Journal of Applied Crystallography最新文献

{"title":"Rapid detection of rare events from <i>in situ</i>X-ray diffraction data using machine learning.","authors":"Weijian Zheng, Jun-Sang Park, Peter Kenesei, Ahsan Ali, Zhengchun Liu, Ian Foster, Nicholas Schwarz, Rajkumar Kettimuthu, Antonino Miceli, Hemant Sharma","doi":"10.1107/S160057672400517X","DOIUrl":"10.1107/S160057672400517X","url":null,"abstract":"<p><p>High-energy X-ray diffraction methods can non-destructively map the 3D microstructure and associated attributes of metallic polycrystalline engineering materials in their bulk form. These methods are often combined with external stimuli such as thermo-mechanical loading to take snapshots of the evolving microstructure and attributes over time. However, the extreme data volumes and the high costs of traditional data acquisition and reduction approaches pose a barrier to quickly extracting actionable insights and improving the temporal resolution of these snapshots. This article presents a fully automated technique capable of rapidly detecting the onset of plasticity in high-energy X-ray microscopy data. The technique is computationally faster by at least 50 times than the traditional approaches and works for data sets that are up to nine times sparser than a full data set. This new technique leverages self-supervised image representation learning and clustering to transform massive data sets into compact, semantic-rich representations of visually salient characteristics (<i>e.g.</i> peak shapes). These characteristics can rapidly indicate anomalous events, such as changes in diffraction peak shapes. It is anticipated that this technique will provide just-in-time actionable information to drive smarter experiments that effectively deploy multi-modal X-ray diffraction methods spanning many decades of length scales.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"1158-1170"},"PeriodicalIF":6.1,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the analysis of two-time correlation functions: equilibrium versus non-equilibrium systems.","authors":"Anastasia Ragulskaya, Vladimir Starostin, Fajun Zhang, Christian Gutt, Frank Schreiber","doi":"10.1107/S1600576724004618","DOIUrl":"10.1107/S1600576724004618","url":null,"abstract":"<p><p>X-ray photon correlation spectroscopy (XPCS) is a powerful tool for the investigation of dynamics covering a broad range of timescales and length scales. The two-time correlation function (TTC) is commonly used to track non-equilibrium dynamical evolution in XPCS measurements, with subsequent extraction of one-time correlations. While the theoretical foundation for the quantitative analysis of TTCs is primarily established for equilibrium systems, where key parameters such as the diffusion coefficient remain constant, non-equilibrium systems pose a unique challenge. In such systems, different projections ('cuts') of the TTC may lead to divergent results if the underlying fundamental parameters themselves are subject to temporal variations. This article explores widely used approaches for TTC calculations and common methods for extracting relevant information from correlation functions, particularly in the light of comparing dynamics in equilibrium and non-equilibrium systems.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"1098-1106"},"PeriodicalIF":6.1,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mix and measure II: joint high-energy laboratory powder diffraction and microtomography for cement hydration studies.","authors":"Jaime Fernandez-Sanchez, Ana Cuesta, Shiva Shirani, Cinthya Redondo-Soto, Angeles G De la Torre, Isabel Santacruz, Ines R Salcedo, Laura Leon-Reina, Miguel A G Aranda","doi":"10.1107/S1600576724004527","DOIUrl":"10.1107/S1600576724004527","url":null,"abstract":"<p><p>Portland cements (PCs) and cement blends are multiphase materials of different fineness, and quantitatively analysing their hydration pathways is very challenging. The dissolution (hydration) of the initial crystalline and amorphous phases must be determined, as well as the formation of labile (such as ettringite), reactive (such as portlandite) and amorphous (such as calcium silicate hydrate gel) components. The microstructural changes with hydration time must also be mapped out. To address this robustly and accurately, an innovative approach is being developed based on <i>in situ</i> measurements of pastes without any sample conditioning. Data are sequentially acquired by Mo <i>K</i>α₁ laboratory X-ray powder diffraction (LXRPD) and microtomography (µCT), where the same volume is scanned with time to reduce variability. Wide capillaries (2 mm in diameter) are key to avoid artefacts, <i>e.g.</i> self-desiccation, and to have excellent particle averaging. This methodology is tested in three cement paste samples: (i) a commercial PC 52.5 R, (ii) a blend of 80 wt% of this PC and 20 wt% quartz, to simulate an addition of supplementary cementitious materials, and (iii) a blend of 80 wt% PC and 20 wt% limestone, to simulate a limestone Portland cement. LXRPD data are acquired at 3 h and 1, 3, 7 and 28 days, and µCT data are collected at 12 h and 1, 3, 7 and 28 days. Later age data can also be easily acquired. In this methodology, the amounts of the crystalline phases are directly obtained from Rietveld analysis and the amorphous phase contents are obtained from mass-balance calculations. From the µCT study, and within the attained spatial resolution, three components (porosity, hydrated products and unhydrated cement particles) are determined. The analyses quantitatively demonstrate the filler effect of quartz and limestone in the hydration of alite and the calcium aluminate phases. Further hydration details are discussed.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"1067-1084"},"PeriodicalIF":6.1,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Determination of α lamellae orientation in a β-Ti alloy using electron backscatter diffraction.","authors":"Petr Harcuba, Jana Šmilauerová, Miloš Janeček, Jan Ilavský, Václav Holý","doi":"10.1107/S160057672400400X","DOIUrl":"10.1107/S160057672400400X","url":null,"abstract":"<p><p>The spatial orientation of α lamellae in a metastable β-Ti matrix of Timetal LCB (Ti-6.8 Mo-4.5 Fe-1.5 Al in wt%) was examined and the orientation of the hexagonal close-packed α lattice in the α lamella was determined. For this purpose, a combination of methods of small-angle X-ray scattering, scanning electron microscopy and electron backscatter diffraction was used. The habit planes of α laths are close to {111}_β, which corresponds to (1320)_α in the hexagonal coordinate system of the α phase. The longest α lamella direction lies approximately along one of the 〈110〉_β directions which are parallel to the specific habit plane. Taking into account the average lattice parameters of the β and α phases in aged conditions in Timetal LCB, it was possible to index all main axes and faces of an α lath not only in the cubic coordinate system of the parent β phase but also in the hexagonal system of the α phase.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"1001-1010"},"PeriodicalIF":6.1,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"X-ray tensor tomography for small-grained polycrystals with strong texture.","authors":"Mads Carlsen, Christian Appel, William Hearn, Martina Olsson, Andreas Menzel, Marianne Liebi","doi":"10.1107/S1600576724004588","DOIUrl":"10.1107/S1600576724004588","url":null,"abstract":"<p><p>Small-angle X-ray tensor tomography and the related wide-angle X-ray tensor tomography are X-ray imaging techniques that tomographically reconstruct the anisotropic scattering density of extended samples. In previous studies, these methods have been used to image samples where the scattering density depends slowly on the direction of scattering, typically modeling the directionality, <i>i.e.</i> the texture, with a spherical harmonics expansion up until order ℓ = 8 or lower. This study investigates the performance of several established algorithms from small-angle X-ray tensor tomography on samples with a faster variation as a function of scattering direction and compares their expected and achieved performance. The various algorithms are tested using wide-angle scattering data from an as-drawn steel wire with known texture to establish the viability of the tensor tomography approach for such samples and to compare the performance of existing algorithms.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"986-1000"},"PeriodicalIF":6.1,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quality assessment of the wide-angle detection option planned at the high-intensity/extended <i>Q</i>-range SANS diffractometer KWS-2 combining experiments and <i>McStas</i> simulations.","authors":"Aurel Radulescu","doi":"10.1107/S160057672400493X","DOIUrl":"10.1107/S160057672400493X","url":null,"abstract":"<p><p>For a reliable characterization of materials and systems featuring multiple structural levels, a broad length scale from a few ångström to hundreds of nanometres must be analyzed and an extended <i>Q</i> range must be covered in X-ray and neutron scattering experiments. For certain samples or effects, it is advantageous to perform such characterization with a single instrument. Neutrons offer the unique advantage of contrast variation and matching by D-labeling, which is of great value in the characterization of natural or synthetic polymers. Some time-of-flight small-angle neutron scattering (TOF-SANS) instruments at neutron spallation sources can cover an extended <i>Q</i> range by using a broad wavelength band and a multitude of detectors. The detectors are arranged to cover a wide range of scattering angles with a resolution that allows both large-scale morphology and crystalline structure to be resolved simultaneously. However, for such analyses, the SANS instruments at steady-state sources operating in conventional monochromatic pinhole mode rely on additional wide-angle neutron scattering (WANS) detectors. The resolution must be tuned via a system of choppers and a TOF data acquisition option to reliably measure the atomic to mesoscale structures. The KWS-2 SANS diffractometer at Jülich Centre for Neutron Science allows the exploration of a wide <i>Q</i> range using conventional pinhole and lens focusing modes and an adjustable resolution Δλ/λ between 2 and 20%. This is achieved through the use of a versatile mechanical velocity selector combined with a variable slit opening and rotation frequency chopper. The installation of WANS detectors planned on the instrument required a detailed analysis of the quality of the data measured over a wide angular range with variable resolution. This article presents an assessment of the WANS performance by comparison with a <i>McStas</i> [Willendrup, Farhi & Lefmann (2004). <i>Physica B</i>, <b>350</b>, E735-E737] simulation of ideal experimental conditions at the instrument.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"1040-1046"},"PeriodicalIF":6.1,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate space-group prediction from composition.","authors":"Vishwesh Venkatraman, Patricia Almeida Carvalho","doi":"10.1107/S1600576724004497","DOIUrl":"10.1107/S1600576724004497","url":null,"abstract":"<p><p>Predicting crystal symmetry simply from chemical composition has remained challenging. Several machine-learning approaches can be employed, but the predictive value of popular crystallographic databases is relatively modest due to the paucity of data and uneven distribution across the 230 space groups. In this work, virtually all crystallographic information available to science has been compiled and used to train and test multiple machine-learning models. Composition-driven random-forest classification relying on a large set of descriptors showed the best performance. The predictive models for crystal system, Bravais lattice, point group and space group of inorganic compounds are made publicly available as easy-to-use software downloadable from https://gitlab.com/vishsoft/cosy.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"975-985"},"PeriodicalIF":6.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patching-based deep-learning model for the inpainting of Bragg coherent diffraction patterns affected by detector gaps.","authors":"Matteo Masto, Vincent Favre-Nicolin, Steven Leake, Tobias Schülli, Marie-Ingrid Richard, Ewen Bellec","doi":"10.1107/S1600576724004163","DOIUrl":"10.1107/S1600576724004163","url":null,"abstract":"<p><p>A deep-learning algorithm is proposed for the inpainting of Bragg coherent diffraction imaging (BCDI) patterns affected by detector gaps. These regions of missing intensity can compromise the accuracy of reconstruction algorithms, inducing artefacts in the final result. It is thus desirable to restore the intensity in these regions in order to ensure more reliable reconstructions. The key aspect of the method lies in the choice of training the neural network with cropped sections of diffraction data and subsequently patching the predictions generated by the model along the gap, thus completing the full diffraction peak. This approach enables access to a greater amount of experimental data for training and offers the ability to average overlapping sections during patching. As a result, it produces robust and dependable predictions for experimental data arrays of any size. It is shown that the method is able to remove gap-induced artefacts on the reconstructed objects for both simulated and experimental data, which becomes essential in the case of high-resolution BCDI experiments.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"966-974"},"PeriodicalIF":6.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>TORO Indexer</i>: a <i>PyTorch</i>-based indexing algorithm for kilohertz serial crystallography.","authors":"Piero Gasparotto, Luis Barba, Hans-Christian Stadler, Greta Assmann, Henrique Mendonça, Alun W Ashton, Markus Janousch, Filip Leonarski, Benjamín Béjar","doi":"10.1107/S1600576724003182","DOIUrl":"10.1107/S1600576724003182","url":null,"abstract":"<p><p>Serial crystallography (SX) involves combining observations from a very large number of diffraction patterns coming from crystals in random orientations. To compile a complete data set, these patterns must be indexed (<i>i.e.</i> their orientation determined), integrated and merged. Introduced here is <i>TORO</i> (<i>Torch</i>-powered robust optimization) <i>Indexer</i>, a robust and adaptable indexing algorithm developed using the <i>PyTorch</i> framework. <i>TORO</i> is capable of operating on graphics processing units (GPUs), central processing units (CPUs) and other hardware accelerators supported by <i>PyTorch</i>, ensuring compatibility with a wide variety of computational setups. In tests, <i>TORO</i> outpaces existing solutions, indexing thousands of frames per second when running on GPUs, which positions it as an attractive candidate to produce real-time indexing and user feedback. The algorithm streamlines some of the ideas introduced by previous indexers like <i>DIALS</i> real-space grid search [Gildea, Waterman, Parkhurst, Axford, Sutton, Stuart, Sauter, Evans & Winter (2014). <i>Acta Cryst.</i> D<b>70</b>, 2652-2666] and <i>XGandalf</i> [Gevorkov, Yefanov, Barty, White, Mariani, Brehm, Tolstikova, Grigat & Chapman (2019). <i>Acta Cryst.</i> A<b>75</b>, 694-704] and refines them using faster and principled robust optimization techniques which result in a concise code base consisting of less than 500 lines. On the basis of evaluations across four proteins, <i>TORO</i> consistently matches, and in certain instances outperforms, established algorithms such as <i>XGandalf</i> and <i>MOSFLM</i> [Powell (1999). <i>Acta Cryst.</i> D<b>55</b>, 1690-1695], occasionally amplifying the quality of the consolidated data while achieving superior indexing speed. The inherent modularity of <i>TORO</i> and the versatility of <i>PyTorch</i> code bases facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"931-944"},"PeriodicalIF":6.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A simple protocol for determining the zone axis direction from selected-area electron diffraction spot patterns of cubic materials.","authors":"Thomas E Weirich","doi":"10.1107/S1600576724004333","DOIUrl":"10.1107/S1600576724004333","url":null,"abstract":"<p><p>Using the well known <i>R_n</i> ratio method, a protocol has been elaborated for determining the lattice direction for the 15 most common cubic zone axis spot patterns. The method makes use of the lengths of the three shortest reciprocal-lattice vectors in each pattern and the angles between them. No prior pattern calibration is required for the method to work, as the <i>R_n</i> ratio method is based entirely on geometric relationships. In the first step the pattern is assigned to one of three possible pattern types according to the angles that are measured between the three reciprocal-lattice vectors. The lattice direction [<i>uvw</i>] and possible Bravais type(s) and Laue indices of the corresponding reflections can then be determined by using lookup tables. In addition to determining the lattice direction, this simple geometric analysis allows one to distinguish between the <i>P</i>, <i>I</i> and <i>F</i> Bravais lattices for spot patterns aligned along [013], [112], [114] and [233]. Moreover, the <i>F</i> lattice can always be uniquely identified from the [011] and [123] patterns.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"57 Pt 4","pages":"1263-1269"},"PeriodicalIF":6.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}