# 14.2. Absorption calculations and experimental corrections¶

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 I_{0} 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 see

- EA Stern and SM Heald. Basic principles and applications of EXAFS.
*Handbook on Synchrotron Radiation*, 1:955–1014, 1983.

## 14.2.1. Absorption Calculation¶

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.

## 14.2.2. McMaster Correction¶

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 Elam 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 k^{2}, 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.

- W. T. Elam, B. D. Ravel, and J. R. Sieber. A new atomic database for X-ray spectroscopic calculations.
*Radiation Physics and Chemistry*, 63:121–128, February 2002. doi:10.1016/S0969-806X(01)00227-4.

For a discussion of the cumulant expansion in EXAFS, see

- Grant Bunker. Application of the ratio method of EXAFS analysis to disordered systems.
*Nuclear Instruments and Methods in Physics Research*, 207(3):437 – 444, 1983. doi:10.1016/0167-5087(83)90655-5.

## 14.2.3. I0 Correction¶

The response of the I_{0} 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 I_{0} signal. There
is no energy response in the I_{f} signal since all atoms
fluoresce at set energies. The energy response of I_{0} 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 I_{0} 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.

## 14.2.4. Self-Absorption Correction¶

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 S^{2}_{0}, 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 S^{2}_{0}.

DEMETER is copyright © 2009-2016 Bruce Ravel – This document is copyright © 2016 Bruce Ravel

This document is licensed under The Creative Commons Attribution-ShareAlike License.

If DEMETER and this document are useful to you, please consider supporting The Creative Commons.