VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3, implementing new features including drawing the external morphology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices. ‡ Present address: National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.
A cross‐platform program, VESTA, has been developed to visualize both structural and volumetric data in multiple windows with tabs. VESTA represents crystal structures by ball‐and‐stick, space‐filling, polyhedral, wireframe, stick, dot‐surface and thermal‐ellipsoid models. A variety of crystal‐chemical information is extractable from fractional coordinates, occupancies and oxidation states of sites. Volumetric data such as electron and nuclear densities, Patterson functions, and wavefunctions are displayed as isosurfaces, bird's‐eye views and two‐dimensional maps. Isosurfaces can be colored according to other physical quantities. Translucent isosurfaces and/or slices can be overlapped with a structural model. Collaboration with external programs enables the user to locate bonds and bond angles in the `graphics area', simulate powder diffraction patterns, and calculate site potentials and Madelung energies. Electron densities determined experimentally are convertible into their Laplacians and electronic energy densities.
A multi-purpose pattern-fitting system, RIETAN-2000, has been extensively utilized to
contribute to many structural studies. It offers a sophisticated structure-refinement technique of
whole-pattern fitting based on the maximum-entropy method (MEM) in combination with a MEM
analysis program PRIMA. We have recently completed a successor system, RIETAN-FP, to
RIETAN-2000, adding new features such as standardization of crystal-structure data, an extended
March-Dollase preferred-orientation function, and automation of imposing restraints on bond
lengths and angles. Further, we have been developing a new three-dimensional visualization system,
VESTA, using wxWidgets as a C++ application framework. VESTA excels in visualization, rendering,
and manipulation of crystal structures and electron/nuclear densities determined by X-ray/
neutron diffraction and electronic-structure calculations. VESTA also enables us to display wave
functions and electrostatic potentials calculated with part of these programs.
A computer program, Dysnomia, for the maximum-entropy method (MEM) has been tested for the evaluation and advancement of MEM-based pattern fitting (MPF). Dysnomia is a successor to PRIMA, which was the only program integrated with RIETAN-FP for MPF. Two types of MEM algorithms, i.e., 0th-order single-pixel approximation and a variant of the Cambridge algorithm, were implemented in Dysnomia in combination with a linear combination of the "generalized F constraints" and arbitrary weighting factors for them. Dysnomia excels PRIMA in computation speed, memory efficiency, and scalability owing to parallel processing and automatic switching of discrete Fourier transform and fast Fourier transform depending on sizes of grids and observed reflections. These features of Dysnomia were evaluated for MPF analyses from X-ray powder diffraction data of three different types of compounds: taurine, Cu 2 CO 3 (OH) 2 (malachite), and Sr 9 In(PO 4 ) 7 . Reliability indices in MPF analyses proved to have been improved by using multiple F constraints and weighting factors based on lattice-plane spacings, d, in comparison with those obtained with PRIMA.
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