Re: [Ifeffit] S02 selection from reviewer

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

mam

On 10/2/2021 12:49 AM, Peng Liu wrote:

Dear IFEFFIT members,

I am sorry to bother you again. I asked about S02 selection for the 
first major revision. I just received the second revision. The reviewer 
is not satisfied with one S02 value for all our samples.

"

1. I am still not satisfied with selected SO2 value (it is set to 0.85). 
SO2 is not transferable between different samples and detection methods. 
It is not possible to use a value obtained from different compound using 
transmission measurement mode to completely different other compound 
measured using fluorescence mode. One method to fix SO2 value is to 
measure diluted solution (to avoid self-absorption) of reference 
material in fluorescence mode. Other is to use multiple spectra fitting 
for all samples of interest (e.g. with Sb(V)) measured using 
fluorescence mode where SO2 parameter is the same for all samples.


At the same time I am confident that CN values 5.6, 7.1 and 6.9 
correspond to CN(Sb-O)=6. I suggest reconsidering the SO2 value for 
measurements in fluorescence mode.


"

We do get the S02 from a similar reference material measured in 
transmission mode, and our samples were all measured in fluorescence 
mode. It is not possible to measure the diluted reference material in 
fluorescence mode in one or two months. If you could give me some 
suggestions, that would be great.



--
Best Regards,

Peng Liu

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Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus

This probably isn't relevant, but Desktop is actually a folder under c:.
On my computer, it's C:\Users\MAMarcus.  I see that 'other Matt' concurs 
with this and seems to be suggesting that your username may have 
non-ASCII characters.  I'm guessing Korean.   Try making a new folder 
under C:\ with only ASCII characters in the name.

mam

On 9/7/2021 6:25 PM, Bang, Shinhyo wrote:

Dear Matthew,

I tried to save a project to "Desktop" which had no parent folder, but 
the same problem occurred. I think the non-ASCII character is not the 
only problem.

Still, I can save onto a usb from now on. Thank you very much.

Best,
Shinhyo

*보낸 사람:* Matt Newville  대신 Ifeffit 


*보낸 날짜:* 2021년 9월 7일 화요일 오후 6:06
*받는 사람:* XAFS Analysis using Ifeffit 
*제목:* Re: [Ifeffit] IFEFFIT file saving issue
Hi Shinhyo,

Again, I would ask to check that the folder you are having trouble 
saving to has any non-ASCII characters. For sure, ifeffit and demeter 
are not going to be able to handle folder or file names with non-ASCII 
characters.


Larch is slightly better at this - it can work with files with names in 
non-ASCII text encodings.  To be clear, the situation with Larch is 
still not ideal, especially on Windows, because
    a) the base installation folder can contain only ASCII characters, 
and cannot contain any spaces (apparently this is some problem

        with other libraries or possibly some other variation on point b).
    b) the concept of "localization" on Windows machines is sort of a 
mess and many libraries (at least, from Python) don't handle this very 
well.  For Larch, we recently had to explicitly set locale to be "simple 
C / ASCII".  That sort (or should!?) mean that you can read/write files 
and folders with non-ASCII characters, though I'm not certain that will 
work for all character encoding sets.  It's possible this will get 
better with time, but it's not something that we can solve.


For ifeffit / demeter there is simply no hope for non-ASCII text to ever 
be handled.



On Tue, Sep 7, 2021 at 7:45 PM Bang, Shinhyo <mailto:shinhyo.b...@wsu.edu>> wrote:


Dear Matthew,

I tried to save the project onto a usb, and it WORKed! Thank you so
much for your help.

Best,
Shinhyo
------------
*보낸 사람:* Matthew Marcus mailto:mamar...@lbl.gov>> 대신 Ifeffit
mailto:ifeffit-boun...@millenia.cars.aps.anl.gov>>
*보낸 날짜:* 2021년 9월 7일 화요일 오후 4:11
*받는 사람:* ifeffit@millenia.cars.aps.anl.gov
<mailto:ifeffit@millenia.cars.aps.anl.gov>
mailto:ifeffit@millenia.cars.aps.anl.gov>>
*제목:* Re: [Ifeffit] IFEFFIT file saving issue
There are other characters that Windoze doesn't like in filenames:
|\/*":<>?
     mam

On 9/7/2021 3:58 PM, Matt Newville wrote:
> Hi Shinhyo, Liane,
> 
> On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo mailto:shinhyo.b...@wsu.edu>

> <mailto:shinhyo.b...@wsu.edu <mailto:shinhyo.b...@wsu.edu>>> wrote:
> 
> Thank you for the response.

> The OS is Windows 10.
> In addition to the symptom that was described aforehand, Athena
> freezes when I try to save the file.
> 
> 
> Is it possible that the folder or file you are saving to has a space or 
> other non-ASCII character in it?  I believe that non-ASCII characters 
> are known to cause problems.
> Can you check whether you can save a file anywhere (maybe even the 
> top-level "C:\" folder)?
> 
> --Matt
> 
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Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus

There are other characters that Windoze doesn't like in filenames: |\/*":<>?
mam

On 9/7/2021 3:58 PM, Matt Newville wrote:

Hi Shinhyo, Liane,

On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo > wrote:


Thank you for the response.
The OS is Windows 10.
In addition to the symptom that was described aforehand, Athena
freezes when I try to save the file.


Is it possible that the folder or file you are saving to has a space or 
other non-ASCII character in it?  I believe that non-ASCII characters 
are known to cause problems.
Can you check whether you can save a file anywhere (maybe even the 
top-level "C:\" folder)?


--Matt

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Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus

Or maybe save onto a USB drive.
mam

On 9/7/2021 3:58 PM, Matt Newville wrote:

Hi Shinhyo, Liane,

On Tue, Sep 7, 2021 at 5:39 PM Bang, Shinhyo > wrote:


Thank you for the response.
The OS is Windows 10.
In addition to the symptom that was described aforehand, Athena
freezes when I try to save the file.


Is it possible that the folder or file you are saving to has a space or 
other non-ASCII character in it?  I believe that non-ASCII characters 
are known to cause problems.
Can you check whether you can save a file anywhere (maybe even the 
top-level "C:\" folder)?


--Matt

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Re: [Ifeffit] IFEFFIT file saving issue

2021-09-07 Thread Matthew Marcus
This may sound like an 'is it plugged in?' sort of suggestion, but I 
wonder if there's a permissions issue.  Perhaps IFEFFIT doesn't have 
write permission where it's trying to write.  It might help people 
diagnose the problem if you were to  specify the OS being used.

mam

On 9/7/2021 3:30 PM, Moreau, Liane Michelle wrote:

Dear fellow XAFS enthusiasts,

My student is running into some trouble in that he can't seem to get any 
files from IFEFFIT (be it project or exported data files) to save on his 
computer. When he saves, no files show up in the folder he has saved to. 
I watched him do this myself to confirm this is indeed the case.


I have never run into this issue, nor have I heard of anyone else having 
this issue previously, but has anyone else run into this issue, and, if 
so, how did they solve it? I imagine there might be something 
incompatible with the student's computer settings somehow, although he 
is able to use the software just fine, it is just that nothing will 
save. He tried uninstalling and reinstalling Demeter, but unfortunately 
that did not fix the problem.


I appreciate any experience anyone can share that might be helpful.

Thank you!

Liane

Liane Moreau, PhD
Assistant Professor
Department of Chemistry
Washington State University
509-335-6073

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Re: [Ifeffit] EXAFS Fitting with 2 CIF files

2021-09-04 Thread Matthew Marcus
Extending what Scott said, I find it useful to make the coefficients 
abs(fracoxide) and abs(1-abs(fracoxide)) to avoid false minima with 
negative S0^2.

mam

On 9/4/2021 1:21 PM, Scott Calvin wrote:

Hi Zihao,

Do it by folding the molar ratio in to the amp parameter for each CIF. Of 
course S02 is part of that parameter, too.

So the amp for PtO2 might be parameterized as S02 * fracoxide and the amp for 
Pt3Fe as S02 * (1-fracoxide)

You could either assume the S02 is the same for the two phases (as I implicitly 
did by writing it with only one S02 variable), or you could use a standard for 
each (from a sample prepared and measured in a similar way) to fix the S02 for 
each phase.

Best,
Scott Calvin
Lehman College of the City University of New York


On Sep 4, 2021, at 4:02 PM, Zihao Yan  wrote:

Dear Ifeffit members:

I have a sample which is a mixture of PtFe and PtO2. In order to do the EXAFS 
fitting, I imported 2 CIF files on Artemis and generated the following 3 paths:
 From PtO2: Pt-O @ 2.07 nm
 From Pt3Fe: Pt-Pt @ 2.736 nm, Pt-Fe @ 2.736 nm
Then, I used these 3 bonds to do the fitting as in the online tutorial (which 
used 1 CIF file). The fitting result is good in terms of R^2 but it is not 
scientifically correct.

I think I didn't set up a parameter which determines the ratio between 
CIF(PtO2) and CIF(Pt3Fe). I mean there should be a parameter that regulates how 
much each CIF contributes to the fitting or the molar ratio between PtO2 and 
Pt3Fe in my system.

Could someone please give me some suggestions on how to do EXAFS fitting with 2 
CIF files? Is there anywhere I can set up the molar ratio between PtO2 and 
Pt3Fe?

Yours sincerely,
Zihao Yan
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Re: [Ifeffit] Manuscript comments regarding EXAFS modeling

2021-08-27 Thread Matthew Marcus
Was there a standard measured that's chemically similar to the unknown? 
 If so, S0^2 could be set by requiring that the CN of the standard be 
what it's known to be.  Often, the dσ² is mostly relevant in terms of 
differences or changes so an error in the absolute value isn't very 
important.  If valence and ligands make such a big difference then it 
would be impossible to measure CNs on samples for which no 
extremely-similar model compounds are available.


Also, it's never been clear to me how doing the fit at three different 
k-powers is better than doing it at just one intermediate value.  The 
idea that it somehow gets you low-k and high-k information in a better 
way seems like an attempt to pull out more independent data points than 
actually exist.  OTOH, proving that you get the same answers, within 
error bars, at different exponents would be a confidence-builder.

mam

On 8/27/2021 7:40 PM, Peng Liu wrote:

Dear Ifeffit members,

I received the following two comments.

"
Comment 1: Authors have fixed the amplitude reduction factor (SO2) to a 
fixed value (0.85). This factor is specific to particular chemical 
compound and sample preparation and quality (mostly homogeneity), 
measurement method (e.g. absorption, fluorescence). Authors can find in 
literature [e.g. Rehr2000] that SO2 for ideal samples (having no other 
effects) represent multielectron effects, which by definition depend on 
valence and ligands. Even more, SO2 is correlated with Debye-Waller 
factor (σ²) and coordination number (CN), so any chosen value will be 
compensated by CN and σ². As coordination numbers are used as 
quantitative indicators in discussion and following conclusions. I would 
request to clarify the selection criteria for SO2 values and advise to 
revise this approach (i.e. not to fix SO2 as the same value for all 
samples). I do not expect drastic changes in obtained CN values, but 
this should be tested.


Comment 2: As I mentioned previously, coordination number (CN) is 
correlated with Debye-Waller factor (σ²). My question is: how this 
correlation is managed (eliminated)? Most probably (in FEFFIT) this is 
done by using 3 separate values for n (1,2,3), where n is a power in 
expression chi(k)*(k^n).

"
I used Artemis for the calculation. 1) Because S02 and CN are 
multiplication relations in the EXAFS equation, as we usually do, we 
fixed S02 to obtain CN for unknown samples. 2) there are outputs 
regarding the correlation between different fitting parameters from 
Artemis. Is there a way to manage or eliminate the correlation as the 
reviewer mentioned using Artemis or Larch?


If you also could give me some suggestions to answer the comments, that 
would also be greatly appreciated.


--
Best Regards,

Peng Liu

School of Environmental Studies

China University of Geosciences, Wuhan, Hubei Province, PR China

https://scholar.google.com/citations?user=qUtyvokJ=en 



http://grzy.cug.edu.cn/049121/zh_CN/index.htm 



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Re: [Ifeffit] [Ext] Farrel Lytle database

2021-07-06 Thread Matthew Marcus
As I recall, not only is the FL Dbase not in a standard format, but the 
format varies according to the vintage of the files.  Also, there's no 
documentation except for the 1-line comment.

mam

On 7/6/2021 9:11 AM, Carlo Segre wrote:

Dear Monica:

The Lytle database is not in a current standard format.  I do have a 
program to convert it but as Edmund has pointed out, you can find better 
and more complete data set on the IXS database or just ask any one of us 
who routinely run Ti edges at a synchrotron.


Carlo

On Tue, Jul 6, 2021 at 9:29 AM Monica Bairagi > wrote:


Hello all:

I am looking forward to standard metal foil data of titanium.

I downloaded the data from the Farrel Lytle database but I can not import 
it into Athena. I looked into the data, it looked wired for me. As Athena 
expects data to be in columns of energy but this data is not recorded by energy 
but by steps of the monochromator rotation stage.
I am wondering if anyone has any idea how to import or transfer the data.
I am attached herewith the data file.

Thanks
Monica Bairagi
Ph.D. Student, Ujjain, India

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Re: [Ifeffit] [Ext] Analyzing EXAFS data on Artemis

2021-05-27 Thread Matthew Marcus
If you go beyond first shell, then you'll need to take into account the 
Se-Se paths in Li2Se.  That may be your best way of detecting Li2Se.

mam

On 5/27/2021 12:03 PM, Carlo Segre wrote:

Hi Deltsidis:

Using Artemis, you can compare the calculated Fourier Transforms of the 
Se-Fe and Se-Li paths to see if the latter will actually be visible.  I 
suspect that it will not if it is an impurity phase with small phase 
fraction.  I would probably start with only Se-Fe and see how well it 
can fit the data.


The eins(T, thetae) is the temperature dependent term.  What is missing 
the static disorder that needs to be added into the sigma^2 to account 
for the temperature independent residual disorder.


Carlo

On Thu, May 27, 2021 at 9:43 AM Alexandros Deltsidis 
mailto:adeltsi...@iesl.forth.gr>> wrote:


Dear mailing list,

I am currently analyzing some EXAFS data. I am studying a Lix(C5H5N)FeSe
system in a temperature grid that extends from 20 K to 300 K and I
have 4
such datasets which correspond to different amount of doping (x). Right
now, im focusing on fitting the 1st coordination cell, in Artemis
for the
Se K-edge. My starting model is the simple P4/nmm FeSe. So, in my system
the 1st coordination cell, in the Se K-edge, corresponds to the Se
(absorber) - Fe (backscatterer) pair. I have 2 questions:
1) I realize now, that I have a certain impurity in the high doping
range
on my system, namely Li2Se. I try to include a scattering path from the
respective Li2Se crystal model in my fits, since a Se (absorber) - Li
(backscatterer) pair is present in the R-range of my fit in the Forward
Fourier Transform. My question here is if this makes sense since Li is
much smaller scatterer compared to Se. In other words, does it make
sense
to look for physical parameters (Li-Se bond length and DW factor
respectively) of a signal (Se-Li) that is "tucked" in below the main
peak
coming from the "majority" Se-Fe signal in the FFT?
2)Also, I'm attempting to extract an Einstein temperature for each of
those datasets, by utilizing the "eins(T, thetae)" function
implemented in
Artemis. What is the equation that is parametrized here? Does it include
the s0^2 offset term that accounts for the overall configuration
disorder
in the system? And if that is the case is there same way to separate it
from the temperature dependent s^2 term?

Thank you in advance,
Deltsidis Alexandros
PS:I am attaching a png. file exported from Artemis that is relative
to my
question 1)

Ph.D candidate,
Institute of Electronic Structure and Laser (IESL),
Foundation for Research and Technology - Hellas
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Re: [Ifeffit] [Ext] Re: XAS question

2020-10-29 Thread Matthew Marcus
It's possible that your data really has a kink in it.  Zoom in on that 
last bit in E space before any background subtraction and see if there's 
something odd-looking.  If there's really an artifactual kink, then 
there's not much you can do.

mam

On 10/29/2020 7:47 AM, Carlo Segre wrote:
I agree, this is a sign of a poor background subtraction.  I find that 
this can be mitigated by cutting back on your spl;ine range for 
background subtraction.  Change it by 0.5 at a time or less and keep 
plotting in k-space.  You might have to lose a bit of range but that 
just means that the data is not good enough to extend that far.


Carlo

On Thu, Oct 29, 2020 at 9:23 AM Edmund Welter > wrote:


Dear Danting,

did you look on the background that is subtracted? I guess it is
your background that is doing something weird here. To look at the
background tick "Background" in the plot. In the region you mention
it should be a smooth line without visible oscillations.

Cheers,

Edmund


On 29.10.20 11:02, Chen, Danting wrote:


Hi Mr/Ms,

__ __

I am a new learner of XAS and meet a problem like before and hope
you can give me some hints.

__ __

__ __

I have a data set after merged and alignment. But at 11-13 A-1,
the amplitude of k is much higher than normal but there seems no
weird points at XAS spectrum. I wonder how I could deal with this
part? If I shorter kmax and it must lose some important information.

__ __

Best Wishes,

Danting

Sent from Mail 
for Windows 10

__ __


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

2020-05-07 Thread Matthew Marcus
sking 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
mailto:srb...@slac.stanford.edu>> 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 L_3 edge (11215.0 eV) as a calibration, the
W L_3 - and L_2 -edges are *10203.4 eV* and *11542.4 eV*,
respectively. 

__ __

When using the Pt L_3 edge (11564.0 eV) as a calibration, the
W L_3 - and L_2 -edges are *10203.3 eV* and *11542.4 eV*,
respectively.

__ __

These observations are thus different than the reported
values of *10207.0 eV* and *11544.0 eV* for the L_3 and L_2
edges, respectively.

__ __

Thanks in advance for the discussion and feedback.

__ __

__ __

Simon R Bare

/Distinguished Scientist/

/SSRL, MS69/

/SLAC National Accelerator Lab/

/2575 Sand Hill Road/

/Menlo Park CA 94025/

__ __

simon.b...@slac.stanford.edu
<mailto:simon.b...@slac.stanford.edu>

Ph: 650-926-2629

__ __




__ __

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

2020-05-05 Thread Matthew Marcus

This paper:
Kraft, S., Stümpel, J., Becker, P., & Kuetgens, U. (1996). High 
resolution x‐ray absorption spectroscopy with absolute energy 
calibration for the determination of absorption edge energies. Review of 
Scientific Instruments, 67(3), 681-687.


has precision measurements of a bunch of edges including the Pt L-edges. 
 It shows an L3 energy of  11562.76(2)eV.  It refers to an older 
tabulation as well.  If you look at various tables, you find energies 
that vary considerably.  For instance, the paper cited above has the Fe 
K-edge as 7110.75eV, while some tabulations have it at 7112.

mam

On 5/5/2020 3:14 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 L_3 edge (11215.0 eV) as a calibration, the W L_3 - 
and L_2 -edges are *10203.4 eV* and *11542.4 eV*, respectively.


When using the Pt L_3 edge (11564.0 eV) as a calibration, the W L_3 - 
and L_2 -edges are *10203.3 eV* and *11542.4 eV*, respectively.


These observations are thus different than the reported values of 
*10207.0 eV* and *11544.0 eV* for the L_3 and L_2 edges, respectively.


Thanks in advance for the discussion and feedback.

Simon R Bare

/Distinguished Scientist/

/SSRL, MS69/

/SLAC National Accelerator Lab/

/2575 Sand Hill Road/

/Menlo Park CA 94025/

simon.b...@slac.stanford.edu 

Ph: 650-926-2629

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Re: [Ifeffit] errors in bond lengths

2020-04-12 Thread Matthew Marcus
Something I've done for analyzing DWF on data taken at several 
temperatures is what I called 'consensus amplitude' fitting.  Here, I 
fitted shells to

k^n*chi[i](k) = exp(-2 dsig2[i] k^2) A(k) sin(phi(k)+2 dr[i]k)

where i is the index to temperature, and the fit parameters are A(k), 
phi(k), dr[i] and dsig2[i].  The obvious ambiguity is solved by 
arbitrarily picking one i, say i=0, to have dsig2[0]=0 and dr[0]=0.
This was done iteratively, starting with A and phi obtained by 
back-transforming the filtered shells.  You can do this with multiple 
shells.  In at least one case, this helped me separate two shells by 
their differing temperature dependence.


Doing this treats the data 'democratically', not taking one of the 
spectra as a reference to which all others are fit.  Also, it doesn't 
overemphasis the low-amplitude parts of the signal, which the log-ratio 
method could do.


Refs: M. A. Marcus, M. P. Andrews, J. Zegenhagen, A. S. Bommannavar, P. 
Montano, "Structure and vibrations of chemically produced Au55 clusters",

PRB 42,3312 (1990)

M. Marcus (that was before I started using my middle initial), "Siting 
and dynamics of Cu impurity in Ti lattice", Solid State Commun. 38, 251 
(1981)


Not a lot of detail in those papers, I'm afraid.  I did do more with 
this method way back when, but it doesn't seem to have made its way into 
the literature.   Back then, I was so naive that I considered a 
conference proceeding to be as good as a PRL, so lost a lot of impact.


mam

On 4/12/2020 8:15 PM, Matt Newville wrote:

Hi George,

I think this will not be a different answer from Matthew's or Anatoly's 
answers, but just reiterate their points.  The Purans et al 2008 PRL 
from 2008 appears to use both non-linear fitting with Feff and EDA 
(which should give basically the same results as Artemis/Ifeffit/Larch, 
though I do not know in detail what error analysis is done), and the 
log-ratio method.  I think they also fit the resulting sigma2 (derived 
from the non-linear fit) to an Einstein model.


The log-ratio method can only determine relative changes in distance, 
coordination number, and sigma2.  The main motivation for using this 
method is that scattering factors in the EXAFS equation will cancel out 
(or mostly cancel out) when comparing two similar experimental spectra.  
In addition, it is often argued that data extraction errors (energy 
scale, background subtraction, etc) would tend to be the same for two 
experimental spectra and so would also mostly cancel out.  There usually 
isn't much analysis of what residual systematic errors happen with the 
log-ratio method.   The working idea is that the ratio of the log of 
isolated single-shell EXAFS chi(k) (or what we would call chi(q) in 
Artemis/Ifeffit/Larch)  amplitudes vs k**2 should be linear (intercept = 
Delta N, slope=Delta sigma2) and the phase difference vs k should also 
be linear (intercept=0 if E0 is truly unchanged, and slope = Delta R).  
  For anyone who actually plots those (even for spectra on the same 
sample), you will probably find that these are "linear-ish", clearly 
showing both "yeah, that could work" and also "maybe not perfectly".


But, if I'm reading this PRL correctly, it looks like they use the 
log-ratio method to compare sigma2 and R of spectra at the same 
temperature but with different isotopes. That does seem like a fine way 
to better determine the subtle differences between those spectra.


--Matt


On Sat, Apr 11, 2020 at 12:41 PM George Sterbinsky 
> wrote:


Hello,

As is well known, EXAFS is more accurate at determining relative
changes in bond lengths than absolute changes in bond lengths due to
cancelation of systematic errors in relative comparisons. When
comparing the relative changes in bond lengths determined from EXAFS
fits, as one might for a temperature series for example, is it
appropriate to use the uncertainties returned by Artemis?

My question arises in part from Phys Rev Lett vol. 100 pg. 055901
(2008), where the authors state that errors for changes in bond
length in a temperature series were determined by empirical means
rather than statistical means. This then raises the question as to
if the authors believe that statistical means would overestimate the
error. My inclination is to think that the uncertainties reported by
Artemis would be appropriate because of the scaling by the square
root of reduced chi squared. However, I want to see what others
think about this before committing to it.

Thank you,
George

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Re: [Ifeffit] errors in bond lengths

2020-04-11 Thread Matthew Marcus
The uncertainties reported by Artemis include as 'noise' the systematic 
deviation of FEFF calculation from the real thing.  Even if FEFF were 
perfect, those FEFF calcs haven't been through the mutilations inflicted 
by data reduction, such as spline fitting.  What I've done when looking 
at closely-related systems such as the same thing at differing 
temperatures is shell-by-shell fitting with one of them as reference.

For an example of this kind of thing, see:

Aruguete, D. M., Marcus, M. A., Li, L.S., Williamson, A., Fakra, S., 
Gygy, F., Galli, G, A, Alivisatos, A. P. (2007)  "Surface structure of 
CdSe nanorods revealed by combined X-ray absorption fine structure 
measurements and ab Initio calculations", J. Phys. Chem. C 111(1),75-79 
and supporting information


The SI has details about how the fits were done.  In this case, the 
different spectra didn't refer to differing temperatures but rather 
different polarization directions.

mam

On 4/11/2020 10:40 AM, George Sterbinsky wrote:

Hello,

As is well known, EXAFS is more accurate at determining relative changes 
in bond lengths than absolute changes in bond lengths due to cancelation 
of systematic errors in relative comparisons. When comparing the 
relative changes in bond lengths determined from EXAFS fits, as one 
might for a temperature series for example, is it appropriate to use the 
uncertainties returned by Artemis?


My question arises in part from Phys Rev Lett vol. 100 pg. 055901 
(2008), where the authors state that errors for changes in bond length 
in a temperature series were determined by empirical means rather than 
statistical means. This then raises the question as to if the authors 
believe that statistical means would overestimate the error. My 
inclination is to think that the uncertainties reported by Artemis would 
be appropriate because of the scaling by the square root of reduced chi 
squared. However, I want to see what others think about this before 
committing to it.


Thank you,
George


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Re: [Ifeffit] what happened to the website?

2020-01-29 Thread Matthew Marcus

OK, thanks.  I figured that you removed it because it's obsolete.

Are you sure the server isn't running Windows 7? :-)

Sincerely,
Matthew Marcus

On 1/29/2020 3:48 PM, Matt Newville wrote:

Hi Matthew,


On Wed, Jan 29, 2020 at 4:39 PM Matthew Marcus mailto:mamar...@lbl.gov>> wrote:

The http://millenia.cars.aps.anl.gov/ website seems to have gone off-line, 
which means that WebAtoms doesn't work anymore.  Is there a replacement?
Of course, I can use the stand-alone Atoms in Demeter.


The webpages appear to be blocked to outside (ie, outside ANL) traffic today.  I've put 
in a complaint ;).  That is, it *should* be working and hopefully will be back soon, but 
the wheels of national labs run slowly and only mostly forward.    FWIW, 
"https://; is now required, but that *should* be automatic and is not the 
problem today.

I don't have an answer for replacement.

--Matt


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Re: [Ifeffit] what happened to the website?

2020-01-29 Thread Matthew Marcus

Quoth the cited doc:
"Assuming you have perl installed on your computer, you will need to install the 
Dancer web framework, perl's YAML tool, Demeter, and all of their dependencies"
This sounds like WAY too much trouble!  I think I'll stick with Demeter 
Stand-Alone Atoms.  WebAtoms had a problem anyway - it wouldn't reliably
handle more than 50 inequivalent sites.  There are complicated mineral 
structures of low symmetry that easily blow past that.

Sincerely,
    Matthew Marcus

On 1/29/2020 3:09 PM, Jo Melville wrote:

If you already have Demeter installed, it's reasonably easy to run a local instance 
of WebAtoms <http://bruceravel.github.io/demeter/documents/SinglePage/wa.html> 
if (like me) you just prefer the interface.

On Wed, Jan 29, 2020 at 5:44 PM Matthew Marcus mailto:mamar...@lbl.gov>> wrote:

The http://millenia.cars.aps.anl.gov/ website seems to have gone off-line, 
which means that WebAtoms doesn't work anymore.  Is there a replacement?
Of course, I can use the stand-alone Atoms in Demeter.
-- 
Sincerely,

          Matthew Marcus
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PhD Candidate, Surendranath Group <http://www.interphases.org/> (2016-)
Contact: (620)-842-8756

/“People think of education as something they can finish.”/

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[Ifeffit] what happened to the website?

2020-01-29 Thread Matthew Marcus

The http://millenia.cars.aps.anl.gov/ website seems to have gone off-line, 
which means that WebAtoms doesn't work anymore.  Is there a replacement?
Of course, I can use the stand-alone Atoms in Demeter.
--
Sincerely,
Matthew Marcus
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Re: [Ifeffit] selection of pixels by criteria

2019-11-21 Thread Matthew Marcus

A suggestion:  Make a scatterplot available, plotting the pixel-by-pixel values 
of any two relevant quantities, and make it
possible to define a polygon mask on that scatterplot.  That often allows 
separation of chemically-distinct areas.

Sincerely,
Matthew Marcus

On 11/21/2019 12:26 PM, Matt Newville wrote:

HI Troy,

Sorry for the late reply -- I think this sort of slipped off my radar screen.


On Sat, Nov 16, 2019 at 2:09 PM E. Rasbury mailto:troy.rasb...@stonybrook.edu>> wrote:

I have used larch some for XRF maps. I like the feature for defining ROI's 
and then looking at the statistics of the data. I have some samples that are an 
intimate mix of two or more phases and I would like to extract pixels based on 
a criteria- like high Sr or low Fe, etc, from across a whole map region. I 
wonder if this feature is available, or would be easy to create on larch?


Like you say, this is not currently available in the Mapviewer GUI.  But it's a 
good suggestion and might be possible to do with a small amount of code.

Would it work for you to say "Make an Area with all pixels where Sr Counts is above some 
value"?  I think that would be easy to generalize from "Sr Counts" to
"Ratio of ROI Counts"  (or "analyzed concentration" once I get that done - a work in 
progress).  If that's right, I think it would be "not hard to add".

--Matt


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[Ifeffit] Anyone use OCEAN?

2019-09-12 Thread Matthew Marcus

OCEAN is the U. Washington program for doing XANES sims using ab-initio, 
Bethe-Salpeter methods 
(http://monalisa.phys.washington.edu/OCEAN/ocean-about.html).
It seems to require a certain amount of experience and expertise to get it to 
produce any result, let alone correct
results.  I wonder if this might be a good forum for getting advice on solving 
problems with this code.  Unlike ABINIT,
which is one of the ab-inito engines OCEAN can use, OCEAN doesn't have a forum 
of its own.
--
Sincerely,
Matthew Marcus
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Re: [Ifeffit] Two analysts, one spectrum, similar outcome?

2019-08-14 Thread Matthew Marcus

Dear Carlo.  Regarding yours of Tue, 13 Aug 2019 21:59:18 -0500 (CDT):

The way I like to put it is that EXAFS works best if you already know most of 
the answer.  You need to have a specific question,
such as 'is there antisite disorder?' or 'Are there edge-sharing octahedra?', 
or 'Which of three structures does this most resemble?'.

I love the idea of blind analysis comparison.

Sincerely,
   Matthew Marcus


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] EXAFS of solid-solution alloy

2019-02-08 Thread Matthew Marcus

Dear Chongchong.  Regarding yours of Fri, 8 Feb 2019 19:36:24 +0900:

For concreteness, let's pretend that A = Mn and B = Co, which differ by 2 in Z. 
 The scattering factors (amp+phase) for Co are very close to those of Mn.  
Thus, you probably can't
distinguish Co from Mn neighbors.  Instead, if you're doing ab-initio fits, I 
suggest doing the fits as if all the scattering atoms were Fe, right in the 
middle.  If you're doing
fits from, say, pure Mn and extracting amp+phase, then you could "correct" to 
Fe by doing theoretical paths for Mn-Mn and Mn-Fe and taking the ratio of amplitudes and 
the difference
in phase and applying these to the Mn-Mn experimental factors.  I used to do 
this all the time back when FEFF wasn't good enough to use without references.  
Why ratio of amps
and differences of phase?  You can think of the scattering factor as a complex 
number Ac = A*exp(i phi), and so Ac(Fe)/Ac(Mn) = 
(A(Fe)/A(Mn))*exp(i(phi(Fe)-phi(Mn))).

To get an idea of what the error in the 'all Fe' assumption is, you could do 
the fits pretending that all the scatterers are Mn and again with all the 
scatterers Co and see how
different the results are.

I imagine that the dsig2 will be smaller for each end-member than in the 
middle, due to lattice distortion as well as the phase difference between A and 
B.  Can you do the EXAFS
at both edges?  If so, any difference between these two will be due to the 
difference in central-atom phase and S0^2 plus any clustering of A with A and B 
with B.  Again, theoretical
sims will tell you how big the difference in central-atom properties is.  You 
can simulate a lattice consisting entirely of A and one in which only the 
absorbing atom is replaced
by a B and apply these differences to the experimental data from each edge.

Sincerely,
   Matthew Marcus

Hi all,

I have some problems in analyzing the EXAFS of solid-solution alloy, let us 
define as A0.5B0.5. I have searched the mailbox but cannot find similar 
discussion yet. So I post the question here and hope to get some suggestion 
from you.


 1. A and B are immiscible metals from the phase diagram, which means that I 
couldn’t get the bulk A0.5B0.5 as a standard reference. In this case, how can I 
estimate the amp for the K-edge of A or B?
 2. A and B are very near (atomic number B-A = 2) in the periodic table. So 
their lattice parameters are quite close to each other. In this case, when I 
tried to fit the 1st shell use A-A and A-B paths at the same time, the 
Happiness parameter becomes worse and the coordination number of A-B is not 
realistic (large errors!).If I fit with only the A-A path or A-B path, I get a 
good fit. However, atomic resolution STEM-EDX maps show the homogenous 
distribution of both A and B atoms. The A-A and A-B bond might have an equal 
ratio. In this case, how can I do the fitting?


Thank you very much in advance!


Sincerely,

Chong


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Re: [Ifeffit] Bump/oscillating pattern at high energies of EXAFS

2018-11-01 Thread Matthew Marcus

Agreed.  The low frequency and high amplitude at the end is implausible as 
EXAFS.

Sincerely,
   Matthew Marcus

It is an effect of inhomogeneity of the sample, that is, the variation in the 
metal density throughout the X-ray beam footprint.
Anatoly



On Thu, Nov 1, 2018 at 5:34 PM Raj kumar mailto:rajr...@gmail.com>> wrote:

Dear All,

I have monitored the growth process of YbVO4 nanoparticles using EXAFS. 
Here, nanoparticles were synthesized in water medium. Both initial and final 
products (EXAFS) of the synthesis were measured using the continuous flow 
approach whereas the intermediate products were recorded, in the glass 
capillary, using the stopped flow. In the attached figure, you can find the 
same (all products). At high energies of EXAFS, both initial and final 
measurements show smooth behavior whereas the oscillating pattern/bump was 
observed for the intermediate states.

Here, my question is: Is the oscillating pattern appearing in the 
intermediate states due to the sedimentation/in-homogeneity of the product in 
the capillary or it is the characteristic of the synthesis?

With regards,
Raj
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Re: [Ifeffit] Interpreting old XANES data with missing standards

2018-06-08 Thread Matthew Marcus

Dear Don.  Regarding yours of Fri, 08 Jun 2018 09:54:40 -0400:

ESRF has a dbase of S XANES, but they're all pretty affected by overabsorption 
("self-absorption").  I think the only reliable way to take such data is in TEY 
mode.
There's a spectrum there for cinnabar (remember, there are multiple polymorphs 
of HgS) and three forms of Fe sulfide plus several more sulfides.  Even the 
transmission spectra are subject to
hole effect, which looks like overabsorption.
Also, if you do take data on sulfides, beware of radiation damage.

Does it really make sense that a silicate glass would have sulfide in it?  I'd 
think that it would have mostly sulfate and maybe sulfite.  Check the peak 
position;
it's a pretty reliable indicator of sulfite vs. sulfate vs. other.

Here are some spectra taken in TEY mode with the calibration gypsum = 2482.75eV.

Sincerely,
   Matthew Marcus

Hello All,

First let me apologize if the question below is inappropriate for this
group, but I don't know of a better set of experts that I can ask.

So, here is some background:

I have some old S K-edge XANES data from NSLS X15B for S-bearing
silicate glasses that was collected by a Ph.D. student who decided to
leave for a good job rather than finishing their degree.  During my
current sabbatical year I have been looking at the data and reading
papers on the topic.  I think that I now understand, at least
qualitatively, the changes in the spectra as a function of iron
concentration in the glasses, but to perform quantitative modelling I
need XANES spectra of MgS and CaS, which we did not think to collect all
those years ago.  I have searched for XANES spectra of MgS and CaS on
the CARS XAFS Data Library and on the XAFS Database at IIT without
success.  I am unaware of other databases available.

Now for for my questions:

1.  Does anyone know of a XANES database that contains MgS and CaS
spectra?  (Or did I miss it in the databases I searched?)

2.  If I cannot find measured MgS and CaS spectra, what do you think
about using calculated spectra (e.g., Zheng et al.,2012, NPJ
Computational Materials, 12 -- which uses FEFF) for quantitative
modelling?


And information, ideas, and suggestions that you may have will be
appreciated.


Wishing you all the best from a spring morning in Montreal,

Don

  



2.4204828E+3 1.3481375E-1
2.4224844E+3 2.1379664E-1
2.4244405E+3 1.0034682E-1
2.4263966E+3 6.0864504E-2
2.4283527E+3 2.3284770E-2
2.4303088E+3 -4.4423012E-4
2.4322649E+3 4.3219621E-3
2.4342210E+3 1.7839984E-2
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2.4381332E+3 1.3531903E-2
2.4400893E+3 -2.1541549E-3
2.4420455E+3 6.4516400E-4
2.4440016E+3 -1.0604154E-1
2.4459577E+3 2.5947752E-2
2.4479138E+3 1.3131741E-3
2.4498699E+3 -1.3334000E-2
2.4518260E+3 6.7262919E-3
2.4537821E+3 1.5119381E-2
2.4557382E+3 -9.0837660E-3
2.4576943E+3 1.4185344E-2
2.4596504E+3 1.0255968E-2
2.4616065E+3 1.0778473E-2
2.4635627E+3 -9.3267548E-3
2.4655188E+3 1.4821698E-2
2.4657189E+3 1.7375247E-2
2.4659191E+3 1.9558202E-2
2.4661192E+3 -9.0770303E-4
2.4663194E+3 -2.0608094E-2
2.4665196E+3 -1.0530884E-2
2.4667197E+3 -1.6217977E-2
2.4669199E+3 -8.8552997E-3
2.4671200E+3 -4.4492973E-3
2.4673202E+3 9.1158992E-3
2.4675204E+3 1.2202778E-2
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2.4681208E+3 8.8804807E-2
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2.4697221E+3 6.7858920E-1
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2.4717237E+3 1.2544375E+0
2.4719239E+3 1.1184622E+0
2.4721241E+3 9.9855791E-1
2.4723242E+3 9.0381839E-1
2.4725244E+3 8.0715872E-1
2.4727245E+3 7.3838810E-1
2.4729247E+3 6.8701761E-1
2.4731249E+3 6.5647131E-1
2.4733250E+3 6.6264678E-1
2.4735252E+3 6.7132830E-1
2.4737253E+3 6.9059683E-1
2.4739255E+3 7.0655582E-1
2.4741257E+3 7.4608062E-1
2.4743258E+3 7.8901739E-1
2.4745260E+3 8.5103375E-1
2.4747261E+3 9.1353422E-1
2.4749263E+3 9.9767993E-1
2.4751265E+3 1.0618783E+0
2.4753266E+3 1.1129009E+0
2.4755268E+3 1.2088946E+0
2.4757269E+3 1.2732357E+0
2.4759271E+3 1.3347068E+0
2.4761273E+3 1.3950683E+0
2.4763274E+3 1.4296208E+0
2.4765276E+3 1.4971378E+0
2.4767277E+3 1.5051599E+0
2.4769279E+3 1.5399133E+0
2.4771281E+3 1.5934019E+0
2.4773282E+3 1.6369189E+0
2.4775284E+3 1.6289419E+0
2.4777285E+3 1.6311694E+0
2.4779287E+3 1.6536179E+0
2.4781289E+3 1.7047408E+0
2.4783290E+3 1.7466130E+0
2.4785292E+3 1.7033940E+0
2.4787293E+3 1.6805148E+0
2.4789295E+3 1.7074040E+0
2.4791297E+3 1.7157318E+0
2.4793298E+3 1.6999374E+0
2.4795300E+3 1.6789126E+0
2.4797301E+3 1.6930139E+0
2.4799303E+3 1.6578313E+0
2.4801305E+3 1.6156245E+0
2.4803306E+3 1.6092837E+0
2.4805308E+3 1.5932398E+0
2.4807309E+3 1.5694943E+0
2.4809311E+3 1.5568848E+0
2.4811313E+3 1.5410127E+0
2.4813314E+3 

Re: [Ifeffit] EXAFS above 5 angstroms

2018-05-21 Thread Matthew Marcus

One of the biggest inhibiting factors for seeing long distances is that there 
are generally many, many paths, which interfere with each other so that you 
don't see much.
OTOH, there are sometimes special circumstances such that one set of paths 
stands out above the crowd and you can sometimes see them.  One example that I 
had was a
Cr bis-arene complex (I think cyclopentadiene, so that Cr was sandwiched 
between two rings).  At RT, it was nothing special, but at 11K, the Cr-Cr 
distance popped out
at 7A.  That also shows the role of vibrations in causing shells to disappear.  
One thing that can give let you see distant shells is focusing by atoms in a 
straight
line in between the absorber and scatterer.  This is sort of like the way a 
galaxy cluster can make it possible to see a very distant galaxy behind it due 
to
gravitational lensing.

Unless you give FEFF realistic MSRD's, then it will tend to overestimate the 
visibility of distant shells.

Depending on which edge you're on, core-hole lifetime can indeed compromise the 
visibility of high shells.  You can see it two ways: the uncertainty principle
shows that the energy resolution is limited by core-hole lifetime, and you can 
also calculate how long it takes for the electron to get to the scatterer and
back again.  If the core hole decays before the round trip is complete, then 
the absorption event doesn't contribute to the EXAFS.  As they say in textbooks,
it is left to the student to verify that these two approaches give you the same 
criterion for the visibility of a distant shell.  This effect is indeed 
significant
for heavy elements, either at the L-edge (5d and actinides) or K-edge (4d and 
up).

Sincerely,
   Matthew Marcus

Daniel,

Those distances are really far away and I think it would really difficult to 
see in EXAFS even with pretty high quality data.  Is there are other 
information from diffraction that suggests these distances?

Chris
**
Dr Christopher Patridge
Assistant Professor
Department of Chemistry
SASE 315
D’Youville College
320 Porter Ave.
Buffalo, NY 14201
716-829-8096 / 315-529-0501
patri...@dyc.edu <mailto:patri...@dyc.edu>




On May 21, 2018, at 7:13 PM, Daniel Sneed <snee...@unlv.nevada.edu 
<mailto:snee...@unlv.nevada.edu>> wrote:

Hello,

This is my first time posting to the mailing list, so please forgive me if I 
did not do it correctly.

I am currently working on EXAFS of tin(IV) oxide, and I have what appears to be 
high quality data out to 9 angstroms or so, but I am having some issues in 
fitting the data above 4 angstroms. I am attempting to verify a crystal 
structure with a= ~6 angstroms, and another structure with a=~9 angstroms. I 
know that there is some inhibiting physics at such long distances, such as 
inelastic scattering, and core-hole lifetime issues that can effect the data. 
My question for the group is, is there any methodical way to deal with these 
issues, other than incorporating Ei and the higher cumulants? Or is it even 
possible to get results from such large R?

Thank you for your time.

regards,

Daniel Sneed
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[Ifeffit] current-amp recommendation

2017-11-14 Thread Matthew Marcus

I've gotten involved with a project in which stabilization of the position of a 
monochromatic, soft X-ray beam is needed.  The
offending frequencies seem to be vibration frequencies like 57 and 116Hz.  We 
have in mind to use a thin Au film with a gap in the
middle, measuring the drain current from the films, much as people normally use 
the jaws of slits.  Now, I'd like to find a couple
of current amplifiers which are small enough so that they can be connected with 
very short cables to the BNC connectors on the
air-side of this detector, and which would have decent frequency response and 
low noise with inputs of the order of 0.1-1nA.
Although this topic is outside the realm of XAFS analysis with IFEFFIT, I 
figure that people on this group might have some
good experience.

mam
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Re: [Ifeffit] XAFS short course in BNL: Nov 1-3, 2017

2017-07-28 Thread Matthew Marcus

Dear Anatoly.  Regarding yours of Fri, 28 Jul 2017 15:43:01 -0400:

The website doesn't work for non-BNL people.  It pops up a login/password 
window for the BNL domain.  I'm assuming that you want people from elsewhere to 
be able to take the course.

I don't know yet whether I'll be able to go.  It does sound interesting.  My 
knowledge of XAS analysis has remained pretty static.  Will there be anything 
that applies
to soft X-rays?  I'm moving to STXM, so will be dealing with soft X-rays.




Sincerely,
   Matthew Marcus

Dear subscribers:

Please share with your group members or others, who may be interested, the 
following information about the short course on XAFS spectroscopy:

Title: *Data Analysis and Modeling of XANES and EXAFS Spectra. Applications to 
Nanomaterials*
Dates: *November 1-3, 2017*
Location: *Brookhaven National Laboratory**
**
*The course is open for applications at this web site:https://www.bnl.gov/exafs2017/ 
<https://mail.bnl.gov/OWA/redir.aspx?C=Cs5LzjKsiYS2QXnknBXt0VXGF6SSe4a5KclqcKrisLz4D2W08NXUCA..=https%3a%2f%2fwww.bnl.gov%2fexafs2017%2f>

The course will be useful for those scientists who are familiar with the 
foundations of XAFS experiment, theory and data analysis, and seek training in 
advanced methods. The course will include lectures, software demonstrations, 
and data analysis sessions. The emphasis will be on applications of XAFS to 
nanomaterials but we will welcome all participants who are interested in modern 
analysis methods. The course instructors will use examples from their research 
during presentations. The topics covered will include:

-Theory of XANES,
-XANES data analysis,
-Structural refinement using XANES, with emphasis on the following methods:
 -Molecular dynamics,
 -Reverse Monte Carlo.
 -Machine Learning methods*
*

During the data analysis practicum on November 3, participants will get an 
opportunity to work with research projects with the help of the course 
instructors.

The course is co-sponsored by BNL and Synchrotron Catalysis Consortium (SCC).

Best regards,

Anatoly*
*
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email: anatoly.fren...@stonybrook.edu 
<https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0ybKTBGBlALcrWeszTCA..=mailto%3ajgchen%40columbia.edu>
http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov <mailto:fren...@bnl.gov>
https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---


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Re: [Ifeffit] E0 on linear combination fitting: fit or not?

2017-05-12 Thread Matthew Marcus

My experience on ALS 10.3.2 is that shifts of up to about 0.5eV are plausible 
and often improve the fit substantially.  I assume you're talking XANES, not 
EXAFS.  6eV
is right out and suggests either a misidentification of the species (false fit) 
or inconsistency of energy cal.  One of my pet peeves is that authors of 
XANES-intensive
papers will often say things like "energy was calibrated using Cu foil" without 
saying what their assumed value was (8978eV? 8048.45eV?).
mam

On 5/12/2017 8:42 AM, Matt Newville wrote:

Hi Pamela,


On Thu, May 11, 2017 at 12:19 PM, Carrillo Sanchez, Pamela > wrote:

__ __

__ __

Hi all, 

__ __

I have gone through the mail archives as well as following the instructions 
of Athena user’s manual as well as Scott Calvin’s book but still I find myself 
with the doubt of how correctly “choose E0”. I have aligned the data and 
standards with the merge of reference foils measurements of the metal (Mn). We 
did not have a reference foil placed while measuring the data so I used the 
merge of the references scans when the standards were measured and they showed 
a consistent energy shift. 

 I have set the same E0 for all the data and standard to the same E0, I 
chose the first peak of the derivative in the data (6MnRh_RED). When I do the 
LCF analysis without ‘fitting E0’ ,  I get a worse fitting than when I choose 
the fit E0 on Athena as well as different types of components on the fitting. 
Which one is the best choice for it ? From what I have read I think that 
without fitting E0 would be the proper one regardless of the “worse fit”. 

__



The recommendation to not fit E0 in linear combination fitting is generally 
preferred, but also assumes that you have all data calibrated to the same 
energy scale.  The concern for fitting E0 in such a linear analysis is that 
energy shifts are often a sign of real chemical effects, not an indication of a 
change in energy calibration.

But, you can definitely use Athena's linear combination fitting to figure out 
what the energy shift is between two spectra on the same material measured with 
different calibrations.

Generally, it's best to measure several standards at the same time, so as to be 
able to assert that their energy scales (and resolution) are consistent.   It's 
OK to measure some samples / standards at different beamlines or different 
sessions at the same beamline as long you're careful about calibrating energy 
consistently (say with the same sample such as metal foil or hard-to-alter 
metal oxide) and the resolutions are similar.  These days most beamlines are 
pretty stable in energy calibration and resolution.

If the standards are well-aligned internally, applying very different E0s to the 
standards is probably not what you want.   Your "fit E0" example shows E0 
shifts varying between ~0 and -6 eV for the different standards.  I think that's kind of 
large - it's possible the energy scales for the standards vary by that much, but you 
might want to double-check that too.

But, if you don't have calibrated standards, I might suggest asking the 
beamline scientist if they have an idea what kinds of energy shifts they expect.


Hope that helps,

--Matt




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Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 21

2017-04-21 Thread Matthew Marcus
scribe via the World Wide Web, visit

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."


Today's Topics:

   1. Re: Ifeffit Digest, Vol 170, Issue 19 (Matt Newville)
   2. Fwd:  Ifeffit Digest, Vol 170, Issue 19 (Matt Newville)
   3. Looking for EXAFS data of Ni2+ ion in aqueous solution (Van Vu)


--

Message: 1
Date: Thu, 20 Apr 2017 21:18:39 -0500
From: Matt Newville <newvi...@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19
Message-ID:
<ca+7esbpewenmlpspnyaxt4j2t1lkjaayua59xcgeblptekt...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Chris,

On Thu, Apr 20, 2017 at 5:02 PM, Christopher Thomas Chantler <
chant...@unimelb.edu.au> wrote:


Note that in general any and every smoothing operation reduces the
information content of the data and its ability to reveal structure.



Well, maybe.  If one has mu(E) measured every 0.01 eV over an 600 eV EXAFS
scan to k=12A^-1, one does not really 60,000 independent measures of the
structure.  Yuji's data wasn't that absurd, but it did have close to 4000
measurements for the full EXAFS spectrum out to k=18^-1.  And to be clear,
there is not anything wrong with that, it's just a matter of how you decide
to treat it.

As the plots attached in Yuji's original message and my replies show, the
resulting chi(k) definitely has is amplitude suppressed when doing a simple
boxcar average of data onto the 0.05 Ang^-1 grid (Athena with Ifeffit).
But when using cubic spline interpolation (Larch), the amplitude of the
EXAFS oscillations are not noticeably suppressed, though the high frequency
noise is also much higher.  Applying a Savitzky-Golay filter prior to the
cubic spline interpolation did not appreciably suppress the EXAFS
oscillations though the high frequency noise was reduced.

Very finely-spaced energy data might reveal is at much higher R than we can
hope to model with EXAFS.  A k-grid of 0.05 Ang^-1 can give frequencies to
31Ang, and so is probably accurate to 16Ang without significant signal
loss.   That is, out to k=18Ang^-1, you really only need 360 samples, but
you'd like these as noise-free as possible.  Having 3600 measurements on a
grid of 0.005 Ang^-1  might give you data out to 160Ang in principle, but
the photo-electron tends to not cooperate.

--Matt
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Message: 2
Date: Thu, 20 Apr 2017 22:33:14 -0500
From: Matt Newville <newvi...@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Fwd:  Ifeffit Digest, Vol 170, Issue 19
Message-ID:
<ca+7esbopsw1p-9hzyyq+yobhcch++cohocyg2z-gexadn3l...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Matthew,


On Thu, Apr 20, 2017 at 5:34 PM, Matthew Marcus <mamar...@lbl.gov> wrote:


Does Athena use a histogramming method for Fourier filtering?



The autobk() in Ifeffit does.  That is, the background mu0(E) and chi(E)
are found at all input energy points.  This is converted to chi(k) at k for
all energy points, and then a boxcar average is applied to give chi(k) on
the standard 0.05 k-grid.  As shown earlier, this diminishes the noise and
also the amplitude of chi(k), especially at higher frequencies.

In Larch, the cubic spline for the background mu0(E)  is found at all input
energy points, but then evaluated at the values on the uniform k-grid.
.


That's what I use.  The idea is that to grid the data we don't interpolate
but take averages over the data appearing within the bin,



 OK, but that boxcar average will blur the data.I definitely see this
with QXAFS (well "continuous") where I can scan continuously but bin the
measurements into 0.05Ang-1 bins -- that *does* reduce the amplitude
compared to binning into 0.02 Ang^-1 bins and compared to step scans, where
one measures at fixed energies, not slewing over an energy range.

The data from SPRing8 was much finer spaced than EXAFS needs -- and boxcar
averaging to 0.05 Ang^-1 does blur the data.



with interpolation only when there aren't any points within a bin. For
those, you have to bridge acr

Re: [Ifeffit] Ifeffit Digest, Vol 170, Issue 19

2017-04-20 Thread Matthew Marcus

Does Athena use a histogramming method for Fourier filtering?  That's what I 
use.  The idea is that to grid the data we don't interpolate but take averages 
over the data appearing within the bin, with interpolation
only when there aren't any points within a bin.  For those, you have to bridge 
across a gap.  This is the best idea I've come up with for using data which may 
be tabulated more finely than the k-grid
of the Fourier filtering process (typically dk=0.05A^-1).

Something I've used in a XANES context but never tried for EXAFS is a 
convolution with a kernel whose width depends on energy, such that it matches 
the sharpest credible feature.  See Manceau, A., Marcus, M. A., Lenoir, T. 
(2014) Estimating the number of pure chemical components in a mixture by X-ray 
absorption spectroscopy. J. Synchrotron Radiat. 21,1140-1147,
specifically the SI.  The notion is that no real feature can be narrower than 
the combination of the core-hole lifetime and instrumental broadening or the 
EXAFS wiggle corresponding to the maximum reasonable path length.  This is done
by transforming the data from E-space to a space in which a constant step in 
the abscissa corresponds to this energy-dependent minimum credible feature 
width.  Of course, in EXAFS this is mostly a constant width in k,
so some kind of smoothing would work if it's a constant kernel in k.  S-G 
smoothing assumes uniform tabulation so unless your data were taken on a 
uniform k-grid, it doesn't really do the right thing.
A problem with this method is that it drops off the very information you need 
to see what your noise floor is.  I put this out there only
for those who insist on smoothing.  I use my data un-smoothed for EXAFS 
analysis, knowing that the treatment of noise and sampling finer than the k-bin 
is not really right.

I don't really see the usefulness of smoothing for XANES or EXAFS analysis, 
though it might be OK for display if not overdone.
mam

On 4/20/2017 3:02 PM, Christopher Thomas Chantler wrote:

Note that in general any and every smoothing operation reduces the information 
content of the data and its ability to reveal structure. Also, many of the 
smoothing algorithms change the data point values at vertices, so change the 
data prior to analysis.


Hence in general avoid unless you know exactly the physical cause requiring 
smoothing.


Best wishes


--
Christopher Chantler, Professor, FAIP, Fellow American Physical Society
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS
President, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783
chant...@unimelb.edu.au 

 chant...@me.com 

http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html 

http://optics.ph.unimelb.edu.au/~chantler/home.html 


---!

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Re: [Ifeffit] Peakfitting CeO2 data in Athena

2016-12-08 Thread Matthew Marcus
The usual justification for using gaussians for peaks, aside from "it
works" is that there's inhomogeneous broadening over and above the
lifetime.  The usual justification for using an arctan for the step is
exactly the opposite.  Instrument broadening is often taken to be
gaussian.  Net result:  A (pseudo)Voight for peaks often works.  One
issue is what to do about the post-white-line peaks, which sometimes
are viewed as the first EXAFS wiggles.  Manceau has a nice paper about
S XANES  (I don't have the ref handy right now) in which he goes
through peak fitting and evaluates its uniqueness.
   mam

On Thu, Dec 8, 2016 at 5:40 AM, Matt Newville
 wrote:
> Hi Stephanie,
>
>
>
> On Wed, Dec 7, 2016 at 12:33 PM, Stephanie Laga 
> wrote:
>>
>> Dear all,
>>
>> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data.
>> I have been using moved the peak fitting function in Athena to model the
>> XANES with an arctan background function and a series of gaussians.
>>
>> Looking through the literature I haven't seen too many specifics to using
>> this approach (rationale for choosing the widths of peaks or how to define
>> the background function). Similarly, doesn't seem to be much rationale for
>> choosing a 4 vs 5 peak fit for the XANES.
>>
>> My main question is then...1) Is there a rational for picking the
>> background function, specifically the height and width (can I let the height
>> vary or should I be keeping a constant arctan through all samples)?
>>
>> Any advice is greatly appreciated!
>>
>> Stephanie
>>
>
> Matthew answered quickly, but sort of changed the subject, suggesting a
> different analysis (LSQ) and then discussing some of the pitfalls of that
> approach.  Your original question is still worth discussing.
>
> There is not a whole lot of justification in using one particular shape for
> the background.  A step broadened as arctan, error function are common and
> seem to work well. Each has some theoretical explanation in that the
> integral of a series of Lorentzian gives an arc-tangent function while the
> integral of a series of Gaussians will give the error function. (If this is
> wrong, can someone please correct?).  If you think as the above edge
> spectrum as a series of finely spaced individual transitions, then these
> functions have some justification.Whether it actually works well in
> detail on a particular spectrum is a separate question.   FWIW, I've also
> seen people use (successfully) a single, very broad Lorentzian for the "main
> edge".
>
> The use of Lorentzians, Gaussians, Voigts, and PseudoVoigts is somewhat more
> justified in that those are how you would expect a single electronic
> transition to appear, especially broadened in the way(s) you'd expect a
> monochromatic X-ray beam to be energy broadened.  Using such functions is
> essentially asserting that there is a single electronic transition at that
> energy, and you want to know it's size and shape.  This is not wrong, but it
> does not inherently include any understanding of what that peak is. For
> pre-edge peaks, it's pretty well-justified, and works pretty well.  For
> peaks on or after the main edge or "white line", it's less justified because
> we know that EXAFS-like effects can be important.
>
> The biggest dangers in the peak-fitting approach are:
>1) one always gets an answer, and that is rarely "no, this is not the
> right model to use".  In fairness, most linear algebra methods used for
> XANES analysis or really most other spectroscopies have the same feature.
>2) interpretation of the results can be challenging, or at least it is
> hard to know when they are misleading.  Again, most linear algebra methods
> used for XANES analysis or really most other spectroscopies have the same
> feature.
>3) it can sort of willfully ignore other parts of the spectra.  In
> fairness, we all do this sort of thing all the time.
>
> Hope that helps.  Peak fitting is not exactly "theoretical XANES analysis",
> but it is not always done in an ad-hoc manner out of ignorance either.
>
> Linear algebra techniques are completely justified too.
>
> Hope that helps,
>
> --Matt Newville
>
>
>
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Re: [Ifeffit] Peakfitting CeO2 data in Athena

2016-12-07 Thread Matthew Marcus

Ce(OH)4 is probably not a well-defined compound.  I wouldn't use it.  I suspect that 
"Ce(OH)4" is really hydrated CeO2 nanos.  I've measured 30nm CeO2 nanos and 
they look like bulk.
mam

On 12/7/2016 11:53 AM, Stephanie Laga wrote:

I had started with LSQ but switched to peak fitting because I was worried about 
the Ce(IV) reference. I have data for bulk CeO2 and Ce(OH)4, but doesn't this 
have some Ce(III) impurity in it? I'm not quite sure how to account for this 
when I do LSQ.

Another challenge I've had is in using the Ce(IV) refs for our nanoparticles, 
which are about 2-5 nm in diameter. Is there a good Ce(IV) ref for nanos that 
are in this size range?

On Wed, Dec 7, 2016 at 2:37 PM, Matthew Marcus <mamar...@lbl.gov 
<mailto:mamar...@lbl.gov>> wrote:

Instead of doing a bunch of peak fitting, try LSQ.  Use CeO2 (bulk or 
nanos) for one reference and some Ce(III) for the other.  Consistency check: 
see that the Ce(III) fraction is consistent over some set of Ce(III) references.
Ce(III) has an assymetric white line, so it doesn't really fit a single 
gaussian.  CeO2, unlike other Ce(IV), has a shoulder on the first peak, and the 
first peak is shifted left a little with respect to other Ce(IV).
mam


On 12/7/2016 10:33 AM, Stephanie Laga wrote:

Dear all,

I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS 
data. I have been using moved the peak fitting function in Athena to model the 
XANES with an arctan background function and a series of gaussians.

Looking through the literature I haven't seen too many specifics to 
using this approach (rationale for choosing the widths of peaks or how to 
define the background function). Similarly, doesn't seem to be much rationale 
for choosing a 4 vs 5 peak fit for the XANES.

My main question is then...1) Is there a rational for picking the 
background function, specifically the height and width (can I let the height 
vary or should I be keeping a constant arctan through all samples)?

Any advice is greatly appreciated!

Stephanie


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Re: [Ifeffit] Peakfitting CeO2 data in Athena

2016-12-07 Thread Matthew Marcus

Instead of doing a bunch of peak fitting, try LSQ.  Use CeO2 (bulk or nanos) 
for one reference and some Ce(III) for the other.  Consistency check: see that 
the Ce(III) fraction is consistent over some set of Ce(III) references.
Ce(III) has an assymetric white line, so it doesn't really fit a single 
gaussian.  CeO2, unlike other Ce(IV), has a shoulder on the first peak, and the 
first peak is shifted left a little with respect to other Ce(IV).
mam

On 12/7/2016 10:33 AM, Stephanie Laga wrote:

Dear all,

I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I 
have been using moved the peak fitting function in Athena to model the XANES 
with an arctan background function and a series of gaussians.

Looking through the literature I haven't seen too many specifics to using this 
approach (rationale for choosing the widths of peaks or how to define the 
background function). Similarly, doesn't seem to be much rationale for choosing 
a 4 vs 5 peak fit for the XANES.

My main question is then...1) Is there a rational for picking the background 
function, specifically the height and width (can I let the height vary or 
should I be keeping a constant arctan through all samples)?

Any advice is greatly appreciated!

Stephanie


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Re: [Ifeffit] Ifeffit Digest, Vol 162, Issue 17

2016-08-12 Thread Matthew Marcus

Topic 3: Incorrect dark current (offset) is just one of many ways that glitches 
can escape being normalized out, and one of the few you can correct in 
software.  Others include but are
not limited to

1.  Any detection-system nonlinearity in I0 or detected channel (F or T).  
This includes deadtime in fluorescence detectors.

2.  Inadequate detection speed in QXAS so that the recording of I0 lags 
behind that of fluorescence (or vice versa if using a Lytle detector or 
similar).

3.  Harmonic/stray beam content varies while going through the glitch.

4.  Beam position or shape varies while going through the glitch.  If the 
crystals are in a diverging beam, then each part of the crystal sees a slightly
different incidence angle, so the exact energy at which the two 
reflections contributing to the glitch both satisfy the Bragg condition varies 
across
the crystal surface, resulting in non-uniform reflection.

There are undoubtely many more.
mam

On 8/12/2016 2:36 PM, Christopher Thomas Chantler wrote:

Topic 1: We have a routine /edit within ifeffit (our modified version) which 
propagates and fits uncertainty.
Working on a couple of minor details before passing it on to Matt and Bruce for 
general use.

Topic 3: Monochromator glitches should be eliminated in absorption spectra 
under normal circumstances if the dark current estimation is well defined. I 
recommend careful measurement and recording of this for all spectra.


Christopher Chantler, Professor, FAIP
Editor-in-Chief, Radiation Physics and Chemistry
Chair, International IUCr Commission on XAFS
President, International Radiation Physics Society
School of Physics, University of Melbourne
Parkville Victoria 3010 Australia
+61-3-83445437 FAX +61-3-93474783
chant...@unimelb.edu.au chant...@me.com
http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html
http://optics.ph.unimelb.edu.au/~chantler/home.html



From: Ifeffit [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of 
ifeffit-requ...@millenia.cars.aps.anl.gov 
[ifeffit-requ...@millenia.cars.aps.anl.gov]
Sent: Friday, 12 August 2016 11:22 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 162, Issue 17

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Today's Topics:

   1. Statistical errors in linear combination fits (Joshua Kas)
   2. Re: Statistical errors in linear combination fits (Bruce Ravel)
   3. Athena interpolation when removing mono glitches
  (Michael Gaultois)
   4. Re: Athena interpolation when removing mono glitches (Bruce Ravel)


--

Message: 1
Date: Thu, 11 Aug 2016 13:31:45 -0700
From: Joshua Kas 
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Statistical errors in linear combination fits
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi All,
I was wondering if it is possible to pass a value for the uncertainty in
the data to Athena when doing linear combination fits. We have calculated
chi^2 values using a simple estimate of the statistical uncertainty, and
find that our values differ by several factors of 10 when compared to the
reported values from Athena. I assume that this has to do with value of the
uncertainty that Athena is using, but I certainly could be mistaken. In any
case, the reduced chi^2 reported by Athena is much smaller than 1, while
the fit is off by fairly large amounts compared to any reasonable estimate
of the statistical error.
Thanks in advance for any help and sorry if this info is already available
in the archives,
Josh Kas
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Message: 2
Date: Thu, 11 Aug 2016 16:43:36 -0400
From: Bruce Ravel 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Statistical errors in linear combination fits
Message-ID: <507e138f-9ab8-9de3-0629-bfd85aad1...@bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 08/11/2016 04:31 PM, Joshua Kas wrote:

I was wondering if it is possible to pass a value for the uncertainty in
the data to Athena when doing linear 

Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-09 Thread Matthew Marcus

Oh, the Demeter menu.  I was looking in Artemis itself.  Thanks!
mam

On 8/9/2016 11:07 AM, Bruce Ravel wrote:

On 08/09/2016 01:50 PM, Matthew Marcus wrote:

This actually results in a bit of inconvenience - if you want to use
ATOMS, you have to load some data into Artemis and pretend you want to
analyze it.


There is a "Stand-alone Atoms" item in the frickin' Start Menu.  How does that 
constitute an inconvenience?  If that's too many clicks for you, drag and drop a shortcut 
to the desktop.

You can use atoms from the command line to read an input or CIF file and write to a file 
or to standard output.  You can use atoms from the command line with the "--wx" 
switch to fire up the stand-alone GUI app.

I acknowledge that the web app that died last January was widely used and that 
I am an unredeemable lay-about for not recreating it.  But your criticism is a 
bit unfair, Matthew.

B


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Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-09 Thread Matthew Marcus

This actually results in a bit of inconvenience - if you want to use ATOMS, you 
have to load some data into Artemis and pretend you want to analyze it.

Another thing for a newbie to beware of - if you have inequivalent sites for 
your absorbing atom, you have to run ATOMS and FEFF separately for each of 
these,
then add the resulting spectra in proportion determined by stoichiometry.  If 
you use a program like Diamond, it tells you the Wyckoff notation (e.g. 12a 
meaning
that a unit cell has 12 such atoms in it, even though they're specified once).  
I think ATOMS can produce a file with each atom listed explicitly (XYZ, I think)
and you could count that.
mam

On 8/9/2016 10:35 AM, Scott Calvin wrote:

Hi Ed,

In case it’s not clear, ATOMS is built in to Artemis. (Long, long ago ATOMS was 
a separate program, so many people still refer to that functionality of Artemis 
by that name.)

—Scott Calvin
Sarah Lawrence College


On Aug 9, 2016, at 12:40 PM, Matthew Marcus <mamar...@lbl.gov> wrote:

There are two different input files which take the extension .inp.  One is the 
feff.inp file, which is the input to FEFF and contains a list of
coordinates (Cartesian, not crystallographic) of all atoms surrounding an 
absorpber atom out to a certain distance.  ATOMS produces this.  The other
is an input file for ATOMS, which has a subset of the information found in a 
CIF file.  ATOMS can save this out as well once you fill in the form, and you
can thus re-use it if, for instance, you want to re-run ATOMS to produce a 
feff.inp file for a different site as absorber.  ATOMS is the only program
I know that produces FEFF files.
mam

On 8/9/2016 9:26 AM, Ed Han wrote:

I see. Thank you for the insight!

Is it possible to create the same .inp or .cif file in FEFF6 (or any of the 
FEFF versions) as well?

Or is the ATOMS program the most recommended software to perform this task?


Regards,
Ed Han

On Mon, Aug 8, 2016 at 5:12 PM, Carlo Segre <se...@iit.edu 
<mailto:se...@iit.edu>> wrote:


   Hi Ed:

   You do not need to start with a CIF file at all.  All you need is the space 
group, the lattice constants and the atomic positions.  You can then fillin the 
blanks for the Atoms program yourself.

   Carlo


   On Mon, 8 Aug 2016, Ed Han wrote:

   Hello All,

   I apologize in advance if this is not the correct method to reply to the
   thread.

   Thank you for your replies and suggestions. I will look further into
   determining the atomic structure of the Hf-Al intermetallics through 
their
   papers.

   Once I obtain this information, how do I go about creating the actual CIF
   file? Can I just open up any arbitrary CIF file and then change the
   parameters and name to match that of the Hf-Al systems?

   Lastly, going through some CIF files from crystallography.net 
<http://crystallography.net>, I notice
   that some of the 3D models from the CIF has a different stoichiometry 
from
   the designated crystal. For example, I have attached a CIF file of SiO2
   that I have found; however, the 3D representation only has 1 Silicon atom
   and 1 Oxygen atom. Do you have any insight on this disparity?

   Regards,
   Ed Han


   --
   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: 312.567.3498 Fax: 312.567.3494 

   se...@iit.edu <mailto:se...@iit.edu>   http://phys.iit.edu/~segre   
se...@debian.org <mailto:se...@debian.org>

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Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-09 Thread Matthew Marcus

There are two different input files which take the extension .inp.  One is the 
feff.inp file, which is the input to FEFF and contains a list of
coordinates (Cartesian, not crystallographic) of all atoms surrounding an 
absorpber atom out to a certain distance.  ATOMS produces this.  The other
is an input file for ATOMS, which has a subset of the information found in a 
CIF file.  ATOMS can save this out as well once you fill in the form, and you
can thus re-use it if, for instance, you want to re-run ATOMS to produce a 
feff.inp file for a different site as absorber.  ATOMS is the only program
I know that produces FEFF files.
mam

On 8/9/2016 9:26 AM, Ed Han wrote:

I see. Thank you for the insight!

Is it possible to create the same .inp or .cif file in FEFF6 (or any of the 
FEFF versions) as well?

Or is the ATOMS program the most recommended software to perform this task?


Regards,
Ed Han

On Mon, Aug 8, 2016 at 5:12 PM, Carlo Segre > wrote:


Hi Ed:

You do not need to start with a CIF file at all.  All you need is the space 
group, the lattice constants and the atomic positions.  You can then fillin the 
blanks for the Atoms program yourself.

Carlo


On Mon, 8 Aug 2016, Ed Han wrote:

Hello All,

I apologize in advance if this is not the correct method to reply to the
thread.

Thank you for your replies and suggestions. I will look further into
determining the atomic structure of the Hf-Al intermetallics through 
their
papers.

Once I obtain this information, how do I go about creating the actual 
CIF
file? Can I just open up any arbitrary CIF file and then change the
parameters and name to match that of the Hf-Al systems?

Lastly, going through some CIF files from crystallography.net 
, I notice
that some of the 3D models from the CIF has a different stoichiometry 
from
the designated crystal. For example, I have attached a CIF file of SiO2
that I have found; however, the 3D representation only has 1 Silicon 
atom
and 1 Oxygen atom. Do you have any insight on this disparity?

Regards,
Ed Han


--
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: 312.567.3498 Fax: 312.567.3494 

se...@iit.edu    http://phys.iit.edu/~segre   
se...@debian.org 

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Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-08 Thread Matthew Marcus

Use ATOMS, which lets you define the structure by filling in a form, then save 
as an ATOMS .inp file.  You don't need the .cif.  I forget whether ATOMS
can save as .cif.

The crystallographic symmetry rules will duplicate the O atom for you.  The CIF 
only shows symmetry-inequivqlent atoms.
mam

On 8/8/2016 3:44 PM, Ed Han wrote:

Hello All,

I apologize in advance if this is not the correct method to reply to the thread.

Thank you for your replies and suggestions. I will look further into 
determining the atomic structure of the Hf-Al intermetallics through their 
papers.

Once I obtain this information, how do I go about creating the actual CIF file? 
Can I just open up any arbitrary CIF file and then change the parameters and 
name to match that of the Hf-Al systems?

Lastly, going through some CIF files from crystallography.net 
, I notice that some of the 3D models from the CIF 
has a different stoichiometry from the designated crystal. For example, I have 
attached a CIF file of SiO2 that I have found; however, the 3D representation only 
has 1 Silicon atom and 1 Oxygen atom. Do you have any insight on this disparity?

Regards,
Ed Han


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Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-08 Thread Matthew Marcus

That's a theoretical paper, so I don't know how reliable those numbers are.  It 
will take Han some care with crystallography to translate the data into 
something
usable by Atoms, i.e. a complete site list.  I suggest starting with structures 
with the same code (e.g. D022) and filling in new parameters per that paper
or experimental ones.
mam

On 8/8/2016 2:15 PM, Bruce Ravel wrote:


Have you read the Colinet & Pasturel paper?  Skimming through it, it seems like 
section III.b along with Fig 1 gives enough information to fill in the Atoms window 
(http://bruceravel.github.io/demeter/documents/Artemis/feff/index.html) by hand.

B


On 08/08/2016 05:02 PM, Ed Han wrote:

Dear All,

In the upcoming fall, my research group plans on performing XAS studies
observing the Hf L3-edge for various Hf-Al intermetallic samples.

In preparation for the experiments, I am looking for CIF files of the
various Hf-Al intermetallic systems, including HfAl3, HfAl2, Hf4Al3, etc.

Upon scavenging through a multitude of crystallographic databases, I was
not able to find any CIF files of Hf-Al intermetallics. However, I have
acquired powder diffraction files (PDF) for said intermetallics.

Seeing as how PDFs cannot be used in Artemis for EXAFS data analysis (to
my knowledge), is there a way to convert PDFs into CIFs? I have attached
one of the PDF files to demonstrate what information it contains.

I would really appreciate your help!

Regards,
Edmund Han





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Re: [Ifeffit] Converting PDF files to CIF files for usage in Artemis

2016-08-08 Thread Matthew Marcus

I'm afraid a PDF file of that sort is useless for EXAFS work because it doesn't 
tell you where the atoms are.  It only tells you the size of the unit cell,
unless you use it to solve the crystal structure yourself, which I don't 
recommend :-)  You need to search the literature for structures which include
the atomic positions and, probably, transcribe them manually into Atoms.  The 
paper referred to in the PDF gives calculated (not experimental) values
for the atomic displacements, from which, with some care, it would be possible 
to figure out coordinates.  However, it would be better to have experimental
data.  A bit of Googling shows that it's not going to be trivial to get all the 
parameters because the papers tend to tell you that the structures are
like other structures, but with certain parameters different, and you'll have 
to fill in the blanks.
mam


On 8/8/2016 2:02 PM, Ed Han wrote:

Dear All,

In the upcoming fall, my research group plans on performing XAS studies 
observing the Hf L3-edge for various Hf-Al intermetallic samples.

In preparation for the experiments, I am looking for CIF files of the various 
Hf-Al intermetallic systems, including HfAl3, HfAl2, Hf4Al3, etc.

Upon scavenging through a multitude of crystallographic databases, I was not 
able to find any CIF files of Hf-Al intermetallics. However, I have acquired 
powder diffraction files (PDF) for said intermetallics.

Seeing as how PDFs cannot be used in Artemis for EXAFS data analysis (to my 
knowledge), is there a way to convert PDFs into CIFs? I have attached one of 
the PDF files to demonstrate what information it contains.

I would really appreciate your help!

Regards,
Edmund Han





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Re: [Ifeffit] Multi-electron peak in Yb

2016-08-04 Thread Matthew Marcus

The samples this guy is interested in are synthetic.  No Cu visible.  Cu XANES 
tends not to have huge white lines, which is what would be
required for the contamination to show as a peak with no detectable edge jump.  
Also, the peak is nowhere near the Cu K-edge.  For similar
reasons, it's not Fe either.
mam

On 8/4/2016 4:20 PM, Matt Newville wrote:

Hi Matthew,


On Thu, Aug 4, 2016 at 2:24 PM, Matthew Marcus <mamar...@lbl.gov 
<mailto:mamar...@lbl.gov>> wrote:

Does anyone know of data on multi-electron peaks at the Yb L3 edge?  One of 
the users here was just running Yb and finds on every spectrum a bump at the 
same
energy.  It's not a Bragg glitch from the sample or an I0 glitch or any 
other obvious artifact.  It reminds me of the two little bumps at Ce.  If 
someone has
analyzed and parameterized this peak as a fraction of edge jump, then it 
would be possible to subtract it off.  The attached papers show exmples for 
almost every
lanthanide *execpt* Yb.


I have not done much work on Yb, and all the measurements I can find are on the 
L2 edge, not the L3 edge.


That's because the L3 edge is at 8944, 30 to 40 eV below the Cu K edge.   In my 
experience, it's really hard to get rid of Cu and Fe as trace contaminants, 
especially in natural samples.Is it possible that what you're seeing is not 
multi-electron excitation by Cu contamination?




For those doing Ce, I've written a program which does the correction, 
essentially as presented in the attached Gomilsek paper.


That sounds useful.

--Matt



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Re: [Ifeffit] determining reasonable fitting parameters

2016-07-27 Thread Matthew Marcus

Oh, so it assumes that chi(k) = (mu(E(k))-spline(k))/const.?  Mine does 
(mu(E(k))-spline(k))/spline(k), which I guess has its own problems - any wiggles
driven in the spline will multiply the EXAFS.  I haven't seen any effect from 
this, though.  Maybe the right thing is (mu(E(k))-spline(k))/smooth(E(k))
where smooth is a smooth post-edge background such as a polynomial or spline 
with fewer knots than the subtraction spline or even a tensioned spline.  I'd
be willing to bet that this refinement will make no detectable difference, 
especially if you do the reference data the same way.  I've found that you can 
do
the most amazingly bogus things and get away with it as long as you do them 
equally to your reference and unknown, especially if the reference is very
similar to the unknown.  Of course, you can't rely on that.
mam

On 7/27/2016 1:45 PM, Bruce Ravel wrote:

On 07/27/2016 04:39 PM, Matthew Marcus wrote:

I'm not sure I get your point about ion-chamber response.  Shouldn't
that normalize out in post-edge spline?


Athena edge-step normalizes (i.e. normalizes by a constant) by default. It does 
not do a functional (or energy dependent) normalization by default in the way 
you are suggesting.


If the I0 chamber gets less sensitive as a function of energy, then the
post-edge background rises by the same amount
as the wiggles get bigger, so it divides out.  Similarly for probe-depth
effects, depending on concentration.  Another
couple of possible sources of amplitude error:
1.The model for the pre-edge background is inaccurate, so that its
extrapolation to the EXAFS region is incorrect.
For instance, if there's a lot of elastic scatter getting into the
fluorescence detector, then the pre-edge is curved,
and if you model that with a straight line fitted near the edge,
them you'll be off far from the edge.  Similarly, in
a long transmission scan, both pre- and post-edge are curved.  My
background-sub program has simple models for thse
shapes which aren't perfect but help.  This effect is really hard to
control for because you have no real way to know
what the 'right' answer is, most of the time.

2.Overabsorption will definitely reduce the amplitude of the
wiggles, and I'm surprise Bruce didn't menntion it.  It looks
much like pinhole effect.  Harmonics do similar things as well in
transmission.


My brain is really tiny and it's getting to be late in the afternoon here.  
It's amazing that many bullet points actually made it into the email!

B



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Re: [Ifeffit] determining reasonable fitting parameters

2016-07-27 Thread Matthew Marcus

I'm not sure I get your point about ion-chamber response.  Shouldn't that 
normalize out in post-edge spline?
If the I0 chamber gets less sensitive as a function of energy, then the 
post-edge background rises by the same amount
as the wiggles get bigger, so it divides out.  Similarly for probe-depth 
effects, depending on concentration.  Another
couple of possible sources of amplitude error:
1.  The model for the pre-edge background is inaccurate, so that its 
extrapolation to the EXAFS region is incorrect.
For instance, if there's a lot of elastic scatter getting into the 
fluorescence detector, then the pre-edge is curved,
and if you model that with a straight line fitted near the edge, them 
you'll be off far from the edge.  Similarly, in
a long transmission scan, both pre- and post-edge are curved.  My 
background-sub program has simple models for thse
shapes which aren't perfect but help.  This effect is really hard to 
control for because you have no real way to know
what the 'right' answer is, most of the time.

2.  Overabsorption will definitely reduce the amplitude of the wiggles, and 
I'm surprise Bruce didn't menntion it.  It looks
much like pinhole effect.  Harmonics do similar things as well in 
transmission.

I still haven't heard how you do EXAFS analysis using the short spectrum from 
Hepheastus.
mam

On 7/27/2016 1:23 PM, Bruce Ravel wrote:

On 07/27/2016 03:53 PM, Neil M Schweitzer wrote:

Thanks to everyone for all the previous responses to my emails, I've
learned a lot in the few weeks I've been on this list! I was hoping
to build off of the last point Bruce made in message 3 below by
asking another question. I am fitting a CeO2 reference from paths
generated by feff from a cif file. Since this is my starting point, I
made SO2 the same for every path (and used the coordination numbers
from the cif file). If I am generating what looks to be a reasonable
fit, but my SO2 is in the 0.55-0.7 range, what is my fit trying to
tell me? Am I doing something wrong in my initial background
subtraction in Athena?

I'm asking about the background subtraction because I recently
discovered that there is a CeO2 reference provided in Hephaestus. I
exported the data, and tried to fit it in Artemis using a similar
methodology I used for my own sample, and I got an even lower SO2. So
I don't think the small SO2 value is an artifact of the way the
experiment was run (although I might be wrong, I wasn't present when
the data was actually collected). The observed difference seems real
because the magnitude of the signal in E-space, k-space, and R-space
is lower for the Hephaestus sample compared to my experimental sample
(see attached image... One note, I'm not sure why the signals are off
set in the Energy plot. The Eo's are the same, and if I plot the
spectra together in E-space alone, they are not offset. Maybe a
bug?).


I don't remember much about the provenance of that CeO2 spectrum.  I
don't remember how calibration was done (or even if it is reliable).
I don't remember much about the sample -- it was a pellet, but I have
no way of knowing if it was homogeneous or even if the particles were
of the size reported.

I guess what I am trying to say is this -- if you trust your CeO2
measurement, you should have more faith in that (or the one Matthew
just sent) than in the one from Hephaestus.

As for your S02 question, here's some of the standard litany:

 + the mean free path used by feff was too long.

 + S02 and sigma^2 are highly correlated.

 + you did a lousy job normalizing the data (although it sure doesn't
   look that way from your picture).

 + your sample had a lot of pinholes.

 + there is some source of loss in CeO2 that is neglected in Feff
   (which is, practically speaking, the same as the mean free path
   comment).  You could try fixing S02 and floating an Ei parameter.
   Or floating both S02 and Ei, although they will be highly
   correlated.

 + There is also an energy response to the ionization chambers at such
   a low energy -- that is, the absorption of the gas in the detector
   is weaker at the end of the spectrum than at the beginning.  In
   fluorescence, that serves to attenuate the edge0step-normalized
   spectrum in a way that looks like an enhancement to sigma^2.  But
   it's an attenuation, which could show up in S02.

I should mention that in my favorite teaching example -- FeS2 -- by
the end of the lecture I have a S02 of something like 0.69.  And I
just walk away from the lecture at that point :) The reason I do so is
that all the rest of the parameters are defensible and I chalk the
small S02 up to one of the points above (along with some enthusiastic
hand waving -- usually it's time for coffee or lunch by the time I've
finished the FeS2 demo!).

B



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[Ifeffit] fitting of S XANES with arctans and gaussians

2016-07-18 Thread Matthew Marcus

I'm trying to fit 37 micro-XANES spectra taken at the S K-edge, using the method 
discussed in the paper by Manceau and Nagy "Quantitative analysis of sulfur 
functional groups
in natural organic matter by XANES spectroscopy", Geochimica et Cosmochimica 
Acta 99 (2012) 206–223.  In this paper, they fit spectra to two arctangents and 6 
gaussians,
with widths of the arctans slaved together and widths of gaussians 1-3 and 4-6 
slaved (or all 6 to one value).  I'm looking for recommendations as to how to 
do the fit.
They give prescriptions for how to set the initial estimates to give robust 
values.  Manceau has told me that 'Athena works quite well', but I don't see 
any obvious way there
to do the parameter constraints called for, or to keep peak heights from going 
negative.  Athena also has a habit of assuming you want it to do the 
normalization
for you; I've already done that and need no further 'help'.  Any ideas?

I've tried using Genplot, but that offers no way to restrain parametsrs to 
ranges to keep them from going nuts.

PCA seems to want 6-8 components, so it's not all that helpful.  These spectra 
were taken at various spots on a biological structure (abalone radula) so 
there's
no sense of sequence which would enable the use of evolving factor analysis or 
something like that.  LCF doesn't give satisfying fits with the references I 
have.

I've attached a couple of the files, truncated to the range Manceau fit 
to.  The originas were taken over the range 2460-2550eV.
mam
2459.8733   0.016383041
2460.1233   0.016094189
2460.3735   0.022025956
2460.6238   0.016678091
2460.8738   0.01631
2461.1240.019483142
2461.3743   0.01770903
2461.6245   0.022848981
2461.8745   0.018562062
2462.1248   0.020740321
2462.3748   0.020652939
2462.6250.017123673
2462.8752   0.025094582
2463.1252   0.019867383
2463.3755   0.022139577
2463.6257   0.023213524
2463.8757   0.020676881
2464.1260.025052877
2464.3762   0.029113997
2464.6262   0.026324339
2464.8765   0.023671083
2465.1267   0.028306101
2465.3767   0.026002042
2465.6270.030652333
2465.8772   0.028775895
2466.1272   0.032816786
2466.3774   0.033937715
2466.6277   0.032948535
2466.8777   0.034721162
2467.1279   0.035310403
2467.3782   0.044202648
2467.6282   0.038343795
2467.8784   0.044291645
2468.1287   0.045460965
2468.3787   0.051915355
2468.6289   0.064561076
2468.8789   0.064293481
2469.1292   0.06745372
2469.3794   0.076904655
2469.6294   0.078936517
2469.8794   0.083785988
2470.1292   0.09224768
2470.3789   0.10311307
2470.6287   0.12705681
2470.8784   0.15507881
2471.1279   0.19775756
2471.3777   0.24674262
2471.6274   0.38095856
2471.8772   0.61600226
2472.1270.95312738
2472.3767   1.3190417
2472.6262   1.579319
2472.8761.6359525
2473.1257   1.5544981
2473.3755   1.4989064
2473.6252   1.5021619
2473.8751.5229028
2474.1245   1.4984316
2474.3743   1.3305453
2474.6241.0569189
2474.8738   0.83871508
2475.1235   0.74043173
2475.3733   0.70619929
2475.6228   0.73935717
2475.8726   0.8194145
2476.1223   0.87513489
2476.3721   0.88144314
2476.6218   0.90261424
2476.8716   0.89132398
2477.1211   0.89018643
2477.3708   0.8967182
2477.6206   0.90281725
2477.8704   0.94701087
2478.1201   0.94702822
2478.3699   0.97867304
2478.6194   1.0008969
2478.8691   1.0092386
2479.1189   1.0287796
2479.3687   1.08442
2479.6184   1.1615053
2479.8679   1.3039225
2480.1179   1.5145243
2480.3674   1.797269
2480.6172   2.0798359
2480.8669   2.2775149
2481.1167   2.3608608
2481.3662   2.3488405
2481.6162.2907579
2481.8657   2.2880797
2482.1155   2.3719938
2482.3652   2.5308979
2482.6152.589304
2482.8645   2.5814075
2483.1143   2.3856504
2483.3642.1799946
2483.6138   1.9504212
2483.8635   1.7527013
2484.1133   1.5563732
2484.3628   1.4446132
2484.6125   1.3397398
2484.8623   1.2488514
2485.1121   1.2062074
2485.3618   1.141425
2485.6116   1.1280848
2485.8611   1.0882412
2486.1108   1.0844127
2486.3606   1.0722013
2486.6104   1.0759245
2486.8601   1.050091
2487.1099   1.0626349
2487.3596   1.0662534
2487.6091   1.0521868
2487.8589   1.0660895
2459.8232   0.0086620357
2460.0735   0.0090417974
2460.3235   0.033545561
2460.5737   0.0085842237
2460.8240.0051017846
2461.0740.011186908
2461.3242   0.017373042
2461.5742   0.015282798
2461.8245   0.020608777
2462.0747   0.030159647
2462.3247   0.037008617
2462.5750.019812036
2462.8250.017694598
2463.0752   0.021219229
2463.3252   0.025639383
2463.5754   

Re: [Ifeffit] No Reference Foil

2016-07-13 Thread Matthew Marcus
Just a caveat - CeO2 and Ce(OH)4 have XANES which isn't  quite the same 
as other Ce4+.  There's a shoulder on the low side, as if it were 
slightly reduced, and the first peak is at a slightly different 
position.  Of course, you can use LCF with CeO2 as one of the  refs if 
you need to.

mam

On 7/13/2016 10:54 AM, fred.mosselm...@diamond.ac.uk wrote:

Dear Neil,

Sorry this may be too exact an interpretation of your English, but if you are 
looking at the exafs  then calibration is normally pretty irrelevant as long as 
it is not wildly out, as you refine E0 anyway in the fitting.
The bond distances will be very little altered by this.

If you are looking at XANES and it is 3/4  then CeL3  as I am sure you know has two 
"white lines" for four and one for three and the ratio of the two peaks can be 
used to
Look at oxidation state mixtures, I think  you should be able to align the 
peaks and fit the area e.g. Burnham AD, Berry AJ, 2014, The effect of oxygen 
fugacity, melt composition, temperature and pressure on the oxidation state of 
cerium in silicate melts, Chemical Geology, Vol:366, ISSN:0009-2541, Pages:52-60

Best wishes
Fred






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Re: [Ifeffit] ISO Calcite + dolomite EXAFS

2016-05-27 Thread Matthew Marcus

Thanks.  I guess you don't have dolomite?

I found the source of my discrepancy with regard to calcite, but not dolomite.
mam

On 5/27/2016 2:49 PM, Anatoly I Frenkel wrote:

I have data for calcite and aragonite. Will send tomorrow.
Anatoly

Sent from my iPhone


On May 27, 2016, at 5:31 PM, Matthew Marcus <mamar...@lbl.gov> wrote:

Does anyone have Ca K-edge EXAFS data they can share for calcite and dolomite?  
I took some, but it seems to disagree with FEFF as to
the position of the Ca-(Ca,Mg) peak.
   mam
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[Ifeffit] ISO Calcite + dolomite EXAFS

2016-05-27 Thread Matthew Marcus

Does anyone have Ca K-edge EXAFS data they can share for calcite and dolomite?  
I took some, but it seems to disagree with FEFF as to
the position of the Ca-(Ca,Mg) peak.
mam
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Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3

2016-04-03 Thread Matthew Marcus

Yup.  In fact, self absorption, in the correct sense, can help reduce 
"self-absorption" in the misnomer sense!  That's how the grazing-exit method 
works.

I might also note that although many elaborate schemes have been proposed for 
correcting for the effect, they all require knowing things about the
sample that you don't always know, e.g. the exact geometry of something that 
isn't planar, or the exact composition.  I find that the simple parameterization
which comes from a thick-planar-sample model works reasonably well as an 
empirical method with an unknown parameter.  Still, I wouldn't necessarily trust
Debye-Waller (ss2) values taken from EXAFS on strongly overabsorbed samples, 
even with a correction that gets the right coordination number.
mam

On 4/3/2016 7:04 PM, Matt Newville wrote:

Hi Matthew,



On Sun, Apr 3, 2016 at 8:13 PM, Matthew Marcus <mamar...@lbl.gov 
<mailto:mamar...@lbl.gov>> wrote:


It shouldn't be called 'self-absorption'.  That's a misnomer, which seems 
to have come from a 1992
paper (Troger, et. al."Full correction of the self-absorption in 
soft-fluorescence extended x-ray-absorption fine structure", PRB 46,3283 (1992).
The effect was described and analyzed in a 1982 paper, which called it an 
"attenuation factor": Goulon, et. al. "On experimental attenuation factors of 
the amplitude
of the EXAFS oscillations in absorption, reflectivity and luminescence 
measurements", J. Physique 43, 539 (1982).

 mam


Thanks!! I completely agree, though I wasn't aware of the historical precedence for the 
mistake.Using "over-absorption" is a far better term.

In X-ray fluorescence,  "self-absorption" actually means the attenuation of 
fluorescence generated within a sample as it travels out of the sample.   For 
over-absorption in XAFS, the issue is measuring absorption in fluorescence mode when the 
concentration of the absorbing element is not infinitesimal or when the sample thickness 
is not infinitesimal.

--Matt


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Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3

2016-04-03 Thread Matthew Marcus


It shouldn't be called 'self-absorption'.  That's a misnomer, which seems to 
have come from a 1992
paper (Troger, et. al."Full correction of the self-absorption in soft-fluorescence 
extended x-ray-absorption fine structure", PRB 46,3283 (1992).
The effect was described and analyzed in a 1982 paper, which called it an "attenuation 
factor": Goulon, et. al. "On experimental attenuation factors of the amplitude
of the EXAFS oscillations in absorption, reflectivity and luminescence 
measurements", J. Physique 43, 539 (1982).

mam

On 4/3/2016 4:56 PM, Matteo Busi wrote:

Hi Bruce,
Thanks for your help, it's really appreciated.
I was trying to keep it simple but it seems I'm just messing around.

What I am trying to do is to perform a new developed self-absorption correction 
using collected fluorescence absorption coefficient data on a CuSO4 
(pentahydrate) capillar (cylinder) and spherical sample with Cu as absorber, 
having different values of molarity and penetration depth.
The correction expression requires these measured quantity:
μX(E) : the absorption coefficient due to a given core excitation of the 
absorbing atom
   - I used the background function for this ( bkg(E))
μo = μ(E) : photoelectric total linear absorption coefficient of the sample at 
incident energy E
- I used the xmu(E) for this
μh = μ(E) :photoelectric total linear absorption coefficient of the sample at 
fluorescence emission Ef
- I used the xmu(Ef) with Ef the K absorption edge of Cu ( 
8.9789 eV)
χ: and here I used the chi(E) values of the exported ascii .xmu file

Hope it's clear now.
Matteo


2016-04-02 19:00 GMT+02:00 >:

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Today's Topics:

1. Re: Ifeffit Digest, Vol 158, Issue 1 (Matt Newville)


--

Message: 1
Date: Fri, 1 Apr 2016 15:56:29 -0500
From: Matt Newville >
To: XAFS Analysis using Ifeffit >
Subject: Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1
Message-ID:
 >
Content-Type: text/plain; charset="utf-8"

Matteo,


On Fri, Apr 1, 2016 at 8:35 AM, Matteo Busi > wrote:

 > Hi Bruce,
 > Now this is clear.
 > In my case the correction I have to perform requires these
 > measured/evaluated parameters: chi, mu (not sure if it's better to work
 > with normmu here) and the background function.
 > Is it physically meaningless to have the mu(k) and bkg(k) data? If that 
is
 > not the case I would like to have these two columns exported in the ascii
 > chi(k) file.
 > So then I can perform the correction and re-import the new corrected
 > chi(k) and make comparison with the uncorrected.
 >
 > Kind regards,
 > Matteo
 >
 >
It would certainly help (and by that I mean "help you get the answers
you're looking for") if you gave us more details about what you're trying
to do rather than ask for how to what you think you want to do.

Just to be clear: Converting from E to k does not involve a Fourier
transform, just
k = sqrt((2m*e/hbar**2)*(E-E0))

for k in Ang^-1 and E in eV, that's  k ~= sqrt(0.262468 
*(E-E0))

I'm not sure what you're trying, but I would image you want to use
normalized mu(E) or at least pre-edge subtracted mu(E).  That is, what we
call mu(E) is typically really -ln(I/I0)
where I and I0 are not the actual intensities before and after the sample,
but counts or counts per time in some detector that samples the flux.
These values include more or less arbitrary scale factors (amplifier gains,
etc) included.  That means that (unless you very careful) mu(E) does not
have meaningful units, certainly not cm^-1 or cm^2/gram.

Normalized mu(E) doesn't have such units either, but it's an easier place
to start.

--Matt

Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 4

2016-02-09 Thread Matthew Marcus

I have an SDD and find very little strength in the escape peak or the Si Ka 
peak.  I have seen Si from the sample.  I can't speak to how well Si XAS works 
because my beamline doesn't go down that far.
mam

On 2/9/2016 10:25 AM, Pierre Lecante wrote:

Hi Pinit,

here is what you can expect from a SDD:

"At X-ray energies greater than silicon K absorption edge, which we have measured 
for crystalline silicon to be 1839 eV, the response function of the device shows two 
distinct peaks in addition to the primary one. One of them at energy /E/_/f/ = 1739 eV is 
due to the silicon fluorescent photons that have escaped far enough from the original 
site of interaction to be detected as a separate event. The other peak centered at energy 
/E/_/e/ = /E/_0 - /E/_/f/ , where /E/_0 is energy of the incident photon, is called an 
escape peak."

So, indeed this shouldn't be a concern if you had a perfect rejection of 
harmonics on your beamline; if not, inelastic scattering of harmonic by the 
sample, even rejected by energy analysis,  should likely induce internal 
fluorescence and escape peaks not observed in TM. Just an hypothesis, but easy 
to check: presence or not of harmonic in your scattering.

Pierre

Le 02/02/2016 23:41, ifeffit-requ...@millenia.cars.aps.anl.gov a écrit :

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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. Re: Could you please give me some information? (Bruce Ravel)
2. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler)
3. Re: Athena with IOS "El Capitan" (Bruce Ravel)
4. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler)


--

Message: 1
Date: Tue, 2 Feb 2016 15:30:45 -0500
From: Bruce Ravel
To: pinit
Cc: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Could you please give me some information?
Message-ID:<56b111f5.7050...@bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 02/01/2016 11:58 PM, pinit wrote:

Dear Bruce,

I am Pinit from SLRI, Thailand. I have some questions concerning the
Si-drift detector.

Could you give me some suggestions if Si-detector can detect the
corrected Si K-edge or not? This is because I have seen a significant
EXAFS signal (higher in amplitude in FT) measured by Si-drift detector
differs from Lytle detector or ionization chambers (TM mode).

Hi Pinit,

Nice to hear from you.  I am CCing my answer to the Ifeffit Mailing
List.  Someone else may have more insight into your question than I
do.  You should CC the list in your response.

I'd probably need to know more about the sample and the nature of the
measurement you made to understand why you are seeing a different
signal with the Si drift detector.

Normally one would expect that he EXAFS would be /attenuated/ either
due to self-absorption or due to the energy dependence of the I0
detector.  That you are seeing a larger EXAFS signal with the Si-drift
seems surprising.

One thing that occurs to me is that the Compton and elastic peaks
probably overlap the Si K alpha ROI quite a bit, even extending into
the EXAFS region.  I would have thought that, too, would serve to
attenuate the EXAFS (but maybe I am thinking about that wrongly).

Perhaps it would help to show us some of the data...?

B






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CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France
Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99
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Re: [Ifeffit] CuO XAS spectrum

2015-12-02 Thread Matthew Marcus

There are two spectra (transmission, probably) in the XAFS Model Compound 
Library http://cars9.uchicago.edu/cgi-bin/newville/Model-Search.cgi .
mam

On 12/2/2015 3:32 PM, Enyuan Hu wrote:

Dear all,

I'm analyzing some Cu compounds spectra and was wondering if anyone has the CuO 
XAS spectrum and is willing to share. Thanks.

best regards,
Enyuan


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Re: [Ifeffit] Unable to run Demeter on EPA computers

2015-10-22 Thread Matthew Marcus

This is an application for an acronym: SIMWA!  Security In My Way Again!
mam

On 10/22/2015 11:46 AM, Matt Noerpel wrote:

Thank you for your time, Bruce.

The IT person tried it with and without the AV running (Symantec) and neither 
worked.  Additionally, the AV does run in Safe Mode.  I agree the problem is 
with our computer setup and not the software.  I will let the list know if we 
figure out what is causing the problem.

Thanks,

Matt

On Wed, Oct 21, 2015 at 1:55 PM, Bruce Ravel > wrote:


Hi Matt,

I am without any further ideas for you.  No one else has reported a
similar situation, other than the recent reports of trouble with AV.
Demeter is used by hundreds of people on Windows, including many
government and government lab employees (like myself).  So I really am
inclined to think that the problem is local, not global.

While I am impressed that your IT person spent so much time and effort
investigating this and I am sympathetic that it was all for naught, I
do want to point out that I don't see anything in the long list of
diagnostics that actually addresses my one suggestion -- namely that
you are seeing some kind of conflict related to AV permissions.

All that said, I am always happy to incorporate changes to the
software and the packaging.  If you can suggest something substantive
that I can do to improve the packaging in a way that will help you
over your hurdle, I am all ears.

B




On 10/21/2015 09:32 AM, Matt Noerpel wrote:

Hello Bruce,

The IT guy just sent me the following report on his efforts to get
Demeter to run.  He was only able to get it to run in Safe Mode and Safe
Mode with Networking.  Here's his full message:

I regret to inform you still no joyL

Here’s a breakdown of what I have been working with:

Symptoms:  When program attempts to execute, it launches the startup
screen briefly, hangs, and then the application is terminated.

Both 32-bit and 64-bit versions

Both patches from the Demeter website

Normal mode

Last known good configuration

Selective startup

Disabled all non-critical local services

Terminated all non-critical system and user processes

Uninstalled Java

Uninstalled .NET framework

Reinstalled Java

Reinstalled .NET framework

Adjusted memory settings for best performance

Verified use has full control of all of their profile data (including
appdata) and installation directory

Attempted as a normal user and administrative user

Windows 95 compatibility mode

Windows 98 compatibility mode

Windows NT 4.0 compatibility mode

Windows 2000 compatibility mode

Windows XP (SP2) compatibility mode

Windows XP (SP3) compatibility mode

Windows Server 2003 (SP1) compatibility mode

Windows Server 2008 (SP1) compatibility mode

Windows Vista compatibility mode

Windows Vista (SP1) compatibility mode

Windows Vista (SP2) compatibility mode

Windows 7

Disabled visual themes

Disabled desktop composition

Disable display scaling on high DPI settings

Install to default location

Install to a specific location C:\demeter (not default)

Workstation was removed from domain and joined to workgroup

Various reboots throughout

It only works in:

Safe mode

Safe mode with networking

Removing the computer from domain into workgroup has no bearing, so we
can rule out EPA group policy.

Also, since it doesn’t even work in clean mode (selective startup mode
with extremely limited drivers), there are no incompatibilities that
exist in Windows.

I was hoping for sure that once we removed from EPA domain that it would
have solved the problem as we were leaning towards that at one point.

I believe that the problem is not on our end.

Unfortunately this problem is outside our scope of control as helpdesk
support.  I’ve talked to a couple other technicians as well.
Nonetheless, thank you for your patience.

I’m certainly available behind the scenes to try anything else, or try
to apply any hotfixes from developers as they are released.  (I did give
you full control of the directory on your computer for future 
reference).

Thanks,


Does this make any sense to anyone?

Thanks,

Matt

On Wed, Oct 14, 2015 at 5:30 PM, Bruce Ravel 
>> wrote:

 On 10/14/2015 05:25 PM, Matt Noerpel wrote:

 Thank you for your prompt reply.  The Ifeffit.dll 

Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)

2015-09-24 Thread Matthew Marcus

I'm not after absolute data, just the edge-jump ratio.  This would have to be 
extracted by peak+arctan fitting because any spectra will have peaks and a very 
limited
range between edges.  If the Chantler numbers are incorrect, then perhaps the 
edge-jump ratio is really 2.

Do you have a reference which can be cited?

I'll try the CXRO tool next, since CXRO specializes in soft X-rays.
mam

On 9/23/2015 11:49 PM, Jana Padeznik Gomilsek wrote:

It is very hard to measure or to calculate absolute absorption data, especially 
in the
vicinity of the absorption edges and especially in the soft x-ray region. 
Therefore there
are significant differences between the tables and I think nobody knows which
are better.
Chantler, for example, says the expected uncertainties of the tables in your 
region are
50 % to 100 % 
(http://physics.nist.gov/PhysRefData/FFast/Text2000/sec06.html#tab2).
I would doubt the Chantler's L3+.1 number, all other numbers look ok - this is 
what you
can get.

jana padeznik gomilsek


Message: 3
Date: Wed, 23 Sep 2015 18:02:08 -0700
From: Matthew Marcus<mamar...@lbl.gov>
To: XAFS Analysis using Ifeffit<ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] Problem with Hephaestus at Ca L-edges
Message-ID:<56034b90.70...@lbl.gov>
Content-Type: text/plain; charset=utf-8; format=flowed

I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca 
using Hephaestus.  I ran into two problems:

1.  The ratio implied by what it says for the unit-edge-step thickness does 
not agree with that derived by computing the absorption (cm^2/gm) above and 
below each edge and
dividing the difference (L3+ - L3-)/(L2+ - L2-).

2.  The results differ wildly depending on which resource I use:

 L3-.1   L3+.1 L2-.1   L2+.1(L1+ - 
L1-)/(L2+ - L2-)
Elam   4759.79627837.796 27478.018 38434.277   2.106375908
Chantler   4322.6   6547.121  32827.61 35436.543   0.852655473
Cromer-Leiberman   4288.52433471.375 32786.294 47072.991   2.042659055

The Henke table doesn't yield an L2 edge jump at all, while the Shaltout yields 
the same results as Cromer-Leiberman. Which one should I trust and why?

This is old-style H. (V0.18), not Demeter.
mam






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Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)

2015-09-24 Thread Matthew Marcus

OK.  Now I get it.  Why use 50eV?  Since lifetime and other broadening is not 
taken into acocunt in any of these tables, why not use a very small number?
mam

On 9/24/2015 11:07 AM, Bruce Ravel wrote:

On 09/24/2015 01:43 PM, Matthew Marcus wrote:

See the attached ppt for the demo.  I think this gives the whole
repeat-by and interpretation.  Am I just missing something?  That would
not be totally surprising.


The algorithms in Hephaestus are pretty dim-witted and tuned (such as they are) 
to getting the calculations more or less right in the hard X-rays.  I don't 
even try to do calculations in the soft x-ray range correctly.  For example, 
the edge step calculations do the calculation at something like +/-50, which is 
a very stupid choice for soft x-ray energies.  That should explain why L2:l3 
ratio is 1.  Presumably also why the L1 step is negative!

See, e.g. 
https://github.com/bruceravel/demeter/blob/master/lib/Demeter/UI/Hephaestus/Formulas.pm#L274

You cannot trust anything Hephaestus has to say about edge jumps below 3-ish 
keV.  Since the +/-50 is hard wired in, the jump ratios will be nonsense for 
any element for which the energy difference between the L2 and L3 edges is less 
than 100 eV.

The Delta mu/rho numbers that you cite are interpolated from the Elam (usually) 
tables and should reliable to whatever extent you consider the table reliable.

B



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Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)

2015-09-24 Thread Matthew Marcus

What I was after was L3/L2, so I don't care about L1.  The attached plot 
doesn't show the jumps for both L2 and L3.

When you say that the edge jumps are 5.8,1.4 and 1.1, are you referring to 
mu(+)/mu(-)?  I was looking for (mu(+)-mu(-))_L3/(mu(+)-mu(-))_L2.

What about that seeming inconsistency between the values H. gives for the 
thickness needed for unit edge step and the cm^2/gm values reported? That seems 
to be a bug indpependent of
the tables used.
mam

On 9/24/2015 9:15 AM, Matt Newville wrote:

Hi Matthew, Jana,

I think the Chantler values, especially in Hephaestus, are not particularly 
robust at the Ca L edges.

To be clear, Elam gives L3, L2, and L1 energies as 346.2, 349.7,  and 438.4 eV, 
and the edge jumps as 5.8, 1.4, and 1.1.  I believe those edge jumps may have 
originated from Shaltout -- maybe Bruce can clarify that.

The Chantler data from the NIST FFast web page (and in Hephaestus) are quite 
sparse.  This is a definitely a problem for using the anomalous scattering 
factors near edges. I've talked with Chris Chantler about this a few times over 
the years.  Not too long ago, he sent me data on a finer grid -- but he also 
told be recently that he hoped to have even better data he could send to me 
soon (all time-scales here on months-to-years here).

I've included the finer data I have from Chantler into Larch. But the results 
for the Ca L edges are still not encouraging.   The attached figure and ASCII 
data file give the results for mu(E) (gr/cm^2) from Elam and from Chantler.  
It's hard to see an L2 edge in either, and Chantler does not show an L1 edge.

FWIW, the script to generate this is:


energies = linspace(300, 500, 101)
muca_chantler = mu_chantler('Ca', energies)
muca_elam = mu_elam('Ca', energies)

newplot(energies, muca_chantler, ymax = 5, label='Chantler')
plot(energies, muca_elam, label='Elam')

info_head = 'Ca edge Energy(eV)  Fyield   EdgeJump'

info_l3 = ' L3   %.1f%.5f%.2f' % xray_edge('Ca', 'L3')
info_l2 = ' L2   %.1f%.5f%.2f' % xray_edge('Ca', 'L2')
info_l1 = ' L1   %.1f%.5f%.2f' % xray_edge('Ca', 'L1')

write_ascii('CaMu.dat', energies, muca_elam, muca_chantler,
  info_head, info_l3, info_l2, info_l1,
  label='Energy  MuCa_Elam  MuCa_Chantler')



I'm not sure that gives a lot of insight except that not trusting Chantler's 
values for these values might be reasonable.



On Thu, Sep 24, 2015 at 10:16 AM, Matthew Marcus <mamar...@lbl.gov 
<mailto:mamar...@lbl.gov>> wrote:

I'm not after absolute data, just the edge-jump ratio.  This would have to 
be extracted by peak+arctan fitting because any spectra will have peaks and a 
very limited
range between edges.  If the Chantler numbers are incorrect, then perhaps 
the edge-jump ratio is really 2.

Do you have a reference which can be cited?

I'll try the CXRO tool next, since CXRO specializes in soft X-rays.
 mam


On 9/23/2015 11:49 PM, Jana Padeznik Gomilsek wrote:

It is very hard to measure or to calculate absolute absorption data, 
especially in the
vicinity of the absorption edges and especially in the soft x-ray 
region. Therefore there
are significant differences between the tables and I think nobody knows 
which
are better.
Chantler, for example, says the expected uncertainties of the tables in 
your region are
50 % to 100 % 
(http://physics.nist.gov/PhysRefData/FFast/Text2000/sec06.html#tab2).
I would doubt the Chantler's L3+.1 number, all other numbers look ok - 
this is what you
can get.

jana padeznik gomilsek

Message: 3
Date: Wed, 23 Sep 2015 18:02:08 -0700
    From: Matthew Marcus<mamar...@lbl.gov <mailto:mamar...@lbl.gov>>
To: XAFS Analysis using Ifeffit<ifeffit@millenia.cars.aps.anl.gov 
<mailto:ifeffit@millenia.cars.aps.anl.gov>>
Subject: [Ifeffit] Problem with Hephaestus at Ca L-edges
Message-ID:<56034b90.70...@lbl.gov <mailto:56034b90.70...@lbl.gov>>
Content-Type: text/plain; charset=utf-8; format=flowed

I wanted to work out the edge-jump ratio between the L3 and L2 
edges of Ca using Hephaestus.  I ran into two problems:

1.  The ratio implied by what it says for the unit-edge-step 
thickness does not agree with that derived by computing the absorption 
(cm^2/gm) above and below each edge and
 dividing the difference (L3+ - L3-)/(L2+ - L2-).

2.  The results differ wildly depending on which resource I use:

  L3-.1   L3+.1 L2-.1   L2+.1
(L1+ - L1-)/(L2+ - L2-)
Elam   4759.79627837.796 27478.018 38434.277   
2.106375908
Chantler   4322.6   6547.121  32827.61 35436.543   
0.8

[Ifeffit] Problem with Hephaestus at Ca L-edges

2015-09-23 Thread Matthew Marcus

I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca 
using Hephaestus.  I ran into two problems:

1.  The ratio implied by what it says for the unit-edge-step thickness does 
not agree with that derived by computing the absorption (cm^2/gm) above and 
below each edge and
dividing the difference (L3+ - L3-)/(L2+ - L2-).

2.  The results differ wildly depending on which resource I use:

   L3-.1   L3+.1 L2-.1   L2+.1(L1+ - L1-)/(L2+ 
- L2-)
Elam   4759.79627837.796 27478.018 38434.277   2.106375908
Chantler   4322.6   6547.121  32827.61 35436.543   0.852655473
Cromer-Leiberman   4288.52433471.375 32786.294 47072.991   2.042659055

The Henke table doesn't yield an L2 edge jump at all, while the Shaltout yields 
the same results as Cromer-Leiberman. Which one should I trust and why?

This is old-style H. (V0.18), not Demeter.
mam
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Re: [Ifeffit] XAFS short course in BNL on Nov 5-7: Save the date

2015-08-07 Thread Matthew Marcus

I figured *that*.  Give me *some* credit :-)

I'm going to Karlsruhe and it's going to be really expensive, so I can't see 
going on another trip in the same FY.  Therefore, even if you don't tell me 
what MCR-ALS is, I'm still not coming, so
you might as well tell me.
mam

On 8/7/2015 3:40 PM, Anatoly I Frenkel wrote:

Can I add some intrigue to this, and not answer?...Just a hint: ALS does not 
stand for Advanced Light Source.
Anatoly

From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Matthew Marcus 
[mamar...@lbl.gov]
Sent: Friday, August 07, 2015 6:23 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] XAFS short course in BNL on Nov 5-7: Save the date

What's MCR-ALS?  I know and use all the other things you mentioned.
 mam

On 8/7/2015 3:06 PM, Anatoly I Frenkel wrote:

Dear IFEFFIT subscribers:

Please save the dates, Nov. 5-7, 2015, of the annual XAFS short course in Brookhaven National 
Laboratory. As many of you may know, we vary our themes from year to year, and we also vary the 
target levels for participants from beginners to intermediate to advanced. This year the target 
level for participants is advanced, as suggested by the course title Advanced 
topics in XAFS data modeling. It is similar in scope to our other courses on this subject 
(the latest one was offered in Brookhaven in 2010) that are available online:

http://www.yu.edu/scc/workshops-courses/

This time the course will be divided in two parts: non-linear analysis methods 
(FEFF theory-based) and linear methods (based on methods of multivariate 
analysis and linear algebra such as LCF, PCA and MCR-ALS).

Nov. 5 (Thursday) and Nov. 6 (Friday) will be devoted to lectures and 
demonstrations of the software.

Nov. 7 (Saturday) will be practical session,  in which registered participants 
will practice problem solving methods discussed in the previous days.

Confirmed instructors are: Alain Michalowicz, Stephen Wasserman, Faisal 
Alamgir, Scott Calvin and Anatoly Frenkel. A full list of instructors and 
additional information on the course will soon appear on BNL web site. 
Participation in the practical data analysis session will be limited to 30 
registered attendees, although auditors are welcome to attend the lectures and 
demonstrations on Thursday and Friday.

For any inquiries please use contact info on the course web that will soon come 
online.

Best regards,

Anatoly Frenkel

Yeshiva University

Anatoly Frenkel, Ph.D.
Professor and Chair, Department of Physics, Yeshiva University
245 Lexington Avenue, New York, NY 10016
https://yu.edu/faculty-bios/frenkel/
Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc
Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.fren...@yu.edu 
mailto:anatoly.fren...@yu.edu


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Re: [Ifeffit] XAFS short course in BNL on Nov 5-7: Save the date

2015-08-07 Thread Matthew Marcus

What's MCR-ALS?  I know and use all the other things you mentioned.
mam

On 8/7/2015 3:06 PM, Anatoly I Frenkel wrote:

Dear IFEFFIT subscribers:

Please save the dates, Nov. 5-7, 2015, of the annual XAFS short course in Brookhaven National 
Laboratory. As many of you may know, we vary our themes from year to year, and we also vary the 
target levels for participants from beginners to intermediate to advanced. This year the target 
level for participants is advanced, as suggested by the course title Advanced 
topics in XAFS data modeling. It is similar in scope to our other courses on this subject 
(the latest one was offered in Brookhaven in 2010) that are available online:

http://www.yu.edu/scc/workshops-courses/

This time the course will be divided in two parts: non-linear analysis methods 
(FEFF theory-based) and linear methods (based on methods of multivariate 
analysis and linear algebra such as LCF, PCA and MCR-ALS).

Nov. 5 (Thursday) and Nov. 6 (Friday) will be devoted to lectures and 
demonstrations of the software.

Nov. 7 (Saturday) will be practical session,  in which registered participants 
will practice problem solving methods discussed in the previous days.

Confirmed instructors are: Alain Michalowicz, Stephen Wasserman, Faisal 
Alamgir, Scott Calvin and Anatoly Frenkel. A full list of instructors and 
additional information on the course will soon appear on BNL web site. 
Participation in the practical data analysis session will be limited to 30 
registered attendees, although auditors are welcome to attend the lectures and 
demonstrations on Thursday and Friday.

For any inquiries please use contact info on the course web that will soon come 
online.

Best regards,

Anatoly Frenkel

Yeshiva University

Anatoly Frenkel, Ph.D.
Professor and Chair, Department of Physics, Yeshiva University
245 Lexington Avenue, New York, NY 10016
https://yu.edu/faculty-bios/frenkel/
Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc
Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.fren...@yu.edu 
mailto:anatoly.fren...@yu.edu


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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus

Do you by any chance has a room-temp spectrum?  Most of our data is taken at RT 
or not much below, and so the LN2 spectrum won't be a perfect match.
mam

On 7/6/2015 9:12 AM, Case Van Genuchten wrote:

Dear Matthew,

Sure, the raw data and/or spectrum can be added to the database.  For this 
sample, the 1st derivative of the Fe foil was 7.112 keV.  I can also provide 
individual scans for the database, if needed.  Is there any interest in the As 
K-edge of this sample, too?  I have that one as well.
Case

On Mon, Jul 6, 2015 at 5:48 PM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

Thanks!  May I add it to the ALS 10.3.2 reference collection?

What is the standard of energy calibration?  Is the Fe metal edge at 
7110.75eV, 7112eV or what?
 mam

On 7/6/2015 7:11 AM, Case Van Genuchten wrote:

Dear Shaofeng,

I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum 
(extracted using SixPack) of scorodite.  The mineral was prepared following the 
procedure outlined in Paktunc et al. (2008).  The data were collected at the 
Stanford Synchrotron Radiation Lightsource in transmission mode with the sample 
housed in a liquid nitrogen cryostat.  You can find additional details on the 
preparation of the sample and data collection from the publication where the 
spectrum is reported and modeled (van Genuchten et al. 2014, Geochimica et 
Cosmochimica Acta).

Please let me know if you have any other questions about data 
collection.

Best,

Case M. van Genuchten
Environmental Geochemistry Laboratory
Institute of Earth Surface Dynamics
University of Lausanne, Lausanne, CH



On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang wangshaof...@iae.ac.cn 
mailto:wangshaof...@iae.ac.cn mailto:wangshaof...@iae.ac.cn 
mailto:wangshaof...@iae.ac.cn wrote:

 Dear all,
 Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
 Thanks in advance.
 Shaofeng
 --
 Shaofeng Wang, Ph.D of Geochemistry
 Environmental Molecular Science Group
 Institute of Applied Ecology, Chinese Academy of Sciences
 Shenyang, 110016, China
wangshaof...@iae.ac.cn mailto:wangshaof...@iae.ac.cn 
mailto:wangshaof...@iae.ac.cn mailto:wangshaof...@iae.ac.cn
www.iae.cas.cn http://www.iae.cas.cn http://www.iae.cas.cn



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Re: [Ifeffit] Fe K edge spectrum of scorodite

2015-07-06 Thread Matthew Marcus

Thanks!  May I add it to the ALS 10.3.2 reference collection?

What is the standard of energy calibration?  Is the Fe metal edge at 7110.75eV, 
7112eV or what?
mam

On 7/6/2015 7:11 AM, Case Van Genuchten wrote:

Dear Shaofeng,

I am attaching the averaged, raw data and Fe K-edge EXAFS spectrum (extracted 
using SixPack) of scorodite.  The mineral was prepared following the procedure 
outlined in Paktunc et al. (2008).  The data were collected at the Stanford 
Synchrotron Radiation Lightsource in transmission mode with the sample housed 
in a liquid nitrogen cryostat.  You can find additional details on the 
preparation of the sample and data collection from the publication where the 
spectrum is reported and modeled (van Genuchten et al. 2014, Geochimica et 
Cosmochimica Acta).

Please let me know if you have any other questions about data collection.

Best,

Case M. van Genuchten
Environmental Geochemistry Laboratory
Institute of Earth Surface Dynamics
University of Lausanne, Lausanne, CH



On Mon, Jul 6, 2015 at 4:02 AM, Shaofeng Wang wangshaof...@iae.ac.cn 
mailto:wangshaof...@iae.ac.cn wrote:

Dear all,
Can anyone have Fe K edge exafs spectrum of scorodite share a copy?
Thanks in advance.
Shaofeng
--
Shaofeng Wang, Ph.D of Geochemistry
Environmental Molecular Science Group
Institute of Applied Ecology, Chinese Academy of Sciences
Shenyang, 110016, China
wangshaof...@iae.ac.cn mailto:wangshaof...@iae.ac.cn
www.iae.cas.cn http://www.iae.cas.cn



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Re: [Ifeffit] Ca EXAFS with Ge220 or InSb111

2015-05-11 Thread Matthew Marcus

I do it just fine with Si111 (ALS 10.3.2).  Do you have some evidence that the 
energy resolution or flux isn't what it should be?  For instance,
have you recorded a S XANES spectrum on sulfate?  That has a sharp, intense 
peak.
mam

On 5/11/2015 8:16 AM, Lisa Bovenkamp wrote:

Hello.
After having some troubles recording a good EXAFS spectrum with some old 
InSb111 crystals
I started wondering if it might be better to use Ge220 instead.
Anybody have some experience with that?

Lisa

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Re: [Ifeffit] SSRL-data

2015-02-04 Thread Matthew Marcus

Seems to me that in this era of nigh-infinite disk space, there's no need for 
binaries for EXAFS files like this.  The ASCII is perfectly fine.
One question to ask:  Is the offset already subtracted from the data count?  I 
assume that it is, because the last column has numbers that are smaller
than the offset numbers.

Another question is which energy to believe.  On 10.3.2, it turns out that the 
requested energy seems to be more accurate than the reported energy.  This
becomes clear when you look at XANES and find it much smoother, especially in 
the derivative, when you use the requested energy.
mam

On 2/1/2015 12:10 PM, Khalid, Syed wrote:

How to handle SSRL, beamline 2-2 data.

Attached is a binary and an ASCII file(with under score A).

Wordpad reads it, first column is time (data point duration), second energy it 
must go to, third real energy where mono went, fourth I0 and fifth It. It is 
gold foil transmission data.

Syed Khalid



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[Ifeffit] S XANES question

2014-11-26 Thread Matthew Marcus

A user on ALS 10.3.2 is taking S K-edge XANES and consistently finding a strong 
peak at 2484eV (calibration: gypsum white line = 2482.75eV).
There's a shoulder at the nominal position of the sulfate peak.  Now, peaks 
below sulfate I can understand, but since there's no such
thing as heptavalent sulfur, what could give a peak *above* the sulfate white 
line?  Anybody ever seen that?  Yes, we checked calibration.
mam
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Re: [Ifeffit] S XANES question

2014-11-26 Thread Matthew Marcus

The gypsum spectrum looks nothing like any spectrum of gypsum or other sulfate 
I've ever seen.  I'm deeply suspicious.
mam

On 11/26/2014 1:36 PM, Lyle Gordon wrote:

Matthew,

Paris et al in 2001 reported higher S K-edge white line energies for SO4 in 
Apatite, 2 eV above Gypsum.

THE VALENCE AND SPECIATION OF SULFUR IN GLASSES
BY X-RAY ABSORPTION SPECTROSCOPY
The Canadian Mineralogist
Vol. 39, pp. 331-339 (2001)

-Lyle

On Wed, Nov 26, 2014 at 12:39 PM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

A user on ALS 10.3.2 is taking S K-edge XANES and consistently finding a 
strong peak at 2484eV (calibration: gypsum white line = 2482.75eV).
There's a shoulder at the nominal position of the sulfate peak.  Now, peaks 
below sulfate I can understand, but since there's no such
thing as heptavalent sulfur, what could give a peak *above* the sulfate 
white line?  Anybody ever seen that?  Yes, we checked calibration.
 mam
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Re: [Ifeffit] S XANES question

2014-11-26 Thread Matthew Marcus

Yup, that's what mine looks like, if done with TEY to avoid overabsorption.  
For calibration, I use FY and take the peak position as
the calibration.  Yours also looks tolerably like the apatite spectrum in the 
cited paper (copied here:
file:///C:/Users/admin/Downloads/02e7e526633b90312500%20(1).pdf), figure 1. 
 It does not look like their
gypsum spectrum.
mam

On 11/26/2014 2:30 PM, Matt Newville wrote:

Hi Matthew, Lyle,

I'm still learning S XANES, but when we've measured gypsum, it looks very 
comparable to the spectra from ID21:
http://www.esrf.eu/UsersAndScience/Experiments/Imaging/ID21/php/gypsum

We often use the spectra from there as references (or when asking: Is this 
standard what we think it is?)

--Matt



On Wed, Nov 26, 2014 at 4:23 PM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

The gypsum spectrum looks nothing like any spectrum of gypsum or other 
sulfate I've ever seen.  I'm deeply suspicious.
 mam

On 11/26/2014 1:36 PM, Lyle Gordon wrote:

Matthew,

Paris et al in 2001 reported higher S K-edge white line energies for 
SO4 in Apatite, 2 eV above Gypsum.

THE VALENCE AND SPECIATION OF SULFUR IN GLASSES
BY X-RAY ABSORPTION SPECTROSCOPY
The Canadian Mineralogist
Vol. 39, pp. 331-339 (2001)

-Lyle

On Wed, Nov 26, 2014 at 12:39 PM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov 
wrote:

 A user on ALS 10.3.2 is taking S K-edge XANES and consistently 
finding a strong peak at 2484eV (calibration: gypsum white line = 2482.75eV).
 There's a shoulder at the nominal position of the sulfate peak.  
Now, peaks below sulfate I can understand, but since there's no such
 thing as heptavalent sulfur, what could give a peak *above* the 
sulfate white line?  Anybody ever seen that?  Yes, we checked calibration.
  mam
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--
--Matt Newville newville at cars.uchicago.edu http://cars.uchicago.edu 
630-252-0431


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Re: [Ifeffit] experimental standard

2014-11-18 Thread Matthew Marcus

You didn't say what you're trying to find out or even which edge you're doing 
this at.  That being the case, it's a little hard to know
what the best strategy is.  A few things come to mind:

1.  If you're looking for the environment of the Ga, then obviously, BaO 
and Ti2O3 aren't terribly useful.  You'd want something
with Ga in an environment similar to that of the unknown.  Is there such a 
thing as BaGa8Ox with the same structure as BaTi8O16, which
I assume is known?  Another possibility is to use as a reference something in 
which instead of Ga as the central atom, you have something
nearby in the periodic table, but in a similar environment.  Ga2O3 would only 
be useful if all you're after is Ga-O and maybe Ga-Ga distances.
Check for other, known oxides in the Ba-Ti-Ga-O system or at least Ba-Ga-O or 
Ti-Ga-O.

2.  If you're after what the Ga does to the environment of the major 
elements, then perhaps you could use BaTi8O16 (if that exists)or
barium titanate.  These would give you the Ba-O, Ti-O, and (Ba,Ti)-(Ba,Ti) 
paths.  My intuitive guess is that if x is small, then you'd be looking
for small changes, so the best standard of all is the x=0 material, if it 
exists.  Fit that, then add in (Ba,Ti)-Ga paths as appropriate and let
the other paths change and see what happens for x 0.

3.  Is the doped material available as a single crystal?  Has the structure 
been solved?  Perhaps that information could be used to constrain
the structure.

4.  The stoichiometry you give, Ba(Ti,Ga)8O16, requires the (Ti,Ga) to be 
in a mixed-valent state (assuming Ba=2, average = 30/8 = 15/4 = 3.75).
That being the case, I'm guessing that the Ga substitutes for the Ti3+, either 
shifting the average valence so that O isn't 16 anymore or just
replacing the Ti3+ until you've replaced it all.  Either way, Ti XANES would be 
informative.   There are many papers about the interpretation
of Ti K-edge XANES.

5.  If my guess about Ga substituting only for Ti3+ is correct, *and* you 
quoted the correct stoichiometry, then,
a)  Something should happen for x2 because you can't get an 
average valence of 3.75 anymore.
b)  If the Ti3+ and Ti4+ sites are different enough, say 
octahedral+tetrahedral, then the Ga EXAFS should look like
that of the Ti3+ only.
c)  Ga3+ is slightly smaller than Ti3+, so you might see a small 
contraction around the Ga relative to the Ti.

Good luck.
mam

On 11/18/2014 2:32 PM, Yun Xu wrote:

Hi all
I have a complex oxide BaTi8-xGaxO16. What standards I should run?
Ga is the dopant. I guess I should run the sample without dopant BaTi8O16 as 
standard, or the simple oxide as BaO, TiO2 Ga2O3?  or is the standard necessary?
Also, I have colleage working on DFT, I assume the theoretical standard is the 
result from the DFT calculation, and by using the coordinates of the atoms, I 
can run FEFF and fit the data.
Thanks
Yun


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Re: [Ifeffit] experimental standard

2014-11-18 Thread Matthew Marcus

It could be Ba K-edge, but you're right that trying to do EXAFS at the Ti edge 
is probably a no-hoper.  You get to k8.5 before you hit the Ba L3-edge,
which would just about be enough to get an average Ti-O distance and maybe 
something about a second shell but not much more.
Anyway, more speculation about intentions is unwarranted until Yun Xu tells us 
what he (? - I can't tell with Chinese names) actually has in mind and what his 
system really is.
mam

On 11/18/2014 3:35 PM, Anatoly I Frenkel wrote:

I think that they study Ga K-edge because Ba L3 and Ti K overlap, hence, those 
are very difficult to refine in such a complex system.
I also think that if your system is a solid solution (it was not obvious but it 
is probably what you imply) then the environment of Ga will have a mixture of 
Ti and Ga somewhere in the r-space and you will have to use a realistic model 
structure to learn how to do this type of an analysis, not a less sophisticated 
experimental standard. The latter may likely not even exist, and if it did, it 
will not be less sophisticated because it will also have a mixture of Ga-Ti and 
Ga-Ga as your unknown material, hence, the same problem.

I would just make sure it is a solid solution and try to make use of XRD data.
They should tell you if it is an isostructural material to one of the pure 
components, or a new structure.
If a new structure, and if you can't do Rietveld refinement, then - theory may 
be the best next step...
If isostructural to something more simple, use that known structure to 
construct FEFF model.

Anatoly


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Matthew Marcus 
[mamar...@lbl.gov]
Sent: Tuesday, November 18, 2014 6:09 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] experimental standard

You didn't say what you're trying to find out or even which edge you're doing 
this at.  That being the case, it's a little hard to know
what the best strategy is.  A few things come to mind:

1.  If you're looking for the environment of the Ga, then obviously, BaO 
and Ti2O3 aren't terribly useful.  You'd want something
with Ga in an environment similar to that of the unknown.  Is there such a 
thing as BaGa8Ox with the same structure as BaTi8O16, which
I assume is known?  Another possibility is to use as a reference something in 
which instead of Ga as the central atom, you have something
nearby in the periodic table, but in a similar environment.  Ga2O3 would only 
be useful if all you're after is Ga-O and maybe Ga-Ga distances.
Check for other, known oxides in the Ba-Ti-Ga-O system or at least Ba-Ga-O or 
Ti-Ga-O.

2.  If you're after what the Ga does to the environment of the major 
elements, then perhaps you could use BaTi8O16 (if that exists)or
barium titanate.  These would give you the Ba-O, Ti-O, and (Ba,Ti)-(Ba,Ti) 
paths.  My intuitive guess is that if x is small, then you'd be looking
for small changes, so the best standard of all is the x=0 material, if it 
exists.  Fit that, then add in (Ba,Ti)-Ga paths as appropriate and let
the other paths change and see what happens for x 0.

3.  Is the doped material available as a single crystal?  Has the structure 
been solved?  Perhaps that information could be used to constrain
the structure.

4.  The stoichiometry you give, Ba(Ti,Ga)8O16, requires the (Ti,Ga) to be 
in a mixed-valent state (assuming Ba=2, average = 30/8 = 15/4 = 3.75).
That being the case, I'm guessing that the Ga substitutes for the Ti3+, either 
shifting the average valence so that O isn't 16 anymore or just
replacing the Ti3+ until you've replaced it all.  Either way, Ti XANES would be 
informative.   There are many papers about the interpretation
of Ti K-edge XANES.

5.  If my guess about Ga substituting only for Ti3+ is correct, *and* you 
quoted the correct stoichiometry, then,
 a)  Something should happen for x2 because you can't get an 
average valence of 3.75 anymore.
 b)  If the Ti3+ and Ti4+ sites are different enough, say 
octahedral+tetrahedral, then the Ga EXAFS should look like
 that of the Ti3+ only.
 c)  Ga3+ is slightly smaller than Ti3+, so you might see a small 
contraction around the Ga relative to the Ti.

Good luck.
 mam

On 11/18/2014 2:32 PM, Yun Xu wrote:

Hi all
I have a complex oxide BaTi8-xGaxO16. What standards I should run?
Ga is the dopant. I guess I should run the sample without dopant BaTi8O16 as 
standard, or the simple oxide as BaO, TiO2 Ga2O3?  or is the standard necessary?
Also, I have colleage working on DFT, I assume the theoretical standard is the 
result from the DFT calculation, and by using the coordinates of the atoms, I 
can run FEFF and fit the data.
Thanks
Yun


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Re: [Ifeffit] problems re-opening Athena project

2014-09-17 Thread Matthew Marcus

There's a combination-fit program on the ALS 10.3.2 website 
https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software .
mam

On 9/17/2014 9:55 AM, Foster, Andrea wrote:

Bruce, thanks for your help...look forward to seeing new version.

FYI I especially am interested using the combinatorics module of Athena's LCF 
to test the uniqueness of some fits.I have a set of 30 models and PCA tells me that a max 
of 5 models should explain the dataset. I have been using SixPack for the fits, but it 
doesn't currently have the option to specify testing the limited set of the permutations  
that I need (I want to test every possible combination of 5 model compounds out of my set 
of 30 models).

andrea


Andrea L. Foster, PhD
U.S. Geological Survey, GMEG Science Center
345 Middlefield Rd., MS 901
Menlo Park, CA 94025
650-329-5437 (t)
650-329-5491 (f)

On Tue, Sep 16, 2014 at 1:36 PM, Bruce Ravel bra...@bnl.gov 
mailto:bra...@bnl.gov wrote:

On 09/15/2014 03:39 PM, Foster, Andrea wrote:

Bruce, attached are some data files...

btw looking through Athena manual I did find lots of helpful
instructions on import, but not specifically on how to import chi(k)
files.  if you could let me know how to do it, that would be great!


Andrea,

The data were helpful.  Thanks.

The thing I discovered is that Athena was making a number of mistakes
related to importing chi(k) data.  The reason for this (this is not an
excuse, just an explanation of what happened) is that I assume that
Athena users will start from raw data so she's much better tested when
starting from raw data.  Import of chi(k) data was kind of an
afterthought for me and, therefore, rather poorly tested.

I think I have put Athena in a better state with respect to importing
chi(k) data.  I even found and fixed a rather serious problem with the
LCF tool after importing chi(k) data.  I think that which was your
original motivation for sufffering through Athena's many shortcomings :)

I need to do some testing on Windows and then I'll need to build a
pre-release package for you to try.  All of that will take a few
days.  But I'll get there.

Thanks for your patience and thanks for reporting the problem in the
first place.  Demeter would be much much worse were it not for patient
people reporting their problems using the codes.

Cheers,
B



--
  Bruce Ravel  --__-- bra...@bnl.gov 
mailto:bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage: http://bruceravel.github.io/__home/ 
http://bruceravel.github.io/home/
  Software: https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/__demeter/ 
http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Principal Component Analysis (PCA) for XANES

2014-07-02 Thread Matthew Marcus

Athena (IFEFFIT package) does it.  So does the ALS Beamline 10.3.2 software 
package at https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software .
If you can't get at it there, I can send the executable and manual.
mam

On 7/1/2014 10:59 PM, Teck Kwang Choo wrote:

Hi Everyone,

Does anyone know what software I should use to perform a Principal Component 
Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The reason I need to 
use this technique is because I have a couple of reference compound spectra but 
am not sure which of those I should use to fit my unknown sample spectrum.

Any help is appreciated.

Thanks and kind regards.


Teck Kwang Choo
PhD Candidate
Department of Chemical Engineering
Room 225, Building 36
Monash University
Mobile No.: 04-11489904


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Re: [Ifeffit] Scattering paths in XANES calculations

2014-06-12 Thread Matthew Marcus

That sounds like an interesting talk.  Is it available?
mam

On 6/12/2014 7:07 AM, Stefanie Roese wrote:

Dear all,
I am performing XANES calculations for silver clusters with FEFF. Aditional to my XANES 
results, I would like to get information about the participating scattering paths and how 
they influence my spectra. In detail I want to get the same pictures that Bruce ravel 
used in his talk a practical introduction to multiple scattering theory from 
page 11. I have performed calculations for XANES using the rpath algorithm to obtain the 
feff.dat files. I already checked, that the course of the rpath spectra  agrees to 
the fms calculations in ordner to make sure that the algorithm converged.

But now I fail at getting the plots with the Energy at the x-axis and the 
normailzed mu at the y-axis likle Bruce did it in his talk. Which program was 
used there? Athena? And how can I get the energy/mu-information out of my 
feffnnn.dat files to compare to the total spectrum? I think I am quite close to 
the solution, but it does not work.

Thanks in advance for every help!
Steffi
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[Ifeffit] Data for Cr selenide?

2014-06-04 Thread Matthew Marcus

Does anyone have EXAFS data to at least k=12 for Cr selenide of known phase?  
I'm working on fitting the EXAFS
of Cr doped into Bi2Se3, and using Feff6L, the S02 comes out to 0.65 if I 
assume a substitutional site, which seems
a bit low.
mam
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Re: [Ifeffit] Fitting EXAFS simulation to experimental

2014-05-29 Thread Matthew Marcus

I wonder if what he was asking about is an automated way of mapping the 
position parameters for a given space group, that is, fractional atomic 
coordinates as listed in a .cif, onto
the various path distances.  As it is now, it's impractically hard to do it 
except for very simple cases.  Maybe what is needed is a language for 
specifying local structures in which
atom positions and occupancies can be given by variables, and the program would 
automatically parameterize the paths.  As a hypothetical toy example, consider 
a simple model of
a substitutional model of Fe in bcc W (atoms chosen more or less at random).  
Here, we suspect that since Fe is a smaller atom than W, the first neighbors 
would be
displaced inward.  Thus, we might have a specification something like

SET a0 = 3.165  /* lattice parameter of pure W */
CENTRAL Fe 0 0 0
ATOM W  /* 1st NN */
POS a0*(1-dist1)*(sqrt(3),sqrt(3),sqrt(3))/2
OCC 1
SS SS1
ATOM W
POS a0*(1-dist1)*(-sqrt(3),sqrt(3),sqrt(3))/2
OCC 1
SS SS1
... add the other 6
ATOM W  /* 2nd NN */
POS a0*(1-dist2)*(1,0,0)
OCC 1
SS SS2
... add the other 5

The program would then automatically compute not only the distances for the SS 
paths, but those for the MS paths as well,
and perhaps even estimate the ss values based on the ss's for the shells.  This 
is a relatively trivial example in which the scripting isn't needed.
However, it gets bigger.  For instance, suppose that some of the 1NN atoms 
might have Fe on them.  Then, the W sites would have
OCC 1-xFe
and there would be ATOM Fe sites specifications like:
ATOM Fe
POS a0*(1-dist1Fe)*(sqrt(3),sqrt(3),sqrt(3))/2
OCC xFe
SS SS1Fe

and the program would automatically work up MS paths with the proper weighting 
for the number of W and Fe atoms involved.

Now, consider an octahedral cage in which the central atom may be off-center:

SET a0 = appropriate value
CENTRAL Ti a0*(d_off,d_off,d_off)/sqrt(3)
ATOM O
POS (a0/2)*(1+d1,d2,d2)
OCC 1
SS SS1
ATOM O
POS (a0/2)*(d2,1+d1,d2)
OCC 1
SS SS1
ATOM O
POS (a0/2)*(d2,d2,1+d1)
OCC 1
SS SS1
ATOM O
POS (a0/2)*(-1+d1,d2,d2)
OCC 1
SS SS1
...

The distortions shown are intended to keep the 3-fold symmetry about 111.  Now, 
when you consider the higher shells, you can see that it could get
pretty messy to work out what the distances would be as a function of d_off, 
even if you don't allow displacements of higher neighbors.
This sort of specification only becomes sort of practical because computers can 
now handle the multitudes of paths which will appear.  Funny
that the Vpath thing should have just got discussed; that tool would be 
extra-important for distorted structures.

For the POS parameters, the above are given in Cartesian coords, but it would 
be good to have the option to do it in crystal coords, invoking
the crystal symmetry.  I'm not sure how to do that for impurities.

I realize that this would be a HUGE job, but whoever does it would win the 
hearts of EXAFS people everywhere :-)
mam

On 5/29/2014 8:14 AM, Matt Newville wrote:

Hi All,

As Scott, Bruce, Anatoly have said, it is certainly possible to map certain 
crystallographic distortions to local structure, and so predict the effect on 
EXAFS, and model EXAFS in terms of those distortions.

But to be clear for the original question, EXAFS is inherently a local structure probe and is not 
actually sensitive to crystallographic parameters.  That is, one *must* make the mapping from 
crystlalographic parameters to local structure, often making important assumptions (such as 
there is a crystal structure and I know what the space group is) that EXAFS 
is not actually able to deny or confirm.

Anyway, yes it is certainly possible to do things like model the extent of a 
tetragonal distortion.

--Matt


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Re: [Ifeffit] Problems in Energy calibration

2014-05-14 Thread Matthew Marcus

Which edge is this for?  I'm guessing MoK since you talk about using a foil for 
calibration.

Could the problem be polarization?  Since MoS2 is a highly anisotropic 
material, you would expect strong dichroism in both XANES and EXAFS regions.

It's possible that the resolutions at the two beamlines are different, so that 
a weak pre-peak might not show on the worse one.

You said something about putting the foil in the sample position.  Was the data 
taken in transmission?  If in fluorescence, then it will be subject to 
over-absorption and the derivative
will look shifted to the left.  If in transmission, and you find that the 
calibration is stable, then I would think that it should be OK.  I work on a 
beamline with no
third foil and it works well.  Another way to check is to inspect I0 for 
monochromator glitches and see if they move.  You can use them as internal 
calibrants.

Whatever you do, note that different people use different reference values for 
edge energies, so whenever showing XANES or quoting energies, you should always 
make
clear that, for instance, the Mo K-edge for Mo foil was taken to be 2.0eV 
(or whatever you use).
mam

On 5/14/2014 1:23 PM, Lei Zhong wrote:

Dear all,

we had beam line time in DESY (Hamburg) and ERSF (Grenoble) for NiMo sulfided 
supported samples. In DESY we got quite nice foil reference but in ERSF we 
failed since the third chamber showed problems. Therefore, we have critical 
issues to do the energy calibration for spectra collected from ERSF. We 
collected spectra for MoS2 crystals. So we are thinking about if it is 
reasonable to compare the spectra of MoS2 for the energy shift and further 
apply the energy calibration. Would you please give me suggestions? Thank you 
in advance.

Q1. In two beam lines, for exactly the same MoS2 crystal, we got difference in 
XANES region. Spectrum from DESY has a weak preedge peak resolved in XANES 
while ERSF doesn't. And the derivative shape of the two spectra for MoS2 
collected from two synchrotrons are not well overlapped. Is it acceptable?

Q2. I tried to overlay the first derivative of the two spectra of MoS2. There 
is a energy shift at 2.5 eV from the different synchrotrons if we take the one 
from DESY as standard. Can I apply the energy shift at 2.5 eV for MoS2 from 
ERSF and then overlay the first derivative of the other NiMo samples with MoS2 
to get the energy calibration? Or should I apply 2.5 eV for all the NiMo 
sulfided samples?

Q3. Since we lost the signal for the foil reference in ERSF, we tried to put 
the foil in the sample position. The first derivatives of the foil spetra from 
time to time overlap quite well. Should we set the energy calibration at 0 
according to the stable foil signal?

Sorry for the long email. Thank you for the time reading it. Hopefully I made 
the questions understandable to you. Looking forward to your answer!

Thanks.

Regards,
Lei
Technical University of Munich


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Re: [Ifeffit] XANES + EXAFS for light elements in diluted samples

2014-05-11 Thread Matthew Marcus

It took some clicking to get from the link below to where there's actually such 
a compilation: http://www.xafs.org/Experiment .  Is that the one you meant?
mam

On 5/11/2014 3:04 PM, Ravel, Bruce wrote:

Federico Boschirini's compilation of the world's XAFS beamlines should help:

http://www.iucr.org/resources/commissions/xafs

B



On May 10, 2014, at 12:04PM, Marcelo Alves wrote:

Dear all,

I am interested in running some measurements of XANES and EXAFS K-edge spectra 
of elements such as  Ca and S sorbed onto commonly found oxisol minerals, i.e 
natural kaolinite, gibbsite, hematite, and goethite. Besides appropiate filters 
to attenuate the fluorescence signals that come from elements such as Al and 
Si, what would the other instrumental conditions (e.g detector type, photon 
flux, etc...) needed for getting usable spectra of those elements in diluted 
samples? Any suggestion on the more adequate beamline to carry out such 
measurements?

Kind regards,

Marcelo.


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Re: [Ifeffit] Peaks in MCA spectra

2014-04-01 Thread Matthew Marcus

OK, I think the other Matt has solved it - it's the L1 peak.  I was confused 
by an inaccurate attempt at reading the energy scale.
Also, I somehow didn't read correctly the branching ratio from Hephaestus.
mam

On 3/31/2014 8:57 PM, George Sterbinsky wrote:

Hi Matt,

Thanks for your reply. Please see below.

On Mon, Mar 31, 2014 at 8:10 PM, Matt Newville newvi...@cars.uchicago.edu 
mailto:newvi...@cars.uchicago.edu wrote:

Hi George,

Calibrated spectra would help, but if we guess the calibration is 0.56
bins/ eV, then we'd have


I've attached a plot of the data showing the x-axis in keV. Also, as requested 
by Zack, I've attached a two column data file.


   line E (eV)   bin #
-
Co La1,2   775  434
O Ka1,2 525  294
C Ka1,2 277  155

which looks  pretty good. This puts the the unknown peak near
380/0.56 which is 678 eV.   Tthat's very close to Co Ll (M1-L3),
which is at 677 eV, and should be a bit less than 10%  of Co La1 and
La2, which is roughly right.


Based on fitting the spectrum with Gaussians, the Co LI is 24% of the La2. As 
you mention, a value of roughly 10% is expected. What could cause such a 
discrepancy?


So, I think it's Co Ll.  That says the sample is just Co, C, and O.
Is that reasonable?


Yes, it is. I think maybe a little fluorine too, but it is very weak as I 
mention in my response to Matthew.


What surprises me is that there is no signal from the elastic peak.
Was that somehow filtered out?


No, if there is an elastic peak it is probably lost under the Co La2.


Thanks,
George

The fact that the counts don't go to
zero between C and O could be many factors, including incomplete
charge collection.  This (and Compton scattering) generally make peaks
have a slightly non-Gaussian shape, with a low-energy tail.






Cheers,

--Matt

On Mon, Mar 31, 2014 at 5:01 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu 
mailto:georgesterbin...@u.northwestern.edu wrote:
  Hello,
 
  I am writing with a general XAS question. It does not necessarily 
pertain to
  Ifeffit, however, I think the topic is something some, maybe most, list
  members will be knowledgeable about. So it seems like this list is a good
  place to post this question.
 
  On to the question. I have attached a plot of a MCA spectrum collected 
with
  a vortex silicon drift detector. The spectrum is actually the average of
  several spectra, all collected in the post edge region of the Co L-edge. 
The
  spectra were averaged to reduce noise. The three peaks result from
  fluorescence from carbon, oxygen, and cobalt. Low-energy shoulders on 
the Co
  and O peaks are also observed. These can be seen as the regions of the
  spectrum that are not well reproduced by the fit. The main reason I 
included
  the fit in the plot is to illustrate the presence of these shoulders,
  particularly in the oxygen florescence, where the additional intensity is
  not so obvious.
 
  I am writing to see if anyone has any suggestion as to what the origins 
of
  these peaks might be. They are not due to additional elements, as they
  appear at the same incident energies as the main florescence peaks, i.e. 
the
  Co shoulder appears at the same incident energies as the main Co peak, 
and
  the O shoulder appears at the same incident energies as the main O peak. 
It
  is possible that the peaks result form other transitions. Considering Co,
  the main peak is due to L3/L2-M4 transitions, and the shoulder is in a
  position that could be consistent with L3/L2-M1 transitions. However, by
  fitting the peaks with Gaussians, one finds an area for the shoulder 
that is
  about 25% of the area of the main peak. This is significantly larger than
  what one might expect from tabulated transition strengths like those 
given
  in Hephaestus.
 
  To summarize, does anyone know what these shoulders might result from if 
not
  lower energy transitions? If they are low energy transitions, why would 
the
  relative transition strengths differ from tabulated values?
 
  Thank you,
  George
 
 
 
 
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Re: [Ifeffit] Peaks in MCA spectra

2014-04-01 Thread Matthew Marcus

I don't think so.  This may be a better question for M. Newville, or whoever 
wrote the program.
mam

On 4/1/2014 9:56 AM, George Sterbinsky wrote:

Hi Matthew,

Hephaestus shows the strength of the Ll emission to be about 10% of the La2 emission. 
When fitting the spectrum as a sum of Gaussians, I find that the area of of the Gaussian 
used to fit the Ll is 24% of that used to fit the La2. What would cause the ratio 
determined from tabulated data to differ from that found in the data I collected? Am I 
misunderstanding the meaning of the strength value in Hephaestus?

Thanks,
George


On Tue, Apr 1, 2014 at 11:45 AM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

OK, I think the other Matt has solved it - it's the L1 peak.  I was 
confused by an inaccurate attempt at reading the energy scale.
Also, I somehow didn't read correctly the branching ratio from Hephaestus.
 mam


On 3/31/2014 8:57 PM, George Sterbinsky wrote:

Hi Matt,

Thanks for your reply. Please see below.

On Mon, Mar 31, 2014 at 8:10 PM, Matt Newville newvi...@cars.uchicago.edu 
mailto:newvi...@cars.uchicago.edu mailto:newville@cars.__uchicago.edu 
mailto:newvi...@cars.uchicago.edu wrote:

 Hi George,

 Calibrated spectra would help, but if we guess the calibration is 
0.56
 bins/ eV, then we'd have


I've attached a plot of the data showing the x-axis in keV. Also, as 
requested by Zack, I've attached a two column data file.


line E (eV)   bin #
 --__---
 Co La1,2   775  434
 O Ka1,2 525  294
 C Ka1,2 277  155

 which looks  pretty good. This puts the the unknown peak near
 380/0.56 which is 678 eV.   Tthat's very close to Co Ll (M1-L3),
 which is at 677 eV, and should be a bit less than 10%  of Co La1 
and
 La2, which is roughly right.


Based on fitting the spectrum with Gaussians, the Co LI is 24% of the 
La2. As you mention, a value of roughly 10% is expected. What could cause such 
a discrepancy?


 So, I think it's Co Ll.  That says the sample is just Co, C, and O.
 Is that reasonable?


Yes, it is. I think maybe a little fluorine too, but it is very weak as 
I mention in my response to Matthew.


 What surprises me is that there is no signal from the elastic peak.
 Was that somehow filtered out?


No, if there is an elastic peak it is probably lost under the Co La2.


Thanks,
George

 The fact that the counts don't go to
 zero between C and O could be many factors, including incomplete
 charge collection.  This (and Compton scattering) generally make 
peaks
 have a slightly non-Gaussian shape, with a low-energy tail.






 Cheers,

 --Matt

 On Mon, Mar 31, 2014 at 5:01 PM, George Sterbinsky
 GeorgeSterbinsky@u.__northwestern.edu 
mailto:georgesterbin...@u.northwestern.edu mailto:GeorgeSterbinsky@u.__northwestern.edu 
mailto:georgesterbin...@u.northwestern.edu wrote:
   Hello,
  
   I am writing with a general XAS question. It does not 
necessarily pertain to
   Ifeffit, however, I think the topic is something some, maybe 
most, list
   members will be knowledgeable about. So it seems like this list 
is a good
   place to post this question.
  
   On to the question. I have attached a plot of a MCA spectrum 
collected with
   a vortex silicon drift detector. The spectrum is actually the 
average of
   several spectra, all collected in the post edge region of the 
Co L-edge. The
   spectra were averaged to reduce noise. The three peaks result 
from
   fluorescence from carbon, oxygen, and cobalt. Low-energy 
shoulders on the Co
   and O peaks are also observed. These can be seen as the regions 
of the
   spectrum that are not well reproduced by the fit. The main 
reason I included
   the fit in the plot is to illustrate the presence of these 
shoulders,
   particularly in the oxygen florescence, where the additional 
intensity is
   not so obvious.
  
   I am writing to see if anyone has any suggestion as to what the 
origins of
   these peaks might be. They are not due to additional elements, 
as they
   appear at the same incident energies as the main florescence 
peaks, i.e. the
   Co shoulder appears at the same incident energies as the main 
Co peak, and
   the O shoulder appears at the same incident energies as the 
main O peak

Re: [Ifeffit] Peaks in MCA spectra

2014-03-31 Thread Matthew Marcus

Hmmm.  An interesting brain-teaser.  Scaling very roughly from the graph, the 
mystery peak shows up at about 715eV.  This is consistent with Fe.
Could there be a background from Fe somewhere in the detection systen?  The 
intensity between the O and Co peaks doesn't really look like
a peak, but just like a background tail, perhaps from the strong Co peak.  It 
seems to be a little to the right of where N (from, for instance,
a kapton window) would be.  I could be wrong, in which case my Fe theory goes 
away.  Now, I thought about an escape peak from Si, but I suspect that
this is really small down here and anyway, the Si L-fluorescence energy is 92eV 
or so, and the extra peak is about 55eV below the main peak.

Did you duck below the Fe edge to see if the peak to the L of Co goes away?

The peaks in the fit seem to be consistently to the left of the ones in the 
data.  Any idea why?  Was the energy scale not a fit parameter?
In order to analyze the 'extra' peaks, it may be useful to optimize the fit to 
the main peaks, then subtract to get the residual, including
the 'extras'.  What would happen if you added Fe and maybe N to the fit?

I admit that I've never done soft X-ray fluorescence, so my ideas come from 
hard X-ray experience, which may not totally apply.
mam

On 3/31/2014 3:01 PM, George Sterbinsky wrote:

Hello,

I am writing with a general XAS question. It does not necessarily pertain to 
Ifeffit, however, I think the topic is something some, maybe most, list members 
will be knowledgeable about. So it seems like this list is a good place to post 
this question.

On to the question. I have attached a plot of a MCA spectrum collected with a 
vortex silicon drift detector. The spectrum is actually the average of several 
spectra, all collected in the post edge region of the Co L-edge. The spectra 
were averaged to reduce noise. The three peaks result from fluorescence from 
carbon, oxygen, and cobalt. Low-energy shoulders on the Co and O peaks are also 
observed. These can be seen as the regions of the spectrum that are not well 
reproduced by the fit. The main reason I included the fit in the plot is to 
illustrate the presence of these shoulders, particularly in the oxygen 
florescence, where the additional intensity is not so obvious.

I am writing to see if anyone has any suggestion as to what the origins of 
these peaks might be. They are not due to additional elements, as they appear 
at the same incident energies as the main florescence peaks, i.e. the Co 
shoulder appears at the same incident energies as the main Co peak, and the O 
shoulder appears at the same incident energies as the main O peak. It is 
possible that the peaks result form other transitions. Considering Co, the main 
peak is due to L3/L2-M4 transitions, and the shoulder is in a position that 
could be consistent with L3/L2-M1 transitions. However, by fitting the peaks 
with Gaussians, one finds an area for the shoulder that is about 25% of the 
area of the main peak. This is significantly larger than what one might expect 
from tabulated transition strengths like those given in Hephaestus.

To summarize, does anyone know what these shoulders might result from if not 
lower energy transitions? If they are low energy transitions, why would the 
relative transition strengths differ from tabulated values?

Thank you,
George





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Re: [Ifeffit] EXAFS with multiple absorbers

2014-02-22 Thread Matthew Marcus

What about the CFAVERAGE card (love that reminder of times gone by)?
mam

On 2/21/2014 7:23 PM, Kevin Jorissen wrote:

Hi Francisco

No.  If you e.g. want to sum contributions from several scatterers with 
different environment/fine structure, the right procedure is to do a separate 
feff calculation for each of these scatterers.

Cheers

Kevin Jorissen



On Feb 21, 2014, at 4:38 PM, Francisco Garcia garcia.ff@gmail.com wrote:

Dear users,

I would like to know if FEFF8 or FEFF9 can compute the EXAFS when multiple 
absorbers are present in the sample.

Thank you.
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Re: [Ifeffit] Absorption-coefficient data repository?

2014-01-27 Thread Matthew Marcus

It won't calculate it accurately in the XANES region because it doesn't know 
about XANES.  What could be done is
to take the smooth parts from Hepheastus and scale by the XANES data.
mam

On 1/27/2014 10:43 AM, Scott Calvin wrote:

Hi Damon,

Hephaestus will calculate that for you. (There are other options, too, but that 
may be the simplest.)

--Scott Calvin
Sarah Lawrence College

On Jan 27, 2014, at 1:30 PM, Damon Turney dtur...@ccny.cuny.edu wrote:


Dear XAFS Community,

I'm looking for values of absorption coefficient (or mass absorption
coefficient) of ZnO in the XANES region of the Zn edge, but all the
publications give XANES plots in arbitrary units, so I have no way
of knowing the absorption coefficient for ZnO.

Does anybody know a data repository where absorption coefficients are
collected?

Thanks,
Damon



--
Damon Turney PhD
Energy Institute, Department of Chemical Engineering
City University of New York
New York, NY 10031
dtur...@che.ccny.cuny.edu
office: (212) 650-5470
cell: (805) 571-3764
fax: (805) 823-4593
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Re: [Ifeffit] How to identify Mn Mn Corner edge paths in Artemis

2014-01-07 Thread Matthew Marcus

Corner-sharing octahedra in birnessite-based structure occur either due to 
interlayer Mn, i.e. Mn which is attached on
top of the layer, over a layer vacancy, or octahedra hanging off the edges of 
sheets.  There is a vast litereature on this,
notably from people like Manceau, Bargar and Webb.  Please refer to their 
papers.  You can get Manceau's papers by going to
his website.  They're all available as PDF.
mam

On 1/7/2014 3:51 AM, fred.mosselm...@diamond.ac.uk wrote:

Hi Sathish,

There are no corner sharing paths in your feff calculation as the perfect 
birnessite model you are using only has edge sharing octahedra. I am not a 
phyllomanganate expert so can't help with a structure suggestion to try but using google 
I would think you could find a structure with corner sharing MnO6.
Then you could take the corner sharing path from there and the edge sharing 
from your original structure.

In Sam Webb's paper he has refined his model to give shell occupancy numbers as 
he has a non totally crystalline structure. This is effectively the path 
degeneracy from the Feff calculation but you cannot refine this number in 
artemis, you have to refine Nmncor  or some other variable the name is 
irrelevant and then define the path occupancy of the corner as 1 and the S02 
for this path as amp * Nmncor .

Bruce's videos are pretty good in getting started in fitting from scratch, 
which is really not the easiest thing to do, so keep going. I assume you have 
watched some of them. 
http://www.diamond.ac.uk/Home/Events/Past_events/XAS-workshop-2011.html?mgnlCK=1339516257183


HTH

Cheers
Fred



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Re: [Ifeffit] fitting a specific k range

2013-12-05 Thread Matthew Marcus

It must be a slow day in the EXAFS world.  Does the term 'topic drift' mean 
anything? :-)
The Wikipedia entry http://en.wikipedia.org/wiki/Hosanna has some examples of 
secular use of the word, FWIW, which I admit isn't much.
mam

On 12/5/2013 2:02 PM, Matt Newville wrote:

Hi Anatoly,

On Thu, Dec 5, 2013 at 12:28 PM, Anatoly I Frenkel afren...@yu.edu wrote:

I object the use of hosannas of adoration. Other than the use of Greek 
mythology, I propose the mailing list to be religion-neutral and tautology-free.


Is Down the rabbit hole OK?   I'm not sure it usually counts as a
religious text to you, but I'm rather fond of Alice's Adventures and
find it to many useful words to live by.  I don't read it as being
True (in the religious sense that De Rerum Natura,The Odyssey, Don
Quixote, Moby Dick, The Lord of the Rings, and the works of Jorge Luis
Borges and Bob Dylan are), but it does seem somewhat more realistic
and useful than some of those other standard texts from antiquity.

That could just be me. I certainly mean no offense to anyone's belief
system ;)

--Matt
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[Ifeffit] Ti or V on hydrous Fe oxides?

2013-12-03 Thread Matthew Marcus

Anyone have reference data for Ti or V sorbed on or substituted in Fe oxides or 
oxyhydroxides?  I'm having trouble finding anything in
the literature.
mam
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Re: [Ifeffit] error in ATOMS

2013-11-13 Thread Matthew Marcus

This still puts the core atoms at huge distances from each other.  This can't 
be right.  I don't know if these
distances cause the problem you're having, but for any reasonable Rmax, no atom 
will be in range of the Ni.  Maybe
it's objecting to making a cluster containing the central atom and no 
scatterers.
mam

On 11/13/2013 11:09 AM, Julius Campecino wrote:

Yes Matt, that is the metal core. I tried translating the coordinates to the 
origin and it is still giving me the same problem. I think this has something 
to do with the attributes/tag after the coordinates. I do not know if some code 
is not working for the Tag. Have you tried running it on your end? These are 
the new coordinates.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10)
! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
title = WT NiSOD
space = P212121
a = 112.260 b = 113.810 c = 128.60
alpha =  90.0   beta =   90.0   gamma =  90.0
core =  Ni  edge =  K   rmax =5.0
atoms
! elem   x  y  z tag   occ.
   Ni0.00.00.0  Ni1.0
   S 0.926001.996000.57400  S 1.0
   S-1.508000.83800   -1.33000  S 1.0
   N-0.64900   -1.95300   -0.24700  N 1.0
   N 0.63900   -2.07000   -3.10800  N 1.0
   N 1.45100   -0.859000.94000  N 1.0

Thanks for your help.

Julius




On Wed, Nov 13, 2013 at 10:09 AM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

Shouldn't ATOMS input coordinates be fractional values?  I wonder if 
putting the S 3000A from center might have something
to do with it.  I'm guessing that this is the metal-sulfer core of a 
protein, right?
 mam


On 11/13/2013 9:58 AM, Julius Campecino wrote:

Hi Chris,

Same problem:

Can't call method quot;attributesquot; on an undefined value at 
/usr/local/lib/perl5/site___perl/5.10.0/Xray/ATP.pm line 342.

Can you try running this input and see if it works for you or not? 
Maybe there is something at my end that is causing this error.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10)
! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
title = WT NiSOD
space = P212121
a = 112.260 b = 113.810 c = 128.60
alpha =  90.0   beta =   90.0   gamma =  90.0
core =  Ni  edge =  K   rmax =5.0
atoms
! elem   x  y  z tag   occ.
Ni3.10300   27.701006.07300  Ni1.0
S 4.02900   29.697006.64700  S 1.0
S 1.59500   28.539004.74300  S 1.0
N 2.45400   25.748005.82600  N 1.0
N 3.74200   25.631002.96500  N 1.0
N 4.55400   26.842007.01300  N 1.0

Thanks for your help!

Julius

On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge patri...@buffalo.edu 
mailto:patri...@buffalo.edu mailto:patri...@buffalo.edu 
mailto:patri...@buffalo.edu wrote:

 Julius,

 I again did not find answer to the error but you could also try 
the following entity of ATOMS on the web which easily allows a huge number of 
sites

http://cars9.uchicago.edu/cgi-__bin/atoms/atoms.cgi 
http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi

 Chris

 **__**
 Dr. Christopher Patridge
 Assistant Professor of Chemistry
 Dept of Math and Natural Science
 D'youville College
 320 Porter Ave., Buffalo, NY 14201
 Phone: 716-829-8096 tel:716-829-8096 tel:716-829-8096 
tel:716-829-8096
Email:_patri...@dyc.edu mailto:email%3a_patri...@dyc.edu 
mailto:patri...@dyc.edu mailto:patri...@dyc.edu_




 On Nov 13, 2013, at 12:19 PM, Julius Campecino jcampec...@gmail.com 
mailto:jcampec...@gmail.com mailto:jcampec...@gmail.com 
mailto:jcampec...@gmail.com wrote:

 Hi everyone,

 Did anyone figure out how to fix Can't call method tag error 
and adding sites? Really a novice on fitting and I badly need help on this to get going. 
Sorry to bother everyone.

 Thanks!

 Julius


 On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino jcampec...@gmail.com 
mailto:jcampec...@gmail.com mailto:jcampec...@gmail.com 
mailto:jcampec...@gmail.com wrote:

 Hi Chris,

 Yeah, I did try add a site but it is not responding. 
Does anyone else experience this problem? Thank you, Chris.

 Julius


 On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge patri

Re: [Ifeffit] modeling significant defects and molecules

2013-10-31 Thread Matthew Marcus

YOu could use ATOMS to make a FEFF file for a simple structure, then copy the 
header from that and replace the atoms list with a set of
coordinates.  You'd have to write a program which would automatically fill in 
the correct IPOTs and symbols, but it's not that hard.
What's annoying is if you have multiple inequivalent absorber atoms, because 
then you have to make individual FEFF files centered about each
one and run FEFF multiple times.  I know that the CFAVERAGE card is supposed to 
take care of that, but I gather that it doesn't work
for XANES.  Anyone have an idea how reliable it is for EXAFS?
mam

On 10/31/2013 9:19 AM, Robert Gordon wrote:

Hi Carl,

You can always use symmetry P1 and specify every atom in the unit cell
in the atoms input.

That can be tedious for a large unit cell, but is achievable.

-R.

On 10/31/2013 11:09 AM, Carl Brozek wrote:

dear listhost,

I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material 
with significant defects that include additional atoms to the unit cell.

Can I simulate this material without making a new cif file? Ideally, I would be 
able to input a DFT-optimized model cluster as xyz coordinates only -- no 
crystallographic information.

This problem seems analogous to modeling discrete molecules. Can molecules be 
simulated by atoms/artemis? I know FEFF is capable of this, but I would like to 
use atoms for making my input file for feff.

Carl



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SB | 2010 | University of Chicago


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Re: [Ifeffit] X-ray natural circular dichroism by FEFF?

2013-09-11 Thread Matthew Marcus
-2.98119-3.628971   O4.69666
2.71415 1.43481-3.628971   O4.75339
   -2.75498 1.54559-3.628971   O4.81125
1.99171 3.97709 1.852031   O4.81811
   -0.40916-1.44312 4.592531   O4.83129
   -1.13161 1.09916 4.592531   O4.85593
1.54125 0.34316 4.592531   O4.85639
   -2.75498-3.62641 1.852031   O4.91638
2.71415-3.73719 1.852031   O4.97627
   -2.03253 4.17531 1.852031   O4.99944
   -4.70539-0.24069 1.852031   O5.06247
3.61508 3.53066-0.888471   O5.13066
1.54125-4.82884-0.888471   O5.14611
4.78798-0.54969 1.852031   O5.16304
0.0-5.17200 0.03   I5.17200
0.0 5.17200 0.03   I5.17200
   -4.74669-2.43150 0.03   I5.33322
4.74669 2.43150 0.03   I5.33322
   -5.15585 1.29738-0.888471   O5.39030
0.0 0.0 5.481003   I5.48100
0.0 0.0-5.481003   I5.48100
4.74669-2.74050 0.03   I5.48100
   -4.74669 2.74050 0.03   I5.48100
1.99171 3.97709-3.628971   O5.74052
1.54125 5.51516-0.888471   O5.79499
   -2.75498-3.62641-3.628971   O5.82324
2.71415-3.73719-3.628971   O5.87390
   -1.58207-2.53476-5.062252   Li   5.87830
   -2.03253 4.17531-3.628971   O5.89354
   -1.58207 2.63724-5.062252   Li   5.92320
   -0.40916 3.72888 4.592531   O5.92987
   -4.70539-0.24069-3.628971   O5.94710
3.16461-0.10326-5.062252   Li   5.97092
   -3.20544-2.08834 4.592531   O5.97723
3.16461 5.06874 0.418752   Li   5.99018
END

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Today's Topics:

1. X-ray natural circular dichroism by FEFF? (Matthew Marcus)


--

Message: 1
Date: Tue, 10 Sep 2013 09:28:44 -0700
From: Matthew Marcus mamar...@lbl.gov
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] X-ray natural circular dichroism by FEFF?
Message-ID: 522f48bc.8090...@lbl.gov
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Can FEFF calculate X-ray natural circular dichroism, which is the XCD that 
comes from structural chirality and not
magnetism?  I suppose I could simply try it, putting in coordinates for some 
simple molecule, but I'd like to know
if any results would be meaningful.
 mam


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End of Ifeffit Digest, Vol 127, Issue 9
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[Ifeffit] X-ray natural circular dichroism by FEFF?

2013-09-10 Thread Matthew Marcus

Can FEFF calculate X-ray natural circular dichroism, which is the XCD that 
comes from structural chirality and not
magnetism?  I suppose I could simply try it, putting in coordinates for some 
simple molecule, but I'd like to know
if any results would be meaningful.
mam
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Re: [Ifeffit] Linear Combination Fitting using ATHENA

2013-08-13 Thread Matthew Marcus

Here are reference spectra.  The calibration is defined with the Fe metal edge 
at 7110.75eV.  The maghemite spectrum has been corrected for mild
overabsorption by reference to magnetite, which is very similar.  The magnetite 
is synthetic Fe3O4 from Aldrich, and done in TEY, so no overabsorption.
The maghemite is from oxidation of Fe oxide nanoparticles and has been verified 
by XRD and comparison with the ETH group's maghemite spectrum.
mam

On 8/13/2013 1:33 AM, Teck Kwang Choo wrote:

Hi all,

@Drew Latta: I was wondering why the end members should be magnetite and 
maghemite. Is it because they are both of inverse-spinel structure, the 
difference only being that the latter has all Fe completely oxidized into 
Fe(III)? Would you be able to provide the standard spectra to me if that is the 
case? Thanks very much!

Previously I have only thought of using hematite (alpha-Fe2O3) and FeO as 
end-members, both representing Fe(III) and Fe(II) respectively without giving 
much thought to the structure Fe takes. I also had my doubts using magnetite 
(Fe3O4) as a standard as it is a mixture of both Fe (II) and Fe (III). But 
thanks to the insights Drew has given, I now think I should take the 
Fe-coordination environment into account with the use of magnetite and 
maghemite as standards.

@Alexandre and Matthew: I have obtained Mossbauer spectra of some of my samples 
but like Drew said, it is not straightforward at this point in time. Will see 
what I can do with the data I have!

Thanks for all your responses! It is greatly appreciated! This forum has been 
more helpful than I thought!

Teck Kwang


On 13 August 2013 01:34, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

While it's true that Mossbauer is the gold standard for Fe valence 
determination, access to the technique isn't all that common, and I don't know
of any facility that can do it on a micro scale.  Is there one?
 mam


On 8/12/2013 7:01 AM, Alexandre dos Santos Anastacio wrote:

Hello,

maybe that fingerprinting technique would be Mossbauer spectroscopy. 
The Fe(II)/Fe(III) ratio comes easily and also there are lots of papers about 
Mg-ferrite, an example:

10.1109/TMAG.2009.2018880 http://dx.doi.org/10.1109/__TMAG.2009.2018880 
http://dx.doi.org/10.1109/TMAG.2009.2018880

Alexandre.




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--
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PhD Student
Department of Chemical Engineering
Room 225, Building 36
Monash University
Mobile No.: 04-11489904


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#%Name: Maghemite nano powder
#%Empirical formula: gamma-Fe3+2O3  /Webmineral
#%Mineral group:  oxides
#%Xtal system: cubic   
#%Edge: K
#%Sample prep: powder on Kapton tape
#%Beamline: ALS 10.3.2, HxV slits = 200x20 um
#%Det:  I0=N2, Fluorescence mode (Ge solid state 7elts)
#%Ref/notes:  Mineralogical Research Company, San Jose, CA-USA. XRD confirmed.
#%Temp: Room temp (28C)
#%Timedate: 6:20 AM 7/3/2007
#%Provider: Matthew A. Marcus, Sirine Fakra.
#%
7.0100066E+3 1.3008636E-3
7.0150081E+3 1.2676025E-3
7.0200096E+3 1.4012953E-3
7.0250111E+3 1.3687201E-3
7.0300126E+3 1.4827145E-3
7.0350141E+3 1.5567103E-3
7.0400156E+3 1.6321360E-3
7.0450172E+3 1.8282378E-3
7.0500187E+3 1.8787587E-3
7.0550202E+3 2.0697013E-3
7.0600217E+3 2.1766526E-3
7.0650232E+3 2.3976456E-3
7.0700247E+3 2.8091858E-3
7.0750262E+3 3.1121079E-3
7.0800277E+3 3.7051882E-3
7.0850292E+3 4.2254896E-3
7.0900307E+3 5.0080461E-3
7.0950323E+3 6.3616899E-3
7.1000338E+3 8.1449022E-3
7.1005339E+3 8.3578735E-3
7.1010341E+3 8.5095725E-3
7.1015342E+3 8.6762463E-3
7.1020344E+3 9.0579738E-3
7.1025345E+3 9.2831028E-3
7.1030347E+3 9.6193633E-3
7.1035348E+3 9.8628340E-3
7.1040350E+3 1.0180513E-2
7.1045351E+3 1.0386116E-2
7.1050353E+3 1.1052578E-2
7.1055355E+3 1.1529281E-2
7.1060356E+3 1.2050395E-2
7.1065358E+3 1.2378185E-2
7.1070359E+3 1.3171965E-2
7.1075361E+3 1.3657637E-2
7.1080362E+3 1.4476360E-2
7.1085364E+3 1.5504986E-2
7.1090365E+3 1.6594136E-2
7.1095367E+3 1.8050181E-2
7.1100368E+3 1.9940670E-2
7.1105370E+3 2.2958282E-2
7.1110371E+3 2.7349793E-2
7.1115373E+3 3.5642680E-2
7.1120374E+3 5.0382320E-2
7.1125376E+3 7.0824214E-2
7.1130377E+3 9.2282370E-2
7.1135379E+3 9.5804412E-2
7.1140380E+3 8.5603494E-2

Re: [Ifeffit] normalization methods

2013-05-16 Thread Matthew Marcus

That 'flattening' function seems over-complicated to me and makes an artificial 
discontinuity, at least in slope, at E0 which is
a somewhat arbitrary quantity.  Why not simply divide by the post-edge 
quadratic (norm(E) = (mu(E)-pre_edge_line(E))/quadratic(E))?
In some cases, where there's a big curvature, it may make sense to divide mu(E) 
by the quadratic, then subtract a pre-edge.  What I've never
solved satisfactorily is the case in which the extrapolation of the pre-edge line 
crosses the post-edge, so mu(E)-pre_edge_line(E)0 for
some part of the range.  I've never understood why this happens.
mam

On 5/16/2013 4:47 AM, Matt Newville wrote:

Hi Matthew, George, Zach,

Thanks for the discussion!

On Wed, May 15, 2013 at 5:41 PM, Matthew Marcus mamar...@lbl.gov wrote:

I'm not sure what 'flattening' means.  Does that mean dividing by a linear
or other polynomial function, fitted to the post-edge?
 mam


Sorry, I should have been clearer.  Standard Athena/Ifeffit is to

   a) regress a pre-edge line to mu(E) (no power laws)
   b) regress a post-edge quadratic
   c) set edge_step = post_edge_quadratic(E0) - pre_edge_line(E0)
   b) set  norm(E)  = (mu(E) - pre_edge_line(E)) / edge_step.

Flattening (Athena only, now backported to larch) fits a quadratic to
the post-edge range (typcically E0+100 to end of data) of norm(E), and
then sets

   flattened(E) =  norm(E) for E= E0
  =  norm(E) - quadratic(E) + quadratic(E0)   for E  E0

I think this was originally meant for display purposes only.

Hopefully Bruce can correct me if I'm wrong on any of the details here.

I think it's fair to say that the Standard Athena/Ifeffit approach
to normalization is simple-minded.  It was designed for EXAFS in an
era when accessing databases seemed like a challenge, so even for
EXAFS it is simple-minded.

Flattening might be better at removing instrumental backgrounds, and
be better for linear analysis of XANES.  The main concern I would have
is the potential for a slight discontinuity at E0, or the potential
strong dependence from the choice of E0.

Using something like bkg_cl() (which matched mu(E) to the data from
the Cromer-Liberman tables) or MBACK (which I believe is similar, but
also accounts for  elastic/Compton leakage into the pre-edge part of
fluorescence spectra).


From my point of view, the question is: what's the best way to do

this?The pre_edge() function in Larch does include an energy
exponent term, and now writes out the flattened array, as above.
It does not include the scaling MAM described, but that would not be
hard.  Reimplementing bkg_cl() would not be too hard, but perhaps
trying to port MBACK would be better. Perhaps all of the above is
best?


--Matt
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Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus

What I typically do for XANES is divide mu-mu_pre_edge_line by a linear 
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge.  If the data 
has obvious curvature in the post-edge, I'll use a higher-order
polynomial.  For transmission data, what sometimes linearizes the background is 
to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward.  All this is, of course, highly subjective 
and one of the reasons for taking extended XANES data (300eV,
for instance).  For short-range XANES, there isn't enough info to do more than 
divide by a constant.  Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) = 
(1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}.  A sign that this degree of 
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if a*(Emax-E0) 
is large.  Don't get me started on overabsorption :-)
mam

On 5/15/2013 7:35 AM, Matt Newville wrote:

Hi Folks,

Over on the github pages for larch, Mauro and Bruce raised an issue
about the flattening in Athena. See
https://github.com/xraypy/xraylarch/issues/44

I've added a flattened output from Larch's pre_edge() function, but
the question has been raised of whether this is better than the
simpler normalized spectra, especially for doing PCA and/or LCF for
XANES.

Currently, the normalized spectra is just (mu -
pre_edge_line)/edge_step. Clearly, a line fitted to the pre-edge of
the spectra is not sufficient to remove all instrumental backgrounds.
In some sense, flattening attempts to do a better job, fitting the
post-edge spectra to a quadratic function.  As Mauro, Bruce, and
Carmelo have pointed out, it is less clear that it is actually better
for XANES analysis.  I think the main concerns are that a) it is so
spectra-specific, and b) it turns on at E0 with a step function.

Bruce suggested doing something more like MBACK or Ifeffit's bkg_cl().
  It would certainly be possible to do some sort of flattening so
that mu follows the expected energy dependence from tabularized mu(E).

Does anyone else have suggestions, opinions, etc?  Feel free to give
them here or at the github page

--Matt
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Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus

The way I commonly do pre-edge is to fit with some form plus a power-law 
singularity representing the initial rise of the edge, then
subtract out that some form.  Now, that form can be either linear, 
linear+E^(-2.7) (for transmission), or linear+ another power-law
singularity centered at the center passband energy of the fluorescence 
detector.  That latter is for fluorescence data which is affected by
the tail of the elastic/Compton peak from the incident energy.  Whichever form 
is taken gets subtraccted from the whole data range, resulting
in data which is pre-edge-subtracted but not yet post-edge normalized.  The 
path then splits; for EXAFS, the usual conversion to k-space, spline
fitting in the post-edge, subtraction and division is done, all interactively.  
Tensioned spline is also available due to request of a prominent user.
For XANES, the post-edge is fit as previously described.  Thus, there's no 
distinction made between data above and below E0 in XANES, whereas
there is such a distinction in EXAFS.
mam

On 5/15/2013 8:25 AM, Matt Newville wrote:

Hi Matthew,

On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus mamar...@lbl.gov wrote:

What I typically do for XANES is divide mu-mu_pre_edge_line by a linear
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge.  If the
data has obvious curvature in the post-edge, I'll use a higher-order
polynomial.  For transmission data, what sometimes linearizes the background
is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward.  All this is, of course, highly
subjective and one of the reasons for taking extended XANES data (300eV,
for instance).  For short-range XANES, there isn't enough info to do more
than divide by a constant.  Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) =
(1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}.  A sign that this degree of
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if
a*(Emax-E0) is large.  Don't get me started on overabsorption :-)
 mam


Thanks -- I should have said that pre_edge() can now do a
victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any
real value).

Still, it seems that the current flattening is somewhere between
better and worse, which is unsettling...  Applying the
flattening polynomial to the pre-edge range definitely seems to give
poor results, but maybe some energy-dependent compromise is possible.

And, of course, over-absorption is next on the list!

--Matt
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Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus

You say that the flipping difference (p - n) is 0 in pre-edge and far post-edge 
regions, which is as it should be, but then say that the
slopes of p- and n- post-edges, considered separately, are different.  I must 
be misunderstanding because those two statements would seem to be
inconsistent.  I wonder if the sensitivity of the TEY changes with magnetic 
field because of the effect of the field on the trajectories of
the outgoing electrons, which would explain the differing curves.  A 
possibility - if you divide the p-XAS by n-XAS, do you get something
which is a smooth curve everywhere but where MCD is expected?  Does that curve 
match in pre- and far post-edge regions?  If that miracle occurs,
then perhaps you could fit that to a polynomial, except in the MCD region, then 
divide the p-XAS by that polynomial, to remove the effect of
the differing sensitivities.

There are people here at ALS, such as Elke Arenholz earenh...@lbl.gov, who do 
this sort of spectroscopy.  I suggest asking her.
mam

On 5/15/2013 9:58 AM, George Sterbinsky wrote:

The question of whether it is appropriate to use flattened data for 
quantitative analysis is something I've been thinking about a lot recently. In 
my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the 
XMCD, I measure XAS with total electron yield detection using a ~70% left or 
right circularly polarized beam and flip the magnetic field on the sample at 
every data point. The goal then, is to subtract the XAS measured in a positive 
field (p-XAS) from XAS measured in a negative field (n-XAS) and get something 
(the XMCD) that is zero in the pre-edge and post-edge regions. I often find 
that after removal of a linear pre-edge, the spectra still have a linearly 
increasing post edge (with EXAFS oscillations superimposed on it), and the 
slope of the n-XAS and p-XAS post-edge lines are different. In this case simply 
multiplying the n-XAS and p-XAS by constants will never give an XMCD spectrum 
that is zero in the post edge region. There is then some component of t


he

XAS background that is not accounted for by linear subtraction and 
multiplication by a constant. It seems to me that flattening could be a good 
way to account for such a background. So is flattening a reasonable thing to do 
in a case such as this, or is there a better way to account for such a 
background?

Thanks,
George


On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

The way I commonly do pre-edge is to fit with some form plus a power-law 
singularity representing the initial rise of the edge, then
subtract out that some form.  Now, that form can be either linear, 
linear+E^(-2.7) (for transmission), or linear+ another power-law
singularity centered at the center passband energy of the fluorescence 
detector.  That latter is for fluorescence data which is affected by
the tail of the elastic/Compton peak from the incident energy.  Whichever 
form is taken gets subtraccted from the whole data range, resulting
in data which is pre-edge-subtracted but not yet post-edge normalized.  The 
path then splits; for EXAFS, the usual conversion to k-space, spline
fitting in the post-edge, subtraction and division is done, all 
interactively.  Tensioned spline is also available due to request of a 
prominent user.
For XANES, the post-edge is fit as previously described.  Thus, there's no 
distinction made between data above and below E0 in XANES, whereas
there is such a distinction in EXAFS.
 mam


On 5/15/2013 8:25 AM, Matt Newville wrote:

Hi Matthew,

On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

What I typically do for XANES is divide mu-mu_pre_edge_line by a 
linear
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge.  
If the
data has obvious curvature in the post-edge, I'll use a higher-order
polynomial.  For transmission data, what sometimes linearizes the 
background
is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward.  All this is, of course, highly
subjective and one of the reasons for taking extended XANES data 
(300eV,
for instance).  For short-range XANES, there isn't enough info to 
do more
than divide by a constant.  Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) =
(1+a*(E-E0))*Sum_on_ref{x[ref]__*muNorm[ref](E)}.  A sign that this 
degree of
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if
a*(Emax-E0) is large.  Don't get me started on overabsorption :-)
  mam


Thanks -- I should have said

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus

OK, I guess I don't know what 'standard normalization' is.  It looks from the 
quotient that you'll need some sort of curved post-edge.
I guess the division didn't work because the electron energy distribution is 
different pre- and post-edge, so the magnetic effects are
different and vary across the edge.  Thus, the shapes of the MCD peaks will be 
at least a little corrupted even if the pre- and post-edge
spectra are taken into account.  I don't know what to do about this.  Did you 
try asking Elke?
mam

On 5/15/2013 11:52 AM, George Sterbinsky wrote:

Hi Matthew,


On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

You say that the flipping difference (p - n) is 0 in pre-edge and far 
post-edge regions, which is as it should be, but then say that the
slopes of p- and n- post-edges, considered separately, are different.  I 
must be misunderstanding because those two statements would seem to be
inconsistent.



Sorry, I think my wording wasn't particularly clear here. What I should have 
said is:

The goal then is to subtract the /normalized/ XAS measured in a positive field 
(p-XAS) from /normalized/ XAS measured in a negative field (n-XAS) and get something (the 
XMCD) that is zero in the pre-edge and post-edge regions. /However, standard 
normalization does not give this result/

Italics indicate new text.

I wonder if the sensitivity of the TEY changes with magnetic field because 
of the effect of the field on the trajectories of
the outgoing electrons, which would explain the differing curves.


I would agree, I think the effect of the magnetic field on the electrons is the 
likely source of the differences in background.

A possibility - if you divide the p-XAS by n-XAS, do you get something
which is a smooth curve everywhere but where MCD is expected?  Does that 
curve match in pre- and far post-edge regions?


No, after division of the p-XAS by the n-XAS (before any normalization), both 
the pre and post-edge regions are smooth, but one would need a step-like 
function to connect them. I've attached a plot showing the result of division.


If that miracle occurs,
then perhaps you could fit that to a polynomial, except in the MCD region, 
then divide the p-XAS by that polynomial, to remove the effect of
the differing sensitivities.

There are people here at ALS, such as Elke Arenholz earenh...@lbl.gov 
mailto:earenh...@lbl.gov, who do this sort of spectroscopy.  I suggest asking 
her.
 mam


Thanks for the suggestion and your reply.

George








On 5/15/2013 9:58 AM, George Sterbinsky wrote:

The question of whether it is appropriate to use flattened data for 
quantitative analysis is something I've been thinking about a lot recently. In 
my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the 
XMCD, I measure XAS with total electron yield detection using a ~70% left or 
right circularly polarized beam and flip the magnetic field on the sample at 
every data point. The goal then, is to subtract the XAS measured in a positive 
field (p-XAS) from XAS measured in a negative field (n-XAS) and get something 
(the XMCD) that is zero in the pre-edge and post-edge regions. I often find 
that after removal of a linear pre-edge, the spectra still have a linearly 
increasing post edge (with EXAFS oscillations superimposed on it), and the 
slope of the n-XAS and p-XAS post-edge lines are different. In this case simply 
multiplying the n-XAS and p-XAS by constants will never give an XMCD spectrum 
that is zero in the post edge region. There is then some
component of the

XAS background that is not accounted for by linear subtraction and 
multiplication by a constant. It seems to me that flattening could be a good 
way to account for such a background. So is flattening a reasonable thing to do 
in a case such as this, or is there a better way to account for such a 
background?

Thanks,
George


On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov 
wrote:

 The way I commonly do pre-edge is to fit with some form plus a 
power-law singularity representing the initial rise of the edge, then
 subtract out that some form.  Now, that form can be either 
linear, linear+E^(-2.7) (for transmission), or linear+ another power-law
 singularity centered at the center passband energy of the 
fluorescence detector.  That latter is for fluorescence data which is affected 
by
 the tail of the elastic/Compton peak from the incident energy. 
 Whichever form is taken gets subtraccted from the whole data range, resulting
 in data which is pre-edge-subtracted but not yet post-edge 
normalized.  The path then splits; for EXAFS, the usual conversion to k-space

Re: [Ifeffit] normalization methods

2013-05-15 Thread Matthew Marcus

I'm not sure what 'flattening' means.  Does that mean dividing by a linear or 
other polynomial function, fitted to the post-edge?
mam

On 5/15/2013 1:43 PM, George Sterbinsky wrote:

By standard normalization, I meant subtraction of a linear pre-edge and 
multiplication by a constant. If this treatment is applied to the XAS spectra 
before subtraction, one does not obtain an XMCD spectrum that goes to zero in 
the post edge region for the data I described. As you noted, that is what would 
be expected given the p-XAS and n-XAS have different slopes in the post-edge 
region.

On the other hand, standard normalization + flattening does result in pre and 
post-edge regions that go to zero, again as one might expect. So perhaps, the 
background modeled by standard normalization + flattening is an accurate 
representation of the real background in some cases and can be used in 
quantitative analysis. Is there reason to believe that cannot be the case?

Thanks,
George




On Wed, May 15, 2013 at 3:04 PM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov wrote:

OK, I guess I don't know what 'standard normalization' is.  It looks from 
the quotient that you'll need some sort of curved post-edge.
I guess the division didn't work because the electron energy distribution 
is different pre- and post-edge, so the magnetic effects are
different and vary across the edge.  Thus, the shapes of the MCD peaks will 
be at least a little corrupted even if the pre- and post-edge
spectra are taken into account.  I don't know what to do about this.  Did 
you try asking Elke?
 mam


On 5/15/2013 11:52 AM, George Sterbinsky wrote:

Hi Matthew,



On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus mamar...@lbl.gov 
mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov 
wrote:

 You say that the flipping difference (p - n) is 0 in pre-edge and 
far post-edge regions, which is as it should be, but then say that the
 slopes of p- and n- post-edges, considered separately, are 
different.  I must be misunderstanding because those two statements would seem 
to be
 inconsistent.



Sorry, I think my wording wasn't particularly clear here. What I should 
have said is:

The goal then is to subtract the /normalized/ XAS measured in a positive 
field (p-XAS) from /normalized/ XAS measured in a negative field (n-XAS) and get 
something (the XMCD) that is zero in the pre-edge and post-edge regions. /However, 
standard normalization does not give this result/


Italics indicate new text.

 I wonder if the sensitivity of the TEY changes with magnetic field 
because of the effect of the field on the trajectories of
 the outgoing electrons, which would explain the differing curves.


I would agree, I think the effect of the magnetic field on the 
electrons is the likely source of the differences in background.

 A possibility - if you divide the p-XAS by n-XAS, do you get 
something
 which is a smooth curve everywhere but where MCD is expected?  
Does that curve match in pre- and far post-edge regions?


No, after division of the p-XAS by the n-XAS (before any 
normalization), both the pre and post-edge regions are smooth, but one would 
need a step-like function to connect them. I've attached a plot showing the 
result of division.


 If that miracle occurs,
 then perhaps you could fit that to a polynomial, except in the MCD 
region, then divide the p-XAS by that polynomial, to remove the effect of
 the differing sensitivities.

 There are people here at ALS, such as Elke Arenholz earenh...@lbl.gov 
mailto:earenh...@lbl.gov mailto:earenh...@lbl.gov mailto:earenh...@lbl.gov, 
who do this sort of spectroscopy.  I suggest asking her.

  mam


Thanks for the suggestion and your reply.

George








 On 5/15/2013 9:58 AM, George Sterbinsky wrote:

 The question of whether it is appropriate to use flattened 
data for quantitative analysis is something I've been thinking about a lot 
recently. In my specific case, I am analyzing XMCD data at the Co L-edge. To 
obtain the XMCD, I measure XAS with total electron yield detection using a ~70% 
left or right circularly polarized beam and flip the magnetic field on the 
sample at every data point. The goal then, is to subtract the XAS measured in a 
positive field (p-XAS) from XAS measured in a negative field (n-XAS) and get 
something (the XMCD) that is zero in the pre-edge and post-edge regions. I 
often find that after removal of a linear pre-edge, the spectra still have a 
linearly increasing post edge (with EXAFS oscillations superimposed on it), and 
the slope of the n-XAS and p-XAS post-edge lines are different. In this case 
simply multiplying the n-XAS and p-XAS by constants

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

2013-03-28 Thread Matthew Marcus

Many years back, when FEFF stopped being free, I was told that the decision was 
not Rehr's but forced by the university.  Blame them.
It's always easier and more pleasant for us to blame faceless university 
beauraucrats than scientists anyway :-)

I agree that FEFF input is broken.  This was, perhaps, inevitable as FEFF 
evolved over the years.  It may be (I haven't studied the matter)
that the old format, which was perfectly good in its day, simply can't 
accommodate new features just by adding new keywords.  I really
can't blame the Project very much for changing the format.  Still, the formats 
are documented, so I don't buy the idea that nothing can be
done with FEFF8 until the Project changes its format or goes open-source.  I 
can understand a reluctance to go open-source because they
now keep tight control over portability and the embodied physics, such that 
everybody knows exactly what 'we used FEFF8.4' means.  If it
went open-source, it may be imagined that there'd be a proliferation of 
versions, some of them with dubious hacks.  One fix I could imagine
the Project doing is to release as open-source an input module for FEFF9, which 
is broken up into separate modules anyway.  That way, people
could have whatever input format they wanted, but the integrity of FEFF would 
be preserved.

As to dielectric response, what is the effect of improving that model on EXAFS 
predictions?  Does it affect the self-energy, hence
lifetime broadening and E0?  I knbow it affects XANES, but that's a whole other 
subject not covered by DemLarchTemis discussions.
mam
mam

On 3/27/2013 7:32 PM, Matt Newville wrote:

Hi Matthew, Bruce,


On Wed, Mar 27, 2013 at 10:33 AM, Matthew Marcus mamar...@lbl.gov wrote:

Some users do have FEFFx (x6l) on their own, so it would be useful to
prepare Artemis/Demeter/Larch... for them and provide
methods for using higher versions if an executable is present.


I completely agree that this would be valuable, and that it's not
quite moot because many people do have Feff8 or Feff9 available to
them.

But, I also want to be clear that I totally agree with Bruce's point
on this as well.  It's really hard to support code that is actually
poorly defined and cannot be changed.  The Feff input file format is a
complete mess, and it's not Bruce's (or my) fault.  In fact, this *is*
what the original question was about.  Feff changed form one awful
form to another -- why is this Bruce's problem to solve? There is
no API or library provided for reading feff.inp.  We are forbidden
from changing it or redistributing a changed version of Feff8.   It
is, to be very clear,  the choice of the Feff project to break these
input files.If we had a Feff8 for EXAFS that could be relied
upon and redistributed, it would be a totally different story.   We
don't.

We've lobbied (begged) for changes in the i/o and freer access to the
code for many, many years.  I can't explain the restrictions in any
rational terms, fathom why this restriction is a priority for John or
anyone else, or understand how anyone who writes scientific software
would use anything except an open-source license.  I've given up on
pestering them about it.  I was told last summer that a version of
Feff8 for EXAFS that we can distribute would be made, but haven't
heard a thing about it since.  It could happen soon  that would be
great.  The license they use is their choice, and I respect that even
if I don't actually like their choice, and actually have real
reservations about the choice being solely theirs to make.
Ultimately, science will demand that all versions of Feff will be made
free or be forgotten.  It is completely believable that Feff6L will be
what is used twenty years from now.  I expect that Feff8 for XANES
calculations codes will never be made free and will be forgotten in
time.

I actually don't have a copy of Feff9.  Kevin J did a great job with
JFEFF, and emulating or including this approach of using a remote
cluster in the analysis codes would be interesting to think about.

From a practical point of view,  it would be easier to reproduce a

similar system than to have to argue about licensing.  Then again,
without the calculation engine being freely available, running it on a
cluster actually seems like a problem... wouldn't you need a license
key or something?  Right, sorry, the Feff license actually makes no
sense -- it's better to not think about this.


What does the multipole self-energy do?  Is that the thing that requires the
dielectric response?  As you point out, the purpose of
the exercise is to analyze unknowns, so by definition one doesn't have the
dielectric response.  We can't expect a program that runs on
a PC to do a proper, all-electrons, excited-state calculation.


Yes, the multipole self-energy uses a better model for the self-energy
based on the dielectric response of the system in the low (electron)
energy regime -- in short, how a free photo-electron will travel

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

2013-03-27 Thread Matthew Marcus

Some users do have FEFFx (x6l) on their own, so it would be useful to prepare 
Artemis/Demeter/Larch... for them and provide
methods for using higher versions if an executable is present.

What does the multipole self-energy do?  Is that the thing that requires the 
dielectric response?  As you point out, the purpose of
the exercise is to analyze unknowns, so by definition one doesn't have the 
dielectric response.  We can't expect a program that runs on
a PC to do a proper, all-electrons, excited-state calculation.

One thing I do is to use experimental data from models as sources of amplitudes 
and phases.  At present, I do this using my own
multishell fit program.  Is there an easy way to do this in your programs?  
What I think would be nice is a subsystem which allows one
to do the filtering and extraction of amp and phase from a model .chi file from 
within the program, rather than having to create
FEFF-path-like files.

As long as we're talking wish-list, I'd love to have some way of defining atom 
positions using symbolic variables and have the system
compute the path distances automatically as functions of those variables.  That 
way, I could, for instance, define a dopant system in terms
of the displacements of the near-neighbors without having to do the geometry by 
hand, which is difficult, tedious and error-prone.
mam

On 3/26/2013 9:24 PM, Matt Newville wrote:

Hi Matthew,

On Tue, 26 Mar 2013, Matthew Marcus wrote:


Just to put my bit in, I believe that the most significant advantage of higher 
FEFF versions for EXAFS analysis is that it results in
more reasonable values for E0 for high-Z elements.  I forget whether the issue 
is high-Z scatterer or absorber.  If you use any of the
common prescriptions for defining E0 with, say, Pt metal in FEFF6l, your fit 
will want large values of enot.  That said, I have not done
a real test by comparing FEFF8 and FEFF6 paths.  Has anyone done that?  It 
would be interesting to know what happens if you simulate a
k^n*chi(k) with one program and fit it with the other.
mam


It's been a very long time since I've tried, but, yes I've made such comparisons in the 
past, as well as comparing Feff6 and Feff8 to the same very good data.

Feff 8 actually has a long history.  Initially, EXAFS was noticeably worse with 
Feff8, but it got better over the years to the point where I think it's hard to 
say that Feff8 is worse than Feff6 for EXAFS.  As you say, E0 is better (though 
still needs refinement), as is S02.  Feff8 also appears that it is better for 
heavy elements (perhaps Z  50, but I'm not sure anyone has looked at that 
carefully).  But: the multi-pole self-energy introduced around Feff8.5 or so can 
make a very large improvement for the EXAFS.  Whether this can be made generally 
applicable is a separate question.

Just to echo some of Bruce's frustration and build on that (and, speaking only 
for myself):  Basically, we're stuck with Feff6 because we do not have access 
to Feff8.  Last I heard, John and Josh were working on this, so that 
Feff8-for-EXAFS would be made freely available.  I haven't seen the code yet, 
but I'm optimistic that it will be released someday.

Once this happens, I'll happily start incorporating this into Larch.  I'd very 
much like to replace the pathfinder (as Bruce has done in Perl for Demeter) so 
that distortions are easier to track, and allow the EXAFS calculation for a 
Path to be done automatically inside the fitting loop.  That will be some real 
work (anyone out there interested in helping?), and could take awhile, but 
could actually make a difference for modeling.

I'm pretty sure that getting the multi-pole self-energies more universally 
useful would be a big help, but I think there still some unknowns there 
(basically -- how well do you have to know the dielectric response for a 
general system?) that have to be worked out.  Getting 1/epsilon for Cu metal is 
one thing (a first step!), but getting it for As sorbed onto ferrihydrite or 
would be more challenging

--Matt
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Re: [Ifeffit] Possible bug in atoms files generation by Artemis

2013-03-27 Thread Matthew Marcus

As I just mentioned to Matt, this conversation is NOT moot because a 
significant fraction of users have bought access.
I wonder if it would be possible to make some sort of 'crippleware' version of 
FEFF(6) which ONLY runs from within DemLarchTemis?
That might make the UW folks a little more comfortable with letting it be 
available.

FEFF9+ will be a harder case because it seems to have been designed to be run 
by the jfeff interface and consists of separate programs
which have to be run in sequence.  I suppose a wrapper could be written to 
orchestrate that.
mam

On 3/27/2013 5:44 AM, Bruce Ravel wrote:

On Tuesday, March 26, 2013 01:21:58 PM Matthew Marcus wrote:

Just to put my bit in, I believe that the most significant advantage of
higher FEFF versions for EXAFS analysis is that it results in more
reasonable values for E0 for high-Z elements.  I forget whether the issue
is high-Z scatterer or absorber.  If you use any of the common
prescriptions for defining E0 with, say, Pt metal in FEFF6l, your fit will
want large values of enot.  That said, I have not done a real test by
comparing FEFF8 and FEFF6 paths.  Has anyone done that?



This is *exactly* my point.  Except, as Matt said, for the rather
limited, unpublished tests made by him and John many years ago, no one
has reported on a substantive test comparing the efficacy of feff6 and
feff8 for analysis of EXAFS.  (Of course, computation of XANES and
other spectroscopies is a different topic entirely.)

Perhaps I would be more interested in fully implementing use of feff8
in my software if someone would offer a better justification than 8
is a bigger number than 6.

FWIW, I agree with Matt that the multi-pole self-energies is a very
promising thing that could have a substantial impact on EXAFS
analysis.  But few of those who claim to want to use feff8 with my
software are actually computing and using the multi-pole
self-energies.

In any case, I do not have permission to redistribute feff8.  So, on a
very real level, this conversation is moot.

B



It would be
interesting to know what happens if you simulate a k^n*chi(k) with one
program and fit it with the other.




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Re: [Ifeffit] How to do with diffraction peak

2012-12-14 Thread Matthew Marcus



On 12/14/2012 4:10 PM, Matt Newville wrote:

Hi Matthew,

On Thu, Dec 13, 2012 at 11:28 PM, Matthew Marcus mamar...@lbl.gov wrote:



You might argue (I would agree) that with multiple measures of
fluorescence you can determine outliers more rigorously.  But I would
also say that then the best thing to do then is to not simply remove
outliers but to take the average AND standard deviation of the samples
and include both in the analysis.  A glitch would then not be removed,
but would be reflected by having a less certain value for that energy
point.



But how do you know what the standard deviation should be for a point you
had to exclude?  I suppose you could
try to come up with some plasuibiity measure which says that it can't be
more different from the results of
interpolation than some amount, a hieuristic measure.  The idea there would
be that you do a best-effort
deglitch and then assign an uncertainty based on how badly you may have done
at it.  This still makes me queasy.
In a typocal case, the glitch dominates over the real signal so you actually
have *no* information about what the signal was
there except for what you know from the surrounding points.  Thus,
attempting to use the glitched-out region is
really an attempted double-use of the surrounding points.  Better to adapt
your methods so that they can deal with
non-uniform tabulation, which you have anyway.


Oh, I meant that for each energy point measured you could use the
different fluorescence channels to compute a mean value for I_f and
standard deviation for I_f, and then propagate both measurement and
uncertainty through the entire analysis.  For a point with a glitch,
the standard deviation would be very high, and so that region of k
space would receive less weight.

I'd view data not measured not as having a value of 0 but having
infinite uncertainty.  In that sense, removing a glitch doesn't do any
harm - we're treating it as if we have no measurement at that energy
point.


If I understand you correctly, you're saying that 'deglitch with reference 
scalers' is OK, but with some additional
error estimate imposed on the points you had to do that to.

I've found no reason to suspect that any artifacts were introduced by this procedure because the 
ratio of the bad to the good
counters is quite slowly-varying except in the glitch region, so interpolation 
is safe.  Therefore, the only extra noise is
shot noise due to counting with fewer elements.  Now, given how non-rigorous 
our treatment of noise is, I think that the
extra noise is not going to influence the fit significantly.

The real problem is what to do when you can't do any kind of signal-based data 
recovery, but have to either
acknowledge that you don't have any data there or make some up and assign some 
sort of uncertainty to your curve-drawing
artistry.





I agree with your larger point that we can definitely afford the CPU
cycles to do better analysis than use something simply because it is
Fast.  I'm not sure that a slow discrete FT would be significantly
different than an FFT, though.  I think (but am listening...) that the
continuous v discrete FT is like classic audiophile snobbery about the
superiority of analog over digital music.  With sufficient sampling
and resolution and dynamic range in the signal, the difference has to
be trivial.  I'm willing to believe that a digital recording has less
dynamic range, but I'm also willing to believe that this is swamped by
my stereo and ears (and I mostly listen to mp3s through cheap
headphones these days, so I clearly am not buying a tube amplifier
anytime soon...).


You're right that the DFT is exactly equivalent to the FFT.  However, the
VSFT is different in that
it works on non-uniformly tabulated data with no interpolation.
I've heard of an AB test in which Golden Ears were challenged with two amps,
one of which was solid-state
and the other also solid-state but with some 2nd-harmonic distortion and (I
think) noise added to simulate
a tube amp.  Guess which won?  Somebody once wrote a parody in which
mercury-filled speaker cables were
advertised for their liquid, shimmering sound, but I digress.


I agree / understand that a VSFT is or can be different from a DFT.
For me the point is that with sufficient sampling and bit depth, the
differences go to zero.  And I think we know how to sample XAFS well
enough.  For digital audio there's a fair argument about bit depth /
dynamic range and whether people can actually detect frequencies about
18KHz.  But there aren't such arguments (yet for EXAFS): no one is
(yet) measuring EXAFS reliably to 50 Ang^-1.


Sampling is exactly the problem - if you have gaps in the data, then you're not 
sampled densely in the
relevant region.  If you assume the data to be band-limited, then you could in 
principle interpolate.  One way to
do that is to do the VSFT and then evaluate the resulting weighted sum of trig 
functions in the bad region.  Unlike DFT,
VSFT defines an inverse

Re: [Ifeffit] How to do with diffraction peak

2012-12-13 Thread Matthew Marcus



You might argue (I would agree) that with multiple measures of
fluorescence you can determine outliers more rigorously.  But I would
also say that then the best thing to do then is to not simply remove
outliers but to take the average AND standard deviation of the samples
and include both in the analysis.  A glitch would then not be removed,
but would be reflected by having a less certain value for that energy


But how do you know what the standard deviation should be for a point you had 
to exclude?  I suppose you could
try to come up with some plasuibiity measure which says that it can't be more 
different from the results of
interpolation than some amount, a hieuristic measure.  The idea there would be 
that you do a best-effort
deglitch and then assign an uncertainty based on how badly you may have done at 
it.  This still makes me queasy.
In a typocal case, the glitch dominates over the real signal so you actually 
have *no* information about what the signal was
there except for what you know from the surrounding points.  Thus, attempting 
to use the glitched-out region is
really an attempted double-use of the surrounding points.  Better to adapt your 
methods so that they can deal with
non-uniform tabulation, which you have anyway.

point.




I agree with your larger point that we can definitely afford the CPU
cycles to do better analysis than use something simply because it is
Fast.  I'm not sure that a slow discrete FT would be significantly
different than an FFT, though.  I think (but am listening...) that the
continuous v discrete FT is like classic audiophile snobbery about the
superiority of analog over digital music.  With sufficient sampling
and resolution and dynamic range in the signal, the difference has to
be trivial.  I'm willing to believe that a digital recording has less
dynamic range, but I'm also willing to believe that this is swamped by
my stereo and ears (and I mostly listen to mp3s through cheap
headphones these days, so I clearly am not buying a tube amplifier
anytime soon...).

You're right that the DFT is exactly equivalent to the FFT.  However, the VSFT 
is different in that
it works on non-uniformly tabulated data with no interpolation.
I've heard of an AB test in which Golden Ears were challenged with two amps, 
one of which was solid-state
and the other also solid-state but with some 2nd-harmonic distortion and (I 
think) noise added to simulate
a tube amp.  Guess which won?  Somebody once wrote a parody in which 
mercury-filled speaker cables were
advertised for their liquid, shimmering sound, but I digress.


But for EXAFS, we know the limits of the signals in k and R (say, 50
Ang^-1 and 25 Ang for extrema), and so can choose samplings that
definitely over-sample enough to not cause significant artifacts.
There can be dynamic range issues (especially with standard
pre-amplifiers and VtoF converters), but I think this is a slightly
separate issue from the glitch problem.


Are you suggesting changes to the methods used to pick points at which to take 
data?  The original discussion
had to do with data which had already been taken.  An example of what you're 
talking about - the QXAS setup on my
beamline scans the mono at a constant angular speed and samples on-the-fly, 
like an on-the-fly fluorescence map
and using the same hardware.  Thus, at the end of the spectrum, to get longer 
dwell times, you have to pick larger
energy steps, which means that you're smearing each point because each point is 
the average over, say, 5eV, rather than
being taken at one enetgy.  However, a simple calculation shows that with 
reasonable stepsizes, you don't lose
anything significant even out to 10A.


Interpolation methods are definitely worth discussing and studying.
I'm not sure that the energy values that happened to have been where
the monochromator was stopped for a measurement of mu(E) are more
sacred or a better sampling of the first shell of an EXAFS spectra
than a set of energies interpolated from those measurements to be on
uniform k grid, provided the the original data isn't woefully
undersampled.  With a typical step size of 0.05Ang^1 you can easily
miss several points and still accurately measure distances up to 5 or
probably even 10 Angstroms.


That's kind of the idea behind the histogram interpolation used in at least 
some FT programs.  Let's say that the
data need to be interpolated on a 0.05A grid, and there happen to be points at 
3.01, 3.03 and 3.04A^-1.  Then,
chi_out(3.00A^-1) = 
(4/5)*chi_in(3.01A^-1)+(2/5)*chi_in(3.03A^-1)+(1/5)*chi_in(3.04A^-1)+ 
contributions from points to the left of 3.00, and
similar for chi_out(3.05A^-1).  If there are no data points between 3.00 and 
3.05, then values are assigned by linear interpolation
from the ones on either side of the 3.00-3.05 interval.

Getting back to the original problem, suppose you have a Bragg glitch whose 
wings go out far enough that you have to lop off the top
of an EXAFS wiggle.  If you try to 

Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus

Here's one last trick that I used to use when I used a plastic scintillator at 
NSLS and didn't have a spinner.  WARNING - this is painful!
I used to tape a piece of Polaroid film to the face of the detector, run 
through a scan, develop the film, see where the white spots
were, and put Pb tape on the detector at those spots.  Told you it was painful! 
 Aside from that, I think Bruce is right - you're screwed
with 1-channel data, especially if the Bragg peaks are broad and/or come in the 
XANES region.  If you have to take data without a spinner or
multi-element detector, the trial-and-error method of changing the sample 
orientation often works to shift the Bragg peaks away from sensitive
parts of the spectrum to where you don't mind too much losing some points.

I have never tried fitting peak shapes to the Bragg peaks (say, a Lorentzian or 
pseudo-Voight plus a smooth polynomial; don't subtract the polynomial).
I suspect that the peak shapes aren't 'nice' enough for that to work reliably.  
The shapes of the tails, for instance, would be influenced by
the angular divergence of the beam onto the sample and into the monochromator 
and any strain.
mam

On 12/12/2012 7:28 AM, Bruce Ravel wrote:

On Tuesday, December 11, 2012 04:08:03 PM Zhaomo Tian wrote:

I got XAFS data for Ag with CO adsorption( using Ag K edge), Ag is thin
film~300nm deposited on Si/SiO2 substrate. But in the original μ(E)
spectra, from 25894-26044eV, four obvious diffraction peaks appear( I
attached the file), and I guess they will influence the quality of fitting.
Is there anyone who knows how to deal with these diffraction peak? Will it
be corrected by smoothing or changing some origin data points in the
original file? I want the modification that will not destroy data analysis
later.


You have received some decent advice on how to post-process your data
to minimize the effect of the diffraction peak.  I think it bears
mentioning that not all prblems are best solved after the fact in
software.  Some problems should be addressed as the data are measured
or even beforehand.

I see from the data file you sent that you were at beamline 10C at
Pohang.  It is hard to tell for certain from the data file or from the
website, but it seems as though you were using a PIPS detector to
measure your fluorescence XAFS.

This is an experimental setup can be a difficult one to combine with a
sample that diffracts.  The sort of PIPS commonly used at an XAS
beamline tends to be of a very large surface area.  That means that
the likelihood of some diffraction peak from the sample hitting the
detector during the measurement is pretty high.  In fact, it happened
4 times for you.  That means you have a lot of data points to
deglitch, were you to follow Kicaj's advice.  Because you used a PIPS
rather than a multi-element detector, you don't have the option of
following any of Matthew's (excellent) advice.

I hate to say it, but I think you are screwed.  The best you can do is
deglitch as best you can.  Because you will be removing so many points
from the data, you will introduce substantial systematic error into
the data set that remains.  I don't really see what you can do about
that at this late date.

So, what might you do the next time you visit the synchrotron to
obtain better data?  In fact, there are number of things that you can
consider at the stages of sample preparation or of data collection.

1. You don't say a lot about the sample or its substrate.  Perhaps you
have a reason that the substrate *must* be crystalline.  Perhaps
not.  Putting your film on an amorphous substrate would obviate the
problem of diffraction from the substrate.  That may be your best
bet.

2. The large size of the PIPS detector is a contributing factor to the
problem.  Simply using a detector with a smaller surface area
reduces (but certainly does not eliminate!) the likelihood of
diffraction peaks hiiting it.  Moving the detector farther away
from the sample would serve the same purpose.  Of course, doing so
would also serve to reduce your count rate, thus reducing the
quality of your data.  There is a cost to everything!

3. Use the 13 element Ge detector instead of the PIPS.  Then you can
simply eliminate channels hit by Bragg peaks or do the
post-processing trick Matthew described.

4. At my beamline, we have users almost every cycle who measure stuff
on crystalline substrates.  Our favorite trick is to mount the
sample on a spinner (e.g. http://dx.doi.org/10.1063/1.1147815) At
my beamline, we actually attach the sample the sort of small DC fan
that is used to cool electronics.  Inexpensive, simple, and
effective!  By keeping the sample constantly in motion, the energy
at which the Bragg condition is met is constantly changing.  This
serves to reduce the effect of the Bragg peak by a few orders of
magnitude by spreading it out in energy.  Usually, it can be made
smaller than 

Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus

I agree about the first point, but what's done is done and the user who started 
this discussion has data which he needs to do something with.

What's Larch?

Why can't ifeffit do what I suggest?  Is it because it uses an algorithm which 
requires uniform tabulation?

One issue with my proposal - post-edge background subtraction (and even 
pre-edge if the Braggie comes at the wrong place) could
be corrupted by gaps in the data.  Imagine if a spline knot falls in a wide gap.

An example of an effect similar to Bragg peaks but not fixable by screwing with 
data acquisition - 2-electron peaks in
ekements like Ce.  For those, you just have to subtract the peaks, but 
fortunately there is literature on how to do that.
mam

On 12/12/2012 3:06 PM, Bruce Ravel wrote:

On Wednesday, December 12, 2012 03:00:41 PM Matthew Marcus wrote:

Hmm.  Another possible way to do it is to delete the bad data points and
then do a slow FT, which would be a fit of  the data, at the points given
with no interpolation, to a sum of sines and cosines.  This would have the
nice feature of using the data as it is and ignoring the bad
stuff.  Filtering would involve multiplying  the sines and cosines by some
window function (in R space) and evaluating them *at the given k-points*,
not on a regular grid.  This of course means that evaluating FEFF paths and
the like is likely to be slow because you don't get to use recursion
relations to evaluate sin(2*R*k(i)+delta) as you would if k(i) are
uniformly tabulated.  Now that computers are a bazillion times faster than
they were when EXAFS analysis traditions were established, maybe that's the
way to go.  What do you think?


I think data should be measured correctly in the first place if at all
possible!  ;)

That said, your suggestion seems completely valid to me.  And, just to
be clear, it's completely impossible with Ifeffit.  Larch, on the
other hand

B



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Re: [Ifeffit] How to do with diffraction peak

2012-12-12 Thread Matthew Marcus



On 12/12/2012 8:03 PM, Matt Newville wrote:

Hi Matthew, Bruce, All,

Sorry for not being able to join this discussion earlier.  I agree
that having glitch-free data is preferred. But I also think it's OK to
simply remove diffraction peaks from XAFS data -- you're just
asserting that you know those values are not good measurements of
mu(E).  I don't see it as all that different from removing obvious
outliers from fluorescence channels from a multi-element detector --
though that has the appeal of keeping good measurements at a
particular energy.


That's kind of my point.  The standard methods, which require uniform 
tabulation, cause you to fill gaps in data by interpolation.
Effectively, you're claiming knowledge of data for which you don't have 
knowledge.  Better to use a method which preserves
agnosticism about the bad data.  The method I described for deglitching with 
reference scalers tries to preserve what information
you do have by allowing you to ignore some channels.  That only works if there 
are 'good' channels to serve as references.






I'm not sure that slow FT versus discrete FT is that important
here, though perhaps I'm missing your meaning.My vies is that The
EXAFS signal is band-limited (finite k range due to F(k) and 1/k, and
finite R range due to F(k), lambda(k),  and 1/R^2), so  that sampling
on reasonably fine grids is going to preserve all the information that
is really there.


Again, FFT requires a uniform tabulation of data in k-space, which is generally 
secured by interpolation.  Traditionally, this has
been histogram interpolation, which tries to take into account the possibility 
of having multiple data points within one of the new
intervals in k.  That method, however, has to 'make up' data when there isn't 
any in one or more intervals.

Actually, there are three possible tiers of speed.  There's FFT, there's 
discrete FT done the slow way by computing the sums as
they appear in the textbook (possibly good if you want a funny grid in R 
space), and then there's what I propose.


I do think that having richer window functions and spectral weightings
would be very useful.   You could view chi(k) data with glitches ias
wanting a window function that had a very small value (possibly zero:
remove this point) exactly at the glitch, but had a large value (~1)
at nearby k-values.

Another (and possibly best) approach is to assign an uncertainty to
each k value of chi.  At the glitch, the uncertainty needs to go way
up, so that not matching that point does not harm the overall fit.


A window function which went to 0 in the glitch region is tantamount to an 
assertion that chi(k)=0 there, which is generally not so
and is probably a lot worse than the error you make by even the lamest 
interpolation through the glitch.  The uncertainty makes more
sense, except that if you filter data, the noise spreads out in a correlated 
manner over adjacent regions.  Also, the tacit assumption
of an uncertainty-based method is that the noise is uncorrelated within the 
high-uncertainty region.  That said, I can imagine that
this is one of those methods that works better than it has any right to.

Now, in my proposed system, how would you fit filtered (q-space) data?  The 
first step is to do the very slow FT (VSFT) on the input
data with no interpolation.  This leads to a set of sines and cosines which 
replicate the data.  I would then apply the window and
do the back-summation of all those sines and cosines at the given points.  This 
will undoubtedly introduce some artifacts near
the edges of the deleted regions simply due to our ignorance of what the data 
really do in there.  Next, in each fit iteration, I would
evaluate the model function at each point, then do the VSFT and filtering 
exactly as had been done on the data, which causes the fit to
have the same artifacts.  Since the VSFT and filter operations are linear, it 
should be possible to pre-compute a kernel which relates the
values of unfiltered data to those of filtered data.  This would be a matrix of 
size Np*Np with Np=# of points.  Using the kernel instead
of evaluating gazillions of trig functions would be reasonably fast; I suspect 
that ifeffit does a similar trick.  Similarly, fitting in
R-space would be accomplished by computing the VSFT on data and model function.

Yes, I know I talk a good game.  Unfortunately, I'm too swamped to attempt 
implementation.  Also, I'd have to reinvent a number of
very well-engineered wheels to do it.


Larch has a separate Transform class used for each dataset in a fit -
this includes the standard FT parameters and fit ranges.  It is
intended to be able to do this sort of advanced windowing (and in
principle, advanced weighting too).  Currently (I'd be ready for a
release but am commissioning our new beamline and am hoping to post a
windows installer by the end of the month)  this has the standard
XAFS window functions, but one can create their own window functions
(for k- and/or 

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