Pattern information extraction from crystal structures

Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summary: Title of program: BilKristal. Catalogue identifier: ADYU_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0. Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland. Licensing provisions: None. Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries. Computer: Personal Computers with Windows operating system. Operating system: Windows XP Professional. RAM: 20-60 MB. No. of lines in distributed program, including test data, etc.:899 779. No. of bytes in distributed program, including test date, etc.:9 271 521. Distribution format:tar.gz. External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL. Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from atomic coordinates of crystal structures. Restrictions: Assumptions are explained in the paper. However, none of them can be considered as a restriction onto the complexity of the problem. Running time: All the examples presented in the paper take less than 30 seconds on a 2.4 GHz Pentium 4 computer. © 2007 Elsevier B.V. All rights reserved

Pattern information extraction from crystal structures

Cataloged from PDF version of article.Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. This work provides a tool that will extract crystal parameters such as primitive vectors, basis vectors and space group from atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work presents a useful tool that help crystallographers, chemists and material scientists to analyze crystal structures efficiently.Okuyan, ErhanM.S

BilKristal 2.0: A tool for pattern information extraction from crystal structures

Cataloged from PDF version of article.We present a revised version of the BilKristal tool of Okuyan et al. (2007). We converted the development environment into Microsoft Visual Studio 2005 in order to resolve compatibility issues. We added multi-core CPU support and improvements are made to graphics functions in order to improve performance. Discovered bugs are fixed and exporting functionality to a material visualization tool is added

A tool for pattern information extraction and defect quantification from crystal structures

In this paper, we present a revised version of BilKristal 2.0 tool. We added defect quantification functionality to assess crystalline defects. We improved visualization capabilities by adding transparency support and runtime visibility sorting. Discovered bugs are fixed and small performance optimizations are made. New version program summary Program title: BilKristal 3.0 Catalogue identifier: ADYU-v3-0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU-v3-0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1868 923 No. of bytes in distributed program, including test data, etc.: 8854 507 Distribution format: tar.gz Programming language: C, C++, Microsoft.NET Framework 2.0 and OpenGL Libraries. Computer: Personal Computers with Windows operating system. Operating system: Windows XP or higher. RAM: 20-60 Megabytes. Classification: 8. Catalogue identifier of previous version: ADYU-v2-0 Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 442 External routines: Microsoft.NET Framework 2.0. For the visualization tool, graphics card driver should also support OpenGL. Does the new version supersede the previous version?: Yes Nature of problem: Determining the crystal structure parameters of a material is a very important issue in crystallography. Knowing the crystal structure parameters helps the understanding of the physical behavior of material. For complex structures, particularly for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be very hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identifies the space group from atomic coordinates of crystal structures. Reasons for new version: Additional features, Compatibility issues with newer development environments, Performance optimizations, Minor bug corrections. Summary of revisions:Defect quantification capability is added. The tool can process the imperfect crystal structures, finds and quantifies the crystalline defects. The tool is capable of finding positional defects, vacancy defects, substitutional impurities and interstitial impurities. The algorithms presented in [3] are used for defect quantification implementation.Transparency support is added to the visualization tool. Users are now allowed to set the transparency of each atom type individually.Runtime visibility sorting functionality is added to facilitate correct transparency computations.Visual Studio 2012 support is added. Visual Studio 2012 specific project files are created and the project is tested with this development environment.In visualization tool, an unused log file was created. This issue is corrected.In visualization tool, some OpenGL calls which are executed at every draw are changed to be executed only when they are needed, improving the visualization performance.Restrictions: Assumptions are explained in [1,2]. However, none of them can be considered as a restriction onto the complexity of the problem. Running time: The tool was able to process input files with more than a million atoms in less than 20 s on a PC with an Athlon quad-core CPU at 3.2 GHz using the default parameter values. References: [1] Erhan Okuyan, Ugur Güdükbay, Oguz Gülseren, Pattern information extraction from crystal structures, Comput. Phys. Comm. 176 (2007) 486. [2] Erhan Okuyan, Ugur Güdükbay, BilKristal 2.0: A tool for pattern information extraction from crystal structures, Comput. Phys. Comm. 185 (2014) 442. [3] Erhan Okuyan, Ugur Güdükbay, Ceyhun Bulutay, Karl-Heinz Heinig, MaterialVis: material visualization tool using direct volume and surface rendering techniques, J. Mol. Graphics Model. 50201450-60. © 2014 The Authors

Information Extraction, Data Integration, and Uncertain Data Management: The State of The Art

Information Extraction, data Integration, and uncertain data management are different areas of research that got vast focus in the last two decades. Many researches tackled those areas of research individually. However, information extraction systems should have integrated with data integration methods to make use of the extracted information. Handling uncertainty in extraction and integration process is an important issue to enhance the quality of the data in such integrated systems. This article presents the state of the art of the mentioned areas of research and shows the common grounds and how to integrate information extraction and data integration under uncertainty management cover

Photonic quasi-crystal LEDs: design, modelling, and optimisation

In this paper we investigate improvement in performance attainable by etching Photonic Crystals and Photonic Quasi-Crystals into the top emitting surface of LEDs. We describe the physical mechanisms of extraction enhancement through ordered surface patterning and investigate benefits in terms of total extraction enhancement, beam directionality, and far field beam quality. Factors such as lattice geometry, etch depth, and epitaxy thickness are investigated. We show that a great variety of far field beam profiles of benefit in applications such as projection TV light engines and direct flat panel display illumination can be obtained simply by adjusting geometric design parameters. Our results show that PCs can provide significant improvement in extraction enhancement for applications requiring non Lambertian beam shapes when etched into standard "production line" epitaxy wafers in comparison to "state of the art" surface roughened thin-GaN LED devices. We investigate PC beam steering effects in these devices confirming that PCs do in fact re-direct light from trapped modes confined within the epi-structure to radiating modes. We also show that by tailoring the thickness of the epi-structure to complement the properties of the photonic crystal, extraction enhancement can be improved by a factor of 9 for some applications

The predicted crystal structure of Li_4C_6O_6, an organic cathode material for Li-ion batteries, from first-principles multi-level computational methods

In this communication, we use first-principles based multi-level computational methods to predict the crystal structure of Li_4C_6O_6, the key intermediate material that can be oxidized to Li_2C_6O_6 or reduced to Li_6C_6O_6. This predicted structure leads to an X-ray diffraction (XRD) pattern in good agreement with experiment, validating the predicted structure. With this structure in hand one can proceed to determine details for the electrochemical properties of these organic electrodes (chemical potential for Li ion as a function of loading and the mechanism for the lithiation/delithiation process) useful in designing optimum systems

Acid/Base Controlled Size Modulation of Capsular Phosphates, Hydroxide Encapsulation, Quantitative and Clean Extraction of Sulfate with Carbonate Capsules of a Tripodal Urea Receptor

A simple tris-(2-aminoethyl) amine based pentafluorophenyl substituted tripodal urea receptor L has been extensively studied as a versatile receptor for various anions. Combined H-1-NMR, Isothermal Titration Calorimetry (ITC) and single crystal X-ray diffraction studies reveal that mononegative anions like F-, OH- and H2PO4- are encapsulated into the pseudocapsular dimeric assemblies of L with 1 : 1 stoichiometry whereas dinegative anions like CO32-, SO42- and HPO42- form tight capsular dimeric assemblies of L with 1 : 2 stoichiometries. Single crystal X-ray diffraction study clearly depicts that the size of the dimer of H2PO4- encapsulated pseudocapsule is 13.8 angstrom whereas the size of the tight HPO42- encapsulated capsular assembly is only 9.9 angstrom. The charge dependent anion encapsulated capsular size modulation of phosphates has been demonstrated by simple acid/base treatment via solution state P-31-NMR and single crystal X-ray diffraction studies. L is also capable of encapsulating hydroxide in its C-3v-symmetric cavity that is achieved upon treating a DMSO solution of L with tetrabutylammonium (TBA) cyanide and characterized by single crystal X-ray diffraction study. To the best of our knowledge this is the first report on the encapsulation of hydroxide in a neutral synthetic receptor. The excellent property of L to quantitatively capture aerial CO2 in the form of CO32- capsules [L-2(CO3)][N(n-Bu)(4)](2) in basic DMSO solution has been utilized to study the liquid-liquid extraction of SO42- from water via anion exchange. Almost quantitative and clean extraction of SO42- from water (99% from extracted pure mass and > 95% shown gravimetrically) has been unambiguously demonstrated by NMR, FT-IR, EDX, XRD and PXRD studies. Selective SO42- extraction is also demonstrated even in the presence of H2PO4- and NO3-. On the other hand the mixtures of L and TBACl (to solubilize L in CHCl3) results impure sulfate extraction even when 1 : 1 L/TBACl is used. Similar impure SO42- extraction is also observed when organic layers containing [L(Cl)][N(n-Bu)(4)] are used as the extractant, obtained upon precipitating SO42- from the extracted mass, [L-2(SO4)][N(n-Bu)(4)](2) in the carbonate capsules method using aqueous BaCl2 solution.Department of Science and TechnologyCSIR, IndiaChemistr