >
>> > Hello All,
>> >
>> > I am having trouble fitting my sample with both Fe5C2 and Fe3O4 as 
>> > standards. Hopefully somebody could help me out and I really appreciate it.
>> >
>> > My iron sample was mainly iron carbide in the core and iron oxide on the 
>> > shell. Fe5C2 has a monoclinic structure and generated complicated FEFF 
>> > paths. Many of the paths have similar distances. I have found some paper 
>> > reported their results as follows, which apparently combined several paths 
>> > together and assume they have similar path length. My first question is 
>> > does someone know how they did it? It seems that combing similar paths 
>> > makes fitting much easier, but I am not sure whether this is a correct way 
>> > to do the fitting.
>> >
>> > My second question is regarding fitting with the two combined model

Re: [Ifeffit] iron carbide fitting with Artemis

[Mike Massey]

I definitely recommend combining multiple atoms of similar distances into the 
same path. That's what you end up with anyway if you use multiple paths, with a 
lot more potential problems in the software.

Sometimes it is beneficial to split a shell of of atoms into two, to capture 
some physical behavior (for example, 2 atoms at 3 Angstroms and 4 atoms at 3.3 
Angstroms, instead of one very disordered shell of 6 atoms at 3.2 Angstroms).

Depending on your data quality, I recommend building a fitting model with maybe 
2-8 total "shells" of atoms at different distances.



Mike


> On Oct 26, 2017, at 12:52 PM, Yunyun Zhou  wrote:
> 
> Hello All,
> 
> I am having trouble fitting my sample with both Fe5C2 and Fe3O4 as standards. 
> Hopefully somebody could help me out and I really appreciate it.
> 
> My iron sample was mainly iron carbide in the core and iron oxide on the 
> shell. Fe5C2 has a monoclinic structure and generated complicated FEFF paths. 
> Many of the paths have similar distances. I have found some paper reported 
> their results as follows, which apparently combined several paths together 
> and assume they have similar path length. My first question is does someone 
> know how they did it? It seems that combing similar paths makes fitting much 
> easier, but I am not sure whether this is a correct way to do the fitting.
> 
> My second question is regarding fitting with the two combined models of Fe5C2 
> and Fe3O4. I haven't fit with two models before. Is it just like what I did 
> in the attached Artemis file? Shall there be any restrictions between the two 
> models and do I have to fix some of the parameters? 
> 
> Thank you very much in advance for your help!
> 
> Best,
> 
> Yunyun Zhou
> 
> Fe5C2 FEff paths:
> 
> 
> Literature reported results:
> 
> 
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Re: [Ifeffit] Athena and "norm" file groups

[Mike Massey]

Thanks for the response! 

For clarification, I'm not really trying to re-normalize the normalized data, 
which is flattened in this case. However, I'm having (terminal) difficulty 
extracting the EXAFS from the normalized groups, because I can't seem to get 
the program to pass a spline through it (even though the spline will pretty 
much be a straight line) and gimme my EXAFS!

All caution will of course be applied in the use of said EXAFS, if I can get 
that far...!


Cheers, thanks again,


Mike




> On Oct 15, 2016, at 1:25 PM, Anatoly Frenkel <anatoly.fren...@stonybrook.edu> 
> wrote:
> 
> I would try to rename .norm by .xmu and see if it will be able to do what you 
> want.
> I would still be cautious doing it because .norm means that the raw data was 
> already altered (pre-edge function was subtrated and slope changed).
> Doing anything like that is possible but not wise because it is not 
> guaranteed that you would obtain the same result as when you start from the 
> raw data directly.
> 
> For example, suppose "norm1" is normalization operation with one set of 
> parameters, and "norm2" - with another. Xmu is the raw absorption coefficient 
> data (obtained from the ratio of detector signals).
> It is not likely that norm2 (xmu) will give the same results as 
> norm2(norm1(xmu)), although the differences may be small. That is the reason, 
> I think, Athena does not allow any ex post factum normalization to the 
> normalized data.
> 
> Anatoly Frenkel
> Stony Brook University
> 
> 
>> On Oct 15, 2016 4:10 PM, "Mike Massey" <mmas...@gmail.com> wrote:
>> Hi everyone,
>> 
>> 
>> Apologies if this has been covered before, I'm just getting around to 
>> upgrading to Demeter. I have a bunch of old project files with a mishmash of 
>> data from different sources, and I'm having trouble getting them to work 
>> fully with the new software.
>> 
>> Any group with a data type of "xmu" (energy space) seems to work as 
>> expected, but any group with a data type of "norm" (normalized data) doesn't 
>> seem to work properly when it comes to spline or post-edge background 
>> subtraction (which is handy if I want to do LCF, for example). Is this a bug 
>> or a feature? Has anybody yet developed a workaround?
>> 
>> Any thoughts or advice would be greatly appreciated. The ultimate workaround 
>> is to use different data, but I'd like to use existing projects if possible 
>> (saves a lot of time and brain damage).
>> 
>> 
>> Cheers, and thanks!
>> 
>> 
>> Mike
>> 
>> 
>> 
>> 
>> 
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[Ifeffit] Athena and "norm" file groups

[Mike Massey]

Hi everyone,


Apologies if this has been covered before, I'm just getting around to upgrading 
to Demeter. I have a bunch of old project files with a mishmash of data from 
different sources, and I'm having trouble getting them to work fully with the 
new software.

Any group with a data type of "xmu" (energy space) seems to work as expected, 
but any group with a data type of "norm" (normalized data) doesn't seem to work 
properly when it comes to spline or post-edge background subtraction (which is 
handy if I want to do LCF, for example). Is this a bug or a feature? Has 
anybody yet developed a workaround?

Any thoughts or advice would be greatly appreciated. The ultimate workaround is 
to use different data, but I'd like to use existing projects if possible (saves 
a lot of time and brain damage).


Cheers, and thanks!


Mike





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