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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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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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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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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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 <ifeffit@millenia.cars.aps.anl.gov>
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] 
<ee11...@leeds.ac.uk<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<tel:%2B44%20%280%29113%2034%2033647>
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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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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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

[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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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 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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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 bra...@bnl.gov 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

[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 bra...@bnl.gov 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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 Ifeffit mailing list
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 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


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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

[Matthew Marcus]

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

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

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

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

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

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

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

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

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

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

Hi All,

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

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

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

--Matt


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Re: [Ifeffit] 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 bro...@mit.edu 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

[Matt Newville]

Hi Matthew,



On Thu, May 29, 2014 at 11:18 AM, Matthew Marcus mamar...@lbl.gov 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 = appropriate value
 CENTRAL Ti a0*(d_off,d_off,d_off)/sqrt(3)
 ATOM O
 POS (a0/2)*(1+d1,d2,d2)
 OCC 1
 SS SS1
 ATOM O
 POS (a0/2)*(d2,1+d1,d2)
 OCC 1
 SS SS1
 ATOM O
 POS (a0/2)*(d2,d2,1+d1)
 OCC 1
 SS SS1
 ATOM O
 POS (a0/2)*(-1+d1,d2,d2)
 OCC 1
 SS SS1
 ...

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

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

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


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

[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 scal...@sarahlawrence.eduwrote:

 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 bro...@mit.edu 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 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 newvi...@cars.uchicago.edu wrote:

 Hi Scott,
 
 On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin scal...@sarahlawrence.edu 
 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 

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

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


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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 bra...@bnl.gov 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 

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

[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 bra...@bnl.gov 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

[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

[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

[Matt Newville]

Scott,

On Thu, Dec 5, 2013 at 11:18 AM, Scott Calvin scal...@sarahlawrence.edu 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

[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]

Hi Anatoly,

On Thu, Dec 5, 2013 at 12:28 PM, Anatoly I Frenkel afren...@yu.edu wrote:
 I object the use of hosannas of adoration. Other than the use of Greek 
 mythology, I propose the mailing list to be religion-neutral and 
 tautology-free.

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

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

--Matt
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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 afren...@yu.edu wrote:

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


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

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

--Matt
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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, fred.mosselm...@diamond.ac.uk 
fred.mosselm...@diamond.ac.uk 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

[Matt Newville]

Hi Scott,

On Thu, Dec 5, 2013 at 4:56 PM, Scott Calvin scal...@sarahlawrence.edu 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

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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 matt.fr...@gmail.com 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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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

[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 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 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 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 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 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 bra...@bnl.gov

To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
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 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

[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

[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 535A
 Upton NY, 11973

 

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

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

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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]

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 bakhshwan1...@yahoo.com 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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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 abhijeetga...@gmail.com 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

[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 standard, how that can be done. Is it possible 

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 
mumble years ago, it was mainstream.
   mam 


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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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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

[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

[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 jrkiz...@ncsu.edu

To: bra...@bnl.gov; XAFS Analysis using Ifeffit 
ifeffit@millenia.cars.aps.anl.gov
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

[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 
ifeffit-boun...@millenia.cars.aps.anl.gov
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
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 fren...@bnl.gov
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
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

[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 
ifeffit-boun...@millenia.cars.aps.anl.gov
  To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
  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 fren...@bnl.gov
  To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
  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]

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 
ifeffit-boun...@millenia.cars.aps.anl.gov 
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov 
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 
ifeffit-boun...@millenia.cars.aps.anl.gov
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
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 fren...@bnl.gov
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
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

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 
ifeffit-boun...@millenia.cars.aps.anl.gov

*To*: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
*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
ifeffit-boun...@millenia.cars.aps.anl.gov
mailto:ifeffit-boun...@millenia.cars.aps.anl.gov
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
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 fren...@bnl.gov
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Sent: Monday, January 04, 2010 6:21 PM
Subject: Re: [Ifeffit] Fitting using Experimental standard


I know of one very obscure

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 procedure

[Matt Newville]

Hi Abhijeet,

On Fri, Apr 24, 2009 at 7:09 AM, abhijeet gaur abhijeetga...@gmail.com 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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Re: [Ifeffit] Fitting procedure

[Matt Newville]

HI Abhijeet,

I think there is a lot of confusion over the method that i used for 
 fitting, So I should make it clear here.
 In this method I fit the first shell by taking into account only first shell 
 R range i.e. 1.5 - 2.7. Then after getting
 a nice fit for the  first shell, I extract its parameters and make them set 
 in Artemis. Then I include the second
 shell by increasing R range to 1.5 - 3.6. In the same manner I fit the first 
 three shells of copper foil and the
 parameters I got for them are reasonably good.
 The problem of high SO2 only lies with one of my foil data which is not as 
 good as other data. For other good
 data I got SO2 value for second shell within the exceptable limit.
 One more thing I want to say is that we can check the corelation between 
 different parameters of shells by
 making them guess during any step of the fitting e.g. during the fitting of 
 second shell we can make any parameter
 of the first shell to vary and check its corelation with them.
 But if I am counting the first shell data twice, I will include only second 
 shell R range after first shell fit.I think it will
  not make any difference to results. If yes please tell me the reasons.

 I want to add some more things I have done
 1) E0 is kept same for all the shells
 2) All other parameters like SO2 , del r , SS2 are calculated separately for
 different shells.
 So. is there problem with taking different SO2  for different shells. Surely
 del r and SO2 will be different for different shells , If I got it right.


I'll assume that you've read all the posts about this.

Since you fit the first shell, then fix these parameters to fit the
second and third shells, why is it that you use an R-range that
includes the first shell?  That's not fitting the second and third
shells, that's fitting the first, second, and third shells, only your
not letting the fit adjust the model for the first shell.  I wouldn't
call this wrong, exactly, but you're not using all you know about the
spectra (that is, that the first shell is well separated from the
second and third, and that you know the R-ranges over which the
different parameters will influence the modeled spectra).  Since
you're choosing variables that can only change a portion of the
spectra (and, as it turns out, the more subtle portion of the
spectra),  the mis-fit to the first shell could easily dominate the
fit to the higher shells.  I think you'd be better off changing the R
range to ignore most of the first shell.

You say the problem with S02 lies only with one data set.  The concern
from the people more experienced in analysis here is not that your
data is noisy, but that having multiple S02 makes a model that is
either non-physical or very hard to understand.   My guess is that
you're varying S02 per shell, but leaving the coordination number N
(path degeneracy) fixed at the nominal values for an fcc solid.  It is
more common (and generally preferred) to use exactly 1 S02 per spectra
(or even the same S02 for a set of spectra on the same edge) and allow
the coordination number to vary.  This is generally easier to
interpret. Since the amplitude for a path is N*S02, the two
approaches are mathematically equivalent.

 One more thing I want to say is that we can check the corelation between 
 different parameters of shells by
 making them guess during any step of the fitting e.g. during the fitting of 
 second shell we can make any parameter
 of the first shell to vary and check its corelation with them.

Yes, that is right.  This is generally a good thing to do.

Cheers,

--Matt
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Re: [Ifeffit] Fitting procedure

[Matt Newville]

Hi Adam,

I am confused by this thread too!

As you say, the original issue involved using S02 for individual
shells of data on Cu foil.  Of course, having separate S02 for each
shell is not usually necessary to model Cu foil -- in fact I can't
think of a case where it is needed.  But  since S02 is 100% with N,
and ~95% correlated with sigma2, it is easy to have S02 vary per shell
if one allows it to happen.Whether that's a good idea or not
depends on how you interpret the results.   Most people choose to fix
a single S02 and vary N.  Lots of people fit spectra with one S02 and
an N for each shell, so I don't think the number of free parameters is
necessarily a big issue.

In a follow-up message, Scott seemed (to me) to be more concerned
about whether it was reasonable to fix parameters for the first
shell  when fitting a second or higher shells, not so much with the
issue of what parameters were being refined.  There weren't explicit
details on what was fixed or what fitting ranges or parameters were
used for the higher shells.  Scott suggested (I believe) that fixing
the first shell and fitting the second shell was not a good idea, and
asked to hear differing views.

I find the approach of fit the first shell, then fix those parameters
and fit the second shell to be a reasonable way to start, so I
responded.   I would not call this approach acceptable, but generally
not preferred -- I would say it has actual merit.  Yes, it is often a
good idea to check a fit to the whole spectrum toward the end of an
analysis.  But in a fit to the whole spectrum, the quality of the fit
to the more subtle features (the finer structure) can often get lost
in the fit to the more dominant features of the spectra.  That is why
we subtract mu0(E), after all.  I don't see Fourier filtering as a bad
idea for analyzing higher shells.

But perhaps I am just not understanding what Scott and Shelly recommend???

--Matt
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Re: [Ifeffit] Fitting procedure

[Scott Calvin]

Hi all,

Well, I'm understanding my own views on this more clearly as the  
conversation continues, so it's been helpful to me!

There are several different issues that have floated through this  
thread, but let me focus on one aspect.

One possible fitting strategy is a shell-by-shell method, in which  
each shell is fit more or less independently. In this method, the R- 
range is chosen to try to correspond to a single shell. Because the  
first shell is often dominant in the spectrum and can leak quite  
significantly into other shells, it is reasonable to fit the first  
shell, and then use those parameters to constrain the leakage from the  
first shell while fitting the second shell. I've rarely used that  
strategy personally, but it seems perfectly reasonable to me, and  
there are cases where it seems like a very good way to go. There are  
no problems with free parameters with this method. For instance, if  
the first shell is fit over the R-range 1.0 to 1.5 angstroms, and the  
second from 1.5 to 2.0, each with its own parameters, then you're not  
cheating to use the results of the first fit to fix the parameters  
for the first shell in the second fit, as those parameters came from  
data you're not currently using. The usual idea that constraints come  
from prior knowledge is satisfied.

On the other hand, I have sometimes seen students in workshops fit the  
first shell, then extend the R-range so that it includes both shells,  
fix the first shell parameters to the results from the prior fit, and  
then do a fit to determine the parameters of the second shell. This is  
the approach I find troubling. It seems to double count data. To be  
specific, the first shell fit might be from 1.0 to 1.5 angstroms, and  
the results would then be used to constrain the first shell in the  
next fit, which would vary second shell parameters but extend from 1.0  
to 2.0. The data from 1.0 to 1.5 has thus been used twice in a manner  
that would cause me some concern.

I am unclear as to which procedure Abhijeet is describing. I initially  
assumed the second, and Matt initially assumed the first; that was  
responsible for some of the confusion.

--Scott Calvin
Sarah Lawrence College



On Apr 18, 2009, at 1:57 PM, Matt Newville wrote:

 Hi Adam,

 I am confused by this thread too!


 I find the approach of fit the first shell, then fix those parameters
 and fit the second shell to be a reasonable way to start, so I
 responded.   I would not call this approach acceptable, but generally
 not preferred -- I would say it has actual merit.  Yes, it is often a
 good idea to check a fit to the whole spectrum toward the end of an
 analysis.  But in a fit to the whole spectrum, the quality of the fit
 to the more subtle features (the finer structure) can often get lost
 in the fit to the more dominant features of the spectra.  That is why
 we subtract mu0(E), after all.  I don't see Fourier filtering as a bad
 idea for analyzing higher shells.

 But perhaps I am just not understanding what Scott and Shelly  
 recommend???

 --Matt
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Re: [Ifeffit] Fitting procedure

[Chappell, Mark A ERDC-EL-MS]

Oops, please ignore my message - sent it to the wrong address!!! 
- 
Message sent via my BlackBerry Wireless Device 




From: ifeffit-boun...@millenia.cars.aps.anl.gov 
To: ifeffit@millenia.cars.aps.anl.gov 
Sent: Sat Apr 18 14:56:35 2009
Subject: Re: [Ifeffit] Fitting procedure 


They're on theur way back to Vicksburg.  I yried to guide them from home but
couldn't figure out where she was.  By 230, she hung it up and turned back
-
Message sent via my BlackBerry Wireless Device


- Original Message -
From: ifeffit-boun...@millenia.cars.aps.anl.gov
ifeffit-boun...@millenia.cars.aps.anl.gov
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Sent: Sat Apr 18 12:57:18 2009
Subject: Re: [Ifeffit] Fitting procedure

Hi Adam,

I am confused by this thread too!

As you say, the original issue involved using S02 for individual
shells of data on Cu foil.  Of course, having separate S02 for each
shell is not usually necessary to model Cu foil -- in fact I can't
think of a case where it is needed.  But  since S02 is 100% with N,
and ~95% correlated with sigma2, it is easy to have S02 vary per shell
if one allows it to happen.Whether that's a good idea or not
depends on how you interpret the results.   Most people choose to fix
a single S02 and vary N.  Lots of people fit spectra with one S02 and
an N for each shell, so I don't think the number of free parameters is
necessarily a big issue.

In a follow-up message, Scott seemed (to me) to be more concerned
about whether it was reasonable to fix parameters for the first
shell  when fitting a second or higher shells, not so much with the
issue of what parameters were being refined.  There weren't explicit
details on what was fixed or what fitting ranges or parameters were
used for the higher shells.  Scott suggested (I believe) that fixing
the first shell and fitting the second shell was not a good idea, and
asked to hear differing views.

I find the approach of fit the first shell, then fix those parameters
and fit the second shell to be a reasonable way to start, so I
responded.   I would not call this approach acceptable, but generally
not preferred -- I would say it has actual merit.  Yes, it is often a
good idea to check a fit to the whole spectrum toward the end of an
analysis.  But in a fit to the whole spectrum, the quality of the fit
to the more subtle features (the finer structure) can often get lost
in the fit to the more dominant features of the spectra.  That is why
we subtract mu0(E), after all.  I don't see Fourier filtering as a bad
idea for analyzing higher shells.

But perhaps I am just not understanding what Scott and Shelly recommend???

--Matt
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Re: [Ifeffit] Fitting procedure

[Kelly, Shelly]

and what we are trying to say is that your method is not generally
accepted as the best way to model data.

 

Shelly

 



From: ifeffit-boun...@millenia.cars.aps.anl.gov
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of abhijeet
gaur
Sent: Friday, April 17, 2009 2:29 AM
To: ifeffit
Subject: [Ifeffit] Fitting procedure

 

Hi all,

 Thanks to all the concerned persons for having such a wonderful
discussion over fitting procedure. I am able to understand the things
better by going through these discussions. But what I am trying to say
is that I had first applied the fitting procedure in which I make the
parameters of all paths( included in the fit) to vary simultaneously,
but the problem is that I am not able to get a good fit and the
parameters for different paths are also coming absurd like very low
amplitude etc. For days I have been trying this method of fitting but
not able to get good results.I tried different models also like Debye 
Einstien model, I used the relation del r= alpha* Reff but it doesn't
work. Then I switch to this the method in which we fit the first shell,
get the parameters fix them and then go for the next shell and in this
way e fix the whole spectra. The results I got are extremely good. Thus
I am using this method. 

 
Abhijeet Gaur

 


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Re: [Ifeffit] Fitting procedure

[Matt Newville]

Shelly wrote:

 ….and what we are trying to say is that your method is not generally
 accepted as the best way to model data.

We are?

If I understand Abhijeet's approach (first fit the first shell, then
fix those parameters, change the R-range to the second shell and fit
that),  it is exactly what I would recommend.

--Matt

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Re: [Ifeffit] Fitting procedure

[Kelly, Shelly]

Okay. Sure, I agree with Matt. But I don't think that this data can be
broken into different shellsotherwise I do not believe that the
model would fail when the entire data range is optimized together.

There could be two reasons that the model fails. Either there are
correlations that were artificially broken by fitting the r-ranges
separately or there is some data that is not accounted for in the model.


I guess I should only talk for myself. I do not generally accept your
fitting method to be the best.  I did say BEST...sometimes best is not
an option.

Shelly

 -Original Message-
 From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-
 boun...@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville
 Sent: Friday, April 17, 2009 9:23 AM
 To: XAFS Analysis using Ifeffit
 Subject: Re: [Ifeffit] Fitting procedure
 
 Shelly wrote:
 
  and what we are trying to say is that your method is not
generally
  accepted as the best way to model data.
 
 We are?
 
 If I understand Abhijeet's approach (first fit the first shell, then
 fix those parameters, change the R-range to the second shell and fit
 that),  it is exactly what I would recommend.
 
 --Matt
 
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Re: [Ifeffit] Fitting procedure

[Adam Webb]

Hi,

Perhaps I am misunderstanding something here. It sounded like the
original problem was that SO2 was too high/low for some shells. It also
sounded like the solution was then to fit each shell separately with its
own set of parameters; SO2, dr, sigma-squared.  I don't think that is
what Matt was saying but I think that was what Abhijeet implied.
However, I may have completely misunderstood what was being done.

If I did understand correctly then I have two concerns.
1. Can you justify having a different SO2 for each shell? I don't know,
I am just asking.
2. In any case, it sounds to me like a recipe for ending up with too
many free parameters. It seems to me that fitting separate pieces is
dangerous. At the very least, at some point the pieces should be put
together and the whole thing fit together.

I can see this method as being reasonable to get starting values for
each shell. However, a good model should work for the total spectrum as
well as for individual pieces. If not, I would be be concerned about the
model.

Cheers,
Adam

Kelly, Shelly wrote:
 Okay. Sure, I agree with Matt. But I don't think that this data can be
 broken into different shellsotherwise I do not believe that the
 model would fail when the entire data range is optimized together.
 
 There could be two reasons that the model fails. Either there are
 correlations that were artificially broken by fitting the r-ranges
 separately or there is some data that is not accounted for in the model.
 
 
 I guess I should only talk for myself. I do not generally accept your
 fitting method to be the best.  I did say BEST...sometimes best is not
 an option.
 
 Shelly
 
 -Original Message-
 From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-
 boun...@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville
 Sent: Friday, April 17, 2009 9:23 AM
 To: XAFS Analysis using Ifeffit
 Subject: Re: [Ifeffit] Fitting procedure

 Shelly wrote:

 and what we are trying to say is that your method is not
 generally
 accepted as the best way to model data.
 We are?

 If I understand Abhijeet's approach (first fit the first shell, then
 fix those parameters, change the R-range to the second shell and fit
 that),  it is exactly what I would recommend.

 --Matt

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Re: [Ifeffit] fitting ReO2

[Zajac, Dariusz]

google helps you ;)
http://www.crystallography.net/
a direct to ReO2 oxide
http://www.crystallography.net/cif/9/9009092.cif?CODSESSION=v2MdMFKIyrKT
wVnjq-bY3VaJxvf


download cif file and open it with artemis

have fun
darek

-Original Message-
From: [EMAIL PROTECTED] 
[mailto:[EMAIL PROTECTED] On Behalf 
Of Edward L. Kunkes
Sent: Wednesday, December 10, 2008 4:23 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] fitting ReO2


Hi everyone,


  I am trying to do a first shell fit of ReO2 - where there 
are 2 different Re-O distances in the first coordination 
shell. Does anyone have an .atoms file or structural 
information for this material that they would be willing to share ?  


Thank you very much for your help.


-Edward Kunkes

Research Assistant 
Department of Chemical Engineering
University of Wisconsin-Madison

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Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

[E. Bosman]

Hi Anatoly,

it's funny for me as an german guy to read your discussion about zeitgeist 
and poltergeist ;-)
I think zeitgeist (the spirit of the time/age) and poltergeist are total 
different things.

Poltergeist:
maybe this is a good definition: Reports of poltergeist activity typically 
feature heavily on raps, bumps, thumps, knocks, footsteps, and bed-shaking, all 
without a discernible point of origin or physical reason for occurrence 
(http://en.wikipedia.org/wiki/Poltergeist). But if you look closer at it, you 
find out that it is a practical joke or nature phenomena like wind, wether 
etc... are the cause.

Ciao,
Eckhard

PS: sorry for the off-topic spam ;-)

 Original-Nachricht 
Datum: Wed, 28 Mar 2007 16:43:35 -0400
Von: Anatoly Frenkel [EMAIL PROTECTED]
An: \'XAFS Analysis using Ifeffit\' ifeffit@millenia.cars.aps.anl.gov
Betreff: Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

 Since I like the sound of my voice too, I will translate the zeitgeist
 from Bruce's email. According to Wikipedia, It is originally a German
 expression that means the spirit (Geist) of the time (Zeit). Can it be
 loosely translate here as poltergeist?
 
 Anatoly
-- 
Feel free - 10 GB Mailbox, 100 FreeSMS/Monat ...
Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail
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Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

[Scott Calvin]

Hi Mario,

There are a couple of different ways to approach the kind of problem 
you describe, although you must be willing to guess at what the local 
environment looks like.

For example, maybe the chemical composition tells you that you have 
an iron oxide. At a minimum, you could use Atoms to make a crystal 
structure for, say, hematite, and then only fit the nearest-neighbor 
paths, perhaps with an unknown coordination number. This can give you 
some information.

Or, following the same example, maybe you think your material might 
be like a disordered hematite. Then you could try to fit the hematite 
structure out for several shells, but with free parameters to account 
for disorder (e.g. you could include vacancies).

The key questions that you should not lose track of:

--What would you like to know about your material?

--What do you think your material might be like?

I think sometimes people forget in particular about the first 
question. EXAFS doesn't answer generic questions very well (tell me 
all about my sample), but it often answers particular questions 
quite effectively (are my iron atoms bonded to oxygen, or sulfur?). 
So if you know what your particular questions are you've got a good 
chance of getting help using Bruce's and Matt's software.

--Scott Calvin
Sarah Lawrence College

At 02:15 PM 3/28/2007, you wrote:
Content-class: urn:content-classes:message
Content-Type: multipart/alternative;
 boundary=_=_NextPart_001_01C77165.0DE07268

Hi Bruce my name is Mario and I was just wondering if your program 
can fir the EXAFS spectra without any atomic positions. Obviously 
the answer is no if you use atoms to create the FEFF file but what 
does one do when we have a semi-crystalline material for which no 
one has attempted the fractional coordinates.

I mean the XRD pattern shows some crystalline but due to the high 
background I would think it would be very hard to do the Rietveld analysis.

So what can one do, can we fit the EXAFS spectra knowing only the 
chemical composition and perhaps the lattice geometry(orthorhombic 
or hexagonal)?



thanks
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Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

[Bruce Ravel]

On Wednesday 28 March 2007 13:15, Mario Gomez wrote:
 Hi Bruce my name is Mario and I was just wondering if your program can fir
 the EXAFS spectra without any atomic positions. Obviously the answer is no
 if you use atoms to create the FEFF file but what does one do when we have
 a semi-crystalline material for which no one has attempted the fractional
 coordinates.

 I mean the XRD pattern shows some crystalline but due to the high
 background I would think it would be very hard to do the Rietveld analysis.

 So what can one do, can we fit the EXAFS spectra knowing only the chemical
 composition and perhaps the lattice geometry(orthorhombic or hexagonal)?

Mario,

Scott's answer was excellent, but I like the sound of my own voice so
I thought I'd answer as well ;-)

The Feff+Ifeffit+Artemis zeitgeist requires a list of atomic
coordinates to begin analysis.  Except in the rare situations, we
don't know the actual arrangement of atoms.  Indeed, to find out is
one of the reasons we might do EXAFS.

As Scott suggested, thinking about what you sample resembles is
usually a good place to start.  Consider amorphous germanium as an
example.  aGe is typically described as a continuous random network of
bonds which are about the same length as the bonds in crystalline Ge.
Because of that, crystalline Ge is a good place to start.  In fact, I
suspect that you could make considerable progress in analyzing aGe
data with that one Feff calculation on the well-ordered material.

EXAFS analysis is something of a creative endeavor -- the trick is to
figure out how to use things that you know to model things that you
don't know.  Reading papers by the folks who answer questions on this
list (Scott Calvin, Shelly Kelly, Anatoly Frenkel, Paul Fons) is a
really good source of ideas for your own work with IfeffitArtemis.

B

-- 
 Bruce Ravel  -- [EMAIL PROTECTED]

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007

 Argonne National Laboratory phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USAfax: (1) 630 252 9793

 My homepage:http://cars9.uchicago.edu/~ravel 
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

[Anatoly Frenkel]

Since I like the sound of my voice too, I will translate the zeitgeist
from Bruce's email. According to Wikipedia, It is originally a German
expression that means the spirit (Geist) of the time (Zeit). Can it be
loosely translate here as poltergeist?

Anatoly



-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bruce Ravel
Sent: Wednesday, March 28, 2007 3:41 PM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Fitting EXAFS with out any atomic coordinates?

On Wednesday 28 March 2007 13:15, Mario Gomez wrote:
 Hi Bruce my name is Mario and I was just wondering if your program can fir
 the EXAFS spectra without any atomic positions. Obviously the answer is no
 if you use atoms to create the FEFF file but what does one do when we have
 a semi-crystalline material for which no one has attempted the fractional
 coordinates.

 I mean the XRD pattern shows some crystalline but due to the high
 background I would think it would be very hard to do the Rietveld
analysis.

 So what can one do, can we fit the EXAFS spectra knowing only the chemical
 composition and perhaps the lattice geometry(orthorhombic or hexagonal)?

Mario,

Scott's answer was excellent, but I like the sound of my own voice so
I thought I'd answer as well ;-)

The Feff+Ifeffit+Artemis zeitgeist requires a list of atomic
coordinates to begin analysis.  Except in the rare situations, we
don't know the actual arrangement of atoms.  Indeed, to find out is
one of the reasons we might do EXAFS.

As Scott suggested, thinking about what you sample resembles is
usually a good place to start.  Consider amorphous germanium as an
example.  aGe is typically described as a continuous random network of
bonds which are about the same length as the bonds in crystalline Ge.
Because of that, crystalline Ge is a good place to start.  In fact, I
suspect that you could make considerable progress in analyzing aGe
data with that one Feff calculation on the well-ordered material.

EXAFS analysis is something of a creative endeavor -- the trick is to
figure out how to use things that you know to model things that you
don't know.  Reading papers by the folks who answer questions on this
list (Scott Calvin, Shelly Kelly, Anatoly Frenkel, Paul Fons) is a
really good source of ideas for your own work with IfeffitArtemis.

B

-- 
 Bruce Ravel  -- [EMAIL PROTECTED]

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007

 Argonne National Laboratory phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USAfax: (1) 630 252 9793

 My homepage:http://cars9.uchicago.edu/~ravel 
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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