There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

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.

VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data

J. Appl. Cryst.の発刊に際して

We report that a layered iron-based compound LaOFeAs undergoes superconducting transition under doping with F- ions at the O2- site. The transition temperature (Tc) exhibits a trapezoid shape dependence on the F- content, with the highest Tc of ∼26 K at ∼11 atom %.

Iron-Based Layered Superconductor La[O1-xFx]FeAs (x = 0.05−0.12) with Tc = 26 K

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.

VESTA: a three-dimensional visualization system for electronic and structural analysis

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.

Three-dimensional Visualization in Powder Diffraction

Raman spectra of anatase have been observed in natural and synthetic crystals. Both crystals show the same spectral features. The Raman band occurring at 516 cm−1 at room temperature is split into two peaks centred at 519 cm−1 and 513 cm−1 at low temperature (73 K). The six Raman active fundamentals predicted by group theory are all observed and assigned. The spectra are analyzed by a simple model considering only short-range forces and the calculated vibrational frequencies are in good agreement with the observed Raman frequencies.

Fujio Izumi

Papers

VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data

VESTA: a three-dimensional visualization system for electronic and structural analysis

Three-dimensional Visualization in Powder Diffraction

Raman spectrum of anatase, TiO2

A Rietveld-Analysis Programm RIETAN-98 and its Applications to Zeolites