Open-access and free articles in Journal of Applied Crystallography
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Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.en-gbCopyright (c) 2022 International Union of CrystallographyInternational Union of CrystallographyInternational Union of CrystallographytextJournal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.https://journals.iucr.orgurn:issn:0021-8898Open-access and free articles in Journal of Applied Crystallographytext/html62002-02-01T00:00+00:00yearlyJournal of Applied Crystallographymed@iucr.orgCopyright (c) 2022 International Union of Crystallographyurn:issn:0021-8898Open-access and free articles in Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
https://journals.iucr.org/j/journalhomepage.html
Still imageOptimization strategies and artifacts of time-involved small-angle neutron scattering experiments
http://scripts.iucr.org/cgi-bin/paper?uz5005
Kinetic small-angle neutron scattering provides access to the microscopic properties of mesoscale systems under slow, periodic perturbations. By interlocking the phases of neutron pulse, sample modulation and detector signal, time-involved small-angle neutron scattering experiments (TISANE) allow one to exploit the neutron velocity spread and record data without major sacrifice in intensity at timescales down to microseconds. This article reviews the optimization strategies of TISANE that arise from specific aspects of the process of data acquisition and data analysis starting from the basic principles of operation. Typical artifacts of data recorded in TISANE due to the choice of time binning and neutron chopper pulse width are illustrated by virtue of the response of the skyrmion lattice in MnSi under periodic changes of the direction of the stabilizing magnetic field.textKinetic small-angle neutron scattering provides access to the microscopic properties of mesoscale systems under slow, periodic perturbations. By interlocking the phases of neutron pulse, sample modulation and detector signal, time-involved small-angle neutron scattering experiments (TISANE) allow one to exploit the neutron velocity spread and record data without major sacrifice in intensity at timescales down to microseconds. This article reviews the optimization strategies of TISANE that arise from specific aspects of the process of data acquisition and data analysis starting from the basic principles of operation. Typical artifacts of data recorded in TISANE due to the choice of time binning and neutron chopper pulse width are illustrated by virtue of the response of the skyrmion lattice in MnSi under periodic changes of the direction of the stabilizing magnetic field.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; SKYRMION; TISANEThis article reviews the opportunities and limitations of time-involved small-angle neutron scattering experiments, with the typical artifacts of the recorded data illustrated by virtue of the response of the skyrmion lattice in MnSi under periodic changes of the direction of the stabilizing field.doi:10.1107/S1600576722009931enOptimization strategies and artifacts of time-involved small-angle neutron scattering experimentsMettus, D.Chacon, A.Bauer, A.Mühlbauer, S.Pfleiderer, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-28552022-11-281600-5767med@iucr.org6December 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersSmall-angle X-ray microdiffraction from fibrils embedded in tissue thin sections
http://scripts.iucr.org/cgi-bin/paper?fs5212
Small-angle X-ray scattering (SAXS) from fibrils embedded in a fixed, thin section of tissue includes contributions from the fibrils, the polymeric matrix surrounding the fibrils, other constituents of the tissue, and cross-terms due to the spatial correlation between fibrils and neighboring molecules. This complex mixture severely limits the amount of information that can be extracted from scattering studies. However, availability of micro- and nano-beams has made the measurement of scattering from very small volumes possible, which, in some cases, may be dominated by a single fibrillar constituent. In such cases, information about the predominant species may be accessible. Nevertheless, even in these cases, the correlations between the positions of fibrils and other constituents have a significant impact on the observed scattering. Here, strategies are proposed to extract partial information about fibril structure and tissue organization on the basis of SAXS from samples of this type. It is shown that the spatial correlation function of the fibril in the direction perpendicular to the fibril axis can be computed and contains information about the predominant fibril structure and the organization of the surrounding tissue matrix. This has significant advantages over approaches based on techniques developed for X-ray solution scattering. Examples of correlation calculations in different types of samples are given to demonstrate the information that can be obtained from these measurements.textSmall-angle X-ray scattering (SAXS) from fibrils embedded in a fixed, thin section of tissue includes contributions from the fibrils, the polymeric matrix surrounding the fibrils, other constituents of the tissue, and cross-terms due to the spatial correlation between fibrils and neighboring molecules. This complex mixture severely limits the amount of information that can be extracted from scattering studies. However, availability of micro- and nano-beams has made the measurement of scattering from very small volumes possible, which, in some cases, may be dominated by a single fibrillar constituent. In such cases, information about the predominant species may be accessible. Nevertheless, even in these cases, the correlations between the positions of fibrils and other constituents have a significant impact on the observed scattering. Here, strategies are proposed to extract partial information about fibril structure and tissue organization on the basis of SAXS from samples of this type. It is shown that the spatial correlation function of the fibril in the direction perpendicular to the fibril axis can be computed and contains information about the predominant fibril structure and the organization of the surrounding tissue matrix. This has significant advantages over approaches based on techniques developed for X-ray solution scattering. Examples of correlation calculations in different types of samples are given to demonstrate the information that can be obtained from these measurements.urn:issn:1600-5767SMALL-ANGLE X-RAY SCATTERING; SAXS; SCANNING MICRODIFFRACTION; AMYLOIDS; ALZHEIMER'S DISEASEThe availability of micro- and nano-X-ray beams makes measurement of scattering from very small volumes possible, opening possibilities for deriving in situ structural information on fibrillar constituents in complex materials and tissues. This work outlines a set of strategies for confronting major technical obstacles to extract useful structural information from scattering derived from these samples.doi:10.1107/S1600576722009955enSmall-angle X-ray microdiffraction from fibrils embedded in tissue thin sectionsNepal, P.Al Bashit, A.Yang, L.Makowski, L.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-21research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767December 20226med@iucr.org1600-5767552022-11-21Preparation of pyrite concentrate powder from the Thackaringa mine for quantitative phase analysis using X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?vb5042
The quantitative phase analysis using X-ray diffraction of pyrite ore concentrate samples extracted from the Thackaringa mine is problematic due to poor particle statistics, microabsorption and preferred orientation. The influence of sample preparation on these issues has been evaluated, with ball milling of the powder found most suitable for accurate and precise quantitative phase analysis. The milling duration and other aspects of sample preparation have been explored, resulting in accurate phase reflection intensities when particle sizes are below 5 µm. Quantitative phase analysis on those samples yielded precise phase fractions with standard deviations below 0.3 wt%. Some discrepancy between the elemental composition obtained using X-ray powder diffraction data and that determined using wavelength-dispersive X-ray fluorescence was found, and is thought to arise from unaccounted for crystalline phase substitution and the possible presence of an amorphous phase. This study provides a methodology for the precise and accurate quantitative phase analysis of X-ray powder diffraction data of pyrite ore concentrate from the Thackaringa mine and a discussion of the limitations of the method. The optimization process reveals the importance of confirming reproducibility on new samples, with as much prior knowledge as possible.textThe quantitative phase analysis using X-ray diffraction of pyrite ore concentrate samples extracted from the Thackaringa mine is problematic due to poor particle statistics, microabsorption and preferred orientation. The influence of sample preparation on these issues has been evaluated, with ball milling of the powder found most suitable for accurate and precise quantitative phase analysis. The milling duration and other aspects of sample preparation have been explored, resulting in accurate phase reflection intensities when particle sizes are below 5 µm. Quantitative phase analysis on those samples yielded precise phase fractions with standard deviations below 0.3 wt%. Some discrepancy between the elemental composition obtained using X-ray powder diffraction data and that determined using wavelength-dispersive X-ray fluorescence was found, and is thought to arise from unaccounted for crystalline phase substitution and the possible presence of an amorphous phase. This study provides a methodology for the precise and accurate quantitative phase analysis of X-ray powder diffraction data of pyrite ore concentrate from the Thackaringa mine and a discussion of the limitations of the method. The optimization process reveals the importance of confirming reproducibility on new samples, with as much prior knowledge as possible.urn:issn:1600-5767X-RAY DIFFRACTION; QUANTITATIVE PHASE ANALYSIS; PYRITE MINERAL; SAMPLE PREPARATIONA method for performing accurate quantitative phase analysis using X-ray powder diffraction of pyrite concentrate mineral samples from the Thackaringa mine has been devised. The sample preparation optimization process is described. Grain size reduction suitable for analysis by the Rietveld method was achieved using ball milling.doi:10.1107/S1600576722009888enPreparation of pyrite concentrate powder from the Thackaringa mine for quantitative phase analysis using X-ray diffractionMcDougall, H.Hibberd, M.Tong, A.Neville, S.Peterson, V.Didier, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-282022-11-28551600-5767med@iucr.org6December 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersAutomatic bad-pixel mask maker for X-ray pixel detectors with application to serial crystallography
http://scripts.iucr.org/cgi-bin/paper?te5097
X-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.textX-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets.urn:issn:1600-5767BAD-PIXEL MASKS; ROBUST MASK MAKER; MACHINE LEARNING; ROBUST STATISTICS; SERIAL CRYSTALLOGRAPHYAttention is focused on perhaps the biggest bottleneck in data analysis for serial crystallography at X-ray free-electron lasers, which has not received serious enough examination to date. An effective and reliable way is presented to identify anomalies in detectors, using machine learning and recently developed mathematical methods in the field referred to as `robust statistics'.doi:10.1107/S1600576722009815enAutomatic bad-pixel mask maker for X-ray pixel detectors with application to serial crystallographySadri, A.Hadian-Jazi, M.Yefanov, O.Galchenkova, M.Kirkwood, H.Mills, G.Sikorski, M.Letrun, R.de Wijn, R.Vakili, M.Oberthuer, D.Komadina, D.Brehm, W.Mancuso, A.P.Carnis, J.Gelisio, L.Chapman, H.N.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-21552022-11-211600-5767med@iucr.org6December 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersProgressive alignment of crystals: reproducible and efficient assessment of crystal structure similarity
http://scripts.iucr.org/cgi-bin/paper?tu5028
During in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis (e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration (Rg) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters (i.e. to minimize Rg) or prioritized reduced RMSD (i.e. via possibly elongated clusters with relatively larger Rg). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK. However, the lower Rg values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.textDuring in silico crystal structure prediction of organic molecules, millions of candidate structures are often generated. These candidates must be compared to remove duplicates prior to further analysis (e.g. optimization with electronic structure methods) and ultimately compared with structures determined experimentally. The agreement of predicted and experimental structures forms the basis of evaluating the results from the Cambridge Crystallographic Data Centre (CCDC) blind assessment of crystal structure prediction, which further motivates the pursuit of rigorous alignments. Evaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a flexible algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration (Rg) as a metric to quantify the shape of the superimposed clusters. It is shown that the absence of metrics to describe cluster shape adds ambiguity to the results of the CCDC blind assessments because it is not possible to determine whether the superposition algorithm has prioritized tightly packed molecular clusters (i.e. to minimize Rg) or prioritized reduced RMSD (i.e. via possibly elongated clusters with relatively larger Rg). For example, it is shown that when the PAC algorithm described here uses single linkage to prioritize molecules for inclusion in the superimposed clusters, the results are nearly identical to those calculated by the widely used program COMPACK. However, the lower Rg values obtained by the use of average linkage are favored for molecule prioritization because the resulting RMSDs more equally reflect the importance of packing along each dimension. It is shown that the PAC algorithm is faster than COMPACK when using a single process and its utility for biomolecular crystals is demonstrated. Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.urn:issn:1600-5767STRUCTURE COMPARISON; CRYSTAL PACKING; CRYSTAL STRUCTURE PREDICTION; RADIUS OF GYRATION; MPI PARALLELIZATIONEvaluating crystal structure packings using coordinate root-mean-square deviation (RMSD) for N molecules (or N asymmetric units) in a reproducible manner requires metrics to describe the shape of the compared molecular clusters to account for alternative approaches used to prioritize selection of molecules. Described here is a fast algorithm called Progressive Alignment of Crystals (PAC) to evaluate crystal packing similarity using coordinate RMSD and introducing the radius of gyration as a metric to quantify the shape of the superimposed clusters.doi:10.1107/S1600576722009670enProgressive alignment of crystals: reproducible and efficient assessment of crystal structure similarityNessler, A.J.Okada, O.Hermon, M.J.Nagata, H.Schnieders, M.J.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-216med@iucr.org1600-5767552022-11-21research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767December 2022Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method
http://scripts.iucr.org/cgi-bin/paper?nb5321
Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R1 values improved by 10–30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.textThree-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R1 values improved by 10–30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.urn:issn:1600-5767POST-COLUMN ENERGY FILTERS; 3D ELECTRON DIFFRACTION; ENERGY-FILTERED 3D ED; MICROCRYSTAL ELECTRON DIFFRACTION; ENERGY-FILTERED MICROED; HAADF; CRYSTAL TRACKING; STRUCTURE DETERMINATIONZero-loss energy-filtered 3D electron diffraction experiments are performed using a post-column energy filter, and both data quality and structures are improved after energy filtration. A novel crystal tracking method is developed, based on a live high-angle annular dark-field image stream. This method can track crystals to achieve high-completeness data sets without adding any additional dose or removing any frames.doi:10.1107/S1600576722009633enImproving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking methodYang, T.Xu, H.Zou, X.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-281600-5767December 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-57672022-11-28556med@iucr.orgEfficient data reduction for time-of-flight neutron scattering experiments on single crystals
http://scripts.iucr.org/cgi-bin/paper?fs5205
Event-mode data collection presents remarkable new opportunities for time-of-flight neutron scattering studies of collective excitations, diffuse scattering from short-range atomic and magnetic structures, and neutron crystallography. In these experiments, large volumes of the reciprocal space are surveyed, often using different wavelengths and counting times. These data then have to be added together, with accurate propagation of the counting errors. This paper presents a statistically correct way of adding and histogramming the data for single-crystal time-of-flight neutron scattering measurements. In order to gain a broader community acceptance, particular attention is given to improving the efficiency of calculations.textEvent-mode data collection presents remarkable new opportunities for time-of-flight neutron scattering studies of collective excitations, diffuse scattering from short-range atomic and magnetic structures, and neutron crystallography. In these experiments, large volumes of the reciprocal space are surveyed, often using different wavelengths and counting times. These data then have to be added together, with accurate propagation of the counting errors. This paper presents a statistically correct way of adding and histogramming the data for single-crystal time-of-flight neutron scattering measurements. In order to gain a broader community acceptance, particular attention is given to improving the efficiency of calculations.urn:issn:1600-5767TIME-OF-FLIGHT NEUTRON SCATTERING; ALGORITHMS; SINGLE CRYSTALSIn neutron scattering experiments, data sets with different statistical significance are collected. A new method is presented to efficiently calculate the weights of single-crystal time-of-flight measurements, and to add together the various contributions.doi:10.1107/S1600576722009645enEfficient data reduction for time-of-flight neutron scattering experiments on single crystalsSavici, A.T.Gigg, M.A.Arnold, O.Tolchenov, R.Whitfield, R.E.Hahn, S.E.Zhou, W.Zaliznyak, I.A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-04December 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papers2022-11-04551600-5767med@iucr.org6Extending MIEZE spectroscopy towards thermal wavelengths
http://scripts.iucr.org/cgi-bin/paper?ei5087
A modulation of intensity with zero effort (MIEZE) setup is proposed for high-resolution neutron spectroscopy at momentum transfers up to 3 Å−1, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons. MIEZE has two prominent advantages compared with classical neutron spin echo. The first is the possibility to investigate spin-depolarizing samples or samples in strong magnetic fields without loss of signal amplitude and intensity. This allows for the study of spin fluctuations in ferromagnets, and facilitates the study of samples with strong spin-incoherent scattering. The second advantage is that multi-analyzer setups can be implemented with comparatively little effort. The use of thermal neutrons increases the range of validity of the spin-echo approximation towards shorter spin-echo times. In turn, the thermal MIEZE option for greater ranges (TIGER) closes the gap between classical neutron spin-echo spectroscopy and conventional high-resolution neutron spectroscopy techniques such as triple-axis, time-of-flight and back-scattering. To illustrate the feasibility of TIGER, this paper presents the details of its implementation at the RESEDA beamline at FRM II by means of an additional velocity selector, polarizer and analyzer.textA modulation of intensity with zero effort (MIEZE) setup is proposed for high-resolution neutron spectroscopy at momentum transfers up to 3 Å−1, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons. MIEZE has two prominent advantages compared with classical neutron spin echo. The first is the possibility to investigate spin-depolarizing samples or samples in strong magnetic fields without loss of signal amplitude and intensity. This allows for the study of spin fluctuations in ferromagnets, and facilitates the study of samples with strong spin-incoherent scattering. The second advantage is that multi-analyzer setups can be implemented with comparatively little effort. The use of thermal neutrons increases the range of validity of the spin-echo approximation towards shorter spin-echo times. In turn, the thermal MIEZE option for greater ranges (TIGER) closes the gap between classical neutron spin-echo spectroscopy and conventional high-resolution neutron spectroscopy techniques such as triple-axis, time-of-flight and back-scattering. To illustrate the feasibility of TIGER, this paper presents the details of its implementation at the RESEDA beamline at FRM II by means of an additional velocity selector, polarizer and analyzer.urn:issn:1600-5767NEUTRON RESONANT SPIN ECHO; MIEZE; QUASIELASTIC SCATTERING; THERMAL NEUTRONSA modulation of intensity with zero effort (MIEZE) setup is proposed for high-resolution neutron spectroscopy at momentum transfers up to 3 Å−1, energy transfers up to 20 meV and an energy resolution in the microelectronvolt range using both thermal and cold neutrons.doi:10.1107/S1600576722009505enExtending MIEZE spectroscopy towards thermal wavelengthsJochum, J.K.Franz, C.Keller, T.Pfleiderer, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-10-27research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767December 20226med@iucr.org1600-57672022-10-2755Euphonic: inelastic neutron scattering simulations from force constants and visualization tools for phonon properties
http://scripts.iucr.org/cgi-bin/paper?in5072
Interpretation of vibrational inelastic neutron scattering spectra of complex systems is frequently reliant on accompanying simulations from theoretical models. Ab initio codes can routinely generate force constants, but additional steps are required for direct comparison with experimental spectra. On modern spectrometers this is a computationally expensive task due to the large data volumes collected. In addition, workflows are frequently cumbersome as the simulation software and experimental data analysis software often do not easily interface to each other. Here a new package, Euphonic, is presented. Euphonic is a robust, easy to use and computationally efficient tool designed to be integrated into experimental software and able to interface directly with the force constant matrix output of ab initio codes.textInterpretation of vibrational inelastic neutron scattering spectra of complex systems is frequently reliant on accompanying simulations from theoretical models. Ab initio codes can routinely generate force constants, but additional steps are required for direct comparison with experimental spectra. On modern spectrometers this is a computationally expensive task due to the large data volumes collected. In addition, workflows are frequently cumbersome as the simulation software and experimental data analysis software often do not easily interface to each other. Here a new package, Euphonic, is presented. Euphonic is a robust, easy to use and computationally efficient tool designed to be integrated into experimental software and able to interface directly with the force constant matrix output of ab initio codes.urn:issn:1600-5767NEUTRON SCATTERING; PHONONS; FORCE CONSTANTS; EUPHONICAn overview of the Euphonic Python package for efficient simulation of inelastic neutron scattering by phonons from force constants is presented.doi:10.1107/S1600576722009256enEuphonic: inelastic neutron scattering simulations from force constants and visualization tools for phonon propertiesFair, R.Jackson, A.Voneshen, D.Jochym, D.Le, D.Refson, K.Perring, T.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-281600-5767December 2022computer programshttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767552022-11-286med@iucr.orgA reverse Monte Carlo algorithm to simulate two-dimensional small-angle scattering intensities
http://scripts.iucr.org/cgi-bin/paper?uz5004
Small-angle scattering (SAS) experiments are a powerful method for studying self-assembly phenomena in nanoscopic materials because of the sensitivity of the technique to structures formed by interactions on the nanoscale. Numerous out-of-the-box options exist for analysing structures measured by SAS but many of these are underpinned by assumptions about the underlying interactions that are not always relevant for a given system. Here, a numerical algorithm based on reverse Monte Carlo simulations is described to model the intensity observed on a SAS detector as a function of the scattering vector. The model simulates a two-dimensional detector image, accounting for magnetic scattering, instrument resolution, particle polydispersity and particle collisions, while making no further assumptions about the underlying particle interactions. By simulating a two-dimensional image that can be potentially anisotropic, the algorithm is particularly useful for studying systems driven by anisotropic interactions. The final output of the algorithm is a relative particle distribution, allowing visualization of particle structures that form over long-range length scales (i.e. several hundred nanometres), along with an orientational distribution of magnetic moments. The effectiveness of the algorithm is shown by modelling a SAS experimental data set studying finite-length chains consisting of magnetic nanoparticles, which assembled in the presence of a strong magnetic field due to dipole interactions.textSmall-angle scattering (SAS) experiments are a powerful method for studying self-assembly phenomena in nanoscopic materials because of the sensitivity of the technique to structures formed by interactions on the nanoscale. Numerous out-of-the-box options exist for analysing structures measured by SAS but many of these are underpinned by assumptions about the underlying interactions that are not always relevant for a given system. Here, a numerical algorithm based on reverse Monte Carlo simulations is described to model the intensity observed on a SAS detector as a function of the scattering vector. The model simulates a two-dimensional detector image, accounting for magnetic scattering, instrument resolution, particle polydispersity and particle collisions, while making no further assumptions about the underlying particle interactions. By simulating a two-dimensional image that can be potentially anisotropic, the algorithm is particularly useful for studying systems driven by anisotropic interactions. The final output of the algorithm is a relative particle distribution, allowing visualization of particle structures that form over long-range length scales (i.e. several hundred nanometres), along with an orientational distribution of magnetic moments. The effectiveness of the algorithm is shown by modelling a SAS experimental data set studying finite-length chains consisting of magnetic nanoparticles, which assembled in the presence of a strong magnetic field due to dipole interactions.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; SMALL-ANGLE X-RAY SCATTERING; MAGNETIC NANOPARTICLES; SUPERPARAMAGNETIC IRON OXIDE NANOPARTICLES; REVERSE MONTE CARLO SIMULATIONSSmall-angle neutron scattering and small-angle X-ray scattering are important experimental techniques for studying the behaviour and properties of materials on the nanoscale. This article describes a numerical algorithm that uses reverse Monte Carlo simulations to model scattering intensities observed on a two-dimensional small-angle scattering detector.doi:10.1107/S1600576722009219enA reverse Monte Carlo algorithm to simulate two-dimensional small-angle scattering intensitiesBarnsley, L.C.Nandakumaran, N.Feoktystov, A.Dulle, M.Fruhner, L.Feygenson, M.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-28552022-11-281600-5767med@iucr.org6December 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersUpdates in SASfit for fitting analytical expressions and numerical models to small-angle scattering patterns
http://scripts.iucr.org/cgi-bin/paper?yr5094
Small-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug-in system for easier adoption by third-party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal. 13, 243–277], and regularization techniques such as the expectation-maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1–22; Richardson (1972) J. Opt. Soc. Am. 62, 55; Lucy (1974). Astron. J. 79, 745; Lucy (1994). Astron. Astrophys. 289, 983–994], which is compared with fits of analytical size distributions via the non-linear least-squares method; and (d) new structure factors, especially for ordered nano- and meso-scaled material systems, as well as the Ornstein–Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small-angle scattering intensity model used for fitting with SASfit.textSmall-angle scattering is an increasingly common method for characterizing particle ensembles in a wide variety of sample types and for diverse areas of application. SASfit has been one of the most comprehensive and flexible curve-fitting programs for decades, with many specialized tools for various fields. Here, a selection of enhancements and additions to the SASfit program are presented that may be of great benefit to interested and advanced users alike: (a) further development of the technical basis of the program, such as new numerical algorithms currently in use, a continuous integration practice for automated building and packaging of the software, and upgrades on the plug-in system for easier adoption by third-party developers; (b) a selection of new form factors for anisotropic scattering patterns and updates to existing form factors to account for multiple scattering effects; (c) a new type of a very flexible distribution called metalog [Keelin (2016). Decis. Anal. 13, 243–277], and regularization techniques such as the expectation-maximization method [Dempster et al. (1977). J. R. Stat. Soc. Ser. B (Methodological), 39, 1–22; Richardson (1972) J. Opt. Soc. Am. 62, 55; Lucy (1974). Astron. J. 79, 745; Lucy (1994). Astron. Astrophys. 289, 983–994], which is compared with fits of analytical size distributions via the non-linear least-squares method; and (d) new structure factors, especially for ordered nano- and meso-scaled material systems, as well as the Ornstein–Zernike solver for numerical determination of particle interactions and the resulting structure factor when no analytical solution is available, with the aim of incorporating its effects into the small-angle scattering intensity model used for fitting with SASfit.urn:issn:1600-5767SMALL-ANGLE SCATTERING; SASFIT; NUMERICAL MODELS; STRUCTURE FACTORS; FORM FACTORS; REGULARIZATION TECHNIQUESRecent enhancements and additions to the SASfit program are discussed, including anisotropic scattering models, flexible distributions, regularization techniques such as the expectation-maximization method, and new structure factors, especially for ordered nano- and meso-scaled material. The Ornstein–Zernike solver for numerical structure factors is also introduced.doi:10.1107/S1600576722009037enUpdates in SASfit for fitting analytical expressions and numerical models to small-angle scattering patternsKohlbrecher, J.Breßler, I.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-216med@iucr.org1600-5767552022-11-21computer programshttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767December 2022Magnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: analytical treatment
http://scripts.iucr.org/cgi-bin/paper?in5070
The magnetization profile and the related magnetic small-angle neutron scattering cross section of a single spherical nanoparticle with Néel surface anisotropy are analytically investigated. A Hamiltonian is employed that comprises the isotropic exchange interaction, an external magnetic field, a uniaxial magnetocrystalline anisotropy in the core of the particle and the Néel anisotropy at the surface. Using a perturbation approach, the determination of the magnetization profile can be reduced to a Helmholtz equation with Neumann boundary condition, whose solution is represented by an infinite series in terms of spherical harmonics and spherical Bessel functions. From the resulting infinite series expansion, the Fourier transform, which is algebraically related to the magnetic small-angle neutron scattering cross section, is analytically calculated. The approximate analytical solution for the spin structure is compared with the numerical solution using the Landau–Lifshitz equation, which accounts for the full nonlinearity of the problem. The signature of the Néel surface anisotropy can be identified in the magnetic neutron scattering observables, but its effect is relatively small, even for large values of the surface anisotropy constant.textThe magnetization profile and the related magnetic small-angle neutron scattering cross section of a single spherical nanoparticle with Néel surface anisotropy are analytically investigated. A Hamiltonian is employed that comprises the isotropic exchange interaction, an external magnetic field, a uniaxial magnetocrystalline anisotropy in the core of the particle and the Néel anisotropy at the surface. Using a perturbation approach, the determination of the magnetization profile can be reduced to a Helmholtz equation with Neumann boundary condition, whose solution is represented by an infinite series in terms of spherical harmonics and spherical Bessel functions. From the resulting infinite series expansion, the Fourier transform, which is algebraically related to the magnetic small-angle neutron scattering cross section, is analytically calculated. The approximate analytical solution for the spin structure is compared with the numerical solution using the Landau–Lifshitz equation, which accounts for the full nonlinearity of the problem. The signature of the Néel surface anisotropy can be identified in the magnetic neutron scattering observables, but its effect is relatively small, even for large values of the surface anisotropy constant.urn:issn:1600-5767MAGNETIC NEUTRON SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MAGNETIC NANOPARTICLES; SURFACE ANISOTROPY; MICROMAGNETICSThe magnetization profile and the ensuing magnetic neutron scattering signal from an inhomogeneously magnetized spherical nanoparticle with Néel surface anisotropy are derived analytically.doi:10.1107/S1600576722008925enMagnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: analytical treatmentAdams, M.P.Michels, A.Kachkachi, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-046med@iucr.org1600-5767552022-11-04research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767December 2022Magnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: atomistic simulations
http://scripts.iucr.org/cgi-bin/paper?in5071
A dilute ensemble of randomly oriented non-interacting spherical nanomagnets is considered, and its magnetization structure and ensuing neutron scattering response are investigated by numerically solving the Landau–Lifshitz equation. Taking into account the isotropic exchange interaction, an external magnetic field, a uniaxial magnetic anisotropy for the particle core, and in particular the Néel surface anisotropy, the magnetic small-angle neutron scattering cross section and pair-distance distribution function are calculated from the obtained equilibrium spin structures. The numerical results are compared with the well known analytical expressions for uniformly magnetized particles and provide guidance to the experimentalist. In addition, the effect of a particle-size distribution function is modelled.textA dilute ensemble of randomly oriented non-interacting spherical nanomagnets is considered, and its magnetization structure and ensuing neutron scattering response are investigated by numerically solving the Landau–Lifshitz equation. Taking into account the isotropic exchange interaction, an external magnetic field, a uniaxial magnetic anisotropy for the particle core, and in particular the Néel surface anisotropy, the magnetic small-angle neutron scattering cross section and pair-distance distribution function are calculated from the obtained equilibrium spin structures. The numerical results are compared with the well known analytical expressions for uniformly magnetized particles and provide guidance to the experimentalist. In addition, the effect of a particle-size distribution function is modelled.urn:issn:1600-5767MAGNETIC NEUTRON SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MAGNETIC NANOPARTICLES; SURFACE ANISOTROPY; MICROMAGNETICSBased on the Landau–Lifshitz equation, atomistic simulations of the magnetic neutron scattering from inhomogeneously magnetized spherical nanoparticles with a strong surface anisotropy are carried out.doi:10.1107/S1600576722008949enMagnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: atomistic simulationsAdams, M.P.Michels, A.Kachkachi, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-11-046med@iucr.org1600-5767552022-11-04research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767December 2022Analysis of time-of-flight small-angle neutron scattering data on mesoscopic crystals such as magnetic vortex lattices
http://scripts.iucr.org/cgi-bin/paper?un5007
Bragg diffracted intensities and q values for crystalline structures with long repeat distances may be obtained by small-angle neutron scattering (SANS) investigations. An account is given of the methods, advantages and disadvantages of obtaining such data by the multichromatic time-of-flight method, compared with the more traditional quasi-monochromatic SANS method. This is illustrated with data obtained from high-magnetic-field measurements on magnetic vortex line lattices in superconductors on the former HFM/EXED instrument at Helmholtz-Zentrum Berlin. The methods have application to other mesoscopic crystalline structures investigated by SANS instruments at pulsed sources.textBragg diffracted intensities and q values for crystalline structures with long repeat distances may be obtained by small-angle neutron scattering (SANS) investigations. An account is given of the methods, advantages and disadvantages of obtaining such data by the multichromatic time-of-flight method, compared with the more traditional quasi-monochromatic SANS method. This is illustrated with data obtained from high-magnetic-field measurements on magnetic vortex line lattices in superconductors on the former HFM/EXED instrument at Helmholtz-Zentrum Berlin. The methods have application to other mesoscopic crystalline structures investigated by SANS instruments at pulsed sources.urn:issn:1600-5767VORTEX LATTICES; SUPERCONDUCTIVITY; TIME-OF-FLIGHT NEUTRON DIFFRACTION; SMALL-ANGLE NEUTRON SCATTERING; SANSA method is presented for extracting quantitative information on superconducting vortex lattices and other mesoscopic structures from time-of-flight small-angle neutron scattering.doi:10.1107/S1600576722008226enAnalysis of time-of-flight small-angle neutron scattering data on mesoscopic crystals such as magnetic vortex latticesCampillo, E.Bartkowiak, M.Prokhnenko, O.Smeibidl, P.Forgan, E.M.Blackburn, E.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-10-0113145med@iucr.org13231600-5767552022-10-01research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767October 2022Epitaxies of Ca sulfates on calcite. II. The main {010}, {001} and {100} forms of bassanite epi-deposited on the {10.4} substrate form of calcite
http://scripts.iucr.org/cgi-bin/paper?gj5284
2D and 3D epitaxies of the main {010}, {001} and {100} forms of deposited bassanite (CaSO4·0.5H2O) on {10.4} calcite (CaCO3) as a substrate are described to provide a theoretical crystallographic background for the replacement of calcite by bassanite both in nature and in the laboratory and by weathering linked to cultural heritage. First, epitaxy in the third dimension, perpendicular to the investigated interfaces, has been verified in order to establish whether adsorption/absorption can occur (as anomalous mixed crystals) at the bassanite/calcite epi-contacts. Secondly, and by applying the Hartman–Perdok method, 2D lattice coincidences have been obtained from the physical-geometric matches of bonds running in the common directions within the elementary slices facing the substrate/deposit interfaces. This research represents the second and more detailed part of a wider program extended to the epi-interactions between the following pairs: (i) {010}-gypsum/{10.4}-calcite (just published); (ii) bassanite/{10.4}-calcite (the present work); and (iii) anhydrite (CaSO4)/{10.4}-calcite (coming soon).text2D and 3D epitaxies of the main {010}, {001} and {100} forms of deposited bassanite (CaSO4·0.5H2O) on {10.4} calcite (CaCO3) as a substrate are described to provide a theoretical crystallographic background for the replacement of calcite by bassanite both in nature and in the laboratory and by weathering linked to cultural heritage. First, epitaxy in the third dimension, perpendicular to the investigated interfaces, has been verified in order to establish whether adsorption/absorption can occur (as anomalous mixed crystals) at the bassanite/calcite epi-contacts. Secondly, and by applying the Hartman–Perdok method, 2D lattice coincidences have been obtained from the physical-geometric matches of bonds running in the common directions within the elementary slices facing the substrate/deposit interfaces. This research represents the second and more detailed part of a wider program extended to the epi-interactions between the following pairs: (i) {010}-gypsum/{10.4}-calcite (just published); (ii) bassanite/{10.4}-calcite (the present work); and (iii) anhydrite (CaSO4)/{10.4}-calcite (coming soon).urn:issn:1600-5767BASSANITE; CALCITE; EPITAXY; TWINS; ANOMALOUS MIXED CRYSTALSA detailed description of 2D and 3D epitaxies of the main {010}, {001} and {100} forms of deposited bassanite (CaSO4·0.5H2O) on {10.4} calcite (CaCO3) is reported.doi:10.1107/S1600576722008196enEpitaxies of Ca sulfates on calcite. II. The main {010}, {001} and {100} forms of bassanite epi-deposited on the {10.4} substrate form of calciteAquilano, D.Bruno, M.Ghignone, S.Pastero, L.Cotellucci, A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-281600-576712962022-09-285551289med@iucr.org1600-5767October 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Using 2D integral breadth to study plastic relaxation in a quasi-lattice-matched HgCdTe/CdZnTe heterostructure
http://scripts.iucr.org/cgi-bin/paper?ei5083
Micro-Laue diffraction has been used to record cross-section profiles on a quasi-lattice-matched HgCdTe/CdZnTe heterostructure as a function of the stress induced by a flexion machine. The heterostructure may be decomposed into four different regions according to depth. Sufficiently far from the interface, the CdZnTe substrate is undisturbed by the HgCdTe layer, while the region situated 10 µm beneath the interface presents an in-plane lattice parameter adjustment to the +0.02% mismatched layer. The layer has a 2 µm critical thickness and, beyond, misfit dislocations induce a large peak broadening whose main direction changes with depth. The same occurs over the whole heterostructure once flexion-induced plastification has started. Consequently, the usual full width at half-maximum or integral breadth is no longer relevant, and only a newly defined and rotationally invariant 2D integral breadth correctly measures the plastification-induced peak broadening. Taking into account only the critical thickness region, a 15.1 ± 0.7 MPa tensile HgCdTe elastic limit was measured, slightly overestimated because of the initial compressive layer stress. It was observed that the plastic onset of the substrate perfectly matches the elastic limit of the layer, despite the fact that the substrate elastic limit is expected to be four times higher: a striking demonstration of the propagation of threading dislocations. The `plastification easiness' is found to be 2.4 times smaller deep inside the substrate than in the layer critical thickness region, while in the substrate lattice adjustment region, the plastification easiness goes from the substrate to the layer value with a 22–25 MPa transition interval. This novel method using the 2D integral breadth allows for easy critical thickness measurement as well as precise plastic onset determination and plastification easiness assessment. It is a quite general method, since it may be applied to the vast class of epitaxial layers for which the critical thickness is larger than the micro-Laue beam size (currently 250 nm).textMicro-Laue diffraction has been used to record cross-section profiles on a quasi-lattice-matched HgCdTe/CdZnTe heterostructure as a function of the stress induced by a flexion machine. The heterostructure may be decomposed into four different regions according to depth. Sufficiently far from the interface, the CdZnTe substrate is undisturbed by the HgCdTe layer, while the region situated 10 µm beneath the interface presents an in-plane lattice parameter adjustment to the +0.02% mismatched layer. The layer has a 2 µm critical thickness and, beyond, misfit dislocations induce a large peak broadening whose main direction changes with depth. The same occurs over the whole heterostructure once flexion-induced plastification has started. Consequently, the usual full width at half-maximum or integral breadth is no longer relevant, and only a newly defined and rotationally invariant 2D integral breadth correctly measures the plastification-induced peak broadening. Taking into account only the critical thickness region, a 15.1 ± 0.7 MPa tensile HgCdTe elastic limit was measured, slightly overestimated because of the initial compressive layer stress. It was observed that the plastic onset of the substrate perfectly matches the elastic limit of the layer, despite the fact that the substrate elastic limit is expected to be four times higher: a striking demonstration of the propagation of threading dislocations. The `plastification easiness' is found to be 2.4 times smaller deep inside the substrate than in the layer critical thickness region, while in the substrate lattice adjustment region, the plastification easiness goes from the substrate to the layer value with a 22–25 MPa transition interval. This novel method using the 2D integral breadth allows for easy critical thickness measurement as well as precise plastic onset determination and plastification easiness assessment. It is a quite general method, since it may be applied to the vast class of epitaxial layers for which the critical thickness is larger than the micro-Laue beam size (currently 250 nm).urn:issn:1600-5767HGCDTE; ELASTIC BEHAVIOUR; PLASTIC DEFORMATION; THIN FILMS; DISLOCATIONSThe newly defined and rotationally invariant 2D integral breadth correctly measures plastification-induced peak broadening during micro-Laue diffraction experiments, and allows for both critical thickness and plastic onset measurements. Applied to the quasi-lattice-matched HgCdTe/CdZnTe heterostructure and taking into account the critical thickness only, it showed that the plastic onset of the rigid substrate perfectly matches the elastic limit of the smooth layer: a striking demonstration of the propagation of threading dislocations.doi:10.1107/S1600576722008184enUsing 2D integral breadth to study plastic relaxation in a quasi-lattice-matched HgCdTe/CdZnTe heterostructureBiquard, X.Tuaz, A.Ballet, P.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-10-01October 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papers552022-10-0113041600-5767med@iucr.org51297In-depth investigations of size and occupancies in cobalt ferrite nanoparticles by joint Rietveld refinements of X-ray and neutron powder diffraction data
http://scripts.iucr.org/cgi-bin/paper?tu5021
Powder X-ray diffraction (PXRD) and neutron powder diffraction (NPD) have been used to investigate the crystal structure of CoFe2O4 nanoparticles prepared via different hydrothermal synthesis routes, with particular attention given to accurately determining the spinel inversion degrees. The study is divided into four parts. In the first part, the investigations focus on the influence of using different diffraction pattern combinations (NPD, Cu-source PXRD and Co-source PXRD) for the structural modelling. It is found that combining PXRD data from a Co source with NPD data offers a robust structural model. The second part of the study evaluates the reproducibility of the employed multipattern Rietveld refinement procedure using different data sets collected on the same sample, as well as on equivalently prepared samples. The refinement procedure gives reproducible results and reveals that the synthesis method is likewise reproducible since only minor differences are noted between the samples. The third part focuses on the structural consequences of (i) the employed heating rate (achieved using three different hydrothermal reactor types) and (ii) changing the cobalt salt in the precursors [aqueous salt solutions of Co(CH3COOH)2, Co(NO3)2 and CoCl2] in the synthesis. It is found that increasing the heating rate causes a change in the crystal structure (unit cell and crystallite sizes) while the Co/Fe occupancy and magnetic parameters remain similar in all cases. Also, changing the type of cobalt salt does not alter the final crystal/magnetic structure of the CoFe2O4 nanoparticles. The last part of this study is a consideration of the chemicals and parameters used in the synthesis of the different samples. All the presented samples exhibit a similar crystal and magnetic structure, with only minor deviations. It is also evident that the refinement method used played a key role in the description of the sample.textPowder X-ray diffraction (PXRD) and neutron powder diffraction (NPD) have been used to investigate the crystal structure of CoFe2O4 nanoparticles prepared via different hydrothermal synthesis routes, with particular attention given to accurately determining the spinel inversion degrees. The study is divided into four parts. In the first part, the investigations focus on the influence of using different diffraction pattern combinations (NPD, Cu-source PXRD and Co-source PXRD) for the structural modelling. It is found that combining PXRD data from a Co source with NPD data offers a robust structural model. The second part of the study evaluates the reproducibility of the employed multipattern Rietveld refinement procedure using different data sets collected on the same sample, as well as on equivalently prepared samples. The refinement procedure gives reproducible results and reveals that the synthesis method is likewise reproducible since only minor differences are noted between the samples. The third part focuses on the structural consequences of (i) the employed heating rate (achieved using three different hydrothermal reactor types) and (ii) changing the cobalt salt in the precursors [aqueous salt solutions of Co(CH3COOH)2, Co(NO3)2 and CoCl2] in the synthesis. It is found that increasing the heating rate causes a change in the crystal structure (unit cell and crystallite sizes) while the Co/Fe occupancy and magnetic parameters remain similar in all cases. Also, changing the type of cobalt salt does not alter the final crystal/magnetic structure of the CoFe2O4 nanoparticles. The last part of this study is a consideration of the chemicals and parameters used in the synthesis of the different samples. All the presented samples exhibit a similar crystal and magnetic structure, with only minor deviations. It is also evident that the refinement method used played a key role in the description of the sample.urn:issn:1600-5767NEUTRON POWDER DIFFRACTION; X-RAY POWDER DIFFRACTION; RESONANCE SCATTERING; SPINEL FERRITES; MAGNETISMCombined neutron and X-ray powder diffraction investigations of CoFe2O4 are reported, aimed at investigating the robustness, reproducibility and reliability of structural parameters from Rietveld refinement.doi:10.1107/S1600576722008123enIn-depth investigations of size and occupancies in cobalt ferrite nanoparticles by joint Rietveld refinements of X-ray and neutron powder diffraction dataHenry, K.Ahlburg, J.V.Andersen, H.L.Granados-Miralles, C.Stingaciu, M.Saura-Múzquiz, M.Christensen, M.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-10-01October 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papers2022-10-01551600-57671350med@iucr.org13365Domain Auto Finder (DAFi) program: the analysis of single-crystal X-ray diffraction data from polycrystalline samples
http://scripts.iucr.org/cgi-bin/paper?iu5028
This paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders. Superposition of numerous reflections originating from a large number of single-crystal domains of the same and/or different (especially unknown) phases usually precludes the sorting of reflections coming from individual domains, making their automatic indexing impossible. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC-XRD data. Further indexing of all found subsets can be easily performed using widely accessible crystallographic packages. As the algorithm neither requires a priori crystallographic information nor is limited by the number of phases or individual domains, DAFi is powerful software to be used for studies of multiphase polycrystalline and microcrystalline (powder) materials. The algorithm is validated by testing on X-ray diffraction data sets obtained from real samples: a multi-mineral basalt rock at ambient conditions and products of the chemical reaction of yttrium and nitrogen in a laser-heated diamond anvil cell at 50 GPa. The high performance of the DAFi algorithm means it can be used for processing SC-XRD data online during experiments at synchrotron facilities.textThis paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders. Superposition of numerous reflections originating from a large number of single-crystal domains of the same and/or different (especially unknown) phases usually precludes the sorting of reflections coming from individual domains, making their automatic indexing impossible. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC-XRD data. Further indexing of all found subsets can be easily performed using widely accessible crystallographic packages. As the algorithm neither requires a priori crystallographic information nor is limited by the number of phases or individual domains, DAFi is powerful software to be used for studies of multiphase polycrystalline and microcrystalline (powder) materials. The algorithm is validated by testing on X-ray diffraction data sets obtained from real samples: a multi-mineral basalt rock at ambient conditions and products of the chemical reaction of yttrium and nitrogen in a laser-heated diamond anvil cell at 50 GPa. The high performance of the DAFi algorithm means it can be used for processing SC-XRD data online during experiments at synchrotron facilities.urn:issn:1600-5767SINGLE-CRYSTAL DOMAIN AUTO FINDER; DAFI; SINGLE-CRYSTAL X-RAY DIFFRACTION; POLYCRYSTALLINE SAMPLES; MULTIPHASE MIXTURESThis paper presents the Domain Auto Finder (DAFi) program and its application to the analysis of single-crystal X-ray diffraction (SC-XRD) data from multiphase mixtures of microcrystalline solids and powders. The DAFi algorithm is designed to quickly find subsets of reflections from individual domains in a whole set of SC-XRD data and neither requires a priori crystallographic information nor is limited by the number of phases or individual domains.doi:10.1107/S1600576722008081enDomain Auto Finder (DAFi) program: the analysis of single-crystal X-ray diffraction data from polycrystalline samplesAslandukov, A.Aslandukov, M.Dubrovinskaia, N.Dubrovinsky, L.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-2813835med@iucr.org13911600-5767552022-09-28computer programshttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767October 2022The Scatman: an approximate method for fast wide-angle scattering simulations
http://scripts.iucr.org/cgi-bin/paper?yr5086
Single-shot coherent diffraction imaging (CDI) is a powerful approach to characterize the structure and dynamics of isolated nanoscale objects such as single viruses, aerosols, nanocrystals and droplets. Using X-ray wavelengths, the diffraction images in CDI experiments usually cover only small scattering angles of a few degrees. These small-angle patterns represent the magnitude of the Fourier transform of the 2D projection of the sample's electron density, which can be reconstructed efficiently but lacks any depth information. In cases where the diffracted signal can be measured up to scattering angles exceeding ∼10°, i.e. in the wide-angle regime, some 3D morphological information of the target is contained in a single-shot diffraction pattern. However, the extraction of the 3D structural information is no longer straightforward and defines the key challenge in wide-angle CDI. So far, the most convenient approach relies on iterative forward fitting of the scattering pattern using scattering simulations. Here the Scatman is presented, an approximate and fast numerical tool for the simulation and iterative fitting of wide-angle scattering images of isolated samples. Furthermore, the open-source software implementation of the Scatman algorithm, PyScatman, is published and described in detail. The Scatman approach, which has already been applied in previous work for forward-fitting-based shape retrieval, adopts the multi-slice Fourier transform method. The effects of optical properties are partially included, yielding quantitative results for small, isolated and weakly interacting samples. PyScatman is capable of computing wide-angle scattering patterns in a few milliseconds even on consumer-level computing hardware, potentially enabling new data analysis schemes for wide-angle coherent diffraction experiments.textSingle-shot coherent diffraction imaging (CDI) is a powerful approach to characterize the structure and dynamics of isolated nanoscale objects such as single viruses, aerosols, nanocrystals and droplets. Using X-ray wavelengths, the diffraction images in CDI experiments usually cover only small scattering angles of a few degrees. These small-angle patterns represent the magnitude of the Fourier transform of the 2D projection of the sample's electron density, which can be reconstructed efficiently but lacks any depth information. In cases where the diffracted signal can be measured up to scattering angles exceeding ∼10°, i.e. in the wide-angle regime, some 3D morphological information of the target is contained in a single-shot diffraction pattern. However, the extraction of the 3D structural information is no longer straightforward and defines the key challenge in wide-angle CDI. So far, the most convenient approach relies on iterative forward fitting of the scattering pattern using scattering simulations. Here the Scatman is presented, an approximate and fast numerical tool for the simulation and iterative fitting of wide-angle scattering images of isolated samples. Furthermore, the open-source software implementation of the Scatman algorithm, PyScatman, is published and described in detail. The Scatman approach, which has already been applied in previous work for forward-fitting-based shape retrieval, adopts the multi-slice Fourier transform method. The effects of optical properties are partially included, yielding quantitative results for small, isolated and weakly interacting samples. PyScatman is capable of computing wide-angle scattering patterns in a few milliseconds even on consumer-level computing hardware, potentially enabling new data analysis schemes for wide-angle coherent diffraction experiments.urn:issn:1600-5767COHERENT DIFFRACTION IMAGING; WIDE-ANGLE SCATTERING; MULTI-SLICE FOURIER TRANSFORM; APPROXIMATE METHODS; HIGH-PERFORMANCE COMPUTINGA fast method for wide-angle coherent scattering simulations of weakly absorbing isolated samples, called the Scatman, is presented. Its quantitative agreement with exact solutions and the low simulation time of its software implementation PyScatman open new perspectives for single-shot 3D coherent diffraction imaging.doi:10.1107/S1600576722008068enThe Scatman: an approximate method for fast wide-angle scattering simulationsColombo, A.Zimmermann, J.Langbehn, B.Möller, T.Peltz, C.Sander, K.Kruse, B.Tümmler, P.Barke, I.Rupp, D.Fennel, T.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-14552022-09-1412461600-5767med@iucr.org12325October 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersFaster and lower-dose X-ray reflectivity measurements enabled by physics-informed modeling and artificial intelligence co-refinement
http://scripts.iucr.org/cgi-bin/paper?yr5088
An approach is presented for analysis of real-time X-ray reflectivity (XRR) process data not just as a function of the magnitude of the reciprocal-space vector q, as is commonly done, but as a function of both q and time. The real-space structures extracted from the XRR curves are restricted to be solutions of a physics-informed growth model and use state-of-the-art convolutional neural networks (CNNs) and differential evolution fitting to co-refine multiple time-dependent XRR curves R(q, t) of a thin film growth experiment. Thereby it becomes possible to correctly analyze XRR data with a fidelity corresponding to standard fits of individual XRR curves, even if they are sparsely sampled, with a sevenfold reduction of XRR data points, or if the data are noisy due to a 200-fold reduction in counting times. The approach of using a CNN analysis and of including prior information through a kinetic model is not limited to growth studies but can be easily extended to other kinetic X-ray or neutron reflectivity data to enable faster measurements with less beam damage.textAn approach is presented for analysis of real-time X-ray reflectivity (XRR) process data not just as a function of the magnitude of the reciprocal-space vector q, as is commonly done, but as a function of both q and time. The real-space structures extracted from the XRR curves are restricted to be solutions of a physics-informed growth model and use state-of-the-art convolutional neural networks (CNNs) and differential evolution fitting to co-refine multiple time-dependent XRR curves R(q, t) of a thin film growth experiment. Thereby it becomes possible to correctly analyze XRR data with a fidelity corresponding to standard fits of individual XRR curves, even if they are sparsely sampled, with a sevenfold reduction of XRR data points, or if the data are noisy due to a 200-fold reduction in counting times. The approach of using a CNN analysis and of including prior information through a kinetic model is not limited to growth studies but can be easily extended to other kinetic X-ray or neutron reflectivity data to enable faster measurements with less beam damage.urn:issn:1600-5767NEUTRON REFLECTIVITY; X-RAY REFLECTIVITY; NEURAL NETWORKS; CO-REFINEMENT; IN SITU MEASUREMENTAn analysis approach for co-refinement of X-ray reflectivity -p0measurement is presented, which works with sparsely sampled or noisy data for seven- to 200-fold speed increases.doi:10.1107/S1600576722008056enFaster and lower-dose X-ray reflectivity measurements enabled by physics-informed modeling and artificial intelligence co-refinementMareček, D.Oberreiter, J.Nelson, A.Kowarik, S.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-10-01med@iucr.org13055552022-10-0113131600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersOctober 20221600-5767From geology to biology: an interdisciplinary course in crystal growth
http://scripts.iucr.org/cgi-bin/paper?dv5001
This contribution shares experience of teaching an interdisciplinary university course in crystal growth with examples ranging from geology to biology. This is an attempt to combine teaching the basics of the classical and non-classical theories of crystallization with impressive examples of crystals growing around us and in the human body, as well as demonstration of the common phenomena in the growth of minerals in nature, crystalline materials in industry and the laboratory, and biomimetic and stimulus-responsive crystals. Lectures are supported by laboratory exercises. Students can also perform an individual research project and present an oral contribution at a mini-conference. Examples of the topics considered in the course are given, and an extensive list of references to papers and web resources is provided, which may be useful to those who want to implement anything from the authors' experience.textThis contribution shares experience of teaching an interdisciplinary university course in crystal growth with examples ranging from geology to biology. This is an attempt to combine teaching the basics of the classical and non-classical theories of crystallization with impressive examples of crystals growing around us and in the human body, as well as demonstration of the common phenomena in the growth of minerals in nature, crystalline materials in industry and the laboratory, and biomimetic and stimulus-responsive crystals. Lectures are supported by laboratory exercises. Students can also perform an individual research project and present an oral contribution at a mini-conference. Examples of the topics considered in the course are given, and an extensive list of references to papers and web resources is provided, which may be useful to those who want to implement anything from the authors' experience.urn:issn:1600-5767CRYSTAL GROWTH; POLYMORPHISM; HIGH PRESSURE; MINERALS; MATERIALS; TEACHING; BIOPOLYMERS; PHARMACEUTICALSThe authors share experience of teaching an interdisciplinary university course in crystal growth with examples ranging from geology to biology.doi:10.1107/S1600576722008032enFrom geology to biology: an interdisciplinary course in crystal growthArkhipov, S.G.Bekker, T.B.Gaydamaka, A.A.Likhacheva, A.Y.Losev, E.A.Boldyreva, E.V.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-10-01med@iucr.org13685552022-10-0113761600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyteaching and educationOctober 20221600-5767Refinements for Bragg coherent X-ray diffraction imaging: electron backscatter diffraction alignment and strain field computation
http://scripts.iucr.org/cgi-bin/paper?te5099
Bragg coherent X-ray diffraction imaging (BCDI) allows the 3D measurement of lattice strain along the scattering vector for specific microcrystals. If at least three linearly independent reflections are measured, the 3D variation of the full lattice strain tensor within the microcrystal can be recovered. However, this requires knowledge of the crystal orientation, which is typically attained via estimates based on crystal geometry or synchrotron microbeam Laue diffraction measurements. Presented here is an alternative method to determine the crystal orientation for BCDI measurements using electron backscatter diffraction (EBSD) to align Fe–Ni and Co–Fe alloy microcrystals on three different substrates. The orientation matrix is calculated from EBSD Euler angles and compared with the orientation determined using microbeam Laue diffraction. The average angular mismatch between the orientation matrices is less than ∼6°, which is reasonable for the search for Bragg reflections. The use of an orientation matrix derived from EBSD is demonstrated to align and measure five reflections for a single Fe–Ni microcrystal via multi-reflection BCDI. Using this data set, a refined strain field computation based on the gradient of the complex exponential of the phase is developed. This approach is shown to increase accuracy, especially in the presence of dislocations. The results demonstrate the feasibility of using EBSD to pre-align BCDI samples and the application of more efficient approaches to determine the full lattice strain tensor with greater accuracy.textBragg coherent X-ray diffraction imaging (BCDI) allows the 3D measurement of lattice strain along the scattering vector for specific microcrystals. If at least three linearly independent reflections are measured, the 3D variation of the full lattice strain tensor within the microcrystal can be recovered. However, this requires knowledge of the crystal orientation, which is typically attained via estimates based on crystal geometry or synchrotron microbeam Laue diffraction measurements. Presented here is an alternative method to determine the crystal orientation for BCDI measurements using electron backscatter diffraction (EBSD) to align Fe–Ni and Co–Fe alloy microcrystals on three different substrates. The orientation matrix is calculated from EBSD Euler angles and compared with the orientation determined using microbeam Laue diffraction. The average angular mismatch between the orientation matrices is less than ∼6°, which is reasonable for the search for Bragg reflections. The use of an orientation matrix derived from EBSD is demonstrated to align and measure five reflections for a single Fe–Ni microcrystal via multi-reflection BCDI. Using this data set, a refined strain field computation based on the gradient of the complex exponential of the phase is developed. This approach is shown to increase accuracy, especially in the presence of dislocations. The results demonstrate the feasibility of using EBSD to pre-align BCDI samples and the application of more efficient approaches to determine the full lattice strain tensor with greater accuracy.urn:issn:1600-5767BRAGG COHERENT X-RAY DIFFRACTION IMAGING; ELECTRON BACKSCATTER DIFFRACTION; STRAIN CALCULATION; PHASE INTERPOLATION; CRYSTAL ORIENTATIONA novel and accurate method to align crystalline samples for Bragg coherent X-ray diffraction imaging using electron backscatter diffraction is presented. An efficient approach using the complex exponential of the phase to calculate the strain is also implemented, for greater accuracy in resolving crystal defects.doi:10.1107/S1600576722007646enRefinements for Bragg coherent X-ray diffraction imaging: electron backscatter diffraction alignment and strain field computationYang, D.Lapington, M.T.He, G.Song, K.Zhang, M.Barker, C.Harder, R.J.Cha, W.Liu, W.Phillips, N.W.Hofmann, F.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-062022-09-06551600-57671195med@iucr.org51184October 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersHTD2: a single-crystal X-ray diffractometer for combined high-pressure/low-temperature experiments at laboratory scale
http://scripts.iucr.org/cgi-bin/paper?iu5026
High-pressure (HP) X-ray diffraction experiments at low temperature (LT) require dedicated instruments as well as non-standard sample environments and measuring strategies. This is especially true when helium cryogenic temperatures below 80 K are targeted. Furthermore, only experiments on single-crystalline samples provide the prerequisites to study subtle structural changes in the p–T phase diagram under extreme LT and HP conditions in greater detail. Due to special hardware requirements, such measurements are usually in the realm of synchrotron beamlines. This contribution describes the design of an LT/HP diffractometer (HTD2) to perform single-crystal X-ray diffraction experiments using a laboratory source in the temperature range 400 > T > 2 K while applying pressures of up to 20 GPa.textHigh-pressure (HP) X-ray diffraction experiments at low temperature (LT) require dedicated instruments as well as non-standard sample environments and measuring strategies. This is especially true when helium cryogenic temperatures below 80 K are targeted. Furthermore, only experiments on single-crystalline samples provide the prerequisites to study subtle structural changes in the p–T phase diagram under extreme LT and HP conditions in greater detail. Due to special hardware requirements, such measurements are usually in the realm of synchrotron beamlines. This contribution describes the design of an LT/HP diffractometer (HTD2) to perform single-crystal X-ray diffraction experiments using a laboratory source in the temperature range 400 > T > 2 K while applying pressures of up to 20 GPa.urn:issn:1600-5767HTD2; LOW TEMPERATURE; HIGH PRESSURE; SINGLE CRYSTALS; INSTRUMENTATIONThe design and operation of a newly commissioned single-crystal X-ray diffractometer (HTD2) are presented. The device enables experiments under simultaneous low-temperature and high-pressure conditions using a laboratory X-ray source.doi:10.1107/S160057672200766XenHTD2: a single-crystal X-ray diffractometer for combined high-pressure/low-temperature experiments at laboratory scaleFischer, A.Langmann, J.Vöst, M.Eickerling, G.Scherer, W.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-281600-576712662022-09-285551255med@iucr.org1600-5767October 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Site dependence of the magnetocaloric effect in Mn5−xFexSi3
http://scripts.iucr.org/cgi-bin/paper?iu5027
The nuclear and magnetic structures of Mn3Fe2Si3 are investigated in the temperature range from 20 to 300 K. The magnetic properties of Mn3Fe2Si3 were measured on a single crystal. The compound undergoes a paramagnetic to antiferromagnetic transition at TN2 ≃ 120 K and an antiferromagnetic to antiferromagnetic transition at TN1 ≃ 69 K. A similar sequence of magnetic phase transitions is found for the parent compound Mn5Si3 upon temperature variation, but the field-driven transition observed in Mn5Si3 is not found in Mn3Fe2Si3, resulting in a strongly reduced magnetocaloric effect. Structurally, the hexagonal symmetry found for both compounds under ambient conditions is preserved in Mn3Fe2Si3 through both magnetic transitions, indicating that the crystal structure is only weakly affected by the magnetic phase transition, in contrast to Mn5Si3 where both transitions distort the nuclear structure. Both compounds feature a collinear high-temperature magnetic phase AF2 and transfer into a non-collinear phase AF1 at low temperature. While one of the distinct crystallographic sites remains disordered in the AF2 phase in the parent compound, the magnetic structure in the AF2 phase involves all magnetic atoms in Mn3Fe2Si3. These observations imply that the distinct sites occupied by the magnetic atoms play an important role in the magnetocaloric behaviour of the family.textThe nuclear and magnetic structures of Mn3Fe2Si3 are investigated in the temperature range from 20 to 300 K. The magnetic properties of Mn3Fe2Si3 were measured on a single crystal. The compound undergoes a paramagnetic to antiferromagnetic transition at TN2 ≃ 120 K and an antiferromagnetic to antiferromagnetic transition at TN1 ≃ 69 K. A similar sequence of magnetic phase transitions is found for the parent compound Mn5Si3 upon temperature variation, but the field-driven transition observed in Mn5Si3 is not found in Mn3Fe2Si3, resulting in a strongly reduced magnetocaloric effect. Structurally, the hexagonal symmetry found for both compounds under ambient conditions is preserved in Mn3Fe2Si3 through both magnetic transitions, indicating that the crystal structure is only weakly affected by the magnetic phase transition, in contrast to Mn5Si3 where both transitions distort the nuclear structure. Both compounds feature a collinear high-temperature magnetic phase AF2 and transfer into a non-collinear phase AF1 at low temperature. While one of the distinct crystallographic sites remains disordered in the AF2 phase in the parent compound, the magnetic structure in the AF2 phase involves all magnetic atoms in Mn3Fe2Si3. These observations imply that the distinct sites occupied by the magnetic atoms play an important role in the magnetocaloric behaviour of the family.urn:issn:1600-5767MAGNETOCALORIC EFFECT; MAGNETIC STRUCTURE; NEUTRON DIFFRACTION; SYNCHROTRON DIFFRACTION; SITE DEPENDENCEThe nuclear and magnetic structures of Mn3Fe2Si3 are determined and the magnetic properties are compared with those of the parent compound Mn5Si3. The results imply that the distinct magnetic sites play an important role in the magnetocaloric behaviour of the family.doi:10.1107/S1600576722007440enSite dependence of the magnetocaloric effect in Mn5−xFexSi3Ait Haddouch, M.Abboushi, N.Sharma, N.Eich, A.Grzechnik, A.Li, C.Tolkiehn, M.Alsamamra, H.Voigt, J.Friese, K.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-062022-09-06551600-57671172med@iucr.org11645October 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersSmall-angle neutron scattering study of mesoscale magnetic disordering and skyrmion phase suppression in the frustrated chiral magnet Co6.75Zn6.75Mn6.5
http://scripts.iucr.org/cgi-bin/paper?uq5003
Co–Zn–Mn chiral cubic magnets display versatile magnetic skyrmion phases, including equilibrium phases stable far above and far below room temperature, and the facile creation of robust far-from-equilibrium skyrmion states. In this system, compositional disorder and magnetic frustration are key ingredients that have profound effects on the chiral magnetism. Reported here are studies of the magnetism in Co6.75Zn6.75Mn6.5 by magnetometry, small-angle neutron scattering (SANS), magnetic diffuse neutron scattering and Lorentz transmission electron microscopy (LTEM). While features in magnetometry and LTEM often give standard indications for skyrmion formation, they are not readily observed from the measurements on this system. Instead, skyrmion lattice correlations are only revealed by SANS, and they are found to form an orientationally disordered structure in a minority fraction of the sample. The majority fraction of the sample always displays orientationally disordered helical spin correlations, which undergo further disordering along the radial direction on cooling below the critical temperature (Tc ≃ 102 K). The near-complete suppression of the skyrmion phase, and the process of disordering on cooling, are attributed to competing magnetic interactions that dominate over the ferromagnetic interaction expected to favour chiral magnetism in this system. These competing interactions start to develop above Tc and become further enhanced towards low temperatures. The present observations of co-existing and disordered magnetic correlations over multiple length scales are not unique to Co6.75Zn6.75Mn6.5 but are seemingly common to the family of Co–Zn–Mn compounds with finite Mn, and their accurate description presents a challenge for theoretical modelling. In addition, this study highlights a need for neutron instrumentation capable of the comprehensive measurement of magnetic correlations over expanded ranges of momentum transfer in such multiple-length-scale magnets.textCo–Zn–Mn chiral cubic magnets display versatile magnetic skyrmion phases, including equilibrium phases stable far above and far below room temperature, and the facile creation of robust far-from-equilibrium skyrmion states. In this system, compositional disorder and magnetic frustration are key ingredients that have profound effects on the chiral magnetism. Reported here are studies of the magnetism in Co6.75Zn6.75Mn6.5 by magnetometry, small-angle neutron scattering (SANS), magnetic diffuse neutron scattering and Lorentz transmission electron microscopy (LTEM). While features in magnetometry and LTEM often give standard indications for skyrmion formation, they are not readily observed from the measurements on this system. Instead, skyrmion lattice correlations are only revealed by SANS, and they are found to form an orientationally disordered structure in a minority fraction of the sample. The majority fraction of the sample always displays orientationally disordered helical spin correlations, which undergo further disordering along the radial direction on cooling below the critical temperature (Tc ≃ 102 K). The near-complete suppression of the skyrmion phase, and the process of disordering on cooling, are attributed to competing magnetic interactions that dominate over the ferromagnetic interaction expected to favour chiral magnetism in this system. These competing interactions start to develop above Tc and become further enhanced towards low temperatures. The present observations of co-existing and disordered magnetic correlations over multiple length scales are not unique to Co6.75Zn6.75Mn6.5 but are seemingly common to the family of Co–Zn–Mn compounds with finite Mn, and their accurate description presents a challenge for theoretical modelling. In addition, this study highlights a need for neutron instrumentation capable of the comprehensive measurement of magnetic correlations over expanded ranges of momentum transfer in such multiple-length-scale magnets.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; SKYRMIONS; CHIRAL MAGNETS; FRUSTRATION; MAGNETIC DISORDER; DIFFUSE SCATTERINGIn the frustrated chiral magnet Co6.75Zn6.75Mn6.5, small-angle neutron scattering reveals that the mesoscale chiral magnetism displays strong disorder and the skyrmion phase is nearly entirely suppressed.doi:10.1107/S1600576722007403enSmall-angle neutron scattering study of mesoscale magnetic disordering and skyrmion phase suppression in the frustrated chiral magnet Co6.75Zn6.75Mn6.5White, J.S.Karube, K.Ukleev, V.Derlet, P.M.Cubitt, R.Dewhurst, C.D.Wildes, A.R.Yu, X.Z.Rønnow, H.M.Tokura, Y.Taguchi, Y.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-14Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersOctober 20221600-5767med@iucr.org121952022-09-14551600-57671231High-resolution 3D X-ray diffraction microscopy: 3D mapping of deformed metal microstructures
http://scripts.iucr.org/cgi-bin/paper?nb5331
Three-dimensional X-ray diffraction microscopy, 3DXRD, has become an established tool for orientation and strain mapping of bulk polycrystals. However, it is limited to a finite spatial resolution of ∼1.5–3 µm. Presented here is a high-resolution modality of the technique, HR-3DXRD, for 3D mapping of submicrometre-sized crystallites or subgrains with high spatial and angular resolution. Specifically, the method is targeted to visualization of metal microstructures at industrially relevant degrees of plastic deformation. Exploiting intrinsic crystallographic properties of such microstructures, the high resolution is obtained by placing a high-resolution imaging detector in between the near-field and far-field regimes. This configuration enables 3D mapping of deformation microstructure by determining the centre of mass and volume of the subgrains and generating maps by tessellation. The setup is presented, together with a data analysis approach. Full-scale simulations are used to determine limitations and to demonstrate HR-3DXRD on realistic phantoms. Misalignments in the setup are shown to cause negligible shifts in the position and orientation of the subgrains. Decreasing the signal-to-noise ratio is observed to lead primarily to a loss in the number of determined diffraction spots. Simulations of an α-Fe sample deformed to a strain of εvM = 0.3 and comprising 828 subgrains show that, despite the high degree of local texture, 772 of the subgrains are retrieved with a spatial accuracy of 0.1 µm and an orientation accuracy of 0.0005°.textThree-dimensional X-ray diffraction microscopy, 3DXRD, has become an established tool for orientation and strain mapping of bulk polycrystals. However, it is limited to a finite spatial resolution of ∼1.5–3 µm. Presented here is a high-resolution modality of the technique, HR-3DXRD, for 3D mapping of submicrometre-sized crystallites or subgrains with high spatial and angular resolution. Specifically, the method is targeted to visualization of metal microstructures at industrially relevant degrees of plastic deformation. Exploiting intrinsic crystallographic properties of such microstructures, the high resolution is obtained by placing a high-resolution imaging detector in between the near-field and far-field regimes. This configuration enables 3D mapping of deformation microstructure by determining the centre of mass and volume of the subgrains and generating maps by tessellation. The setup is presented, together with a data analysis approach. Full-scale simulations are used to determine limitations and to demonstrate HR-3DXRD on realistic phantoms. Misalignments in the setup are shown to cause negligible shifts in the position and orientation of the subgrains. Decreasing the signal-to-noise ratio is observed to lead primarily to a loss in the number of determined diffraction spots. Simulations of an α-Fe sample deformed to a strain of εvM = 0.3 and comprising 828 subgrains show that, despite the high degree of local texture, 772 of the subgrains are retrieved with a spatial accuracy of 0.1 µm and an orientation accuracy of 0.0005°.urn:issn:1600-5767X-RAY IMAGING; X-RAY DIFFRACTION; 3DXRD; STRUCTURAL MATERIALSA full-field X-ray diffraction contrast method is presented (high-resolution 3D X-ray diffraction), for 3D mapping of plastically deformed microstructures. The essence of the method is the introduction of a 2D detector in the optical mid-field regime. The properties and limitations of the method are estimated by numerical simulations.doi:10.1107/S1600576722007361enHigh-resolution 3D X-ray diffraction microscopy: 3D mapping of deformed metal microstructuresKutsal, M.Poulsen, H.F.Winther, G.Sørensen, H.O.Detlefs, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-3051125med@iucr.org11381600-5767552022-08-30research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767October 2022Radial spin echo small-angle neutron scattering method: concept and performance
http://scripts.iucr.org/cgi-bin/paper?tu5024
A novel spin echo small-angle neutron scattering (SESANS) concept based on a rotationally symmetric magnetic field geometry is introduced. The proposed method is similar to the conventional linear SESANS technique but uses longitudinal precession fields and field gradients in a radial direction, as typically found in neutron spin echo (NSE) spectrometers. Radial SESANS could thus be implemented as an add-on to NSE setups. The neutron trajectory through the instrument is encoded with the help of radial gradients generated by radial shifters, which are coils placed in the beam area similar to Fresnel coils. The present work introduces the setup of the instrument and explores its performance and the relationship between the encoded momentum transfer and the precession angle. The results indicate that radial SESANS is only sensitive to scattering along the radial direction and thus measures the projected correlation function along this direction as a function of the spin echo length, defined similarly to linear SESANS. For an evaluation of the performance of the setup, the case of scattering from solid spheres is considered and the results calculated for the radial and linear SESANS cases are compared. Also discussed is the implementation of the radial magnetic field geometry in spin echo modulated small-angle neutron scattering.textA novel spin echo small-angle neutron scattering (SESANS) concept based on a rotationally symmetric magnetic field geometry is introduced. The proposed method is similar to the conventional linear SESANS technique but uses longitudinal precession fields and field gradients in a radial direction, as typically found in neutron spin echo (NSE) spectrometers. Radial SESANS could thus be implemented as an add-on to NSE setups. The neutron trajectory through the instrument is encoded with the help of radial gradients generated by radial shifters, which are coils placed in the beam area similar to Fresnel coils. The present work introduces the setup of the instrument and explores its performance and the relationship between the encoded momentum transfer and the precession angle. The results indicate that radial SESANS is only sensitive to scattering along the radial direction and thus measures the projected correlation function along this direction as a function of the spin echo length, defined similarly to linear SESANS. For an evaluation of the performance of the setup, the case of scattering from solid spheres is considered and the results calculated for the radial and linear SESANS cases are compared. Also discussed is the implementation of the radial magnetic field geometry in spin echo modulated small-angle neutron scattering.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; POLARIZED NEUTRONS; SPIN ECHO SMALL-ANGLE NEUTRON SCATTERING; LARMOR LABELLINGThe concept of a radially symmetric spin echo small-angle neutron scattering (SESANS) setup is introduced and analyzed.doi:10.1107/S1600576722007245enRadial spin echo small-angle neutron scattering method: concept and performanceKadletz, E.Bouwman, W.G.Pappas, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-24research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767October 202210725med@iucr.org1600-576710842022-08-2455The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability
http://scripts.iucr.org/cgi-bin/paper?dv5002
Within science, of which crystallography is a key part, there are questions posed to all fields that challenge the trust in results. The US National Academies of Sciences, Engineering and Medicine published a thorough report in 2019 on the Reproducibility and Replicability of Science: replicability being where a totally new study attempts to confirm if a phenomenon can be seen independently of another study. Data reuse is a key term in the FAIR data accord [Wilkinson et al. (2016). Sci. Data, 3, 160018], where the acronym FAIR means findable, accessible, interoperable and reusable. In the social sciences, the acronym FACT (namely fairness, accuracy, confidentiality and transparency) has emerged, the idea being that data should be FACTual to ensure trust [van der Aalst et al. (2017). Bus. Inf. Syst. Eng. 59, 311–313]. A distinction also must be made between accuracy and precision; indeed, the authors' lectures at the European Crystallography School ECS6 independently emphasized the need for use of other methods as well as crystal structure analysis to establish accuracy in biological and chemical/material functional contexts. The efforts by disparate science communities to introduce new terms to ensure trust have merit for discussion in crystallographic teaching commissions and possible adoption by crystallographers too.textWithin science, of which crystallography is a key part, there are questions posed to all fields that challenge the trust in results. The US National Academies of Sciences, Engineering and Medicine published a thorough report in 2019 on the Reproducibility and Replicability of Science: replicability being where a totally new study attempts to confirm if a phenomenon can be seen independently of another study. Data reuse is a key term in the FAIR data accord [Wilkinson et al. (2016). Sci. Data, 3, 160018], where the acronym FAIR means findable, accessible, interoperable and reusable. In the social sciences, the acronym FACT (namely fairness, accuracy, confidentiality and transparency) has emerged, the idea being that data should be FACTual to ensure trust [van der Aalst et al. (2017). Bus. Inf. Syst. Eng. 59, 311–313]. A distinction also must be made between accuracy and precision; indeed, the authors' lectures at the European Crystallography School ECS6 independently emphasized the need for use of other methods as well as crystal structure analysis to establish accuracy in biological and chemical/material functional contexts. The efforts by disparate science communities to introduce new terms to ensure trust have merit for discussion in crystallographic teaching commissions and possible adoption by crystallographers too.urn:issn:1600-5767TRUST; RELIABILITY; REPRODUCIBILITY; REPLICABILITY; REUSEAcross the sciences, generic monitors of trust in results from science are being introduced. As educators and researchers, the authors consider these terms within the context of biological and chemical crystal structure analyses.doi:10.1107/S1600576722007208enThe four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusabilityHelliwell, J.R.Massera, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-24Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/teaching and educationOctober 20221600-5767med@iucr.org135152022-08-24551600-57671358X-ray diffraction imaging of fully packaged n–p–n transistors under accelerated ageing conditions
http://scripts.iucr.org/cgi-bin/paper?te5102
X-ray diffraction imaging was used to monitor the local strains that developed around individual n–p–n bipolar transistors within fully encapsulated packages under conditions of extremely high forward bias to simulate accelerated ageing. Die warpage associated with the packaging was observed to relax systematically as the polymer became viscous due to the temperature rise associated with the dissipation of heat in the transistor. The direct image size and intensity from the individual transistors were interpreted in terms of a model in which local thermal expansion is treated as a cylindrical inclusion of distorted material, contrast arising principally from lattice tilt. The extension of the thermal strain image along the emitter with increasing power dissipation was ascribed to the effect of current crowding in the emitter region. Weaker large-area contrast associated with the base–collector region was interpreted as arising from the smaller change in effective misorientation at the high X-ray energy of thermal lattice dilation in the base region.textX-ray diffraction imaging was used to monitor the local strains that developed around individual n–p–n bipolar transistors within fully encapsulated packages under conditions of extremely high forward bias to simulate accelerated ageing. Die warpage associated with the packaging was observed to relax systematically as the polymer became viscous due to the temperature rise associated with the dissipation of heat in the transistor. The direct image size and intensity from the individual transistors were interpreted in terms of a model in which local thermal expansion is treated as a cylindrical inclusion of distorted material, contrast arising principally from lattice tilt. The extension of the thermal strain image along the emitter with increasing power dissipation was ascribed to the effect of current crowding in the emitter region. Weaker large-area contrast associated with the base–collector region was interpreted as arising from the smaller change in effective misorientation at the high X-ray energy of thermal lattice dilation in the base region.urn:issn:1600-5767X-RAY DIFFRACTION IMAGING; CURRENT CROWDING; THERMAL DILATION; SILICON DEVICESX-ray diffraction imaging contrast from individual silicon n–p–n bipolar transistors within fully encapsulated packages under conditions of extremely high forward bias is interpreted as arising from the effects of current crowding in the emitter region.doi:10.1107/S1600576722007142enX-ray diffraction imaging of fully packaged n–p–n transistors under accelerated ageing conditionsTanner, B.K.Danilewsky, A.McNally, P.J.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-30med@iucr.org11395552022-08-3011461600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersOctober 20221600-5767A comparison of deep-learning-based inpainting techniques for experimental X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?jl5040
The implementation is proposed of image inpainting techniques for the reconstruction of gaps in experimental X-ray scattering data. The proposed methods use deep learning neural network architectures, such as convolutional autoencoders, tunable U-Nets, partial convolution neural networks and mixed-scale dense networks, to reconstruct the missing information in experimental scattering images. In particular, the recovered pixel intensities are evaluated against their corresponding ground-truth values using the mean absolute error and the correlation coefficient metrics. The results demonstrate that the proposed methods achieve better performance than traditional inpainting algorithms such as biharmonic functions. Overall, tunable U-Net and mixed-scale dense network architectures achieved the best reconstruction performance among all the tested algorithms, with correlation coefficient scores greater than 0.9980.textThe implementation is proposed of image inpainting techniques for the reconstruction of gaps in experimental X-ray scattering data. The proposed methods use deep learning neural network architectures, such as convolutional autoencoders, tunable U-Nets, partial convolution neural networks and mixed-scale dense networks, to reconstruct the missing information in experimental scattering images. In particular, the recovered pixel intensities are evaluated against their corresponding ground-truth values using the mean absolute error and the correlation coefficient metrics. The results demonstrate that the proposed methods achieve better performance than traditional inpainting algorithms such as biharmonic functions. Overall, tunable U-Net and mixed-scale dense network architectures achieved the best reconstruction performance among all the tested algorithms, with correlation coefficient scores greater than 0.9980.urn:issn:1600-5767X-RAY SCATTERING; IMAGE INPAINTING; DEEP LEARNING; MIXED-SCALE DENSE NETWORKS; TUNABLE U-NETSA number of machine-learning-based algorithms are presented for the reconstruction of gaps in experimental X-ray scattering images through inpainting approaches.doi:10.1107/S1600576722007105enA comparison of deep-learning-based inpainting techniques for experimental X-ray scatteringChavez, T.Roberts, E.J.Zwart, P.H.Hexemer, A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-28med@iucr.org127752022-09-28551600-57671288Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersOctober 20221600-5767Specific analysis of highly absorbing nanoporous powder by small-angle X-ray scattering
http://scripts.iucr.org/cgi-bin/paper?ge5112
The characterization of nanoporous powders of highly absorbing compounds by small-angle X-ray scattering (SAXS) involves overcoming several difficulties before quantitative information related to the porous texture, such as the specific surface and the porous volume, can be derived. In this article, first, the contribution of the grain facet reflectivity and scattering from the bulk of a grain with the density of ThO2, a highly absorbing material, were calculated. Microporous ThO2 powder having micrometric grain size was characterized, in which the scattering signal is predominant. A high-resolution synchrotron instrument was used in order to cover a wider q range and minimize the absorption effect, and the results were compared with those obtained using a laboratory X-ray source. Concerning the absorption problem existing with a laboratory X-ray source, a new and robust experimental method was proposed to correctly determine the scattering intensity of the highly absorbing granular samples on an absolute scale. This method allows one to calculate accurately the porous volume and the specific surface via Porod's law and the invariant using a laboratory SAXS instrument. This last result opens new perspectives for the characterization of the volume and the specific surface of highly absorbing actinide oxide powders.textThe characterization of nanoporous powders of highly absorbing compounds by small-angle X-ray scattering (SAXS) involves overcoming several difficulties before quantitative information related to the porous texture, such as the specific surface and the porous volume, can be derived. In this article, first, the contribution of the grain facet reflectivity and scattering from the bulk of a grain with the density of ThO2, a highly absorbing material, were calculated. Microporous ThO2 powder having micrometric grain size was characterized, in which the scattering signal is predominant. A high-resolution synchrotron instrument was used in order to cover a wider q range and minimize the absorption effect, and the results were compared with those obtained using a laboratory X-ray source. Concerning the absorption problem existing with a laboratory X-ray source, a new and robust experimental method was proposed to correctly determine the scattering intensity of the highly absorbing granular samples on an absolute scale. This method allows one to calculate accurately the porous volume and the specific surface via Porod's law and the invariant using a laboratory SAXS instrument. This last result opens new perspectives for the characterization of the volume and the specific surface of highly absorbing actinide oxide powders.urn:issn:1600-5767SMALL-ANGLE X-RAY SCATTERING; HIGHLY ABSORBING POROUS POWDERS; REFLECTIVITY AND SCATTERING CONTRIBUTIONS; ABSOLUTE SCATTERING INTENSITYThe contributions of grain facet reflectivity and scattering from the bulk of a grain of highly absorbing material were calculated as a function of sample characteristics. To test these results, the scattering intensity of a grain of microporous ThO2 was experimentally characterized by small-angle X-ray scattering using a synchrotron source. In addition, a new experimental method to probe the porous texture of nanoporous powders of highly absorbing compounds using a laboratory X-ray instrument has been proposed.doi:10.1107/S1600576722006987enSpecific analysis of highly absorbing nanoporous powder by small-angle X-ray scatteringLu, Z.Rébiscoul, D.Narayanan, T.Zemb, T.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-0611545med@iucr.org1600-576711632022-09-0655research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767October 2022Bond-length distributions in ionically bonded materials with decomposition by coordination environment
http://scripts.iucr.org/cgi-bin/paper?gj5278
The distributions are analysed of the bond lengths between cations and anions in nitrides, oxides and fluorides for which structural data are available in the Crystallography Open Database (https://www.crystallography.net/cod/). The distributions are decomposed according to analysis of the coordination environments of the cations, which are offered in the tool ChemEnv [Waroquiers, George, Horton, Schenk, Persson, Rignanese, Gonze & Hautier (2020). Acta Cryst. B76, 683–695]. The distributions show how well the concept of ionic radius works. Chemical trends can be observed from the obtained distributions. For example, the bond-length distribution for Sc—O is similar to that for Zr—O. The distributions for Mo—O and V—O show noteworthy similarity. Resources for reproducing all of the results are available at https://github.com/tkotani/CEBond, with additional results for nitrides and fluorides.textThe distributions are analysed of the bond lengths between cations and anions in nitrides, oxides and fluorides for which structural data are available in the Crystallography Open Database (https://www.crystallography.net/cod/). The distributions are decomposed according to analysis of the coordination environments of the cations, which are offered in the tool ChemEnv [Waroquiers, George, Horton, Schenk, Persson, Rignanese, Gonze & Hautier (2020). Acta Cryst. B76, 683–695]. The distributions show how well the concept of ionic radius works. Chemical trends can be observed from the obtained distributions. For example, the bond-length distribution for Sc—O is similar to that for Zr—O. The distributions for Mo—O and V—O show noteworthy similarity. Resources for reproducing all of the results are available at https://github.com/tkotani/CEBond, with additional results for nitrides and fluorides.urn:issn:1600-5767BOND-LENGTH DISTRIBUTIONS; IONIC RADII; CRYSTALLOGRAPHY OPEN DATABASE; CHEMENV; STATISTICSTo aid understanding of the idea of the ionic radius, a statistical analysis of the bond-length distributions for real crystal structures in the Crystallography Open Database is presented. A package to reproduce the results is freely available from https://github.com/tkotani/CEBond.doi:10.1107/S1600576722006884enBond-length distributions in ionically bonded materials with decomposition by coordination environmentSawada, M.Iwamoto, R.Kotani, T.Sakakibara, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-09-061600-576713672022-09-065551359med@iucr.org1600-5767October 2022teaching and educationJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Digitization of imaging plates from Guinier powder X-ray diffraction cameras
http://scripts.iucr.org/cgi-bin/paper?vb5036
A Guinier camera equipped with an imaging plate is used to investigate and eliminate the sources of instrumental errors affecting the quality of the obtained scanned Guinier data. A program with a graphical user interface is presented which converts the data of the scanned images into different standard file formats for powder X-ray patterns containing intensities, their standard deviations and the diffraction angles. The program also allows for manual and automatic correction of the 2θ scale against a known reference material. It is shown using LaB6 that the exported X-ray diffraction patterns provide a 2θ scale reproducible enough to allow for averaging diffractograms obtained from different exposures of the imaging plate for the same sample. As shown on a mixture of NaCl and sodalite, the quality of the produced data is sufficient for Rietveld refinement. The software including source code is made available under a free software license.textA Guinier camera equipped with an imaging plate is used to investigate and eliminate the sources of instrumental errors affecting the quality of the obtained scanned Guinier data. A program with a graphical user interface is presented which converts the data of the scanned images into different standard file formats for powder X-ray patterns containing intensities, their standard deviations and the diffraction angles. The program also allows for manual and automatic correction of the 2θ scale against a known reference material. It is shown using LaB6 that the exported X-ray diffraction patterns provide a 2θ scale reproducible enough to allow for averaging diffractograms obtained from different exposures of the imaging plate for the same sample. As shown on a mixture of NaCl and sodalite, the quality of the produced data is sufficient for Rietveld refinement. The software including source code is made available under a free software license.urn:issn:1600-5767IPREADER SOFTWARE; GUINIER CAMERAS; IMAGING PLATES (IPS); DIFFRACTION PATTERN CONVERSION INTO DATA COLUMNS; POWDER X-RAY DIFFRACTION; DATA PROCESSING; GUINIER METHODA program for the digitization of Guinier powder diffraction images is described, which works with images from both optical and laser scanners. Thus, processing of data from storage-phosphor-based imaging plates and Ag-based photographic films is possible.doi:10.1107/S160057672200677XenDigitization of imaging plates from Guinier powder X-ray diffraction camerasNasir, J.Steinbrück, N.Xu, K.Engelen, B.Schmedt auf der Günne, J.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-24research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767October 202210975med@iucr.org1600-576711032022-08-2455GenX 3: the latest generation of an established tool
http://scripts.iucr.org/cgi-bin/paper?ge5118
Since its publication more than 15 years ago the GenX software has been continuously developed and has established itself as a standard package for analyzing X-ray and neutron reflectometry data. The evolution of the software during the last two major revisions is reported here. This includes a simplified model builder for beginners, simple samples, additional sample models, statistical error analysis and the use of just-in-time compilation modules for the reflectometry kernel to achieve higher performance. In addition, the influence of experimental errors on the reflectivity curve is discussed, and new features are described that allow the user to include these in the error statistics to improve the fitting and uncertainty estimation.textSince its publication more than 15 years ago the GenX software has been continuously developed and has established itself as a standard package for analyzing X-ray and neutron reflectometry data. The evolution of the software during the last two major revisions is reported here. This includes a simplified model builder for beginners, simple samples, additional sample models, statistical error analysis and the use of just-in-time compilation modules for the reflectometry kernel to achieve higher performance. In addition, the influence of experimental errors on the reflectivity curve is discussed, and new features are described that allow the user to include these in the error statistics to improve the fitting and uncertainty estimation.urn:issn:1600-5767REFLECTOMETRY; SURFACE X-RAY DIFFRACTION; NEUTRON ANALYSIS; X-RAY ANALYSISImprovements to the GenX program are discussed, including performance, model building and error analysis.doi:10.1107/S1600576722006653enGenX 3: the latest generation of an established toolGlavic, A.Björck, M.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-30med@iucr.org106342022-07-30551600-57671071Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/computer programsAugust 20221600-5767Temperature dependence in Bragg edge neutron transmission measurements
http://scripts.iucr.org/cgi-bin/paper?in5052
A systematic study has been carried out to investigate the neutron transmission signal as a function of sample temperature. In particular, the experimentally determined wavelength-dependent neutron attenuation spectra for a martensitic steel at temperatures ranging from 21 to 700°C are compared with simulated data. A theoretical description that includes the Debye–Waller factor in order to describe the temperature influence on the neutron cross sections was implemented in the nxsPlotter software and used for the simulations. The analysis of the attenuation coefficients at varying temperatures shows that the missing contributions due to elastic and inelastic scattering can be clearly distinguished: while the elastically scattered intensities decrease with higher temperatures, the inelastically scattered intensities increase, and the two can be separated from each other by analysing unique sharp features in the form of Bragg edges. This study presents the first systematic approach to quantify this effect and can serve as a basis , for example, to correct measurements taken during in situ heat treatments, in many cases being a prerequisite for obtaining quantifiable results.textA systematic study has been carried out to investigate the neutron transmission signal as a function of sample temperature. In particular, the experimentally determined wavelength-dependent neutron attenuation spectra for a martensitic steel at temperatures ranging from 21 to 700°C are compared with simulated data. A theoretical description that includes the Debye–Waller factor in order to describe the temperature influence on the neutron cross sections was implemented in the nxsPlotter software and used for the simulations. The analysis of the attenuation coefficients at varying temperatures shows that the missing contributions due to elastic and inelastic scattering can be clearly distinguished: while the elastically scattered intensities decrease with higher temperatures, the inelastically scattered intensities increase, and the two can be separated from each other by analysing unique sharp features in the form of Bragg edges. This study presents the first systematic approach to quantify this effect and can serve as a basis , for example, to correct measurements taken during in situ heat treatments, in many cases being a prerequisite for obtaining quantifiable results.urn:issn:1600-5767NEUTRON BRAGG EDGE IMAGING; DEBYE-WALLER FACTOR; TEMPERATURE-DEPENDENT NEUTRON TRANSMISSION; SUPER MARTENSITIC STAINLESS STEELA systematic study was carried out to investigate the neutron transmission signal as a function of sample temperature. In particular, the experimentally determined wavelength-dependent neutron attenuation spectra for a martensitic steel at temperatures ranging from 21 to 700°C are compared with simulated data.doi:10.1107/S1600576722006549enTemperature dependence in Bragg edge neutron transmission measurementsAl-Falahat, A.M.Kardjilov, N.Woracek, R.Boin, M.Markötter, H.Kuhn, L.T.Makowska, M.Strobl, M.Pfretzschner, B.Banhart, J.Manke, I.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-30August 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papers552022-07-309281600-5767med@iucr.org4919Describing small-angle scattering profiles by a limited set of intensities
http://scripts.iucr.org/cgi-bin/paper?vg5144
Small-angle scattering (SAS) probes the size and shape of particles at low resolution through the analysis of the scattering of X-rays or neutrons passing through a solution of particles. One approach to extracting structural information from SAS data is the indirect Fourier transform (IFT). The IFT approach parameterizes the real-space pair distribution function [P(r)] of a particle using a set of basis functions, which simultaneously determines the scattering profile [I(q)] using corresponding reciprocal-space basis functions. This article presents an extension of an IFT algorithm proposed by Moore [J. Appl. Cryst. (1980), 13, 168–175] which used a trigonometric series to describe the basis functions, where the real-space and reciprocal-space basis functions are Fourier mates. An equation is presented relating the Moore coefficients to the intensities of the SAS profile at specific positions, as well as a series of new equations that describe the size and shape parameters of a particle from this distinct set of intensity values. An analytical real-space regularizer is derived to smooth the P(r) curve and ameliorate systematic deviations caused by series termination. Regularization is commonly used in IFT methods though not described in Moore's original approach, which is particularly susceptible to such effects. The algorithm is provided as a script, denss.fit_data.py, as part of the DENSS software package for SAS, which includes both command line and interactive graphical interfaces. Results of the program using experimental data show that it is as accurate as, and often more accurate than, existing tools.textSmall-angle scattering (SAS) probes the size and shape of particles at low resolution through the analysis of the scattering of X-rays or neutrons passing through a solution of particles. One approach to extracting structural information from SAS data is the indirect Fourier transform (IFT). The IFT approach parameterizes the real-space pair distribution function [P(r)] of a particle using a set of basis functions, which simultaneously determines the scattering profile [I(q)] using corresponding reciprocal-space basis functions. This article presents an extension of an IFT algorithm proposed by Moore [J. Appl. Cryst. (1980), 13, 168–175] which used a trigonometric series to describe the basis functions, where the real-space and reciprocal-space basis functions are Fourier mates. An equation is presented relating the Moore coefficients to the intensities of the SAS profile at specific positions, as well as a series of new equations that describe the size and shape parameters of a particle from this distinct set of intensity values. An analytical real-space regularizer is derived to smooth the P(r) curve and ameliorate systematic deviations caused by series termination. Regularization is commonly used in IFT methods though not described in Moore's original approach, which is particularly susceptible to such effects. The algorithm is provided as a script, denss.fit_data.py, as part of the DENSS software package for SAS, which includes both command line and interactive graphical interfaces. Results of the program using experimental data show that it is as accurate as, and often more accurate than, existing tools.urn:issn:1600-5767SMALL-ANGLE SCATTERING; INDIRECT FOURIER TRANSFORM; SOLUTION SCATTERING; PAIR DISTRIBUTION FUNCTIONAn indirect Fourier transform method is presented which describes a solution scattering profile from a reduced set of intensities. Equations are derived to fit the experimental profile using least squares and to calculate commonly used size and shape parameters directly from the reduced set of intensities, along with associated uncertainties. An analytical equation is derived enabling regularization of the real-space pair distribution function. Convenient software is provided to perform all described calculations.doi:10.1107/S1600576722006598enDescribing small-angle scattering profiles by a limited set of intensitiesGrant, T.D.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-30Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersOctober 20221600-5767med@iucr.org111652022-08-30551600-57671124Brittle fracture studied by ultra-high-speed synchrotron X-ray diffraction imaging
http://scripts.iucr.org/cgi-bin/paper?vb5040
In situ investigations of cracks propagating at up to 2.5 km s−1 along an (001) plane of a silicon single crystal are reported, using X-ray diffraction megahertz imaging with intense and time-structured synchrotron radiation. The studied system is based on the Smart Cut process, where a buried layer in a material (typically Si) is weakened by microcracks and then used to drive a macroscopic crack (10−1 m) in a plane parallel to the surface with minimal deviation (10−9 m). A direct confirmation that the shape of the crack front is not affected by the distribution of the microcracks is provided. Instantaneous crack velocities over the centimetre-wide field of view were measured and showed an effect of local heating by the X-ray beam. The post-crack movements of the separated wafer parts could also be observed and explained using pneumatics and elasticity. A comprehensive view of controlled fracture propagation in a crystalline material is provided, paving the way for the in situ measurement of ultra-fast strain field propagation.textIn situ investigations of cracks propagating at up to 2.5 km s−1 along an (001) plane of a silicon single crystal are reported, using X-ray diffraction megahertz imaging with intense and time-structured synchrotron radiation. The studied system is based on the Smart Cut process, where a buried layer in a material (typically Si) is weakened by microcracks and then used to drive a macroscopic crack (10−1 m) in a plane parallel to the surface with minimal deviation (10−9 m). A direct confirmation that the shape of the crack front is not affected by the distribution of the microcracks is provided. Instantaneous crack velocities over the centimetre-wide field of view were measured and showed an effect of local heating by the X-ray beam. The post-crack movements of the separated wafer parts could also be observed and explained using pneumatics and elasticity. A comprehensive view of controlled fracture propagation in a crystalline material is provided, paving the way for the in situ measurement of ultra-fast strain field propagation.urn:issn:1600-5767X-RAY DIFFRACTION; ION IMPLANTATION; CRACK-FRONT SHAPECrack propagation in a silicon single-crystal wafer is tracked in situ using synchrotron-based ultra-high speed X-ray diffraction imaging. The high spatio-temporal resolution reached in diffraction imaging mode allows for assessing different parameters such as crack velocity or post crack movements of the separated wafers.doi:10.1107/S1600576722006537enBrittle fracture studied by ultra-high-speed synchrotron X-ray diffraction imagingPetit, A.Pokam, S.Mazen, F.Tardif, S.Landru, D.Kononchuk, O.Ben Mohamed, N.Olbinado, M.P.Rack, A.Rieutord, F.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-30med@iucr.org4911552022-07-309181600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersAugust 20221600-5767Observation of in-plane shear stress fields in off-axis SiC wafers by birefringence imaging
http://scripts.iucr.org/cgi-bin/paper?vb5039
For the nondestructive characterization of SiC wafers for power device application, birefringence imaging is one of the promising methods. In the present study, it is demonstrated that birefringence image contrast variation in off-axis SiC wafers corresponds to the in-plane shear stress under conditions slightly deviating from crossed Nicols according to both theoretical consideration and experimental observation. The current results indicate that the characterization of defects in SiC wafers is possible to achieve by birefringence imaging.textFor the nondestructive characterization of SiC wafers for power device application, birefringence imaging is one of the promising methods. In the present study, it is demonstrated that birefringence image contrast variation in off-axis SiC wafers corresponds to the in-plane shear stress under conditions slightly deviating from crossed Nicols according to both theoretical consideration and experimental observation. The current results indicate that the characterization of defects in SiC wafers is possible to achieve by birefringence imaging.urn:issn:1600-5767BIREFRINGENCE; DEFECT CHARACTERIZATION; SILICON CARBIDETheoretical consideration and experimental demonstration reveal that the contrast variation in a birefringence image of an off-axis SiC wafer corresponds to the in-plane shear stress field.doi:10.1107/S1600576722006483enObservation of in-plane shear stress fields in off-axis SiC wafers by birefringence imagingHarada, S.Murayama, K.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-30August 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/short communications2022-07-30551600-57671032med@iucr.org41029Parameter inversion of a polydisperse system in small-angle scattering
http://scripts.iucr.org/cgi-bin/paper?jl5041
A general method to invert parameter distributions of a polydisperse system using data acquired from a small-angle scattering (SAS) experiment is presented. The forward problem, i.e. calculating the scattering intensity given the distributions of any causal parameters of a theoretical model, is generalized as a multi-linear map, characterized by a high-dimensional Green tensor that represents the complete scattering physics. The inverse problem, i.e. finding the maximum-likelihood estimation of the parameter distributions (in free form) given the scattering intensity (either a curve or an image) acquired from an experiment, is formulated as a constrained nonlinear programming (NLP) problem. This NLP problem is solved with high accuracy and efficiency via several theoretical and computational enhancements, such as an automatic data scaling for accuracy preservation and GPU acceleration for large-scale multi-parameter systems. Six numerical examples are presented, including both synthetic tests and solutions to real neutron and X-ray data sets, where the method is compared with several existing methods in terms of their generality, accuracy and computational cost. These examples show that SAS inversion is subject to a high degree of non-uniqueness of solution or structural ambiguity. With an ultra-high accuracy, the method can yield a series of near-optimal solutions that fit data to different acceptable levels.textA general method to invert parameter distributions of a polydisperse system using data acquired from a small-angle scattering (SAS) experiment is presented. The forward problem, i.e. calculating the scattering intensity given the distributions of any causal parameters of a theoretical model, is generalized as a multi-linear map, characterized by a high-dimensional Green tensor that represents the complete scattering physics. The inverse problem, i.e. finding the maximum-likelihood estimation of the parameter distributions (in free form) given the scattering intensity (either a curve or an image) acquired from an experiment, is formulated as a constrained nonlinear programming (NLP) problem. This NLP problem is solved with high accuracy and efficiency via several theoretical and computational enhancements, such as an automatic data scaling for accuracy preservation and GPU acceleration for large-scale multi-parameter systems. Six numerical examples are presented, including both synthetic tests and solutions to real neutron and X-ray data sets, where the method is compared with several existing methods in terms of their generality, accuracy and computational cost. These examples show that SAS inversion is subject to a high degree of non-uniqueness of solution or structural ambiguity. With an ultra-high accuracy, the method can yield a series of near-optimal solutions that fit data to different acceptable levels.urn:issn:1600-5767SMALL-ANGLE SCATTERING; POLYDISPERSITY; INVERSION; NEUTRON SCATTERING; X-RAY SCATTERING; NONLINEAR PROGRAMMINGAn accurate and efficient method for model- and form-free inversion of a polydisperse small-angle scattering system is presented. It supports an arbitrary number of model parameters and both 1D and 2D intensity observations.doi:10.1107/S1600576722006379enParameter inversion of a polydisperse system in small-angle scatteringLeng, K.King, S.Snow, T.Rogers, S.Markvardsen, A.Maheswaran, S.Thiyagalingam, J.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-01August 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papers552022-08-019771600-5767med@iucr.org4966Electron diffraction characterization of nanocrystalline materials using a Rietveld-based approach. Part I. Methodology
http://scripts.iucr.org/cgi-bin/paper?nb5328
Transmission electron microscopy is a powerful experimental tool, very effective for the complete characterization of nanocrystalline materials by employing a combination of imaging, spectroscopy and diffraction techniques. Electron powder diffraction (EPD) pattern fingerprinting in association with chemical information from spectroscopy can be used to deduce the identity of the crystalline phases. Furthermore, EPD has similar potential to X-ray powder diffraction (XRPD) for extracting additional information regarding material specimens, such as microstructural features and defect structures. The aim of this paper is to extend a full-pattern fitting procedure, broadly used for analysing XRPD patterns, to EPD. The interest of this approach is twofold: in the first place, the relatively short times involved with data acquisition allow one to speed up the characterization procedures. This is a particularly interesting aspect in the case of metastable structures or kinetics studies. Moreover, the reduced sampling volumes involved with electron diffraction analyses can better reveal surface alteration layers in the analysed specimen which might be completely overlooked by conventional bulk techniques. The first step forward to have an effective application of the proposed methodology concerns establishing a reliable calibration protocol to take into correct account the instrumental effects and thus separate them from those determined by the structure, microstructure and texture of the analysed samples. In this paper, the methodology for determining the instrumental broadening of the diffraction lines is demonstrated through a full quantitative analysis based on the Rietveld refinement of the EPD. In this regard, a CeO2 nanopowder reference specimen has been used. The results provide indications also on the specific features that a good calibration standard should have.textTransmission electron microscopy is a powerful experimental tool, very effective for the complete characterization of nanocrystalline materials by employing a combination of imaging, spectroscopy and diffraction techniques. Electron powder diffraction (EPD) pattern fingerprinting in association with chemical information from spectroscopy can be used to deduce the identity of the crystalline phases. Furthermore, EPD has similar potential to X-ray powder diffraction (XRPD) for extracting additional information regarding material specimens, such as microstructural features and defect structures. The aim of this paper is to extend a full-pattern fitting procedure, broadly used for analysing XRPD patterns, to EPD. The interest of this approach is twofold: in the first place, the relatively short times involved with data acquisition allow one to speed up the characterization procedures. This is a particularly interesting aspect in the case of metastable structures or kinetics studies. Moreover, the reduced sampling volumes involved with electron diffraction analyses can better reveal surface alteration layers in the analysed specimen which might be completely overlooked by conventional bulk techniques. The first step forward to have an effective application of the proposed methodology concerns establishing a reliable calibration protocol to take into correct account the instrumental effects and thus separate them from those determined by the structure, microstructure and texture of the analysed samples. In this paper, the methodology for determining the instrumental broadening of the diffraction lines is demonstrated through a full quantitative analysis based on the Rietveld refinement of the EPD. In this regard, a CeO2 nanopowder reference specimen has been used. The results provide indications also on the specific features that a good calibration standard should have.urn:issn:1600-5767TRANSMISSION ELECTRON MICROSCOPY; INSTRUMENTAL BROADENING FUNCTIONS; RIETVELD REFINEMENTQuantitative microstructural characterization of nanocrystalline materials based on Rietveld refinement of electron diffraction patterns has been used to explore sample characteristics. The electron microscope instrumental effects have been considered.doi:10.1107/S1600576722006367enElectron diffraction characterization of nanocrystalline materials using a Rietveld-based approach. Part I. MethodologySinha, A.Bortolotti, M.Ischia, G.Lutterotti, L.Gialanella, S.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-01med@iucr.org49532022-08-01551600-5767965Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersAugust 20221600-5767Magnetic nanoprecipitates and interfacial spin disorder in zero-field-annealed Ni50Mn45In5 Heusler alloys as seen by magnetic small-angle neutron scattering
http://scripts.iucr.org/cgi-bin/paper?uz5003
Shell ferromagnetism is a new functional property of certain off-stoichiometric Ni–Mn–In Heusler alloys, with a potential application in non-volatile magnetic memories and recording media. One key challenge in this field remains the determination of the structural and magnetic properties of the nanoprecipitates that are the result of an annealing-induced segregation process. Thanks to its unique mesoscopic length scale sensitivity, magnetic small-angle neutron scattering appears to be a powerful technique to disclose the microstructure of such annealing-induced nanoprecipitates. In this study, the microstructure of a zero-field-annealed off-stoichiometric Ni50Mn45In5 Heusler alloy is investigated by unpolarized magnetic small-angle neutron scattering. The neutron data analysis reveals a significant spin-misalignment scattering, which is mainly related to the formation of annealing-induced ferromagnetic nanoprecipitates in an antiferromagnetic matrix. These particles represent a source of perturbation which, due to dipolar stray fields, gives rise to canted spin moments in the surroundings of the particle–matrix interface. The presence of anticorrelations in the computed magnetic correlation function reflects the spatial perturbation of the magnetization vector around the nanoprecipitates. The magnetic field dependence of the zero crossing and the minima of the magnetic correlation function are qualitatively explained using the law of approach to ferromagnetic saturation for inhomogeneous spin states. More specifically, at remanence, the nanoprecipitates act magnetically as one superdefect with a correlation length that lies outside the experimental q range, whereas near saturation the magnetization distribution follows each individual nanoprecipitate. Analysis of the neutron data yields an estimated size of 30 nm for the spin-canted region and a value of about 75 nm for the magnetic core of the individual nanoprecipitates.textShell ferromagnetism is a new functional property of certain off-stoichiometric Ni–Mn–In Heusler alloys, with a potential application in non-volatile magnetic memories and recording media. One key challenge in this field remains the determination of the structural and magnetic properties of the nanoprecipitates that are the result of an annealing-induced segregation process. Thanks to its unique mesoscopic length scale sensitivity, magnetic small-angle neutron scattering appears to be a powerful technique to disclose the microstructure of such annealing-induced nanoprecipitates. In this study, the microstructure of a zero-field-annealed off-stoichiometric Ni50Mn45In5 Heusler alloy is investigated by unpolarized magnetic small-angle neutron scattering. The neutron data analysis reveals a significant spin-misalignment scattering, which is mainly related to the formation of annealing-induced ferromagnetic nanoprecipitates in an antiferromagnetic matrix. These particles represent a source of perturbation which, due to dipolar stray fields, gives rise to canted spin moments in the surroundings of the particle–matrix interface. The presence of anticorrelations in the computed magnetic correlation function reflects the spatial perturbation of the magnetization vector around the nanoprecipitates. The magnetic field dependence of the zero crossing and the minima of the magnetic correlation function are qualitatively explained using the law of approach to ferromagnetic saturation for inhomogeneous spin states. More specifically, at remanence, the nanoprecipitates act magnetically as one superdefect with a correlation length that lies outside the experimental q range, whereas near saturation the magnetization distribution follows each individual nanoprecipitate. Analysis of the neutron data yields an estimated size of 30 nm for the spin-canted region and a value of about 75 nm for the magnetic core of the individual nanoprecipitates.urn:issn:1600-5767MAGNETIC NEUTRON SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MAGNETIC STRUCTURES; MATERIALS SCIENCE; HEUSLER ALLOYSMagnetic-field-dependent small-angle neutron scattering is employed to disclose the zero-field annealing-induced spin disorder around magnetic nanoprecipitates in an off-stoichiometric Ni50Mn45In5 Heusler alloy.doi:10.1107/S1600576722006355enMagnetic nanoprecipitates and interfacial spin disorder in zero-field-annealed Ni50Mn45In5 Heusler alloys as seen by magnetic small-angle neutron scatteringBersweiler, M.Bender, P.Peral, I.Pratami Sinaga, E.Honecker, D.Alba Venero, D.Titov, I.Michels, A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-15https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersAugust 20221600-5767med@iucr.org7134552022-07-157211600-5767A semi-supervised deep-learning approach for automatic crystal structure classification
http://scripts.iucr.org/cgi-bin/paper?tu5018
The structural solution problem can be a daunting and time-consuming task. Especially in the presence of impurity phases, current methods, such as indexing, become more unstable. In this work, the novel approach of semi-supervised learning is applied towards the problem of identifying the Bravais lattice and the space group of inorganic crystals. The reported semi-supervised generative deep-learning model can train on both labeled data, i.e. diffraction patterns with the associated crystal structure, and unlabeled data, i.e. diffraction patterns that lack this information. This approach allows the models to take advantage of the troves of unlabeled data that current supervised learning approaches cannot, which should result in models that can more accurately generalize to real data. In this work, powder diffraction patterns are classified into all 14 Bravais lattices and 144 space groups (the number is limited due to sparse coverage in crystal structure databases), which covers more crystal classes than other studies. The reported models also outperform current deep-learning approaches for both space group and Bravais lattice classification using fewer training data.textThe structural solution problem can be a daunting and time-consuming task. Especially in the presence of impurity phases, current methods, such as indexing, become more unstable. In this work, the novel approach of semi-supervised learning is applied towards the problem of identifying the Bravais lattice and the space group of inorganic crystals. The reported semi-supervised generative deep-learning model can train on both labeled data, i.e. diffraction patterns with the associated crystal structure, and unlabeled data, i.e. diffraction patterns that lack this information. This approach allows the models to take advantage of the troves of unlabeled data that current supervised learning approaches cannot, which should result in models that can more accurately generalize to real data. In this work, powder diffraction patterns are classified into all 14 Bravais lattices and 144 space groups (the number is limited due to sparse coverage in crystal structure databases), which covers more crystal classes than other studies. The reported models also outperform current deep-learning approaches for both space group and Bravais lattice classification using fewer training data.urn:issn:1600-5767MACHINE LEARNING; POWDER NEUTRON DIFFRACTION; SEMI-SUPERVISED; INDEXINGA semi-supervised model to predict crystal structures from powder neutron diffraction patterns has been developed. The models have higher accuracies than current approaches while covering more space groups.doi:10.1107/S1600576722006069enA semi-supervised deep-learning approach for automatic crystal structure classificationLolla, S.Liang, H.Kusne, A.G.Takeuchi, I.Ratcliff, W.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-28med@iucr.org88242022-07-28551600-5767889Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersAugust 20221600-5767Neutron interference from a split-crystal interferometer
http://scripts.iucr.org/cgi-bin/paper?tu5022
The first successful operation of a neutron interferometer with a separate beam-recombining crystal is reported. This result was achieved at the neutron interferometry setup S18 at the ILL in Grenoble by a collaboration between TU Wien, ILL, Grenoble, and INRIM, Torino. While previous interferometers have been machined out of a single-crystal block, in this work two crystals were successfully aligned on nanoradian and picometre scales, as required to obtain neutron interference. As a decisive proof-of-principle demonstration, this opens the door to a new generation of neutron interferometers and exciting applications.textThe first successful operation of a neutron interferometer with a separate beam-recombining crystal is reported. This result was achieved at the neutron interferometry setup S18 at the ILL in Grenoble by a collaboration between TU Wien, ILL, Grenoble, and INRIM, Torino. While previous interferometers have been machined out of a single-crystal block, in this work two crystals were successfully aligned on nanoradian and picometre scales, as required to obtain neutron interference. As a decisive proof-of-principle demonstration, this opens the door to a new generation of neutron interferometers and exciting applications.urn:issn:1600-5767NEUTRON INTERFEROMETRY; SPLIT-CRYSTAL INTERFEROMETERS; SILICON CRYSTALS; ATOMIC SCALE POSITIONINGThis article reports the first successful operation of a neutron interferometer with a separate beam-recombining crystal. This result is a proof-of-principle demonstration showing that new-generation neutron interferometers and applications are possible.doi:10.1107/S1600576722006082enNeutron interference from a split-crystal interferometerLemmel, H.Jentschel, M.Abele, H.Lafont, F.Guerard, B.Sasso, C.P.Mana, G.Massa, E.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-158704med@iucr.org8751600-5767552022-07-15research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767August 2022Indexing of superimposed Laue diffraction patterns using a dictionary–branch–bound approach
http://scripts.iucr.org/cgi-bin/paper?nb5318
X-ray Laue diffraction is an important method for characterizing the local crystallographic orientation and elastic strain in polycrystalline materials. Existing analysis methods are designed mainly to index a single or a few Laue diffraction pattern(s) recorded in a detector image. In this work, a novel method called dictionary–branch–bound (DBB) is presented to determine the crystallographic orientations of multiple crystals simultaneously illuminated by a parallel X-ray incident beam, using only the spot positions in a detector image. DBB is validated for simulated X-ray Laue diffraction data. In the simulation, up to 100 crystals with random crystallographic orientations are simultaneously illuminated. Fake spots are randomly added to the detector image to test the robustness of DBB. Additionally, spots are randomly removed to test the resilience of DBB against true spots that are undetected due to background noise and/or spot overlap. Poisson noise is also added to test the sensitivity of DBB to less accurate positions of detected spots. In all cases except the most challenging one, a perfect indexing with a mean angular error below 0.08° is obtained. To demonstrate the potential of DBB further, it is applied to synchrotron microdiffraction data. Finally, guidelines for using DBB in experimental data are provided.textX-ray Laue diffraction is an important method for characterizing the local crystallographic orientation and elastic strain in polycrystalline materials. Existing analysis methods are designed mainly to index a single or a few Laue diffraction pattern(s) recorded in a detector image. In this work, a novel method called dictionary–branch–bound (DBB) is presented to determine the crystallographic orientations of multiple crystals simultaneously illuminated by a parallel X-ray incident beam, using only the spot positions in a detector image. DBB is validated for simulated X-ray Laue diffraction data. In the simulation, up to 100 crystals with random crystallographic orientations are simultaneously illuminated. Fake spots are randomly added to the detector image to test the robustness of DBB. Additionally, spots are randomly removed to test the resilience of DBB against true spots that are undetected due to background noise and/or spot overlap. Poisson noise is also added to test the sensitivity of DBB to less accurate positions of detected spots. In all cases except the most challenging one, a perfect indexing with a mean angular error below 0.08° is obtained. To demonstrate the potential of DBB further, it is applied to synchrotron microdiffraction data. Finally, guidelines for using DBB in experimental data are provided.urn:issn:1600-5767LAUE DIFFRACTION; SUPERIMPOSED PATTERNS; INDEXING; CRYSTALLOGRAPHIC ORIENTATIONSA method is developed to determine multiple simultaneously illuminated crystallographic orientations producing superimposed Laue diffraction patterns on a single detector image, using only spot positions. Tests performed on simulated data show the capability of indexing at least 100 crystals, even if fake spots are added, true spots are removed and noise is added. Further validation on synchrotron microdiffraction data is also provided.doi:10.1107/S1600576722006021enIndexing of superimposed Laue diffraction patterns using a dictionary–branch–bound approachSeret, A.Gao, W.Juul Jensen, D.Godfrey, A.Zhang, Y.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-2451085med@iucr.org10961600-5767552022-08-24research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767October 2022Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules
http://scripts.iucr.org/cgi-bin/paper?yr5084
X-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.textX-ray free-electron lasers (XFELs) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges in terms of both experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classifiers using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. Skopi is a resource to aid feasibility studies and advance the development of algorithms for noncrystalline experiments at XFEL facilities.urn:issn:1600-5767SINGLE-PARTICLE IMAGING; FLUCTUATION X-RAY SCATTERING; HOLOGRAPHY; FREE-ELECTRON LASERS; SIMULATIONThe Skopi software package provides tools to generate realistic simulations of coherent X-ray diffractive imaging of noncrystalline biological samples, which in turn will aid algorithm development for a range of experiments at X-ray free-electron laser sources.doi:10.1107/S1600576722005994enSkopi: a simulation package for diffractive imaging of noncrystalline biomoleculesPeck, A.Chang, H.-Y.Dujardin, A.Ramalingam, D.Uervirojnangkoorn, M.Wang, Z.Mancuso, A.Poitevin, F.Yoon, C.H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-15August 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papers552022-07-1510101600-5767med@iucr.org41002Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package
http://scripts.iucr.org/cgi-bin/paper?te5094
The design of X-ray optics based on diffraction from crystals depends on the accurate calculation of the structure factors of their Bragg reflections over a wide range of temperatures. In general, the temperature dependence of the lattice parameters, the atomic positions and the atomic thermal vibrations is both anisotropic and nonlinear. Implemented here is a software package for precise and flexible calculation of structure factors for dynamical diffraction. α-Quartz is used as an example because it presents the challenges mentioned above and because it is being considered for use in high-resolution X-ray spectroscopy. The package is designed to be extended easily to other crystals by adding new material files, which are kept separate from the package's stable core. Python 3 was chosen as the language to allow the easy integration of this code into existing packages. The importance of a correct anisotropic treatment of the atomic thermal vibrations is demonstrated by comparison with an isotropic Debye model. Discrepancies between the two models can be as much as 5% for strong reflections and considerably larger (even to the level of 100%) for weak reflections. A script for finding Bragg reflections that backscatter X-rays of a given energy within a given temperature range is demonstrated. The package and example scripts are available on request. Also discussed, in detail, are the various conventions related to the proper description of chiral quartz.textThe design of X-ray optics based on diffraction from crystals depends on the accurate calculation of the structure factors of their Bragg reflections over a wide range of temperatures. In general, the temperature dependence of the lattice parameters, the atomic positions and the atomic thermal vibrations is both anisotropic and nonlinear. Implemented here is a software package for precise and flexible calculation of structure factors for dynamical diffraction. α-Quartz is used as an example because it presents the challenges mentioned above and because it is being considered for use in high-resolution X-ray spectroscopy. The package is designed to be extended easily to other crystals by adding new material files, which are kept separate from the package's stable core. Python 3 was chosen as the language to allow the easy integration of this code into existing packages. The importance of a correct anisotropic treatment of the atomic thermal vibrations is demonstrated by comparison with an isotropic Debye model. Discrepancies between the two models can be as much as 5% for strong reflections and considerably larger (even to the level of 100%) for weak reflections. A script for finding Bragg reflections that backscatter X-rays of a given energy within a given temperature range is demonstrated. The package and example scripts are available on request. Also discussed, in detail, are the various conventions related to the proper description of chiral quartz.urn:issn:1600-5767QUARTZ; X-RAYS; STRUCTURE FACTORS; PYTHONA Python 3 software package for precise calculation of X-ray structure factors of α-quartz over a wide temperature range is presented. α-Quartz was chosen because of its practical application in high-resolution X-ray spectroscopy, but this software package can be easily extended to other crystals.doi:10.1107/S1600576722005945enCalculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 packageSutter, J.P.Pittard, J.Filik, J.Baron, A.Q.R.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-2810281600-5767552022-07-2841011med@iucr.org1600-5767August 2022research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyTowards real-time analysis of liquid jet alignment in serial femtosecond crystallography
http://scripts.iucr.org/cgi-bin/paper?ap5045
Liquid sample delivery systems are used extensively for serial femtosecond crystallography at X-ray free-electron lasers (XFELs). However, misalignment of the liquid jet and the XFEL beam leads to the X-rays either partially or completely missing the sample, resulting in sample wastage and a loss of experiment time. Implemented here is an algorithm to analyse optical images using machine vision to determine whether there is overlap of the X-ray beam and liquid jet. The long-term goal is to use the output from this algorithm to implement an automated feedback mechanism to maintain constant alignment of the X-ray beam and liquid jet. The key elements of this jet alignment algorithm are discussed and its performance is characterized by comparing the results with a manual analysis of the optical image data. The success rate of the algorithm for correctly identifying hits is quantified via a similarity metric, the Dice coefficient. In total four different nozzle designs were used in this study, yielding an overall Dice coefficient of 0.98.textLiquid sample delivery systems are used extensively for serial femtosecond crystallography at X-ray free-electron lasers (XFELs). However, misalignment of the liquid jet and the XFEL beam leads to the X-rays either partially or completely missing the sample, resulting in sample wastage and a loss of experiment time. Implemented here is an algorithm to analyse optical images using machine vision to determine whether there is overlap of the X-ray beam and liquid jet. The long-term goal is to use the output from this algorithm to implement an automated feedback mechanism to maintain constant alignment of the X-ray beam and liquid jet. The key elements of this jet alignment algorithm are discussed and its performance is characterized by comparing the results with a manual analysis of the optical image data. The success rate of the algorithm for correctly identifying hits is quantified via a similarity metric, the Dice coefficient. In total four different nozzle designs were used in this study, yielding an overall Dice coefficient of 0.98.urn:issn:1600-5767MACHINE VISION; AUTOMATION; LIQUID JET ALIGNMENT; IMAGE PROCESSINGA novel strategy is presented for sample jet alignment using machine vision for liquid-jet-based sample delivery systems. Feedback using height-resolution images from an optical microscope positioned perpendicular to the path of the X-ray beam enables tracking of the relative alignment of the liquid jet and X-ray beam.doi:10.1107/S1600576722005891enTowards real-time analysis of liquid jet alignment in serial femtosecond crystallographyPatel, J.Round, A.Bielecki, J.Doerner, K.Kirkwood, H.Letrun, R.Schulz, J.Sikorski, M.Vakili, M.de Wijn, R.Peele, A.Mancuso, A.P.Abbey, B.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-08-01med@iucr.org9444552022-08-019521600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersAugust 20221600-5767Gwaihir: Jupyter Notebook graphical user interface for Bragg coherent diffraction imaging
http://scripts.iucr.org/cgi-bin/paper?te5096
Bragg coherent X-ray diffraction is a nondestructive method for probing material structure in three dimensions at the nanoscale, with unprecedented resolution in displacement and strain fields. This work presents Gwaihir, a user-friendly and open-source tool to process and analyze Bragg coherent X-ray diffraction data. It integrates the functionalities of the existing packages bcdi and PyNX in the same toolbox, creating a natural workflow and promoting data reproducibility. Its graphical interface, based on Jupyter Notebook widgets, combines an interactive approach for data analysis with a powerful environment designed to link large-scale facilities and scientists.textBragg coherent X-ray diffraction is a nondestructive method for probing material structure in three dimensions at the nanoscale, with unprecedented resolution in displacement and strain fields. This work presents Gwaihir, a user-friendly and open-source tool to process and analyze Bragg coherent X-ray diffraction data. It integrates the functionalities of the existing packages bcdi and PyNX in the same toolbox, creating a natural workflow and promoting data reproducibility. Its graphical interface, based on Jupyter Notebook widgets, combines an interactive approach for data analysis with a powerful environment designed to link large-scale facilities and scientists.urn:issn:1600-5767X-RAY DIFFRACTION; COHERENCE; PHASE RETRIEVAL; JUPYTER NOTEBOOK; GRAPHICAL USER INTERFACESIn a world where data are steadily made more available, Gwaihir is a tool that overcomes multiple issues by bridging remote access, cluster computing and a user-friendly interface, consequentially improving the link between synchrotrons and their users for Bragg coherent diffraction imaging.doi:10.1107/S1600576722005854enGwaihir: Jupyter Notebook graphical user interface for Bragg coherent diffraction imagingSimonne, D.Carnis, J.Atlan, C.Chatelier, C.Favre-Nicolin, V.Dupraz, M.Leake, S. J.Zatterin, E.Resta, A.Coati, A.Richard, M. I.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-151600-5767August 2022computer programshttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography10541600-5767552022-07-1510454med@iucr.orgMuMag2022: a software tool for analyzing magnetic field dependent unpolarized small-angle neutron scattering data of bulk ferromagnets
http://scripts.iucr.org/cgi-bin/paper?ei5079
The MATLAB-based software tool MuMag2022 is presented for the analysis of magnetic-field-dependent unpolarized small-angle neutron scattering (SANS) data of bulk ferromagnets such as elemental nanocrystalline ferromagnets, magnetic nanocomposites or magnetic steels. On the basis of the micromagnetic theory for the magnetic SANS cross section, the program analyzes unpolarized total (nuclear and magnetic) SANS data within the approach-to-saturation regime. The main features of MuMag2022 are the estimation of the exchange-stiffness constant, and of the strength and spatial structure of the magnetic anisotropy field and the magnetostatic field due to longitudinal magnetization fluctuations. MuMag2022 is open source and available as a standalone executable for Windows at https://mumag.uni.lu.textThe MATLAB-based software tool MuMag2022 is presented for the analysis of magnetic-field-dependent unpolarized small-angle neutron scattering (SANS) data of bulk ferromagnets such as elemental nanocrystalline ferromagnets, magnetic nanocomposites or magnetic steels. On the basis of the micromagnetic theory for the magnetic SANS cross section, the program analyzes unpolarized total (nuclear and magnetic) SANS data within the approach-to-saturation regime. The main features of MuMag2022 are the estimation of the exchange-stiffness constant, and of the strength and spatial structure of the magnetic anisotropy field and the magnetostatic field due to longitudinal magnetization fluctuations. MuMag2022 is open source and available as a standalone executable for Windows at https://mumag.uni.lu.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; MICROMAGNETISM; MAGNETIC MATERIALS; NANOCOMPOSITESThe MATLAB-based software tool MuMag2022 is presented for the analysis of magnetic-field-dependent unpolarized small-angle neutron scattering data of bulk ferromagnets such as elemental nanocrystalline ferromagnets, magnetic nanocomposites or magnetic steels.doi:10.1107/S1600576722005349enMuMag2022: a software tool for analyzing magnetic field dependent unpolarized small-angle neutron scattering data of bulk ferromagnetsAdams, M.P.Bersweiler, M.Jefremovas, E.M.Michels, A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-2810554med@iucr.org10621600-5767552022-07-28computer programshttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767August 2022Dislocation substructures in pure aluminium after creep deformation as studied by electron backscatter diffraction
http://scripts.iucr.org/cgi-bin/paper?te5088
In the present work, electron backscatter diffraction was used to determine the microscopic dislocation structures generated during creep (with tests interrupted at the steady state) in pure 99.8% aluminium. This material was investigated at two different stress levels, corresponding to the power-law and power-law breakdown regimes. The results show that the formation of subgrain cellular structures occurs independently of the crystallographic orientation. However, the density of these cellular structures strongly depends on the grain crystallographic orientation with respect to the tensile axis direction, with 〈111〉 grains exhibiting the highest densities at both stress levels. It is proposed that this behaviour is due to the influence of intergranular stresses, which is different in 〈111〉 and 〈001〉 grains.textIn the present work, electron backscatter diffraction was used to determine the microscopic dislocation structures generated during creep (with tests interrupted at the steady state) in pure 99.8% aluminium. This material was investigated at two different stress levels, corresponding to the power-law and power-law breakdown regimes. The results show that the formation of subgrain cellular structures occurs independently of the crystallographic orientation. However, the density of these cellular structures strongly depends on the grain crystallographic orientation with respect to the tensile axis direction, with 〈111〉 grains exhibiting the highest densities at both stress levels. It is proposed that this behaviour is due to the influence of intergranular stresses, which is different in 〈111〉 and 〈001〉 grains.urn:issn:1600-5767CREEP; PURE ALUMINIUM; ELECTRON BACKSCATTER DIFFRACTION (EBSD); CELLULAR STRUCTURES; POWER LAW AND POWER-LAW BREAKDOWNIn the present work, electron backscatter diffraction is used to investigate the influence of crystal orientation and stress level on the dislocation structures generated during primary and steady-state creep in pure aluminium (99.8%). The goal is to characterize features of the microstructure with a statistically sound approach.doi:10.1107/S1600576722005209enDislocation substructures in pure aluminium after creep deformation as studied by electron backscatter diffractionSerrano-Munoz, I.Fernández, R.Saliwan-Neumann, R.González-Doncel, G.Bruno, G.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-05August 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papers2022-07-05551600-5767869med@iucr.org4860Small-angle X-ray scattering: characterization of cubic Au nanoparticles using Debye's scattering formula
http://scripts.iucr.org/cgi-bin/paper?yr5077
A versatile software package in the form of a Python extension, named CDEF (computing Debye's scattering formula for extraordinary form factors), is proposed to calculate approximate scattering profiles of arbitrarily shaped nanoparticles for small-angle X-ray scattering (SAXS). CDEF generates a quasi-randomly distributed point cloud in the desired particle shape and then applies the open-source software DEBYER for efficient evaluation of Debye's scattering formula to calculate the SAXS pattern (https://github.com/j-from-b/CDEF). If self-correlation of the scattering signal is not omitted, the quasi-random distribution provides faster convergence compared with a true-random distribution of the scatterers, especially at higher momentum transfer. The usage of the software is demonstrated for the evaluation of scattering data of Au nanocubes with rounded edges, which were measured at the four-crystal monochromator beamline of PTB at the synchrotron radiation facility BESSY II in Berlin. The implementation is fast enough to run on a single desktop computer and perform model fits within minutes. The accuracy of the method was analyzed by comparison with analytically known form factors and verified with another implementation, the SPONGE, based on a similar principle with fewer approximations. Additionally, the SPONGE coupled to McSAS3 allows one to retrieve information on the uncertainty of the size distribution using a Monte Carlo uncertainty estimation algorithm.textA versatile software package in the form of a Python extension, named CDEF (computing Debye's scattering formula for extraordinary form factors), is proposed to calculate approximate scattering profiles of arbitrarily shaped nanoparticles for small-angle X-ray scattering (SAXS). CDEF generates a quasi-randomly distributed point cloud in the desired particle shape and then applies the open-source software DEBYER for efficient evaluation of Debye's scattering formula to calculate the SAXS pattern (https://github.com/j-from-b/CDEF). If self-correlation of the scattering signal is not omitted, the quasi-random distribution provides faster convergence compared with a true-random distribution of the scatterers, especially at higher momentum transfer. The usage of the software is demonstrated for the evaluation of scattering data of Au nanocubes with rounded edges, which were measured at the four-crystal monochromator beamline of PTB at the synchrotron radiation facility BESSY II in Berlin. The implementation is fast enough to run on a single desktop computer and perform model fits within minutes. The accuracy of the method was analyzed by comparison with analytically known form factors and verified with another implementation, the SPONGE, based on a similar principle with fewer approximations. Additionally, the SPONGE coupled to McSAS3 allows one to retrieve information on the uncertainty of the size distribution using a Monte Carlo uncertainty estimation algorithm.urn:issn:1600-5767SMALL-ANGLE X-RAY SCATTERING; NON-SPHERICAL NANOPARTICLES; DEBYE SCATTERING EQUATIONThe Python extension CDEF is a suitable evaluation tool for experimentalists to calculate single-particle small-angle X-ray scattering profiles with satisfactory accuracy, as shown by comparison with common well-known analytical form factors. Using different complex cubic models, a direct comparison between CDEF and the already established SPONGE with respect to the size distribution of imperfect Au nanocubes showed a clear agreement of the results.doi:10.1107/S160057672200499XenSmall-angle X-ray scattering: characterization of cubic Au nanoparticles using Debye's scattering formulaDeumer, J.Pauw, B.R.Marguet, S.Skroblin, D.Taché, O.Krumrey, M.Gollwitzer, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-15August 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papers552022-07-1510011600-5767med@iucr.org9934MoloVol: an easy-to-use program for analyzing cavities, volumes and surface areas of chemical structures
http://scripts.iucr.org/cgi-bin/paper?yr5079
Cavities are a ubiquitous feature of chemical structures encountered in various fields ranging from supramolecular chemistry to molecular biology. They are involved in the encapsulation, transport and transformation of guest molecules, thus necessitating a precise and accessible tool for estimating and visualizing their size and shape. MoloVol, a free user-parametrizable open-source software, developed for calculating a range of geometric features for both unit-cell and isolated structures, is presented here. MoloVol utilizes up to two spherical probes to define cavities, surfaces and volumes. The program was optimized by combining an octree data structure with voxel-partitioned space, allowing for even high-resolution protein structure calculations on reasonable timescales. MoloVol comes with a user-friendly graphic interface along with a command-line interface for high-throughput calculations. It was written in C++ and is available on Windows, macOS and Linux distributions.textCavities are a ubiquitous feature of chemical structures encountered in various fields ranging from supramolecular chemistry to molecular biology. They are involved in the encapsulation, transport and transformation of guest molecules, thus necessitating a precise and accessible tool for estimating and visualizing their size and shape. MoloVol, a free user-parametrizable open-source software, developed for calculating a range of geometric features for both unit-cell and isolated structures, is presented here. MoloVol utilizes up to two spherical probes to define cavities, surfaces and volumes. The program was optimized by combining an octree data structure with voxel-partitioned space, allowing for even high-resolution protein structure calculations on reasonable timescales. MoloVol comes with a user-friendly graphic interface along with a command-line interface for high-throughput calculations. It was written in C++ and is available on Windows, macOS and Linux distributions.urn:issn:1600-5767COMPUTER PROGRAMS; VOLUME; SURFACE AREA; CAVITIES; VOIDSMoloVol is a free program for calculating volumes and surface areas of molecules and their cavities.doi:10.1107/S1600576722004988enMoloVol: an easy-to-use program for analyzing cavities, volumes and surface areas of chemical structuresMaglic, J.B.Lavendomme, R.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-2310334med@iucr.org10441600-5767552022-06-23computer programshttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767August 2022The Radon transform as a tool for 3D reciprocal-space mapping of epitaxial microcrystals
http://scripts.iucr.org/cgi-bin/paper?nb5319
This work presents a new approach suitable for mapping reciprocal space in three dimensions with standard laboratory equipment and a typical X-ray diffraction setup. The method is based on symmetric and coplanar high-resolution X-ray diffraction, ideally realized using 2D X-ray pixel detectors. The processing of experimental data exploits the Radon transform commonly used in medical and materials science. It is shown that this technique can also be used for diffraction mapping in reciprocal space even if a highly collimated beam is not available. The application of the method is demonstrated for various types of epitaxial microcrystals on Si substrates. These comprise partially fused SiGe microcrystals that are tens of micrometres high, multiple-quantum-well structures grown on SiGe microcrystals and pyramid-shaped GaAs/Ge microcrystals on top of Si micropillars.textThis work presents a new approach suitable for mapping reciprocal space in three dimensions with standard laboratory equipment and a typical X-ray diffraction setup. The method is based on symmetric and coplanar high-resolution X-ray diffraction, ideally realized using 2D X-ray pixel detectors. The processing of experimental data exploits the Radon transform commonly used in medical and materials science. It is shown that this technique can also be used for diffraction mapping in reciprocal space even if a highly collimated beam is not available. The application of the method is demonstrated for various types of epitaxial microcrystals on Si substrates. These comprise partially fused SiGe microcrystals that are tens of micrometres high, multiple-quantum-well structures grown on SiGe microcrystals and pyramid-shaped GaAs/Ge microcrystals on top of Si micropillars.urn:issn:1600-5767RADON TRANSFORM; X-RAY DIFFRACTION; PATTERNED SI SUBSTRATES; GE MICROCRYSTALS; RECIPROCAL-SPACE MAPPINGDifferent types of epitaxially grown microcrystals on Si are used for the demonstration of 3D reciprocal-space map reconstruction using the Radon transform. With this technique, high-resolution diffraction reciprocal-space maps in three dimensions can be collected efficiently even with a standard laboratory setup.doi:10.1107/S1600576722004885enThe Radon transform as a tool for 3D reciprocal-space mapping of epitaxial microcrystalsMeduňa, M.Isa, F.Bressan, F.von Känel, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-05Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersAugust 20221600-5767med@iucr.org82342022-07-05551600-5767836Small-angle neutron scattering applied to low-dose neutron-irradiated Fe–Cr alloys and ferritic martensitic steel Eurofer97
http://scripts.iucr.org/cgi-bin/paper?uq5001
Ferritic/martensitic (F/M) Fe–Cr-based steels are candidates for applications in nuclear fission and fusion. Previous experimental results for neutron-irradiated binary Fe–Cr alloys and high-dose neutron-irradiated F/M steels contributed greatly to the understanding of the irradiation behaviour of these groups of materials. However, some details still need to be addressed. Such gaps are related to the effect of secondary alloying and impurity elements, such as Ni and Si, as well as the dose dependence at lower neutron doses [e.g. in the range 0.1–1 displacements per atom (dpa)]. This input is essential, for example, for multiscale modelling of irradiation effects or the evaluation of nuclear fission or fusion components at the first stages of operation. Using small-angle neutron scattering, three issues are addressed: (1) the effect of Cr undersaturation (5% Cr) and supersaturation (14% Cr) on the formation of irradiation-induced solute atom clusters/precipitates in low-dose neutron-irradiated Fe–Cr alloys in the presence of intentionally added levels of Ni, Si and P; (2) the effect of irradiation temperature (290°C versus 450°C); and (3) the effect of neutron dose in the range 0.06–0.6 dpa on the irradiation response of the reduced-activation F/M 9%Cr steel Eurofer97. The irradiation-enhanced formation of Cr-rich α′-phase particles was found to be the dominant effect for supersaturated Fe–14Cr–NiSiP at both irradiation temperatures. In contrast, α′ formation is impossible in Fe–5Cr–NiSiP, for which the pronounced irradiation effects observed at 0.1 dpa are mainly attributed to added Ni, Si and P. Finally, Eurofer97 exhibits an exceptionally weak irradiation effect at low neutron doses, the reasons for which are also considered.textFerritic/martensitic (F/M) Fe–Cr-based steels are candidates for applications in nuclear fission and fusion. Previous experimental results for neutron-irradiated binary Fe–Cr alloys and high-dose neutron-irradiated F/M steels contributed greatly to the understanding of the irradiation behaviour of these groups of materials. However, some details still need to be addressed. Such gaps are related to the effect of secondary alloying and impurity elements, such as Ni and Si, as well as the dose dependence at lower neutron doses [e.g. in the range 0.1–1 displacements per atom (dpa)]. This input is essential, for example, for multiscale modelling of irradiation effects or the evaluation of nuclear fission or fusion components at the first stages of operation. Using small-angle neutron scattering, three issues are addressed: (1) the effect of Cr undersaturation (5% Cr) and supersaturation (14% Cr) on the formation of irradiation-induced solute atom clusters/precipitates in low-dose neutron-irradiated Fe–Cr alloys in the presence of intentionally added levels of Ni, Si and P; (2) the effect of irradiation temperature (290°C versus 450°C); and (3) the effect of neutron dose in the range 0.06–0.6 dpa on the irradiation response of the reduced-activation F/M 9%Cr steel Eurofer97. The irradiation-enhanced formation of Cr-rich α′-phase particles was found to be the dominant effect for supersaturated Fe–14Cr–NiSiP at both irradiation temperatures. In contrast, α′ formation is impossible in Fe–5Cr–NiSiP, for which the pronounced irradiation effects observed at 0.1 dpa are mainly attributed to added Ni, Si and P. Finally, Eurofer97 exhibits an exceptionally weak irradiation effect at low neutron doses, the reasons for which are also considered.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; FE-CR ALLOYS; FERRITIC MARTENSITIC STEEL; NEUTRON IRRADIATIONCharacteristics of irradiation-induced nanofeatures derived from magnetic small-angle neutron scattering are reported for low-dose neutron-irradiated Fe–(5–14)Cr–NiSiP model alloys and the reduced-activation ferritic/martensitic 9Cr steel Eurofer97.doi:10.1107/S1600576722004800enSmall-angle neutron scattering applied to low-dose neutron-irradiated Fe–Cr alloys and ferritic martensitic steel Eurofer97Ulbricht, A.Heinemann, A.Bergner, F.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-15med@iucr.org7024552022-06-157121600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersAugust 20221600-5767Multivariate versus traditional quantitative phase analysis of X-ray powder diffraction and fluorescence data of mixtures showing preferred orientation and microabsorption
http://scripts.iucr.org/cgi-bin/paper?nb5320
In materials and earth science, but also in chemistry, pharmaceutics and engineering, the quantification of elements and crystal phases in solid samples is often essential for a full characterization of materials. The most frequently used techniques for this purpose are X-ray fluorescence (XRF) for elemental analysis and X-ray powder diffraction (XRPD) for phase analysis. In both methods, relations between signal and quantity do exist but they are expressed in terms of complex equations including many parameters related to both sample and instruments, and the dependence on the active element or phase amounts to be determined is convoluted among those parameters. Often real-life samples hold relations not suitable for a direct quantification and, therefore, estimations based only on the values of the relative intensities are affected by large errors. Preferred orientation (PO) and microabsorption (MA) in XRPD cannot usually be avoided, and traditional corrections in Rietveld refinement, such as the Brindley MA correction, are not able, in general, to restore the correct phase quantification. In this work, a multivariate approach, where principal component analysis is exploited alone or combined with regression methods, is used on XRPD profiles collected on ad hoc designed mixtures to face and overcome the typical problems of traditional approaches. Moreover, the partial or no known crystal structure (PONKCS) method was tested on XRPD data, as an example of a hybrid approach between Rietveld and multivariate approaches, to correct for the MA effect. Particular attention is given to the comparison and selection of both method and pre-process, the two key steps for good performance when applying multivariate methods to obtain reliable quantitative estimations from XRPD data, especially when MA and PO are present. A similar approach was tested on XRF data to deal with matrix effects and compared with the more classical fundamental-parameter approach. Finally, useful indications to overcome the difficulties of the general user in managing the parameters for a successful application of multivariate approaches for XRPD and XRF data analysis are given.textIn materials and earth science, but also in chemistry, pharmaceutics and engineering, the quantification of elements and crystal phases in solid samples is often essential for a full characterization of materials. The most frequently used techniques for this purpose are X-ray fluorescence (XRF) for elemental analysis and X-ray powder diffraction (XRPD) for phase analysis. In both methods, relations between signal and quantity do exist but they are expressed in terms of complex equations including many parameters related to both sample and instruments, and the dependence on the active element or phase amounts to be determined is convoluted among those parameters. Often real-life samples hold relations not suitable for a direct quantification and, therefore, estimations based only on the values of the relative intensities are affected by large errors. Preferred orientation (PO) and microabsorption (MA) in XRPD cannot usually be avoided, and traditional corrections in Rietveld refinement, such as the Brindley MA correction, are not able, in general, to restore the correct phase quantification. In this work, a multivariate approach, where principal component analysis is exploited alone or combined with regression methods, is used on XRPD profiles collected on ad hoc designed mixtures to face and overcome the typical problems of traditional approaches. Moreover, the partial or no known crystal structure (PONKCS) method was tested on XRPD data, as an example of a hybrid approach between Rietveld and multivariate approaches, to correct for the MA effect. Particular attention is given to the comparison and selection of both method and pre-process, the two key steps for good performance when applying multivariate methods to obtain reliable quantitative estimations from XRPD data, especially when MA and PO are present. A similar approach was tested on XRF data to deal with matrix effects and compared with the more classical fundamental-parameter approach. Finally, useful indications to overcome the difficulties of the general user in managing the parameters for a successful application of multivariate approaches for XRPD and XRF data analysis are given.urn:issn:1600-5767X-RAY POWDER DIFFRACTION; QUANTITATIVE PHASE ANALYSIS; RIETVELD REFINEMENT; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; X-RAY FLUORESCENCE; PREFERRED ORIENTATION; MICROABSORPTIONA case study on the use of both multivariate statistics and traditional methods for ill-conditioned powder samples (microabsorption and preferred orientation) using X-ray fluorescence and diffraction data is presented. Indications and recipes on how to exploit multivariate methods to limit and overcome the difficulties of real-world industrial samples and control the analytical error are given.doi:10.1107/S1600576722004708enMultivariate versus traditional quantitative phase analysis of X-ray powder diffraction and fluorescence data of mixtures showing preferred orientation and microabsorptionLopresti, M.Mangolini, B.Milanesio, M.Caliandro, R.Palin, L.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-07-054837med@iucr.org1600-57678502022-07-0555research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767August 2022A new model to describe small-angle neutron scattering from foams
http://scripts.iucr.org/cgi-bin/paper?ei5082
The modelling of scattering data from foams is very challenging due to the complex structure of foams and is therefore often reduced to the fitting of single peak positions or feature mimicking. This article presents a more elaborate model to describe the small-angle neutron scattering (SANS) data from foams. The model takes into account the geometry of the foam bubbles and is based on an incoherent superposition of the reflectivity curves arising from the foam films and the small-angle scattering (SAS) contribution from the plateau borders. The model is capable of describing the complete scattering curve of a foam stabilized by the standard cationic surfactant tetradecyltrimethylammonium bromide (C14TAB) with different water contents, i.e. different drainage states, and provides information on the thickness distribution of liquid films inside the foam. The mean film thickness decreases with decreasing water content because of drainage, from 28 to 22 nm, while the polydispersity increases. These results are in good agreement with the film thicknesses of individual horizontal foam films studied with a thin-film pressure balance.textThe modelling of scattering data from foams is very challenging due to the complex structure of foams and is therefore often reduced to the fitting of single peak positions or feature mimicking. This article presents a more elaborate model to describe the small-angle neutron scattering (SANS) data from foams. The model takes into account the geometry of the foam bubbles and is based on an incoherent superposition of the reflectivity curves arising from the foam films and the small-angle scattering (SAS) contribution from the plateau borders. The model is capable of describing the complete scattering curve of a foam stabilized by the standard cationic surfactant tetradecyltrimethylammonium bromide (C14TAB) with different water contents, i.e. different drainage states, and provides information on the thickness distribution of liquid films inside the foam. The mean film thickness decreases with decreasing water content because of drainage, from 28 to 22 nm, while the polydispersity increases. These results are in good agreement with the film thicknesses of individual horizontal foam films studied with a thin-film pressure balance.urn:issn:1600-5767FOAMS; FOAM FILMS; SMALL-ANGLE NEUTRON SCATTERING; NEUTRON REFLECTOMETRY; THIN-FILM PRESSURE BALANCESA new model for the interpretation of small-angle neutron scattering data from aqueous foams is presented and validated using experimental data from a model foam system.doi:10.1107/S1600576722004691enA new model to describe small-angle neutron scattering from foamsKühnhammer, M.Braun, L.Ludwig, M.Soltwedel, O.Chiappisi, L.Klitzing, R. vonInternational Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-231600-57677682022-06-23557584med@iucr.org1600-5767August 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn–Hilliard-type simulations using auto-encoder networks
http://scripts.iucr.org/cgi-bin/paper?vh5158
Machine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid–liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn–Hilliard-type simulations of liquid–liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm. The method presented here is a first step towards handling large amounts of dynamic data measured at high-brilliance synchrotron and X-ray free-electron laser sources, facilitating fast comparison with phase field models of phase separation.textMachine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid–liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn–Hilliard-type simulations of liquid–liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm. The method presented here is a first step towards handling large amounts of dynamic data measured at high-brilliance synchrotron and X-ray free-electron laser sources, facilitating fast comparison with phase field models of phase separation.urn:issn:1600-5767PROTEIN DYNAMICS; X-RAY PHOTON CORRELATION SPECTROSCOPY; XPCS; CAHN-HILLIARD; AUTO-ENCODERS; MACHINE LEARNINGTwo-time correlation maps are classified in a simulation framework using an auto-encoder network.doi:10.1107/S1600576722004435enAutomated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn–Hilliard-type simulations using auto-encoder networksTimmermann, S.Starostin, V.Girelli, A.Ragulskaya, A.Rahmann, H.Reiser, M.Begam, N.Randolph, L.Sprung, M.Westermeier, F.Zhang, F.Schreiber, F.Gutt, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-15August 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papers552022-06-157571600-5767med@iucr.org4751The effect of transverse wavefront width on specular neutron reflection
http://scripts.iucr.org/cgi-bin/paper?ge5117
In the analysis of neutron scattering measurements of condensed matter structure, it normally suffices to treat the incident and scattered neutron beams as if composed of incoherent distributions of plane waves with wavevectors of different magnitudes and directions that are taken to define an instrumental resolution. However, despite the wide-ranging applicability of this conventional treatment, there are cases, such as specular neutron reflectometry, in which the structural length scales of the scattering object require that the wavefunction of an individual neutron in the beam be described by a spatially localized packet – in particular with respect to the transverse extent of its wavefronts (i.e. normal to the packet's mean direction of propagation). It is shown in the present work that neutron diffraction patterns observed for periodic transmission phase gratings, as well as specular reflection measurements from patterned thin films with repeat units of the order of micrometres, can be accurately described by associating an individual neutron with a wave packet and treating a beam as a collection of independent packets. In these cases, accurate analysis requires that the transverse spatial extent of a neutron packet wavefront be accounted for in addition to the angular divergence of the beam that is characterized by a distribution of packet mean wavevector directions. It is shown how a measure of the effective transverse spatial extent of the neutron packet – over which its wavefronts are of sufficient uniformity to produce coherent scattering – can be determined by employing reference diffraction gratings and patterned thin films of known structure and composition.textIn the analysis of neutron scattering measurements of condensed matter structure, it normally suffices to treat the incident and scattered neutron beams as if composed of incoherent distributions of plane waves with wavevectors of different magnitudes and directions that are taken to define an instrumental resolution. However, despite the wide-ranging applicability of this conventional treatment, there are cases, such as specular neutron reflectometry, in which the structural length scales of the scattering object require that the wavefunction of an individual neutron in the beam be described by a spatially localized packet – in particular with respect to the transverse extent of its wavefronts (i.e. normal to the packet's mean direction of propagation). It is shown in the present work that neutron diffraction patterns observed for periodic transmission phase gratings, as well as specular reflection measurements from patterned thin films with repeat units of the order of micrometres, can be accurately described by associating an individual neutron with a wave packet and treating a beam as a collection of independent packets. In these cases, accurate analysis requires that the transverse spatial extent of a neutron packet wavefront be accounted for in addition to the angular divergence of the beam that is characterized by a distribution of packet mean wavevector directions. It is shown how a measure of the effective transverse spatial extent of the neutron packet – over which its wavefronts are of sufficient uniformity to produce coherent scattering – can be determined by employing reference diffraction gratings and patterned thin films of known structure and composition.urn:issn:1600-5767SPECULAR NEUTRON REFLECTIVITY; WAVE PACKETS; TRANSVERSE COHERENT EXTENTThe role that the transverse coherent extent of a neutron packet wavefunction plays in the analysis of specular neutron reflectivity is examined both theoretically and experimentally. It is shown how, in practice, the transverse coherent extent of an individual neutron packet wavefront can be measured and distinguished from the effects of geometrical angular divergence for a beam composed of a collection of such independent packets.doi:10.1107/S160057672200440XenThe effect of transverse wavefront width on specular neutron reflectionMajkrzak, C.F.Berk, N.F.Maranville, B.B.Dura, J.A.Jach, T.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-231600-57678122022-06-23554787med@iucr.org1600-5767August 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/Small-angle neutron scattering by spatially inhomogeneous ferromagnets with a nonzero average uniaxial anisotropy
http://scripts.iucr.org/cgi-bin/paper?uz5002
Micromagnetic small-angle neutron scattering theory is well established for analyzing spin-misalignment scattering data of bulk ferromagnets. Here, this theory is extended to allow for a global uniaxial magnetic anisotropy (texture) of the material, in addition to the already included random zero-average local anisotropy. Macroscopic cross sections and spin-misalignment response functions are computed analytically for several practically relevant mutual anisotropy and external magnetic field orientations in both parallel and perpendicular scattering geometries for field magnitudes both above and below the rotational saturation. Some of these expressions are tested on published experimental data of magnetic-field-annealed Vitroperm and plastically deformed Ni, allowing determination of the corresponding global uniaxial anisotropy quality factors.textMicromagnetic small-angle neutron scattering theory is well established for analyzing spin-misalignment scattering data of bulk ferromagnets. Here, this theory is extended to allow for a global uniaxial magnetic anisotropy (texture) of the material, in addition to the already included random zero-average local anisotropy. Macroscopic cross sections and spin-misalignment response functions are computed analytically for several practically relevant mutual anisotropy and external magnetic field orientations in both parallel and perpendicular scattering geometries for field magnitudes both above and below the rotational saturation. Some of these expressions are tested on published experimental data of magnetic-field-annealed Vitroperm and plastically deformed Ni, allowing determination of the corresponding global uniaxial anisotropy quality factors.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; SANS; MICROMAGNETICS; ANISOTROPYMacroscopic spin-misalignment small-angle neutron scattering cross sections and response functions are computed analytically for a material with global uniaxial magnetic anisotropy (texture). The resulting expressions are tested against previously published experimental data.doi:10.1107/S160057672200437XenSmall-angle neutron scattering by spatially inhomogeneous ferromagnets with a nonzero average uniaxial anisotropyZaporozhets, V.D.Oba, Y.Michels, A.Metlov, K.L.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-011600-5767June 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-57676002022-06-01555923med@iucr.orgRobust approaches for model-free small-angle scattering data analysis
http://scripts.iucr.org/cgi-bin/paper?uz5001
The small-angle neutron scattering data of nanostructured magnetic samples contain information regarding their chemical and magnetic properties. Often, the first step to access characteristic magnetic and structural length scales is a model-free investigation. However, due to measurement uncertainties and a restricted q range, a direct Fourier transform usually fails and results in ambiguous distributions. To circumvent these problems, different methods have been introduced to derive regularized, more stable correlation functions, with the indirect Fourier transform being the most prominent approach. Here, the indirect Fourier transform is compared with the singular value decomposition and an iterative algorithm. These approaches are used to determine the correlation function from magnetic small-angle neutron scattering data of a powder sample of iron oxide nanoparticles; it is shown that with all three methods, in principle, the same correlation function can be derived. Each method has certain advantages and disadvantages, and thus the recommendation is to combine these three approaches to obtain robust results.textThe small-angle neutron scattering data of nanostructured magnetic samples contain information regarding their chemical and magnetic properties. Often, the first step to access characteristic magnetic and structural length scales is a model-free investigation. However, due to measurement uncertainties and a restricted q range, a direct Fourier transform usually fails and results in ambiguous distributions. To circumvent these problems, different methods have been introduced to derive regularized, more stable correlation functions, with the indirect Fourier transform being the most prominent approach. Here, the indirect Fourier transform is compared with the singular value decomposition and an iterative algorithm. These approaches are used to determine the correlation function from magnetic small-angle neutron scattering data of a powder sample of iron oxide nanoparticles; it is shown that with all three methods, in principle, the same correlation function can be derived. Each method has certain advantages and disadvantages, and thus the recommendation is to combine these three approaches to obtain robust results.urn:issn:1600-5767SMALL-ANGLE SCATTERING; CORRELATION FUNCTIONS; FOURIER TRANSFORM; MAGNETIC NANOPARTICLES; MODULATION OF INTENSITY WITH ZERO EFFORT; MIEZE; RESEDAThree different approaches are compared for determination of the correlation function from the small-angle neutron scattering data of a powder sample of iron oxide nanoparticles.doi:10.1107/S1600576722004356enRobust approaches for model-free small-angle scattering data analysisBender, P.Honecker, D.Bersweiler, M.Costo, R.Kahmann, T.Ludwig, F.Leiner, J.Jochum, J.K.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-28med@iucr.org58632022-05-28551600-5767591Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersJune 20221600-5767Insights into a dual-phase steel microstructure using EBSD and image-processing-based workflow
http://scripts.iucr.org/cgi-bin/paper?nb5326
Quantitative metallography to understand the morphology of different crystallographic phases in a material often rests on the segmentation and classification of electron backscatter diffraction (EBSD) maps. Image analysis offers rich toolboxes to perform such tasks based on `scalar' images. Embracing the entire wealth of information provided by crystallography, operations such as erosion, dilation, interpolation, smoothing and segmentation require generalizations to do justice to the very nature of crystal orientations (e.g. preserving properties like frame indifference). The present study gives such extensions based on quaternion representation of crystal orientations. A dual-phase stainless steel specimen is used to illustrate the different steps of such a procedure.textQuantitative metallography to understand the morphology of different crystallographic phases in a material often rests on the segmentation and classification of electron backscatter diffraction (EBSD) maps. Image analysis offers rich toolboxes to perform such tasks based on `scalar' images. Embracing the entire wealth of information provided by crystallography, operations such as erosion, dilation, interpolation, smoothing and segmentation require generalizations to do justice to the very nature of crystal orientations (e.g. preserving properties like frame indifference). The present study gives such extensions based on quaternion representation of crystal orientations. A dual-phase stainless steel specimen is used to illustrate the different steps of such a procedure.urn:issn:1600-5767ELECTRON BACKSCATTER DIFFRACTION (EBSD); ORIENTATIONS; DUPLEX STAINLESS STEELS; SEGMENTATION; CLASSIFICATION; IMAGE ANALYSIS; MICROSTRUCTURES; CRYSTALLOGRAPHIC PHASESIn this article, an image-analysis-based method is applied to electron backscatter diffraction (EBSD) data in order to recover specific properties in a complex microstructure, and some new dedicated tools are developed and compared with existing methods.doi:10.1107/S1600576722004265enInsights into a dual-phase steel microstructure using EBSD and image-processing-based workflowMollens, M.Roux, S.Hild, F.Guery, A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-016013med@iucr.org6101600-5767552022-06-01research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767June 2022LaueNN: neural-network-based hkl recognition of Laue spots and its application to polycrystalline materials
http://scripts.iucr.org/cgi-bin/paper?nb5322
A feed-forward neural-network-based model is presented to index, in real time, the diffraction spots recorded during synchrotron X-ray Laue microdiffraction experiments. Data dimensionality reduction is applied to extract physical 1D features from the 2D X-ray diffraction Laue images, thereby making it possible to train a neural network on the fly for any crystal system. The capabilities of the LaueNN model are illustrated through three examples: a two-phase nanostructure, a textured high-symmetry specimen deformed in situ and a polycrystalline low-symmetry material. This work provides a novel way to efficiently index Laue spots in simple and complex recorded images in <1 s, thereby opening up avenues for the realization of real-time analysis of synchrotron Laue diffraction data.textA feed-forward neural-network-based model is presented to index, in real time, the diffraction spots recorded during synchrotron X-ray Laue microdiffraction experiments. Data dimensionality reduction is applied to extract physical 1D features from the 2D X-ray diffraction Laue images, thereby making it possible to train a neural network on the fly for any crystal system. The capabilities of the LaueNN model are illustrated through three examples: a two-phase nanostructure, a textured high-symmetry specimen deformed in situ and a polycrystalline low-symmetry material. This work provides a novel way to efficiently index Laue spots in simple and complex recorded images in <1 s, thereby opening up avenues for the realization of real-time analysis of synchrotron Laue diffraction data.urn:issn:1600-5767SYNCHROTRON X-RAY LAUE MICRODIFFRACTION; NEURAL NETWORKS; HKL RECOGNITIONAn efficient neural network architecture to index Laue spots in synchrotron Laue microdiffraction patterns is presented. The efficiency and predictive capability of the model makes it applicable to real-time indexing of Laue microdiffraction data.doi:10.1107/S1600576722004198enLaueNN: neural-network-based hkl recognition of Laue spots and its application to polycrystalline materialsPurushottam Raj Purohit, R.R.P.Tardif, S.Castelnau, O.Eymery, J.Guinebretière, R.Robach, O.Ors, T.Micha, J.-S.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-15August 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papers2022-06-15551600-5767750med@iucr.org7374Optimizing experimental design in neutron reflectometry
http://scripts.iucr.org/cgi-bin/paper?ge5107
Using the Fisher information (FI), the design of neutron reflectometry experiments can be optimized, leading to greater confidence in parameters of interest and better use of experimental time [Durant, Wilkins, Butler & Cooper (2021). J. Appl. Cryst. 54, 1100–1110]. In this work, the FI is utilized in optimizing the design of a wide range of reflectometry experiments. Two lipid bilayer systems are investigated to determine the optimal choice of measurement angles and liquid contrasts, in addition to the ratio of the total counting time that should be spent measuring each condition. The reduction in parameter uncertainties with the addition of underlayers to these systems is then quantified, using the FI, and validated through the use of experiment simulation and Bayesian sampling methods. For a `one-shot' measurement of a degrading lipid monolayer, it is shown that the common practice of measuring null-reflecting water is indeed optimal, but that the optimal measurement angle is dependent on the deuteration state of the monolayer. Finally, the framework is used to demonstrate the feasibility of measuring magnetic signals as small as 0.01 μB per atom in layers only 20 Å thick, given the appropriate experimental design, and that the time to reach a given level of confidence in the small magnetic moment is quantifiable.textUsing the Fisher information (FI), the design of neutron reflectometry experiments can be optimized, leading to greater confidence in parameters of interest and better use of experimental time [Durant, Wilkins, Butler & Cooper (2021). J. Appl. Cryst. 54, 1100–1110]. In this work, the FI is utilized in optimizing the design of a wide range of reflectometry experiments. Two lipid bilayer systems are investigated to determine the optimal choice of measurement angles and liquid contrasts, in addition to the ratio of the total counting time that should be spent measuring each condition. The reduction in parameter uncertainties with the addition of underlayers to these systems is then quantified, using the FI, and validated through the use of experiment simulation and Bayesian sampling methods. For a `one-shot' measurement of a degrading lipid monolayer, it is shown that the common practice of measuring null-reflecting water is indeed optimal, but that the optimal measurement angle is dependent on the deuteration state of the monolayer. Finally, the framework is used to demonstrate the feasibility of measuring magnetic signals as small as 0.01 μB per atom in layers only 20 Å thick, given the appropriate experimental design, and that the time to reach a given level of confidence in the small magnetic moment is quantifiable.urn:issn:1600-5767NEUTRON REFLECTIVITY; NEUTRON REFLECTOMETRY; EXPERIMENTAL DESIGN; FISHER INFORMATION; INFORMATION THEORYAn approach for optimal experimental design of neutron reflectivity experiments using metrics derived from the Fisher information is presented. This is demonstrated on a range of systems including lipid bilayers and magnetic heterostructures, and it is shown that small (or large) changes to the experimental setup can result in drastically reduced experimental count times.doi:10.1107/S1600576722003831enOptimizing experimental design in neutron reflectometryDurant, J.H.Wilkins, L.Cooper, J.F.K.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-06-23med@iucr.org4769552022-06-237811600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersAugust 20221600-5767Automating ALCHEMI at the nano-scale using software compatible with PC-controlled transmission electron microscopy
http://scripts.iucr.org/cgi-bin/paper?jl5035
Atom location by channeling-enhanced microanalysis (ALCHEMI) is a technique to obtain atom-site-specific information on constituent elements in a crystalline sample by acquiring a set of core electron transition spectra while tilting the incident beam. This methodology has been extended to a more quantitative technique called high-angular-resolution electron-channeled X-ray/electron spectroscopy (HARECXS/HARECES). There is a growing demand for analyzing smaller areas, such as small particles and multilayers. However, the minimum size of a region of interest probed by the present hardware-assisted automated HARECXS/HARECES scheme is limited to no smaller than 1 µm, not only by the size of the electron probe and its convergence angle but also by the movement of the probe position associated with the beam tilt due to aberrations of the hardware system. Herein, QED (quantitative electron diffraction), a commercial plug-in working on an integrated software platform, Gatan Microscopy Suite, was modified to enable the calibration and control of the probe to resolve the aforementioned limitation. In addition, a more sophisticated scheme for QED was developed to realize the ALCHEMI method for energy-dispersive X-ray spectroscopy, electron energy-loss spectroscopy or both concurrently. This allows access to ALCHEMI and its derivative methods, automatically executed with any type of current PC-controlled commercial microscope on an area as small as 30 nm, without modifying the hardware system.textAtom location by channeling-enhanced microanalysis (ALCHEMI) is a technique to obtain atom-site-specific information on constituent elements in a crystalline sample by acquiring a set of core electron transition spectra while tilting the incident beam. This methodology has been extended to a more quantitative technique called high-angular-resolution electron-channeled X-ray/electron spectroscopy (HARECXS/HARECES). There is a growing demand for analyzing smaller areas, such as small particles and multilayers. However, the minimum size of a region of interest probed by the present hardware-assisted automated HARECXS/HARECES scheme is limited to no smaller than 1 µm, not only by the size of the electron probe and its convergence angle but also by the movement of the probe position associated with the beam tilt due to aberrations of the hardware system. Herein, QED (quantitative electron diffraction), a commercial plug-in working on an integrated software platform, Gatan Microscopy Suite, was modified to enable the calibration and control of the probe to resolve the aforementioned limitation. In addition, a more sophisticated scheme for QED was developed to realize the ALCHEMI method for energy-dispersive X-ray spectroscopy, electron energy-loss spectroscopy or both concurrently. This allows access to ALCHEMI and its derivative methods, automatically executed with any type of current PC-controlled commercial microscope on an area as small as 30 nm, without modifying the hardware system.urn:issn:1600-5767ELECTRON CHANNELING; SITE-SELECTIVE MICROANALYSIS; NANO-SCALE ANALYSIS; AUTOMATED PROBE SHIFT CORRECTION; ENERGY-DISPERSIVE X-RAY SPECTROSCOPY; ELECTRON ENERGY-LOSS SPECTROSCOPYA software-control system has been developed that enables access to site-selective energy-dispersive X-ray spectroscopy/electron energy-loss spectroscopy measurements from a sub-micrometre area by automatically and concurrently tilting the beam and acquiring spectra.doi:10.1107/S1600576722003818enAutomating ALCHEMI at the nano-scale using software compatible with PC-controlled transmission electron microscopyIshizuka, A.Ohtsuka, M.Muto, S.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-252022-05-25551600-5767557med@iucr.org5513June 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersSAXSDOG: open software for real-time azimuthal integration of 2D scattering images
http://scripts.iucr.org/cgi-bin/paper?jl5036
In situ small- and wide-angle scattering experiments at synchrotrons often result in massive quantities of data within just seconds. Especially during such beamtimes, processing of the acquired data online, without appreciable delay, is key to obtaining feedback on the failure or success of the experiment. This had led to the development of SAXSDOG, a Python-based environment for real-time azimuthal integration of large-area scattering images. The software is primarily designed for dedicated data pipelines: once a scattering image is transferred from the detector onto the storage unit, it is automatically integrated and pre-evaluated using integral parameters within milliseconds. The control and configuration of the underlying server-based processes is achieved via a graphical user interface, SAXSLEASH, which visualizes the resulting 1D data together with integral classifiers in real time. SAXSDOG further includes a portable `take-home' version for users that runs on standalone computers, enabling its use in laboratories or at the preferred workspace.textIn situ small- and wide-angle scattering experiments at synchrotrons often result in massive quantities of data within just seconds. Especially during such beamtimes, processing of the acquired data online, without appreciable delay, is key to obtaining feedback on the failure or success of the experiment. This had led to the development of SAXSDOG, a Python-based environment for real-time azimuthal integration of large-area scattering images. The software is primarily designed for dedicated data pipelines: once a scattering image is transferred from the detector onto the storage unit, it is automatically integrated and pre-evaluated using integral parameters within milliseconds. The control and configuration of the underlying server-based processes is achieved via a graphical user interface, SAXSLEASH, which visualizes the resulting 1D data together with integral classifiers in real time. SAXSDOG further includes a portable `take-home' version for users that runs on standalone computers, enabling its use in laboratories or at the preferred workspace.urn:issn:1600-5767COMPUTER PROGRAMS; SMALL-ANGLE X-RAY SCATTERING; SAXS; AZIMUTHAL INTEGRATION; SAXSDOGThe open-source software SAXSDOG performs a real-time azimuthal integration of 2D scattering images reaching peak integration performance at current hardware limits.doi:10.1107/S1600576722003685enSAXSDOG: open software for real-time azimuthal integration of 2D scattering imagesBurian, M.Meisenbichler, C.Naumenko, D.Amenitsch, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-282022-05-28551600-5767685med@iucr.org3677June 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/computer programsOptimization and inference of bin widths for histogramming inelastic neutron scattering spectra
http://scripts.iucr.org/cgi-bin/paper?in5064
A data-driven bin-width optimization for the histograms of measured data sets based on inhomogeneous Poisson processes was developed in a neurophysiology study [Shimazaki & Shinomoto (2007). Neural Comput. 19, 1503–1527], and a subsequent study [Muto, Sakamoto, Matsuura, Arima & Okada (2019). J. Phys. Soc. Jpn, 88, 044002] proposed its application to inelastic neutron scattering (INS) data. In the present study, the results of the method on experimental INS time-of-flight data collected under different measurement conditions from a copper single crystal are validated. The extrapolation of the statistics on a given data set to other data sets with different total counts precisely infers the optimal bin widths on the latter. The histograms with the optimized bin widths statistically verify two fine-spectral-feature examples in the energy and momentum transfer cross sections: (i) the existence of phonon band gaps; and (ii) the number of plural phonon branches located close to each other. This indicates that the applied method helps in the efficient and rigorous observation of spectral structures important in physics and materials science like novel forms of magnetic excitation and phonon states correlated to thermal conductivities.textA data-driven bin-width optimization for the histograms of measured data sets based on inhomogeneous Poisson processes was developed in a neurophysiology study [Shimazaki & Shinomoto (2007). Neural Comput. 19, 1503–1527], and a subsequent study [Muto, Sakamoto, Matsuura, Arima & Okada (2019). J. Phys. Soc. Jpn, 88, 044002] proposed its application to inelastic neutron scattering (INS) data. In the present study, the results of the method on experimental INS time-of-flight data collected under different measurement conditions from a copper single crystal are validated. The extrapolation of the statistics on a given data set to other data sets with different total counts precisely infers the optimal bin widths on the latter. The histograms with the optimized bin widths statistically verify two fine-spectral-feature examples in the energy and momentum transfer cross sections: (i) the existence of phonon band gaps; and (ii) the number of plural phonon branches located close to each other. This indicates that the applied method helps in the efficient and rigorous observation of spectral structures important in physics and materials science like novel forms of magnetic excitation and phonon states correlated to thermal conductivities.urn:issn:1600-5767DATA-DRIVEN SCIENCE; HISTOGRAM BIN-WIDTH OPTIMIZATION; INELASTIC NEUTRON SCATTERING; INHOMOGENEOUS POISSON POINT PROCESSES; STATISTICAL SPECTRAL-FEATURE VALIDATION; EXPERIMENT DESIGNBin widths for histograms of inelastic neutron scattering (INS) spectra are optimized for a given data set and inferred for other data sets of different total counts. After verification of the results on INS experimental and simulated data sets, utilization of the method and further improvement are discussed.doi:10.1107/S1600576722003624enOptimization and inference of bin widths for histogramming inelastic neutron scattering spectraTatsumi, K.Inamura, Y.Kofu, M.Kiyanagi, R.Shimazaki, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-25med@iucr.org5333552022-05-255431600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papersJune 20221600-5767pdCIFplotter: visualizing powder diffraction data in pdCIF format
http://scripts.iucr.org/cgi-bin/paper?yr5087
A description is given of the program pdCIFplotter. This program is used for visualizing powder diffraction data and models published in powder CIF format (pdCIF). In particular, support for the visualization of multi-pattern data sets, such as in situ diffraction experiments, is provided by means of stack and surface plots. pdCIFplotter is written in Python 3 and can run wherever a compatible runtime is available. TOPAS macros for the production of pdCIF files are also presented.textA description is given of the program pdCIFplotter. This program is used for visualizing powder diffraction data and models published in powder CIF format (pdCIF). In particular, support for the visualization of multi-pattern data sets, such as in situ diffraction experiments, is provided by means of stack and surface plots. pdCIFplotter is written in Python 3 and can run wherever a compatible runtime is available. TOPAS macros for the production of pdCIF files are also presented.urn:issn:1600-5767POWDER DIFFRACTION; DATA VISUALIZATION; CIF; PDCIFA program is described for visualizing powder diffraction data and models published in powder CIF format.doi:10.1107/S1600576722003478enpdCIFplotter: visualizing powder diffraction data in pdCIF formatRowles, M.R.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-25552022-05-256371600-5767med@iucr.org3631June 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyCIF applicationsUniaxial polarization analysis of bulk ferromagnets: theory and first experimental results
http://scripts.iucr.org/cgi-bin/paper?un5004
On the basis of Brown's static equations of micromagnetics, the uniaxial polarization of the scattered neutron beam of a bulk magnetic material is computed. The approach considers a Hamiltonian that takes into account the isotropic exchange interaction, the antisymmetric Dzyaloshinskii–Moriya interaction, magnetic anisotropy, the dipole–dipole interaction and the effect of an applied magnetic field. In the high-field limit, the solutions for the magnetization Fourier components are used to obtain closed-form results for the spin-polarized small-angle neutron scattering (SANS) cross sections and the ensuing polarization. The theoretical expressions are compared with experimental data on a soft magnetic nanocrystalline alloy. The micromagnetic SANS theory provides a general framework for polarized real-space neutron methods, and it may open up a new avenue for magnetic neutron data analysis on magnetic microstructures.textOn the basis of Brown's static equations of micromagnetics, the uniaxial polarization of the scattered neutron beam of a bulk magnetic material is computed. The approach considers a Hamiltonian that takes into account the isotropic exchange interaction, the antisymmetric Dzyaloshinskii–Moriya interaction, magnetic anisotropy, the dipole–dipole interaction and the effect of an applied magnetic field. In the high-field limit, the solutions for the magnetization Fourier components are used to obtain closed-form results for the spin-polarized small-angle neutron scattering (SANS) cross sections and the ensuing polarization. The theoretical expressions are compared with experimental data on a soft magnetic nanocrystalline alloy. The micromagnetic SANS theory provides a general framework for polarized real-space neutron methods, and it may open up a new avenue for magnetic neutron data analysis on magnetic microstructures.urn:issn:1600-5767POLARIZED NEUTRON SCATTERING; UNIAXIAL POLARIZATION ANALYSIS; SMALL-ANGLE NEUTRON SCATTERING; MICROMAGNETICS; MAGNETIC NANOCOMPOSITESBased on the continuum theory of micromagnetics, theoretical expressions for the polarization of the scattered neutron beam in uniaxial small-angle neutron scattering have been derived and their predictions tested by analyzing experimental data on a soft magnetic nanocrystalline alloy. The here-presented theoretical framework forms the basis for polarized real-space methods such as spin-echo small-angle neutron scattering, spin-echo modulated small-angle neutron scattering and polarized neutron dark-field contrast imaging.doi:10.1107/S1600576722003508enUniaxial polarization analysis of bulk ferromagnets: theory and first experimental resultsMalyeyev, A.Titov, I.Dewhurst, C.Suzuki, K.Honecker, D.Michels, A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-28research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767June 20223569med@iucr.org1600-57675852022-05-2855Towards kilohertz synchrotron coherent diffractive imaging
http://scripts.iucr.org/cgi-bin/paper?yr5083
X-ray coherent diffractive imaging (CDI) techniques have been applied with widespread impact to study nanoscale material properties. New fast framing detectors may reveal dynamics that occur at millisecond timescales. This work demonstrates by simulation that kilohertz synchrotron CDI is possible, by making use of redundant information from static parts of the image field. Reconstruction ambiguities are strongly suppressed by applying a spatiotemporal constraint, obviating the need for slower methods of introducing diversity such as ptychography. The relationship between image fidelity and time resolution is investigated and shows that dynamics an order of magnitude faster can be reconstructed, compared with conventional CDI.textX-ray coherent diffractive imaging (CDI) techniques have been applied with widespread impact to study nanoscale material properties. New fast framing detectors may reveal dynamics that occur at millisecond timescales. This work demonstrates by simulation that kilohertz synchrotron CDI is possible, by making use of redundant information from static parts of the image field. Reconstruction ambiguities are strongly suppressed by applying a spatiotemporal constraint, obviating the need for slower methods of introducing diversity such as ptychography. The relationship between image fidelity and time resolution is investigated and shows that dynamics an order of magnitude faster can be reconstructed, compared with conventional CDI.urn:issn:1600-5767COHERENT DIFFRACTIVE IMAGING; COHERENT X-RAY IMAGING; KHZ X-RAY IMAGING; NANOSCALE DYNAMICS; PHASE RETRIEVALThis work shows how spatiotemporal redundancy can overcome the twin-image stagnation mode in coherent diffractive imaging, and explores the relationship between detector frame rate and signal-to-noise ratio in the application of imaging nanoscale dynamic behaviour at kHz frame rates.doi:10.1107/S1600576722003466enTowards kilohertz synchrotron coherent diffractive imagingHinsley, G.N.Kewish, C.M.van Riessen, G.A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-081600-57674832022-05-08553479med@iucr.org1600-5767June 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/DISEMM: a tool for the investigation of elasto-plastic behaviour on polycrystalline samples using X-ray and neutron diffraction
http://scripts.iucr.org/cgi-bin/paper?in5063
The software DISEMM is designed to analyse diffraction data from in situ loading experiments on polycrystalline samples for the determination of single-crystal elastic constants (SECs) and elasto-plastic self-consistent (EPSC) modelling of lattice strains. The SECs can be obtained from powder-diffraction elastic constants using a variety of grain-to-grain interaction models, namely Voigt, Reuss, Hill, Kröner, de Wit and Matthies approaches. The texture of the polycrystalline sample can be taken into account using the orientation distribution function of the grains. For the analysis of two-phase materials, an approach was implemented to calculate the stress transfer between the phases and its impact on the apparent elastic properties. The calculated SECs can then be used as input into the EPSC model, which allows the user to predict the elasto-plastic behaviour for comparison with experimental lattice strain data and to investigate the activation of individual slip systems. For this purpose, critical resolved shear stresses and hardening parameters are adapted iteratively.textThe software DISEMM is designed to analyse diffraction data from in situ loading experiments on polycrystalline samples for the determination of single-crystal elastic constants (SECs) and elasto-plastic self-consistent (EPSC) modelling of lattice strains. The SECs can be obtained from powder-diffraction elastic constants using a variety of grain-to-grain interaction models, namely Voigt, Reuss, Hill, Kröner, de Wit and Matthies approaches. The texture of the polycrystalline sample can be taken into account using the orientation distribution function of the grains. For the analysis of two-phase materials, an approach was implemented to calculate the stress transfer between the phases and its impact on the apparent elastic properties. The calculated SECs can then be used as input into the EPSC model, which allows the user to predict the elasto-plastic behaviour for comparison with experimental lattice strain data and to investigate the activation of individual slip systems. For this purpose, critical resolved shear stresses and hardening parameters are adapted iteratively.urn:issn:1600-5767SINGLE-CRYSTAL ELASTIC CONSTANTS; ELASTO-PLASTIC SELF-CONSISTENT (EPSC) MODELLING; DISEMM; MECHANICAL MODELLINGDISEMM is a software tool to analyse neutron or X-ray diffraction data on polycrystalline samples collected under mechanical load, combining the determination of single-crystal elastic constants and the methods of elasto-plastic self-consistent modelling in one package.doi:10.1107/S1600576722003314enDISEMM: a tool for the investigation of elasto-plastic behaviour on polycrystalline samples using X-ray and neutron diffractionHeldmann, A.Hofmann, M.Hoelzel, M.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-08Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/computer programsJune 20221600-5767med@iucr.org65632022-05-08551600-5767662A multipurpose laboratory diffractometer for operando powder X-ray diffraction investigations of energy materials
http://scripts.iucr.org/cgi-bin/paper?ap5043
Laboratory X-ray diffractometers are among the most widespread instruments in research laboratories around the world and are commercially available in different configurations and setups from various manufacturers. Advances in detector technology and X-ray sources push the data quality of in-house diffractometers and enable the collection of time-resolved scattering data during operando experiments. Here, the design and installation of a custom-built multipurpose laboratory diffractometer for the crystallographic characterization of battery materials are reported. The instrument is based on a Huber six-circle diffractometer equipped with a molybdenum microfocus rotating anode with 2D collimated parallel-beam X-ray optics and an optional two-bounce crystal monochromator. Scattered X-rays are detected with a hybrid single-photon-counting area detector (PILATUS 300K-W). An overview of the different diffraction setups together with the main features of the beam characteristics is given. Example case studies illustrate the flexibility of the research instrument for time-resolved operando powder X-ray diffraction experiments as well as the possibility to collect higher-resolution data suitable for diffraction line-profile analysis.textLaboratory X-ray diffractometers are among the most widespread instruments in research laboratories around the world and are commercially available in different configurations and setups from various manufacturers. Advances in detector technology and X-ray sources push the data quality of in-house diffractometers and enable the collection of time-resolved scattering data during operando experiments. Here, the design and installation of a custom-built multipurpose laboratory diffractometer for the crystallographic characterization of battery materials are reported. The instrument is based on a Huber six-circle diffractometer equipped with a molybdenum microfocus rotating anode with 2D collimated parallel-beam X-ray optics and an optional two-bounce crystal monochromator. Scattered X-rays are detected with a hybrid single-photon-counting area detector (PILATUS 300K-W). An overview of the different diffraction setups together with the main features of the beam characteristics is given. Example case studies illustrate the flexibility of the research instrument for time-resolved operando powder X-ray diffraction experiments as well as the possibility to collect higher-resolution data suitable for diffraction line-profile analysis.urn:issn:1600-5767POWDER X-RAY DIFFRACTION; INSTRUMENTATION; OPERANDO; ENERGY MATERIALS; DIFFRACTOMETERS; AREA DETECTORSThis paper describes the design and implementation of an in-house laboratory powder X-ray diffractometer tailored for structural investigations of energy materials. The performance characteristics of the diffractometer together with some example research applications are presented.doi:10.1107/S1600576722003089enA multipurpose laboratory diffractometer for operando powder X-ray diffraction investigations of energy materialsGeßwein, H.Stüble, P.Weber, D.Binder, J.R.Mönig, R.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-163503med@iucr.org5141600-5767552022-05-16research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767June 20223D-printed equipment to decouple (powder) X-ray diffraction sample preparation and measurement
http://scripts.iucr.org/cgi-bin/paper?oc5019
An alternative storage method to separate sample preparation from single-crystal and powder X-ray diffraction measurements at home source diffractometers is described. For single crystals, a setup is presented which allows storage of preselected crystals under cryogenic and ambient temperatures. For powders, a disposable sample holder is introduced. The method is suitable for the storage of air- and moisture-sensitive samples. Equipment made of biodegradable polylactic acid is produced by 3D printing and can be adapted to individual needs. As 3D printers are widely available at research institutions nowadays, models of the presented equipment are provided for the reader to allow easy reproduction.textAn alternative storage method to separate sample preparation from single-crystal and powder X-ray diffraction measurements at home source diffractometers is described. For single crystals, a setup is presented which allows storage of preselected crystals under cryogenic and ambient temperatures. For powders, a disposable sample holder is introduced. The method is suitable for the storage of air- and moisture-sensitive samples. Equipment made of biodegradable polylactic acid is produced by 3D printing and can be adapted to individual needs. As 3D printers are widely available at research institutions nowadays, models of the presented equipment are provided for the reader to allow easy reproduction.urn:issn:1600-57673D PRINTING; CRYO-STORAGE; SINGLE CRYSTALS; POWDERS; DIFFRACTION; HOME SOURCESA method to separate sample preparation from X-ray diffraction and powder X-ray diffraction measurements is presented. The necessary equipment is accessible at low cost by 3D printing.doi:10.1107/S160057672200293Xen3D-printed equipment to decouple (powder) X-ray diffraction sample preparation and measurementFuß, F.Rieckert, M.Steinhauer, S.Liesegang, M.Thiele, G.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-04-291600-5767June 2022laboratory notesJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-57676922022-04-29556863med@iucr.orgBragg coherent diffraction imaging of single 20 nm Pt particles at the ID01-EBS beamline of ESRF
http://scripts.iucr.org/cgi-bin/paper?te5091
Electronic or catalytic properties can be modified at the nanoscale level. Engineering efficient and specific nanomaterials requires the ability to study their complex structure–property relationships. Here, Bragg coherent diffraction imaging was used to measure the three-dimensional shape and strain of platinum nanoparticles with a diameter smaller than 30 nm, i.e. significantly smaller than any previous study. This was made possible by the realization of the Extremely Brilliant Source of ESRF, The European Synchrotron. This work demonstrates the feasibility of imaging the complex structure of very small particles in three dimensions and paves the way towards the observation of realistic catalytic particles.textElectronic or catalytic properties can be modified at the nanoscale level. Engineering efficient and specific nanomaterials requires the ability to study their complex structure–property relationships. Here, Bragg coherent diffraction imaging was used to measure the three-dimensional shape and strain of platinum nanoparticles with a diameter smaller than 30 nm, i.e. significantly smaller than any previous study. This was made possible by the realization of the Extremely Brilliant Source of ESRF, The European Synchrotron. This work demonstrates the feasibility of imaging the complex structure of very small particles in three dimensions and paves the way towards the observation of realistic catalytic particles.urn:issn:1600-5767BRAGG COHERENT DIFFRACTION IMAGING; EXTREMELY BRILLIANT SOURCE; STRUCTURE; PT PARTICLES; THREE-DIMENSIONAL; NANOSCALEThis work demonstrates three-dimensional Bragg coherent diffraction imaging of single 20 nm Pt particles at the ID01-EBS beamline of ESRF.doi:10.1107/S1600576722002886enBragg coherent diffraction imaging of single 20 nm Pt particles at the ID01-EBS beamline of ESRFRichard, M.-I.Labat, S.Dupraz, M.Li, N.Bellec, E.Boesecke, P.Djazouli, H.Eymery, J.Thomas, O.Schülli, T.U.Santala, M.K.Leake, S.J.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-05-163621med@iucr.org6251600-5767552022-05-16short communicationshttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1600-5767June 2022CELLOPT: improved unit-cell parameters for electron diffraction data of small-molecule crystals
http://scripts.iucr.org/cgi-bin/paper?yr5082
Electron diffraction enables structure determination of organic small molecules using crystals that are too small for conventional X-ray crystallography. However, because of uncertainties in the experimental parameters, notably the detector distance, the unit-cell parameters and the geometry of the structural models are typically less accurate and precise compared with results obtained by X-ray diffraction. Here, an iterative procedure to optimize the unit-cell parameters obtained from electron diffraction using idealized restraints is proposed. The cell optimization routine has been implemented as part of the structure refinement, and a gradual improvement in lattice parameters and data quality is demonstrated. It is shown that cell optimization, optionally combined with geometrical corrections for any apparent detector distortions, benefits refinement of electron diffraction data in small-molecule crystallography and leads to more accurate structural models.textElectron diffraction enables structure determination of organic small molecules using crystals that are too small for conventional X-ray crystallography. However, because of uncertainties in the experimental parameters, notably the detector distance, the unit-cell parameters and the geometry of the structural models are typically less accurate and precise compared with results obtained by X-ray diffraction. Here, an iterative procedure to optimize the unit-cell parameters obtained from electron diffraction using idealized restraints is proposed. The cell optimization routine has been implemented as part of the structure refinement, and a gradual improvement in lattice parameters and data quality is demonstrated. It is shown that cell optimization, optionally combined with geometrical corrections for any apparent detector distortions, benefits refinement of electron diffraction data in small-molecule crystallography and leads to more accurate structural models.urn:issn:1600-5767ELECTRON DIFFRACTION; PRECISION OF UNIT-CELL PARAMETERS; CRYSTAL STRUCTURE DETERMINATION; COMPENSATION FOR EXPERIMENTAL AND INSTRUMENTAL ERRORSIterative optimization of the unit-cell parameters improves the refinement of organic small-molecule structures using electron diffraction data.doi:10.1107/S160057672200276XenCELLOPT: improved unit-cell parameters for electron diffraction data of small-molecule crystalsGruene, T.Clabbers, M.T.B.Luebben, J.Chin, J.M.Reithofer, M.R.Stowasser, F.Alker, A.M.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-04-29552022-04-296551600-5767med@iucr.org3647June 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographycomputer programsScipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data
http://scripts.iucr.org/cgi-bin/paper?yr5085
Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.textThree-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.urn:issn:1600-5767ELECTRON DIFFRACTION; 3D ED; MICROED; DATA PROCESSING; COMPUTER PROGRAMSThe design and usage of Scipion-ED, a graphical user interface program for processing and analysis of three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) data, are presented. A study of the influence of data merging strategies on the ability to resolve unmodelled features of tetragonal lysozyme is included as an illustration of the advantages of Scipion-ED.doi:10.1107/S1600576722002758enScipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED dataBengtsson, V.E.G.Pacoste, L.Rosa-Trevin, J.M. de laHofer, G.Zou, X.Xu, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-04-22June 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographycomputer programs552022-04-226461600-5767med@iucr.org3638Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasers
http://scripts.iucr.org/cgi-bin/paper?te5090
Single particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It is proposed that this task could be formulated as an image-classification problem and solved using convolutional neural network (CNN) architectures. Two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall. The CNNs are also combined with expectation-maximization (EM) selection as well as size filtering. It is observed that the CNN selections have lower contrast in power spectral density functions relative to the EM selection used in previous work. However, the reconstruction of the CNN-based selections gives similar results. Introducing CNNs into SPI experiments allows the reconstruction pipeline to be streamlined, enables researchers to classify patterns on the fly, and, as a consequence, enables them to tightly control the duration of their experiments. Incorporating non-standard artificial-intelligence-based solutions into an existing SPI analysis workflow may be beneficial for the future development of SPI experiments.textSingle particle imaging (SPI) at X-ray free-electron lasers is particularly well suited to determining the 3D structure of particles at room temperature. For a successful reconstruction, diffraction patterns originating from a single hit must be isolated from a large number of acquired patterns. It is proposed that this task could be formulated as an image-classification problem and solved using convolutional neural network (CNN) architectures. Two CNN configurations are developed: one that maximizes the F1 score and one that emphasizes high recall. The CNNs are also combined with expectation-maximization (EM) selection as well as size filtering. It is observed that the CNN selections have lower contrast in power spectral density functions relative to the EM selection used in previous work. However, the reconstruction of the CNN-based selections gives similar results. Introducing CNNs into SPI experiments allows the reconstruction pipeline to be streamlined, enables researchers to classify patterns on the fly, and, as a consequence, enables them to tightly control the duration of their experiments. Incorporating non-standard artificial-intelligence-based solutions into an existing SPI analysis workflow may be beneficial for the future development of SPI experiments.urn:issn:1600-5767CONVOLUTIONAL NEURAL NETWORKS; SINGLE-PARTICLE IMAGING; CLASSIFICATION OF DIFFRACTION PATTERNS; X-RAY FREE-ELECTRON LASERSA convolutional neural network is applied for the single-hit diffraction-pattern classification step in single-particle-imaging experiments at X-ray free-electron lasers. This approach can be employed not only after the experiment but, importantly, also during an experiment and can significantly reduce the size of data storage for further analysis stages.doi:10.1107/S1600576722002667enClassification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasersAssalauova, D.Ignatenko, A.Isensee, F.Trofimova, D.Vartanyants, I.A.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-04-22med@iucr.org44432022-04-22551600-5767454Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersJune 20221600-5767Lower uncertainty bounds of diffraction-based nanoparticle sizes
http://scripts.iucr.org/cgi-bin/paper?tu5019
A self-consistent analysis is reported of traditional diffraction-based particle size determination techniques applied to synthetic diffraction profiles generated with the Patterson approach. The results show that dimensions obtained from traditional techniques utilizing peak fitting or Fourier analysis for single-crystal nanoparticles have best-case error bounds of around 5%. For arbitrarily shaped particles, lower error magnitudes are possible only if the zeroes of the thickness fringes are used. The errors for sizes obtained by integral-breadth- and Fourier-decomposition-based techniques depend on the shape of the diffracting domains. In the case of integral-breadth analysis, crystal shapes which scatter more intensity into the central peak of the rocking curve have lower size errors. For Fourier-decomposition analysis, crystals which have non-uniform distributions of chord lengths exhibit nonlinearities in the initial ranges of the normalized Fourier cosine coefficient versus column length (|AL| versus L) plots, even when the entire rocking curve is used in the decomposition. It is recommended that, in routine analysis, all domain size determination techniques should be applied to all reflections in a diffraction pattern. If there is significant divergence among these results, the `average particle size(s)' obtained might not be reliable.textA self-consistent analysis is reported of traditional diffraction-based particle size determination techniques applied to synthetic diffraction profiles generated with the Patterson approach. The results show that dimensions obtained from traditional techniques utilizing peak fitting or Fourier analysis for single-crystal nanoparticles have best-case error bounds of around 5%. For arbitrarily shaped particles, lower error magnitudes are possible only if the zeroes of the thickness fringes are used. The errors for sizes obtained by integral-breadth- and Fourier-decomposition-based techniques depend on the shape of the diffracting domains. In the case of integral-breadth analysis, crystal shapes which scatter more intensity into the central peak of the rocking curve have lower size errors. For Fourier-decomposition analysis, crystals which have non-uniform distributions of chord lengths exhibit nonlinearities in the initial ranges of the normalized Fourier cosine coefficient versus column length (|AL| versus L) plots, even when the entire rocking curve is used in the decomposition. It is recommended that, in routine analysis, all domain size determination techniques should be applied to all reflections in a diffraction pattern. If there is significant divergence among these results, the `average particle size(s)' obtained might not be reliable.urn:issn:1600-5767DIFFRACTION; PARTICLE SIZE DETERMINATION; SCHERRER APPROACH; INTEGRAL BREADTH; FOURIER ANALYSISThe errors for particle sizes obtained by integral-breadth- and Fourier-decomposition-based techniques depend on the shape of the diffracting domains.doi:10.1107/S1600576722002564enLower uncertainty bounds of diffraction-based nanoparticle sizesNoyan, İ.C.Öztürk, H.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-04-291600-57674702022-04-29554553med@iucr.org1600-5767June 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/A drug-discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screening
http://scripts.iucr.org/cgi-bin/paper?ap5042
In X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitrogen or propane. Protocols for protein crystal cryoprotection are based on either increasing the environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Several salt solutions were screened to identify KF13 as optimal. Cryoprotection using the KF13 protocol is non-invasive to the crystal, high throughput and easy to implement, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug-discovery projects which use very large compound or fragment libraries. An application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.textIn X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitrogen or propane. Protocols for protein crystal cryoprotection are based on either increasing the environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Several salt solutions were screened to identify KF13 as optimal. Cryoprotection using the KF13 protocol is non-invasive to the crystal, high throughput and easy to implement, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug-discovery projects which use very large compound or fragment libraries. An application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.urn:issn:1600-5767CRYOPROTECTION; HIGH THROUGHPUT; DEHYDRATION; CRYSTALS; PROTEINSA one-step dehydration-based protein crystal cryoprotection protocol is presented. It is suitable for both low- and high-throughput projects, and may also benefit ligand occupancy and diffraction resolution. This same procedure can also be applied to discover new crystal hits from clear drops of already vapour diffusion equilibrated crystallization screening plates.doi:10.1107/S1600576722002382enA drug-discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screeningBellini, D.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-04-02April 20221600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallographyresearch papers552022-04-023791600-5767med@iucr.org3702Neural network analysis of neutron and X-ray reflectivity data: automated analysis using mlreflect, experimental errors and feature engineering
http://scripts.iucr.org/cgi-bin/paper?vh5156
The Python package mlreflect is demonstrated, which implements an optimized pipeline for the automated analysis of reflectometry data using machine learning. The package combines several training and data treatment techniques discussed in previous publications. The predictions made by the neural network are accurate and robust enough to serve as good starting parameters for an optional subsequent least-mean-squares (LMS) fit of the data. For a large data set of 242 reflectivity curves of various thin films on silicon substrates, the pipeline reliably finds an LMS minimum very close to a fit produced by a human researcher with the application of physical knowledge and carefully chosen boundary conditions. The differences between simulated and experimental data and their implications for the training and performance of neural networks are discussed. The experimental test set is used to determine the optimal noise level during training. The extremely fast prediction times of the neural network are leveraged to compensate for systematic errors by sampling slight variations in the data.textThe Python package mlreflect is demonstrated, which implements an optimized pipeline for the automated analysis of reflectometry data using machine learning. The package combines several training and data treatment techniques discussed in previous publications. The predictions made by the neural network are accurate and robust enough to serve as good starting parameters for an optional subsequent least-mean-squares (LMS) fit of the data. For a large data set of 242 reflectivity curves of various thin films on silicon substrates, the pipeline reliably finds an LMS minimum very close to a fit produced by a human researcher with the application of physical knowledge and carefully chosen boundary conditions. The differences between simulated and experimental data and their implications for the training and performance of neural networks are discussed. The experimental test set is used to determine the optimal noise level during training. The extremely fast prediction times of the neural network are leveraged to compensate for systematic errors by sampling slight variations in the data.urn:issn:1600-5767REFLECTOMETRY; DATA ANALYSIS; MACHINE LEARNING; PYTHONA Python-based analysis pipeline for the fast analysis of X-ray and neutron reflectivity data using neural networks is presented.doi:10.1107/S1600576722002230enNeural network analysis of neutron and X-ray reflectivity data: automated analysis using mlreflect, experimental errors and feature engineeringGreco, A.Starostin, V.Edel, E.Munteanu, V.Rußegger, N.Dax, I.Shen, C.Bertram, F.Hinderhofer, A.Gerlach, A.Schreiber, F.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-04-021600-5767April 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-57673692022-04-02553622med@iucr.orgStructure evolution of nanodiamond aggregates: a SANS and USANS study
http://scripts.iucr.org/cgi-bin/paper?ge5110
Ultra-small-angle neutron scattering (USANS) and small-angle neutron scattering (SANS) measurements, covering length scales from micrometres to nanometres, were made to investigate the structure of nanodiamonds (NDs) and their suspensions. These nanodiamonds were produced by two different techniques, namely by the detonation method and by the laser ablation of a carbon–hydrocarbon mixture. The (U)SANS results indicated the presence of structures four orders of magnitude larger than the dimensions of a single ND particle, consisting of aggregations of ND particles. This aggregation of the ND particles was studied by employing the contrast variation technique. Two different solvents, namely H2O and dimethyl sulfoxide (and their deuterated counterparts), were used to understand the role of hydrogen in the shape and size of the aggregates. The analysis of experimental data from SANS measurements also reveals the ND particles to have an ellipsoidal structure. Using a defined shape model and the SANS contrast variation technique, it was possible to characterize the non-diamond outer shell of the particles and determine the outer layer thickness. This clarification of the structure of the NDs will allow better preparation of suspensions/samples for various applications. Understanding the structure of NDs at multiple length scales also provides crucial knowledge of particle–particle interaction and its effect on the aggregation structures.textUltra-small-angle neutron scattering (USANS) and small-angle neutron scattering (SANS) measurements, covering length scales from micrometres to nanometres, were made to investigate the structure of nanodiamonds (NDs) and their suspensions. These nanodiamonds were produced by two different techniques, namely by the detonation method and by the laser ablation of a carbon–hydrocarbon mixture. The (U)SANS results indicated the presence of structures four orders of magnitude larger than the dimensions of a single ND particle, consisting of aggregations of ND particles. This aggregation of the ND particles was studied by employing the contrast variation technique. Two different solvents, namely H2O and dimethyl sulfoxide (and their deuterated counterparts), were used to understand the role of hydrogen in the shape and size of the aggregates. The analysis of experimental data from SANS measurements also reveals the ND particles to have an ellipsoidal structure. Using a defined shape model and the SANS contrast variation technique, it was possible to characterize the non-diamond outer shell of the particles and determine the outer layer thickness. This clarification of the structure of the NDs will allow better preparation of suspensions/samples for various applications. Understanding the structure of NDs at multiple length scales also provides crucial knowledge of particle–particle interaction and its effect on the aggregation structures.urn:issn:1600-5767NANODIAMONDS; COLD NEUTRON SOURCES; DETONATION NDS; SMALL-ANGLE NEUTRON SCATTERING; LASER SYNTHESIS TECHNIQUENanodiamonds (NDs) produced by two different techniques have been studied by ultra-small- (USANS) and small-angle neutron scattering (SANS): (i) produced by the detonation of explosives in an oxygen-deficient atmosphere (TNT + hexogen), which results in the production of detonation nanodiamonds, and (ii) produced by laser ablation of a carbon–hydrocarbon mixture. The size distribution of the particles and the composition of the outer layers are expected to vary depending on the source of the NDs.doi:10.1107/S1600576722002084enStructure evolution of nanodiamond aggregates: a SANS and USANS studyKabir, I.I.Osborn, J.C.Lu, W.Mata, J.P.Rehm, C.Yeoh, G.H.Ersez, T.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-03-25April 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papers2022-03-25551600-5767361med@iucr.org3532Performance of the new biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon Source
http://scripts.iucr.org/cgi-bin/paper?ge5116
Recent developments in the instrumentation and data analysis of synchrotron small-angle X-ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small- and wide-angle X-ray scattering (SAXS–WAXS or SWAXS). The endstation features an in-vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size-exclusion chromatography system incorporating several optical probes including a UV–Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS–WAXS data collection and data reduction for high-throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal-model fittings to the data in the q range ∼0.005–2.0 Å−1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration-dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.textRecent developments in the instrumentation and data analysis of synchrotron small-angle X-ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small- and wide-angle X-ray scattering (SAXS–WAXS or SWAXS). The endstation features an in-vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size-exclusion chromatography system incorporating several optical probes including a UV–Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS–WAXS data collection and data reduction for high-throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal-model fittings to the data in the q range ∼0.005–2.0 Å−1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration-dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.urn:issn:1600-5767SMALL-ANGLE X-RAY SCATTERING; WIDE-ANGLE X-RAY SCATTERING; SAXS-WAXS; SWAXS; ONLINE SIZE EXCLUSION CHROMATOGRAPHY; INTEGRATED UV-VIS ABSORPTION AND REFRACTOMETRY; BIOMOLECULAR SOLUTION SCATTERINGA new endstation for biological small- and wide-angle X-ray scattering is detailed, which provides development opportunities for studying correlated local and global structures of biomolecules in solution.doi:10.1107/S1600576722001923enPerformance of the new biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon SourceShih, O.Liao, K.-F.Yeh, Y.-Q.Su, C.-J.Wang, C.-A.Chang, J.-W.Wu, W.-R.Liang, C.-C.Lin, C.-Y.Lee, T.-H.Chang, C.-H.Chiang, L.-C.Chang, C.-F.Liu, D.-G.Lee, M.-H.Liu, C.-Y.Hsu, T.-W.Mansel, B.Ho, M.-C.Shu, C.-Y.Lee, F.Yen, E.Lin, T.-C.Jeng, U.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-03-18Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersApril 20221600-5767med@iucr.org23402022-03-18551600-5767352The FUSION protein crystallization screen
http://scripts.iucr.org/cgi-bin/paper?ei5076
The success and speed of atomic structure determination of biological macromolecules by X-ray crystallography depends critically on the availability of diffraction-quality crystals. However, the process of screening crystallization conditions often consumes large amounts of sample and time. An innovative protein crystallization screen formulation called FUSION has been developed to help with the production of useful crystals. The concept behind the formulation of FUSION was to combine the most efficient components from the three MORPHEUS screens into a single screen using a systematic approach. The resulting formulation integrates 96 unique combinations of crystallization additives. Most of these additives are small molecules and ions frequently found in crystal structures of the Protein Data Bank (PDB), where they bind proteins and complexes. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins. In the process, two crystal forms not currently in the PDB for the proteins α-amylase and avidin were discovered.textThe success and speed of atomic structure determination of biological macromolecules by X-ray crystallography depends critically on the availability of diffraction-quality crystals. However, the process of screening crystallization conditions often consumes large amounts of sample and time. An innovative protein crystallization screen formulation called FUSION has been developed to help with the production of useful crystals. The concept behind the formulation of FUSION was to combine the most efficient components from the three MORPHEUS screens into a single screen using a systematic approach. The resulting formulation integrates 96 unique combinations of crystallization additives. Most of these additives are small molecules and ions frequently found in crystal structures of the Protein Data Bank (PDB), where they bind proteins and complexes. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins. In the process, two crystal forms not currently in the PDB for the proteins α-amylase and avidin were discovered.urn:issn:1600-5767X-RAY CRYSTALLOGRAPHY; MACROMOLECULAR CRYSTALLIZATION; CRYSTALLIZATION SCREENS; PROTEIN CRYSTALSThe FUSION protein crystallization screen, which integrates 96 unique combinations of additives, is presented and its efficiency is demonstrated.doi:10.1107/S1600576722001765enThe FUSION protein crystallization screenGorrec, F.Bellini, D.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-03-111600-5767April 2022research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-57673192022-03-11552310med@iucr.orgEfficient solution of particle shape functions for the analysis of powder total scattering data
http://scripts.iucr.org/cgi-bin/paper?jl5028
Structural characterization of powder samples via total scattering methods, in either real or reciprocal space, must take into account the effect of particle shape. Here, the shape contribution of a set of ideally isolated particles to the small-angle scattering (SAS) component of the intensity profile is modelled using the shape function [Svergun & Koch (2003). Rep. Prog. Phys. 66, 1735–1782]. The shape function is obtained by orientational averaging of common volume functions (CVFs) for a discrete set of directions. The effects of particle size and size dispersity are accounted for via scaling of the CVFs and their convolution with the underlying probability distribution. The method is applied to shapes with CVFs expressed analytically or by using discrete tables. The accurate calculation of SAS particle shape contributions up to large momentum transfer demonstrates the reliability and flexibility of modelling shape functions from sets of CVFs. The algorithm presented here is computationally efficient and can be directly incorporated into existing routines for analysis of powder total scattering data.textStructural characterization of powder samples via total scattering methods, in either real or reciprocal space, must take into account the effect of particle shape. Here, the shape contribution of a set of ideally isolated particles to the small-angle scattering (SAS) component of the intensity profile is modelled using the shape function [Svergun & Koch (2003). Rep. Prog. Phys. 66, 1735–1782]. The shape function is obtained by orientational averaging of common volume functions (CVFs) for a discrete set of directions. The effects of particle size and size dispersity are accounted for via scaling of the CVFs and their convolution with the underlying probability distribution. The method is applied to shapes with CVFs expressed analytically or by using discrete tables. The accurate calculation of SAS particle shape contributions up to large momentum transfer demonstrates the reliability and flexibility of modelling shape functions from sets of CVFs. The algorithm presented here is computationally efficient and can be directly incorporated into existing routines for analysis of powder total scattering data.urn:issn:1600-5767SHAPE FUNCTIONS; SMALL-ANGLE SCATTERING; TOTAL SCATTERING; PAIR DISTRIBUTION FUNCTIONS; COMMON VOLUME FUNCTIONSParticle shape functions are necessary to model powder scattering data that are in the form of intensity profiles and pair distribution functions. Here, an efficient method is presented to compute particle shape functions by orientational averaging of common volume functions. Contributions from particle size and size dispersity are accounted for via scaling and convolution.doi:10.1107/S1600576722001261enEfficient solution of particle shape functions for the analysis of powder total scattering dataLeonardi, A.Neder, R.Engel, M.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-03-183391600-5767552022-03-183292med@iucr.org1600-5767April 2022research papershttps://creativecommons.org/licenses/by/4.0/Journal of Applied CrystallographyMagnetic Small-Angle Neutron Scattering. A Probe for Mesoscale Magnetism Analysis. By Andreas Michels. Oxford University Press, 2021. Pp. 384. Price (hardback) GBP 80.00. ISBN 9780198855170.
http://scripts.iucr.org/cgi-bin/paper?xo0186
texturn:issn:1600-5767BOOK REVIEWS; MAGNETIC SMALL-ANGLE NEUTRON SCATTERING; MESOSCALE MAGNETISMBook review.doi:10.1107/S1600576722001029enMagnetic Small-Angle Neutron Scattering. A Probe for Mesoscale Magnetism Analysis. By Andreas Michels. Oxford University Press, 2021. Pp. 384. Price (hardback) GBP 80.00. ISBN 9780198855170.Disch, S.International Union of Crystallographytext/html2022-02-27April 20221600-5767Journal of Applied Crystallographybook reviews2022-02-27551600-5767443med@iucr.org4422The very small angle neutron scattering instrument at the National Institute of Standards and Technology
http://scripts.iucr.org/cgi-bin/paper?ge5109
A description and the performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology are presented. The measurement range of the instrument extends over three decades of momentum transfer q from 2 × 10−4 to 0.7 Å−1. The entire scattering angle range from 8 × 10−5 to π/6 rad (30°) can be measured simultaneously using three separate detector carriages on rails holding nine 2D detector arrays. Versatile choices of collimation options and neutron wavelength selection allow the q resolution and beam intensity to be optimized for the needs of the experiment. High q resolution is achieved using multiple converging-beam collimation with circular pinholes combined with refractive lenses and prisms. Relaxed vertical resolution with much higher beam intensity can be achieved with narrow slit collimation and a broad wavelength range chosen by truncating the moderator source distribution below 4 Å with a Be crystalline filter and above 8 Å with a supermirror deflector. Polarized beam measurements with full polarization analysis are also provided by a high-performance supermirror polarizer and spin flipper, capable of producing flipping ratios of over 100, along with a high-efficiency 3He polarization analyzer.textA description and the performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology are presented. The measurement range of the instrument extends over three decades of momentum transfer q from 2 × 10−4 to 0.7 Å−1. The entire scattering angle range from 8 × 10−5 to π/6 rad (30°) can be measured simultaneously using three separate detector carriages on rails holding nine 2D detector arrays. Versatile choices of collimation options and neutron wavelength selection allow the q resolution and beam intensity to be optimized for the needs of the experiment. High q resolution is achieved using multiple converging-beam collimation with circular pinholes combined with refractive lenses and prisms. Relaxed vertical resolution with much higher beam intensity can be achieved with narrow slit collimation and a broad wavelength range chosen by truncating the moderator source distribution below 4 Å with a Be crystalline filter and above 8 Å with a supermirror deflector. Polarized beam measurements with full polarization analysis are also provided by a high-performance supermirror polarizer and spin flipper, capable of producing flipping ratios of over 100, along with a high-efficiency 3He polarization analyzer.urn:issn:1600-5767SMALL-ANGLE NEUTRON SCATTERING; VSANS; INSTRUMENTATION; NEUTRON OPTICSA description and the performance of the very small angle neutron scattering diffractometer at the National Institute of Standards and Technology are presented.doi:10.1107/S1600576722000826enThe very small angle neutron scattering instrument at the National Institute of Standards and TechnologyBarker, J.Moyer, J.Kline, S.Jensen, G.Cook, J.Gagnon, C.Kelley, E.Chabot, J.P.Maliszewskyj, N.Parikh, C.Chen, W.Murphy, R.P.Glinka, C.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-02-27research papersJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767April 20222271med@iucr.org1600-57672832022-02-2755QUANTAS: a Python software for the analysis of thermodynamics and elastic behavior of solids from ab initio quantum mechanical simulations and experimental data
http://scripts.iucr.org/cgi-bin/paper?vb5027
Mineralogy, petrology and materials science are fundamental disciplines not only for the basic knowledge and classification of solid phases but also for their technological applications, which are becoming increasingly demanding and challenging. Characterization and design of materials are of utmost importance and usually need knowledge of the thermodynamics and mechanical stability of solids. Alongside well known experimental approaches, in recent years the advances in both quantum mechanical methods and computational power have placed theoretical investigations as a complementary useful and powerful tool in this kind of study. In order to aid both theoreticians and experimentalists, an open-source Python-based software, QUANTAS, has been developed. QUANTAS provides a fast, flexible, easy-to-use and extensible platform for calculating the thermodynamics and elastic behavior of crystalline solid phases, starting from both experimental and ab initio data.textMineralogy, petrology and materials science are fundamental disciplines not only for the basic knowledge and classification of solid phases but also for their technological applications, which are becoming increasingly demanding and challenging. Characterization and design of materials are of utmost importance and usually need knowledge of the thermodynamics and mechanical stability of solids. Alongside well known experimental approaches, in recent years the advances in both quantum mechanical methods and computational power have placed theoretical investigations as a complementary useful and powerful tool in this kind of study. In order to aid both theoreticians and experimentalists, an open-source Python-based software, QUANTAS, has been developed. QUANTAS provides a fast, flexible, easy-to-use and extensible platform for calculating the thermodynamics and elastic behavior of crystalline solid phases, starting from both experimental and ab initio data.urn:issn:1600-5767QUANTAS COMPUTER PROGRAM; SOLID PHASES; THERMODYNAMICS; EQUATIONS OF STATE; SECOND-ORDER ELASTIC CONSTANTS; QUANTUM MINERALOGYThis paper presents QUANTAS, an open-source Python-based software aimed at providing a fast, flexible and easy-to-use framework to calculate the thermodynamics and elastic properties of crystalline solids. QUANTAS could be of use for researchers involved in various fields of solid-state chemistry, physics and mineralogy.doi:10.1107/S1600576722000085enQUANTAS: a Python software for the analysis of thermodynamics and elastic behavior of solids from ab initio quantum mechanical simulations and experimental dataUlian, G.Valdrè, G.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-02-101600-5767April 2022computer programsJournal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-57673962022-02-10552386med@iucr.orgOptical demonstration of crystallography and reciprocal space using laser diffraction from Au microdisc arrays
http://scripts.iucr.org/cgi-bin/paper?oc5016
Crystallography is an invaluable tool in materials science, solid state physics and protein science. Understanding crystallography requires grasping the powerful but abstract concept of reciprocal space. Here a simple but insightful experiment using a laser pointer and Au microdisc arrays to explore and illustrate Bragg diffraction and reciprocal space is demonstrated. The Au microdisc arrays were manufactured using standard semiconductor fabrication techniques. The flexibility of the array design allows the demonstration of basic concepts such as lattice and atomic form factor, but also more advanced ones such as quasicrystal and shape function.textCrystallography is an invaluable tool in materials science, solid state physics and protein science. Understanding crystallography requires grasping the powerful but abstract concept of reciprocal space. Here a simple but insightful experiment using a laser pointer and Au microdisc arrays to explore and illustrate Bragg diffraction and reciprocal space is demonstrated. The Au microdisc arrays were manufactured using standard semiconductor fabrication techniques. The flexibility of the array design allows the demonstration of basic concepts such as lattice and atomic form factor, but also more advanced ones such as quasicrystal and shape function.urn:issn:1600-5767TEACHING; EDUCATION; DIFFRACTION; RECIPROCAL SPACEA simple experiment to explore and illustrate Bragg diffraction and reciprocal space using a laser pointer and Au microdisc arrays is demonstrated. The flexibility of the array design allows the demonstration of basic concepts such as lattice and atomic form factor, but also more advanced ones such as quasicrystal and shape function.doi:10.1107/S1600576721013492enOptical demonstration of crystallography and reciprocal space using laser diffraction from Au microdisc arraysChayanun, L.Gustafson, J.Wallentin, J.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-02-012022-02-01551600-5767171med@iucr.org1168February 20221600-5767Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/teaching and educationA new library of 3D models and problems for teaching crystallographic symmetry generated through Blender for use with 3D printers or Sketchfab
http://scripts.iucr.org/cgi-bin/paper?oc5017
A new and growing library of 3D models that can be utilized to illustrate many important concepts in the field of crystallography is presented. These models are accessible in the classroom via computers and smartphones and offer significant advantages over 2D depictions found in crystallography textbooks. Through the use of Blender, a free 3D modeling and animation program, over 100 new models focusing on different aspects of crystallographic education have been created. To simplify distribution/access, all of these models have been uploaded to Sketchfab, a model hosting and viewing web site that works similarly to YouTube. The current set of models is also given as a list in the supporting information. All of these models are free to view in a web browser or through a smartphone application. Additionally, all of these models are freely downloadable through the supporting information and Sketchfab, and users are encouraged to download and modify these models to best suit their needs. This library of models is part of the authors' ongoing outreach program to provide 3D models for free for educational purposes, and the authors offer their services to create additional models and moderate this library as additional requests or critiques are provided.textA new and growing library of 3D models that can be utilized to illustrate many important concepts in the field of crystallography is presented. These models are accessible in the classroom via computers and smartphones and offer significant advantages over 2D depictions found in crystallography textbooks. Through the use of Blender, a free 3D modeling and animation program, over 100 new models focusing on different aspects of crystallographic education have been created. To simplify distribution/access, all of these models have been uploaded to Sketchfab, a model hosting and viewing web site that works similarly to YouTube. The current set of models is also given as a list in the supporting information. All of these models are free to view in a web browser or through a smartphone application. Additionally, all of these models are freely downloadable through the supporting information and Sketchfab, and users are encouraged to download and modify these models to best suit their needs. This library of models is part of the authors' ongoing outreach program to provide 3D models for free for educational purposes, and the authors offer their services to create additional models and moderate this library as additional requests or critiques are provided.urn:issn:1600-57673D MODELS; 3D ANIMATIONS; EDUCATIONThis work details a set of newly made and maintained 3D models for the purpose of teaching crystallography. These models are all freely downloadable and viewable online through Sketchfab.doi:10.1107/S1600576721013236enA new library of 3D models and problems for teaching crystallographic symmetry generated through Blender for use with 3D printers or SketchfabAristov, M.M.Geng, H.Pavelic, A.Berry, J.F.International Union of Crystallographytext/html2022-02-01February 20221600-5767Journal of Applied Crystallographyteaching and education2022-02-01551600-5767179med@iucr.org1172Performance of the time-resolved ultra-small-angle X-ray scattering beamline with the Extremely Brilliant Source
http://scripts.iucr.org/cgi-bin/paper?jl5029
The new technical features and enhanced performance of the ID02 beamline with the Extremely Brilliant Source (EBS) at the ESRF are described. The beamline enables static and kinetic investigations of a broad range of systems from ångström to micrometre size scales and down to the sub-millisecond time range by combining different small-angle X-ray scattering techniques in a single instrument. In addition, a nearly coherent beam obtained in the high-resolution mode allows multispeckle X-ray photon correlation spectroscopy measurements down to the microsecond range over the ultra-small- and small-angle regions. While the scattering vector (of magnitude q) range covered is the same as before, 0.001 ≤ q ≤ 50 nm−1 for an X-ray wavelength of 1 Å, the EBS permits relaxation of the collimation conditions, thereby obtaining a higher flux throughput and lower background. In particular, a coherent photon flux in excess of 1012 photons s−1 can be routinely obtained, allowing dynamic studies of relatively dilute samples. The enhanced beam properties are complemented by advanced pixel-array detectors and high-throughput data reduction pipelines. All these developments together open new opportunities for structural, dynamic and kinetic investigations of out-of-equilibrium soft matter and biophysical systems.textThe new technical features and enhanced performance of the ID02 beamline with the Extremely Brilliant Source (EBS) at the ESRF are described. The beamline enables static and kinetic investigations of a broad range of systems from ångström to micrometre size scales and down to the sub-millisecond time range by combining different small-angle X-ray scattering techniques in a single instrument. In addition, a nearly coherent beam obtained in the high-resolution mode allows multispeckle X-ray photon correlation spectroscopy measurements down to the microsecond range over the ultra-small- and small-angle regions. While the scattering vector (of magnitude q) range covered is the same as before, 0.001 ≤ q ≤ 50 nm−1 for an X-ray wavelength of 1 Å, the EBS permits relaxation of the collimation conditions, thereby obtaining a higher flux throughput and lower background. In particular, a coherent photon flux in excess of 1012 photons s−1 can be routinely obtained, allowing dynamic studies of relatively dilute samples. The enhanced beam properties are complemented by advanced pixel-array detectors and high-throughput data reduction pipelines. All these developments together open new opportunities for structural, dynamic and kinetic investigations of out-of-equilibrium soft matter and biophysical systems.urn:issn:1600-5767SMALL-ANGLE X-RAY SCATTERING; SAXS; ULTRA-SMALL-ANGLE X-RAY SCATTERING; USAXS; X-RAY PHOTON CORRELATION SPECTROSCOPY; XPCS; TIME-RESOLVED STUDIESThe new technical features and improved performance of the time-resolved ultra-small-angle X-ray scattering beamline at the ESRF are presented. The beamline enables static and time-resolved investigations from ångström to micrometre size scales down to the sub-millisecond time range and coherent scattering studies in the ultra-small-angle region. Among the main applications are the elucidation of static and transient hierarchical structures in soft matter and biophysical systems, and the dynamics of out-of-equilibrium complex fluids.doi:10.1107/S1600576721012693enPerformance of the time-resolved ultra-small-angle X-ray scattering beamline with the Extremely Brilliant SourceNarayanan, T.Sztucki, M.Zinn, T.Kieffer, J.Homs-Puron, A.Gorini, J.Van Vaerenbergh, P.Boesecke, P.International Union of Crystallographytext/htmlhttps://creativecommons.org/licenses/by/4.0/2022-02-01Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/research papersFebruary 20221600-5767med@iucr.org1982022-02-01551600-5767111