Hi Nino,

On Tue, Apr 12, 2016 at 9:08 PM, pereira <ninorpereira@gmail.com> wrote:

Hi All,

new to this list and to the field, so please be patient and kind
and helpful in any response you may have. So far everyone I've
reached on this topic has been extraordinary good. I still have to
learn the lore though.

I'd like to compute the x-ray transmission as function of the x-ray
energy, for a particular mass per unit area of a substance, say Zn.
In the XAS data base I find Zn foil at room temperature, recently measured
and even more recently put into the data base just in time for
my purpose. Thank you! The question is: is there a ready-made program
to use those data? I see that your community has a whole slew of
programs that do the opposite, go from the attenuation and/or fluorescence
measured on a beam line to the attenuation coefficient, apparently without
having to know the mass per unit area of the filter. I see Demeter,
Athena, Larch, and various others but they all seem to go the wrong
way for (and much further than) what I need.

Instead, I'd like to pick up the data you guys measured on the synchrotron,
and convert those into the X-ray transmission of a filter for which I select
the mass per unit area.

In trying to figure out how to do this I look at the graphs in the database,
and the numbers behind Zn foil.xdi.

The graph on the top left side gives the "Raw XAFS" (y, say) as function of energy.
I interpret that as y = - ln (itrans/i0), where i0 and itrans are in Zn foil.xdi
as the intensity of the incoming x-ray beam, and the beam behind the
particular filter. Far from the edge, at 9600 eV, I see i0=93769.049842
and itrans=56429.849906, so that y=0.508. I can't tell from the graph whether this
is indeed the case, so I go to the NIST tables. They give 35.05 cm^2/g on the
low side of the edge. Then, the mass per unit area of this particular foil
must have been 14.5 mg/cm^2.

At 10000 eV the same thing gives y=3.603. This is pretty close to what I
see in the graph, so I'm tempted to think that guessing "Raw XAFS"= ln(i0/itrans).
However, for (mu/rho) NIST gives 233.1 cm^2/g, so I get for the foil's mass
per unit area 16 mg/cm^2. Not quite right.

Any comments on what I might have done wrong?

It seems to me that by measuring the transmission of a particular filter on
some X-ray source we might have available would then in effect measure
the mass per unit area, so that this can be taken into account by simply
exponentiating itrans/i0 with the right exponent ( = multiplying the
logs with the right factor).

Is something like this already implemented in one of your programs? If so,
which one?

For XANES and EXAFS we (most of us, anyway) tend to not care about the value of the mass attenuation in cm^2/gr, though we do pay attention to total attenuation in cm^-1, at least insofar as we get the sample thickness correct. The measurements we report are rarely in true units, as I0 is typically a sampled current from an upstream ion chamber and I1 is a sampled current from a downstream ion chamber -- we don't bother converting these numbers to flux just before and just after the sample -- we know there are arbitrary scale factors, but they tend to cancel out.

The step in the reported -log(I1/I0) should be a good measure of the edge step in mu*x, and we typically aim for value around 1 (so that going across the edge changes the attenuation by 1/e).

I think what you want are good values for mass attenuation for the Zn K edge. These are tabulated and available in the Hephaestus program (that is part of the Demeter package), and also in Larch.    For example, in Larch, you could do
   larch> en = linspace(9500, 10000, 501)
     larch> mu = mu_elam(30, en)
     larch> plot(en, mu)

Here, mu (in cm^2/gr) will go from about 35 below the edge to about 250 above the edge. Of course, these tables are atomic, and have no chemical or structural effects included. But, a simple offset and scaling of the measured mu to match these atomic values should be pretty good.

Hephaestus also has a nice calculator for the 1/e thickness of a sample (in your case, filter) of a given composition and density, at a particular energy.

Hope that helps!

--Matt