# [Ifeffit] Basic questions about the preliminary data processing in Athena

Haifeng Li hli211 at uic.edu
Tue Aug 14 18:21:23 CDT 2018

```Hi, Carlo,

Thanks for your physical explanation for the calibration.

I have another question. I measured the same element at different
beamlines. So if I want to compare different samples measured at different
beamlines, how should I do for this situation given the possible different
calibration methods? I know alignment is very important and just shifting
the energy by calibrating would have issue.

Here I mean different calibration methods is dedicated for my element
ruthenium Ru with E0 of 22117 eV. The derivative curve show it has two
peaks. One beamline used the first one for calibration. The other used the
second. Another used the middle number between the two peaks by claiming
that the peaks stand for oxidation state with one peak for one oxidation
state and multiple peaks for multiple oxidation states. Here for Ru metal
with one oxidation state, since the main peak splits into two, the middle
energy between the two peaks was chose as the E0. Attached is the file of
Ru foil for more information. I do not know which one should be right. In
the manual, it shows choosing the first maximum point as the edge energy.
How should I choose the edge energy? Maybe I think too much. It does not
matter as the calibration is consistency.

The reference data from different calibration methods can be aligned very
well. This is another confusing part. Does the calibration would affect the
alignment?

Haifeng

On Mon, Jul 23, 2018 at 10:48 AM, Carlo Segre <segre at iit.edu> wrote:

>
> The calibration should be done at the beamline with a foil.  Once that is
> done, then you don't really want to change it.  Remember that just shifting
> the energy is not actually the correct way to do a shift.  The energy shift
> is a non-linear function of the angle (Bragg's Law) and so when you shift
> energy you are really distorting Chi(k) since that is also a non-linear
> function of energy (E^1/2).  Yes, it is usually a small effect but I prefer
> not to apply too many shifts in energy if possible.
>
> I assume that the calibrate function is the same as the align except the
> E-shift is left at zero and a correction is applied permanently to the data.
>
> Carlo
>
>
> On Mon, 23 Jul 2018, Haifeng Li wrote:
>
> Hi, Carlo,
>>
>>
>> I may ask you more questions. Why you do not recommend to calibrate the
>> data? Calibration is used to find the E0 and match it to the literature
>> data. What is the real difference between calibration and alignment?
>>
>> Thanks,
>>
>> Haifeng
>>
>> On Sun, Jul 22, 2018 at 5:30 PM, Carlo Segre <segre at iit.edu> wrote:
>>
>>
>>> Hello Haifeng:
>>>
>>> Personally, I would not calibrate the data but merely align the
>>> references
>>> of A2 and A3 to the reference of A1 and similarly align B2 and B3
>>> references to that of B1.  Once merged, you can then aligh the reference
>>> of
>>> the merged B samples to that of the merged A samples.
>>>
>>> If you keep the references then you can always align data taken at a
>>> leter
>>> time to these data sets.  If the energy of your reference is a small bit
>>> off from the tabulated value, that is OK as long as all the data being
>>> compared has aligned references.
>>>
>>> Carlo
>>>
>>>
>>> On Sun, 22 Jul 2018, Haifeng Li wrote:
>>>
>>> Dear ALL,
>>>
>>>>
>>>> I am a beginner in Athena. Recently I got the spectra and I am confusing
>>>> about the data calibration and alignment. The manual shows that
>>>> calibrate
>>>> the reference data of one scan and align other reference data to that
>>>> calibrated one.
>>>>
>>>> Here I want to show examples. I have two samples A and B, Each sample
>>>> has
>>>> three scans with the corresponding reference data. For sample A, 1st
>>>> scan
>>>> is calibrated and the other two scans are aligned to 1st scan. Then
>>>> merge
>>>> them into merged A. The same procedures for sample B and get merged B.
>>>> If
>>>> I
>>>> want to compare XANES of sample A and B, do I need to align the merged
>>>> reference data between A and B? If so, why? My understanding is that all
>>>> scans (original data and merged data) in sample A and B are calibrated
>>>> to
>>>> standard edge energy. Why do they need to align?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Haifeng
>>>>
>>>>
>>>> --
>>> Carlo U. Segre -- Duchossois Leadership Professor of Physics
>>> Interim Chair, Department of Chemistry
>>> Director, Center for Synchrotron Radiation Research and Instrumentation
>>> Illinois Institute of Technology
>>> Voice: 312.567.3498            Fax: 312.567.3494
>>> segre at iit.edu   http://phys.iit.edu/~segre   segre at debian.org
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
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>>>
>>>
>>
> --
> Carlo U. Segre -- Duchossois Leadership Professor of Physics
> Interim Chair, Department of Chemistry
> Director, Center for Synchrotron Radiation Research and Instrumentation
> Illinois Institute of Technology
> Voice: 312.567.3498            Fax: 312.567.3494
> segre at iit.edu   http://phys.iit.edu/~segre   segre at debian.org
>
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