Included in ATOMS is absorption data for the elements from various
sources. Using this and the crystallographic information from
atoms.inp, ATOMS is able to make several
calculations useful for XAFS analysis. It approximates the absorption
depth and edge step size of the material at the edge energy of the
core atom and estimates three corrections needed for the analysis of
XAFS data. These corrections are the “McMaster
correction”, the energy response of the I0 chamber in a fluorescence
experiment, and the self-absorption of a thick material in a
fluorescence experiment. All of these numbers are written at the top
of the output file. For more information on these calculations consult
Chapter 10 of *Handbook of Synchrotron Radiation,
v.1*.

Proper sample preparation for an XAFS experiment requires knowledge of the absorption depth and edge step size of the material of interest. The statistics of data collection can be optimized by choosing the correct sample thickness. It is also necessary to avoid distortions to the data due to thickness and large particle size effects.

ATOMS calculates the total cross section of the material above the
edge energy of the central atom and divides by the unit cell
volume. The number obtained, μ_{total}, has units of
cm^{-1}. Thus, if `x` is the thickness of
the sample in cm, the x-ray beam passing through the sample will be
attenuated by exp(μ_{total} * `x`).

ATOMS also calculates the change in cross section of the central atom below and above the absorption edge and divides by the unit cell volume. This number, Δμ, multiplied by the sample thickness in cm gives the approximate edge step in a transmission experiment.

The density of the material is also reported. This number assumes that the bulk material will have the same density as the unit cell. It is included as an aid to sample preparation.

Typically, XAFS data is normalized to a single number representing the size of the edge step. While there are compelling reasons to use this simple normalization, it can introduce an important distortion to the amplitude of the χ(k) extracted from the absorption data. This distortion comes from energy response of the bare atom absorption of the central atom. This is poorly approximated away from the edge by a single number. Because this affects the amplitude of χ(k) and not the phase, it can be corrected by including a Debye-Waller factor and a fourth cumulant in the analysis of the data. These two “McMaster corrections” are intended to be additive corrections to any thermal or structural disorder included in the analysis of the XAFS.

ATOMS uses data from McMaster to construct the bare atom
absorption for the central atom. ATOMS then regresses a quadratic
polynomial in energy to the natural logarithm of the constructed
central atom absorption. Because energy and photo-electron wave number
are simply related, E is proportional to k², the coefficients of
this regression can be related to the XAFS Debye-Waller factor and
fourth cumulant. The coefficient of the term linear in energy equals
`sigma_MM^2` and the coefficient of the quadratic term equals `4/3 * ``sigma_MM^4`. The values of `sigma_MM^2` and
`sigma_MM^4` are written at the top of the output file.

The response of the I₀ chamber varies with energy during an XAFS
experiment. In a fluorescence experiment, the absorption signal is
obtained by normalizing the I_{f} signal by the I₀ signal. There
is no energy response in the I_{f} signal since all atoms fluoresce
at set energies. The energy response of I₀ is ignored by this
normalization. At low energies this can be a significant effect. Like
the McMaster correction, this effect attenuates the amplitude of
χ(k) and is is well approximated by an additional Debye-Waller
factor and fourth cumulant.

ATOMS uses the values of the nitrogen, argon and krypton keywords
in atoms.inp to determine the content of the
I₀ chamber by pressure. It assumes that the remainder of the
chamber is filled with helium. It then uses McMaster's data to
construct the energy response of the chamber and regresses a
polynomial to it in the manner described above. `sigma_I0^2` and
are also
written at the top of the output file and intended as additive
corrections in the analysis.

If the thickness of a sample is large compared to absorption length of the sample and the absorbing atom is sufficiently concentrated in the sample, then the amplitude of the χ(k) extracted from the data taken on it in fluorescence will be distorted by self-absorption effects in a way that is easily estimated. The absorption depth of the material might vary significantly through the absorption edge and the XAFS wiggles. The correction for this effect is well approximated as

1 + mu_abs / (mu_background+mu_fluor)

where μ_{background} is the absorption of the
non-resonant atoms in the material and μ_{fluo} is the total
absorption of the material at the fluorescent energy of the absorbing
atom. ATOMS constructs this function using the McMaster tables
then regresses a polynomial to it in the manner described above.
`sigma_self^2` and `sigma_self^4` are written at the top of the output file and
intended as additive corrections in the analysis. Because the size of
the edge step is affected by self-absorption, the amplitude of
χ(k) is attenuated when normalized to the edge step. Since the
amplitude is a measure of S²₀, this is an important effect. The
number reported in feff.inp as the amplitude
factor is intended to be a multiplicative correction to the data or to
the measured S²₀.