Pub Date : 2024-09-01Epub Date: 2024-07-29DOI: 10.1107/S2053273324005643
Agatha Kristel Abila, Ma Louise Antonette De Las Peñas, Mark Tomenes
An edge-n-coloring of a uniform tiling {cal T} is uniform if for any two vertices of {cal T} there is a symmetry of {cal T} that preserves the colors of the edges and maps one vertex onto the other. This paper gives a method based on group theory and color symmetry theory to arrive at uniform edge-n-colorings of uniform tilings. The method is applied to give a complete enumeration of uniform edge-n-colorings of the uniform tilings of the Euclidean plane, for which the results point to a total of 114 colorings, n = 1, 2, 3, 4, 5. Examples of uniform edge-n-colorings of tilings in the hyperbolic plane and two-dimensional sphere are also presented.
{"title":"On uniform edge-n-colorings of tilings.","authors":"Agatha Kristel Abila, Ma Louise Antonette De Las Peñas, Mark Tomenes","doi":"10.1107/S2053273324005643","DOIUrl":"10.1107/S2053273324005643","url":null,"abstract":"<p><p>An edge-n-coloring of a uniform tiling {cal T} is uniform if for any two vertices of {cal T} there is a symmetry of {cal T} that preserves the colors of the edges and maps one vertex onto the other. This paper gives a method based on group theory and color symmetry theory to arrive at uniform edge-n-colorings of uniform tilings. The method is applied to give a complete enumeration of uniform edge-n-colorings of the uniform tilings of the Euclidean plane, for which the results point to a total of 114 colorings, n = 1, 2, 3, 4, 5. Examples of uniform edge-n-colorings of tilings in the hyperbolic plane and two-dimensional sphere are also presented.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"367-378"},"PeriodicalIF":1.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-07-15DOI: 10.1107/S2053273324006569
Dmitry Chernyshov, Kenneth P Marshall, Erlend Tiberg North, Chloe A Fuller, David S Wragg
The atomic pair distribution function (PDF) is a real-space representation of the structure of a material. Experimental PDFs are obtained using a Fourier transform from total scattering data which may or may not have Bragg diffraction peaks. The determination of Bragg peak resolution in scattering data from the fundamental physical parameters of the diffractometer used is well established, but after the Fourier transform from reciprocal to direct space, these contributions are harder to identify. Starting from an existing definition of the resolution function of large-area detectors for X-ray diffraction, this approach is expanded into direct space. The effect of instrumental parameters on PDF peak resolution is developed mathematically, then studied with modelling and comparison with experimental PDFs of LaB6 from measurements made in different-sized capillaries.
原子对分布函数(PDF)是材料结构的实空间表示。实验 PDF 是通过对可能有或可能没有布拉格衍射峰的总散射数据进行傅立叶变换获得的。根据所用衍射仪的基本物理参数来确定散射数据中的布拉格峰分辨率是行之有效的方法,但在从倒数空间到直接空间的傅立叶变换之后,这些贡献就很难确定了。从 X 射线衍射大面积探测器分辨率函数的现有定义出发,这种方法被扩展到直接空间。仪器参数对 PDF 峰值分辨率的影响以数学方式进行了阐述,然后通过建模和与在不同尺寸毛细管中测量的 LaB6 实验 PDF 的比较进行了研究。
{"title":"Instrumental broadening and the radial pair distribution function with 2D detectors.","authors":"Dmitry Chernyshov, Kenneth P Marshall, Erlend Tiberg North, Chloe A Fuller, David S Wragg","doi":"10.1107/S2053273324006569","DOIUrl":"10.1107/S2053273324006569","url":null,"abstract":"<p><p>The atomic pair distribution function (PDF) is a real-space representation of the structure of a material. Experimental PDFs are obtained using a Fourier transform from total scattering data which may or may not have Bragg diffraction peaks. The determination of Bragg peak resolution in scattering data from the fundamental physical parameters of the diffractometer used is well established, but after the Fourier transform from reciprocal to direct space, these contributions are harder to identify. Starting from an existing definition of the resolution function of large-area detectors for X-ray diffraction, this approach is expanded into direct space. The effect of instrumental parameters on PDF peak resolution is developed mathematically, then studied with modelling and comparison with experimental PDFs of LaB<sub>6</sub> from measurements made in different-sized capillaries.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"358-366"},"PeriodicalIF":1.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11363166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-08DOI: 10.1107/S2053273324007253
Adam Morawiec
Neutron time-of-flight transmission spectra of mosaic crystals contain Bragg dips, i.e., minima at wavelengths corresponding to diffraction reflections. The positions of the dips are used for investigating crystal lattices. By rotating the sample around a fixed axis and recording a spectrum at each rotation step, the intensity of the transmitted beam is obtained as a function of the rotation angle and wavelength. The questions addressed in this article concern the determination of lattice parameters and orientations of centrosymmetric crystals from such data. It is shown that if the axis of sample rotation is inclined to the beam direction, the reflection positions unambiguously determine reciprocal-lattice vectors, which is not the case when the axis is perpendicular to the beam. Having a set of such vectors, one can compute the crystal orientation or lattice parameters using existing indexing software. The considerations are applicable to arbitrary Laue symmetry. The work contributes to the automation of the analysis of diffraction data obtained in the neutron imaging mode.
{"title":"Indexing neutron transmission spectra of a rotating crystal.","authors":"Adam Morawiec","doi":"10.1107/S2053273324007253","DOIUrl":"10.1107/S2053273324007253","url":null,"abstract":"<p><p>Neutron time-of-flight transmission spectra of mosaic crystals contain Bragg dips, i.e., minima at wavelengths corresponding to diffraction reflections. The positions of the dips are used for investigating crystal lattices. By rotating the sample around a fixed axis and recording a spectrum at each rotation step, the intensity of the transmitted beam is obtained as a function of the rotation angle and wavelength. The questions addressed in this article concern the determination of lattice parameters and orientations of centrosymmetric crystals from such data. It is shown that if the axis of sample rotation is inclined to the beam direction, the reflection positions unambiguously determine reciprocal-lattice vectors, which is not the case when the axis is perpendicular to the beam. Having a set of such vectors, one can compute the crystal orientation or lattice parameters using existing indexing software. The considerations are applicable to arbitrary Laue symmetry. The work contributes to the automation of the analysis of diffraction data obtained in the neutron imaging mode.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"379-386"},"PeriodicalIF":1.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-06-07DOI: 10.1107/S2053273324003292
Johannes Dallmann, Jonas Graetz, Rainer Hock
Analytical calculations of absorption corrections for X-ray powder diffraction experiments on non-ideal samples with surface roughness, porosity or absorption contrasts from multiple phases require complex mathematical models to represent their material distribution. In a computational approach to this problem, a practicable ray-tracing algorithm is formulated which is capable of simulating angle-dependent absorption corrections in reflection geometry for any given rasterized sample model. Single or multiphase systems with arbitrary surface roughness, porosity and spatial distribution of the phases in any combination can be modeled on a voxel grid by assigning respective values to each voxel. The absorption corrections are calculated by tracing the attenuation of X-rays along their individual paths via a modified shear-warp algorithm. The algorithm is presented in detail and the results of simulated absorption corrections on samples with various surface modulations are discussed in the context of published experimental results.
对表面粗糙度、孔隙率或多相吸收对比的非理想样品进行 X 射线粉末衍射实验的吸收修正分析计算,需要复杂的数学模型来表示其材料分布。针对这一问题的计算方法制定了一种实用的光线跟踪算法,该算法能够模拟任何给定光栅化样品模型在反射几何中与角度相关的吸收修正。单相或多相系统具有任意的表面粗糙度、孔隙率和任意组合的相的空间分布,可以通过给每个象素分配各自的值在象素网格上建模。吸收修正的计算方法是通过改进的剪切-剪切算法追踪 X 射线沿各自路径的衰减情况。本文详细介绍了该算法,并结合已公布的实验结果,讨论了对具有各种表面调制的样品进行吸收修正的模拟结果。
{"title":"Universal simulation of absorption effects for X-ray diffraction in reflection geometry.","authors":"Johannes Dallmann, Jonas Graetz, Rainer Hock","doi":"10.1107/S2053273324003292","DOIUrl":"10.1107/S2053273324003292","url":null,"abstract":"<p><p>Analytical calculations of absorption corrections for X-ray powder diffraction experiments on non-ideal samples with surface roughness, porosity or absorption contrasts from multiple phases require complex mathematical models to represent their material distribution. In a computational approach to this problem, a practicable ray-tracing algorithm is formulated which is capable of simulating angle-dependent absorption corrections in reflection geometry for any given rasterized sample model. Single or multiphase systems with arbitrary surface roughness, porosity and spatial distribution of the phases in any combination can be modeled on a voxel grid by assigning respective values to each voxel. The absorption corrections are calculated by tracing the attenuation of X-rays along their individual paths via a modified shear-warp algorithm. The algorithm is presented in detail and the results of simulated absorption corrections on samples with various surface modulations are discussed in the context of published experimental results.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"315-328"},"PeriodicalIF":1.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11216610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-05-31DOI: 10.1107/S2053273324002730
Felix N Chukhovskii
Fundamental equations describing the X-ray and electron diffraction scattering in imperfect crystals have been derived in the form of the matrix Fredholm-Volterra integral equation of the second kind. A theoretical approach has been developed using the perfect-crystal Green function formalism. In contrast, another approach utilizes the wavefield eigenfunctions related to the diagonalized matrix propagators of the conventional Takagi-Taupin and Howie-Whelan equations. Using the Liouville-Neumann-type series formalism for building up the matrix Fredholm-Volterra integral equation solutions, the general resolvent function solutions of the X-ray and electron diffraction boundary-valued Cauchy problems have been obtained. Based on the resolvent-type solutions, the aim is to reveal the features of the diffraction scattering onto the crystal lattice defects, including the mechanisms of intra- and interbranch wave scattering in the strongly deformed regions in the vicinity of crystal lattice defect cores. Using the two-stage resolvent solution of the second order, this approach has been supported by straightforward calculation of the electron bright- and dark-field contrasts of an edge dislocation in a thick foil. The results obtained for the bright- and dark-field profiles of the edge dislocation are discussed and compared with analogous ones numerically calculated by Howie & Whelan [Proc. R. Soc. A (1962), 267, 206].
描述不完全晶体中 X 射线和电子衍射散射的基本方程是以矩阵 Fredholm-Volterra 第二种积分方程的形式推导出来的。一种理论方法是利用完美晶体的格林函数形式主义。相反,另一种方法则利用了与传统高木-陶平方程和豪伊-惠兰方程的对角化矩阵传播者相关的波场特征函数。利用 Liouville-Neumann 型数列形式建立矩阵 Fredholm-Volterra 积分方程解,得到了 X 射线和电子衍射边界值考奇问题的一般解析函数解。基于解析型解法,目的是揭示衍射散射到晶格缺陷上的特征,包括晶格缺陷核心附近强变形区域的支内和支间波散射机制。利用二阶的两级解析解,通过直接计算厚箔中边缘位错的电子亮场和暗场对比,支持了这一方法。本文讨论了边缘位错的明场和暗场剖面,并与 Howie 和 Whelan [Proc. R. Soc. A (1962), 267, 206] 的类似数值计算结果进行了比较。
{"title":"Development of an innovative diffraction scattering theory of X-rays and electrons in imperfect crystals.","authors":"Felix N Chukhovskii","doi":"10.1107/S2053273324002730","DOIUrl":"10.1107/S2053273324002730","url":null,"abstract":"<p><p>Fundamental equations describing the X-ray and electron diffraction scattering in imperfect crystals have been derived in the form of the matrix Fredholm-Volterra integral equation of the second kind. A theoretical approach has been developed using the perfect-crystal Green function formalism. In contrast, another approach utilizes the wavefield eigenfunctions related to the diagonalized matrix propagators of the conventional Takagi-Taupin and Howie-Whelan equations. Using the Liouville-Neumann-type series formalism for building up the matrix Fredholm-Volterra integral equation solutions, the general resolvent function solutions of the X-ray and electron diffraction boundary-valued Cauchy problems have been obtained. Based on the resolvent-type solutions, the aim is to reveal the features of the diffraction scattering onto the crystal lattice defects, including the mechanisms of intra- and interbranch wave scattering in the strongly deformed regions in the vicinity of crystal lattice defect cores. Using the two-stage resolvent solution of the second order, this approach has been supported by straightforward calculation of the electron bright- and dark-field contrasts of an edge dislocation in a thick foil. The results obtained for the bright- and dark-field profiles of the edge dislocation are discussed and compared with analogous ones numerically calculated by Howie & Whelan [Proc. R. Soc. A (1962), 267, 206].</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"305-314"},"PeriodicalIF":1.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141178211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-06-27DOI: 10.1107/S2053273324004352
Il Hun Kim, Il Hwan Kim, Kum Ok Jang, Song Won Kim
This paper proposes a new order parameter model which satisfactorily explains complicated symmetry changes, the temperature-pressure (T-P) phase diagram and elastic anomalies observed experimentally with the improper ferroelastic phase transitions in multiferroic KMnF3 single crystal. First, it is shown that the order parameter model is transformed according to the four-dimensional reducible representation of the wavevector star channel group. Second, based on the order parameter model and the singularity theory, the sixth-order structurally stable Landau potential model is constructed. Finally, the theoretical T-P phase diagram is plotted and the elastic anomalies possible for each of the phase transitions are discussed.
{"title":"A new order parameter model for the improper ferroelastic phase transitions in KMnF<sub>3</sub> single crystal.","authors":"Il Hun Kim, Il Hwan Kim, Kum Ok Jang, Song Won Kim","doi":"10.1107/S2053273324004352","DOIUrl":"10.1107/S2053273324004352","url":null,"abstract":"<p><p>This paper proposes a new order parameter model which satisfactorily explains complicated symmetry changes, the temperature-pressure (T-P) phase diagram and elastic anomalies observed experimentally with the improper ferroelastic phase transitions in multiferroic KMnF<sub>3</sub> single crystal. First, it is shown that the order parameter model is transformed according to the four-dimensional reducible representation of the wavevector star channel group. Second, based on the order parameter model and the singularity theory, the sixth-order structurally stable Landau potential model is constructed. Finally, the theoretical T-P phase diagram is plotted and the elastic anomalies possible for each of the phase transitions are discussed.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"329-338"},"PeriodicalIF":1.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141453791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-06-25DOI: 10.1107/S2053273324004418
Ryoko Oishi-Tomiyasu
In ab initio indexing, for a given diffraction/scattering pattern, the unit-cell parameters and the Miller indices assigned to reflections in the pattern are determined simultaneously. `Ab initio' means a process performed without any good prior information on the crystal lattice. Newly developed ab initio indexing software is frequently reported in crystallography. However, it is not widely recognized that use of a Bravais lattice determination method, which is tolerant of experimental errors, can simplify indexing algorithms and increase their success rates. One of the goals of this article is to collect information on the lattice-basis reduction theory and its applications. The main result is a Bravais lattice determination algorithm for 2D lattices, along with a mathematical proof that it works even for parameters containing large observational errors. It uses two lattice-basis reduction methods that seem to be optimal for different symmetries, similarly to the algorithm for 3D lattices implemented in the CONOGRAPH software. In indexing, a method for error-stable unit-cell identification is also required to exclude duplicate solutions. Several methods are introduced to measure the difference in unit cells known in crystallography and mathematics.
在 ab initio 索引中,对于给定的衍射/散射图样,要同时确定单位晶胞参数和分配给图案中反射的米勒指数。所谓 "非初始",是指在没有任何关于晶格的可靠信息的情况下进行的过程。晶体学领域经常报道新开发的ab initio 索引软件。然而,人们并没有普遍认识到,使用可容忍实验误差的布拉维晶格确定方法可以简化索引算法并提高其成功率。本文的目的之一是收集有关晶格基础还原理论及其应用的信息。主要成果是二维网格的布拉维网格确定算法,以及该算法即使在参数包含较大观测误差时也有效的数学证明。它使用了两种格子基础还原方法,这两种方法似乎是不同对称性的最佳方法,类似于 CONOGRAPH 软件中实现的三维格子算法。在索引过程中,还需要一种误差稳定的单元格识别方法来排除重复解。本文介绍了几种测量晶体学和数学中已知单元格差异的方法。
{"title":"Ideas of lattice-basis reduction theory for error-stable Bravais lattice determination and abinitio indexing.","authors":"Ryoko Oishi-Tomiyasu","doi":"10.1107/S2053273324004418","DOIUrl":"10.1107/S2053273324004418","url":null,"abstract":"<p><p>In ab initio indexing, for a given diffraction/scattering pattern, the unit-cell parameters and the Miller indices assigned to reflections in the pattern are determined simultaneously. `Ab initio' means a process performed without any good prior information on the crystal lattice. Newly developed ab initio indexing software is frequently reported in crystallography. However, it is not widely recognized that use of a Bravais lattice determination method, which is tolerant of experimental errors, can simplify indexing algorithms and increase their success rates. One of the goals of this article is to collect information on the lattice-basis reduction theory and its applications. The main result is a Bravais lattice determination algorithm for 2D lattices, along with a mathematical proof that it works even for parameters containing large observational errors. It uses two lattice-basis reduction methods that seem to be optimal for different symmetries, similarly to the algorithm for 3D lattices implemented in the CONOGRAPH software. In indexing, a method for error-stable unit-cell identification is also required to exclude duplicate solutions. Several methods are introduced to measure the difference in unit cells known in crystallography and mathematics.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"339-350"},"PeriodicalIF":1.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01Epub Date: 2024-05-28DOI: 10.1107/S2053273324003097
Dmitry G Stepenshchikov, Anton D Pavlushin
The shape of a flat-faceted octahedral crystal can be uniquely defined by the measured distances between pairs of its parallel facets and the length of one of its false edges. In total, only five numerical values are involved in this approach. Some interdependencies of parameters that allow one to control the correctness of measurements were derived. The proposed method is suitable for describing the shape as full-faceted, or as incomplete octahedral crystals (e.g. diamond) with unequally developed facets. This so-called `real crystal form' can be considered as one of the typomorphic features of minerals, connecting the dissymmetry to the anisotropy of the host rock. The measurement results can be used in crystallo-morphological analysis, restoration of the lost crystal shape in the case of man-made damage and in the practice of diamond prospecting.
{"title":"The description of octahedral crystals using five parameters.","authors":"Dmitry G Stepenshchikov, Anton D Pavlushin","doi":"10.1107/S2053273324003097","DOIUrl":"10.1107/S2053273324003097","url":null,"abstract":"<p><p>The shape of a flat-faceted octahedral crystal can be uniquely defined by the measured distances between pairs of its parallel facets and the length of one of its false edges. In total, only five numerical values are involved in this approach. Some interdependencies of parameters that allow one to control the correctness of measurements were derived. The proposed method is suitable for describing the shape as full-faceted, or as incomplete octahedral crystals (e.g. diamond) with unequally developed facets. This so-called `real crystal form' can be considered as one of the typomorphic features of minerals, connecting the dissymmetry to the anisotropy of the host rock. The measurement results can be used in crystallo-morphological analysis, restoration of the lost crystal shape in the case of man-made damage and in the practice of diamond prospecting.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"351-354"},"PeriodicalIF":1.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141157116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-01Epub Date: 2024-04-29DOI: 10.1107/S2053273324002523
Maxwell Christopher Day, Ali Rostami, Frank Christopher Hawthorne
Following the work of Day & Hawthorne [Acta Cryst. (2022), A78, 212-233] and Day et al. [Acta Cryst. (2024), A80, 258-281], the program GraphT-T has been developed to embed graphical representations of observed and hypothetical chains of (SiO4)4- tetrahedra into 2D and 3D Euclidean space. During embedding, the distance between linked vertices (T-T distances) and the distance between unlinked vertices (T...T separations) in the resultant unit-distance graph are restrained to the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is restrained to be equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. The notional interactions between vertices are described by a 3D spring-force algorithm in which the attractive forces between linked vertices behave according to Hooke's law and the repulsive forces between unlinked vertices behave according to Coulomb's law. Embedding parameters (i.e. spring coefficient, k, and Coulomb's constant, K) are iteratively refined during embedding to determine if it is possible to embed a given graph to produce a unit-distance graph with T-T distances and T...T separations that are compatible with the observed T-T distances and T...T separations in crystal structures. The resultant unit-distance graphs are denoted as compatible and may form crystal structures if and only if all distances between linked vertices (T-T distances) agree with the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. If the unit-distance graph does not satisfy these conditions, it is considered incompatible and the corresponding chain of tetrahedra is unlikely to form crystal structures. Using GraphT-T, Day et al. [Acta Cryst. (2024), A80, 258-281] have shown that several topological properties of chain graphs influence the flexibility (and rigidity) of the corresponding chains of Si tetrahedra and may explain why particular compatible chain arrangements (and the minerals in which they occur) are more common than others and/or why incompatible chain arrangements do not occur in crystals despite being topologically possible.
{"title":"GraphT-T (V1.0Beta), a program for embedding and visualizing periodic graphs in 3D Euclidean space.","authors":"Maxwell Christopher Day, Ali Rostami, Frank Christopher Hawthorne","doi":"10.1107/S2053273324002523","DOIUrl":"https://doi.org/10.1107/S2053273324002523","url":null,"abstract":"<p><p>Following the work of Day & Hawthorne [Acta Cryst. (2022), A78, 212-233] and Day et al. [Acta Cryst. (2024), A80, 258-281], the program GraphT-T has been developed to embed graphical representations of observed and hypothetical chains of (SiO<sub>4</sub>)<sup>4-</sup> tetrahedra into 2D and 3D Euclidean space. During embedding, the distance between linked vertices (T-T distances) and the distance between unlinked vertices (T...T separations) in the resultant unit-distance graph are restrained to the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is restrained to be equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. The notional interactions between vertices are described by a 3D spring-force algorithm in which the attractive forces between linked vertices behave according to Hooke's law and the repulsive forces between unlinked vertices behave according to Coulomb's law. Embedding parameters (i.e. spring coefficient, k, and Coulomb's constant, K) are iteratively refined during embedding to determine if it is possible to embed a given graph to produce a unit-distance graph with T-T distances and T...T separations that are compatible with the observed T-T distances and T...T separations in crystal structures. The resultant unit-distance graphs are denoted as compatible and may form crystal structures if and only if all distances between linked vertices (T-T distances) agree with the average observed distance between linked Si tetrahedra (3.06±0.15 Å) and the minimum separation between unlinked vertices is equal to or greater than the minimum distance between unlinked Si tetrahedra (3.713 Å) in silicate minerals. If the unit-distance graph does not satisfy these conditions, it is considered incompatible and the corresponding chain of tetrahedra is unlikely to form crystal structures. Using GraphT-T, Day et al. [Acta Cryst. (2024), A80, 258-281] have shown that several topological properties of chain graphs influence the flexibility (and rigidity) of the corresponding chains of Si tetrahedra and may explain why particular compatible chain arrangements (and the minerals in which they occur) are more common than others and/or why incompatible chain arrangements do not occur in crystals despite being topologically possible.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":"80 Pt 3","pages":"282-292"},"PeriodicalIF":1.8,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140846642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}