In a broad project designed to examine uranium transport by surface water from Sierra Peña Blanca to Laguna del Cuervo in the Chihuahuan Desert, sediments from intermittent streams and the lagoon have been extracted and studied. Two samples were sediments from the high area of the Sierra, close to the uranium deposit “El Nopal.” Moreover, 23 core segments extracted for dating sediments were analyzed to consider changes in the fine component concentrations. The techniques of scanning electron microscopy–energy dispersive X-ray spectroscopy, XRD in a conventional diffractometer, and high-resolution synchrotron XRD analysis were applied. The crystallographic objective of the present work was to evaluate the functionality of various methodologies when applied to cases of a detailed analysis of many polyphase samples with cryptocrystals. The methods for processing the experimental data were the Rietveld method in the current multi-pattern variant of the Fullprof program and the degree of crystallinity method for the rapid estimation of the proportion of cryptocrystals in a mixture. This last technique was developed with an ad hoc software package deposited in the GitLab public repository.

To study uranium transport by surface water from Sierra Peña Blanca to Laguna del Cuervo in the Chihuahuan Desert, sediments from intermittent streams and the lagoon have been extracted and studied. Two samples are sediments from the high area of ​​the Sierra, close to the uranium deposit “El Nopal.” Moreover, 23 segments of a sedimentary core were analyzed to study changes in the fine component concentrations. The techniques of scanning electron microscopy-energy dispersive X-ray spectroscopy, XRD in a conventional diffractometer, and high-resolution synchrotron XRD analysis were applied. The crystallographic objective has been to evaluate the functionality of various methodologies when applied to cases of detailed analysis of many polyphase samples with cryptocrystals. The methods for processing the experimental data have been the Rietveld method, in the current multi-pattern variant of the Fullprof program, and the Degree of Crystallinity method for rapid estimation of the proportion of cryptocrystals in a mixture. This last technique has been developed with an Ad-Hoc software package, which has been deposited in the public repository GitLab.

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

Crystallographic algorithms and computer programs play significant roles in materials’ characterization. A software package for the quantitative characterization of crystallographic texture, under axial symmetry conditions, is presented. The proposed methodology is intended for use with both electrons and high-energy synchrotron X-rays. Three different programs are introduced. Anaelu and Grazing are based on the Rietveld modelling approach. Dianne follows the Bunge’s symmetrized spherical harmonics method. A SrTiO3 model sample is proposed as a hypothetical study case.

A computer-aided methodology for the approximate prediction of axially textured polycrystals' properties is presented. The input data for the developed application consist of: (a) the two-dimensional diffraction pattern of the material under investigation and (b) the tensors of the elasto-piezo-dielectric properties of the single crystal case. Program ANAELU 2.0 allows the determination of the fiber axis inverse pole figure by means of a Rietveld-type procedure. The Material Properties Open Database (MPOD, http://mpod.cimav.edu.mx) provides free access to the experimentally determined values of the tensor properties for several crystal species. Practical estimates of polycrystals' properties may be obtained by averaging single crystals' properties tensors, with the orientation distribution function (the symmetry-axis inverse pole figure, in fiber textures) as a weight factor. This treatment, with the application of the Voigt, Reuss and Hill approaches, requires special precautions when it comes to the coupling properties (e.g. piezoelectricity, magnetostriction, magnetoelectricity). Some key physical, mathematical and computational aspects related to the considered topic are discussed. Program GISELLE systematizes the calculation of polycrystal properties under the considered treatments. The application of the proposed methodology to real-world events is illustrated by means of a case study. (C) 2019 SECV. Published by Elsevier Espana, S.L.U.

A tensor formalism for the calculation of effective polycrystal properties associated with polar tensors of up to 4th rank is presented. Sample fiber symmetry is assumed. The Hill approach, via Voigt and Reuss approximations, is followed. The article contains a compact summary of the required mathematical background. The necessary considerations for the treatment of the so-called coupling properties, particularly piezoelectricity, are considered. Focus is put on the elasto-piezo-dielectric case. The analysis of an experimental study from the literature is presented. The article includes a link to the system of programs developed during the investigation. The methodology and the programs described in this article represent tools for the approximate prediction of the properties to be expected in piezoceramics.

The estimation of physical properties in textured polycrystals is reviewed. “Principal” properties, which relate actions and responses within the same subsystem (electric, elastic, …), as well as “coupling” properties (e.g., piezomagnetism), linking actions, and responses associated with various subsystems (magneto‐elastic, thermo‐electric, …) are analyzed. Tensor ranks from 1 to 4, with polar and axial characteristics are considered. Virtual‐time inversion (the case of magnetoelectricity) is taken into account. Matrix and surface representations are considered. Significant differences in the effect of texture on properties arise from the diversity of properties tensors ranks and polar/axial natures. To predict the effective values of coupling properties, precautions required for application of the Voigt, Reuss, and Hill approximations are pointed out. At all stages of the proposed methodology, a symmetrized spherical harmonics treatment of the orientation distribution functions, the inverse pole figures and (single‐ and polycrystals) physical properties is applied. For the case of magnetostriction, a functional program for estimating polycrystal performance is included as Supporting Information. The input data are the single‐crystal property coefficients and the polycrystal inverse pole figure parameters. The coincidence of predicted magnetostriction coefficients with experimentally measured values is satisfactory. Recently established considerations regarding the characterization of coupling properties in complex materials are divulged.

The ANAELU program is part of the current trend towards 2D diffraction patterns processing. ANAELU is open source, distributed under MPL license. The basic conception of the program is that the user proposes the crystalline structure of the phase under study and the inverse pole figure of the considered texture. With this data, using the tools of mathematical texture analysis, the program simulates and graphically represents the 2D-XRD pattern of the model sample. An important feature of the considered patterns is the distribution of intensities along the Debye rings. The visual comparison between observed and calculated patterns is the criterion of correctness of the proposed model. The program has been successfully used in the characterization of materials for electronic applications, alloys and minerals. Some limitations that have been detected in the use of ANAELU are the limited number of input formats that it is able to read, the program relative slowness, the non-consideration of the diffraction background and the poor portability. The present update consists in the improvement of the raised aspects. ANAELU-2.0 presents the following innovations. (a) A new GUI has been created, in WxPython, associated with a system for reading experimental patterns through the FabIO library. The current system reads patterns in the most internationally used formats. (b) The calculation of diffraction patterns, from the generation of the unit cell to the diffracted intensities, has been translated to FORTRAN 2003 with systematic use of the CRYSFML library. This change reduces the running time by one order. (c) Various routines (Laplacian softening, spherical harmonics) have been introduced to model the two-dimensional background. (d) The current version, ANAELU2.0, can be distributed by means of stable executable packages in Windows, LINUX and IOS wraped by MiniConda.

The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

The mathematics required to comprehend much of crystallography is widely taught in the senior years of secondary schooling in many countries, at the same time, there is consternation regarding perceived losses in interest in STEM (Science, Technological, Engineering and Mathematics) subjects, and worse, a failure to engage a significant proportion of young women in these topics in the first instance.In observing the beautiful patterns which result from Laue diffraction experiments we have been encouraged to explore the possibility of employing tools originally developed to analyse experimental patterns[1, 2] as a conduit through which students may be engaged in the exploration of a mathematically based subject.The aesthetically pleasing demonstrations of real-life examples can be shown while the modifications which occur with changing orientation or cell dimensions can be explored.In the context of the current New South Wales Higher School Certificate, conic sections appear as a topic of study and the relevance of Conics to the interpretation of Laue patterns is an appealing example of the application of what might otherwise appear to be an obscure branch of geometry.

An algorithm for modelling the background for each Bragg reflection in a series of X-ray diffraction images containing Debye–Scherrer diffraction from ice in the sample is presented. The method involves the use of a global background model which is generated from the complete X-ray diffraction data set. Fitting of this model to the background pixels is then performed for each reflection independently. The algorithm uses a static background model that does not vary over the course of the scan. The greatest improvement can be expected for data where ice rings are present throughout the data set and the local background shape at the size of a spot on the detector does not exhibit large time-dependent variation. However, the algorithm has been applied to data sets whose background showed large pixel variations (variance/mean > 2) and has been shown to improve the results of processing for these data sets. It is shown that the use of a simple flat-background model as in traditional integration programs causes systematic bias in the background determination at ice-ring resolutions, resulting in an overestimation of reflection intensities at the peaks of the ice rings and an underestimation of reflection intensities either side of the ice ring. The new global background-model algorithm presented here corrects for this bias, resulting in a noticeable improvement in R factors following refinement.

The ANAELU program is part of the current trend towards 2D diffraction patterns processing.ANAELU is open source, distributed under MPL

The Material Properties Open Database (MPOD, http://mpod.cimav.edu.mx) is a functional element of the web-based open databases system linked with Crystallography.MPOD delivers single-crystal tensor properties in several representations, ranging from numerical matrices to 3D printing.Longitudinal moduli surfaces can be displayed in computers as well as in smart cell phones.Properties are stored as ".mpod" files.IUCr formatting standards (CIF) are followed.The original paper containing the data is cited.Structural and experimental information is also registered and linked.The MPOD system includes a physical properties dictionary with pertinent constitutive equations respecting Vol.D of the International Tables when possible."Coupling properties", e.g.piezo-effects and magnetoelectricity, represent interactions linking different subsystems in a material.The implications of crystal symmetry in physical properties are systematically taken into account.Matrices' elements and longitudinal moduli surfaces are checked for consistency with the Neumann Principle.The representation of magnetic coupling properties and their link with magnetic symmetry concepts represent newly added features of MPOD.Color-symmetry and time-inversion considerations add complexity and interest to the task of systematizing the reception, validation and representation of this family of properties.The representation of polycrystals' properties constitutes a current challenge for the MPOD international group.Work on the systematization of the Voigt, Reuss and Hill approximations is described.The MPOD presentation includes a real-time demonstration of the database possibilities.

In macromolecular crystallography, integration programs - such as DIALS (Waterman et al. 2013) - are used to estimate the intensities of Bragg reflections recorded on a series of X-ray diffraction images. The reflection intensities are estimated using the following procedure. A model for the shape of the reflection profile is estimated from a set of strong reflections. This model is then applied to each reflection in order to estimate the size and shape of the reflection on the detector surface and to label each pixel as either foreground or background. The intensity of each reflection is then estimated (in the case of summation integration) by summing the total counts minus the estimated background counts in the foreground region. Since the background level under the reflection peak cannot be measured directly, it is estimated from the surrounding background pixels assuming a given model.

A method for estimating the background under each reflection during integration that is robust in the presence of pixel outliers is presented. The method uses a generalized linear model approach that is more appropriate for use with Poisson distributed data than traditional approaches to pixel outlier handling in integration programs. The algorithm is most applicable to data with a very low background level where assumptions of a normal distribution are no longer valid as an approximation to the Poisson distribution. It is shown that traditional methods can result in the systematic underestimation of background values. This then results in the reflection intensities being overestimated and gives rise to a change in the overall distribution of reflection intensities in a dataset such that too few weak reflections appear to be recorded. Statistical tests performed during data reduction may mistakenly attribute this to merohedral twinning in the crystal. Application of the robust generalized linear model algorithm is shown to correct for this bias.