The effect of self-consistent potentials on EXAFS analysis.

A theory program intended for use with extended X-ray-absorption fine structure (EXAFS) spectroscopy and based on the popular FEFF8 is presented. It provides an application programming interface designed to make it easy to integrate high-quality theory into EXAFS analysis software. This new code is then used to examine the impact of self-consistent scattering potentials on EXAFS data analysis by methodical testing of theoretical fitting standards against a curated suite of measured EXAFS data. For each data set, the results of a fit are compared using a well characterized structural model and theoretical fitting standards computed both with and without self-consistent potentials. It is demonstrated that the use of self-consistent potentials has scant impact on the results of the EXAFS analysis.

XAFS Data Interchange: A single spectrum XAFS data file format.

We propose a standard data format for the interchange of XAFS data. The XAFS Data Interchange (XDI) standard is meant to encapsulate a single spectrum of XAFS along with relevant metadata. XDI is a text-based format with a simple syntax which clearly delineates metadata from the data table in a way that is easily interpreted both by a computer and by a human. The metadata header is inspired by the format of an electronic mail header, representing metadata names and values as an associative array. The data table is represented as columns of numbers. This format can be imported as is into most existing XAFS data analysis, spreadsheet, or data visualization programs. Along with a specification and a dictionary of metadata types, we provide an application-programming interface written in C and bindings for programming dynamic languages.

Muffin-tin potentials in EXAFS analysis.

Muffin-tin potentials are the standard tool for calculating the potential surface of a cluster of atoms for use in the analysis of extended X-ray absorption fine-structure (EXAFS) data. The set of Cartesian coordinates used to define the positions of atoms in the cluster and to calculate the muffin-tin potentials is commonly also used to enumerate the scattering paths used in the EXAFS data analysis. In this paper, it is shown that these muffin-tin potentials are sufficiently robust to be used to examine quantitatively contributions to the EXAFS data from scattering geometries not represented in the original cluster.

Emission Ghost Imaging: reconstruction with data augmentation.

Ghost Imaging enables 2D reconstruction of an object even though particles transmitted or emitted by the object of interest are detected with a single pixel detector without spatial resolution. This is possible because for the particular implementation of ghost imaging presented here, the incident beam is spatially modulated with a non-configurable attenuating mask whose orientation is varied (e.g. via transverse displacement or rotation) in the course of the ghost imaging experiment. Each orientation yields a distinct spatial pattern in the attenuated beam. In many cases, ghost imaging reconstructions can be dramatically improved by factoring the measurement matrix which consists of measured attenuated incident radiation for each of many orientations of the mask at each pixel to be reconstructed as the product of an orthonormal matrix Qand an upper triangular matrix R provided that the number of orientations of the mask (N) is greater than or equal to the number of pixels (P) reconstructed. For the N

Towards data format standardization for X-ray absorption spectroscopy.

A working group on data format standardization for X-ray absorption spectroscopy (XAS) has recently formed under the auspices of the International X-ray Absorption Society and the XAFS Commission of the International Union of Crystallography. This group of beamline scientists and XAS practitioners has been tasked to propose data format standards to meet the needs of the world-wide XAS community. In this report, concepts for addressing three XAS data storage needs are presented: a single spectrum interchange format, a hierarchical format for multispectral X-ray experiment, and a relational database format for XAS data libraries.

Correction: Synthesis and characterisation of brannerite compositions (U0.9Ce0.1)1-x M x Ti2O6 (M = Gd3+, Ca2+) for the immobilisation of MOX residues.

[This corrects the article DOI: 10.1039/C7RA11742F.].

Performance of a four-element Si drift detector for X-ray absorption fine-structure spectroscopy: resolution, maximum count rate, and dead-time correction with incorporation into the ATHENA data analysis software.

The performance of a four-element Si drift detector for energy-dispersive fluorescence-yield X-ray absorption fine-structure measurements is reported, operating at the National Institute of Standards and Technology beamline X23A2 at the National Synchrotron Light Source. The detector can acquire X-ray absorption fine-structure spectra with a throughput exceeding 4 x 10(5) counts per second per detector element (>1.6 x 10(6) total counts per second summed over all four channels). At this count rate the resolution at 6 keV is approximately 220 eV, which adequately resolves the Mn Kalpha and Kbeta fluorescence lines. Accurate dead-time correction is demonstrated, and it has been incorporated into the ATHENA data analysis program. To maintain counting efficiency and high signal to background, it is suggested that the incoming count rate should not exceed approximately 70% of the maximum throughput.

Simultaneous XAFS measurements of multiple samples.

A four-channel ionization chamber has been designed, constructed and tested. This ionization chamber allows X-ray absorption spectra to be collected in transmission from up to four samples simultaneously. This results in spectra that are free of systematic uncertainty in relative energy alignment introduced by scan-to-scan stability of the monochromator or of numerical uncertainty associated with a post-processing alignment algorithm, allowing, in a single shot, an absolute measure of edge shift between four samples of different valence. As four samples can be measured in parallel, the time expended over the course of an experiment to cycle the measurement environment between its rest state and the measurement condition is substantially reduced. The ionization chamber is simple in design and could be implemented at virtually any XAFS beamline with a horizontal fan of radiation such as that provided by a bend magnet or wiggler.

A synchrotron X-ray spectroscopy study of titanium co-ordination in explosive melt glass derived from the trinity nuclear test.

The speciation of Ti in trinitite, the explosive melt glass derived from the Trinity Test of 16th of July 1945, was investigated by X-ray absorption spectroscopy (XAS). Ti K-edge XANES showed that Ti was present in the Ti(iv) oxidation state for all samples. Fitting of pre-edge features by Gaussian functions and comparison with standards of known Ti coordination revealed significant variation in Ti coordination environment between samples. The variation of Ti coordination may be attributed to several factors including specific local chemistry and thermal histories of samples, in keeping with the highly heterogeneous microstructure of trinitite and the arkosic sand source material.

Local atomic order and hierarchical polar nanoregions in a classical relaxor ferroelectric.

The development of useful structure-function relationships for materials that exhibit correlated nanoscale disorder requires adequately large atomistic models which today are obtained mainly via theoretical simulations. Here, we exploit our recent advances in structure-refinement methodology to demonstrate how such models can be derived directly from simultaneous fitting of 3D diffuse- and total-scattering data, and we use this approach to elucidate the complex nanoscale atomic correlations in the classical relaxor ferroelectric PbMg1/3Nb2/3O3 (PMN). Our results uncover details of ordering of Mg and Nb and reveal a hierarchical structure of polar nanoregions associated with the Pb and Nb displacements. The magnitudes of these displacements and their alignment vary smoothly across the nanoregion boundaries. No spatial correlations were found between the chemical ordering and the polar nanoregions. This work highlights a broadly applicable nanoscale structure-refinement method and provides insights into the structure of PMN that require rethinking its existing contentious models.

Synthesis and characterisation of brannerite compositions (U0.9Ce0.1)1-x M x Ti2O6 (M = Gd3+, Ca2+) for the immobilisation of MOX residues.

A suite of uranium brannerites for the disposal of MOX residues, formulated (U0.9Ce0.1)1-x M x Ti2O6 (M = Ca2+ and/or Gd3+), were prepared using a mixed oxide route under oxidising, inert and reducing atmospheres (air, argon and H2/N2). Gd3+ was added to act as a neutron absorber in the final Pu bearing wasteform and Ce added to function as a structural analogue for Pu. X-ray powder diffraction of the synthesised specimens found that phase distribution was strongly affected by the processing atmosphere and Gd content. In all cases prototypical brannerite was formed, accompanied by different secondary phases dependent on processing atmosphere. Microstructural analysis (SEM) of the sintered samples confirmed the results of the X-ray powder diffraction. Bulk XANES found that Ti remained in the Ti4+ oxidation state whereas Ce was uniformly reduced to the Ce3+ oxidation state regardless of processing conditions or stoichiometry. Micro-focus XANES was used to determine U oxidation in the brannerite phase and showed that U oxidised to higher U oxidation states to charge compensate. It was concluded that the charge balance mechanism was a combination of U oxidation and A-site vacancies.

Diamond sensors and polycapillary lenses for X-ray absorption spectroscopy.

Diamond sensors are evaluated as incident beam monitors for X-ray absorption spectroscopy experiments. These single crystal devices pose a challenge for an energy-scanning experiment using hard X-rays due to the effect of diffraction from the crystalline sensor at energies which meet the Bragg condition. This problem is eliminated by combination with polycapillary lenses. The convergence angle of the beam exiting the lens is large compared to rocking curve widths of the diamond. A ray exiting one capillary from the lens meets the Bragg condition for any reflection at a different energy from the rays exiting adjacent capillaries. This serves to broaden each diffraction peak over a wide energy range, allowing linear measurement of incident intensity over the range of the energy scan. Extended X-ray absorption fine structure data are measured with a combination of a polycapillary lens and a diamond incident beam monitor. These data are of comparable quality to data measured without a lens and with an ionization chamber monitoring the incident beam intensity.

Deposition of uranium precipitates in dolomitic gravel fill.

Uranium-containing precipitates have been observed in a dolomitic gravel fill near the Department of Energy (DOE) S-3 Ponds former waste disposal site as a result of exposure to acidic (pH 3.4) groundwater contaminated with U (33 mg L(-1)), Al3+ (900 mg L(-1)), and NO3- (14 000 mg L(-1)). The U containing precipitates fluoresce a bright green under ultraviolet (UV) short-wave light which identify U-rich coatings on the gravel. Scanning electron microscopy (SEM) microprobe analysis show U concentration ranges from 1.6-19.8% (average of 7%) within the coatings with higher concentrations at the interface of the dolomite fragments. X-ray absorption near edge structure spectroscopy (XANES) indicate that the U is hexavalent and extended X-ray absorption fine structure spectroscopy (EXAFS) shows that the uranyl is coordinated by carbonate. The exact nature of the uranyl carbonates are difficult to determine, but some are best described by a split K(+)-like shell similar to grimselite [K4Na(UO2)(CO3)3 x H2O] and other regions are better described by a single Ca(2+)-like shell similar to liebigite [Ca2(UO2)(CO3)3 x 11(H2O)] or andersonite [Na2CaUO2(CO3)3 x 6H2O]. The U precipitates are found in the form of white to light yellow cracked-formations as coatings on the dolomite gravel and as detached individual precipitates, and are associated with amorphous basalumnite [Al4(SO4)(OH)10 x 4H2O].

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT.

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.

ATOMS: crystallography for the X-ray absorption spectroscopist.

ATOMS is a user application providing crystallographic functionality useful to x-ray absorption spectroscopists. ATOMS is also a set of reusable, object-oriented software modules written in the Perl programming language providing crystallographic functionality and access to databases of absorption coefficients and anomalous scattering factors. The main use of the ATOMS program is to generate input data for the ab initio, multiple scattering, x-ray absorption spectroscopy code FEFF. However the code offers many additional features, including useful calculations involving absorption coefficients and simulations of Diffraction Anomalous Fine-Structure (DAFS) spectra. Command line, graphical, and web-based interfaces to the code are offered as part of the standard distribution. As Perl runs on a wide variety of common computer platforms, ATOMS itself is a cross platform application. All text presented to the user can be internationalized - support for four languages is currently included in the package. Development of ATOMS is active - a FEFF interface, structure visualization, and additional crystallographic calculations are among the future developments.

Valence selective DAFS measurements of Mn in La1/3Ca2/3MnO3.

The manganese perovskite system La(1-x)Ca(x)MnO3 displays a complex phase diagram of structural, magnetic, and transport properties with varying Ca concentration. At x = 2/3 and at low temperature, the system is antiferromagnetic with Mn4+ and Mn3+ ions occupying special positions in a charge-ordered supperlattice. The charge ordering transition at about 260 K is characterized by the appearance of satellite peaks around certain strong normal lattice reflections. The normal lattice reflections are due to scattering from planes containing Mn4+ and Mn3+ ions in nearly stoichiometric proportion, however the superlattice reflections are due to scattering from planes containing only Mn4+ ions. By measuring Diffraction Anomalous Fine-Structure spectral on a superlattice reflection and its associated normal lattice reflection, it is possible to isolate absorption-like spectra for the two Mn sites. Due to the weak intensity of these superlattice reflections, we were unable to obtain high quality near-edge spectra for the superlattice reflection measured. However, the data offer useful information about the local electronic structures of the two Mn ions.

Diffraction anomalous fine-structure spectroscopy at beamline BM2 at the European Synchrotron Radiation Facility.

Diffraction anomalous fine-structure (DAFS) spectroscopy uses resonant elastic X-rays scattering as an atomic, shell and site-selective probe that provides information on the electronic structure and the local atomic environment as well as on the long-range-ordered crystallographic structure. A DAFS experiment consists of measuring the Bragg peak intensities as a function of the energy of the incoming X-ray beam. The French CRG (Collaborative Research Group) beamline BM2-D2AM (Diffraction Diffusion Anomale Multi-longueurs d'Onde) at the ESRF (European Synchrotron Radiation Facility) has developed a state-of-the-art energy scan diffraction set-up. In this article the requirements for obtaining reliable DAFS data are presented and recent technical achievements are reported.