Dear Scott,
 
this is exactly why I was confused about alignment, since I want to see that shift!!
Thank you so much for your precious help. it is very clear now..
 
With best wishes,
Ornella
 
> From: ifeffit-request@millenia.cars.aps.anl.gov
> Subject: Ifeffit Digest, Vol 92, Issue 13
> To: ifeffit@millenia.cars.aps.anl.gov
> Date: Thu, 14 Oct 2010 17:54:36 -0500
>
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> Today's Topics:
>
> 1. Re: calibration/aligment...2 (Scott Calvin)
> 2. Re: MPSE (Joshua Kas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 14 Oct 2010 11:37:43 -0700
> From: Scott Calvin <dr.scott.calvin@gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] calibration/aligment...2
> Message-ID: <04C38483-D6F6-4F2D-B206-AFFB25B30429@gmail.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> DelSp="yes"
>
> Thanks, Ornella, that clarifies what you're doing.
>
> My recommendation is to look closely at the 6 reference spectra and
> see if there appears to be a systematic energy shift between them. For
> example, each spectrum might be shifted by about 0.3 eV from the
> spectrum before it. Or the first two spectra might appear aligned, but
> then the third through sixth are shifted by 1.5 eV. In either of those
> cases, you should align them. In my second example, I might throw out
> the second spectrum as an additional precaution (if the shift occurred
> "all at once," it might have occurred during the scan before which it
> appears). In either case, it doesn't really matter which scan you
> choose to align to (and calibrate, if you have a way of doing that).
>
> If, on the other hand, the 6 reference spectra appear to basically
> overplot except for random noise, I would not try to align them further.
>
> I would treat the 6 spectra for the electrolysed solution similarly--
> align them to each other if there is a systematic energy shift.
>
> What you should not do, in my opinion, is to align the electrolysed
> scans to the reference scans. You actually expect there to be a
> chemical shift between the two sets of data, and aligning one to the
> other would remove that!
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Oct 14, 2010, at 11:00 AM, ornella smila castro wrote:
>
> > 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
>
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> ------------------------------
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> Message: 2
> Date: Thu, 14 Oct 2010 15:54:30 -0700
> From: Joshua Kas <joshua.j.kas@gmail.com>
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] MPSE
> Message-ID:
> <AANLkTinMa226iuG5zRGvA4i8kS-6yJ3xiAu1=uJO1ONK@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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@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 --------------
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> > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101013/5f98fa0a/attachment.html
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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<61NhHsCR1n9LDyqdDBfJUuKUzw%2BCJHmLPP5z@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
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit@millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
> > End of Ifeffit Digest, Vol 92, Issue 11
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