Re: [Ifeffit] Fitting mechanism of Artemis

[Matt Newville]

Hi Konstantin,



On Fri, Oct 6, 2023 at 3:11 AM  wrote:

> Dear all,
> I have a general question regarding the mechanism employed in the fitting
> procedures implemented in Artemis.
> How exactly is performed a fit?



That is a pretty open-ended question to be able to answer with precision.
Is the question more about how fitting works in general, or about what is
modeled and allowed to change in the mode for EXAFS?

There are plenty of writeups and resources on both topics, including
program documentation.

Do we have a fixed central atom (absorbing/emitting atom) and only the
> distances to the
> neighbors included in the probed pathways are varied, i.e. by varying the
> coordinates of the corresponding neighbor atoms, or during
> the fitting process Artemis can vary the position of the absorption center
> too?



Within the context of the software here, the answer is sort of that the
central atom is fixed.

The way we model EXAFS is effectively (more below,  as some might object to
this) as a 1-dimensional problem.  Single scattering EXAFS depends only on
the scalar distance between the atoms (or path length for the
photo-electron).  Now, some aspects of EXAFS scattering definitely depend
on more than just distance.  The Z of the scattering atom definitely has a
large effect. The angle of the X-ray polarization vector with the
three-dimensional bond direction can also have an effect.   These are
folded into the scattering amplitude and phase shift.   But even the
disorder terms, sigma^2, and so on, are really capturing the disorder in R,
not the 3-D disorder.

For sure, multiple-scattering paths will have 3D information baked into
them. With Feff and the way we use it, this 3D info *is* folded into the
scattering amplitudes and phase shifts calculated for a path and all we
really vary is the distribution of path lengths for those paths.

In 1-D, it does not matter whether the absorber or scatterer moves, the
only thing that matters is the distance.  In fact, to the extent that
neighboring atoms move together in the same direction, there is no effect
on the EXAFS -- an atom in a solution or melt will have EXAFS (it might be
weak, but it does not fall to 0 at a phase transition).  EXAFS is much more
sensitive to "optical phonons" (neighboring atoms moving in opposite
direction) than to "acoustic phonons" (neighboring atoms moving in the same
direction).

Now, one can take a reverse-monte-carlo approach: calculate a lot of
different local structures, sum the EXAFS for each calculation, and see
which is best.   One can also do something sort of in-between:  calculate a
set of "undistorted paths" and one or more sets of "distorted paths" and
then do a linear (or for some multiple-scattering case, quadratic) model to
combine these.


Could the procedure be constrained in such a way that the scattering
> pathways are adjusted by only varying the coordinates of the central atom?
>

Yes. In fact, this has been done several times.  If you imagine a metal ion
(let's say Ti) surrounded by six neighbors (let's say O) in an octahedron,
a common thing to try to model is if that Ti atom moves away from the
center of the octahedron, say in a perovskite-like structure.

For the simplest case (ie, what I would start with ;)), you could calculate
the EXAFS with Ti at the center of a perfect octahedron and get 6
equivalent paths, and add those to give the EXAFS.  If the octahedron is
distorted, you might have 2, 3, 4, or 6 paths.  Let's go all the way to
"general" 6 paths.   Each path would use a different Feff calculation (or a
copy).  You would not be limited to varying the change in each of the six
path lengths (our 'delr' parameter) to have the same delr for all paths.
Instead, you could define 3 new fitting variables, let's say "dx", "dy",
and "dz" for the displacement of the absorbing Ti from the position used in
the Feff calculation (let's just call that "origin").

If you only have "dz", then one path gets shorter by dz, one gets longer by
dz, and the other four get longer by sqrt(reff*2 + dz**2), where "reff" is
the magic "R used for each path Feff calculation.   I'll leave the more
general case for you ;).

Hope that gets you started,

--Matt
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Re: [Ifeffit] Fitting mechanism of Artemis

[Edmund Welter]

Dear Konstantin,

why would you want to do that? If you change the distance between A-B 
you the distance between B-A changes by the same amount. If you move the 
absorber away from let's say the centre of an octaeder you would split 
the (next) nearest neighbours shell into different shells with different 
distances. If the differences are large enough and the resolution of 
your EXAFS spectrum sufficient you would see more than one (first 
neighbours) peak in the FT of your EXAFS spectrum. But that would be 
another model that you would feed into FEFF before you start your second 
fit. Technically you would fneed to define the position of all atoms in 
your model in world-coordinates. So the absorber would no longer be at 
0,0,0. I would guess that this would make the computation and the model 
more complex or at least less intuitive.


Best regards,

Edmund


On 06.10.23 10:09, bi...@phys.uni-sofia.bg wrote:

Dear all,
I have a general question regarding the mechanism employed in the fitting
procedures implemented in Artemis.
How exactly is performed a fit? Do we have a fixed
central atom (absorbing/emitting atom) and only the distances to the
neighbors included in the probed pathways are varied, i.e. by varying the
coordinates of the corresponding neighbor atoms, or during
the fitting process Artemis can vary the position of the absorption center
too? Could the procedure be constrained in such a way that the scattering
pathways are adjusted by only varying the coordinates of the central atom?

With kind regards,
Konstantin Bikov
PhD Student at the Physics Department
of the University of Sofia, Bulgaria

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[Ifeffit] Fitting mechanism of Artemis

[bikov]

Dear all,
I have a general question regarding the mechanism employed in the fitting
procedures implemented in Artemis.
How exactly is performed a fit? Do we have a fixed
central atom (absorbing/emitting atom) and only the distances to the
neighbors included in the probed pathways are varied, i.e. by varying the
coordinates of the corresponding neighbor atoms, or during
the fitting process Artemis can vary the position of the absorption center
too? Could the procedure be constrained in such a way that the scattering
pathways are adjusted by only varying the coordinates of the central atom?

With kind regards,
Konstantin Bikov
PhD Student at the Physics Department
of the University of Sofia, Bulgaria

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Re: [Ifeffit] Fitting multiple spectra simultaneously with Larch

[Matt Newville]

Hi Casey,


Sorry for the late reply - I see that you asked this question 2 weeks ago
- I think I got the same question from someone else by private email the
same day  I have had this question several times this summer.  Anyway,
sorry for missing this.

Larch can definitely fit multiple spectra at one time, co-refining
parameters.   An example of fitting 3 datasets (Cu K edge at 3
temperatures) is at

https://github.com/xraypy/xraylarch/blob/master/examples/feffit/doc_feffit3.lar

That is, you create several "Feffit datasets".  Each of these has a group
for the chi(k) data, a "transform" that gives the Fourier (or Wavelet)
Transform configuration and the fitting ranges, and a list of Feff Paths.

Different data sets can use the same transform and reuse Feff Paths. You
will also have a Parameter Group with all the variables and other
Parameters used to calculate the Path Parameters for each Feff Path.
Anyway, yes, Larch can definitely fit multiple datasets.

But: The XAS Viewer GUI does not currently (yet?) support this -- it helps
build a model, do the fit, and inspect the results for one dataset.  It
also helps write out the larch script to do the fit.  One approach could be
to use that:  use the GUI for "simple stuff" and interactive data
exploration, but use a script for more complicated and involved analyses.

I'm not opposed to adding fitting of multiple data sets in the XAS Viewer
GUI, but implementing it in the current GUI framework seems challenging (it
was definitely challenging for Artemis too).   I've heard some good
suggestions, but I'd be curious to hear (either here or via private email)
what others would like to see or suggest.

I guess that question really extends to other aspects of Larch and XAS
Viewer: if there are features, analysis approaches, or GUI tools that you
think could be better, let me know.

On Mon, Sep 12, 2022 at 11:30 AM Van Stappen, Casey M <
casey.vanstap...@austin.utexas.edu> wrote:

> Dear Ifeffit team,
>
>
>
> I’d like to fit multiple EXAFS spectra simultaneously in Larch using
> several common parameters/relative restraints, but have not found a way to
> do so (yet). I’ve gone through Dr. Matt Newville’s youtube tutorials
> (generally very helpful), but this topic doesn’t seem to have been covered.
> Any suggestions? Thanks!
>
>
>
> Best,
>
>
>
> Casey Van Stappen
>
>
>
> 
>
> Dr. Casey Van Stappen
>
> University of Texas at Austin
>
> Robert A. Welch Hall, 4.318
>
> 2350 Speedway
>
> Austin, TX 78705
>
> USA
>
>
>
> Phone: +1 (512) 775-2658
>
> E-mail: casey.vanstap...@austin.utexas.edu
>
>
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-- 
--Matt Newville  630-327-7411
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Re: [Ifeffit] Fitting multiple spectra simultaneously with Larch

[Andy Zhang]

Hi Casey,

You can find some examples on the webpage
https://xraypy.github.io/xraylarch/xafs_feffit.html#example-1-simple-fit-with-1-path
.

Have a nice evening!

Best,
Harry

--
Harry Zhang
Eindhoven University of Technology
5612 AZ, Eindhoven, The Netherlands



On Mon, Sep 12, 2022 at 6:30 PM Van Stappen, Casey M <
casey.vanstap...@austin.utexas.edu> wrote:

> Dear Ifeffit team,
>
>
>
> I’d like to fit multiple EXAFS spectra simultaneously in Larch using
> several common parameters/relative restraints, but have not found a way to
> do so (yet). I’ve gone through Dr. Matt Newville’s youtube tutorials
> (generally very helpful), but this topic doesn’t seem to have been covered.
> Any suggestions? Thanks!
>
>
>
> Best,
>
>
>
> Casey Van Stappen
>
>
>
> 
>
> Dr. Casey Van Stappen
>
> University of Texas at Austin
>
> Robert A. Welch Hall, 4.318
>
> 2350 Speedway
>
> Austin, TX 78705
>
> USA
>
>
>
> Phone: +1 (512) 775-2658
>
> E-mail: casey.vanstap...@austin.utexas.edu
>
>
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[Ifeffit] Fitting multiple spectra simultaneously with Larch

[Van Stappen, Casey M]

Dear Ifeffit team,

I’d like to fit multiple EXAFS spectra simultaneously in Larch using several 
common parameters/relative restraints, but have not found a way to do so (yet). 
I’ve gone through Dr. Matt Newville’s youtube tutorials (generally very 
helpful), but this topic doesn’t seem to have been covered. Any suggestions? 
Thanks!

Best,

Casey Van Stappen


Dr. Casey Van Stappen
University of Texas at Austin
Robert A. Welch Hall, 4.318
2350 Speedway
Austin, TX 78705
USA

Phone: +1 (512) 775-2658
E-mail: casey.vanstap...@austin.utexas.edu

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Re: [Ifeffit] Fitting in Wavelet transform space ?

[Matt Newville]

Hi Samy,

On Wed, Jul 10, 2019 at 2:08 AM Samy Ould-Chikh 
wrote:

> Dear colleagues,
>
> I have been using more and more wavelet transform in parallel of EXAFS
> fitting.
> In addition of the statistical parameters provided after the fit, I try
> also to compare the wavelet transform of experimental data against various
> structural models to choose the best.
> Absolutely nothing new here.
>
> After applying the wavelet transform to tens of structural model in a row
> which was bit long, I asked myself this question:
> Why can't we simply fit the experimental spectra in "wavelet space"
> instead of R space/k-space ?
> Does someone know about a code already doing it ?
>

Yes, Larch supports fitting in (Cauchy) wavelet space.  Basically, you set
the fitting space to 'w'  and specify the k- and R-ranges for the transform:

trans = feffit_transform(fitspace='w', rmin=1.2, rmax=3.0, kmin=2.5,
kmax=15, kweight=2, dk=5, windows='kaiser') . # wavelet

dataset = feffit_dataset(data=my_datagroup, pathlist=[path1, path2],
transform=trans)

result = feffit(parameters, dataset)

For example, see
https://github.com/xraypy/xraylarch/blob/master/examples/feffit/doc_feffit_wavelet_fit.lar


>
> Best Regards,
> Samy Ould-Chikh
>
> KAUST Catalysis Center
> Bldg.3,Level 4, #4231
> 4700 King Abdullah University of Science & Technology
> Thuwal 23955-6900
> Kingdom of Saudi Arabia
>
> Tel: +966 12 8084486
> E-mail: samy.ouldch...@kaust.edu.sa
> Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx
>
>
>
>
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--Matt
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[Ifeffit] Fitting in Wavelet transform space ?

[Samy Ould-Chikh]

Dear colleagues,

I have been using more and more wavelet transform in parallel of EXAFS fitting.
In addition of the statistical parameters provided after the fit, I try also to 
compare the wavelet transform of experimental data against various structural 
models to choose the best.
Absolutely nothing new here.

After applying the wavelet transform to tens of structural model in a row which 
was bit long, I asked myself this question:
Why can't we simply fit the experimental spectra in "wavelet space" instead of 
R space/k-space ?
Does someone know about a code already doing it ?


Best Regards,
Samy Ould-Chikh
 
KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia
 
Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx




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Re: [Ifeffit] Fitting Problems in Artemis version 0.9.26

[Scott Calvin]

Dear Huan,

Neither of those sound like a flaw in Artemis to me. 

1) Fitting with a range that goes below Rbkg means fitting to a part of the 
data’s Fourier transform that has been suppressed by background subtraction, 
even though the theory’s Fourier transform has not been similarly suppressed. 
That will yield a misleading fit. If the newer version of Artemis does a check 
to prevent this, that’s actually an improvement.

2) This could always happen—you may just not happen to have seen it before. 
Using abs() doesn’t make the variable you are fitting positive; it makes the 
result which is used in the fit (the “path parameter”) positive. So if, for 
example, Artemis reports ss1 = -0.002, that means it used +0.002 in the fit.

Best,
Scott Calvin

> On Jun 28, 2018, at 10:03 PM, LIU HUAN  wrote:
> 
> Dear Dr. Ravel,
> 
> I want to ask you that when I use the new version "Artemis 0.9.26" I have two 
> problems. (1) The fitting Range was reported to be a error that the Rmin 
> should be larger than the Rkbg value. It makes that the fitting range cannot 
> be smaller than 0.9 (the Rkbg value is 0.9). (2) When Fitting the 
> Debye–Waller factor  (ss) and coordination number (N), although I use "abs()" 
> to make it to be positive, but the fitting results still be negative. But I 
> did not meet these problems in the old version in Artemis 0.8.012. I am 
> wondering that whether could you tell me how to solve these problems. Thank 
> you so much.
> 
> Sincerely,
> Huan
> 
> Huan Liu
> School of  Earth Sciences and Engineering 
> Nanjing University 
> 163 Xianlin Road, Nanjing, Jiangsu, 210023 
> P. R. China
> 
> Tel  86-15861809073
> Email: huanliu_ea...@hotmail.com 
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[Ifeffit] Fitting Problems in Artemis version 0.9.26

[LIU HUAN]

Dear Dr. Ravel,


I want to ask you that when I use the new version "Artemis 0.9.26" I have two 
problems. (1) The fitting Range was reported to be a error that the Rmin should 
be larger than the Rkbg value. It makes that the fitting range cannot be 
smaller than 0.9 (the Rkbg value is 0.9). (2) When Fitting the Debye�CWaller 
factor  (ss) and coordination number (N), although I use "abs()" to make it to 
be positive, but the fitting results still be negative. But I did not meet 
these problems in the old version in Artemis 0.8.012. I am wondering that 
whether could you tell me how to solve these problems. Thank you so much.


Sincerely,

Huan


Huan Liu
School of  Earth Sciences and Engineering
Nanjing University
163 Xianlin Road, Nanjing, Jiangsu, 210023
P. R. China

Tel  86-15861809073
Email: huanliu_ea...@hotmail.com
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Re: [Ifeffit] Fitting sorption EXAFS data in Artemis

[Gemma Woodward [ee11glw]]

Thanks a lot!

Gemma Woodward

PhD Student
Cohen Geochemistry
Earth Surface Science Institute
School of Earth and Environment
University of Leeds
Leeds LS2 9JT

Telephone: +44 (0)113 34 33647
Twitter: @glw_93<https://twitter.com/glw_93>
Website: http://www.see.leeds.ac.uk/people/g.woodward

From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of 
Alexey Boubnov
Sent: 08 February 2017 12:49
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Fitting sorption EXAFS data in Artemis

Dear Gemma,

you indeed want a feff-input with a central Co on/in a kaolinite matrix. You 
should define the location of the Co ion - the simplest assumptions would be 
substitution of an Al or Si.

Import the cif and run ATOMS to create the kaolinite structure. Then replace 
either Al or Si with Co (index 0) in the atom list and change the atom with 
index 0 to Co with its atomic number. Then run FEFF and do the fitting!

Before running FEFF, control the atoms list and visualise your structure in a 
molecular program (e.g. Mercury) to make sure that the structure is as you 
wanted - Artemis sometimes builds the structures incorrectly. To export an atom 
list in .xyz format, Theory --> FEFF --> write special output --> xyz, save the 
list as a .xyz text file and open it in e.g. Mercury. If you get errors, try 
another cif file of kaolinite.

All the best!
Alexey

2017-02-08 12:18 GMT+01:00 Gemma Woodward [ee11glw] 
mailto:ee11...@leeds.ac.uk>>:
Hi all

I have EXAFS data for Co sorbed to kaolinite and want to fit this using 
artemis. I have a kaolinite cif file but am unsure where to go from here to 
include the Co so I get Co-Al/Si pathways. In the atoms window do I add a Co 
into the table at the bottom and make it the core atom?

Thanks

Gemma Woodward

PhD Student
Cohen Geochemistry
Earth Surface Science Institute
School of Earth and Environment
University of Leeds
Leeds LS2 9JT

Telephone: +44 (0)113 34 33647
Twitter: @glw_93
Website: http://www.see.leeds.ac.uk/people/g.woodward



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Re: [Ifeffit] Fitting sorption EXAFS data in Artemis

[Alexey Boubnov]

Dear Gemma,

you indeed want a feff-input with a central Co on/in a kaolinite matrix.
You should define the location of the Co ion - the simplest assumptions
would be substitution of an Al or Si.

Import the cif and run ATOMS to create the kaolinite structure. Then
replace either Al or Si with Co (index 0) in the atom list and change the
atom with index 0 to Co with its atomic number. Then run FEFF and do the
fitting!

Before running FEFF, control the atoms list and visualise your structure in
a molecular program (e.g. Mercury) to make sure that the structure is as
you wanted - Artemis sometimes builds the structures incorrectly. To export
an atom list in .xyz format, Theory --> FEFF --> write special output -->
xyz, save the list as a .xyz text file and open it in e.g. Mercury. If you
get errors, try another cif file of kaolinite.

All the best!
Alexey

2017-02-08 12:18 GMT+01:00 Gemma Woodward [ee11glw] :

> Hi all
>
> I have EXAFS data for Co sorbed to kaolinite and want to fit this using
> artemis. I have a kaolinite cif file but am unsure where to go from here to
> include the Co so I get Co-Al/Si pathways. In the atoms window do I add a
> Co into the table at the bottom and make it the core atom?
>
> Thanks
>
> Gemma Woodward
>
> PhD Student
> Cohen Geochemistry
> Earth Surface Science Institute
> School of Earth and Environment
> University of Leeds
> Leeds LS2 9JT
>
> Telephone: +44 (0)113 34 33647
> Twitter: @glw_93
> Website: http://www.see.leeds.ac.uk/people/g.woodward
>
>
>
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[Ifeffit] Fitting sorption EXAFS data in Artemis

[Gemma Woodward [ee11glw]]

Hi all

I have EXAFS data for Co sorbed to kaolinite and want to fit this using 
artemis. I have a kaolinite cif file but am unsure where to go from here to 
include the Co so I get Co-Al/Si pathways. In the atoms window do I add a Co 
into the table at the bottom and make it the core atom?

Thanks

Gemma Woodward 

PhD Student
Cohen Geochemistry
Earth Surface Science Institute
School of Earth and Environment
University of Leeds
Leeds LS2 9JT

Telephone: +44 (0)113 34 33647
Twitter: @glw_93
Website: http://www.see.leeds.ac.uk/people/g.woodward



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Re: [Ifeffit] fitting of S XANES with arctans and gaussians

[Matt Newville]

On Tue, Jul 19, 2016 at 6:38 AM, Jon Wade  wrote:

>
> I can’t recommend  LMFIT in python enough  (or Larch - never used it mind,
> but see no reason why I haven’t).
>
> Its well documented, easy to use and, best of all, its FREE!  :)
>
>
> https://lmfit.github.io/lmfit-py/builtin_models.html#builtin-models-chapter
>
> https://lmfit.github.io/lmfit-py/builtin_models.html#example-3-fitting-multiple-peaks-and-using-prefixes
>
>
> all the best
>
> Jon
>
>
There are (IMHO) pretty good peak fitting methods in Larch, and a GUI for
fitting XANES with Larch and LMFIT is actually a top priority for me. It's
in progress (I was working on it some yesterday), but not yet fully
working.  This will allow features like constraining multiple peaks to have
the same widths, etc.

Feature requests, suggestions, or help are most welcome.

--Matt
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Re: [Ifeffit] fitting of S XANES with arctans and gaussians

[Jon Wade]

I can’t recommend  LMFIT in python enough  (or Larch - never used it mind, but 
see no reason why I haven’t).

Its well documented, easy to use and, best of all, its FREE!  :)


https://lmfit.github.io/lmfit-py/builtin_models.html#builtin-models-chapter
https://lmfit.github.io/lmfit-py/builtin_models.html#example-3-fitting-multiple-peaks-and-using-prefixes


all the best

Jon



On 19 Jul 2016, at 14:26, Robert Gordon 
mailto:ragor...@alumni.sfu.ca>> wrote:

Hi Matthew,

WinXAS, (Commercial program by Thorsten Ressler) does possess the capabilities 
you are seeking
but it costs E$200 for an academic/gov't license.

-R.



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Re: [Ifeffit] fitting of S XANES with arctans and gaussians

[Robert Gordon]

Hi Matthew,

WinXAS, (Commercial program by Thorsten Ressler) does possess the 
capabilities you are seeking

but it costs E$200 for an academic/gov't license.

-R.

On 7/19/2016 5:21 AM, Bruce Ravel wrote:

On 07/18/2016 11:10 PM, Matthew Marcus wrote:

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?


Matthew,

As for the pre-normalized data, you are supposed to be able to tell 
Athena at the time of import that the data are normalized mu(E).


http://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units 



If that doesn't work, let me know.

As for constraints in the peak fitting, that is certainly not 
implemented in Athena.  I am not quite sure why Alain thinks otherwise.


HTH,
B





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Re: [Ifeffit] fitting of S XANES with arctans and gaussians

[Bruce Ravel]

On 07/18/2016 11:10 PM, Matthew Marcus wrote:

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?


Matthew,

As for the pre-normalized data, you are supposed to be able to tell 
Athena at the time of import that the data are normalized mu(E).


http://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units

If that doesn't work, let me know.

As for constraints in the peak fitting, that is certainly not 
implemented in Athena.  I am not quite sure why Alain thinks otherwise.


HTH,
B



--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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[Ifeffit] fitting of S XANES with arctans and gaussians

[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&Nagy 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   0.

Re: [Ifeffit] Fitting parameters corrleations between variables

[Matt Newville]

Hi Pushkar,


On Mon, Nov 23, 2015 at 11:28 PM, pushkar shejwalkar <
pshejwalkar2...@gmail.com> wrote:

> Dear Matt,
>   Thank you very much for your response. One more question. What value of
> corelation is acceptable/publishable?
>

A correlation > 0.999 is probably an indication of duplicate parameters in
a model, but it's common to publish parameters (say, N and sigma2 or E0 and
R) that are correlated by more than 0.9.   The correlation simply measures
the amount by which a parameters best-fit value would change if another
parameter was changed away from its best-fit value.   The uncertainties
take these correlations into account.


> also having a correlation number means the fit is not finished and I
> should change the values of variable that are correlated? is that so?
>

No.  The fit is (or "can be") finished.  The reported best-fit values are
really the best values found, and the reported uncertainties are those that
increase the best chi-square by reduced chi-square, taking into account the
correlation.The correlation does not indicate a bad model or a bad fit,
it's just a consequence of the complex model and limited data for XAFS.

Hope that helps,

--Matt
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Re: [Ifeffit] Fitting parameters corrleations between variables

[pushkar shejwalkar]

Dear Matt,
  Thank you very much for your response. One more question. What value of
corelation is acceptable/publishable? also having a correlation number
means the fit is not finished and I should change the values of variable
that are correlated? is that so?
Best
Pushkar

On Tue, Nov 24, 2015 at 1:48 PM, Matt Newville 
wrote:

> Pushkar,
>
> On Mon, Nov 23, 2015 at 8:59 PM, pushkar shejwalkar <
> pshejwalkar2...@gmail.com> wrote:
>
>> Dear All,
>> I am trying to fit in Pd compound and the fit that I obtained looks
>> kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These
>> standards were collected and fitted simultaneously and I got the SO2 value
>> there as 0.67 with Pd foil coordination number as 12 which is correct when
>> considered Pd foil CN. Next while fitting the actual sample (unknown) I
>> used the formula in SO2 column as amp*N1 and put amp as 0.67 and N as 1. I
>> kept N1 as variable (Guess). same I did for the second shell of Pd-O with
>> N2. amp is kept on SET value of 0.67. After fitting I received the N1 and
>> N2 value as 5.6 (0.5) and 1.6 (0.7) (roughly). however, when I checked the
>> correlations between the variables I got the values as given in the log
>> file attached. I saw there is some correlation between bkg01_01 and N2 and
>> many such correlations between bkg values. I have so far never seen such
>> correlations. What are the implications of these correlations? does this
>> means that my fitting assumptions are incorrect. does correlations values
>> in negative indicates something?
>>
>
> Correlation between two variables A and B means that if you changed one
> variable (A) away from its best-fit value, you could improve that fit by
> changing the other variable (B).  In fact the correlation tells you by how
> much, and (from the sign) in what direction that change would be.
>
> A correlation of 0 means that if one changed A, B would not need to change
> at all. A correlation of 1 would mean that a change in A by 1 standard
> error (the reported error), B would have to change by 1 standard error.
> And, again, the sign gives the direction of that change.
>
> Having correlated values does not mean that your assumptions are incorrect.
>
> Thank you very much for the input. By the way my RBKG is 1.2 in athena and
>> I used this same file for fitting purpose and on artemis I used rmin 1.2
>> and rmax 3.4. All these information are in log file attached
>> Any help in understanding this is appreciated.
>>
>> --
>> Best Regards,
>> Pushkar Shejwalkar.
>> Post-doctoral -Researcher,
>> Tokyo Engineering University,
>> Tokyo-to
>> Japan
>>
>>
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>>
>
> --Matt
>
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>


-- 
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,
Tokyo Engineering University,
Tokyo-to
Japan
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Re: [Ifeffit] Fitting parameters corrleations between variables

[Matt Newville]

Pushkar,

On Mon, Nov 23, 2015 at 8:59 PM, pushkar shejwalkar <
pshejwalkar2...@gmail.com> wrote:

> Dear All,
> I am trying to fit in Pd compound and the fit that I obtained looks
> kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These
> standards were collected and fitted simultaneously and I got the SO2 value
> there as 0.67 with Pd foil coordination number as 12 which is correct when
> considered Pd foil CN. Next while fitting the actual sample (unknown) I
> used the formula in SO2 column as amp*N1 and put amp as 0.67 and N as 1. I
> kept N1 as variable (Guess). same I did for the second shell of Pd-O with
> N2. amp is kept on SET value of 0.67. After fitting I received the N1 and
> N2 value as 5.6 (0.5) and 1.6 (0.7) (roughly). however, when I checked the
> correlations between the variables I got the values as given in the log
> file attached. I saw there is some correlation between bkg01_01 and N2 and
> many such correlations between bkg values. I have so far never seen such
> correlations. What are the implications of these correlations? does this
> means that my fitting assumptions are incorrect. does correlations values
> in negative indicates something?
>

Correlation between two variables A and B means that if you changed one
variable (A) away from its best-fit value, you could improve that fit by
changing the other variable (B).  In fact the correlation tells you by how
much, and (from the sign) in what direction that change would be.

A correlation of 0 means that if one changed A, B would not need to change
at all. A correlation of 1 would mean that a change in A by 1 standard
error (the reported error), B would have to change by 1 standard error.
And, again, the sign gives the direction of that change.

Having correlated values does not mean that your assumptions are incorrect.

Thank you very much for the input. By the way my RBKG is 1.2 in athena and
> I used this same file for fitting purpose and on artemis I used rmin 1.2
> and rmax 3.4. All these information are in log file attached
> Any help in understanding this is appreciated.
>
> --
> Best Regards,
> Pushkar Shejwalkar.
> Post-doctoral -Researcher,
> Tokyo Engineering University,
> Tokyo-to
> Japan
>
>
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>

--Matt
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[Ifeffit] Fitting parameters corrleations between variables

[pushkar shejwalkar]

Dear All,
I am trying to fit in Pd compound and the fit that I obtained looks
kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These
standards were collected and fitted simultaneously and I got the SO2 value
there as 0.67 with Pd foil coordination number as 12 which is correct when
considered Pd foil CN. Next while fitting the actual sample (unknown) I
used the formula in SO2 column as amp*N1 and put amp as 0.67 and N as 1. I
kept N1 as variable (Guess). same I did for the second shell of Pd-O with
N2. amp is kept on SET value of 0.67. After fitting I received the N1 and
N2 value as 5.6 (0.5) and 1.6 (0.7) (roughly). however, when I checked the
correlations between the variables I got the values as given in the log
file attached. I saw there is some correlation between bkg01_01 and N2 and
many such correlations between bkg values. I have so far never seen such
correlations. What are the implications of these correlations? does this
means that my fitting assumptions are incorrect. does correlations values
in negative indicates something?
Thank you very much for the input. By the way my RBKG is 1.2 in athena and
I used this same file for fitting purpose and on artemis I used rmin 1.2
and rmax 3.4. All these information are in log file attached
Any help in understanding this is appreciated.

-- 
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,
Tokyo Engineering University,
Tokyo-to
Japan


Pd and O of PdOAc2 fitting using different fitting parameters	and N1N2 values.log
Description: Binary data
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Re: [Ifeffit] fitting mixture

[Bruce Ravel]

On 10/05/2014 10:42 AM, kaziz sameh wrote:

hi,
i want to fit Pd2Au36 in KPd edge with artemis. from the data spectrum
and  think there is a mixture of Pd in staple and in centre. could you
help me how to do the fitting mixture.



I have the same advice for you that I had for this person:

https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04636.html

EXAFS analysis isn't simply a matter of learning which buttons to push. 
 You need to develop some understanding of the physics and the methods 
of the technique before diving into challenging analysis problems.


B

--
 Bruce Ravel   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/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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[Ifeffit] fitting mixture

[kaziz sameh]

hi,
i want to fit Pd2Au36 in KPd edge with artemis. from the data spectrum and  
think there is a mixture of Pd in staple and in centre. could you help me how 
to do the fitting mixture.___
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Re: [Ifeffit] Fitting EXAFS simulation to experimental

[Carl Brozek]

Hi Scott,

Thanks a lot for the insight. It seems like it'll take a bit of work, but
I'm happy to hear it's doable.

best,
Carl


On Thu, May 29, 2014 at 12:54 PM, Scott Calvin wrote:

> Dear Carl,
>
> The short answer is yes, but it takes a little bit of effort.
>
> One method is to actually figure out how stretching the c-axis impacts the
> lengths of each path geometrically, and then use the functions determine to
> express the delr's of each path in terms of the change in c. This method is
> rigorously correct, but requires digging in to the geometry, and entering
> somewhat lengthy expressions for many of the scattering paths.
>
> A related method is to in effect use a first-order approximation of those
> changes. To do that, create two atoms files with slightly different values
> of c. Generate the corresponding paths, and see how the reff of those paths
> changes. For example, changing c by 0.01 might result in a certain path
> having a reff change by 0.014. Use the ratio of the change in reff to the
> change in c to scale the delr of those paths with respect to a guessed
> parameter delc. In the example I just provided the delr of the path in
> question would be chosen to be 1.4*delc.
>
> The second method is, of course, approximate, but for small changes in a
> parameter such as c can work pretty well, and can be easier to implement
> than the first.
>
> --Scott Calvin
> Sarah Lawrence College
>
>
> On May 29, 2014, at 12:33 PM, Carl Brozek  wrote:
>
> > Dear All,
> >
> > Thank you for your responses so far and I apologize for not being
> clearer.
> >
> > Here is the problem at hand: I have a material that is best thought of
> as organic, graphene-like 2-D sheets connected by infinite chains of Fe-S.
> Based on PXRD and other techniques, we know the structure of the AB plane
> (the 2-D organic part), but we aren't able to make sense of what is going
> on with the Fe-S chain. We can simulate the PXRD based on proposed .cif
> files, but it's off most likely because of the c direction (Fe-S chain).
> >
> > We collected Fe K edge XAS to tease out Fe-S bond angles and distances,
> hoping we could feed this into our simulation for the PXRD to improve the
> fit.
> >
> > Modifying the ATOMS input by hand, by constructing different reasonable
> geometries, was improving the simulation, but using a error minimization
> fitting program would be best.
> >
> > So, is it possible to vary specific angles and distances between atoms
> along the c-direction only in an error minimization program based on our
> experimental data?
> >
> > I apologize if you have already responded to this reformulated question.
> >
> > best,
> > Carl
>
>
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>



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SB | 2010 | University of Chicago
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Re: [Ifeffit] Fitting EXAFS simulation to experimental

[Matt Newville]

Hi Matthew,



On Thu, May 29, 2014 at 11:18 AM, Matthew Marcus  wrote:

> 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.


I completely agree.


>  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.


This is an excellent suggestion...


>  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 = 
> 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
>
>
Yes, that's a very nice way to do it, and I think such a distortion
language would be a great way to map the problem to EXAFS.  I think such
ideas have been kicked around for a long time, and I'm pretty sure
something like this was part of Bruce's motivation for Virtual Paths.

A confounding, persistent issue for many years was that Feff's pathfinder
(purposely?) loses all information about the atomic positions for a path.
Basically, the pathfinder needs to be able to retain the full path in order
to model distortions in the way you're talking about.  I believe Bruce's
pathfinder in Artemis does this.

I agree it's real work, but would be highly useful.

--Matt
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Re: [Ifeffit] Fitting EXAFS simulation to experimental

[Scott Calvin]

Dear Carl,

The short answer is yes, but it takes a little bit of effort.

One method is to actually figure out how stretching the c-axis impacts the 
lengths of each path geometrically, and then use the functions determine to 
express the delr's of each path in terms of the change in c. This method is 
rigorously correct, but requires digging in to the geometry, and entering 
somewhat lengthy expressions for many of the scattering paths.

A related method is to in effect use a first-order approximation of those 
changes. To do that, create two atoms files with slightly different values of 
c. Generate the corresponding paths, and see how the reff of those paths 
changes. For example, changing c by 0.01 might result in a certain path having 
a reff change by 0.014. Use the ratio of the change in reff to the change in c 
to scale the delr of those paths with respect to a guessed parameter delc. In 
the example I just provided the delr of the path in question would be chosen to 
be 1.4*delc.

The second method is, of course, approximate, but for small changes in a 
parameter such as c can work pretty well, and can be easier to implement than 
the first.

--Scott Calvin
Sarah Lawrence College


On May 29, 2014, at 12:33 PM, Carl Brozek  wrote:

> Dear All,
> 
> Thank you for your responses so far and I apologize for not being clearer.
> 
> Here is the problem at hand: I have a material that is best thought of as 
> organic, graphene-like 2-D sheets connected by infinite chains of Fe-S. Based 
> on PXRD and other techniques, we know the structure of the AB plane (the 2-D 
> organic part), but we aren't able to make sense of what is going on with the 
> Fe-S chain. We can simulate the PXRD based on proposed .cif files, but it's 
> off most likely because of the c direction (Fe-S chain).
> 
> We collected Fe K edge XAS to tease out Fe-S bond angles and distances, 
> hoping we could feed this into our simulation for the PXRD to improve the 
> fit. 
> 
> Modifying the ATOMS input by hand, by constructing different reasonable 
> geometries, was improving the simulation, but using a error minimization 
> fitting program would be best.
> 
> So, is it possible to vary specific angles and distances between atoms along 
> the c-direction only in an error minimization program based on our 
> experimental data?
> 
> I apologize if you have already responded to this reformulated question.
> 
> best,
> Carl 


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Re: [Ifeffit] Fitting EXAFS simulation to experimental

[Carl Brozek]

Dear All,

Thank you for your responses so far and I apologize for not being clearer.

Here is the problem at hand: I have a material that is best thought of as
organic, graphene-like 2-D sheets connected by infinite chains of Fe-S.
Based on PXRD and other techniques, we know the structure of the AB plane
(the 2-D organic part), but we aren't able to make sense of what is going
on with the Fe-S chain. We can simulate the PXRD based on proposed .cif
files, but it's off most likely because of the c direction (Fe-S chain).

We collected Fe K edge XAS to tease out Fe-S bond angles and distances,
hoping we could feed this into our simulation for the PXRD to improve the
fit.

Modifying the ATOMS input by hand, by constructing different reasonable
geometries, was improving the simulation, but using a error minimization
fitting program would be best.

So, is it possible to vary specific angles and distances between atoms
along the c-direction only in an error minimization program based on our
experimental data?

I apologize if you have already responded to this reformulated question.

best,
Carl


On Wed, May 28, 2014 at 6:58 PM, Carl Brozek  wrote:

> Dear listhost,
>
> I'm using Artemis as a front end for ATOMS and FEFF and I would like to
> build a simulated EXAFS spectrum based on experimental data I have. I know
> how to generate a simulation based on a .cif or .xyz file, but is it
> possible to vary parameters in these input geometries to best match the
> experimental?
>
> Has someone implemented this in artemis or matlab?
>
> thanks,
> Carl
>
> --
> PhD Candidate | Chemistry | MIT
> SB | 2010 | University of Chicago
>



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Re: [Ifeffit] Fitting EXAFS simulation to experimental

[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 = 
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] Fitting EXAFS simulation to experimental

[Matt Newville]

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] Fitting EXAFS simulation to experimental

[Anatoly I Frenkel]

Yes, it is possible to vary atomic positions in the fitting process and 
evaluate their effect on the fit, or just use them as adjustable parameters in 
the fit as any other fitting variables.

This process was historically started by Yizhak Yacoby (see papers from his 
group in the 1990s), who introduced structural distortions into the fit.

We had a somewhat similar approach in this work:

https://pubweb.bnl.gov/~frenkel/KNbO3/kno.pdf

where we have parameterized the fractional coordinates of oxygen atoms in the 
perovskite structure and traced their effect on EXAFS equation (most 
non-trivially, on the scattering amplitude of multiple scattering (Equations 
6,7)  paths, the rest was pretty trivial: Equations 4,5).

I think Bruce also had done such parameterization in some of his papers and in 
his Thesis.

Anatoly


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Scott Calvin 
[scal...@sarahlawrence.edu]
Sent: Thursday, May 29, 2014 10:40 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Fitting EXAFS simulation to experimental

Hi Carl,

I'm not sure what level you were asking your question from. Bruce provided an 
answer to one interpretation of the question.

If the question is, however, "has anyone written an automated script that 
allows the user to choose parameters given to ATOMS as fitting parameters for 
all space groups," then my answer is that I'm not aware of that having been 
done.

For example, it is very easy to make the lattice parameter for a cubic space 
group be a fitting parameter, as changes to it will result in a uniform 
fractional change to the length of all paths, and the reff keyword makes it 
easy to implement a uniform fractional change. Plenty of people have computed 
the relationship between ATOMS parameters and path parameters for specific 
geometries (including more complicated ones), and used that for fitting.

But in each case that requires some effort to think about the geometry 
involved. That's different from having a script that allows you to designate a 
shift in, say, the x-coordinate in fractional coordinates of one kind of atom 
in the input file and automatically have that result in the generation of the 
correct function of that fitting parameter in each of the paths used in FEFF, 
including multiple-scattering paths. And that's the thing that I don't think 
currently exists.

--Scott Calvin
Sarah Lawrence College

On May 29, 2014, at 9:04 AM, Bruce Ravel  wrote:

> On 05/28/2014 06:58 PM, Carl Brozek wrote:
>> Dear listhost,
>>
>> I'm using Artemis as a front end for ATOMS and FEFF and I would like to
>> build a simulated EXAFS spectrum based on experimental data I have. I
>> know how to generate a simulation based on a .cif or .xyz file, but is
>> it possible to vary parameters in these input geometries to best match
>> the experimental?
>>
>> Has someone implemented this in artemis or matlab?
>>
>> thanks,
>
>
> Carl,
>
> In Artemis, this is called a VPath.
>
>   http://bruceravel.github.io/demeter/artug/plot/vpaths.html
>
> You will need to import data of some sort because a VPath is created
> from paths that have been associated with a data set.
>
> Run Feff.  Drag and drop any number of paths from the Path tab in the
> Feff window onto your data Window.  Mark the paths paths you want to
> include in your VPath by clicking their little check buttons.  From
> the Actions menu, select "Make VPath from marked".  This will prompt
> you for a name for the VPath and insert the VPath into the plotting
> list, as described in the page whose URL is given above.
>
> As for varying structural parameters, that is what we call a "fit".
> You can parameterize the various Delta R parameters to represent
> changes in lattice positions.  There are plenty of examples of this
> using Ifeffit -- Daniel Haskel's papers on cuprate superconductors, my
> own papers on titanate perovskites, lots of work buy Anatoly Frenkel
> on various catalyst materials, Sam Webb's work on manganites, just to
> name a few.
>
> B
>
>
>
> --
>  Bruce Ravel   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://xafs.org/BruceRavel
>  Software:https://github.com/bruceravel
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Re: [Ifeffit] Fitting EXAFS simulation to experimental

[Scott Calvin]

Hi Carl,

I'm not sure what level you were asking your question from. Bruce provided an 
answer to one interpretation of the question.

If the question is, however, "has anyone written an automated script that 
allows the user to choose parameters given to ATOMS as fitting parameters for 
all space groups," then my answer is that I'm not aware of that having been 
done.

For example, it is very easy to make the lattice parameter for a cubic space 
group be a fitting parameter, as changes to it will result in a uniform 
fractional change to the length of all paths, and the reff keyword makes it 
easy to implement a uniform fractional change. Plenty of people have computed 
the relationship between ATOMS parameters and path parameters for specific 
geometries (including more complicated ones), and used that for fitting.

But in each case that requires some effort to think about the geometry 
involved. That's different from having a script that allows you to designate a 
shift in, say, the x-coordinate in fractional coordinates of one kind of atom 
in the input file and automatically have that result in the generation of the 
correct function of that fitting parameter in each of the paths used in FEFF, 
including multiple-scattering paths. And that's the thing that I don't think 
currently exists.

--Scott Calvin
Sarah Lawrence College
 
On May 29, 2014, at 9:04 AM, Bruce Ravel  wrote:

> On 05/28/2014 06:58 PM, Carl Brozek wrote:
>> Dear listhost,
>> 
>> I'm using Artemis as a front end for ATOMS and FEFF and I would like to
>> build a simulated EXAFS spectrum based on experimental data I have. I
>> know how to generate a simulation based on a .cif or .xyz file, but is
>> it possible to vary parameters in these input geometries to best match
>> the experimental?
>> 
>> Has someone implemented this in artemis or matlab?
>> 
>> thanks,
> 
> 
> Carl,
> 
> In Artemis, this is called a VPath.
> 
>   http://bruceravel.github.io/demeter/artug/plot/vpaths.html
> 
> You will need to import data of some sort because a VPath is created
> from paths that have been associated with a data set.
> 
> Run Feff.  Drag and drop any number of paths from the Path tab in the
> Feff window onto your data Window.  Mark the paths paths you want to
> include in your VPath by clicking their little check buttons.  From
> the Actions menu, select "Make VPath from marked".  This will prompt
> you for a name for the VPath and insert the VPath into the plotting
> list, as described in the page whose URL is given above.
> 
> As for varying structural parameters, that is what we call a "fit".
> You can parameterize the various Delta R parameters to represent
> changes in lattice positions.  There are plenty of examples of this
> using Ifeffit -- Daniel Haskel's papers on cuprate superconductors, my
> own papers on titanate perovskites, lots of work buy Anatoly Frenkel
> on various catalyst materials, Sam Webb's work on manganites, just to
> name a few.
> 
> B
> 
> 
> 
> -- 
>  Bruce Ravel   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://xafs.org/BruceRavel
>  Software:https://github.com/bruceravel
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Re: [Ifeffit] Fitting EXAFS simulation to experimental

[Bruce Ravel]

On 05/28/2014 06:58 PM, Carl Brozek wrote:

Dear listhost,

I'm using Artemis as a front end for ATOMS and FEFF and I would like to
build a simulated EXAFS spectrum based on experimental data I have. I
know how to generate a simulation based on a .cif or .xyz file, but is
it possible to vary parameters in these input geometries to best match
the experimental?

Has someone implemented this in artemis or matlab?

thanks,



Carl,

In Artemis, this is called a VPath.

  http://bruceravel.github.io/demeter/artug/plot/vpaths.html

You will need to import data of some sort because a VPath is created
from paths that have been associated with a data set.

Run Feff.  Drag and drop any number of paths from the Path tab in the
Feff window onto your data Window.  Mark the paths paths you want to
include in your VPath by clicking their little check buttons.  From
the Actions menu, select "Make VPath from marked".  This will prompt
you for a name for the VPath and insert the VPath into the plotting
list, as described in the page whose URL is given above.

As for varying structural parameters, that is what we call a "fit".
You can parameterize the various Delta R parameters to represent
changes in lattice positions.  There are plenty of examples of this
using Ifeffit -- Daniel Haskel's papers on cuprate superconductors, my
own papers on titanate perovskites, lots of work buy Anatoly Frenkel
on various catalyst materials, Sam Webb's work on manganites, just to
name a few.

B



--
 Bruce Ravel   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://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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[Ifeffit] Fitting EXAFS simulation to experimental

[Carl Brozek]

Dear listhost,

I'm using Artemis as a front end for ATOMS and FEFF and I would like to
build a simulated EXAFS spectrum based on experimental data I have. I know
how to generate a simulation based on a .cif or .xyz file, but is it
possible to vary parameters in these input geometries to best match the
experimental?

Has someone implemented this in artemis or matlab?

thanks,
Carl

-- 
PhD Candidate | Chemistry | MIT
SB | 2010 | University of Chicago
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Re: [Ifeffit] fitting a specific k range

[Scott Calvin]

Hi Matt,

Yes--we clearly disagree. 

The word "complaining" has come up a couple of times. I didn't think of it that 
way, although clearly it's coming off that way. I said it was my least favorite 
warning, and that usually one of the first things I tell students to do is to 
change the preferences to turn it off. That isn't a complaint--it's a 
description of what I do. I think descriptions of the actual behavior of users, 
whatever their level of expertise, is useful to developers and community. If 
that's counterproductive, wouldn't it also be counterproductive to say "I never 
use the button for corrected Fourier transform, because I think it encourages 
confusion" or "I don't see what the benefit is to fitting in k or q space, and 
so I don't do it?" 

> Having a warning about this is vastly preferable to not having such a warning.


To be clear, my view is that false positives can indeed be a significant 
problem--the medical community, for example, knows this very well. I've 
repeatedly witnessed people starting out with Artemis who fall in to a pattern 
of ignoring all warnings because of this particular false positive.

It seems to me that a user has to know a bit more to generate the true positive 
in this case than the false one. They have to add free parameters for paths 
outside the fitting range--Artemis doesn't do that for them. And then they get 
another strong sign that something has gone wrong because, as you say, the 
error bars blow up. So, unlike the consequences that can come from treating the 
false positive as a true one (removing a path that actually contributes 
significantly to the fitting range), in the case of a true positive it will at 
least be clear something is wrong. The message helps diagnose the problem, but 
the lack of the message wouldn't cause someone to think everything is 
hunky-dory when it's not (unless they don't even understand the concept and 
importance of error bars) .

So yes, it's closer to my view that the rule is always wrong and not worth 
fixing, although of course that's a bit oversimplified. For certain kinds of 
fitting strategies, it can be useful, and it's good that the software offers it 
as an option. But I don't think it should be the default option, as I think it 
confuses or misleads novices more often than it helps them. So I would suggest 
that the out of the box behavior for the warning to be off.

That's not an attack on the software in general, or on the warning feature it 
includes. It is my opinion, and it seems to me that this mailing list is an 
appropriate place to express that kind of opinion.

--Scott Calvin
Sarah Lawrence College

On Dec 6, 2013, at 12:29 AM, Matt Newville  wrote:

> Hi Scott,
> 
> On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin  
> wrote:
>> I love the warnings Artemis gives! They're not just for novices--they often 
>> catch when I've made a dumb mistake somewhere. I praise them, defend them, 
>> and generally think Bruce has done a wonderful thing by having them.
>> 
>> The out of range default warning, however, I find counterproductive and 
>> confusing to novices. There are two reasons for my opinion (and it is, of 
>> course, my opinion--as Bruce points out, if others differ, they can set the 
>> defaults differently.) One has to do with the kind of example I mentioned 
>> earlier. Here's the other reason:
>> 
>> The default behavior is to warn if there is a path beyond 1.1 times the top 
>> of the range, correct? (It's kind of a pain for me right now to fire up the 
>> most recent version of Artemis, so I can't actually easily confirm that at 
>> the moment.) The default R-max is, if I recall correctly, 3.0 angstroms. 
>> Thus, by default, a warning is generated if there is a path above 3.3 
>> angstroms in the list.
>> 
>> But, as we know, the path list uses distances which are half path lengths, 
>> while the Fourier transform range is in terms of the conjugate variable to 
>> k. For edges around the third row of the periodic table, the peaks 
>> corresponding to a path tend to show up about 0.3 to 0.5 angstroms lower in 
>> the Fourier transform than their half path-length. And, of course, that's 
>> just the peak--the path has significant amplitude a bit below (and above) 
>> that.
>> 
>> So, a novice user fires up Artemis, imports her data, and uses atoms to 
>> generate a feff file. Because she's appropriately thoughtful about what 
>> she's doing, she looks at what the unfitted paths of the FEFF calculation 
>> look like. She sees the fitting range goes up to 3 angstroms, and then 
>> selects all the paths that contribute significant amplitude to that range. 
>> That might include a path with a half path length of 3.4 angstroms. She then 
>> runs a fit--and Artemis gives her a warning that something may be wrong.
>> 
>> At that point, she could stick to her guns and tell the fit to continue. 
>> Since that's going to happen with pretty much every fit she runs, it becomes 
>> very tempting not to read

Re: [Ifeffit] fitting a specific k range

[Matt Newville]

Hi Scott,

On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin  wrote:
> I love the warnings Artemis gives! They're not just for novices--they often 
> catch when I've made a dumb mistake somewhere. I praise them, defend them, 
> and generally think Bruce has done a wonderful thing by having them.
>
> The out of range default warning, however, I find counterproductive and 
> confusing to novices. There are two reasons for my opinion (and it is, of 
> course, my opinion--as Bruce points out, if others differ, they can set the 
> defaults differently.) One has to do with the kind of example I mentioned 
> earlier. Here's the other reason:
>
> The default behavior is to warn if there is a path beyond 1.1 times the top 
> of the range, correct? (It's kind of a pain for me right now to fire up the 
> most recent version of Artemis, so I can't actually easily confirm that at 
> the moment.) The default R-max is, if I recall correctly, 3.0 angstroms. 
> Thus, by default, a warning is generated if there is a path above 3.3 
> angstroms in the list.
>
> But, as we know, the path list uses distances which are half path lengths, 
> while the Fourier transform range is in terms of the conjugate variable to k. 
> For edges around the third row of the periodic table, the peaks corresponding 
> to a path tend to show up about 0.3 to 0.5 angstroms lower in the Fourier 
> transform than their half path-length. And, of course, that's just the 
> peak--the path has significant amplitude a bit below (and above) that.
>
> So, a novice user fires up Artemis, imports her data, and uses atoms to 
> generate a feff file. Because she's appropriately thoughtful about what she's 
> doing, she looks at what the unfitted paths of the FEFF calculation look 
> like. She sees the fitting range goes up to 3 angstroms, and then selects all 
> the paths that contribute significant amplitude to that range. That might 
> include a path with a half path length of 3.4 angstroms. She then runs a 
> fit--and Artemis gives her a warning that something may be wrong.
>
> At that point, she could stick to her guns and tell the fit to continue. 
> Since that's going to happen with pretty much every fit she runs, it becomes 
> very tempting not to read the warning each time, but just dismiss it. And at 
> that point, if there's a highly useful warning, she'll miss it.
>
> Or, she could decide that she's the novice, and what she's doing isn't that 
> unusual, so maybe she shouldn't be including that path at 3.4 angstroms, and 
> take it out. She is now getting distorted results, because she's leaving out 
> a path that has significant amplitude in the region.

It's reasonable to question whether the threshold for such a warning
is too conservative or to suggest (better yet, issue a pull request
for) a fix for a particular feature.  Saying (as you did) that turning
the warning off "usually one of the first things" you teach students
seems counterproductive.   To be clear, you did not teach them to
change the default value of reff_margin. I would have said Mend it,
don't End it.   Perhaps the rule should be (Reff+0.5)*1.1?  But this
was not your suggestion.  Your suggestion was to ignore the rule.

If you are relying on these codes for your work, and teaching others
to use them, and find things you don't like or could be improved, it
is your responsibility to provide constructive, specific feedback and
fixes to the actual code.  Yes, I actually do mean you, Scott.   This
would be the perfect place for you to contribute.  See
 https://github.com/bruceravel/demeter/blob/master/lib/Demeter/Fit/Sanity.pm
 
https://github.com/bruceravel/demeter/blob/master/lib/Demeter/configuration/warnings.demeter_conf

> I think, not just from personal preference, but also from a consideration of 
> what is best for people learning to use
> the software, that the warning is set too conservatively. And I'm not even 
> clear what misstep it's trying to prevent.

I cannot tell if you are joking.   It is, of course, to prevent one
from including paths (say, the second and third shells with variable
parameters when the R range being fit (say the first shell) will not
allow those variables to alter the fit.  Having such variables can
grossly distort the fit and will generally prevent good error bars
from being calculated.  I agree that it's not so much the presence of
Paths well beyond Rmax as it is the presence of variables that only
affect Paths outside the fitting range.  But that is much harder to
automatically detect, and the case described above is a likely way to
get into that situation.  Having a warning about this is vastly
preferable to not having such a warning.

The details of the thresholds may be tweaked, but you didn't complain
about the details of the rules, but the existence of the rule itself.

Perhaps your view is that this rule is just always wrong and not worth
fixing, but I think many of us would disagree with you.

--Matt

___

Re: [Ifeffit] fitting a specific k range

[Scott Calvin]

I love the warnings Artemis gives! They're not just for novices--they often 
catch when I've made a dumb mistake somewhere. I praise them, defend them, and 
generally think Bruce has done a wonderful thing by having them.

The out of range default warning, however, I find counterproductive and 
confusing to novices. There are two reasons for my opinion (and it is, of 
course, my opinion--as Bruce points out, if others differ, they can set the 
defaults differently.) One has to do with the kind of example I mentioned 
earlier. Here's the other reason:

The default behavior is to warn if there is a path beyond 1.1 times the top of 
the range, correct? (It's kind of a pain for me right now to fire up the most 
recent version of Artemis, so I can't actually easily confirm that at the 
moment.) The default R-max is, if I recall correctly, 3.0 angstroms. Thus, by 
default, a warning is generated if there is a path above 3.3 angstroms in the 
list.

But, as we know, the path list uses distances which are half path lengths, 
while the Fourier transform range is in terms of the conjugate variable to k. 
For edges around the third row of the periodic table, the peaks corresponding 
to a path tend to show up about 0.3 to 0.5 angstroms lower in the Fourier 
transform than their half path-length. And, of course, that's just the 
peak--the path has significant amplitude a bit below (and above) that. 

So, a novice user fires up Artemis, imports her data, and uses atoms to 
generate a feff file. Because she's appropriately thoughtful about what she's 
doing, she looks at what the unfitted paths of the FEFF calculation look like. 
She sees the fitting range goes up to 3 angstroms, and then selects all the 
paths that contribute significant amplitude to that range. That might include a 
path with a half path length of 3.4 angstroms. She then runs a fit--and Artemis 
gives her a warning that something may be wrong.

At that point, she could stick to her guns and tell the fit to continue. Since 
that's going to happen with pretty much every fit she runs, it becomes very 
tempting not to read the warning each time, but just dismiss it. And at that 
point, if there's a highly useful warning, she'll miss it.

Or, she could decide that she's the novice, and what she's doing isn't that 
unusual, so maybe she shouldn't be including that path at 3.4 angstroms, and 
take it out. She is now getting distorted results, because she's leaving out a 
path that has significant amplitude in the region.

I think, not just from personal preference, but also from a consideration of 
what is best for people learning to use the software, that the warning is set 
too conservatively. And I'm not even clear what misstep it's trying to prevent.

--Scott Calvin
Sarah Lawrence College

On Dec 5, 2013, at 2:32 PM,  
 wrote:

> 
> 
> What I find reassuring about Bruce's warnings is they allow you to think 
> properly about what you are doing. Fortunately, unlike Chris, I am not of a 
> size where I have to worry about falling down rabbit holes, unless American 
> rabbits are much bigger than English ones.
> I would commend Matt's original question as it opened a debate with 3 of the 
> mainstays of the list. That may not have been the intention but it makes 
> interesting reading for us mailing list voyeurs.
> 
> Cheers
> Fred
> Sent from Samsung tablet


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Re: [Ifeffit] fitting a specific k range

[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  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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Re: [Ifeffit] fitting a specific k range

[Matt Newville]

Hi Anatoly,

On Thu, Dec 5, 2013 at 12:28 PM, Anatoly I Frenkel  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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Re: [Ifeffit] fitting a specific k range

[fred.mosselmans]

What I find reassuring about Bruce's warnings is they allow you to think 
properly about what you are doing. Fortunately, unlike Chris, I am not of a 
size where I have to worry about falling down rabbit holes, unless American 
rabbits are much bigger than English ones.
I would commend Matt's original question as it opened a debate with 3 of the 
mainstays of the list. That may not have been the intention but it makes 
interesting reading for us mailing list voyeurs.

Cheers
Fred
Sent from Samsung tablet

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Re: [Ifeffit] fitting a specific k range

[Matt Newville]

Scott,

On Thu, Dec 5, 2013 at 11:18 AM, Scott Calvin  wrote:
> First, a disclaimer--I haven't looked at the data Matt sent (it's a busy time 
> of year!), but I disagree in a general sense with my reading of what Bruce 
> wrote (perhaps I am reading it wrong). In particular, I disagree with this 
> statement:
>
>> Given that you are fitting in q-space, it is completely unreasonable (from a 
>> numerical perspective) to expect that the fit could possibly reproduce a 
>> feature that you have (intentionally or otherwise) filtered out of the data.
>>
>> To say that another way, given how you constructed the fit, you got a good 
>> fit.  You made the fit in a way that it cannot possibly reproduce the 
>> feature you are asking about, thus your question is ill-posed.
>
> To explain why, suppose I am fitting a standard--for the sake of a simple 
> example, suppose it's copper. I include in my model paths out to 7 angstroms, 
> including multiple-scattering paths, and use a Debye model for the MSRDs. 
> It's possible to do a pretty good job in that kind of fit with just a few 
> free parameters: S02, E0, an isotropic lattice expansion, and a Debye 
> temperature. Now, suppose I perform the fit from 1 to 3.5 angstroms. Usually, 
> the fit will do a pretty good job reproducing features well above 3.5 
> angstroms, because they're in the model (the paths are included) even though 
> they're not in the fitting range. That's true for features in k-space that 
> are caused by high-R paths too, of course.
>
> In fact, that kind of fit is particularly valuable to me, because it strongly 
> suggests I've got the model right--I've essentially hid the high-R data from 
> the numerical routines, so if it fits that region well anyway, it's probably 
> because the model itself is a good one.
>
> While I defend that principle as a very important one, I'm not claiming it 
> applies in Matt's case--it probably doesn't. To reproduce features at high-R, 
> it IS necessary to have a model (i.e. paths) that cover the high-R 
> contribution, and it sounds like Matt does not have those paths included in 
> his model. But it's not necessary to FIT up to high R.

I agree that if a model fitted to data over some limited range of data
(either k or R, or even some external variable)  matches data well
outside that range, that is a good feature of the model.  But what if
it doesn't match the data outside that range? As you say, model
that matches data over a very limited range can be useful, but mostly
in the context for how it extrapolates outside that range.

Back to Matt's point: using a sharp feature in chi(k) can be a
reasonable spectroscopic approach to identifying particular phases of
materials (mineral phases for example).But to actually model any
of these sharp features in chi(k) would require a large R range for
the data, and might require many paths.   Trying to model such a
limited range while ignoring data outside that range is not a good
idea.

> P.S. My least favorite warning that Artemis provides is the one that tells 
> you that you're including paths outside the fitting region, for just this 
> reason. It's easy enough to change the preferences so that Artemis doesn't 
> give that warning, and it's usually one of the first things I have my 
> students do when they're first learning to fit.

When teaching students to drive a car is showing them how to put a
piece of electrical tape over the Check Engine light the first thing
you do?   Generally, false positives warnings are preferable to having
no warnings.

--Matt

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Re: [Ifeffit] fitting a specific k range

[Anatoly I Frenkel]

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.
How about "you should consider praise or adoration", instead of "you should 
consider hosannas of gratitude".
Anatoly 


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Bruce Ravel 
[bra...@bnl.gov]
Sent: Thursday, December 05, 2013 1:19 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] fitting a specific k range

On 12/05/2013 12:18 PM, Scott Calvin wrote:
> While I defend that principle as a very important one, I'm not
> claiming it applies in Matt's case--it probably doesn't. To reproduce
> features at high-R, it IS necessary to have a model (i.e. paths) that
> cover the high-R contribution, and it sounds like Matt does not have
> those paths included in his model. But it's not necessary to FIT up
> to high R.

It doesn't apply.  Matt filtered his data.  Matt used paths that only
include Fourier components within the filtered band.  To suggest that
it may somehow be reasonable that the fit could turn out other than
how it did runs a real risk of misleading this fellow who is,
apparently, a newcomer to EXAFS analysis.

> P.S. My least favorite warning that Artemis provides is the one that
> tells you that you're including paths outside the fitting region, for
> just this reason. It's easy enough to change the preferences so that
> Artemis doesn't give that warning, and it's usually one of the first
> things I have my students do when they're first learning to fit.

OK.  Whatever.  Instead of complaining about this, perhaps you should
consider hosannas of gratitude that I make it possible, easy even, to
accommodate preferences different from my own.

B


--
  Bruce Ravel   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://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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Re: [Ifeffit] fitting a specific k range

[Jensen, Mark P.]

Besides, that's a (very common) misuse of the word hosanna.



-Original Message-
From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Anatoly I 
Frenkel
Sent: Thursday, December 05, 2013 12:29 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] fitting a specific k range

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.
How about "you should consider praise or adoration", instead of "you should 
consider hosannas of gratitude".
Anatoly 


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Bruce Ravel 
[bra...@bnl.gov]
Sent: Thursday, December 05, 2013 1:19 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] fitting a specific k range

On 12/05/2013 12:18 PM, Scott Calvin wrote:
> While I defend that principle as a very important one, I'm not 
> claiming it applies in Matt's case--it probably doesn't. To reproduce 
> features at high-R, it IS necessary to have a model (i.e. paths) that 
> cover the high-R contribution, and it sounds like Matt does not have 
> those paths included in his model. But it's not necessary to FIT up to 
> high R.

It doesn't apply.  Matt filtered his data.  Matt used paths that only include 
Fourier components within the filtered band.  To suggest that it may somehow be 
reasonable that the fit could turn out other than how it did runs a real risk 
of misleading this fellow who is, apparently, a newcomer to EXAFS analysis.

> P.S. My least favorite warning that Artemis provides is the one that 
> tells you that you're including paths outside the fitting region, for 
> just this reason. It's easy enough to change the preferences so that 
> Artemis doesn't give that warning, and it's usually one of the first 
> things I have my students do when they're first learning to fit.

OK.  Whatever.  Instead of complaining about this, perhaps you should consider 
hosannas of gratitude that I make it possible, easy even, to accommodate 
preferences different from my own.

B


--
  Bruce Ravel   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://xafs.org/BruceRavel
  Software:https://github.com/bruceravel
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Re: [Ifeffit] fitting a specific k range

[Chris Patridge]

Bruce,

Without those friendly warnings (reminders), beginners would likely fall down 
several rabbit holes before understanding many of the important steps necessary 
to get meaningful answers in EXAFS.  
I know I would have.

Chris
***
Dr. Christopher Patridge
Assistant Professor
Department of Math and Natural Sciences 
D'youville College
Contact: 315-529-0501

On Dec 5, 2013, at 1:19 PM, Bruce Ravel  wrote:

> On 12/05/2013 12:18 PM, Scott Calvin wrote:
>> While I defend that principle as a very important one, I'm not
>> claiming it applies in Matt's case--it probably doesn't. To reproduce
>> features at high-R, it IS necessary to have a model (i.e. paths) that
>> cover the high-R contribution, and it sounds like Matt does not have
>> those paths included in his model. But it's not necessary to FIT up
>> to high R.
> 
> It doesn't apply.  Matt filtered his data.  Matt used paths that only
> include Fourier components within the filtered band.  To suggest that
> it may somehow be reasonable that the fit could turn out other than
> how it did runs a real risk of misleading this fellow who is,
> apparently, a newcomer to EXAFS analysis.
> 
>> P.S. My least favorite warning that Artemis provides is the one that
>> tells you that you're including paths outside the fitting region, for
>> just this reason. It's easy enough to change the preferences so that
>> Artemis doesn't give that warning, and it's usually one of the first
>> things I have my students do when they're first learning to fit.
> 
> OK.  Whatever.  Instead of complaining about this, perhaps you should
> consider hosannas of gratitude that I make it possible, easy even, to
> accommodate preferences different from my own.
> 
> B
> 
> 
> -- 
> Bruce Ravel   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://xafs.org/BruceRavel
> Software:https://github.com/bruceravel
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Re: [Ifeffit] fitting a specific k range

[Bruce Ravel]

On 12/05/2013 12:18 PM, Scott Calvin wrote:

While I defend that principle as a very important one, I'm not
claiming it applies in Matt's case--it probably doesn't. To reproduce
features at high-R, it IS necessary to have a model (i.e. paths) that
cover the high-R contribution, and it sounds like Matt does not have
those paths included in his model. But it's not necessary to FIT up
to high R.


It doesn't apply.  Matt filtered his data.  Matt used paths that only
include Fourier components within the filtered band.  To suggest that
it may somehow be reasonable that the fit could turn out other than
how it did runs a real risk of misleading this fellow who is,
apparently, a newcomer to EXAFS analysis.


P.S. My least favorite warning that Artemis provides is the one that
tells you that you're including paths outside the fitting region, for
just this reason. It's easy enough to change the preferences so that
Artemis doesn't give that warning, and it's usually one of the first
things I have my students do when they're first learning to fit.


OK.  Whatever.  Instead of complaining about this, perhaps you should
consider hosannas of gratitude that I make it possible, easy even, to
accommodate preferences different from my own.

B


--
 Bruce Ravel   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://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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Re: [Ifeffit] fitting a specific k range

[Scott Calvin]

First, a disclaimer--I haven't looked at the data Matt sent (it's a busy time 
of year!), but I disagree in a general sense with my reading of what Bruce 
wrote (perhaps I am reading it wrong). In particular, I disagree with this 
statement:

> Given that you are fitting in q-space, it is completely unreasonable (from a 
> numerical perspective) to expect that the fit could possibly reproduce a 
> feature that you have (intentionally or otherwise) filtered out of the data.
> 
> To say that another way, given how you constructed the fit, you got a good 
> fit.  You made the fit in a way that it cannot possibly reproduce the feature 
> you are asking about, thus your question is ill-posed.

To explain why, suppose I am fitting a standard--for the sake of a simple 
example, suppose it's copper. I include in my model paths out to 7 angstroms, 
including multiple-scattering paths, and use a Debye model for the MSRDs. It's 
possible to do a pretty good job in that kind of fit with just a few free 
parameters: S02, E0, an isotropic lattice expansion, and a Debye temperature. 
Now, suppose I perform the fit from 1 to 3.5 angstroms. Usually, the fit will 
do a pretty good job reproducing features well above 3.5 angstroms, because 
they're in the model (the paths are included) even though they're not in the 
fitting range. That's true for features in k-space that are caused by high-R 
paths too, of course.

In fact, that kind of fit is particularly valuable to me, because it strongly 
suggests I've got the model right--I've essentially hid the high-R data from 
the numerical routines, so if it fits that region well anyway, it's probably 
because the model itself is a good one.

While I defend that principle as a very important one, I'm not claiming it 
applies in Matt's case--it probably doesn't. To reproduce features at high-R, 
it IS necessary to have a model (i.e. paths) that cover the high-R 
contribution, and it sounds like Matt does not have those paths included in his 
model. But it's not necessary to FIT up to high R.

--Scott Calvin
Sarah Lawrence College

P.S. My least favorite warning that Artemis provides is the one that tells you 
that you're including paths outside the fitting region, for just this reason. 
It's easy enough to change the preferences so that Artemis doesn't give that 
warning, and it's usually one of the first things I have my students do when 
they're first learning to fit.

On Dec 5, 2013, at 10:11 AM, Bruce Ravel  wrote:

> 
> Matt,
> 
> At the risk of coming off sounding a bit mean, I don't think you are
> asking a very well-posed question.
> 
> Examining the history of this project, I see that you are fitting in q
> space.  Like Matt, this is not my favorite choice, but there is
> nothing horribly wrong about it, so long as you understand what you
> are doing.
> 
> What is problematic is your expectation that, in doing so, you should
> be better able to fit a particular feature in k space.  If you examine
> the data in k and q space, you will see that the act of Fourier
> filtering the data (i.e. plotting in q space) has the effect of
> suppressing the wiggle at 5 inv. Ang. that you are asking about.
> Given that you are fitting in q-space, it is completely unreasonable
> (from a numerical perspective) to expect that the fit could possibly
> reproduce a feature that you have (intentionally or otherwise)
> filtered out of the data.
> 
> To say that another way, given how you constructed the fit, you got a
> good fit.  You made the fit in a way that it cannot possibly reproduce
> the feature you are asking about, thus your question is ill-posed.
> 
> I think the deeper problem is that you don't have a deep grasp of what
> happens in Fourier analysis.  So let's talk about that a bit.
> 
> When you do the transform from k to R-space, you are representing the
> frequency spectrum contained in the original data.  Slow wiggling
> features in the original data give rise to the low-R
> (i.e. low-frequency) features in the chi(R) data.  Fast wiggling
> features in chi(k) give rise to high-R features in chi(R).  Your
> wiggle at 5 inv. Ang. looks to my eye like a pretty high frequency
> feature.
> 
> When you do the backwards transform from k to R with a restricted R
> range (in your case, from 1 to 3.5), you are filtering frequencies out
> of the data.  The chi(q) data only contains those frequencies from the
> original chi(k) spectrum that fall in your R range.
> 
> What I am suggesting is that the wiggle in question is due to Fourier
> components beyond 3.5 Ang in chi(R).
> 
> So, how would you reproduce that feature in chi(k)?  That's simple --
> fit features in the data beyond 3.5 in chi(R).  That is, do an actual
> good job of fitting the small signal from 3.5 to 5 Ang in R.
> 
> Of course, that's going to be difficult to do in a statistically
> robust manner because the signal is very small, there will be quite a
> large number of paths contributing to that region, and the
> parameteri

Re: [Ifeffit] fitting a specific k range

[Chris Patridge]

Matt,

Outside of the question of fitting the data, can you collect absorption data on 
the additional 3+ metal you are adding the material?  

Chris
 
***
Dr. Christopher Patridge
Assistant Professor
Department of Math and Natural Sciences 
D'youville College
Contact: 315-529-0501

On Dec 5, 2013, at 10:11 AM, Bruce Ravel  wrote:

> 
> Matt,
> 
> At the risk of coming off sounding a bit mean, I don't think you are
> asking a very well-posed question.
> 
> Examining the history of this project, I see that you are fitting in q
> space.  Like Matt, this is not my favorite choice, but there is
> nothing horribly wrong about it, so long as you understand what you
> are doing.
> 
> What is problematic is your expectation that, in doing so, you should
> be better able to fit a particular feature in k space.  If you examine
> the data in k and q space, you will see that the act of Fourier
> filtering the data (i.e. plotting in q space) has the effect of
> suppressing the wiggle at 5 inv. Ang. that you are asking about.
> Given that you are fitting in q-space, it is completely unreasonable
> (from a numerical perspective) to expect that the fit could possibly
> reproduce a feature that you have (intentionally or otherwise)
> filtered out of the data.
> 
> To say that another way, given how you constructed the fit, you got a
> good fit.  You made the fit in a way that it cannot possibly reproduce
> the feature you are asking about, thus your question is ill-posed.
> 
> I think the deeper problem is that you don't have a deep grasp of what
> happens in Fourier analysis.  So let's talk about that a bit.
> 
> When you do the transform from k to R-space, you are representing the
> frequency spectrum contained in the original data.  Slow wiggling
> features in the original data give rise to the low-R
> (i.e. low-frequency) features in the chi(R) data.  Fast wiggling
> features in chi(k) give rise to high-R features in chi(R).  Your
> wiggle at 5 inv. Ang. looks to my eye like a pretty high frequency
> feature.
> 
> When you do the backwards transform from k to R with a restricted R
> range (in your case, from 1 to 3.5), you are filtering frequencies out
> of the data.  The chi(q) data only contains those frequencies from the
> original chi(k) spectrum that fall in your R range.
> 
> What I am suggesting is that the wiggle in question is due to Fourier
> components beyond 3.5 Ang in chi(R).
> 
> So, how would you reproduce that feature in chi(k)?  That's simple --
> fit features in the data beyond 3.5 in chi(R).  That is, do an actual
> good job of fitting the small signal from 3.5 to 5 Ang in R.
> 
> Of course, that's going to be difficult to do in a statistically
> robust manner because the signal is very small, there will be quite a
> large number of paths contributing to that region, and the
> parameterization of many paths for such a small signal is likely not
> to be very robust.  EXAFS is hard!
> 
> Hope that helps,
> B
> 
> 
> On 12/04/2013 02:17 PM, Matt Frith wrote:
>> Dear All,
>> 
>> I need some help in fitting an amorphous iron oxyhydoxide sample.  I am
>> having difficulty producing a good fit, particularly in the k=4-6 range.
>> Fitting this region well is very important for me, because if I add
>> another metal(+3 oxidation state) into my system, this is where I
>> observe the most quantifiable changes (The shoulder @ 5 A^-1 and the min
>> @ 5.6 A^-1). Thus far I have been unable to fit the shoulder well enough
>> to make meaningful comparisons.
>> 
>> I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1
>> and Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths.
>> Attached is an Artemis file (P41_006_merge_norm_TRANS.fpj) for an
>> amorphous Fe oxyhydroxide sample (Fe only, no other metals). The data
>> was collected at the Fe K-edge.
>> 
>> *Is there a way to fit just this region (k~4-6 range) in k? If so what
>> is the best method for doing this? If not, does anyone have suggestions
>> as to how I can improve my fitting? Should I fit the data in k since the
>> shoulder is less evident in kq?*
>> 
>> Thank you for your time.
>> 
>> Sincerely,
>> 
>> Matt Frith
>> 
>> 
>> 
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>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
> 
> 
> -- 
> Bruce Ravel   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://xafs.org/BruceRavel
> Software:https://github.com/bruceravel
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Re: [Ifeffit] fitting a specific k range

[Bruce Ravel]

Matt,

At the risk of coming off sounding a bit mean, I don't think you are
asking a very well-posed question.

Examining the history of this project, I see that you are fitting in q
space.  Like Matt, this is not my favorite choice, but there is
nothing horribly wrong about it, so long as you understand what you
are doing.

What is problematic is your expectation that, in doing so, you should
be better able to fit a particular feature in k space.  If you examine
the data in k and q space, you will see that the act of Fourier
filtering the data (i.e. plotting in q space) has the effect of
suppressing the wiggle at 5 inv. Ang. that you are asking about.
Given that you are fitting in q-space, it is completely unreasonable
(from a numerical perspective) to expect that the fit could possibly
reproduce a feature that you have (intentionally or otherwise)
filtered out of the data.

To say that another way, given how you constructed the fit, you got a
good fit.  You made the fit in a way that it cannot possibly reproduce
the feature you are asking about, thus your question is ill-posed.

I think the deeper problem is that you don't have a deep grasp of what
happens in Fourier analysis.  So let's talk about that a bit.

When you do the transform from k to R-space, you are representing the
frequency spectrum contained in the original data.  Slow wiggling
features in the original data give rise to the low-R
(i.e. low-frequency) features in the chi(R) data.  Fast wiggling
features in chi(k) give rise to high-R features in chi(R).  Your
wiggle at 5 inv. Ang. looks to my eye like a pretty high frequency
feature.

When you do the backwards transform from k to R with a restricted R
range (in your case, from 1 to 3.5), you are filtering frequencies out
of the data.  The chi(q) data only contains those frequencies from the
original chi(k) spectrum that fall in your R range.

What I am suggesting is that the wiggle in question is due to Fourier
components beyond 3.5 Ang in chi(R).

So, how would you reproduce that feature in chi(k)?  That's simple --
fit features in the data beyond 3.5 in chi(R).  That is, do an actual
good job of fitting the small signal from 3.5 to 5 Ang in R.

Of course, that's going to be difficult to do in a statistically
robust manner because the signal is very small, there will be quite a
large number of paths contributing to that region, and the
parameterization of many paths for such a small signal is likely not
to be very robust.  EXAFS is hard!

Hope that helps,
B


On 12/04/2013 02:17 PM, Matt Frith wrote:

Dear All,

I need some help in fitting an amorphous iron oxyhydoxide sample.  I am
having difficulty producing a good fit, particularly in the k=4-6 range.
Fitting this region well is very important for me, because if I add
another metal(+3 oxidation state) into my system, this is where I
observe the most quantifiable changes (The shoulder @ 5 A^-1 and the min
@ 5.6 A^-1). Thus far I have been unable to fit the shoulder well enough
to make meaningful comparisons.

I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1
and Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths.
Attached is an Artemis file (P41_006_merge_norm_TRANS.fpj) for an
amorphous Fe oxyhydroxide sample (Fe only, no other metals). The data
was collected at the Fe K-edge.

*Is there a way to fit just this region (k~4-6 range) in k? If so what
is the best method for doing this? If not, does anyone have suggestions
as to how I can improve my fitting? Should I fit the data in k since the
shoulder is less evident in kq?*

Thank you for your time.

Sincerely,

Matt Frith



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--
 Bruce Ravel   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://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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Re: [Ifeffit] fitting a specific k range

[Matt Newville]

Hi Matt,

On Wed, Dec 4, 2013 at 1:17 PM, Matt Frith  wrote:
> Dear All,
>
>
> I need some help in fitting an amorphous iron oxyhydoxide sample.  I am
> having difficulty producing a good fit, particularly in the k=4-6 range.
> Fitting this region well is very important for me, because if I add another
> metal(+3 oxidation state) into my system, this is where I observe the most
> quantifiable changes (The shoulder @ 5 A^-1 and the min @ 5.6 A^-1). Thus
> far I have been unable to fit the shoulder well enough to make meaningful
> comparisons.
>
>
>
> I have been fitting in kq with kmin=2.566 And kmax=10.877, and Rmin=1 and
> Rmax=3.5, and using the goethite O1.1, Fe.1, and Fe.3 paths. Attached is an
> Artemis file (P41_006_merge_norm_TRANS.fpj) for an amorphous Fe oxyhydroxide
> sample (Fe only, no other metals). The data was collected at the Fe K-edge.
>
>
> Is there a way to fit just this region (k~4-6 range) in k? If so what is the
> best method for doing this? If not, does anyone have suggestions as to how I
> can improve my fitting? Should I fit the data in k since the shoulder is
> less evident in kq?
>
> Thank you for your time.
>
> Sincerely,
>
> Matt Frith

I haven't looked at your project, but yes, you can restrict the fit k
range.  Just use kmin=4,kmax=6.   That said, I would not recommend
using such a short k-range.  For one thing, if you get a fit that does
match your data well in this region but doesn't match outside this
region, would you call it a good fit?   I sure hope not.

In general, any "features" that appear in chi(k) are a mixture of many
distances, and you may have to go out very far in R to accurately
reproduce them.   There are cases where you only have to consider a
split second or third shell to reproduce a diagnostic k space feature
for some mineral phase, but again, the better approach is to describe
this as a structural (R space) feature that translates into a
spectroscopic (k space) one.

Someone may be able to come up with a good counter-argument, but I
recommend not ever fitting in "k" space or "q" space -- just fit in R
space.

--Matt
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[Ifeffit] questions related to ifeffit fitting

[davood dar]

Respected Sir,



I am new in the field of EXAFS. I have few questions regarding
to IFEFFIT i.e., fitting of theoretical models to the  experimental EXAFS
data.

1.What is the ideal value of R- factor for any fit.

2.  ** Can we use (fit) the theoretical model generated from square
pyramidal structure to EXAFS  data of  octahedral structure by assigning
degeneracy of 2 for the apical atom. OR using octalhedral for square planar
by not using apical path



Yours faithfully

Davood Ah. Dar

EXAFS research scholar

India
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[Ifeffit] questions regarding to ifeffit fitting

[davood dar]

Respected Sir,



I am new in the field of EXAFS. I have few questions regarding
to IFEFFIT i.e., fitting of theoretical models to the  experimental EXAFS
data.

1.   What is the ideal value of R- factor for any fit.

2.  *   * Can we use (fit) the theoretical model generated from square
pyramidal structure to EXAFS  data of  octahedral structure by assigning
degeneracy of 2 for the apical atom. OR using octalhedral for square planar
by not using apical path



Yours faithfully

Davood Ah. Dar

EXAFS research scholar

India
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Re: [Ifeffit] Fitting XANES spectrun with standards (Adrien Couet)

[adrien couet]

Thanks for the answer Bruce!

I think one thing I did not understand about the single fit is that it
tries to use all standards (although some of the standard's weights can be
equal to 0 in the results), which can be detrimental to the fitting. Thanks
a lot for the precisions, things are clearer now!

-- 
Adrien Couet
Graduate Student
Dept of Nuclear Engineering, Penn State University
+1 814 865 9709
axc1...@psu.edu
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Re: [Ifeffit] Fitting XANES spectrun with standards (Adrien Couet)

[Bruce Ravel]

On Friday, June 29, 2012 03:56:24 PM adrien couet wrote:
> Going back to the original question, I did select 8 standards for both
> cases (single fit with "fit this group" and combination of fits with "fit
> all combinations"), which gives me 247 combinations (see Excel file
> attached).
> In the case of the single fit I get a R-factor of 2.0x10-3 whereas for the
> best fit from the combinations I got 1.8x10-3 (the weights of each
> standards are also different in both cases).

My answer is still the same.

It is quite possible that I am not understanding your explanation, but
it seems as though you are comparing the best fit from the
combinatorial sequence with the individual fit that uses all 8
standards.

B


-- 

 Bruce Ravel   bra...@bnl.gov

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

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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Re: [Ifeffit] Fitting XANES spectrun with standards

[Bruce Ravel]

Adrien,

For starters, I am not very happy with your data.  With such short
pre- and post-edge ranges, I really doubt that you can reliably
normalize any of your data.  Without relilable normalization, I would
doubt any result you get from LCF.  In fact, if presented with data of
such limited range in a manuscript for review, I would be hard-pressed
to recommend publication.

But that is not the point of your question.

You have not given quite enough information about what you did, but I
have a guess as to the "problem".

"Fit all combinations" does a sequence of fits using all combinations
up to some number.  The default is four.  Using this default and your
set of 8 standards, that means the number of fits performed is
8-choose-4 + 8-choose-3 + 8-choose-2 = 70 + 56 + 28 = 154.  That is,
that bit of automation will attempt to find the best fit of the 154
ways of combining 4, 3, or 2 of the standards.  There are various ways
to tweak the total number of fits done in the combinatorial sequence.

As I said, you have not been clear about what steps you took, but it
would seem that you are comparing the results of that combinatorial
sequence of up to 4 standards with the result of fitting all 8
standards to your data.

Those are not and should not be the same.

The combinatorial fitting is just a wrapper around the normal fit.  In
this case, the combinatorial thing just does the normal fit 154 times.

If my assessment is not correct, you did something different, and you
think you have found a problem -- that's fine.  The software gets
better thanks to good bug reports.  Please remember that I need to be
able to reproduce on my computer EXACTLY what you did to expose the
problem. 

B


On Friday, June 29, 2012 10:30:57 AM adrien couet wrote:
> Hi all,
> 
> I am having some troubles when I fit XANES spectra with a library of
> standards. The unknown spectrum has been processed (background removal,
> normalization,...).
> 
> If I understand correctly the documentation, I have two ways to fit the
> unknown spectra:
> 
> - using "fit this group" and I will get the best fit using my standards
> library
> - using "fit all combinations" and I will get all the different fit results
> from the best to the worst.
> 
> However, it appears that the result given by "fit this group" does not
> correspond to the best fit given by "fit all combinations" (it often
> corresponds to a higher R factor fit), and thus "fit this group" does not
> give me the best fit possible. Are these two fitting processes using a
> different fitting algorithm?
> 
> I attached one example to this email. I am using a library of 8 different
> Fe standards to fit the unknown spectra.
> 
> Thanks for your attention


-- 

 Bruce Ravel   bra...@bnl.gov

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

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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Re: [Ifeffit] Fitting pre-edge feature in Fe XANES

[Erik Farquhar]

Hi Sharon,

In addition to Bruce's excellent advice on treating pre-edge analysis as a
generic fitting problem, you may also want to have a look at an earlier
systematic survey of Fe pre-edge analysis:  Westre, et al., J. Am. Chem. 
Soc. 1997, 119, 6297-6314 DOI: 10.1021/ja964352a. Note the constrained 
fitting range in that paper, which simplified the fitting problem a bit since 
they 
did not need to worry about accurately fitting the edge step and bumps 
along the rising edge using step functions and the like.

The only useful application of EXAFSPAK to your problem would be
to fit the pre-edge data using the EDG_FIT program of that package (this
was used in the Westre paper referred to above). This program has 
something of a learning curve to use well. If you have another peak-
fitting program that you like, then it's best to stick with that one.

Good luck,
Erik

--
Erik Farquhar, Ph.D.
Case Center for
Synchrotron Biosciences
Brookhaven National
Lab
NSLS, Building
725A-X3
Upton, NY 
11973
efarqu...@bnl.gov
+1-631-344-8174



From: "shb...@berkeley.edu" 
To: ifeffit@millenia.cars.aps.anl.gov 
Sent: Friday, June 8, 2012 2:18 PM
Subject: [Ifeffit] Fitting pre-edge feature in Fe XANES

Dear All:

I would like to attempt fits to the pre-edge features of a set of Fe
K-edge XANES spectra for Fe(II) samples that show partial oxidation with
the goal of determining whether Fe(III) exists in octahedral or
tetrahedral coordination (e.g. Wilke et al., American Mineralogist, 2001).

Broadly, the fitting procedure involves extracting the pre-edge feature
from the edge using a spline function and then deconvoluting this feature
using a set of pseudo-voigt functions.

I believe that I can use the LCF module in Sixpack to fit the feature
using the pseudo-voigt functions, but I'm having trouble extracting the
pre-edge feature.

I've tried using the spline function in Sixpack (and Athena), but I don't
have enough options to modify the spline. It seems to me that I need to
use a very rigid spline (for instance, one with only 3 or so knots), and
that the options in Sixpack and Athena don't allow for this.

I heard the program exafspak would allow me more freedom to control the
spline function, but I haven't been able to successfully download the
program, let alone use it. So, my questions are the following:

(1) Is there a program other than exafspak that I could use to fit a
spline to my data where I would have more control over the spline options?
I would prefer not to use exafspak since my knowledge of unix is nil.

(2) Has anyone used exafspak on a mac? I'm using OS 10.5.8 and I'd
appreciate any tips you might be able to give me on installing the
program. I followed the directions for installation provided on the
website, but the command to install the program (i.e. "add_exafs") wasn't
recognized.

Thanks for your help!

Sharon




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Re: [Ifeffit] Fitting pre-edge feature in Fe XANES

[Bruce Ravel]

On Friday, June 08, 2012 11:18:25 AM shb...@berkeley.edu wrote:
> I've tried using the spline function in Sixpack (and Athena), but I don't
> have enough options to modify the spline. It seems to me that I need to
> use a very rigid spline (for instance, one with only 3 or so knots), and
> that the options in Sixpack and Athena don't allow for this.

Sharon,

That is not the problem that the spline in Ifeffit (and therefore in
Athena and Sixpack) is designed to solve.  The purpose of Ifeffit's
spline is to isolate the chi(k) from mu(E) and it only aims to do so
reliably above 2 or so inverse Angstroms.  There are reasons for that:

 1. There are information theoretic limits to how much freedom the
chi(k) isolation spline should have.  In general, it cannot have
enough freedom to reliably go down the edge -- which is the
fastest changing part of the data.

 2. We typically do our EXAFS analysis starting a few inv. Ang above
k=0, so in practice Ifeffit's spline does what we want.

 3. The theory for EXAFS analysis is probably unreliable below 2 or 3
inv Ang, but quite reliable above that.  So if the spline cannot
isolate chi(k) below 2 or 3 and the theory cannot be trusted below
2 or 3, nothing is lost for EXAFS analysis.

So, I think your problem is that you are trying to use the wrong tool
for the job.  You want to treat your XANES data as a generic peak
fitting problem.  There are many, many options for that.  You don't
really need to rely upon software written explicitly for XAS data,
although many of them do some kind of peak fitting.  Athena does, for
example, using thinsg like arctangents and gaussians, although it is
perhaps not the strongest part of that program.  A general peak
fitting problem can be dealt with in something like Matlab or
Mathematica.  It can probably be done reasonably well in Excel.
Whatever

Step-like functions (like an arctangent) are often used to model the
edge.  I suppose you could use a spline for that, but it may be
challenging to give the spline enough freedom to follow the step-like
shape but not enough freedom that it wants to follow the peaks in the
egde.  That's the nice thing about an arctangent or an error function
-- purely a broadened step.

HTH,
B


-- 

 Bruce Ravel   bra...@bnl.gov

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

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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[Ifeffit] Fitting pre-edge feature in Fe XANES

[shbone]

Dear All:

I would like to attempt fits to the pre-edge features of a set of Fe
K-edge XANES spectra for Fe(II) samples that show partial oxidation with
the goal of determining whether Fe(III) exists in octahedral or
tetrahedral coordination (e.g. Wilke et al., American Mineralogist, 2001).

Broadly, the fitting procedure involves extracting the pre-edge feature
from the edge using a spline function and then deconvoluting this feature
using a set of pseudo-voigt functions.

I believe that I can use the LCF module in Sixpack to fit the feature
using the pseudo-voigt functions, but I'm having trouble extracting the
pre-edge feature.

I've tried using the spline function in Sixpack (and Athena), but I don't
have enough options to modify the spline. It seems to me that I need to
use a very rigid spline (for instance, one with only 3 or so knots), and
that the options in Sixpack and Athena don't allow for this.

I heard the program exafspak would allow me more freedom to control the
spline function, but I haven't been able to successfully download the
program, let alone use it. So, my questions are the following:

(1) Is there a program other than exafspak that I could use to fit a
spline to my data where I would have more control over the spline options?
I would prefer not to use exafspak since my knowledge of unix is nil.

(2) Has anyone used exafspak on a mac? I'm using OS 10.5.8 and I'd
appreciate any tips you might be able to give me on installing the
program. I followed the directions for installation provided on the
website, but the command to install the program (i.e. "add_exafs") wasn't
recognized.

Thanks for your help!

Sharon




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Re: [Ifeffit] fitting sulphur using standards by Athena

[Matthew Marcus]

To reiterate a point which is often not understood - dilution won't fix overabsorption if the particles of the concentrated material 
which are mixed in with the diluent are too big.  For concentrated S compounds, "too big" is in the low microns.
When I run a S standard, I do it in total electron yield to avoid this problem.  When I fit a S spectrum, I use a crude 
oveabsorption model with a single parameter which is treated as an unknown fitting parameter, with the assumption

that the reference spectra were collected in a way which avoids overabsorption.
   mam
- Original Message - 
From: "Bruce Ravel" 

To: "XAFS Analysis using Ifeffit" 
Sent: Tuesday, February 14, 2012 6:07 AM
Subject: Re: [Ifeffit] fitting sulphur using standards by Athena



On Tuesday, February 14, 2012 07:55:54 am 陈娟 wrote:

As I known, the spectra for standard diluted with BN and non-diluted are
different. The peak of the non-diluted is low due to self-absorption, as
shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur
to about 3%. For dilution, the position of the peak is also changed.
Therefore the non-diluted s1 spectra isnot the real spectra of
dibenzothiophene. The question is what percentage should I dilute the
standard to get the credible spectra for the standards?and how to explain
the peak position change?


Although this sort of thing can be approximated from tables of
absorption coefficients, the advice I usually give to my users is to
prepare a series of samples of diminishing concetrations and measure
then.

Having a good intuition for sample preparation and the effects of poor
sample preparation is always important and even more so for low energy
edges.  The best way to develop that intuition is by doing the
experiment yourself.


Can I use Athena to counteract the self-absorption and get the
credible spectra for sdandards?


Yes it can -- in principle.  Doing a good job of self absorption
correction requires a lot of knowledge about your sample and its
matrix -- often more than one has.

The use of the self absorption tool is explained in the Athena
document.  I have also written a lecture on this topic.  Go to

 https://github.com/bruceravel/XAS-Education/downloads

and download the "selfabs.pdf" file.

B


--

Bruce Ravel   bra...@bnl.gov

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

My homepage:http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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Re: [Ifeffit] fitting sulphur using standards by Athena

[Bruce Ravel]

On Tuesday, February 14, 2012 07:55:54 am 陈娟 wrote:
> As I known, the spectra for standard diluted with BN and non-diluted are
> different. The peak of the non-diluted is low due to self-absorption, as
> shown in the figure below. S1 is non-diluted and s1_10 is diluted sulphur
> to about 3%. For dilution, the position of the peak is also changed.
> Therefore the non-diluted s1 spectra isnot the real spectra of
> dibenzothiophene. The question is what percentage should I dilute the
> standard to get the credible spectra for the standards?and how to explain
> the peak position change? 

Although this sort of thing can be approximated from tables of
absorption coefficients, the advice I usually give to my users is to
prepare a series of samples of diminishing concetrations and measure
then.

Having a good intuition for sample preparation and the effects of poor
sample preparation is always important and even more so for low energy
edges.  The best way to develop that intuition is by doing the
experiment yourself.

> Can I use Athena to counteract the self-absorption and get the
> credible spectra for sdandards?

Yes it can -- in principle.  Doing a good job of self absorption
correction requires a lot of knowledge about your sample and its
matrix -- often more than one has.

The use of the self absorption tool is explained in the Athena
document.  I have also written a lecture on this topic.  Go to 

  https://github.com/bruceravel/XAS-Education/downloads

and download the "selfabs.pdf" file.

B


-- 

 Bruce Ravel   bra...@bnl.gov

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

 My homepage:http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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Re: [Ifeffit] Fitting on Athena

[Matt Newville]

Niken,

Have you compared MBACK to using the 'CLnorm' normalization in Athena
(found under "Background Removal Additional Parameters")?   The
algorithms are not identical, but have a lot in common, and would
probably make it easier to compare with other data in Athena.   If I
understand correctly, your sulfur spectra were not collected in
fluorescence with a solid-state detector, so that part of what MBACK
is really good at doesn't apply, and the CLnorm normalization is
pretty close to other part of MBACK.

I'd be interested to know if you or anyone else has done a careful
study comparing MBACK, CLnorm, and other normalization procedures.

--Matt
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Re: [Ifeffit] Fitting on Athena

[Bruce Ravel]

On Wednesday, September 07, 2011 07:52:38 pm Niken Wijaya wrote:
> I think I have to clarify that I used MBACK to do the normalization 
> instead of ATHENA. This might as well explain why I got such a high 
> value of y-axis offset, why you think I did not choose the right 
> parameters for the "pre-edge" and "normalization range" and also why I 
> imported the data as normalized mu(E) rather than mu(E). As mentioned in 
> the manual, doing normalization in Athena is very subjective, tiny 
> difference in the point chosen for both the "pre-edge region" and 
> "normalization range" will result in different normalized spectra. Due 
> to lack of experience in processing XAFS spectra and noisy spectra 
> obtained, I was planning to eliminate this problem by using MBACK. My 
> initial plan was to combine the benefit I can get from both ATHENA and 
> MBACK. So, I did the normalization using MBACK, then do the 
> self-absorption correction and fit the normalized spectra in ATHENA. 
> However, looking at your comment, LCF in ATHENA requires edge-step 
> normalization, by saying that, does it mean that I cannot normalized my 
> spectra using MBACK then fit them in ATHENA?

Niken,

So, you want to use MBACK because it is less subjective than Autobk.
How, then, do you then plan to do your self absorption correction in a
similarly and defensibly rigorous manner?  I am suspicious that you
have not thought this through very well.

Your original email suggested that you believed there to be a problem
with Athena.  A cursory examination of your work -- once you actually
did the favor of posting a project file -- made it clear to me that
you are not using the program correctly.  Indeed, in one of your
emails, you made it clear that you have never read the documentation.

I am unaware of a bug in Athena that precludes using data normalized
outside of Athena to do LCF within Athena.  That may not be the mornal
mode of operation, but it is a reasonable thing to want to do.  You
must take care to import the data correctly and verify that the form
of your data has been preserved before performing the LCF.  If you
expect the program to magically do what you want rather then observing
how the program actually behaves, it is unlikely that you will be
satisfied with the results.

Is it possible that there is a bug that precludes Athena from doing
this thing?  Of course.  A quick examination of the archives of this
mailing list should make it clear that my software is *way* less than
perfect.  So far, you have not given me any reason to belive that's
the case.

B




-- 

 Bruce Ravel   bra...@bnl.gov

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

 My homepage:http://xafs.org/BruceRavel
 EXAFS software:  http://cars9.uchicago.edu/ifeffit/Demeter
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Re: [Ifeffit] Fitting on Athena

[Niken Wijaya]

On 7/09/2011 7:24 AM, Bruce Ravel wrote:

On Sunday, September 04, 2011 08:52:30 pm Niken Wijaya wrote:

1. As you can see on the figure (i.e. filename: ifeffitlist-sample1
fitting), the intensity of the fitting spectra is higher than the actual
sample. This is I believe due to the higher intensity of the individual
standard compounds when compared to the spectra of my samples (i.e.
filename: ifeffitlist-intensity). This is the case for every fitting I
did for my sample so I am just not sure with the fitting results.

Well, there are a lot of problems contributing to your confusion.

One thing that probably doesn't help, but which certainly isn't the
central problem, is that you have extremely large values for the
y-axis offset parameter of several of the standards.  This makes it
difficult to plot normalized spectra in an unconfusing way.

Your central problem is that, for most of the data groups, the values
of parameters for the pre-edge and normalization lines are not well
chosen.  It would seem that you trusted the default values without
checking them.  See

   http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html

In your case, the default values resulted in unusably short ranges for
thepre-edge line or the post-edge line or both.  The moral of this
story is to plot the data with its pre- and post-edge lines to verify
that the values result in sensible normalization.  See

   http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/plot/tabs.html

You also had a problem that some of your data were somehow imported as
normalized mu(E) rather than as mu(E) or xanes(E).  See

   
http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/columns.html#datatypesandenergyunits

This is usually not a good idea as it tells Athena that your data are
already reliably normalized and should not be further processed.
Those data, however, were not unit edge-step normalized, which is what
the LCF utility requires.  The way to fix that in an existing Athena
project file is explained just a little further down on that same
page.

Once I fixed the datatype for all of your groups and performed a
sensible normalization for your data, I got the LCF fit shown in the
attached image.  Not great, but not the ridiculous result you were
getting with so many things done wrongly in your project file.

I think that the underlying problem is that you expected Athena to
magically do the right thing with your data without verifying its
results.  Or, perhaps, you plowed forward without fully understanding
how to use the program.  The documentation isn't exactly exciting
reading, but it doesn't completely suck.  You might want to bookmark
its URL.



2. If we see figure "ifeffitlist-sample39", we can see that the spectra
has different slopes on the pre and post-edge region. When I used MBACK
for background removal, the normalized spectra is weird, illustrated in
"sample39-fig-norm.pdf". What is the best way to fix this issue? I have
5 samples with this feature that I cannot process due to the weird
normalized spectra.

Well, MBACk isn't my thing, so I can only comment on it in general
terms.  I suspect that you would get better results if you severely
truncated your data, say from about 2455 to 2515.  Something wonky
happens in that spectrum at the beginning and the end.  I suspect that
MBACK is having trouble figuring out what part of the data is actually
the edge step.


3. Regarding the self-absorption correction, I was not aware that Athena
has this function. I will have a look at the manual again. Thank you for
letting me know.

   http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/process/sa.html

Again, not exciting ... doesn't suck ... bookmark.

Here's a talk I gave at the University of Ghent last January on the
topic of self-absortion corrections.  It may be of some help to you:

   http://cars9.uchicago.edu/~ravel/misc/selfabs.pdf


4. With the 3rd derivative spectrum, I did indeed derive it from the
normalized values. As you can see from the file I attached earlier, from
the experts points of view, do you think I should go on with the Nth
derivative spectra or due to the very low signal-to-noise ratio of the
spectra, I should just focus on the absorption spectra?

I don't really have an opinion one way or the other about the 3rd
derivative.  The folks from Stanford and CLS who do a lot of sulfur
work have made extensive use of the 3rd derivative and they are really
smart people.  I haven't done a lot of S work in my own career and
none of Athena's users have ever asked for a 3rd derivative option, so
Athena doesn't currently do that.

B

PS: Doesn't it just blow your mind how there is a strong correlation
between quality and clarity of the question and specificity of the
answer?  Amazing...!




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Hi Bruce,

I think I have to clarify 

Re: [Ifeffit] Fitting on Athena

[Bruce Ravel]

On Sunday, September 04, 2011 08:52:30 pm Niken Wijaya wrote:
> 1. As you can see on the figure (i.e. filename: ifeffitlist-sample1 
> fitting), the intensity of the fitting spectra is higher than the actual 
> sample. This is I believe due to the higher intensity of the individual 
> standard compounds when compared to the spectra of my samples (i.e. 
> filename: ifeffitlist-intensity). This is the case for every fitting I 
> did for my sample so I am just not sure with the fitting results.

Well, there are a lot of problems contributing to your confusion.

One thing that probably doesn't help, but which certainly isn't the
central problem, is that you have extremely large values for the
y-axis offset parameter of several of the standards.  This makes it
difficult to plot normalized spectra in an unconfusing way.

Your central problem is that, for most of the data groups, the values
of parameters for the pre-edge and normalization lines are not well
chosen.  It would seem that you trusted the default values without
checking them.  See

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html

In your case, the default values resulted in unusably short ranges for
thepre-edge line or the post-edge line or both.  The moral of this
story is to plot the data with its pre- and post-edge lines to verify
that the values result in sensible normalization.  See

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/plot/tabs.html

You also had a problem that some of your data were somehow imported as
normalized mu(E) rather than as mu(E) or xanes(E).  See

  
http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/columns.html#datatypesandenergyunits

This is usually not a good idea as it tells Athena that your data are
already reliably normalized and should not be further processed.
Those data, however, were not unit edge-step normalized, which is what
the LCF utility requires.  The way to fix that in an existing Athena
project file is explained just a little further down on that same
page.

Once I fixed the datatype for all of your groups and performed a
sensible normalization for your data, I got the LCF fit shown in the
attached image.  Not great, but not the ridiculous result you were
getting with so many things done wrongly in your project file.

I think that the underlying problem is that you expected Athena to
magically do the right thing with your data without verifying its
results.  Or, perhaps, you plowed forward without fully understanding
how to use the program.  The documentation isn't exactly exciting
reading, but it doesn't completely suck.  You might want to bookmark
its URL.


> 2. If we see figure "ifeffitlist-sample39", we can see that the spectra 
> has different slopes on the pre and post-edge region. When I used MBACK 
> for background removal, the normalized spectra is weird, illustrated in 
> "sample39-fig-norm.pdf". What is the best way to fix this issue? I have 
> 5 samples with this feature that I cannot process due to the weird 
> normalized spectra.

Well, MBACk isn't my thing, so I can only comment on it in general
terms.  I suspect that you would get better results if you severely
truncated your data, say from about 2455 to 2515.  Something wonky
happens in that spectrum at the beginning and the end.  I suspect that
MBACK is having trouble figuring out what part of the data is actually
the edge step.

> 3. Regarding the self-absorption correction, I was not aware that Athena 
> has this function. I will have a look at the manual again. Thank you for 
> letting me know.

  http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/process/sa.html

Again, not exciting ... doesn't suck ... bookmark.

Here's a talk I gave at the University of Ghent last January on the
topic of self-absortion corrections.  It may be of some help to you:

  http://cars9.uchicago.edu/~ravel/misc/selfabs.pdf

> 4. With the 3rd derivative spectrum, I did indeed derive it from the 
> normalized values. As you can see from the file I attached earlier, from 
> the experts points of view, do you think I should go on with the Nth 
> derivative spectra or due to the very low signal-to-noise ratio of the 
> spectra, I should just focus on the absorption spectra?

I don't really have an opinion one way or the other about the 3rd
derivative.  The folks from Stanford and CLS who do a lot of sulfur
work have made extensive use of the 3rd derivative and they are really
smart people.  I haven't done a lot of S work in my own career and
none of Athena's users have ever asked for a 3rd derivative option, so
Athena doesn't currently do that.

B

PS: Doesn't it just blow your mind how there is a strong correlation
between quality and clarity of the question and specificity of the
answer?  Amazing...!


-- 

 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 5

[Ifeffit] Fitting on Athena

[bruceravel1]

Niken Wijaya writes:
 > Hi Everyone,
 > 
 > I am facing a lot of problems when I am trying to fit my sample's
 > spectra with my standards one. Initially, I used Athena to do the
 > background subtraction, but the fitting results are just too "funny".
 > The fitting does not really fit the actual spectra. Since I am analyzing
 > Sulphur and many papers has reported how it is prone to self-absorption
 > effect, I thought, probably if I am using a better background
 > subtraction such as MBACK, I would get a better results. So I decided to
 > use it for the normalization and unlike in Athena, the normalized
 > intensity of the spectra does not equal to 1. By saying this, the
 > intensity of my standard models is way higher than the actual samples.
 > Hence, when I use Athena to fit my real spectra, I would not get a good
 > results. I have also tried using the 3rd derivative of my absorption
 > spectra, but the fitting results are even worse. The intensity of the
 > "fit" spectra is way higher than the actual spectra of my samples that I
 > am trying to fit it with. In fact, when I stack the spectra from the
 > standards and the sample together, the 3rd derivative peak of the
 > samples is almost completely flat due to the very high intensity of the
 > standards themselves.
 > 
 > What did I do wrong? and what can I do to fix it? I have also attached
 > my samples and standards spectra.
 > 
 > Thank you very much for the assistance.

Hi Niken,

It's a little hard to know what's going on.  The reason that we like
having Athena project files attached to these postings is because it
is then much easier to evaluate the provenance of the problem.  That
is, the Athena project file retains some of the history of the data.
We can evaluate how you have processed the data to arrive at the point
of having a problem with the analysis.

Given the text files you have attached, it is very difficult to know
how to advise you because it is very difficult to understand the
problem you are having.  I know that you tried to explain the problem,
but a picture is, as they say, worth a thousand (unlear, slightly
rambly) words.

That said, I do have a few comments.

1. There are good reasons to use an algorithm like MBACK rather than
   the simpler pre- and post-edge normalizaton that Athena offers.
   Fixing the problem of self-absorption is not one of those reasons.
   Self-absorption makes the fine structure oscillations smaller.  No
   normalization algorithm will magically undo that problem.

   Although Athena (or other software) might have a tool for
   correcting self-absorption, the only really good way of dealing
   with that problem is to not have it inthe first place.  For some
   samples, self absorption is unavoidable.  But if it is possible to
   modify your sample to minimize that effect, then you should most
   certainly do so.

2. The third derivative might be a useful tool, as you say.  It is,
   however, esential that you make your Nth derivative spectrum
   (regardless of the value of N) on normalized data or else the data
   you examine will not be on the same scale.  Another issue with high
   order derivatives is that they tend to amplify the size of the
   noise with respect to the signal.  One of your spectra has that
   problem.  Analysis of derivative spectra is one of the few
   situations in which I think that smoothing is helpful and
   defensible.

If you choose to pursue this issue further here on the mailing list, I
encourage you not only to add a project file, but to avoid the sort of
fuzzy language you used in this posting.  Saying things like "funny
fitting results" and "way higher intensities" is just to unclear and
subjective.  It often helps to attach a screenshot to better
demonstrate what you are trying to say.

B


-- 
 Bruce Ravel  brucerav...@gmail.com
 Homepage --- http://xafs.org/BruceRavel
 EXAFS software - http://github.com/bruceravel/demeter/
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[Ifeffit] Fitting bond lengths without a known FEFF file

[Hana]

Dear list experts,
Here is another challenging question for me; can someone help?
I have soil samples, trying to fit the first shell, I have 3 different optional 
bond lengths, which might give a lot of information. Now I have two questions:

1. If I do not know of specific structure (XRD implies a very amorphous 
material), so no specific FEFF file that I can use. what would be my way to 
determine the parameters for IFEFFIT (Deg, Reff, amp,...)?

2. Is there any option to fit the 3 bond lengths together (no dependency that I 
can think of...)? Should I fit all pairs, then accordingly assume one 
component; 
'set' it and fit the other two as fractions of 1 (N+(1-N)? 

Thanks!!

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[Ifeffit] fitting

[mohamed sobhy]

- Forwarded Message 
From: mohamed sobhy 
To: ifeffit@millenia.cars.aps.anl.gov
Sent: Thu, May 20, 2010 4:14:18 PM
Subject: [Ifeffit] fitting


Dear all thanks for your help and explanation about the background
I
fitted my data after removing the background and in the attached file I
got this fitting, although all the values are good but I think the coordination 
number should be less than 8 (for the first shell) due to irradiation.
So how can I get the right coordination number?
How to improve the fitting of second shell?
thanks  



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[Ifeffit] fitting

[mohamed sobhy]

Dear all thanks for your help and explanation about the background
I
fitted my data after removing the background and in the attached file I
got this fitting, although all the values are good but I think the coordination 
number should be less than 8 (for the first shell) due to irradiation.
So how can I get the right coordination number?
How to improve the fitting of second shell?
thanks  


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Re: [Ifeffit] fitting

[Iztok Arčon]

Dear Mohamed,

There is an example of CeO2 EXAFS analysis, taking into account 
background problems,

in the following paper:
*J. Padežnik Gomilšek, I. Kozjek-Škofic, N. Bukovec, A. Kodre
*/X-ray absorption study of CeO2 and Ce/V mixed oxide thin films 
obtained by sol-gel deposition. /*

*Thin solid films,  vol. 446, issue 1, (2004) 117-123.
regards
Iztok Arcon

mohamed sobhy wrote:


Dear all
I am trying to use artemis to do fitting to CeO2. But really I cant 
get the right way to do that.
During the fitting, I am using amp as set and change in N degeneracy 
of the path. attached is the best fit i got but it still not good and 
the chi-square is 41.109065479

so can you suggest me what to do

thanks

Mohamed




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--
Iztok Arcon
University of Nova Gorica
Vipavska 13, POB 301
5001 Nova Gorica, Slovenia

tel: +386 5 331 5227
fax: +386 5 331 5240
e-mail: iztok.ar...@ung.si
http://www.ung.si/~arcon
http://www.ung.si/~arcon/xas

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Re: [Ifeffit] fitting

[Bruce Ravel]

On Thursday 13 May 2010, 05:21:02 pm, mohamed sobhy wrote:

> Dear all
> I am trying to use artemis to do fitting to CeO2. But really I cant get the
>  right way to do that. During the fitting, I am using amp as set and change
>  in N degeneracy of the path. attached is the best fit i got but it still
>  not good and the chi-square is 41.109065479 so can you suggest me what to
>  do

Mohamed,

I think you need to do some homework.

Along with Shelly's suggestion, I suspect that you need to read up on the 
meaning of the Rbkg parameter in Athena.  There is some discussion of this in 
the Athena manual.  Shelly's book chapter is very useful.

I suggest you also read up on what's been written about how to interpret chi-
square.  Look through the stuff at xafs.org.  Matt, Shelly, and Scott -- as 
well as myself and others -- have written extensively about how to think about 
chi-square.  It is not obvious just from looking at a picture that there is 
anything wrong with your fit.

B

-- 
 Bruce Ravel   bra...@bnl.gov

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

 My homepage:http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
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Re: [Ifeffit] fitting

[shelly Kelly]

I agree. 

To see if the problem is at high k, just make three copies of the data and then 
ft it with larger values for kmax.  That would indicate noise as the 
problem.

You can do the same at low k by adjusting kmin. That would indicate a problem 
with the background.

You can find examples of these methods in my book chapter.  Send me an 
email and I'll send it to you.

Tht
Shelly



-- Sent from my Palm Prē
On May 13, 2010 4:53 PM, Stefan Mangold <stefan.mang...@iss.fzk.de> 
wrote: 

Hello,
to ideas coming into my mind without an look at your data:
1. Very noisy data ... (may produce to many peaks)2. problems with the 
background correction
regards
Stefan
Am 13.05.2010 um 23:34 schrieb María Elena Montero Cabrera:I don't know 
anything about CeO2, but...for me there is something wrong since the Athena 
fitting, because there are too many peaks below the main one, and specially 
below 1 A. Am I right or not?

Maria Elena 


2010/5/13 Frenkel, Anatoly <fren...@bnl.gov>

There is a large number of articles explaining how to fit CeO2 including 
discussions why multi-electron excitatoins complicate the fit, and some of 
those authors (e.g., A. Soldatov, but also M. Benfatto) propose first principle 
methods that account for those.


Some papers even show that ignoring those contributions may give a decent fit, 
but you should be aware of the multitudes of theoretical issues surrounding 
EXAFS modeling of this system before trying it on your own.



Anatoly











From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of mohamed sobhy

Sent: Thu 5/13/2010 5:21 PM

To: ifeffit@millenia.cars.aps.anl.gov

Subject: [Ifeffit] fitting





Dear all

I am trying to use artemis to do fitting to CeO2. But really I cant get the 
right way to do that.

During the fitting, I am using amp as set and change in N degeneracy of the 
path. attached is the best fit i got but it still not good and the chi-square 
is 41.109065479

so can you suggest me what to do



thanks



Mohamed








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-- 
María Elena

Dra. María Elena Montero Cabrera
Departamento de Medio Ambiente y Energía
Centro de Investigación en Materiales Avanzados (CIMAV)
Miguel de Cervantes 120, Compl. Ind. Chihuahua

Chihuahua CP 31109, Chih. México
Tel (614) 4391123

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--
Dr. Stefan Mangold
Institut für Synchrotronstrahlung
Forschungszentrum Karlsruhe
Tel.: +49-7247-826073



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Re: [Ifeffit] fitting

[Stefan Mangold]

Hello,

to ideas coming into my mind without an look at your data:

1. Very noisy data ... (may produce to many peaks)
2. problems with the background correction

regards

Stefan

Am 13.05.2010 um 23:34 schrieb María Elena Montero Cabrera:

> I don't know anything about CeO2, but...for me there is something wrong since 
> the Athena fitting, because there are too many peaks below the main one, and 
> specially below 1 A. Am I right or not?
> 
> Maria Elena 
> 
> 2010/5/13 Frenkel, Anatoly 
> There is a large number of articles explaining how to fit CeO2 including 
> discussions why multi-electron excitatoins complicate the fit, and some of 
> those authors (e.g., A. Soldatov, but also M. Benfatto) propose first 
> principle methods that account for those.
> Some papers even show that ignoring those contributions may give a decent 
> fit, but you should be aware of the multitudes of theoretical issues 
> surrounding EXAFS modeling of this system before trying it on your own.
> 
> Anatoly
> 
> 
> 
> 
> 
> From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of mohamed sobhy
> Sent: Thu 5/13/2010 5:21 PM
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: [Ifeffit] fitting
> 
> 
> Dear all
> I am trying to use artemis to do fitting to CeO2. But really I cant get the 
> right way to do that.
> During the fitting, I am using amp as set and change in N degeneracy of the 
> path. attached is the best fit i got but it still not good and the chi-square 
> is 41.109065479
> so can you suggest me what to do
> 
> thanks
> 
> Mohamed
> 
> 
> 
> 
> ___
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> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> 
> 
> 
> 
> -- 
> María Elena
> 
> Dra. María Elena Montero Cabrera
> Departamento de Medio Ambiente y Energía
> Centro de Investigación en Materiales Avanzados (CIMAV)
> Miguel de Cervantes 120, Compl. Ind. Chihuahua
> Chihuahua CP 31109, Chih. México
> Tel (614) 4391123
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> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

--
Dr. Stefan Mangold
Institut für Synchrotronstrahlung
Forschungszentrum Karlsruhe
Tel.: +49-7247-826073

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Re: [Ifeffit] fitting

[Frenkel, Anatoly]

Then what I wrote is an overkill...
Anatoly
 


From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of María Elena 
Montero Cabrera
Sent: Thu 5/13/2010 5:34 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] fitting


I don't know anything about CeO2, but...for me there is something wrong since 
the Athena fitting, because there are too many peaks below the main one, and 
specially below 1 A. Am I right or not?

Maria Elena 


2010/5/13 Frenkel, Anatoly 


There is a large number of articles explaining how to fit CeO2 
including discussions why multi-electron excitatoins complicate the fit, and 
some of those authors (e.g., A. Soldatov, but also M. Benfatto) propose first 
principle methods that account for those.
Some papers even show that ignoring those contributions may give a 
decent fit, but you should be aware of the multitudes of theoretical issues 
surrounding EXAFS modeling of this system before trying it on your own.

Anatoly





From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of mohamed 
sobhy
Sent: Thu 5/13/2010 5:21 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] fitting



Dear all
I am trying to use artemis to do fitting to CeO2. But really I cant get 
the right way to do that.
During the fitting, I am using amp as set and change in N degeneracy of 
the path. attached is the best fit i got but it still not good and the 
chi-square is 41.109065479
so can you suggest me what to do

thanks

Mohamed





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-- 
María Elena

Dra. María Elena Montero Cabrera
Departamento de Medio Ambiente y Energía
Centro de Investigación en Materiales Avanzados (CIMAV)
Miguel de Cervantes 120, Compl. Ind. Chihuahua
Chihuahua CP 31109, Chih. México
Tel (614) 4391123

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Re: [Ifeffit] fitting

[María Elena Montero Cabrera]

I don't know anything about CeO2, but...for me there is something wrong
since the Athena fitting, because there are too many peaks below the main
one, and specially below 1 A. Am I right or not?

Maria Elena

2010/5/13 Frenkel, Anatoly 

> There is a large number of articles explaining how to fit CeO2 including
> discussions why multi-electron excitatoins complicate the fit, and some of
> those authors (e.g., A. Soldatov, but also M. Benfatto) propose first
> principle methods that account for those.
> Some papers even show that ignoring those contributions may give a decent
> fit, but you should be aware of the multitudes of theoretical issues
> surrounding EXAFS modeling of this system before trying it on your own.
>
> Anatoly
>
>
>
> 
>
> From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of mohamed sobhy
> Sent: Thu 5/13/2010 5:21 PM
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: [Ifeffit] fitting
>
>
> Dear all
> I am trying to use artemis to do fitting to CeO2. But really I cant get the
> right way to do that.
> During the fitting, I am using amp as set and change in N degeneracy of the
> path. attached is the best fit i got but it still not good and the
> chi-square is 41.109065479
> so can you suggest me what to do
>
> thanks
>
> Mohamed
>
>
>
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>


-- 
María Elena

Dra. María Elena Montero Cabrera
Departamento de Medio Ambiente y Energía
Centro de Investigación en Materiales Avanzados (CIMAV)
Miguel de Cervantes 120, Compl. Ind. Chihuahua
Chihuahua CP 31109, Chih. México
Tel (614) 4391123
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Re: [Ifeffit] fitting

[Frenkel, Anatoly]

There is a large number of articles explaining how to fit CeO2 including 
discussions why multi-electron excitatoins complicate the fit, and some of 
those authors (e.g., A. Soldatov, but also M. Benfatto) propose first principle 
methods that account for those.
Some papers even show that ignoring those contributions may give a decent fit, 
but you should be aware of the multitudes of theoretical issues surrounding 
EXAFS modeling of this system before trying it on your own. 
 
Anatoly
 




From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of mohamed sobhy
Sent: Thu 5/13/2010 5:21 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] fitting


Dear all 
I am trying to use artemis to do fitting to CeO2. But really I cant get the 
right way to do that.
During the fitting, I am using amp as set and change in N degeneracy of the 
path. attached is the best fit i got but it still not good and the chi-square 
is 41.109065479
so can you suggest me what to do

thanks

Mohamed



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[Ifeffit] fitting

[mohamed sobhy]

Dear all 
I am trying to use artemis to do fitting to CeO2. But really I cant get the 
right way to do that.
During the fitting, I am using amp as set and change in N degeneracy of the 
path. attached is the best fit i got but it still not good and the chi-square 
is 41.109065479
so can you suggest me what to do

thanks

Mohamed


  

athena.emf
Description: Binary data
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Re: [Ifeffit] fitting simultaneously two different K-edges

[Matt Newville]

Dear Maria,

If you haven't already done so, I would suggest that you begin by
separately fitting the data for each edge on each sample.  This will
give you a good understanding of the local structure around each metal
ion.   Once you have this intimacy with the structural models, you
will be able to tell what might be constrained between the two
different metal atoms.   Once you get to that point, getting the
software to combine the fits will not seem very hard ;).


--Matt


2010/5/1 María Elena Montero Cabrera :
> Dear friends, Sam Webb, Bruce Ravel or any other,
>
> I have XAFS measurements, performed at SSRL at room temperature, of three
> compounds. All compounds have multielemental character and I have K-edge
> XAFS of two elements in each compound. It is desirable to make IFEFFIT
> fitting of both edges simultaneously. In all cases random solution of
> competing elements is assumed, but there are ferroelectricity,
> superconductivity or magnetic behaviors that are desirable to be explained.
> In each case, XAFS would confirm or reject the random character of the
> solution. I am not such an expert for resolving by myself how to fit
> together two edges using Artemis software. I'll present each case in the
> following:
>
> 1. rutheno-cuprate (Ru1-xNbx)Sr2Eu1.4 Ce0.6Cu2O10+δ compounds series was
> studied in both Ru and Nb K-edges. Changes in interatomic distances that
> could be obtained by EXAFS would tell something about oxygen octahedra
> around Ru and Nb.
>
> 2. g-Fe1-xCrxO3 maghemite for x=0.25, 0.5 and 0.75 was investigated by XAFS
> in both Fe and Cr K-edges. Possible distortion of oxygen octahedra around
> both Fe(III) and Cr(III) cations would tell something about not confirmed
> ferroelectricity.
>
> 3. LaFeNiTiO3 has been confirmed to display magnetic behavior and was
> studied by its Fe and Ti K-edges. Interatomic distances that could be
> obtained by EXAFS are interesting for checking possible preferential
> occupation of sites by Fe or Ti atoms.
>
> Would any of you, please, suggest how to use Artemis or Sixpack for solving
> these problems?
>
> Sincerely yours
>
> --
> María Elena
>
> Dra. María Elena Montero Cabrera
> Departamento de Medio Ambiente y Energía
> Centro de Investigación en Materiales Avanzados (CIMAV)
> Miguel de Cervantes 120, Compl. Ind. Chihuahua
> Chihuahua CP 31109, Chih. México
> Tel (614) 4391123
>
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>
>
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Re: [Ifeffit] fitting simultaneously two different K-edges

[Bruce Ravel]

Maria Elena,

This paper by Scott Calvin is a good place to start nderstanding
multiple data set fitting:

  S. Calvin, et al., Phys Rev B, 66:22, (2002) p. 224405

It is, of course, on a rather different system from the ones you
mention below, but the ideas are excellent and well explained.  The
concepts should be transferable to your measurements.

B



On Saturday 01 May 2010 12:53:44 pm María Elena Montero Cabrera wrote:
> Dear friends, Sam Webb, Bruce Ravel or any other,
> 
> I have XAFS measurements, performed at SSRL at room temperature, of three
> compounds. All compounds have multielemental character and I have K-edge
> XAFS of two elements in each compound. It is desirable to make IFEFFIT
> fitting of both edges simultaneously. In all cases random solution of
> competing elements is assumed, but there are ferroelectricity,
> superconductivity or magnetic behaviors that are desirable to be explained.
> In each case, XAFS would confirm or reject the random character of the
> solution. I am not such an expert for resolving by myself how to fit
> together two edges using Artemis software. I'll present each case in the
> following:
> 
> 1. rutheno-cuprate (Ru1-xNbx)Sr2Eu1.4 Ce0.6Cu2O10+δ compounds series was
> studied in both Ru and Nb K-edges. Changes in interatomic distances that
> could be obtained by EXAFS would tell something about oxygen octahedra
> around Ru and Nb.
> 
> 2. g-Fe1-xCrxO3 maghemite for x=0.25, 0.5 and 0.75 was investigated by XAFS
> in both Fe and Cr K-edges. Possible distortion of oxygen octahedra around
> both Fe(III) and Cr(III) cations would tell something about not confirmed
> ferroelectricity.
> 
> 3. LaFeNiTiO3 has been confirmed to display magnetic behavior and was
> studied by its Fe and Ti K-edges. Interatomic distances that could be
> obtained by EXAFS are interesting for checking possible preferential
> occupation of sites by Fe or Ti atoms.
> 
> Would any of you, please, suggest how to use Artemis or Sixpack for solving
> these problems?
> Sincerely yours
> 

-- 

 Bruce Ravel   bra...@bnl.gov

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

 My homepage:http://xafs.org/BruceRavel
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
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[Ifeffit] fitting simultaneously two different K-edges

[María Elena Montero Cabrera]

Dear friends, Sam Webb, Bruce Ravel or any other,

I have XAFS measurements, performed at SSRL at room temperature, of three
compounds. All compounds have multielemental character and I have K-edge
XAFS of two elements in each compound. It is desirable to make IFEFFIT
fitting of both edges simultaneously. In all cases random solution of
competing elements is assumed, but there are ferroelectricity,
superconductivity or magnetic behaviors that are desirable to be explained.
In each case, XAFS would confirm or reject the random character of the
solution. I am not such an expert for resolving by myself how to fit
together two edges using Artemis software. I'll present each case in the
following:

1. rutheno-cuprate (Ru1-xNbx)Sr2Eu1.4 Ce0.6Cu2O10+δ compounds series was
studied in both Ru and Nb K-edges. Changes in interatomic distances that
could be obtained by EXAFS would tell something about oxygen octahedra
around Ru and Nb.

2. g-Fe1-xCrxO3 maghemite for x=0.25, 0.5 and 0.75 was investigated by XAFS
in both Fe and Cr K-edges. Possible distortion of oxygen octahedra around
both Fe(III) and Cr(III) cations would tell something about not confirmed
ferroelectricity.

3. LaFeNiTiO3 has been confirmed to display magnetic behavior and was
studied by its Fe and Ti K-edges. Interatomic distances that could be
obtained by EXAFS are interesting for checking possible preferential
occupation of sites by Fe or Ti atoms.

Would any of you, please, suggest how to use Artemis or Sixpack for solving
these problems?
Sincerely yours

-- 
María Elena

Dra. María Elena Montero Cabrera
Departamento de Medio Ambiente y Energía
Centro de Investigación en Materiales Avanzados (CIMAV)
Miguel de Cervantes 120, Compl. Ind. Chihuahua
Chihuahua CP 31109, Chih. México
Tel (614) 4391123
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Re: [Ifeffit] fitting

[Shelly Kelly]

Hi Mohamed:

It is hard to help you without some more information. The coordination
number (CN) is a little bit complicated by the high correlation it has
with the value for S02, degeneracy, and the normalization edge step.
You have to have all of those things correct to get the CN correct.
If you are just starting out, I'd suggest reading my book chapter and
some of the tutorials on the www.xafs.org web site.  If you send me an
email, I'll send you my book chapter.

Cheers,
Shelly Kelly
dr.sdke...@gmail.com


On Thu, Apr 22, 2010 at 1:50 PM, mohamed sobhy  wrote:
> Dear all
> I am trying to fit some data of coordination number 8, but I always find the
> fitting of the first shell give the coordination number only about 0.5.
> I do not know what is wrong. Do I need to fit first and second and third
> shells altogether, and if that is right how Can I do that??
> Thanks
>
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>
>
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[Ifeffit] fitting

[mohamed sobhy]

Dear all 
I am trying to fit some data of coordination number 8, but I always find the 
fitting of the first shell give the coordination number only about 0.5.
I
do not know what is wrong. Do I need to fit first and second and third
shells altogether, and if that is right how Can I do that??
Thanks


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Re: [Ifeffit] Fitting results

[Shelly Kelly]

Hi Abhijeet,

I think that there is a problem with you structure for Cu2O.  Each Cu
atoms must be coordinated by more than just two O atoms in the first
shell.

Shelly

On Thu, Jan 21, 2010 at 1:28 AM, Abhijeet Gaur  wrote:
> Hello Sir,
>    I had done fitting of a Cu2O data taken at SSRL EXAFS
> beamline in transmission mode, Stanford, by my research guide
>    Dr. B. D. Shrivastava.
>    I had used here the fiting procedure as discussed before in
> this mailing list. The fitted curves are coming   nice, but the
>   values of some fitting parameters are not reliable as shown
> bold below.
>   amp = 0.4898160   +/-  0.0469990    (1.)
>   enot    = 7.6843630   +/-  0.4828620    (0.)
>   alpha   = 0.0022670   +/-  0.0030950    (0.)
>   ss011   = 0.0003280   +/-  0.0013130    (0.0030)
>   sscu11  = 0.0174780   +/-  0.0016220    (0.0030)
>   sscu11o11   = 0.0470530   +/-  0.0655560    (0.0030)
>   ss012   = 0.0070100   +/-  0.0044660    (0.0030)
>   sscu12  = 0.0186980   +/-  0.0093570    (0.0030)
>   ss013cu11   = 0.0088980   +/-  0.0190580    (0.0030)
>   sscu13  = 0.0196150   +/-  0.0062940    (0.0030)
>   sscu13012   = 0.0084870   +/-  0.0067030    (0.0030)
>   sscu11cu11  = 0.0071110   +/-  0.0132390    (0.0030)
>   sscu12cu11  = 0.0111440   +/-  0.0139470    (0.0030)
> Def parameters (using "FEFF0: Path 1: [O1_1]"):
>   delr    = 0.0041920
>
> So, if someone can please tell me that where I had done wrong or what should
> I do to make things right I will be very thankful.The Artemis project
> file is attached herewith.
>
>    With regards
>     Abhijeet Gaur
>     Research Scholar
>     School of Studies in Physics
>     Vikram University, Ujjain (INDIA)
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Re: [Ifeffit] Fitting using Experimental standard

[Matthew]

The very valid question whenever the topic of empirical standards
comes up is "Why do you think you need it?"  I am unconvinced that
empirical standards are ever needed.  Of course, I am also unconvinced
that I am right in saying that!  So who knows...?  There is some
evidence that empirical standards might be preferable in certain
specific cases, such as the case in which a hydrogen atom is collinear
or nearly collinear with an absorber and scatterer.


From a the persepective of "guy who writes programs" I suppose the

fact that there is interest in having the capability of using
empirical standards is itself good enough reason to include it.


One reason I can think of is when the unknown is in some sense close to a model, for instance, a glass compared with a corresponding 
crystal, a dilute solid solution compared with an appropriate compound, if one exists,
or a nanoparticle compared with bulk.  In that case, one might argue that Nature's calculation might be more accurate than FEFF, and 
that the use of a model will automatically correct for artifacts in the extraction of the (filtered) shell.

I will grant that this is now a niche technique whereas, when I started 
 years ago, it was mainstream.
   mam 


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Re: [Ifeffit] Fitting using Experimental standard

[Bruce Ravel]

On Monday 04 January 2010 10:16:15 pm you wrote:
> Dear all,
> Can somebody please explain to me what is theoretical standard and what is
> experimental standard. My understanding of theoretical standard is the
> crystallographic data. However, it is first time I heard experimental
> standard.
> Thanks
>

While certainly not wrong, I don't think any of the answers given last
night answered Fiona's question as I would have liked.

The paradigm for interpreting EXAFS data offered by a real-space
multiple scattering program like Feff relies upon the so-called path
expansion.  This means that the EXAFS from a given configuration of
atoms can be expressed as the sum of the contributions from each
scattering path.  That is

  chi_total(k) = sum_over_all_paths [ chi_path(k) ]

In this language, a "scattering path" is some closed loop wherein the
photoelectron ejected from the atom by the incident photon scatters
from one or more atoms in the cluster before closing the loop back at
the absorbing atom.

For each such path, chi(k) is evaluated like so:

N S_0^2 F(k)
  chi(k) = - sin( 2kR + phi(k) ) exp( -2k^2sigma^2 )
  2kR^2

There is also an exponetial term considering the photoelectron
mean-free-path that I am neglecting in this discussion.  There might
also, in some approaches, be additional disorder terms expressed as
cumulants, adding an additional term to the sine and an additional
exponential term. 

In a fitting program like Artemis, the parameters of this equation
come in two flavors.  

One flavor includes the terms 2R (the length of the path), sigma^2
(the mean square disorder about that path length), N (the number of
such paths), S_0^2 (the amplitude reduction factor that has to do with
the details of the behavior of the other electrons in the system), and
a handful of others.  The parameters of this type are the things that
may be parameterized in Artemis to yield answers to questions such as
"What is the coordination number of the absorber?" and "How far is the
absorber from the atoms in the second coordination shell?"

The other flavor of parameters includes the terms F(k) and phi(k).
These are the scattering amplitude and phase shift.  These are
k-dependent functions that have to do with the details of the atomic
species of the absorber and scatterer(s), the number of legs that the
scattering path has, and the angles through which the photoelectron
scatters as it traverses the path.  In Artemis, parameters of this
type are computed by Feff and typically not altered during the
course of the fit.  That is, Artemis takes the Feff calculations of
the various F(k) and phi(k) functions as gospel and uses them as the
basis for determining the values of the first flavor of parameters.

Abhijeet's original question was whether Artemis is only able to
determine the F(k) and phi(k) functions using a Feff calculation or if
it is able to somehow extract approximations of F(k) and phi(k) from
another set of experimental data using a technique like those
discussed by Matthew and Anatoly.

The short answer is "no, Artemis cannot use experimentally extracted
F(k) and phi(k) functions -- it does require the use of Feff."

The longer answer is that Matthew's request from his last email of the
night -- that someone code up a way to automate the extraction the
F(k) and phi(k) from experimental data and save it in a form that
Artemis or some other Feff-using program could use -- has long been on
my list of potential things to do with my software and may actually
happen one of these days.

The very valid question whenever the topic of empirical standards
comes up is "Why do you think you need it?"  I am unconvinced that
empirical standards are ever needed.  Of course, I am also unconvinced
that I am right in saying that!  So who knows...?  There is some
evidence that empirical standards might be preferable in certain
specific cases, such as the case in which a hydrogen atom is collinear
or nearly collinear with an absorber and scatterer.

>From a the persepective of "guy who writes programs" I suppose the
fact that there is interest in having the capability of using
empirical standards is itself good enough reason to include it.

HTH,
B

PS: Please note that, strictly speaking, I was describing Feff,
Ifeffit, and Artemis.  Other real-space multiple scattering programs
and other fitting programms using Feff incorporate important
differences from what I explained above.  But the bottom line
distinction between theoretical and empirical standards is about the
same in all cases.



> Fiona R. Kizewski
> Ph.D. Candidate
> Department of Chemistry
> North Carolina State University
> Raleigh North Carolina 27695
> 
> > On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:
> >> Generally the fitting is done using theoretical standards. For that in
> >> Artemis, we give input as crystallographic data. But If we want to use
> >> an
> >> experimental standard instead of
> >> theoretical stan

Re: [Ifeffit] Fitting using Experimental standard

[Matthew Marcus]

I wonder if some kind soul with some programming time to spare (ha ha) could 
write a program to do that.  It would be relatively simple,
but does need the knowledge of how to write a FEFF path.  It would ask 
questions like where the phase and amp files are, what k-power
was used, what the distance is, which path number to use, etc. then write out 
the ASCII path in the appropriate directory for Artemis.
A potential problem is what to do about the data range, since a normal FEFF 
path goes from k=0 to k=20 (from memory) and most data doesn't.
Also, there would be a problem if the reference-compound data didn't go as far 
as the data one is trying to fit because Artemis would have
no obvious way of knowing that the "FEFF path" is bogus beyond a certain 
k-range.  I guess the program would have to ask for the data
file being fitted and issue a warning, or just let the user find out the hard 
way :-)
mam

On 1/4/2010 8:05 PM, Frenkel, Anatoly wrote:

I doctored FEFF path.
Not sure if Artemis offers anything better and less intrusive than this 
trick but I think it is still the only way to use experimental standards 
for fits (other than the ratio method that is implemented in athena as 
Bruce desribed, which is used for monoatomic shells only).

A.



*From*: ifeffit-boun...@millenia.cars.aps.anl.gov 


*To*: XAFS Analysis using Ifeffit 
*Sent*: Mon Jan 04 22:54:30 2010
*Subject*: Re: [Ifeffit] Fitting using Experimental standard

Ah, I see.  I think Artemis has some way of putting in experimental 
phase and amp, but that may be just to make a "corrected" FT.  Is that so?
Otherwise, I suppose it should be possible to write a fake FEFF path 
file and read it in.  I guess that's what you did.

mam

- Original Message -
*From:* Frenkel, Anatoly <mailto:fren...@bnl.gov>
*To:* ifeffit@millenia.cars.aps.anl.gov
<mailto:ifeffit@millenia.cars.aps.anl.gov>
*Sent:* Monday, January 04, 2010 7:43 PM
*Subject:* Re: [Ifeffit] Fitting using Experimental standard

Thank you, Matthew.
As they say in Russia, everything new is well forgotten old.
Seriously, that paper was really how to use FEFFIT for both
experimental and theoretical standards, not just theoretical.

A.


- Original Message -
From: ifeffit-boun...@millenia.cars.aps.anl.gov
<mailto:ifeffit-boun...@millenia.cars.aps.anl.gov>
mailto:ifeffit-boun...@millenia.cars.aps.anl.gov>>
To: XAFS Analysis using Ifeffit 
    Sent: Mon Jan 04 22:34:56 2010
Subject: Re: [Ifeffit] Fitting using Experimental standard

You're describing the way many of us, including me, used to analyze
data before FEFF became as reliable and easy to use (courtesy of
Artemis and the like) as it is now.  As shown in the paper,
you extract amplitude and phase from model compounds, by
back-transforming filtered shells, then use those to fit data.  Multiple
data sets aren't new, either; I used to do that with data taken on
dilute solid solutions at different temperatures.  Another trick I
used to use a lot was if I didn't have a standard for the right
pair of atoms, I'd use FEFF to get the difference in scattering
factors (phase+amp)
between the pair I wanted and a nearby (in Z) pair I had data for. 
For instance, you can get CuAl2 as  a compound and extract the

phase+amp for Cu as the central atom and Al as the scatterer.  You
can't do
that for Cu and Si because there's no Si-rich intermetallic in the
CuSi system.  Therefore, you can do:

Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al)
Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al)

and get a "semi-empirical" Cu->Si "standard".  Why the +- for phase
and the */ for amp?  You can think of it as extrapolating the
log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the
measured chi is the Im().
This expresses everything in terms of relatively slowly-varying
quantities and treats amp and phi as parts of the same quantity,
which they really are.

One of the programs available from the ALS beamline 10.3.2 website
http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is
called EXAFSfit and does this sort of fitting to amp and phase.  You
feed it amp and phases which
come from the FT program, also available at the website.  The amp
and phase files are simple 2-column ASCII, thus readable anywhere.
mam
- Original Message -
    From: "Frenkel, Anatoly" 
To: "XAFS Analysis using Ifeffit" 
Sent: Monday, January 04, 2010 6:21 PM
Subject: Re: [Ifeffit] Fitting using Experimental standard


I know of one very obscure conference proceeding

Re: [Ifeffit] Fitting using Experimental standard

[Frenkel, Anatoly]

I doctored FEFF path.
Not sure if Artemis offers anything better and less intrusive than this trick 
but I think it is still the only way to use experimental standards for fits 
(other than the ratio method that is implemented in athena as Bruce desribed, 
which is used for monoatomic shells only).
A.





From: ifeffit-boun...@millenia.cars.aps.anl.gov 
 
To: XAFS Analysis using Ifeffit  
Sent: Mon Jan 04 22:54:30 2010
Subject: Re: [Ifeffit] Fitting using Experimental standard 


Ah, I see.  I think Artemis has some way of putting in experimental phase and 
amp, but that may be just to make a "corrected" FT.  Is that so?
Otherwise, I suppose it should be possible to write a fake FEFF path file and 
read it in.  I guess that's what you did.
mam

- Original Message - 
From: Frenkel, Anatoly <mailto:fren...@bnl.gov>  
To: ifeffit@millenia.cars.aps.anl.gov 
Sent: Monday, January 04, 2010 7:43 PM
    Subject: Re: [Ifeffit] Fitting using Experimental standard


Thank you, Matthew.
As they say in Russia, everything new is well forgotten old.
Seriously, that paper was really how to use FEFFIT for both 
experimental and theoretical standards, not just theoretical.

A.


- Original Message -
From: ifeffit-boun...@millenia.cars.aps.anl.gov 

To: XAFS Analysis using Ifeffit 
Sent: Mon Jan 04 22:34:56 2010
    Subject: Re: [Ifeffit] Fitting using Experimental standard

You're describing the way many of us, including me, used to analyze 
data before FEFF became as reliable and easy to use (courtesy of
Artemis and the like) as it is now.  As shown in the paper,
you extract amplitude and phase from model compounds, by 
back-transforming filtered shells, then use those to fit data.  Multiple
data sets aren't new, either; I used to do that with data taken on
dilute solid solutions at different temperatures.  Another trick I used 
to use a lot was if I didn't have a standard for the right
pair of atoms, I'd use FEFF to get the difference in scattering factors 
(phase+amp)
between the pair I wanted and a nearby (in Z) pair I had data for.  For 
instance, you can get CuAl2 as  a compound and extract the
phase+amp for Cu as the central atom and Al as the scatterer.  You 
can't do
that for Cu and Si because there's no Si-rich intermetallic in the CuSi 
system.  Therefore, you can do:

Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al)
Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al)

and get a "semi-empirical" Cu->Si "standard".  Why the +- for phase and 
the */ for amp?  You can think of it as extrapolating the
log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the 
measured chi is the Im().
This expresses everything in terms of relatively slowly-varying 
quantities and treats amp and phi as parts of the same quantity,
which they really are.

One of the programs available from the ALS beamline 10.3.2 website 
http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is
called EXAFSfit and does this sort of fitting to amp and phase.  You 
feed it amp and phases which
come from the FT program, also available at the website.  The amp and 
phase files are simple 2-column ASCII, thus readable anywhere.
mam
- Original Message -
From: "Frenkel, Anatoly" 
To: "XAFS Analysis using Ifeffit" 
Sent: Monday, January 04, 2010 6:21 PM
Subject: Re: [Ifeffit] Fitting using Experimental standard


I know of one very obscure conference proceeding describing what you 
are looking for. It was written during pre-Artemis times but
the method can be used with Artemis, of course.

A. I. Frenkel, M. Vairavamurthy, and M. Newville,
A study of the coordination environment in aqueous cadmium-thiol 
complexes by EXAFS spectroscopy: experimental vs. theoretical
standards
J. Synchrotron Rad., 8 , 669-771 (2001).

The link to PDF is here:
https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf

Anatoly



From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet 
gaur
Sent: Mon 1/4/2010 9:15 AM
To: ifeffit
Subject: [Ifeffit] Fitting using Experimental standard


A very happy new year to all

Generally the fitting is done using theoretical standards. For that in 
Artemis, we give input as crystallographic data. But If we
want to use an ex

Re: [Ifeffit] Fitting using Experimental standard

[Matthew]

Re: [Ifeffit] Fitting using Experimental standardAh, I see.  I think Artemis 
has some way of putting in experimental phase and amp, but that may be just to 
make a "corrected" FT.  Is that so?
Otherwise, I suppose it should be possible to write a fake FEFF path file and 
read it in.  I guess that's what you did.
mam
  - Original Message - 
  From: Frenkel, Anatoly 
  To: ifeffit@millenia.cars.aps.anl.gov 
  Sent: Monday, January 04, 2010 7:43 PM
  Subject: Re: [Ifeffit] Fitting using Experimental standard


  Thank you, Matthew.
  As they say in Russia, everything new is well forgotten old.
  Seriously, that paper was really how to use FEFFIT for both experimental and 
theoretical standards, not just theoretical.

  A.


  - Original Message -
  From: ifeffit-boun...@millenia.cars.aps.anl.gov 

  To: XAFS Analysis using Ifeffit 
  Sent: Mon Jan 04 22:34:56 2010
  Subject: Re: [Ifeffit] Fitting using Experimental standard

  You're describing the way many of us, including me, used to analyze data 
before FEFF became as reliable and easy to use (courtesy of
  Artemis and the like) as it is now.  As shown in the paper,
  you extract amplitude and phase from model compounds, by back-transforming 
filtered shells, then use those to fit data.  Multiple
  data sets aren't new, either; I used to do that with data taken on
  dilute solid solutions at different temperatures.  Another trick I used to 
use a lot was if I didn't have a standard for the right
  pair of atoms, I'd use FEFF to get the difference in scattering factors 
(phase+amp)
  between the pair I wanted and a nearby (in Z) pair I had data for.  For 
instance, you can get CuAl2 as  a compound and extract the
  phase+amp for Cu as the central atom and Al as the scatterer.  You can't do
  that for Cu and Si because there's no Si-rich intermetallic in the CuSi 
system.  Therefore, you can do:

  Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al)
  Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al)

  and get a "semi-empirical" Cu->Si "standard".  Why the +- for phase and the 
*/ for amp?  You can think of it as extrapolating the
  log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured 
chi is the Im().
  This expresses everything in terms of relatively slowly-varying quantities 
and treats amp and phi as parts of the same quantity,
  which they really are.

  One of the programs available from the ALS beamline 10.3.2 website 
http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is
  called EXAFSfit and does this sort of fitting to amp and phase.  You feed it 
amp and phases which
  come from the FT program, also available at the website.  The amp and phase 
files are simple 2-column ASCII, thus readable anywhere.
  mam
  - Original Message -
  From: "Frenkel, Anatoly" 
  To: "XAFS Analysis using Ifeffit" 
  Sent: Monday, January 04, 2010 6:21 PM
  Subject: Re: [Ifeffit] Fitting using Experimental standard


  I know of one very obscure conference proceeding describing what you are 
looking for. It was written during pre-Artemis times but
  the method can be used with Artemis, of course.

  A. I. Frenkel, M. Vairavamurthy, and M. Newville,
  A study of the coordination environment in aqueous cadmium-thiol complexes by 
EXAFS spectroscopy: experimental vs. theoretical
  standards
  J. Synchrotron Rad., 8 , 669-771 (2001).

  The link to PDF is here:
  https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf

  Anatoly

  

  From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet gaur
  Sent: Mon 1/4/2010 9:15 AM
  To: ifeffit
  Subject: [Ifeffit] Fitting using Experimental standard


  A very happy new year to all

  Generally the fitting is done using theoretical standards. For that in 
Artemis, we give input as crystallographic data. But If we
  want to use an experimental standard instead of
  theoretical standard, how that can be done. Is it possible to use 
experimental standard in Artemis? or we have to use some other
  method.

  with thanks
  Abhijeet Gaur
  School of Studies in Physics
  Vikram University, Ujjain (India)





  



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Re: [Ifeffit] Fitting using Experimental standard

[Frenkel, Anatoly]

Thank you, Matthew.
As they say in Russia, everything new is well forgotten old.
Seriously, that paper was really how to use FEFFIT for both experimental and 
theoretical standards, not just theoretical.

A.


- Original Message -
From: ifeffit-boun...@millenia.cars.aps.anl.gov 

To: XAFS Analysis using Ifeffit 
Sent: Mon Jan 04 22:34:56 2010
Subject: Re: [Ifeffit] Fitting using Experimental standard

You're describing the way many of us, including me, used to analyze data before 
FEFF became as reliable and easy to use (courtesy of 
Artemis and the like) as it is now.  As shown in the paper,
you extract amplitude and phase from model compounds, by back-transforming 
filtered shells, then use those to fit data.  Multiple 
data sets aren't new, either; I used to do that with data taken on
dilute solid solutions at different temperatures.  Another trick I used to use 
a lot was if I didn't have a standard for the right 
pair of atoms, I'd use FEFF to get the difference in scattering factors 
(phase+amp)
between the pair I wanted and a nearby (in Z) pair I had data for.  For 
instance, you can get CuAl2 as  a compound and extract the 
phase+amp for Cu as the central atom and Al as the scatterer.  You can't do
that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. 
 Therefore, you can do:

Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al)
Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al)

and get a "semi-empirical" Cu->Si "standard".  Why the +- for phase and the */ 
for amp?  You can think of it as extrapolating the 
log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured 
chi is the Im().
This expresses everything in terms of relatively slowly-varying quantities and 
treats amp and phi as parts of the same quantity, 
which they really are.

One of the programs available from the ALS beamline 10.3.2 website 
http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is 
called EXAFSfit and does this sort of fitting to amp and phase.  You feed it 
amp and phases which
come from the FT program, also available at the website.  The amp and phase 
files are simple 2-column ASCII, thus readable anywhere.
mam
- Original Message - 
From: "Frenkel, Anatoly" 
To: "XAFS Analysis using Ifeffit" 
Sent: Monday, January 04, 2010 6:21 PM
Subject: Re: [Ifeffit] Fitting using Experimental standard


I know of one very obscure conference proceeding describing what you are 
looking for. It was written during pre-Artemis times but 
the method can be used with Artemis, of course.

A. I. Frenkel, M. Vairavamurthy, and M. Newville,
A study of the coordination environment in aqueous cadmium-thiol complexes by 
EXAFS spectroscopy: experimental vs. theoretical 
standards
J. Synchrotron Rad., 8 , 669-771 (2001).

The link to PDF is here:
https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf

Anatoly



From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet gaur
Sent: Mon 1/4/2010 9:15 AM
To: ifeffit
Subject: [Ifeffit] Fitting using Experimental standard


A very happy new year to all

Generally the fitting is done using theoretical standards. For that in Artemis, 
we give input as crystallographic data. But If we 
want to use an experimental standard instead of
theoretical standard, how that can be done. Is it possible to use experimental 
standard in Artemis? or we have to use some other 
method.

with thanks
Abhijeet Gaur
School of Studies in Physics
Vikram University, Ujjain (India)








> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> 

___
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Re: [Ifeffit] Fitting using Experimental standard

[Matthew]

An experimental standard is an EXAFS spectrum of a known compound.  If you pick the right known compound (and if such exists) then 
you have an isolatable shell consisting only of scattering from one kind of atom, with
the others being at distances sufficiently different so that one can Fourier-filter them out.  Nowadays, a more standard procedure 
is to fit your standard compound using Artemis or the like, then use that fit as a starting point
for a fit to the unknown.  The accuracy with which the fit to the standard reproduces the known (crystallographic) values tells you 
how well EXAFS worked in the case of your compound.  Also, the coordination number you get
for the dominant shell, relative to what it's "supposed to be", tells you the S0^2.  If you get strange values like 0.1 or 20 then 
you know something's wrong.  If you get plausible numbers, you can think about substituting those in
for the S02 in the unknown and taking the resultant amplitudes as coordination numbers.  Similarly, if the model compound is really 
similar to the unknown, you can start your fit to the unknown using the values for E0 and Ds2 you got from the

model.
   mam
- Original Message - 
From: "Fiona R. Kizewski" 

To: ; "XAFS Analysis using Ifeffit" 

Sent: Monday, January 04, 2010 7:16 PM
Subject: Re: [Ifeffit] Fitting using Experimental standard



Dear all,
Can somebody please explain to me what is theoretical standard and what is
experimental standard. My understanding of theoretical standard is the
crystallographic data. However, it is first time I heard experimental
standard.
Thanks

Fiona R. Kizewski
Ph.D. Candidate
Department of Chemistry
North Carolina State University
Raleigh North Carolina 27695





On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:


Generally the fitting is done using theoretical standards. For that in
Artemis, we give input as crystallographic data. But If we want to use
an
experimental standard instead of
theoretical standard, how that can be done. Is it possible to use
experimental standard in Artemis? or we have to use some other method.



Artemis does not do fitting with experimental standards, although Athena
does
have a dialog for doing log-ratio/phase-difference analysis.

B
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Re: [Ifeffit] Fitting using Experimental standard

[Matthew]

You're describing the way many of us, including me, used to analyze data before FEFF became as reliable and easy to use (courtesy of 
Artemis and the like) as it is now.  As shown in the paper,
you extract amplitude and phase from model compounds, by back-transforming filtered shells, then use those to fit data.  Multiple 
data sets aren't new, either; I used to do that with data taken on
dilute solid solutions at different temperatures.  Another trick I used to use a lot was if I didn't have a standard for the right 
pair of atoms, I'd use FEFF to get the difference in scattering factors (phase+amp)
between the pair I wanted and a nearby (in Z) pair I had data for.  For instance, you can get CuAl2 as  a compound and extract the 
phase+amp for Cu as the central atom and Al as the scatterer.  You can't do

that for Cu and Si because there's no Si-rich intermetallic in the CuSi system. 
 Therefore, you can do:

Amp(Cu->Si) = Amp_exp(Cu->Al)*Amp_Feff(Cu->Si)/Amp_Feff(Cu->Al)
Phi(Cu->Si) = Phi_exp(Cu->Al)+Phi_Feff(Cu->Si)-Phi_Feff(Cu->Al)

and get a "semi-empirical" Cu->Si "standard".  Why the +- for phase and the */ for amp?  You can think of it as extrapolating the 
log of a complex signal chi~(k) = Amp(k)*exp(i*Phi(k)), of which the measured chi is the Im().
This expresses everything in terms of relatively slowly-varying quantities and treats amp and phi as parts of the same quantity, 
which they really are.


One of the programs available from the ALS beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm is 
called EXAFSfit and does this sort of fitting to amp and phase.  You feed it amp and phases which

come from the FT program, also available at the website.  The amp and phase 
files are simple 2-column ASCII, thus readable anywhere.
   mam
- Original Message - 
From: "Frenkel, Anatoly" 

To: "XAFS Analysis using Ifeffit" 
Sent: Monday, January 04, 2010 6:21 PM
Subject: Re: [Ifeffit] Fitting using Experimental standard


I know of one very obscure conference proceeding describing what you are looking for. It was written during pre-Artemis times but 
the method can be used with Artemis, of course.


A. I. Frenkel, M. Vairavamurthy, and M. Newville,
A study of the coordination environment in aqueous cadmium-thiol complexes by EXAFS spectroscopy: experimental vs. theoretical 
standards

J. Synchrotron Rad., 8 , 669-771 (2001).

The link to PDF is here:
https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf

Anatoly



From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet gaur
Sent: Mon 1/4/2010 9:15 AM
To: ifeffit
Subject: [Ifeffit] Fitting using Experimental standard


A very happy new year to all

Generally the fitting is done using theoretical standards. For that in Artemis, we give input as crystallographic data. But If we 
want to use an experimental standard instead of
theoretical standard, how that can be done. Is it possible to use experimental standard in Artemis? or we have to use some other 
method.


with thanks
Abhijeet Gaur
School of Studies in Physics
Vikram University, Ujjain (India)









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Re: [Ifeffit] Fitting using Experimental standard

[Scott Calvin]

Hi Fiona,

An experimental standard is a spectrum of a known material (the term  
is also often used for the known material itself, in addition to its  
spectrum). If you use Athena to do a linear combination fit, you are  
most commonly using experimental standards to do it.


A theoretical standard is a theoretically simulated spectrum of some  
structure. Thus, the theoretical standard is not the crystallographic  
data itself, although that data can serve as a basis for generating a  
theoretical standard using software such as FEFF.


--Scott Calvin
Sarah Lawrence College

On Jan 4, 2010, at 7:16 PM, Fiona R. Kizewski wrote:


Dear all,
Can somebody please explain to me what is theoretical standard and  
what is

experimental standard. My understanding of theoretical standard is the
crystallographic data. However, it is first time I heard experimental
standard.
Thanks


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Re: [Ifeffit] Fitting using Experimental standard

[Fiona R. Kizewski]

Dear all,
Can somebody please explain to me what is theoretical standard and what is
experimental standard. My understanding of theoretical standard is the
crystallographic data. However, it is first time I heard experimental
standard.
Thanks

Fiona R. Kizewski
Ph.D. Candidate
Department of Chemistry
North Carolina State University
Raleigh North Carolina 27695




> On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:
>
>> Generally the fitting is done using theoretical standards. For that in
>> Artemis, we give input as crystallographic data. But If we want to use
>> an
>> experimental standard instead of
>> theoretical standard, how that can be done. Is it possible to use
>> experimental standard in Artemis? or we have to use some other method.
>>
>
> Artemis does not do fitting with experimental standards, although Athena
> does
> have a dialog for doing log-ratio/phase-difference analysis.
>
> B
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Re: [Ifeffit] Fitting using Experimental standard

[Frenkel, Anatoly]

I know of one very obscure conference proceeding describing what you are 
looking for. It was written during pre-Artemis times but the method can be used 
with Artemis, of course.
 
A. I. Frenkel, M. Vairavamurthy, and M. Newville, 
A study of the coordination environment in aqueous cadmium-thiol complexes by 
EXAFS spectroscopy: experimental vs. theoretical standards 
J. Synchrotron Rad., 8 , 669-771 (2001).
 
The link to PDF is here:
https://pubweb.bnl.gov/~frenkel/EXP-FEFF/thiols.pdf
 
Anatoly
 


From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of abhijeet gaur
Sent: Mon 1/4/2010 9:15 AM
To: ifeffit
Subject: [Ifeffit] Fitting using Experimental standard


A very happy new year to all 
 
Generally the fitting is done using theoretical standards. For that in Artemis, 
we give input as crystallographic data. But If we want to use an experimental 
standard instead of 
theoretical standard, how that can be done. Is it possible to use experimental 
standard in Artemis? or we have to use some other method. 
 
with thanks
Abhijeet Gaur
School of Studies in Physics
Vikram University, Ujjain (India)
 
 
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Re: [Ifeffit] Fitting using Experimental standard

[Bruce Ravel]

On Monday 04 January 2010, 09:15:37 am, abhijeet gaur wrote:

> Generally the fitting is done using theoretical standards. For that in
> Artemis, we give input as crystallographic data. But If we want to use an
> experimental standard instead of
> theoretical standard, how that can be done. Is it possible to use
> experimental standard in Artemis? or we have to use some other method.
> 

Artemis does not do fitting with experimental standards, although Athena does 
have a dialog for doing log-ratio/phase-difference analysis.

B
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[Ifeffit] Fitting using Experimental standard

[abhijeet gaur]

A very happy new year to all

Generally the fitting is done using theoretical standards. For that in
Artemis, we give input as crystallographic data. But If we want to use an
experimental standard instead of
theoretical standard, how that can be done. Is it possible to use
experimental standard in Artemis? or we have to use some other method.

with thanks
Abhijeet Gaur
School of Studies in Physics
Vikram University, Ujjain (India)
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Re: [Ifeffit] Fitting Cu2O

[umesh palikundwar]

> Hi all,
> I am fitting Cu2O data. But when I fit the first shell using the
> first path, I got the guess value for SS parameter negative which is around
> -0.0028 and also the guessed value for SO2 parameter comes out to be around
> 0.52. Are these values logically correct as I am getting a nice fit.
> Also when I use the same SS parameter but with positive sign for the
> first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to
> be 0.61.
> When I fit the higher shells by using the same SO2 and Enot value for
> other paths, the value of SS parameter for these paths is coming very high ,
> i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher
> values of SS parameter correct. The resulting figure is attached.
> 
> with thanks
> 
> Abhijeet Gaur
> 
> School of Studies in Physics
> 
> Vikram University, Ujjain, INDIA.


Dear Abhijit,

 

 The parameters So2 and SS are highly correlated. The negative value of SS does 
not make any physical significance. It may be due that Artemis is conveging for 
lower value of So2. In your case (So2=0.552 or 0.61) it is very low. Generelly, 
it should be in the range of 0.7 to 1. It will be better if you fix So2 for the 
standard value calulated theoretically in the literature or you can try to get 
approximated value of SS for So2 around 0.8 to 0.9. 

 

regards

 

Umesh Palikundwar

Department of Physics

RTM Nagpur University,

Nagpur-440033 

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Re: [Ifeffit] Fitting Cu2O

[Carlo Segre]

Hi Abhijeet:

I wasnot able to view the BMP.  Perhaps a PNG or JGP would be a better 
format.  in any case, a figure is very hard to assess.  My incilnation is 
to say that you hve something very wrong with your fitting if your SS is 
negative.  This is not really very physical.

If you could attache your artemis project file, it would allow others to 
anszer your questions more effectively.

Carlo

On Fri, 3 Jul 2009, abhijeet gaur wrote:

> Hi all,
> I am fitting Cu2O data. But when I fit the first shell using the
> first path, I got the guess value for SS parameter negative which is around
> -0.0028 and also the guessed value for SO2 parameter comes out to be around
> 0.52. Are these values logically correct as I am getting a nice fit.
>  Also when I use the same SS parameter but with positive sign for the
> first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to
> be 0.61.
> When I fit the higher shells by using the same SO2 and Enot value for
> other paths, the value of SS parameter for these paths is coming very high ,
> i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher
> values of SS parameter correct. The resulting figure is attached.
>
> with thanks
>
> Abhijeet Gaur
>
> School of Studies in Physics
>
> Vikram University, Ujjain, INDIA.
>

-- 
Carlo U. Segre -- Professor of Physics
Associate Dean for Graduate Admissions, Graduate College
Illinois Institute of Technology
Voice: 312.567.3498Fax: 312.567.3494
se...@iit.edu   http://www.iit.edu/~segre   se...@debian.org
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[Ifeffit] Fitting Cu2O

[abhijeet gaur]

Hi all,
 I am fitting Cu2O data. But when I fit the first shell using the
first path, I got the guess value for SS parameter negative which is around
-0.0028 and also the guessed value for SO2 parameter comes out to be around
0.52. Are these values logically correct as I am getting a nice fit.
  Also when I use the same SS parameter but with positive sign for the
first shell i.e., 0.0028, the guessed value for SO2 parameter comes out to
be 0.61.
 When I fit the higher shells by using the same SO2 and Enot value for
other paths, the value of SS parameter for these paths is coming very high ,
i.e., 0.016 - 0.021. But the fit seems to be quiet good. Are these higher
values of SS parameter correct. The resulting figure is attached.

with thanks

Abhijeet Gaur

School of Studies in Physics

Vikram University, Ujjain, INDIA.
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[Ifeffit] Fitting procedure

[abhijeet gaur]

Hello Matt Sir,
Thanks a lot. I will include the error bars in fitted
value for sure.

 with regards

 Abhijeet Gaur
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Re: [Ifeffit] Fitting procedure

[Matt Newville]

Hi Abhijeet,

On Fri, Apr 24, 2009 at 7:09 AM, abhijeet gaur  wrote:
> Hello Matt Sir,
>   Thanks a lot for your valuable sugestions. I had
> fitted the Cu foil spectra as you suggested. I had taken same SO2 value for
> all the paths and after fitting the first shell , making its parameter fix
> when fitting second shell I changed the fit R range 2.9- 3.7 in order to
> make the contribution of first shell negligible. I got a nice fit.  The
> values of different parameters I got are as follows :
> E 0=2.90 eV   ,  SO2= 0.72
>  1st shell  R = 2.54, delR= -0.011, SS2=0.0083
>  2nd shell R= 3.69,   delR= 0.080,  SS2=0.0088
> The experimental data is taken at room temperature.
> Are these parameters within the experimental error limit. Please tell me
>   with regards
>   Abhijeet Gaur
>

Those values seem like the right range for room temperature Cu to me.
Channeling those who taught me: be sure to include error bars in those
fitted values!

--Matt
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[Ifeffit] Fitting procedure

[abhijeet gaur]

Hello Matt Sir,
  Thanks a lot for your valuable sugestions. I had
fitted the Cu foil spectra as you suggested. I had taken same SO2 value for
all the paths and after fitting the first shell , making its parameter fix
when fitting second shell I changed the fit R range 2.9- 3.7 in order to
make the contribution of first shell negligible. I got a nice fit.  The
values of different parameters I got are as follows :
E 0=2.90 eV   ,  SO2= 0.72
 1st shell  R = 2.54, delR= -0.011, SS2=0.0083
 2nd shell R= 3.69,   delR= 0.080,  SS2=0.0088
The experimental data is taken at room temperature.
Are these parameters within the experimental error limit. Please tell me
  with regards
  Abhijeet Gaur
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