PDFfit2 and PDFgui: computer programs for studying nanostructure in crystals (original) (raw)
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Crystal structure solution from experimentally determined atomic pair distribution functions
Journal of Applied Crystallography, 2010
The paper describes an extension of the Liga algorithm for structure solution from atomic pair distribution function (PDF), to handle periodic crystal structures with multiple elements in the unit cell. The procedure is performed in 2 separate stepsat first the Liga algorithm is used to find unit cell sites consistent with pair distances extracted from the experimental PDF. In the second step the assignment of atom species over cell sites is solved by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron x-ray PDF data from 16 test samples. The structure solution was successful for 14 samples including cases with enlarged super cells. The algorithm success rate and the reasons for failed cases are discussed together with enhancements that should improve its convergence and usability.
WinCSD: software package for crystallographic calculations (Version 4)
Journal of Applied Crystallography, 2014
The fourth version of the program packageWinCSDis multi-purpose computer software for crystallographic calculations using single-crystal and powder X-ray and neutron diffraction data. The software environment and the graphical user interface are built using the platform of the Microsoft .NET Framework, which grants independence from changing Windows operating systems and allows for transferring to other operating systems. Graphic applications use the three-dimensional OpenGL graphics language.WinCSDcovers the complete spectrum of crystallographic calculations, including powder diffraction pattern deconvolution, crystal structure solution and refinement in 3 + dspace, refinement of the multipole model and electron density studies from diffraction data, and graphical representation of crystallographic information.
2006
Summary of Completed Work The project web site has been established at http://nanocrystallography.research.pdx.edu/ and the NWACC logo is displayed at this site prominently At http://nanocrystallography.research.pdx.edu/CIF-searchable/ we provide access to a local version of the free Crystallography Open Database (COD), which contains the records of approximately 11,000 structure determinations. Queries of this database can be downloaded in the standard Crystallographic Information File (CIF) format and displayed by the free java based program Jmol. For details see the attached manuscripts of a paper in the peer reviewed international Journal of Materials Education (appendix A) and of a paper that is going to be published on the website of Symposium KK: Education in Nanoscience and Engineering, http://www.mrs.org/s\_mrs/doc.asp?CID=3336&DID=167381 (appendix B) and to be presented orally at that symposium on ABSTRACT Crystallographic databases for inorganic materials that are freely a...
OLEX : new software for visualization and analysis of extended crystal structures
Journal of Applied Crystallography, 2003
We have developed new software (OLEX) for the visualization and analysis of extended crystal structures. This software has a Windows-compatible mousedriven graphical interface which gives full control over all structural elements. OLEX provides the user with tools to construct topological networks, visualize interpenetrating or overlapping fragments, and analyse networks constructed fully or partially by exploiting short interactions. It is also easy to generate conventional ellipsoid, ball-and-stick or packing plots.
CURVIS : a program to study and analyse crystallographic structures and phase transitions
Journal of Applied Crystallography, 2005
The visualization of scientific data is, nowadays, of extreme importance. Phase transitions, the topology of a crystallographic system, the electron density distribution inside a lattice or the changes in crystal structure during phase transitions cannot be fully investigated without the help of proper visualization. The program CURVIS (downloadable free of charge upon request) was developed as a tool for investigating crystal structures and occurring transitions. In this tool, some features are implemented to analyse, display and manage the three-dimensional structure of crystals and single molecules. More importantly, CURVIS can generate and handle hyperbolic surfaces in three dimensions, and provide specific routines to perform calculations of curvature and energy of such surfaces. The most important features are (i) file format conversion (with assignment of the atom types and atomic charges), (ii) surface calculation and (iii) curvature and surface-energy analysis.
CCDC 1509229: Experimental Crystal Structure Determination
2016
An entry from the Cambridge Structural Database, the world's repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Journal of Applied Crystallography - J APPL CRYST, 2007
SUPERFLIP is a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data. Structure solution from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure. SUPERFLIP is written in Fortran90 and is distributed as a source code and as precompiled binaries. It has been successfully compiled and tested on a variety of operating systems.