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) 2023 International Union of CrystallographyInternational Union of CrystallographyInternational Union of Crystallographytexthttps://journals.iucr.orgOpen-access and free articles in Journal of Applied CrystallographyJournal 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.urn:issn:0021-8898text/htmlyearly2002-02-01T00:00+00:006med@iucr.orgJournal of Applied Crystallographyurn:issn:0021-8898Copyright (c) 2023 International Union of CrystallographyOpen-access and free articles in Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
https://journals.iucr.org/j/journalhomepage.html
Still imageHAT: a high-energy surface X-ray diffraction analysis toolkit
http://scripts.iucr.org/cgi-bin/paper?vb5044
This work introduces the high-energy surface X-ray diffraction analysis toolkit (HAT), an open-source cross-platform software package written in Python to allow the extraction and processing of high-energy surface X-ray diffraction (HESXRD) data sets. Thousands of large-area detector images are collected in a single HESXRD scan, corresponding to billions of pixels and hence reciprocal space positions. HAT is an optimized reciprocal space binner that implements a graphical user interface to allow the easy and interactive exploration of HESXRD data sets. Regions of reciprocal space can be selected with movable and resizable masks in multiple views and are projected onto different axes to allow the creation of reciprocal space maps and the extraction of crystal truncation rods. Current and future versions of HAT can be downloaded and used free of charge.DATA ANALYSIS; DATA REDUCTION; RECIPROCAL SPACE MAPPING; HIGH-ENERGY SURFACE X-RAY DIFFRACTION; CRYSTAL TRUNCATION RODShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHarlow, G.S.Pfaff, S.Abbondanza, G.Hegedüs, Z.Lienert, U.Lundgren, E.texturn:issn:1600-5767HAT: a high-energy surface X-ray diffraction analysis toolkitThis work introduces the high-energy surface X-ray diffraction analysis toolkit (HAT), an open-source cross-platform software package written in Python to allow the extraction and processing of high-energy surface X-ray diffraction (HESXRD) data sets. Thousands of large-area detector images are collected in a single HESXRD scan, corresponding to billions of pixels and hence reciprocal space positions. HAT is an optimized reciprocal space binner that implements a graphical user interface to allow the easy and interactive exploration of HESXRD data sets. Regions of reciprocal space can be selected with movable and resizable masks in multiple views and are projected onto different axes to allow the creation of reciprocal space maps and the extraction of crystal truncation rods. Current and future versions of HAT can be downloaded and used free of charge.doi:10.1107/S16005767230000922023-02-01text/htmlComputer software for the analysis and extraction of high-energy surface X-ray diffraction data is presented.https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography13212023-02-013121600-5767computer programs1600-576756February 2023med@iucr.orgData reduction for X-ray serial crystallography using machine learning
http://scripts.iucr.org/cgi-bin/paper?te5101
Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large-scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the `bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.SERIAL CRYSTALLOGRAPHY; DATA REDUCTION; MACHINE LEARNING; FEATURE EXTRACTIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenRahmani, V.Nawaz, S.Pennicard, D.Setty, S.P.R.Graafsma, H.texturn:issn:1600-5767Data reduction for X-ray serial crystallography using machine learningSerial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large-scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the `bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.doi:10.1107/S16005767220117482023-02-01text/htmlA machine learning method for distinguishing good and bad images in serial crystallography is presented. To reduce the computational cost, this uses the oriented FAST and rotated BRIEF feature extraction method from computer vision to detect image features, followed by a multilayer perceptron (neural network) to classify the images.1600-57671600-5767research papers2023-02-01213200https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1February 2023med@iucr.org56Extracting the morphology of gold bipyramids from small-angle X-ray scattering experiments via form factor modelling
http://scripts.iucr.org/cgi-bin/paper?jl5056
Accurate shape description is a challenge in materials science. Small-angle X-ray scattering (SAXS) can provide the shape, size and polydispersity of nanoparticles by form factor modelling. However, simple geometric models such as the ellipsoid may not be enough to describe objects with complex shapes. This work shows that the form factor of gold nanobipyramids is accurately described by a truncated bicone model, which is validated by comparison with transmission electron microscopy (TEM) data for nine different synthesis batches; the average shape parameters (width, height and truncation) and the sample polydispersity are obtained. In contrast, the ellipsoid model yields worse fits of the SAXS data and exhibits systematic discrepancies with the TEM results.SMALL-ANGLE X-RAY SCATTERING; SAXS; COLLOIDS; BIPYRAMIDS; FORM FACTORS; TRANSMISSION ELECTRON MICROSCOPY; TEMhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLyu, J.Goldmann, C.Hamon, C.Constantin, D.texturn:issn:1600-5767Extracting the morphology of gold bipyramids from small-angle X-ray scattering experiments via form factor modellingAccurate shape description is a challenge in materials science. Small-angle X-ray scattering (SAXS) can provide the shape, size and polydispersity of nanoparticles by form factor modelling. However, simple geometric models such as the ellipsoid may not be enough to describe objects with complex shapes. This work shows that the form factor of gold nanobipyramids is accurately described by a truncated bicone model, which is validated by comparison with transmission electron microscopy (TEM) data for nine different synthesis batches; the average shape parameters (width, height and truncation) and the sample polydispersity are obtained. In contrast, the ellipsoid model yields worse fits of the SAXS data and exhibits systematic discrepancies with the TEM results.doi:10.1107/S16005767220116692023-02-01text/htmlThe use of the bicone model is validated for extracting the form factor of gold bipyramids in solution from small-angle X-ray scattering data.1600-57671600-5767research papers2212023-02-01214https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1February 2023med@iucr.org56Machine learning for scattering data: strategies, perspectives and applications to surface scattering
http://scripts.iucr.org/cgi-bin/paper?jo5077
Machine learning (ML) has received enormous attention in science and beyond. Discussed here are the status, opportunities, challenges and limitations of ML as applied to X-ray and neutron scattering techniques, with an emphasis on surface scattering. Typical strategies are outlined, as well as possible pitfalls. Applications to reflectometry and grazing-incidence scattering are critically discussed. Comment is also given on the availability of training and test data for ML applications, such as neural networks, and a large reflectivity data set is provided as reference data for the community.SURFACE SCATTERING; X-RAY DIFFRACTION; NEUTRON SCATTERING; MACHINE LEARNING; DATA ANALYSIShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHinderhofer, A.Greco, A.Starostin, V.Munteanu, V.Pithan, L.Gerlach, A.Schreiber, F.texturn:issn:1600-5767Machine learning for scattering data: strategies, perspectives and applications to surface scatteringMachine learning (ML) has received enormous attention in science and beyond. Discussed here are the status, opportunities, challenges and limitations of ML as applied to X-ray and neutron scattering techniques, with an emphasis on surface scattering. Typical strategies are outlined, as well as possible pitfalls. Applications to reflectometry and grazing-incidence scattering are critically discussed. Comment is also given on the availability of training and test data for ML applications, such as neural networks, and a large reflectivity data set is provided as reference data for the community.doi:10.1107/S16005767220115662023-02-01text/htmlThe status, opportunities, challenges and limitations of machine learning are discussed as applied to X-ray and neutron scattering techniques, with an emphasis on surface scattering.56February 2023med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography12023-02-011131600-5767topical reviews1600-5767Advice on describing Bayesian analysis of neutron and X-ray reflectometry
http://scripts.iucr.org/cgi-bin/paper?yr5098
As a result of the availability of modern software and hardware, Bayesian analysis is becoming more popular in neutron and X-ray reflectometry analysis. The understandability and replicability of these analyses may be harmed by inconsistencies in how the probability distributions central to Bayesian methods are represented in the literature. Herein advice is provided on how to report the results of Bayesian analysis as applied to neutron and X-ray reflectometry. This includes the clear reporting of initial starting conditions, the prior probabilities, the results of any analysis and the posterior probabilities that are the Bayesian equivalent of the error bar, to enable replicability and improve understanding. It is believed that this advice, grounded in the authors' experience working in the field, will enable greater analytical reproducibility in the work of the reflectometry community, and improve the quality and usability of results.REFLECTOMETRY; REFLECTIVITY; BAYESIAN ANALYSIS; FAIR DATA STANDARDShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMcCluskey, A.R.Caruana, A.J.Kinane, C.J.Armstrong, A.J.Arnold, T.Cooper, J.F.K.Cortie, D.L.Hughes, A.V.Moulin, J.-F.Nelson, A.R.J.Potrzebowski, W.Starostin, V.texturn:issn:1600-5767Advice on describing Bayesian analysis of neutron and X-ray reflectometryAs a result of the availability of modern software and hardware, Bayesian analysis is becoming more popular in neutron and X-ray reflectometry analysis. The understandability and replicability of these analyses may be harmed by inconsistencies in how the probability distributions central to Bayesian methods are represented in the literature. Herein advice is provided on how to report the results of Bayesian analysis as applied to neutron and X-ray reflectometry. This includes the clear reporting of initial starting conditions, the prior probabilities, the results of any analysis and the posterior probabilities that are the Bayesian equivalent of the error bar, to enable replicability and improve understanding. It is believed that this advice, grounded in the authors' experience working in the field, will enable greater analytical reproducibility in the work of the reflectometry community, and improve the quality and usability of results.doi:10.1107/S16005767220114262023-02-01text/htmlThe members of the Open Reflectometry Standards Organisation outline their best practice for reporting the results of Bayesian analysis of reflectometry measurements. Following this advice will enable greater reproducibility and improve understanding.https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1172023-02-01121600-5767feature articles1600-576756February 2023med@iucr.orgSpecimen-displacement correction for powder X-ray diffraction in Debye–Scherrer geometry with a flat area detector
http://scripts.iucr.org/cgi-bin/paper?vb5047
The effect of small changes in the specimen-to-detector distance on the unit-cell parameters is examined for synchrotron powder diffraction in Debye–Scherrer (transmission) geometry with a flat area detector. An analytical correction equation is proposed to fix the shift in 2θ values due to specimen capillary displacement. This equation does not require the use of an internal reference material, is applied during the Rietveld refinement step, and is analogous to the specimen-displacement correction equations for Bragg–Brentano and curved-detector Debye–Scherrer geometry experiments, but has a different functional form. The 2θ correction equation is compared with another specimen-displacement correction based on the use of an internal reference material in which new integration and calibration parameters of area-detector images are determined. Example data sets showing the effect of a 3.3 mm specimen displacement on the unit-cell parameters for 25°C CeO2, including both types of displacement correction, are described. These experiments were performed at powder X-ray diffraction beamlines at the National Synchrotron Light Source II at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory.DEBYE-SCHERRER; TRANSMISSION; SPECIMEN-TO-DETECTOR DISTANCE; DISPLACEMENT CORRECTION EQUATION; POWDER X-RAY DIFFRACTION; AREA DETECTORShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHulbert, B.S.Kriven, W.M.texturn:issn:1600-5767Specimen-displacement correction for powder X-ray diffraction in Debye–Scherrer geometry with a flat area detectorThe effect of small changes in the specimen-to-detector distance on the unit-cell parameters is examined for synchrotron powder diffraction in Debye–Scherrer (transmission) geometry with a flat area detector. An analytical correction equation is proposed to fix the shift in 2θ values due to specimen capillary displacement. This equation does not require the use of an internal reference material, is applied during the Rietveld refinement step, and is analogous to the specimen-displacement correction equations for Bragg–Brentano and curved-detector Debye–Scherrer geometry experiments, but has a different functional form. The 2θ correction equation is compared with another specimen-displacement correction based on the use of an internal reference material in which new integration and calibration parameters of area-detector images are determined. Example data sets showing the effect of a 3.3 mm specimen displacement on the unit-cell parameters for 25°C CeO2, including both types of displacement correction, are described. These experiments were performed at powder X-ray diffraction beamlines at the National Synchrotron Light Source II at Brookhaven National Laboratory and the Advanced Photon Source at Argonne National Laboratory.doi:10.1107/S16005767220113602023-02-01text/htmlAn analytical correction equation is proposed to fix the shift in 2θ values caused by specimen capillary displacements for powder diffraction experiments in Debye–Scherrer (transmission) geometry with a flat area detector. The accuracy of this equation and the corresponding corrections were verified by comparing it with a correction based on new integration parameters from an internal reference material.https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography12023-02-011661601600-5767research papers1600-576756February 2023med@iucr.orgSmall-angle X-ray scattering intensity of multiscale models of spheroids
http://scripts.iucr.org/cgi-bin/paper?jl5051
The microstructure of heterogeneous catalysts often consists of multiscale aggregates of nanoparticles, some of which are highly anisotropic. Therefore, small-angle X-ray scattering, in classical or anomalous mode, is a valuable tool to characterize this kind of material. Yet, the classical exploitation of the scattered intensities through form and structure factors or by means of Boolean models of spheres is questionable. Here, it is proposed to interpret the scattered intensities through the use of multiscale Boolean models of spheroids. The numerical procedure to compute scattered intensities of such models is given and then validated on asymptotic diluted Boolean models, and its applicability is demonstrated for the characterization of alumina catalyst supports.SMALL-ANGLE X-RAY SCATTERING; BOOLEAN MODELS; MULTISCALE AGGREGATES; CATALYSTS; SUPPORTS; SPHEROIDShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenDuchêne, P.Humbert, S.Sorbier, L.Moreaud, M.texturn:issn:1600-5767Small-angle X-ray scattering intensity of multiscale models of spheroidsThe microstructure of heterogeneous catalysts often consists of multiscale aggregates of nanoparticles, some of which are highly anisotropic. Therefore, small-angle X-ray scattering, in classical or anomalous mode, is a valuable tool to characterize this kind of material. Yet, the classical exploitation of the scattered intensities through form and structure factors or by means of Boolean models of spheres is questionable. Here, it is proposed to interpret the scattered intensities through the use of multiscale Boolean models of spheroids. The numerical procedure to compute scattered intensities of such models is given and then validated on asymptotic diluted Boolean models, and its applicability is demonstrated for the characterization of alumina catalyst supports.doi:10.1107/S16005767220113592023-02-01text/htmlSmall-angle X-ray scattering intensity is simulated for multiscale Boolean models of spheroids.56med@iucr.orgFebruary 2023Journal of Applied Crystallography1https://creativecommons.org/licenses/by/4.0/2372023-02-01246research papers1600-57671600-5767Design research with the use of visual and symmetry analysis in indigenous woven textiles
http://scripts.iucr.org/cgi-bin/paper?in5067
Since ca the 1990s, there have been developments in the weaving process for making tin chok fabrics in the Long district, Phrae province, northern Thailand, with the aim of reducing the production time and increasing the production capacity with respect to poverty alleviation and cultural revitalization. In this article, the symmetry patterns in tin chok fabrics in a collection of 17 vintage (traditional) skirts held in the Komol Antique Textile Museum, in the Long district, are examined to determine how to distinguish tin chok fabrics woven by the integrated method from those woven by the traditional method. The research includes visual and symmetry analysis, literature review, fieldwork, and the creation of a pattern booklet. This research reveals that the hem, which is one of the four parts (supplementary part one, the main part, supplementary part two and the hem) of the detachable tin chok, is key to distinguishing the fabrics made by the two methods. The four parts of tin chok made by the integrated method will always have a common vertical axis of symmetry, whereas the vertical axes of symmetry of the hem of a fabric made by the traditional method may not be aligned with the motifs in the other three parts. The frieze groups of the individual parts of the 17 vintage (traditional) skirts are decoded and possible corresponding patterns for weaving by the integrated method are generated.DESIGN VISUALIZATION; FRIEZE GROUPS; VISUAL ANAYSIS; SYMMETRY ANALYSIS; TRADITIONAL WEAVING; TEXTILE PATTERNShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenChudasri, D.Sukantamala, N.texturn:issn:1600-5767Design research with the use of visual and symmetry analysis in indigenous woven textilesSince ca the 1990s, there have been developments in the weaving process for making tin chok fabrics in the Long district, Phrae province, northern Thailand, with the aim of reducing the production time and increasing the production capacity with respect to poverty alleviation and cultural revitalization. In this article, the symmetry patterns in tin chok fabrics in a collection of 17 vintage (traditional) skirts held in the Komol Antique Textile Museum, in the Long district, are examined to determine how to distinguish tin chok fabrics woven by the integrated method from those woven by the traditional method. The research includes visual and symmetry analysis, literature review, fieldwork, and the creation of a pattern booklet. This research reveals that the hem, which is one of the four parts (supplementary part one, the main part, supplementary part two and the hem) of the detachable tin chok, is key to distinguishing the fabrics made by the two methods. The four parts of tin chok made by the integrated method will always have a common vertical axis of symmetry, whereas the vertical axes of symmetry of the hem of a fabric made by the traditional method may not be aligned with the motifs in the other three parts. The frieze groups of the individual parts of the 17 vintage (traditional) skirts are decoded and possible corresponding patterns for weaving by the integrated method are generated.doi:10.1107/S16005767220111532023-02-01text/htmlThis research examines a type of traditional handwoven skirt from northern Thailand, with the aim of distinguishing the fabrics made by the faster integrated method from those made by the traditional method. Visual and symmetry analysis have been employed to inspect the fabric patterns, the design structure and the symmetries.2023-02-019481https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography11600-57671600-5767research papers56February 2023med@iucr.orgExperimental setup for high-resolution characterization of crystal optics for coherent X-ray beam applications
http://scripts.iucr.org/cgi-bin/paper?ei5086
Stanford Synchrotron Radiation Lightsource serves a wide scientific community with its variety of X-ray capabilities. Recently, a wiggler X-ray source located at beamline 10-2 has been employed to perform high-resolution rocking curve imaging (RCI) of diamond and silicon crystals. X-ray RCI is invaluable for the development of upcoming cavity-based X-ray sources at SLAC, including the cavity-based X-ray free-electron laser and X-ray laser oscillator. In this paper, the RCI apparatus is described and experimental results are provided to validate its design. Future improvements of the setup are also discussed.BRAGG CRYSTALS; ROCKING CURVE IMAGING; DARWIN WIDTH; CAVITY-BASED X-RAY SOURCEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHalavanau, A.Margraf, R.Robles, R.MacArthur, J.Qu, Z.Marcus, G.Wu, J.Sato, T.Zhu, D.Takacs, C.J.Arthur, R.Kraynis, O.Johnson, B.Rabedeau, T.texturn:issn:1600-5767Experimental setup for high-resolution characterization of crystal optics for coherent X-ray beam applicationsStanford Synchrotron Radiation Lightsource serves a wide scientific community with its variety of X-ray capabilities. Recently, a wiggler X-ray source located at beamline 10-2 has been employed to perform high-resolution rocking curve imaging (RCI) of diamond and silicon crystals. X-ray RCI is invaluable for the development of upcoming cavity-based X-ray sources at SLAC, including the cavity-based X-ray free-electron laser and X-ray laser oscillator. In this paper, the RCI apparatus is described and experimental results are provided to validate its design. Future improvements of the setup are also discussed.doi:10.1107/S16005767220109982023-02-01text/htmlThe article presents the rocking curve imaging instrument at Stanford Synchrotron Radiation Lightsource beamline 10-2, which is used to characterize diamond and silicon crystals for Bragg optics applications.med@iucr.orgFebruary 2023561600-5767research papers1600-57671552023-02-01159Journal of Applied Crystallography1https://creativecommons.org/licenses/by/4.0/xrd_simulator: 3D X-ray diffraction simulation software supporting 3D polycrystalline microstructure morphology descriptions
http://scripts.iucr.org/cgi-bin/paper?nb5332
An open source Python package named xrd_simulator, capable of simulating geometrical interactions between a monochromatic X-ray beam and a polycrystalline microstructure, is described and demonstrated. The software can simulate arbitrary intragranular lattice variations of single crystals embedded within a multiphase 3D aggregate by making use of a tetrahedral mesh representation where each element holds an independent lattice. By approximating the X-ray beam as an arbitrary convex polyhedral region in space and letting the sample be moved continuously through arbitrary rigid motions, data from standard and non-standard measurement sequences can be simulated. This implementation is made possible through analytical solutions to a modified, time-dependent version of the Laue equations. The software, which primarily targets three-dimensional X-ray diffraction microscopy (high-energy X-ray diffraction microscopy) type experiments, enables the numerical exploration of which sample quantities can and cannot be reconstructed for a given acquisition scheme. Similarly, xrd_simulator targets investigations of different measurement sequences in relation to optimizing both experimental run times and sampling.X-RAY DIFFRACTION; 3DXRD; SIMULATION TOOLS; POLYCRYSTALLINE MICROSTRUCTURE; COMPUTER PROGRAMShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHenningsson, A.Hall, S.A.texturn:issn:1600-5767xrd_simulator: 3D X-ray diffraction simulation software supporting 3D polycrystalline microstructure morphology descriptionsAn open source Python package named xrd_simulator, capable of simulating geometrical interactions between a monochromatic X-ray beam and a polycrystalline microstructure, is described and demonstrated. The software can simulate arbitrary intragranular lattice variations of single crystals embedded within a multiphase 3D aggregate by making use of a tetrahedral mesh representation where each element holds an independent lattice. By approximating the X-ray beam as an arbitrary convex polyhedral region in space and letting the sample be moved continuously through arbitrary rigid motions, data from standard and non-standard measurement sequences can be simulated. This implementation is made possible through analytical solutions to a modified, time-dependent version of the Laue equations. The software, which primarily targets three-dimensional X-ray diffraction microscopy (high-energy X-ray diffraction microscopy) type experiments, enables the numerical exploration of which sample quantities can and cannot be reconstructed for a given acquisition scheme. Similarly, xrd_simulator targets investigations of different measurement sequences in relation to optimizing both experimental run times and sampling.doi:10.1107/S16005767220110012023-02-01text/htmlAn open source Python package named xrd_simulator, developed to address the need for 3D microstructure morphology simulation in 3DXRD-type experiments, is described and demonstrated.1600-57671600-5767computer programs2922023-02-01282https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography1February 2023med@iucr.org56Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
http://scripts.iucr.org/cgi-bin/paper?te5103
Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal–organic compounds and network structures such as covalent organic frameworks and metal–organic frameworks is now possible in a hybrid mode such as IAM–TAAM or HAR–TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.QUANTUM CRYSTALLOGRAPHY; ASPHERICAL ATOM REFINEMENT; TRANSFERABLE ASPHERICAL ATOM MODEL; TAAM; MATTS; HIRSHFELD ATOM REFINEMENT; HAR; NOSPHERA2; DISORDER; STRUCTURE REFINEMENThttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenJha, K.K.Kleemiss, F.Chodkiewicz, M.L.Dominiak, P.M.texturn:issn:1600-5767Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-offAspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal–organic compounds and network structures such as covalent organic frameworks and metal–organic frameworks is now possible in a hybrid mode such as IAM–TAAM or HAR–TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.doi:10.1107/S16005767220108832023-02-01text/htmlIt is now possible to integrate the transferable aspherical atom model (TAAM) with NoSpherA2 and refine X-ray diffraction data of disordered, twinned, co-crystal, covalent organic framework and metal–salt structures in a short period of time. A new hybrid approach, allowing a combination of the independent atom model, Hirshfeld atom refinement and TAAM in one structure refinement, is introduced which benefits from the advantages of each method.56February 2023med@iucr.org2023-02-01127116https://creativecommons.org/licenses/by/4.0/1Journal of Applied Crystallography1600-57671600-5767research papersSpatz: the time-of-flight neutron reflectometer with vertical sample geometry at the OPAL research reactor
http://scripts.iucr.org/cgi-bin/paper?xx5008
The Spatz neutron beam instrument is the second time-of-flight neutron reflectometer to be installed at the OPAL research reactor. The instrument was formerly the V18 BioRef reflectometer at the BER-II reactor in Berlin and was transferred to Australia in 2016. Subsequently the instrument was re-installed in the neutron guide hall of the OPAL reactor at the end position of the CG2B cold-neutron guide and recommissioned. The instrument performance has not been compromised by the move, with reflectivity achieved down to 10−7 and good counting statistics within a reasonable time frame using a wavelength range of 2–20 Å. Several different samples at the solid–air interface and the solid–liquid interface have been measured to demonstrate the instrument's capabilities.NEUTRON REFLECTOMETRY; INSTRUMENT COMMISSIONING; SURFACES; INTERFACES; TIME OF FLIGHThttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLe Brun, A.P.Huang, T.-Y.Pullen, S.Nelson, A.R.J.Spedding, J.Holt, S.A.texturn:issn:1600-5767Spatz: the time-of-flight neutron reflectometer with vertical sample geometry at the OPAL research reactorThe Spatz neutron beam instrument is the second time-of-flight neutron reflectometer to be installed at the OPAL research reactor. The instrument was formerly the V18 BioRef reflectometer at the BER-II reactor in Berlin and was transferred to Australia in 2016. Subsequently the instrument was re-installed in the neutron guide hall of the OPAL reactor at the end position of the CG2B cold-neutron guide and recommissioned. The instrument performance has not been compromised by the move, with reflectivity achieved down to 10−7 and good counting statistics within a reasonable time frame using a wavelength range of 2–20 Å. Several different samples at the solid–air interface and the solid–liquid interface have been measured to demonstrate the instrument's capabilities.doi:10.1107/S160057672201086X2023-02-01text/htmlThe performance of the Spatz neutron reflectometer is demonstrated. It has a variable wavelength resolution to suit experimental needs for reflectometry at air–solid and solid–liquid interfaces.252023-02-0118https://creativecommons.org/licenses/by/4.0/1Journal of Applied Crystallography1600-57671600-5767research papers56February 2023med@iucr.orgCombining reverse Monte Carlo analysis of X-ray scattering and extended X-ray absorption fine structure spectra of very small nanoparticles
http://scripts.iucr.org/cgi-bin/paper?jl5055
Finite size effects in partial pair distribution functions generate artefacts in the scattering structure factor and scattering intensity. It is shown how they can be overcome using a binned version of the Debye scattering equation. Accordingly, reverse Monte Carlo simulations are used for very small nanoparticles of LaFeO3 with diameters below 10 nm to simultaneously analyse X-ray scattering data and extended X-ray absorption fine structure spectra at the La K and Fe K edges. The structural information obtained is consistent regarding local structure and long-range order.EXTENDED X-RAY ABSORPTION FINE STRUCTURE; EXAFS; WIDE-ANGLE X-RAY SCATTERING; WAXS; REVERSE MONTE CARLO; RMC; NANOCRYSTALS; LAFEO3https://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenWinterer, M.Geiß, J.texturn:issn:1600-5767Combining reverse Monte Carlo analysis of X-ray scattering and extended X-ray absorption fine structure spectra of very small nanoparticlesFinite size effects in partial pair distribution functions generate artefacts in the scattering structure factor and scattering intensity. It is shown how they can be overcome using a binned version of the Debye scattering equation. Accordingly, reverse Monte Carlo simulations are used for very small nanoparticles of LaFeO3 with diameters below 10 nm to simultaneously analyse X-ray scattering data and extended X-ray absorption fine structure spectra at the La K and Fe K edges. The structural information obtained is consistent regarding local structure and long-range order.doi:10.1107/S16005767220108582023-02-01text/htmlComputing scattering intensity using the Debye scattering equation after binning interatomic distances avoids finite size artefacts and is efficient enough for simultaneous refinement of scattering data and extended X-ray absorption spectra by reverse Monte Carlo simulations.https://creativecommons.org/licenses/by/4.0/1Journal of Applied Crystallography1092023-02-011031600-5767research papers1600-576756February 2023med@iucr.orgSmall-angle neutron scattering of long-wavelength magnetic modulations in reduced sample dimensions
http://scripts.iucr.org/cgi-bin/paper?uq5006
Magnetic small-angle neutron scattering (SANS) is ideally suited to providing direct reciprocal-space information on long-wavelength magnetic modulations, such as helicoids, solitons, merons or skyrmions. SANS of such structures in thin films or micro-structured bulk materials is strongly limited by the tiny scattering volume vis a vis the prohibitively high background scattering by the substrate and support structures. Considering near-surface scattering just above the critical angle of reflection, where unwanted signal contributions due to substrate or support structures become very small, it is established that the scattering patterns of the helical, conical, skyrmion lattice and fluctuation-disordered phases in a polished bulk sample of MnSi are equivalent for conventional transmission and near-surface SANS geometries. This motivates the prediction of a complete repository of scattering patterns expected for thin films in the near-surface SANS geometry for each orientation of the magnetic order with respect to the scattering plane.SMALL-ANGLE NEUTRON SCATTERING; NEAR-SURFACE SANS; MAGNETISM; NON-COLLINEAR MAGNETISM; THIN FILMS; SKYRMIONS; MNSIhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenCauser, G.L.Chacon, A.Heinemann, A.Pfleiderer, C.texturn:issn:1600-5767Small-angle neutron scattering of long-wavelength magnetic modulations in reduced sample dimensionsMagnetic small-angle neutron scattering (SANS) is ideally suited to providing direct reciprocal-space information on long-wavelength magnetic modulations, such as helicoids, solitons, merons or skyrmions. SANS of such structures in thin films or micro-structured bulk materials is strongly limited by the tiny scattering volume vis a vis the prohibitively high background scattering by the substrate and support structures. Considering near-surface scattering just above the critical angle of reflection, where unwanted signal contributions due to substrate or support structures become very small, it is established that the scattering patterns of the helical, conical, skyrmion lattice and fluctuation-disordered phases in a polished bulk sample of MnSi are equivalent for conventional transmission and near-surface SANS geometries. This motivates the prediction of a complete repository of scattering patterns expected for thin films in the near-surface SANS geometry for each orientation of the magnetic order with respect to the scattering plane.doi:10.1107/S16005767220107552023-02-01text/htmlNear-surface SANS is discussed for its potential as a probe of long-wavelength magnetic modulations in specimens with reduced sample dimensions.352023-02-0126https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography11600-57671600-5767research papers56February 2023med@iucr.orgKinematic scattering by nanocrystals
http://scripts.iucr.org/cgi-bin/paper?xx5007
Various formulations are compared which describe diffraction from ultra-thin single-crystal films in the symmetric scattering configuration, showing that, for this thickness range, several implicit assumptions in these formulations are no longer satisfied. Consequently, the position, integrated intensity and integral breadth of a diffraction peak cannot be related to the lattice spacing of the material or the number of unit cells along the diffraction vector using traditional analysis methods. Some simple equations are proposed to obtain the correct values of these parameters for this specific sample/diffraction geometry combination. More generally, the development of rigorous formalisms for analyzing diffraction from nanocrystals is proposed.X-RAY DIFFRACTION; NANOCRYSTALS; KINEMATIC SCATTERINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenThomas, O.Noyan, I.C.texturn:issn:1600-5767Kinematic scattering by nanocrystalsVarious formulations are compared which describe diffraction from ultra-thin single-crystal films in the symmetric scattering configuration, showing that, for this thickness range, several implicit assumptions in these formulations are no longer satisfied. Consequently, the position, integrated intensity and integral breadth of a diffraction peak cannot be related to the lattice spacing of the material or the number of unit cells along the diffraction vector using traditional analysis methods. Some simple equations are proposed to obtain the correct values of these parameters for this specific sample/diffraction geometry combination. More generally, the development of rigorous formalisms for analyzing diffraction from nanocrystals is proposed.doi:10.1107/S160057672201069X2023-02-01text/htmlThis work compares various formulations which describe diffraction from ultra-thin single-crystal films and shows that, for this thickness range, several implicit assumptions in these formulations are no longer satisfied. This has important consequences for the analysis of diffraction patterns from nanocrystals.1600-5767research papers1600-57671282023-02-01134Journal of Applied Crystallography1https://creativecommons.org/licenses/by/4.0/med@iucr.orgFebruary 202356Pressure cells for in situ neutron total scattering: time and real-space resolution during deuterium absorption
http://scripts.iucr.org/cgi-bin/paper?ei5089
In situ gas-loading sample holders for two-dimensionally arranged detectors in time-of-flight neutron total scattering experiments have been developed to investigate atomic arrangements during deuterium absorption using time and real-space resolution. A single-crystal sapphire container was developed that allows conditions of 473 K and 10 MPa hydrogen gas pressure. High-resolution transient measurements detected deuterium absorption by palladium that proceeded within a few seconds. A double-layered container with thick- and thin-walled vanadium allowed conditions of 423 K and 10 MPa hydrogen gas pressure. The deuterium occupation sites of a lanthanum–nickel–aluminium alloy are discussed in detail on the basis of real-space high-resolution data obtained from in situ neutron scattering measurements and reverse Monte Carlo structural modeling.IN SITU NEUTRON TOTAL SCATTERING; PAIR DISTRIBUTION FUNCTIONS; HYDROGEN STORAGE; REVERSE MONTE CARLO METHODShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenIkeda, K.Ohshita, H.Otomo, T.Sakaki, K.Kim, H.Nakamura, Y.Machida, A.Von Dreele, R.B.texturn:issn:1600-5767Pressure cells for in situ neutron total scattering: time and real-space resolution during deuterium absorptionIn situ gas-loading sample holders for two-dimensionally arranged detectors in time-of-flight neutron total scattering experiments have been developed to investigate atomic arrangements during deuterium absorption using time and real-space resolution. A single-crystal sapphire container was developed that allows conditions of 473 K and 10 MPa hydrogen gas pressure. High-resolution transient measurements detected deuterium absorption by palladium that proceeded within a few seconds. A double-layered container with thick- and thin-walled vanadium allowed conditions of 423 K and 10 MPa hydrogen gas pressure. The deuterium occupation sites of a lanthanum–nickel–aluminium alloy are discussed in detail on the basis of real-space high-resolution data obtained from in situ neutron scattering measurements and reverse Monte Carlo structural modeling.doi:10.1107/S16005767220105612022-12-01text/htmlIn situ gas-loading sample holders for two-dimensionally arranged detectors in time-of-flight neutron total scattering experiments have been developed for the structural analysis of the deuterium absorption process using time and real-space resolution.16312022-12-0116396Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767research papers1600-576755med@iucr.orgDecember 2022Multiscale magnetization in cobalt-doped ferrite nanocubes
http://scripts.iucr.org/cgi-bin/paper?un5008
The magnetization of cobalt ferrite nanocubes of similar size, but with varying Co/Fe ratio, is extensively characterized on atomistic and nanoscopic length scales. Combination of X-ray diffraction, Mössbauer spectroscopy, magnetization measurements and polarized small-angle neutron scattering (SANS) reveals that a lower amount of cobalt leads to an enhanced magnetization. At the same time, magnetic SANS confirms no or negligible near-surface spin disorder in these highly crystalline, homogeneously magnetized nanoparticles, resulting in an exceptionally hard magnetic material with high coercivity.MAGNETIC SMALL-ANGLE NEUTRON SCATTERING; NANOPARTICLES; FERRITE; COERCIVITY; MOSSBAUER SPECTROSCOPY; NEAR-SURFACE SPIN DISORDERhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenZákutná, D.Fischer, A.Dresen, D.Nižňanský, D.Honecker, D.Disch, S.texturn:issn:1600-5767Multiscale magnetization in cobalt-doped ferrite nanocubesThe magnetization of cobalt ferrite nanocubes of similar size, but with varying Co/Fe ratio, is extensively characterized on atomistic and nanoscopic length scales. Combination of X-ray diffraction, Mössbauer spectroscopy, magnetization measurements and polarized small-angle neutron scattering (SANS) reveals that a lower amount of cobalt leads to an enhanced magnetization. At the same time, magnetic SANS confirms no or negligible near-surface spin disorder in these highly crystalline, homogeneously magnetized nanoparticles, resulting in an exceptionally hard magnetic material with high coercivity.doi:10.1107/S16005767220102872022-12-01text/htmlA set of cuboidal cobalt ferrite nanoparticles with exceptionally high crystallinity is presented, expressed by homogeneous magnetization with negligible near-surface spin disorder as observed by magnetic small-angle neutron scattering.55December 2022med@iucr.org2022-12-0116301622https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography61600-57671600-5767research papersReconstruction algorithms for grain mapping by laboratory X-ray diffraction contrast tomography
http://scripts.iucr.org/cgi-bin/paper?jl5050
X-ray-based non-destructive 3D grain mapping techniques are well established at synchrotron facilities. To facilitate everyday access to grain mapping instruments, laboratory diffraction contrast tomography (LabDCT), using a laboratory-based conical polychromatic X-ray beam, has been developed and commercialized. Yet the currently available LabDCT grain reconstruction methods are either ill-suited for handling a large number of grains or require a commercial licence bound to a specific instrument. To promote the availability of LabDCT, grain reconstruction methods have been developed with multiple reconstruction algorithms based on both forward and back calculations. The different algorithms are presented in detail and their efficient implementation using parallel computing is described. The performance of different reconstruction methods is assessed on synthetic data. The code to implement all the described algorithms has been made publicly accessible with the intention of fostering the development of grain mapping techniques on widely available laboratory instruments.DIFFRACTION CONTRAST TOMOGRAPHY; GRAIN MAPPING; RECONSTRUCTION ALGORITHMS; 3D IMAGING; FORWARD CALCULATIONS; BACK CALCULATIONShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenFang, H.Ludwig, W.Lhuissier, P.texturn:issn:1600-5767Reconstruction algorithms for grain mapping by laboratory X-ray diffraction contrast tomographyX-ray-based non-destructive 3D grain mapping techniques are well established at synchrotron facilities. To facilitate everyday access to grain mapping instruments, laboratory diffraction contrast tomography (LabDCT), using a laboratory-based conical polychromatic X-ray beam, has been developed and commercialized. Yet the currently available LabDCT grain reconstruction methods are either ill-suited for handling a large number of grains or require a commercial licence bound to a specific instrument. To promote the availability of LabDCT, grain reconstruction methods have been developed with multiple reconstruction algorithms based on both forward and back calculations. The different algorithms are presented in detail and their efficient implementation using parallel computing is described. The performance of different reconstruction methods is assessed on synthetic data. The code to implement all the described algorithms has been made publicly accessible with the intention of fostering the development of grain mapping techniques on widely available laboratory instruments.doi:10.1107/S16005767220102142022-12-01text/htmlGrain reconstruction methods based on both forward and back calculations have been developed for laboratory-based diffraction contrast tomography. These methods are computationally efficient and can give good orientation and spatial accuracies, and the code is open source.1600-57671600-5767research papers2022-12-0116631652https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography6December 2022med@iucr.org55Shape-induced superstructure formation in concentrated ferrofluids under applied magnetic fields
http://scripts.iucr.org/cgi-bin/paper?uq5005
The field-induced ordering of concentrated ferrofluids based on spherical and cuboidal maghemite nanoparticles is studied using small-angle neutron scattering, revealing a qualitative effect of the faceted shape on the interparticle interactions as shown in the structure factor and correlation lengths. Whereas a spatially disordered hard-sphere interaction potential with a short correlation length is found for ∼9 nm spherical nanoparticles, nanocubes of a comparable particle size exhibit a more pronounced interparticle interaction and the formation of linear arrangements. Analysis of the anisotropic two-dimensional pair distance correlation function gives insight into the real-space arrangement of the nanoparticles. On the basis of the short interparticle distances found here, oriented attachment, i.e. a face-to-face arrangement of the nanocubes, is likely. The unusual field dependence of the interparticle correlations suggests a field-induced structural rearrangement.FERROFLUIDS; NANOCUBES; DIPOLAR INTERACTIONS; SMALL-ANGLE NEUTRON SCATTERING; MAGNETIC SANShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBender, P.Wetterskog, E.Salazar-Alvarez, G.Bergström, L.Hermann, R.P.Brückel, T.Wiedenmann, A.Disch, S.texturn:issn:1600-5767Shape-induced superstructure formation in concentrated ferrofluids under applied magnetic fieldsThe field-induced ordering of concentrated ferrofluids based on spherical and cuboidal maghemite nanoparticles is studied using small-angle neutron scattering, revealing a qualitative effect of the faceted shape on the interparticle interactions as shown in the structure factor and correlation lengths. Whereas a spatially disordered hard-sphere interaction potential with a short correlation length is found for ∼9 nm spherical nanoparticles, nanocubes of a comparable particle size exhibit a more pronounced interparticle interaction and the formation of linear arrangements. Analysis of the anisotropic two-dimensional pair distance correlation function gives insight into the real-space arrangement of the nanoparticles. On the basis of the short interparticle distances found here, oriented attachment, i.e. a face-to-face arrangement of the nanocubes, is likely. The unusual field dependence of the interparticle correlations suggests a field-induced structural rearrangement.doi:10.1107/S16005767220100932022-12-01text/htmlIn-field small-angle neutron scattering reveals superstructure formation in a concentrated dispersion of spherical and cuboidal iron oxide nanoparticles.Journal of Applied Crystallography6https://creativecommons.org/licenses/by/4.0/16132022-12-011621research papers1600-57671600-576755med@iucr.orgDecember 2022Small-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.SMALL-ANGLE X-RAY SCATTERING; SAXS; SCANNING MICRODIFFRACTION; AMYLOIDS; ALZHEIMER'S DISEASEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenNepal, P.Al Bashit, A.Yang, L.Makowski, L.texturn:issn:1600-5767Small-angle X-ray microdiffraction from fibrils embedded in tissue thin sectionsSmall-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.doi:10.1107/S16005767220099552022-11-21text/htmlThe 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.1600-5767research papers1600-57672022-11-216Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/med@iucr.orgDecember 202255Optimization 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.SMALL-ANGLE NEUTRON SCATTERING; SKYRMION; TISANEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMettus, D.Chacon, A.Bauer, A.Mühlbauer, S.Pfleiderer, C.texturn:issn:1600-5767Optimization strategies and artifacts of time-involved small-angle neutron scattering experimentsKinetic 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.doi:10.1107/S16005767220099312022-11-28text/htmlThis 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.2022-11-28https://creativecommons.org/licenses/by/4.0/6Journal of Applied Crystallography1600-57671600-5767research papers55December 2022med@iucr.orgPreparation 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.X-RAY DIFFRACTION; QUANTITATIVE PHASE ANALYSIS; PYRITE MINERAL; SAMPLE PREPARATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMcDougall, H.Hibberd, M.Tong, A.Neville, S.Peterson, V.Didier, C.texturn:issn:1600-5767Preparation of pyrite concentrate powder from the Thackaringa mine for quantitative phase analysis using X-ray diffractionThe 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.doi:10.1107/S16005767220098882022-11-28text/htmlA 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.1600-5767research papers1600-57672022-11-28Journal of Applied Crystallography6https://creativecommons.org/licenses/by/4.0/med@iucr.orgDecember 202255Automatic 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.BAD-PIXEL MASKS; ROBUST MASK MAKER; MACHINE LEARNING; ROBUST STATISTICS; SERIAL CRYSTALLOGRAPHYhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSadri, 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.texturn:issn:1600-5767Automatic bad-pixel mask maker for X-ray pixel detectors with application to serial crystallographyX-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.doi:10.1107/S16005767220098152022-11-21text/htmlAttention 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'.1600-57671600-5767research papers2022-11-21https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography6December 2022med@iucr.org55Progressive 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.STRUCTURE COMPARISON; CRYSTAL PACKING; CRYSTAL STRUCTURE PREDICTION; RADIUS OF GYRATION; MPI PARALLELIZATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenNessler, A.J.Okada, O.Hermon, M.J.Nagata, H.Schnieders, M.J.texturn:issn:1600-5767Progressive alignment of crystals: reproducible and efficient assessment of crystal structure similarityDuring 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.doi:10.1107/S16005767220096702022-11-21text/htmlEvaluating 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.https://creativecommons.org/licenses/by/4.0/6Journal of Applied Crystallography2022-11-211600-5767research papers1600-576755December 2022med@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.TIME-OF-FLIGHT NEUTRON SCATTERING; ALGORITHMS; SINGLE CRYSTALShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSavici, A.T.Gigg, M.A.Arnold, O.Tolchenov, R.Whitfield, R.E.Hahn, S.E.Zhou, W.Zaliznyak, I.A.texturn:issn:1600-5767Efficient data reduction for time-of-flight neutron scattering experiments on single crystalsEvent-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.doi:10.1107/S16005767220096452022-11-04text/htmlIn 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.55December 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/6Journal of Applied Crystallography2022-11-041600-5767research papers1600-5767Improving 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.POST-COLUMN ENERGY FILTERS; 3D ELECTRON DIFFRACTION; ENERGY-FILTERED 3D ED; MICROCRYSTAL ELECTRON DIFFRACTION; ENERGY-FILTERED MICROED; HAADF; CRYSTAL TRACKING; STRUCTURE DETERMINATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenYang, T.Xu, H.Zou, X.texturn:issn:1600-5767Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking methodThree-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.doi:10.1107/S16005767220096332022-11-28text/htmlZero-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.https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography62022-11-281600-5767research papers1600-576755December 2022med@iucr.orgExtending 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.NEUTRON RESONANT SPIN ECHO; MIEZE; QUASIELASTIC SCATTERING; THERMAL NEUTRONShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenJochum, J.K.Franz, C.Keller, T.Pfleiderer, C.texturn:issn:1600-5767Extending MIEZE spectroscopy towards thermal wavelengthsA 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.doi:10.1107/S16005767220095052022-10-27text/htmlA 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.55med@iucr.orgDecember 20226Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/2022-10-27research papers1600-57671600-5767Euphonic: 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.NEUTRON SCATTERING; PHONONS; FORCE CONSTANTS; EUPHONIChttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenFair, R.Jackson, A.Voneshen, D.Jochym, D.Le, D.Refson, K.Perring, T.texturn:issn:1600-5767Euphonic: inelastic neutron scattering simulations from force constants and visualization tools for phonon propertiesInterpretation 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.doi:10.1107/S16005767220092562022-11-28text/htmlAn overview of the Euphonic Python package for efficient simulation of inelastic neutron scattering by phonons from force constants is presented.med@iucr.orgDecember 202255computer programs1600-57671600-5767Journal of Applied Crystallography6https://creativecommons.org/licenses/by/4.0/2022-11-28A 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.SMALL-ANGLE NEUTRON SCATTERING; SMALL-ANGLE X-RAY SCATTERING; MAGNETIC NANOPARTICLES; SUPERPARAMAGNETIC IRON OXIDE NANOPARTICLES; REVERSE MONTE CARLO SIMULATIONShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBarnsley, L.C.Nandakumaran, N.Feoktystov, A.Dulle, M.Fruhner, L.Feygenson, M.texturn:issn:1600-5767A reverse Monte Carlo algorithm to simulate two-dimensional small-angle scattering intensitiesSmall-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.doi:10.1107/S16005767220092192022-11-28text/htmlSmall-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.55med@iucr.orgDecember 20226Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/2022-11-28research papers1600-57671600-5767Updates 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.SMALL-ANGLE SCATTERING; SASFIT; NUMERICAL MODELS; STRUCTURE FACTORS; FORM FACTORS; REGULARIZATION TECHNIQUEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenKohlbrecher, J.Breßler, I.texturn:issn:1600-5767Updates in SASfit for fitting analytical expressions and numerical models to small-angle scattering patternsSmall-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.doi:10.1107/S16005767220090372022-11-21text/htmlRecent 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.55December 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography62022-11-211600-5767computer programs1600-5767Magnetic 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.MAGNETIC NEUTRON SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MAGNETIC NANOPARTICLES; SURFACE ANISOTROPY; MICROMAGNETICShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAdams, M.P.Michels, A.Kachkachi, H.texturn:issn:1600-5767Magnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: analytical treatmentThe 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.doi:10.1107/S16005767220089252022-11-04text/htmlThe magnetization profile and the ensuing magnetic neutron scattering signal from an inhomogeneously magnetized spherical nanoparticle with Néel surface anisotropy are derived analytically.2022-11-04https://creativecommons.org/licenses/by/4.0/6Journal of Applied Crystallography1600-57671600-5767research papers55December 2022med@iucr.orgMagnetic 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.MAGNETIC NEUTRON SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MAGNETIC NANOPARTICLES; SURFACE ANISOTROPY; MICROMAGNETICShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAdams, M.P.Michels, A.Kachkachi, H.texturn:issn:1600-5767Magnetic neutron scattering from spherical nanoparticles with Néel surface anisotropy: atomistic simulationsA 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.doi:10.1107/S16005767220089492022-11-04text/htmlBased 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.December 2022med@iucr.org551600-5767research papers1600-5767https://creativecommons.org/licenses/by/4.0/6Journal of Applied Crystallography2022-11-04Analysis 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.VORTEX LATTICES; SUPERCONDUCTIVITY; TIME-OF-FLIGHT NEUTRON DIFFRACTION; SMALL-ANGLE NEUTRON SCATTERING; SANShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenCampillo, E.Bartkowiak, M.Prokhnenko, O.Smeibidl, P.Forgan, E.M.Blackburn, E.texturn:issn:1600-5767Analysis of time-of-flight small-angle neutron scattering data on mesoscopic crystals such as magnetic vortex latticesBragg 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.doi:10.1107/S16005767220082262022-10-01text/htmlA method is presented for extracting quantitative information on superconducting vortex lattices and other mesoscopic structures from time-of-flight small-angle neutron scattering.Journal of Applied Crystallography5https://creativecommons.org/licenses/by/4.0/131413232022-10-01research papers1600-57671600-576755med@iucr.orgOctober 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).BASSANITE; CALCITE; EPITAXY; TWINS; ANOMALOUS MIXED CRYSTALShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAquilano, D.Bruno, M.Ghignone, S.Pastero, L.Cotellucci, A.texturn:issn:1600-5767Epitaxies of Ca sulfates on calcite. II. The main {010}, {001} and {100} forms of bassanite epi-deposited on the {10.4} substrate form of calcite2D 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).doi:10.1107/S16005767220081962022-09-28text/htmlA 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.med@iucr.orgOctober 2022551600-5767research papers1600-576712892022-09-281296Journal of Applied Crystallography5https://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).HGCDTE; ELASTIC BEHAVIOUR; PLASTIC DEFORMATION; THIN FILMS; DISLOCATIONShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBiquard, X.Tuaz, A.Ballet, P.texturn:issn:1600-5767Using 2D integral breadth to study plastic relaxation in a quasi-lattice-matched HgCdTe/CdZnTe heterostructureMicro-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).doi:10.1107/S16005767220081842022-10-01text/htmlThe 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.med@iucr.orgOctober 202255research papers1600-57671600-5767Journal of Applied Crystallography5https://creativecommons.org/licenses/by/4.0/12972022-10-011304In-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.NEUTRON POWDER DIFFRACTION; X-RAY POWDER DIFFRACTION; RESONANCE SCATTERING; SPINEL FERRITES; MAGNETISMhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHenry, K.Ahlburg, J.V.Andersen, H.L.Granados-Miralles, C.Stingaciu, M.Saura-Múzquiz, M.Christensen, M.texturn:issn:1600-5767In-depth investigations of size and occupancies in cobalt ferrite nanoparticles by joint Rietveld refinements of X-ray and neutron powder diffraction dataPowder 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.doi:10.1107/S16005767220081232022-10-01text/htmlCombined 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.55med@iucr.orgOctober 2022Journal of Applied Crystallography5https://creativecommons.org/licenses/by/4.0/13362022-10-011350research papers1600-57671600-5767Domain 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.SINGLE-CRYSTAL DOMAIN AUTO FINDER; DAFI; SINGLE-CRYSTAL X-RAY DIFFRACTION; POLYCRYSTALLINE SAMPLES; MULTIPHASE MIXTUREShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAslandukov, A.Aslandukov, M.Dubrovinskaia, N.Dubrovinsky, L.texturn:issn:1600-5767Domain Auto Finder (DAFi) program: the analysis of single-crystal X-ray diffraction data from polycrystalline samplesThis 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.doi:10.1107/S16005767220080812022-09-28text/htmlThis 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.55med@iucr.orgOctober 202213832022-09-2813915Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767computer programs1600-5767The 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.COHERENT DIFFRACTION IMAGING; WIDE-ANGLE SCATTERING; MULTI-SLICE FOURIER TRANSFORM; APPROXIMATE METHODS; HIGH-PERFORMANCE COMPUTINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenColombo, A.Zimmermann, J.Langbehn, B.Möller, T.Peltz, C.Sander, K.Kruse, B.Tümmler, P.Barke, I.Rupp, D.Fennel, T.texturn:issn:1600-5767The Scatman: an approximate method for fast wide-angle scattering simulationsSingle-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.doi:10.1107/S16005767220080682022-09-14text/htmlA 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.55October 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography52022-09-14124612321600-5767research papers1600-5767Faster 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.NEUTRON REFLECTIVITY; X-RAY REFLECTIVITY; NEURAL NETWORKS; CO-REFINEMENT; IN SITU MEASUREMENThttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMareček, D.Oberreiter, J.Nelson, A.Kowarik, S.texturn:issn:1600-5767Faster and lower-dose X-ray reflectivity measurements enabled by physics-informed modeling and artificial intelligence co-refinementAn 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.doi:10.1107/S16005767220080562022-10-01text/htmlAn 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.med@iucr.orgOctober 2022551600-5767research papers1600-5767130513132022-10-015Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/From 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.CRYSTAL GROWTH; POLYMORPHISM; HIGH PRESSURE; MINERALS; MATERIALS; TEACHING; BIOPOLYMERS; PHARMACEUTICALShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenArkhipov, S.G.Bekker, T.B.Gaydamaka, A.A.Likhacheva, A.Y.Losev, E.A.Boldyreva, E.V.texturn:issn:1600-5767From geology to biology: an interdisciplinary course in crystal growthThis 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.doi:10.1107/S16005767220080322022-10-01text/htmlThe authors share experience of teaching an interdisciplinary university course in crystal growth with examples ranging from geology to biology.55October 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/5Journal of Applied Crystallography2022-10-01137613681600-5767teaching and education1600-5767HTD2: 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.HTD2; LOW TEMPERATURE; HIGH PRESSURE; SINGLE CRYSTALS; INSTRUMENTATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenFischer, A.Langmann, J.Vöst, M.Eickerling, G.Scherer, W.texturn:issn:1600-5767HTD2: a single-crystal X-ray diffractometer for combined high-pressure/low-temperature experiments at laboratory scaleHigh-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.doi:10.1107/S160057672200766X2022-09-28text/htmlThe 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.2022-09-2812661255https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography51600-57671600-5767research papers55October 2022med@iucr.orgRefinements 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.BRAGG COHERENT X-RAY DIFFRACTION IMAGING; ELECTRON BACKSCATTER DIFFRACTION; STRAIN CALCULATION; PHASE INTERPOLATION; CRYSTAL ORIENTATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenYang, D.Lapington, M.T.He, G.Song, K.Zhang, M.Barker, C.Harder, R.J.Cha, W.Liu, W.Phillips, N.W.Hofmann, F.texturn:issn:1600-5767Refinements for Bragg coherent X-ray diffraction imaging: electron backscatter diffraction alignment and strain field computationBragg 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.doi:10.1107/S16005767220076462022-09-06text/htmlA 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.55October 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography511952022-09-0611841600-5767research papers1600-5767Site 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.MAGNETOCALORIC EFFECT; MAGNETIC STRUCTURE; NEUTRON DIFFRACTION; SYNCHROTRON DIFFRACTION; SITE DEPENDENCEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAit Haddouch, M.Abboushi, N.Sharma, N.Eich, A.Grzechnik, A.Li, C.Tolkiehn, M.Alsamamra, H.Voigt, J.Friese, K.texturn:issn:1600-5767Site dependence of the magnetocaloric effect in Mn5−xFexSi3The 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.doi:10.1107/S16005767220074402022-09-06text/htmlThe 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.https://creativecommons.org/licenses/by/4.0/5Journal of Applied Crystallography2022-09-06117211641600-5767research papers1600-576755October 2022med@iucr.orgSmall-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.SMALL-ANGLE NEUTRON SCATTERING; SKYRMIONS; CHIRAL MAGNETS; FRUSTRATION; MAGNETIC DISORDER; DIFFUSE SCATTERINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenWhite, 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.texturn:issn:1600-5767Small-angle neutron scattering study of mesoscale magnetic disordering and skyrmion phase suppression in the frustrated chiral magnet Co6.75Zn6.75Mn6.5Co–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.doi:10.1107/S16005767220074032022-09-14text/htmlIn 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.12312022-09-141219https://creativecommons.org/licenses/by/4.0/5Journal of Applied Crystallography1600-57671600-5767research papers55October 2022med@iucr.orgHigh-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°.X-RAY IMAGING; X-RAY DIFFRACTION; 3DXRD; STRUCTURAL MATERIALShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenKutsal, M.Poulsen, H.F.Winther, G.Sørensen, H.O.Detlefs, C.texturn:issn:1600-5767High-resolution 3D X-ray diffraction microscopy: 3D mapping of deformed metal microstructuresThree-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°.doi:10.1107/S16005767220073612022-08-30text/htmlA 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.Journal of Applied Crystallography5https://creativecommons.org/licenses/by/4.0/112511382022-08-30research papers1600-57671600-576755med@iucr.orgOctober 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.SMALL-ANGLE NEUTRON SCATTERING; POLARIZED NEUTRONS; SPIN ECHO SMALL-ANGLE NEUTRON SCATTERING; LARMOR LABELLINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenKadletz, E.Bouwman, W.G.Pappas, C.texturn:issn:1600-5767Radial spin echo small-angle neutron scattering method: concept and performanceA 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.doi:10.1107/S16005767220072452022-08-24text/htmlThe concept of a radially symmetric spin echo small-angle neutron scattering (SESANS) setup is introduced and analyzed.October 2022med@iucr.org551600-5767research papers1600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography52022-08-2410841072The 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.TRUST; RELIABILITY; REPRODUCIBILITY; REPLICABILITY; REUSEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHelliwell, J.R.Massera, C.texturn:issn:1600-5767The four Rs and crystal structure analysis: reliability, reproducibility, replicability and reusabilityWithin 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.doi:10.1107/S16005767220072082022-08-24text/htmlAcross 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.teaching and education1600-57671600-57675Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/13512022-08-241358med@iucr.orgOctober 202255X-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.X-RAY DIFFRACTION IMAGING; CURRENT CROWDING; THERMAL DILATION; SILICON DEVICEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenTanner, B.K.Danilewsky, A.McNally, P.J.texturn:issn:1600-5767X-ray diffraction imaging of fully packaged n–p–n transistors under accelerated ageing conditionsX-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.doi:10.1107/S16005767220071422022-08-30text/htmlX-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.October 2022med@iucr.org551600-57671600-5767research papers2022-08-3011461139https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography5A 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.X-RAY SCATTERING; IMAGE INPAINTING; DEEP LEARNING; MIXED-SCALE DENSE NETWORKS; TUNABLE U-NETShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenChavez, T.Roberts, E.J.Zwart, P.H.Hexemer, A.texturn:issn:1600-5767A comparison of deep-learning-based inpainting techniques for experimental X-ray scatteringThe 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.doi:10.1107/S16005767220071052022-09-28text/htmlA number of machine-learning-based algorithms are presented for the reconstruction of gaps in experimental X-ray scattering images through inpainting approaches.October 2022med@iucr.org551600-5767research papers1600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography512882022-09-281277Specific 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.SMALL-ANGLE X-RAY SCATTERING; HIGHLY ABSORBING POROUS POWDERS; REFLECTIVITY AND SCATTERING CONTRIBUTIONS; ABSOLUTE SCATTERING INTENSITYhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLu, Z.Rébiscoul, D.Narayanan, T.Zemb, T.texturn:issn:1600-5767Specific analysis of highly absorbing nanoporous powder by small-angle X-ray scatteringThe 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.doi:10.1107/S16005767220069872022-09-06text/htmlThe 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.https://creativecommons.org/licenses/by/4.0/5Journal of Applied Crystallography2022-09-06116311541600-5767research papers1600-576755October 2022med@iucr.orgBond-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.BOND-LENGTH DISTRIBUTIONS; IONIC RADII; CRYSTALLOGRAPHY OPEN DATABASE; CHEMENV; STATISTICShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSawada, M.Iwamoto, R.Kotani, T.Sakakibara, H.texturn:issn:1600-5767Bond-length distributions in ionically bonded materials with decomposition by coordination environmentThe 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.doi:10.1107/S16005767220068842022-09-06text/htmlTo 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.55October 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/5Journal of Applied Crystallography13672022-09-0613591600-5767teaching and education1600-5767Digitization 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.IPREADER SOFTWARE; GUINIER CAMERAS; IMAGING PLATES (IPS); DIFFRACTION PATTERN CONVERSION INTO DATA COLUMNS; POWDER X-RAY DIFFRACTION; DATA PROCESSING; GUINIER METHODhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenNasir, J.Steinbrück, N.Xu, K.Engelen, B.Schmedt auf der Günne, J.texturn:issn:1600-5767Digitization of imaging plates from Guinier powder X-ray diffraction camerasA 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.doi:10.1107/S160057672200677X2022-08-24text/htmlA 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.55med@iucr.orgOctober 2022Journal of Applied Crystallography5https://creativecommons.org/licenses/by/4.0/109711032022-08-24research papers1600-57671600-5767GenX 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.REFLECTOMETRY; SURFACE X-RAY DIFFRACTION; NEUTRON ANALYSIS; X-RAY ANALYSIShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenGlavic, A.Björck, M.texturn:issn:1600-5767GenX 3: the latest generation of an established toolSince 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.doi:10.1107/S16005767220066532022-07-30text/htmlImprovements to the GenX program are discussed, including performance, model building and error analysis.55August 2022med@iucr.org2022-07-3010711063https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography41600-57671600-5767computer programsTemperature 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.NEUTRON BRAGG EDGE IMAGING; DEBYE-WALLER FACTOR; TEMPERATURE-DEPENDENT NEUTRON TRANSMISSION; SUPER MARTENSITIC STAINLESS STEELhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAl-Falahat, A.M.Kardjilov, N.Woracek, R.Boin, M.Markötter, H.Kuhn, L.T.Makowska, M.Strobl, M.Pfretzschner, B.Banhart, J.Manke, I.texturn:issn:1600-5767Temperature dependence in Bragg edge neutron transmission measurementsA 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.doi:10.1107/S16005767220065492022-07-30text/htmlA 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.August 2022med@iucr.org551600-57671600-5767research papers9282022-07-30919https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography4Describing 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.SMALL-ANGLE SCATTERING; INDIRECT FOURIER TRANSFORM; SOLUTION SCATTERING; PAIR DISTRIBUTION FUNCTIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenGrant, T.D.texturn:issn:1600-5767Describing small-angle scattering profiles by a limited set of intensitiesSmall-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.doi:10.1107/S16005767220065982022-08-30text/htmlAn 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.1600-5767research papers1600-5767111611242022-08-30Journal of Applied Crystallography5https://creativecommons.org/licenses/by/4.0/med@iucr.orgOctober 202255Brittle 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.X-RAY DIFFRACTION; ION IMPLANTATION; CRACK-FRONT SHAPEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenPetit, A.Pokam, S.Mazen, F.Tardif, S.Landru, D.Kononchuk, O.Ben Mohamed, N.Olbinado, M.P.Rack, A.Rieutord, F.texturn:issn:1600-5767Brittle fracture studied by ultra-high-speed synchrotron X-ray diffraction imagingIn 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.doi:10.1107/S16005767220065372022-07-30text/htmlCrack 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.August 2022med@iucr.org551600-5767research papers1600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography42022-07-30918911Observation 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.BIREFRINGENCE; DEFECT CHARACTERIZATION; SILICON CARBIDEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHarada, S.Murayama, K.texturn:issn:1600-5767Observation of in-plane shear stress fields in off-axis SiC wafers by birefringence imagingFor 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.doi:10.1107/S16005767220064832022-07-30text/htmlTheoretical 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.55med@iucr.orgAugust 2022Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/102910322022-07-30short communications1600-57671600-5767Parameter 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.SMALL-ANGLE SCATTERING; POLYDISPERSITY; INVERSION; NEUTRON SCATTERING; X-RAY SCATTERING; NONLINEAR PROGRAMMINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLeng, K.King, S.Snow, T.Rogers, S.Markvardsen, A.Maheswaran, S.Thiyagalingam, J.texturn:issn:1600-5767Parameter inversion of a polydisperse system in small-angle scatteringA 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.doi:10.1107/S16005767220063792022-08-01text/htmlAn 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.1600-5767research papers1600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography42022-08-01977966August 2022med@iucr.org55Electron 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.TRANSMISSION ELECTRON MICROSCOPY; INSTRUMENTAL BROADENING FUNCTIONS; RIETVELD REFINEMENThttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSinha, A.Bortolotti, M.Ischia, G.Lutterotti, L.Gialanella, S.texturn:issn:1600-5767Electron diffraction characterization of nanocrystalline materials using a Rietveld-based approach. Part I. MethodologyTransmission 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.doi:10.1107/S16005767220063672022-08-01text/htmlQuantitative 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.9539652022-08-01Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/1600-5767research papers1600-576755med@iucr.orgAugust 2022Magnetic 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.MAGNETIC NEUTRON SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MAGNETIC STRUCTURES; MATERIALS SCIENCE; HEUSLER ALLOYShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBersweiler, M.Bender, P.Peral, I.Pratami Sinaga, E.Honecker, D.Alba Venero, D.Titov, I.Michels, A.texturn:issn:1600-5767Magnetic nanoprecipitates and interfacial spin disorder in zero-field-annealed Ni50Mn45In5 Heusler alloys as seen by magnetic small-angle neutron scatteringShell 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.doi:10.1107/S16005767220063552022-07-15text/htmlMagnetic-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.August 2022med@iucr.org551600-57671600-5767research papers7212022-07-15713https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography4A 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.MACHINE LEARNING; POWDER NEUTRON DIFFRACTION; SEMI-SUPERVISED; INDEXINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLolla, S.Liang, H.Kusne, A.G.Takeuchi, I.Ratcliff, W.texturn:issn:1600-5767A semi-supervised deep-learning approach for automatic crystal structure classificationThe 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.doi:10.1107/S16005767220060692022-07-28text/htmlA 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.med@iucr.orgAugust 202255research papers1600-57671600-57674Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/8822022-07-28889Neutron 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.NEUTRON INTERFEROMETRY; SPLIT-CRYSTAL INTERFEROMETERS; SILICON CRYSTALS; ATOMIC SCALE POSITIONINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLemmel, H.Jentschel, M.Abele, H.Lafont, F.Guerard, B.Sasso, C.P.Mana, G.Massa, E.texturn:issn:1600-5767Neutron interference from a split-crystal interferometerThe 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.doi:10.1107/S16005767220060822022-07-15text/htmlThis 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.55August 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/4Journal of Applied Crystallography2022-07-158758701600-5767research papers1600-5767Indexing 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.LAUE DIFFRACTION; SUPERIMPOSED PATTERNS; INDEXING; CRYSTALLOGRAPHIC ORIENTATIONShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSeret, A.Gao, W.Juul Jensen, D.Godfrey, A.Zhang, Y.texturn:issn:1600-5767Indexing of superimposed Laue diffraction patterns using a dictionary–branch–bound approachX-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.doi:10.1107/S16005767220060212022-08-24text/htmlA 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.1600-57671600-5767research papers2022-08-2410961085https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography5October 2022med@iucr.org55Skopi: 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.SINGLE-PARTICLE IMAGING; FLUCTUATION X-RAY SCATTERING; HOLOGRAPHY; FREE-ELECTRON LASERS; SIMULATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenPeck, A.Chang, H.-Y.Dujardin, A.Ramalingam, D.Uervirojnangkoorn, M.Wang, Z.Mancuso, A.Poitevin, F.Yoon, C.H.texturn:issn:1600-5767Skopi: a simulation package for diffractive imaging of noncrystalline biomoleculesX-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.doi:10.1107/S16005767220059942022-07-15text/htmlThe 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.1600-5767research papers1600-576710022022-07-151010Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/med@iucr.orgAugust 202255Towards 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.MACHINE VISION; AUTOMATION; LIQUID JET ALIGNMENT; IMAGE PROCESSINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenPatel, 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.texturn:issn:1600-5767Towards real-time analysis of liquid jet alignment in serial femtosecond crystallographyLiquid 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.doi:10.1107/S16005767220058912022-08-01text/htmlA 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.55August 2022med@iucr.org2022-08-01952944https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography41600-57671600-5767research papersCalculating 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.QUARTZ; X-RAYS; STRUCTURE FACTORS; PYTHONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSutter, J.P.Pittard, J.Filik, J.Baron, A.Q.R.texturn:issn:1600-5767Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 packageThe 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.doi:10.1107/S16005767220059452022-07-28text/htmlA 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.med@iucr.orgAugust 202255research papers1600-57671600-5767Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/10112022-07-281028Gwaihir: 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.X-RAY DIFFRACTION; COHERENCE; PHASE RETRIEVAL; JUPYTER NOTEBOOK; GRAPHICAL USER INTERFACEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSimonne, D.Carnis, J.Atlan, C.Chatelier, C.Favre-Nicolin, V.Dupraz, M.Leake, S. J.Zatterin, E.Resta, A.Coati, A.Richard, M. I.texturn:issn:1600-5767Gwaihir: Jupyter Notebook graphical user interface for Bragg coherent diffraction imagingBragg 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.doi:10.1107/S16005767220058542022-07-15text/htmlIn 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.10542022-07-151045https://creativecommons.org/licenses/by/4.0/4Journal of Applied Crystallography1600-57671600-5767computer programs55August 2022med@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.SMALL-ANGLE NEUTRON SCATTERING; MICROMAGNETISM; MAGNETIC MATERIALS; NANOCOMPOSITEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAdams, M.P.Bersweiler, M.Jefremovas, E.M.Michels, A.texturn:issn:1600-5767MuMag2022: a software tool for analyzing magnetic field dependent unpolarized small-angle neutron scattering data of bulk ferromagnetsThe 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.doi:10.1107/S16005767220053492022-07-28text/htmlThe 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.med@iucr.orgAugust 2022551600-5767computer programs1600-5767105510622022-07-28Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/Dislocation 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.CREEP; PURE ALUMINIUM; ELECTRON BACKSCATTER DIFFRACTION (EBSD); CELLULAR STRUCTURES; POWER LAW AND POWER-LAW BREAKDOWNhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenSerrano-Munoz, I.Fernández, R.Saliwan-Neumann, R.González-Doncel, G.Bruno, G.texturn:issn:1600-5767Dislocation substructures in pure aluminium after creep deformation as studied by electron backscatter diffractionIn 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.doi:10.1107/S16005767220052092022-07-05text/htmlIn 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.med@iucr.orgAugust 202255research papers1600-57671600-5767Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/8608692022-07-05Small-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.SMALL-ANGLE X-RAY SCATTERING; NON-SPHERICAL NANOPARTICLES; DEBYE SCATTERING EQUATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenDeumer, J.Pauw, B.R.Marguet, S.Skroblin, D.Taché, O.Krumrey, M.Gollwitzer, C.texturn:issn:1600-5767Small-angle X-ray scattering: characterization of cubic Au nanoparticles using Debye's scattering formulaA 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.doi:10.1107/S160057672200499X2022-07-15text/htmlThe 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.55med@iucr.orgAugust 2022Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/9932022-07-151001research papers1600-57671600-5767MoloVol: 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.COMPUTER PROGRAMS; VOLUME; SURFACE AREA; CAVITIES; VOIDShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMaglic, J.B.Lavendomme, R.texturn:issn:1600-5767MoloVol: an easy-to-use program for analyzing cavities, volumes and surface areas of chemical structuresCavities 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.doi:10.1107/S16005767220049882022-06-23text/htmlMoloVol is a free program for calculating volumes and surface areas of molecules and their cavities.August 2022med@iucr.org551600-5767computer programs1600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography410442022-06-231033The 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.RADON TRANSFORM; X-RAY DIFFRACTION; PATTERNED SI SUBSTRATES; GE MICROCRYSTALS; RECIPROCAL-SPACE MAPPINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMeduňa, M.Isa, F.Bressan, F.von Känel, H.texturn:issn:1600-5767The Radon transform as a tool for 3D reciprocal-space mapping of epitaxial microcrystalsThis 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.doi:10.1107/S16005767220048852022-07-05text/htmlDifferent 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.1600-5767research papers1600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography48362022-07-05823August 2022med@iucr.org55Small-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.SMALL-ANGLE NEUTRON SCATTERING; FE-CR ALLOYS; FERRITIC MARTENSITIC STEEL; NEUTRON IRRADIATIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenUlbricht, A.Heinemann, A.Bergner, F.texturn:issn:1600-5767Small-angle neutron scattering applied to low-dose neutron-irradiated Fe–Cr alloys and ferritic martensitic steel Eurofer97Ferritic/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.doi:10.1107/S16005767220048002022-06-15text/htmlCharacteristics 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 Eurofer97.55med@iucr.orgAugust 20224Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/7022022-06-15712research papers1600-57671600-5767Multivariate 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.X-RAY POWDER DIFFRACTION; QUANTITATIVE PHASE ANALYSIS; RIETVELD REFINEMENT; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; X-RAY FLUORESCENCE; PREFERRED ORIENTATION; MICROABSORPTIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLopresti, M.Mangolini, B.Milanesio, M.Caliandro, R.Palin, L.texturn:issn:1600-5767Multivariate versus traditional quantitative phase analysis of X-ray powder diffraction and fluorescence data of mixtures showing preferred orientation and microabsorptionIn 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.doi:10.1107/S16005767220047082022-07-05text/htmlA 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.1600-57671600-5767research papers2022-07-05850837https://creativecommons.org/licenses/by/4.0/4Journal of Applied CrystallographyAugust 2022med@iucr.org55A 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.FOAMS; FOAM FILMS; SMALL-ANGLE NEUTRON SCATTERING; NEUTRON REFLECTOMETRY; THIN-FILM PRESSURE BALANCEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenKühnhammer, M.Braun, L.Ludwig, M.Soltwedel, O.Chiappisi, L.Klitzing, R. vontexturn:issn:1600-5767A new model to describe small-angle neutron scattering from foamsThe 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.doi:10.1107/S16005767220046912022-06-23text/htmlA 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.7582022-06-237684Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767research papers1600-576755med@iucr.orgAugust 2022The 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.SPECULAR NEUTRON REFLECTIVITY; WAVE PACKETS; TRANSVERSE COHERENT EXTENThttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMajkrzak, C.F.Berk, N.F.Maranville, B.B.Dura, J.A.Jach, T.texturn:issn:1600-5767The effect of transverse wavefront width on specular neutron reflectionIn 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.doi:10.1107/S160057672200440X2022-06-23text/htmlThe 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.8122022-06-23787https://creativecommons.org/licenses/by/4.0/4Journal of Applied Crystallography1600-57671600-5767research papers55August 2022med@iucr.orgAutomated 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.PROTEIN DYNAMICS; X-RAY PHOTON CORRELATION SPECTROSCOPY; XPCS; CAHN-HILLIARD; AUTO-ENCODERS; MACHINE LEARNINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenTimmermann, 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.texturn:issn:1600-5767Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn–Hilliard-type simulations using auto-encoder networksMachine 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.doi:10.1107/S16005767220044352022-06-15text/htmlTwo-time correlation maps are classified in a simulation framework using an auto-encoder network.55August 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography42022-06-157577511600-5767research papers1600-5767Small-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.SMALL-ANGLE NEUTRON SCATTERING; SANS; MICROMAGNETICS; ANISOTROPYhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenZaporozhets, V.D.Oba, Y.Michels, A.Metlov, K.L.texturn:issn:1600-5767Small-angle neutron scattering by spatially inhomogeneous ferromagnets with a nonzero average uniaxial anisotropyMicromagnetic 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.doi:10.1107/S160057672200437X2022-06-01text/htmlMacroscopic 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.55med@iucr.orgJune 20223Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/5922022-06-01600research papers1600-57671600-5767Robust 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.SMALL-ANGLE SCATTERING; CORRELATION FUNCTIONS; FOURIER TRANSFORM; MAGNETIC NANOPARTICLES; MODULATION OF INTENSITY WITH ZERO EFFORT; MIEZE; RESEDAhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBender, P.Honecker, D.Bersweiler, M.Costo, R.Kahmann, T.Ludwig, F.Leiner, J.Jochum, J.K.texturn:issn:1600-5767Robust approaches for model-free small-angle scattering data analysisThe 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.doi:10.1107/S16005767220043562022-05-28text/htmlThree 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.55June 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography32022-05-285915861600-5767research papers1600-5767Insights 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.ELECTRON BACKSCATTER DIFFRACTION (EBSD); ORIENTATIONS; DUPLEX STAINLESS STEELS; SEGMENTATION; CLASSIFICATION; IMAGE ANALYSIS; MICROSTRUCTURES; CRYSTALLOGRAPHIC PHASEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMollens, M.Roux, S.Hild, F.Guery, A.texturn:issn:1600-5767Insights into a dual-phase steel microstructure using EBSD and image-processing-based workflowQuantitative 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.doi:10.1107/S16005767220042652022-06-01text/htmlIn 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.3Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/6016102022-06-01research papers1600-57671600-576755med@iucr.orgJune 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.SYNCHROTRON X-RAY LAUE MICRODIFFRACTION; NEURAL NETWORKS; HKL RECOGNITIONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenPurushottam Raj Purohit, R.R.P.Tardif, S.Castelnau, O.Eymery, J.Guinebretière, R.Robach, O.Ors, T.Micha, J.-S.texturn:issn:1600-5767LaueNN: neural-network-based hkl recognition of Laue spots and its application to polycrystalline materialsA 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.doi:10.1107/S16005767220041982022-06-15text/htmlAn 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.55August 2022med@iucr.org2022-06-15750737https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography41600-57671600-5767research papersAutomating 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.ELECTRON CHANNELING; SITE-SELECTIVE MICROANALYSIS; NANO-SCALE ANALYSIS; AUTOMATED PROBE SHIFT CORRECTION; ENERGY-DISPERSIVE X-RAY SPECTROSCOPY; ELECTRON ENERGY-LOSS SPECTROSCOPYhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenIshizuka, A.Ohtsuka, M.Muto, S.texturn:issn:1600-5767Automating ALCHEMI at the nano-scale using software compatible with PC-controlled transmission electron microscopyAtom 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.doi:10.1107/S16005767220038182022-05-25text/htmlA 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.https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography35572022-05-255511600-5767research papers1600-576755June 2022med@iucr.orgOptimizing 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.NEUTRON REFLECTIVITY; NEUTRON REFLECTOMETRY; EXPERIMENTAL DESIGN; FISHER INFORMATION; INFORMATION THEORYhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenDurant, J.H.Wilkins, L.Cooper, J.F.K.texturn:issn:1600-5767Optimizing experimental design in neutron reflectometryUsing 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.doi:10.1107/S16005767220038312022-06-23text/htmlAn 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.med@iucr.orgAugust 202255research papers1600-57671600-5767Journal of Applied Crystallography4https://creativecommons.org/licenses/by/4.0/7692022-06-23781SAXSDOG: 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.COMPUTER PROGRAMS; SMALL-ANGLE X-RAY SCATTERING; SAXS; AZIMUTHAL INTEGRATION; SAXSDOGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBurian, M.Meisenbichler, C.Naumenko, D.Amenitsch, H.texturn:issn:1600-5767SAXSDOG: open software for real-time azimuthal integration of 2D scattering imagesIn 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.doi:10.1107/S16005767220036852022-05-28text/htmlThe open-source software SAXSDOG performs a real-time azimuthal integration of 2D scattering images reaching peak integration performance at current hardware limits.1600-5767computer programs1600-5767https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography32022-05-28685677June 2022med@iucr.org55Optimization 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.DATA-DRIVEN SCIENCE; HISTOGRAM BIN-WIDTH OPTIMIZATION; INELASTIC NEUTRON SCATTERING; INHOMOGENEOUS POISSON POINT PROCESSES; STATISTICAL SPECTRAL-FEATURE VALIDATION; EXPERIMENT DESIGNhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenTatsumi, K.Inamura, Y.Kofu, M.Kiyanagi, R.Shimazaki, H.texturn:issn:1600-5767Optimization and inference of bin widths for histogramming inelastic neutron scattering spectraA 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.doi:10.1107/S16005767220036242022-05-25text/htmlBin 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.research papers1600-57671600-5767Journal of Applied Crystallography3https://creativecommons.org/licenses/by/4.0/5335432022-05-25med@iucr.orgJune 202255Uniaxial 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.POLARIZED NEUTRON SCATTERING; UNIAXIAL POLARIZATION ANALYSIS; SMALL-ANGLE NEUTRON SCATTERING; MICROMAGNETICS; MAGNETIC NANOCOMPOSITEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenMalyeyev, A.Titov, I.Dewhurst, C.Suzuki, K.Honecker, D.Michels, A.texturn:issn:1600-5767Uniaxial polarization analysis of bulk ferromagnets: theory and first experimental resultsOn 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.doi:10.1107/S16005767220035082022-05-28text/htmlBased 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.2022-05-28585569https://creativecommons.org/licenses/by/4.0/3Journal of Applied Crystallography1600-57671600-5767research papers55June 2022med@iucr.orgTowards 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.COHERENT DIFFRACTIVE IMAGING; COHERENT X-RAY IMAGING; KHZ X-RAY IMAGING; NANOSCALE DYNAMICS; PHASE RETRIEVALhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHinsley, G.N.Kewish, C.M.van Riessen, G.A.texturn:issn:1600-5767Towards kilohertz synchrotron coherent diffractive imagingX-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.doi:10.1107/S16005767220034662022-05-08text/htmlThis 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.1600-5767research papers1600-57674794832022-05-08Journal of Applied Crystallography3https://creativecommons.org/licenses/by/4.0/med@iucr.orgJune 202255pdCIFplotter: 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.POWDER DIFFRACTION; DATA VISUALIZATION; CIF; PDCIFhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenRowles, M.R.texturn:issn:1600-5767pdCIFplotter: visualizing powder diffraction data in pdCIF formatA 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.doi:10.1107/S16005767220034782022-05-25text/htmlA program is described for visualizing powder diffraction data and models published in powder CIF format.https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography32022-05-256376311600-5767CIF applications1600-576755June 2022med@iucr.orgDISEMM: 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.SINGLE-CRYSTAL ELASTIC CONSTANTS; ELASTO-PLASTIC SELF-CONSISTENT (EPSC) MODELLING; DISEMM; MECHANICAL MODELLINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenHeldmann, A.Hofmann, M.Hoelzel, M.texturn:issn:1600-5767DISEMM: a tool for the investigation of elasto-plastic behaviour on polycrystalline samples using X-ray and neutron diffractionThe 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.doi:10.1107/S16005767220033142022-05-08text/htmlDISEMM 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.6566622022-05-08Journal of Applied Crystallography3https://creativecommons.org/licenses/by/4.0/1600-5767computer programs1600-576755med@iucr.orgJune 2022A 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.POWDER X-RAY DIFFRACTION; INSTRUMENTATION; OPERANDO; ENERGY MATERIALS; DIFFRACTOMETERS; AREA DETECTORShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenGeßwein, H.Stüble, P.Weber, D.Binder, J.R.Mönig, R.texturn:issn:1600-5767A multipurpose laboratory diffractometer for operando powder X-ray diffraction investigations of energy materialsLaboratory 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.doi:10.1107/S16005767220030892022-05-16text/htmlThis 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.1600-57671600-5767research papers2022-05-16514503https://creativecommons.org/licenses/by/4.0/3Journal of Applied CrystallographyJune 2022med@iucr.org553D-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.3D PRINTING; CRYO-STORAGE; SINGLE CRYSTALS; POWDERS; DIFFRACTION; HOME SOURCEShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenFuß, F.Rieckert, M.Steinhauer, S.Liesegang, M.Thiele, G.texturn:issn:1600-57673D-printed equipment to decouple (powder) X-ray diffraction sample preparation and measurementAn 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.doi:10.1107/S160057672200293X2022-04-29text/htmlA 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.55June 2022med@iucr.orghttps://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography36922022-04-296861600-5767laboratory notes1600-5767Bragg 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.BRAGG COHERENT DIFFRACTION IMAGING; EXTREMELY BRILLIANT SOURCE; STRUCTURE; PT PARTICLES; THREE-DIMENSIONAL; NANOSCALEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenRichard, 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.texturn:issn:1600-5767Bragg coherent diffraction imaging of single 20 nm Pt particles at the ID01-EBS beamline of ESRFElectronic 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.doi:10.1107/S16005767220028862022-05-16text/htmlThis work demonstrates three-dimensional Bragg coherent diffraction imaging of single 20 nm Pt particles at the ID01-EBS beamline of ESRF.55med@iucr.orgJune 20223Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/6216252022-05-16short communications1600-57671600-5767CELLOPT: 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.ELECTRON DIFFRACTION; PRECISION OF UNIT-CELL PARAMETERS; CRYSTAL STRUCTURE DETERMINATION; COMPENSATION FOR EXPERIMENTAL AND INSTRUMENTAL ERRORShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenGruene, T.Clabbers, M.T.B.Luebben, J.Chin, J.M.Reithofer, M.R.Stowasser, F.Alker, A.M.texturn:issn:1600-5767CELLOPT: improved unit-cell parameters for electron diffraction data of small-molecule crystalsElectron 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.doi:10.1107/S160057672200276X2022-04-29text/htmlIterative optimization of the unit-cell parameters improves the refinement of organic small-molecule structures using electron diffraction data.June 2022med@iucr.org551600-57671600-5767computer programs6552022-04-29647https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography3Scipion-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.ELECTRON DIFFRACTION; 3D ED; MICROED; DATA PROCESSING; COMPUTER PROGRAMShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBengtsson, V.E.G.Pacoste, L.Rosa-Trevin, J.M. de laHofer, G.Zou, X.Xu, H.texturn:issn:1600-5767Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED dataThree-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.doi:10.1107/S16005767220027582022-04-22text/htmlThe 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.6386462022-04-223Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767computer programs1600-576755med@iucr.orgJune 2022Classification 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.CONVOLUTIONAL NEURAL NETWORKS; SINGLE-PARTICLE IMAGING; CLASSIFICATION OF DIFFRACTION PATTERNS; X-RAY FREE-ELECTRON LASERShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenAssalauova, D.Ignatenko, A.Isensee, F.Trofimova, D.Vartanyants, I.A.texturn:issn:1600-5767Classification of diffraction patterns using a convolutional neural network in single-particle-imaging experiments performed at X-ray free-electron lasersSingle 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.doi:10.1107/S16005767220026672022-04-22text/htmlA 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.4442022-04-224543Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767research papers1600-576755med@iucr.orgJune 2022Lower 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.DIFFRACTION; PARTICLE SIZE DETERMINATION; SCHERRER APPROACH; INTEGRAL BREADTH; FOURIER ANALYSIShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenNoyan, İ.C.Öztürk, H.texturn:issn:1600-5767Lower uncertainty bounds of diffraction-based nanoparticle sizesA 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.doi:10.1107/S16005767220025642022-04-29text/htmlThe errors for particle sizes obtained by integral-breadth- and Fourier-decomposition-based techniques depend on the shape of the diffracting domains.55med@iucr.orgJune 20224552022-04-294703Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/1600-5767research papers1600-5767A 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.CRYOPROTECTION; HIGH THROUGHPUT; DEHYDRATION; CRYSTALS; PROTEINShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenBellini, D.texturn:issn:1600-5767A drug-discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screeningIn 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.doi:10.1107/S16005767220023822022-04-02text/htmlA 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.1600-5767research papers1600-57673702022-04-023792Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/med@iucr.orgApril 202255Neural 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.REFLECTOMETRY; DATA ANALYSIS; MACHINE LEARNING; PYTHONhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenGreco, A.Starostin, V.Edel, E.Munteanu, V.Rußegger, N.Dax, I.Shen, C.Bertram, F.Hinderhofer, A.Gerlach, A.Schreiber, F.texturn:issn:1600-5767Neural network analysis of neutron and X-ray reflectivity data: automated analysis using mlreflect, experimental errors and feature engineeringThe 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.doi:10.1107/S16005767220022302022-04-02text/htmlA Python-based analysis pipeline for the fast analysis of X-ray and neutron reflectivity data using neural networks is presented.research papers1600-57671600-57672Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/4.0/3622022-04-02369med@iucr.orgApril 202255Structure 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.NANODIAMONDS; COLD NEUTRON SOURCES; DETONATION NDS; SMALL-ANGLE NEUTRON SCATTERING; LASER SYNTHESIS TECHNIQUEhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenKabir, I.I.Osborn, J.C.Lu, W.Mata, J.P.Rehm, C.Yeoh, G.H.Ersez, T.texturn:issn:1600-5767Structure evolution of nanodiamond aggregates: a SANS and USANS studyUltra-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.doi:10.1107/S16005767220020842022-03-25text/htmlNanodiamonds (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.https://creativecommons.org/licenses/by/4.0/2Journal of Applied Crystallography2022-03-253613531600-5767research papers1600-576755April 2022med@iucr.orgPerformance 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.SMALL-ANGLE X-RAY SCATTERING; WIDE-ANGLE X-RAY SCATTERING; SAXS-WAXS; SWAXS; ONLINE SIZE EXCLUSION CHROMATOGRAPHY; INTEGRATED UV-VIS ABSORPTION AND REFRACTOMETRY; BIOMOLECULAR SOLUTION SCATTERINGhttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenShih, 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.texturn:issn:1600-5767Performance of the new biological small- and wide-angle X-ray scattering beamline 13A at the Taiwan Photon SourceRecent 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.doi:10.1107/S16005767220019232022-03-18text/htmlA 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.55April 2022med@iucr.org3522022-03-18340https://creativecommons.org/licenses/by/4.0/2Journal of Applied Crystallography1600-57671600-5767research papersThe 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.X-RAY CRYSTALLOGRAPHY; MACROMOLECULAR CRYSTALLIZATION; CRYSTALLIZATION SCREENS; PROTEIN CRYSTALShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenGorrec, F.Bellini, D.texturn:issn:1600-5767The FUSION protein crystallization screenThe 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.doi:10.1107/S16005767220017652022-03-11text/htmlThe FUSION protein crystallization screen, which integrates 96 unique combinations of additives, is presented and its efficiency is demonstrated.April 2022med@iucr.org551600-57671600-5767research papers3192022-03-11310https://creativecommons.org/licenses/by/4.0/Journal of Applied Crystallography2Efficient 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.SHAPE FUNCTIONS; SMALL-ANGLE SCATTERING; TOTAL SCATTERING; PAIR DISTRIBUTION FUNCTIONS; COMMON VOLUME FUNCTIONShttps://creativecommons.org/licenses/by/4.0/International Union of CrystallographyenLeonardi, A.Neder, R.Engel, M.texturn:issn:1600-5767Efficient solution of particle shape functions for the analysis of powder total scattering dataStructural 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.doi:10.1107/S16005767220012612022-03-18text/htmlParticle 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.1600-5767research papers1600-57673292022-03-18339Journal of Applied Crystallography2https://creativecommons.org/licenses/by/4.0/med@iucr.orgApril 202255