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, μtotal, 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(μtotal * 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 If signal by the I₀ signal. There is no energy response in the If 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 μbackground is the absorption of the non-resonant atoms in the material and μfluo 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.