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共71条结果
  • 1.

    【2hr】XGANDALF – extended gradient descent algorithm for lattice finding

    包量

    机译 XGANDALF –用于晶格寻找的扩展梯度下降算法
    摘要：Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real-time feedback during serial crystallography experiments. It is implemented in an open-source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
  • 2.

    【2hr】Theoretical study of the properties of X-ray diffraction moiré fringes. II. Illustration of angularly integrated moiré images

    包量

    机译 X射线衍射莫尔条纹特性的理论研究。二。角度整合的莫尔图像的插图
    • 作者：Jun-ichi Yoshimura
    • 刊名：Acta Crystallographica. Section A Foundations and Advances
    • -1年第Pt 4期
    摘要：Using a theory of X-ray diffraction moiré fringes developed in a previous paper, labelled Part I [Yoshimura (2015). Acta Cryst. A>71, 368–381], the X-ray moiré images of a silicon bicrystal having a weak curvature strain and an interspacing gap, assumed to be integrated for an incident-wave angular width, are simulation-computed over a wide range of crystal thicknesses and incident-wave angular width, likely under practical experimental conditions. Along with the simulated moiré images, the graphs of characteristic quantities on the moiré images are presented for a full understanding of them. The treated moiré images are all of rotation moiré. Mo Kα1 radiation and the 220 reflection were assumed in the simulation. The results of this simulation show that fringe patterns, which are significantly modified from simple straight fringes of rotation moiré, appear in some ranges of crystal thicknesses and incident-wave angular width, due to a combined effect of Pendellösung oscillation and an added phase difference from the interspacing gap, under the presence of a curvature strain. The moiré fringes which slope to the perpendicular direction to the diffraction vector in spite of the assumed condition of rotation moiré, and fringe patterns where low-contrast bands are produced with a sharp bend of fringes arising along the bands are examples of the modified fringe pattern. This simulation study provides a wide theoretical survey of the type of bicrystal moiré image produced under a particular condition.
  • 3.

    【2hr】Experimentally obtained and computer-simulated X-ray asymmetric eight-beam pinhole topographs for a silicon crystal

    包量

    机译 实验获得的计算机模拟的X射线非对称八光束针孔地形图
    摘要：In this study, experimentally obtained eight-beam pinhole topographs for a silicon crystal using synchrotron X-rays were compared with computer-simulated images, and were found to be in good agreement. The experiment was performed with an asymmetric all-Laue geometry. However, the X-rays exited from both the bottom and side surfaces of the crystal. The simulations were performed using two different approaches: one was the integration of the n-beam Takagi–Taupin equation, and the second was the fast Fourier transformation of the X-ray amplitudes obtained by solving the eigenvalue problem of the n-beam Ewald–Laue theory as reported by Kohn & Khikhlukha [Acta Cryst. (2016), A>72, 349–356] and Kohn [Acta Cryst. (2017), A>73, 30–38].
  • 4.

    【2hr】Full real-space analysis of a dodecagonal quasicrystal

    包量

    机译 十二边形准晶体的完整实空间分析
    摘要：The atomically resolved real-space structure of a long-range-ordered dodecagonal quasicrystal is determined based on scanning tunnelling microscopy. For the BaTiO3-derived oxide quasicrystal which spontaneously forms on a Pt(111) surface, 8100 atomic positions have been determined and are compared with an ideal Niizeki–Gähler tiling. Although the Niizeki–Gähler tiling has a complex three-element structure, the abundance of the triangle, square and rhomb tiling elements in the experimental data closely resembles the ideal frequencies. Similarly, the frequencies of all possible next-neighbour tiling combinations are, within the experimental uncertainty, identical to the ideal tiling. The angular and orientational distributions of all individual tiling elements show the characteristics of the dodecagonal quasicrystal. In contrast, the analysis of the orientation of characteristic and more complex tiling combinations indicates the partial decomposition of the quasicrystal into small patches with locally reduced symmetry. These, however, preserve the long-range quasicrystal coherence. The symmetry reduction from dodecagonal to sixfold is assigned to local interaction with the threefold substrate. It leads to atomic flips which preserve the number of quasicrystal tiling elements.
  • 5.

    【2hr】Principles of weakly ordered domains in intermetallics: the cooperative effects of atomic packing and electronics in Fe2Al5

    包量

    机译 金属间化合物中弱序畴的原理：Fe2Al5中原子堆积和电子的协同效应
    摘要：Many complex intermetallic structures feature a curious juxtaposition of domains with strict 3D periodicity and regions of much weaker order or incommensurability. This article explores the basic principles leading to such arrangements through an investigation of the weakly ordered channels of Fe2Al5. It starts by experimentally confirming the earlier crystallographic model of the high-temperature form, in which nearly continuous columns of electron density corresponding to disordered Al atoms emerge. Then electronic structure calculations on ordered models are used to determine the factors leading to the formation of these columns. These calculations reveal electronic pseudogaps near 16 electrons/Fe atom, an electron concentration close to the Al-rich side of the phase’s homogeneity range. Through a reversed approximation Molecular Orbital (raMO) analysis, these pseudogaps are correlated with the filling of 18-electron configurations on the Fe atoms with the support of isolobal σ Fe–Fe bonds. The resulting preference for 16 electrons/Fe requires a fractional number of Al atoms in the Fe2Al5 unit cell. Density functional theory–chemical pressure (DFT-CP) analysis is then applied to investigate how this nonstoichiometry is accommodated. The CP schemes reveal strong quadrupolar distributions on the Al atoms of the channels, suggestive of soft atomic motions along the undulating electron density observed in the Fourier map that allow the Al positions to shift easily in response to compositional changes. Such a combination of preferred electron counts tied to stoichiometry and continuous paths of CP quadrupoles could provide predictive indicators for the emergence of channels of disordered or incommensurately spaced atoms in intermetallic structures.
  • 6.

    【2hr】Grazing-incidence small-angle X-ray scattering study of correlated lateral density fluctuations in W/Si multilayers

    包量

    机译 W / Si多层膜中相关横向密度波动的掠入射小角X射线散射研究
    摘要：A structural characterization of W/Si multilayers using X-ray reflectivity (XRR), scanning transmission electron microscopy (STEM) and grazing-incidence small-angle X-ray scattering (GISAXS) is presented. STEM images revealed lateral, periodic density fluctuations in the Si layers, which were further analysed using GISAXS. Characteristic parameters of the fluctuations such as average distance between neighbouring fluctuations, average size and lateral distribution of their position were obtained by fitting numerical simulations to the measured scattering images, and these parameters are in good agreement with the STEM observations. For the numerical simulations the density fluctuations were approximated as a set of spheroids distributed inside the Si layers as a 3D para­crystal (a lattice of spheroids with short-range ordering but lacking any long-range order). From GISAXS, the density of the material inside the density fluctuations is calculated to be 2.07 g cm−3 which is 89% of the bulk value of the deposited layer (2.33 g cm−3).
  • 7.

    【2hr】Resolving 500 nm axial separation by multi-slice X-ray ptychography

    包量

    机译 多层X射线分型术解决500 nm轴向分离
    摘要：Multi-slice X-ray ptychography offers an approach to achieve images with a nanometre-scale resolution from samples with thicknesses larger than the depth of field of the imaging system by modeling a thick sample as a set of thin slices and accounting for the wavefront propagation effects within the specimen. Here, we present an experimental demonstration that resolves two layers of nanostructures separated by 500 nm along the axial direction, with sub-10 nm and sub-20 nm resolutions on two layers, respectively. Fluorescence maps are simultaneously measured in the multi-modality imaging scheme to assist in decoupling the mixture of low-spatial-frequency features across different slices. The enhanced axial sectioning capability using correlative signals obtained from multi-modality measurements demonstrates the great potential of the multi-slice ptychography method for investigating specimens with extended dimensions in 3D with high resolution.
  • 8.

    【2hr】High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm

    包量

    机译 高速张量层析成像：迭代重建张量层析成像（IRTT）算法
    摘要：The recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), >527, 349–352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction.
  • 9.

    【2hr】CO2 adsorption in Y zeolite: a structural and dynamic view by a novel principal-component-analysis-assisted in situ single-crystal X-ray diffraction experiment

    包量

    机译 Y沸石中的CO2吸附：一种新颖的主成分分析辅助原位单晶X射线衍射实验的结构和动力学视图
    摘要：The increasing efficiency of detectors and brightness of X-rays in both laboratory and large-scale facilities allow the collection of full single-crystal X-ray data sets within minutes. The analysis of these ‘crystallographic big data’ requires new tools and approaches. To answer these needs, the use of principal component analysis (PCA) is proposed to improve the efficiency and speed of the analysis. Potentialities and limitations of PCA were investigated using single-crystal X-ray diffraction (XRD) data collected in situ on Y zeolite, in which CO2, acting as an active species, is thermally adsorbed while cooling from 300 to 200 K. For the first time, thanks to the high sensitivity of single-crystal XRD, it was possible to determine the sites where CO2 is adsorbed, the increase in their occupancy while the temperature is decreased, and the correlated motion of active species, i.e. CO2, H2O and Na+. PCA allowed identification and elimination of problematic data sets, and better understanding of the trends of the occupancies of CO2, Na+ and water. The quality of the data allowed for the first time calculation of the enthalpy (ΔH) and entropy (ΔS) of the CO2 adsorption by applying the van ’t Hoff equation to in situ single-crystal data. The calculation of thermodynamic values was carried out by both traditional and PCA-based approaches, producing comparable results. The obtained ΔH value is significant and involves systems (CO2 and Y zeolite) with no toxicity, superb stability and chemical inertness. Such features, coupled with the absence of carbonate formation and framework inertness upon adsorption, were demonstrated for the bulk crystal by the single-crystal experiment, and suggest that the phenomenon can be easily reversed for a large number of cycles, with CO2 released on demand. The main advantages of PCA-assisted analysis reside in its speed and in the possibility of it being applied directly to raw data, possibly as an ‘online’ data-quality test during data collection, without any a priori knowledge of the crystal structure.
  • 10.

    【2hr】Aspherical scattering factors for SHELXL – model implementation and application

    包量

    机译 SHELXL的非球面散射因子–模型实施和应用
    摘要：A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.
  • 11.

    【2hr】Rotational switches in the two-dimensional fullerene quasicrystal

    包量

    机译 二维富勒烯准晶体中的旋转开关
    摘要：One of the essential components of molecular electronic circuits are switching elements that are stable in two different states and can ideally be switched on and off many times. Here, distinct buckminsterfullerenes within a self-assembled monolayer, forming a two-dimensional dodecagonal quasicrystal on a Pt-terminated Pt3Ti(111) surface, are identified to form well separated molecular rotational switching elements. Employing scanning tunneling microscopy, the molecular-orbital appearance of the fullerenes in the quasicrystalline monolayer is resolved. Thus, fullerenes adsorbed on the 36 vertex configuration are identified to exhibit a distinctly increased mobility. In addition, this finding is verified by differential conductance measurements. The rotation of these mobile fullerenes can be triggered frequently by applied voltage pulses, while keeping the neighboring molecules immobile. An extensive analysis reveals that crystallographic and energetic constraints at the molecule/metal interface induce an inequality of the local potentials for the 36 and 32.4.3.4 vertex sites and this accounts for the switching ability of fullerenes on the 36 vertex sites. Consequently, a local area of the 8/3 approximant in the two-dimensional fullerene quasicrystal consists of single rotational switching fullerenes embedded in a matrix of inert molecules. Furthermore, it is deduced that optimization of the intermolecular interactions between neighboring fullerenes hinders the realization of translational periodicity in the fullerene monolayer on the Pt-terminated Pt3Ti(111) surface.
  • 12.

    【2hr】Selling reduction versus Niggli reduction for crystallographic lattices

    包量

    机译 出售还原与Niggli还原的晶格
    摘要：The unit-cell reduction described by Selling and used by Delone (whose early publications were under the spelling Delaunay) is explained in a simple form. The transformations needed to implement the reduction are listed. The simplicity of this reduction contrasts with the complexity of Niggli reduction.
  • 13.

    【2hr】Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector. Corrigendum

    包量

    机译 使用Timepix量子面积直接电子检测器在室温下通过电子衍射从头算结构确定有机药物化合物的纳米晶体。更正
    摘要：Corrections are made to Table 1 in the article by .
  • 14.

    【2hr】Specular reflection intensity modulated by grazing-incidence diffraction in a wide angular range

    包量

    机译 在宽角度范围内通过掠入射衍射调制的镜面反射强度
    摘要：Grazing-incidence X-ray diffraction (GID) is a well known technique for the characterization of crystal surfaces. A theoretical study has been performed of the sensitivity of GID to the structure of a crystal surface and distorted nanometre-thin surface layers. To simulate GID from crystals that have a complex subsurface structure, a matrix formalism of the dynamical diffraction theory has been applied. It has been found that the azimuthal rocking curves of a crystal that has a distorted subsurface, measured over a wide angular range, show asymmetric thickness oscillations with two distinguishable sets of frequencies: one corresponding to the diffraction in the single-crystal subsurface layer and the second corresponding to the diffraction in the single-crystal substrate. Therefore, azimuthal rocking curves allow characterization of the subsurface structure of a single crystal. Furthermore, thickness oscillations induced by evanescent diffraction modulate the specular reflection intensity, showing high-intensity modulations. This will potentially allow implementation of subsurface crystal characterization using, for instance, a laboratory-scale X-ray diffractometer.
  • 15.

    【2hr】Response to Fraser Wark’s comments on A new theory for X-ray diffraction

    包量

    机译 回应Fraser＆Wark关于X射线衍射新理论的评论
    • 作者：Paul F. Fewster
    • 刊名：Acta Crystallographica. Section A Foundations and Advances
    • -1年第Pt 5期
    摘要：The criticisms of my theory, as given by Fraser & Wark [(2018), Acta Cryst. A>74, ], are built on a misunderstanding of the concept and the methodology I have used. The assumption they have made rules out my description from which they conclude that my theory is proved to be wrong. They assume that I have misunderstood the diffraction associated with the shape of a crystal and my calculation is only relevant to a parallelepiped and even that I have got wrong. It only appears wrong to Fraser & Wark because the effect I predict has nothing to do with the crystal shape. The effect though can be measured as well as the crystal shape effects. This response describes my reasoning behind the theory, how it can be related to the Ewald sphere construction, and the build-up of the full diffraction pattern from all the scatterers in a stack of planes. It is the latter point that makes the Fraser & Wark analysis incomplete. The description given in this article describes my approach much more precisely with reference to the Ewald sphere construction. Several experiments are described that directly measure the predictions of the new theory, which are explained with reference to the Ewald sphere description. In its simplest terms the new theory can be considered as giving a thickness to the Ewald sphere surface, whereas in the conventional theory it has no thickness. Any thickness immediately informs us that the scattering from a peak at the Bragg angle does not have to be in the Bragg condition to be observed. I believe the conventional theory is a very good approximation, but as soon as it is tested with careful experiments it is shown to be incomplete. The new theory puts forward the idea that there is persistent intensity at the Bragg scattering angle outside the Bragg condition. This intensity is weak (∼10−5) but can be observed in careful laboratory experiments, despite being on the limit of observation, yet it has a profound impact on how we should interpret diffraction patterns.
  • 16.

    【2hr】A group-theoretical approach to enumerating magnetoelectric and multiferroic couplings in perovskites

    包量

    机译 枚举钙钛矿中磁电和多铁耦合的群论方法
    摘要：A group-theoretical approach is used to enumerate the possible couplings between magnetism and ferroelectric polarization in the parent perovskite structure. It is shown that third-order magnetoelectric coupling terms must always involve magnetic ordering at the A and B sites which either transforms both as R-point or both as X-point time-odd irreducible representations (irreps). For fourth-order couplings it is demonstrated that this criterion may be relaxed allowing couplings involving irreps at X-, M- and R-points which collectively conserve crystal momentum, producing a magnetoelectric effect arising from only B-site magnetic order. In this case, exactly two of the three irreps entering the order parameter must be time-odd irreps and either one or all must be odd with respect to inversion symmetry. It is possible to show that the time-even irreps in this triad must transform as one of: X1 +, M3,5 − or R5 +, corresponding to A-site cation order, A-site antipolar displacements or anion rocksalt ordering, respectively. This greatly reduces the search space for type-II multiferroic perovskites. Similar arguments are used to demonstrate how weak ferromagnetism may be engineered and a variety of schemes are proposed for coupling this to ferroelectric polarization. The approach is illustrated with density functional theory calculations on magnetoelectric couplings and, by considering the literature, suggestions are given of which avenues of research are likely to be most promising in the design of novel magnetoelectric materials.
  • 17.

    【2hr】A method to estimate statistical errors of properties derived from charge-density modelling

    包量

    机译 一种估计由电荷密度模型得出的特性的统计误差的方法
    摘要：Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance–covariance matrix issued from the least-squares refinement. This ‘SSD methodology’ procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling.
  • 18.

    【2hr】Quasicrystals: What do we know? What do we want to know? What can we know?

    包量

    机译 准晶体：我们知道什么？我们想知道什么？我们能知道些什么？
    • 作者：Walter Steurer
    • 刊名：Acta Crystallographica. Section A Foundations and Advances
    • -1年第Pt 1期
    摘要：More than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.
  • 19.

    【2hr】... formula ...-module defects in crystals

    包量

    机译 ...公式...晶体中的模块缺陷
    摘要：An analysis is presented of the new types of defects that can appear in crystalline structures where the positions of the atoms and the unit cell belong to the same -module, i.e. are irrational projections of an N > 3-dimensional (N-D) lattice Λ as in the case of quasicrystals. Beyond coherent irrationally oriented twins already discussed in a previous paper [Quiquandon et al. (2016). Acta Cryst. A>72, 55–61], new two-dimensional translational defects are expected, the translation vectors of which, being projections of nodes of Λ, have irrational coordinates with respect to the unit-cell reference frame. Partial dislocations, called here module dislocations, are the linear defects bounding these translation faults. A specific case arises when the Burgers vector >B is the projection of a non-zero vector of Λ that is perpendicular to the physical space. This new kind of dislocation is called a scalar dislocation since, because its Burgers vector in physical space is zero, it generates no displacement field and has no interaction with external stress fields and other dislocations.
  • 20.

    【2hr】High-resolution X-ray diffraction with no sample preparation

    包量

    机译 无需样品制备的高分辨率X射线衍射
    摘要：It is shown that energy-dispersive X-ray diffraction (EDXRD) implemented in a back-reflection geometry is extremely insensitive to sample morphology and positioning even in a high-resolution configuration. This technique allows high-quality X-ray diffraction analysis of samples that have not been prepared and is therefore completely non-destructive. The experimental technique was implemented on beamline B18 at the Diamond Light Source synchrotron in Oxfordshire, UK. The majority of the experiments in this study were performed with pre-characterized geological materials in order to elucidate the characteristics of this novel technique and to develop the analysis methods. Results are presented that demonstrate phase identification, the derivation of precise unit-cell parameters and extraction of microstructural information on unprepared rock samples and other sample types. A particular highlight was the identification of a specific polytype of a muscovite in an unprepared mica schist sample, avoiding the time-consuming and difficult preparation steps normally required to make this type of identification. The technique was also demonstrated in application to a small number of fossil and archaeological samples. Back-reflection EDXRD implemented in a high-resolution configuration shows great potential in the crystallographic analysis of cultural heritage artefacts for the purposes of scientific research such as provenancing, as well as contributing to the formulation of conservation strategies. Possibilities for moving the technique from the synchrotron into museums are discussed. The avoidance of the need to extract samples from high-value and rare objects is a highly significant advantage, applicable also in other potential research areas such as palaeontology, and the study of meteorites and planetary materials brought to Earth by sample-return missions.
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