[Ifeffit] MPSE

[Joshua Kas]

Hi Mehmet,
The documentation in feff9 for MPSE is (obviously) not very good. What you
will need, to start, is a calculation of the bulk loss function L(E) =
-Im[1/epsilon(E)] for your material. I can discuss the details with you over
email if you like.
Cheers,
Josh Kas

joshua.j.kas at gmail.com



> 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
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101013/5f98fa0a/attachment.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Thu, 14 Oct 2010 09:46:13 +0000
> From: ornella smila castro <sornella at hotmail.com>
> To: <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] calibration/alignment
> Message-ID: <SNT118-W28EB06506AEEA22C66F3DECB560 at 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101014/9779e9be/attachment-0001.htm
> >
>
> ------------------------------
>
> Message: 3
> Date: Thu, 14 Oct 2010 07:04:17 -0700
> From: Scott Calvin <dr.scott.calvin at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] calibration/alignment
> Message-ID: <9A87D9FF-2ABE-429A-BDC1-D6026F690223 at 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 at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] calibration/alignment
> Message-ID:
>        <AANLkTi=_61NhHsCR1n9LDyqdDBfJUuKUzw+CJHmLPP5z at mail.gmail.com<61NhHsCR1n9LDyqdDBfJUuKUzw%2BCJHmLPP5z at 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 at 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 at 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 at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] calibration/alignment
> Message-ID: <D201B821-E95E-4C3E-8F85-14DD3EB9E3C0 at 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
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 92, Issue 11
> ***************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101014/ecaa544f/attachment.html>