Dear all,

i want to run FEFF with the many pole self energy MPSE. In the documentation
to FEFF9 is written that I have to use the formula detailed in
'EpsInvFormula.ps' to calculate the optical constants.

Where can I get this file?

Many thanks

Mehmet from University Duisburg-Essen in Germany

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Message: 2
Date: Thu, 14 Oct 2010 09:46:13 +0000
From: ornella smila castro <sornella@hotmail.com>
To: <ifeffit@millenia.cars.aps.anl.gov>
Subject: [Ifeffit] calibration/alignment
Message-ID: <SNT118-W28EB06506AEEA22C66F3DECB560@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"

Hi everyone,

I am trying to do some data processing with Athena but I am already stuck at the first step. The thing is: I read the worked example section of the "Athena's user guide" and on the example on the iron foil, it is mentioned to calibrate the data at the right energy (until here evrything is fine) but then it is said to align the data. Can anyone explain to me what does "alignment" exactly means, and what is the aim of "aligning the data". The data that I have collected were through a channel through which a solution flow (~200 microliters/hr) so I am not convinced that alignment makes sense.

Many thanks,
Ornel
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Message: 3
Date: Thu, 14 Oct 2010 07:04:17 -0700
From: Scott Calvin <dr.scott.calvin@gmail.com>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] calibration/alignment
Message-ID: <9A87D9FF-2ABE-429A-BDC1-D6026F690223@gmail.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hi Ornel,

Alignment is used to compensate for monochromators that do not
maintain stable energy calibration between scans. In conventional
measurements, you'll generally have several scans that are supposed to
be of the same sample under identical conditions, and those scans may
need to be aligned with each other. That is not the case for a time
series, which is what I think you are saying you have.

So in a time series, how do you compensate for any energy drift of the
monochromator? If you are recording a simultaneous reference spectrum,
you can align the reference spectra to each other. (Athena
automatically will shift the sample spectra by the same amount that
the reference spectra are shifted.)

If you have a time series but don't have a simultaneous reference
spectra, it becomes tougher. If you collected a reference spectrum
before and after the time series, you could try to interpolate any
shift that's seen, although that's dicey; shifts sometimes occur in
jumps. But if there's no shift, you're probably OK!

If you have a time series and no reference at all, or a reference only
before the series, you're out of luck. You're relying then on the
assumption of energy stability, which on some beamlines might be
OK...but it is best to confirm that by at least measuring a reference
before and after.

--Scott Calvin
Sarah Lawrence College

On Oct 14, 2010, at 2:46 AM, ornella smila castro wrote:

> Hi everyone,
>
> I am trying to do some data processing with Athena but I am already
> stuck at the first step. The thing is: I read the worked example
> section of the "Athena's user guide" and on the example on the iron
> foil, it is mentioned to calibrate the data at the right energy
> (until here evrything is fine) but then it is said to align the
> data. Can anyone explain to me what does "alignment" exactly means,
> and what is the aim of "aligning the data". The data that I have
> collected were through a channel through which a solution flow (~200
> microliters/hr) so I am not convinced that alignment makes sense.
>
> Many thanks,
> Ornel
> <ATT00001..txt>

------------------------------

Message: 4
Date: Thu, 14 Oct 2010 09:39:28 -0500
From: Matt Newville <newville@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] calibration/alignment
Message-ID:
<AANLkTi=_61NhHsCR1n9LDyqdDBfJUuKUzw+CJHmLPP5z@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Ornel,

Alignment here means to make sure that the energy scale has not
drifted between different scans. At many (especially older)
facilities, it is not too unusual to have the apparent energy scale
drift around a bit over time.

Sometimes a reference sample is measured simultaneously specifically
for detecting such drifts. Generally one asserts that the recorded
energies were offset from one scan to another by a constant amount
that happened between one scan and other (ie, not during a scan).
This assumption might be justified from a mechanical point-of-view,
but is rarely tested in practice.

It is easy for the data processing to simply add a constant to all
energies of one scan until it looks like the energies align with
another scan. For small shifts (a few eV or so), this is probably
fine. Consequently, this easy procedure is commonly done even though
the underlying assumptions are rarely tested and the procedure is
loses accuracy for large shifts.

If you don't think you need to do this, then you're probably right.
The corollary is that if you do think you need to do this all the
time, and that the energy shift is larger than a few eV, then there is
probably something wrong, and you should look carefully at whether
"shift by a constant energy" is even reasonable.

If you're just getting started, I would say to not worry about energy
alignment until it becomes an obvious problem.

--Matt

On Thu, Oct 14, 2010 at 4:46 AM, ornella smila castro
<sornella@hotmail.com> wrote:
> Hi everyone,
>
> I am trying to do some data processing with Athena but I am already stuck at
> the first step. The thing is:?I read the worked example section of the
> "Athena's user guide" and on the example on the iron foil, it is mentioned
> to calibrate the data at the right energy (until here evrything is fine)?but
> then it is?said to align the data. Can anyone explain to me what does
> "alignment" exactly means, and what is the aim of "aligning the data".?? The
> data that I have collected?were?through a channel through which a solution
> flow (~200 microliters/hr)?so I am not convinced that alignment makes
> sense.
>
> Many thanks,
> Ornel
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>

------------------------------

Message: 5
Date: Thu, 14 Oct 2010 08:48:21 -0700
From: Scott Calvin <dr.scott.calvin@gmail.com>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] calibration/alignment
Message-ID: <D201B821-E95E-4C3E-8F85-14DD3EB9E3C0@gmail.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

On Oct 14, 2010, at 7:39 AM, Matt Newville wrote:

> If you're just getting started, I would say to not worry about energy
> alignment until it becomes an obvious problem.

A cautionary tale (with details made up, since I don't remember them!)
from when I was just starting out as to what constitutes an "obvious
problem":

I collected five transmission EXAFS scans on the same sample. The
scans were on top of each other when I looked at the graph, so I
merged them...and proceeded to get somewhat screwy fits.

The problem? I only looked at the graph across the whole spectra--say,
1500 eV. It turns out there was about a 0.7 eV shift between each scan
and the next one, for a total of roughly 3 eV . That was small enough
so as to be invisible when looked at on that scale. When I looked at
just the XANES, though, the shift did become "obvious." I aligned the
spectra and merged them, and suddenly the problems in the fit went away!

Since then, I've seen the same thing happen with students to whom I am
teaching the technique.

On the other hand, there's no magic "blessing" given by the process of
alignment. Suppose I have ten scans of very noisy data, and no
reference. If I used the auto-align procedure in Athena, it sometimes
shifts a scan 0.3 eV one way, sometimes 0.2 eV the other way, with no
apparent rhyme or reason. Looking at the graphs, even zoomed in, just
shows a bunch of noisy data roughly on top of each other. In that
case, there's no reason to believe there are actual shifts between
scans, and I would NOT align them prior to merging.

Finally, beamline scientists usually have a very good idea whether
their line is prone to drifts. Ask them!

--Scott Calvin
Sarah Lawrence College

------------------------------

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End of Ifeffit Digest, Vol 92, Issue 11
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