Hi Matt and Scott,
 
First, thank you so much for replying to my questions.
I realised that I should have been a bit more accurate on the type of experiments I am doing.  
To start with, I am doing electrochemistry combined with EXAFS. I am using an integrated electrolysis/EXAFS cell. Our experiments are as follow: in the case of this experiment in particular, we have a solution of ruthenium-based compound that we flow through a channel through which the beam passes and that we call "reference". we record let's say 6 spectra in a row (we use a flow in order to avoid beam damage on our sample).we didn't do any reference spectra (if you mean running a scan of a Ru foil before starting the actual experiment). then, we make up a new solution  but this time we electrolysed the solution (by applying a potential) in order to get the cationic produced species. (the obtained spectra will therefore be a mixture of the neutral and the cationic species). and we record as well a set of 6 spectra.
Here is what I did and what I was wondering if it was the right thing to do: I have considered the first spectra of the first set of scans as the reference for calibration/alignment. is it ok?
Thus, I am wondering if when I process the second set of data (electrolysed solution), which spectra I should take as a starting point for calibrating/aligning my second series of scans: the one I used for the first serie or the first of the second set of scans?

I hope this is clear...
 
Thanks again for your help,
Ornella
 
> From: ifeffit-request@millenia.cars.aps.anl.gov
> Subject: Ifeffit Digest, Vol 92, Issue 11
> To: ifeffit@millenia.cars.aps.anl.gov
> Date: Thu, 14 Oct 2010 12:00:01 -0500
>
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> Today's Topics:
>
> 1. MPSE (Mehmet Kaya)
> 2. calibration/alignment (ornella smila castro)
> 3. Re: calibration/alignment (Scott Calvin)
> 4. Re: calibration/alignment (Matt Newville)
> 5. Re: calibration/alignment (Scott Calvin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 13 Oct 2010 12:23:06 +0200
> From: "Mehmet Kaya" <mehmet.kaya@uni-due.de>
> To: <ifeffit@millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] MPSE
> Message-ID: <000401cb6ac0$a110d0d0$e3327270$@kaya@uni-due.de>
> Content-Type: text/plain; charset="us-ascii"
>
> 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
> -------------- next part --------------
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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
> ***************************************