General overview of LASE

What is LASE?

LASE is a software dedicated to the X-Ray Absorption spectra analysis. It can run on any computer with unix and X-Window, or with Windows (95 or higher). In both case, it offers a userfriendly graphical interface, which allows to visualize in real time the effects of various parameters, while offering a great liberty to the user.

LASE was first designed at LURE, for the analysis of bioinorganical samples studied by X-ray absorption spectroscopy. Hence, it is especially suited for this kind of samples: proteins, transition metals complexes,...

Currently, LASE offers tools for analysis and treatment of spectra in three main categories:

These points are presented with more details hereafter.

EXAFS oscillations extraction

LASE offers various tools to treat the experimental data and extracting the EXAFS oscillations. Especially, it also includes statistical tools to handle the informations coming from the repeated measurements of a sample spectrum.

Experimental data loading

• experimental files with transmission, fluorescence or electron detection, from various experimental lines (LURE, ESRF mainly).
• possibility to keep I₀ and I₁, and to recompute the signal from corrected I₀ or I₁.
• experiments with many detectors are handled (including mixt experiments with absorption and fluorescence), with creation of one spectrum by detector or automatic average, and selection of really used detectors.

Whole spectrum handling

• Energie corrections, linear or with use of the Bragg-law,
• derivation, integration, interpolation, truncature,...,
• glitch removal with polynomial or spline interpolation,
• normalisation using 1 or 2 points or with µ₀ modelisation,
• search for edge energie (and related edge), using the maximum of the first derivative,
• sorting, handling of multiple-points.

Statistical analysis of the spectra

• Average spectrum of n experimental spectra, with standard deviation on each point,
• Optionnal visualisation of individual error bars for each spectrum,
• error bars are propagated all along the data reduction,
• error bars can even be propagated across Fourier filtering, with computation of the whole covariance matrix,
• basic statistical tools: average, standard deviations, distribution analysis (histograms, Kolmogorov-Smirnov test for normal distribution).

EXAFS oscillations extraction

• At each step, result is shown in real time after parameter change,
• background (matrix) absorption modelled by a Victoreen function (complete or truncated), a polynomial function, least-square fitted to the preedge region defined by the user,

• three-step removal of µ₀: E-space polynomial, then k-space polynomial, then smoothing spline. Everything is under user control.

• parameter changes can be automatically forwarded to ulterior steps of the extraction, including Fourier-transform,
• kⁿ weigthing, with n = 0 to 9,
• normalisation with the modelled µ₀, or with theoretical µ₀ (Victoreen, McMaster,...)

Spectrum filtering

It is done with the classical Fourier transformation procedure.

• Free selection of the apodisation function ("window") among several ones: rectangular, gaussian, Hanning, Hamming, Norton-Beer, Kaiser-Bessel,...,
• complete definition of the R and k intervals and steps,
• phase and amplitude corrections before Fourier transform, on demand,
• computation with fast algorithm or, directly on experimental data, with classical integral estimation,
• error bars can be computed on real and imaginary part of the TF and TFI,
• free selection of the R-space filter among the several filtering functions,
• real time visualisation of the window influence on the Fourier transform,
• apodisation function is memorised with the TF, to correct for it simply
• phases and amplitudes can be isolated when doing the inverse Fourier transform

LASE offers tools to help in the creation of the structural model needed to compute the theoretical EXAFS spectra that will be used in the fitting step. Presently, these models can be used for creating FEFF input files.

For its models, LASE works with "molecules": a molecule is a set of atoms grouped for a logical reason: molecule in the chemical meaning, but also unit cell(s) or other association. In that molecule one or more atoms can be defined as "absorbing": an absorbing atom represent the atom studied with the X-ray spectroscopy and regroups a set of models (including scattering paths for electrons) and experimental data.

Structural data loading

It is possible to load in LASE structural data from the *.cor files (Cambridge Cristallographic Databank), the *.pdb files (Protein Data Bank) and simple free-format ASCII files. With the help of the babel software, that can convert various formats into the pdb file format, it is possible to load practically any structural file in LASE.

A structural model can also be created directly in LASE, starting with orthonormal coordinates or fractionnar cristallographic coordinates. For some space groups (P1, P-1, P21, C2/c, Pnma,...), symmetries are handled. Several cells can be generated at once.

Structural model visualisation

If OpenGL is present (MESA works quite well), one can view in LASE the structural model

It is then possible to know atomic coordinates, distances and angles between atoms simply by clicking them. It is also possible to add or remove atoms to the FEFF model in the same way. If there is an absorber atom with a model, the experimental and modelled spectra are also shown. The various scattering paths, and their contribution to the EXAFS signal after fitting, can also be drawn.

FEFF model creation

LASE offers a graphical user interface to parameter almost all FEFF-6 options, except the OVERLAP one.

The structural model creation can be done automatically starting with the structural informations created in LASE, including all atoms or atoms closer than a given distance of the absorbing atom. The model can then be edited using the above dialog boxes.

With LASE, it is possible to fit in k-space (that is, EXAFS oscillations) with or without error-bars weighting. This fit relies on the path-decomposition of the EXAFS formula (in the case of just single scattering is present, a path is equivalent to a reflector atoms shell).

For each path, it is possible to fit its degeneracy (N, number of neighbours), Debye-Waller factor, length (R, distance) and four cumulants accounting for asymetries in statistical or thermal disorder. If required, one can also fit individual mean-free-path and edge-energy corrections.

Are also fitted a global edge-energy correction and the electronic amplitude reduction factor (S₀²).

While fitting, the fitted spectrum is redrawn in real time, to follow on screen the minimisation procedure.

FEFF results usage

LASE can read paths.dat files created by FEFF to construct the structural model (if not already known), the various reflexion paths and their phases and amplitudes.

Results validation

LASE offers tools for performing a Monte-Carlo study of the fitting results, to obtain the average value and error bars on the fitted parameters, with no other hypothesis than the gaussian distribution of the experimental errors.