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

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.

http://cars9.uchicago.edu/xafs_school/Material/Articles/Horae%20JSR2005.pdf

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT.

Accelerating the discovery of advanced materials is essential for human welfare and sustainable, clean energy. In this paper, we introduce the Materials Project (www.materialsproject.org), a core program of the Materials Genome Initiative that uses high-throughput computing to uncover the properties of all known inorganic materials. This open dataset can be accessed through multiple channels for both interactive exploration and data mining. The Materials Project also seeks to create open-source platforms for developing robust, sophisticated materials analyses. Future efforts will enable users to perform ‘‘rapid-prototyping’’ of new materials in silico, and provide researchers with new avenues for cost-effective, data-driven materials design. © 2013 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

/pdf/commentary-the-materials-project-a-materials-genome-approach-3kpccfz11d.pdf

Commentary: The Materials Project: A materials genome approach to accelerating materials innovation

Jenny Schneider,*,† Masaya Matsuoka,‡ Masato Takeuchi,‡ Jinlong Zhang, Yu Horiuchi,‡ Masakazu Anpo,‡ and Detlef W. Bahnemann*,† †Institut fur Technische Chemie, Leibniz Universitaẗ Hannover, Callinstrasse 3, D-30167 Hannover, Germany ‡Faculty of Engineering, Osaka Prefecture University, 1 Gakuen-cho, Sakai Osaka 599-8531, Japan Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, Shanghai 200237, China

Understanding TiO2 photocatalysis: mechanisms and materials.

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 self-consistent real-space multiple-scattering (RSMS) approach for calculations of x-ray-absorption near-edge structure (XANES) is presented and implemented in an ab initio code applicable to arbitrary aperiodic or periodic systems This approach yields a quantitative interpretation of XANES based on simultaneous, self-consistent-field (SCF) calculations of local electronic structure and x-ray absorption spectra, which include full multiple scattering from atoms within a small cluster and the contributions of high-order MS from scatterers outside that cluster In addition, the code includes a SCF estimate of the Fermi energy and an account of orbital occupancy and charge transfer We also present a qualitative, scattering-theoretic interpretation of XANES Sample applications are presented for cubic BN, ${\mathrm{UF}}_{6},$ Pu hydrates, and distorted ${\mathrm{PbTiO}}_{3}$ Limitations and various extensions are also discussed

Real-space multiple-scattering calculation and interpretation of x-ray-absorption near-edge structure

Dramatic advances in the understanding of x-ray absorption fine structure (XAFS) have been made over the past few decades, which have led ultimately to a highly quantitative theory. This review covers these developments from a unified multiple-scattering viewpoint. The authors focus on extended x-ray absorption fine structure (EXAFS) well above an x-ray edge, and, to a lesser extent, on x-ray absorption near-edge structure (XANES) closer to an edge. The discussion includes both formal considerations, derived from a many-electron formulation, and practical computational methods based on independent-electron models, with many-body effects lumped into various inelastic losses and energy shifts. The main conceptual issues in XAFS theory are identified and their relative importance is assessed; these include the convergence of the multiple-scattering expansion, curved-wave effects, the scattering potential, inelastic losses, self-energy shifts, and vibrations and structural disorder. The advantages and limitations of current computational approaches are addressed, with particular regard to quantitative experimental comparisons.

Theoretical approaches to x-ray absorption fine structure

A high-order multiple-scattering (MS) approach to the calculation of polarized x-ray-absorption spectra, which includes both x-ray-absorption fine structure and x-ray-absorption near-edge structure, is presented. Efficient calculations in arbitrary systems are carried out by using a curved-wave MS path formalism that ignores negligible paths, and has an energy-dependent self-energy and MS Debye-Waller factors. Embedded-atom background absorption calculations on an absolute energy scale are included. The theory is illustrated for metallic Cu, Cd, and Pt. For these cases the MS expansion is found to converge to within typical experimental accuracy, both to experiment and to full MS theories (e.g., band structure), by using only a few dozen important paths, which are primarily single-scattering, focusing, linear, and triangular.

Multiple-scattering calculations of x-ray-absorption spectra

Theoretical X-ray Absorption Fine Structure Standards

High-order scattering is found to be essential for the convergence of the multiple-scattering (MS) theory of x-ray-absorption fine structure, both in the near-edge and the extended regimes. These contributions are calculated using an ab initio curved-wave scattering-matrix formalism. Convergence to full MS accuracy is demonstrated for fcc Cu, as well as for molecular ${\mathrm{O}}_{2}$ and ${\mathrm{N}}_{2}$, where our approach provides a high-order MS interpretation of the ${\mathrm{\ensuremath{\sigma}}}^{\mathrm{*}}$ shape resonances.

John J. Rehr

Papers

Real-space multiple-scattering calculation and interpretation of x-ray-absorption near-edge structure

Theoretical approaches to x-ray absorption fine structure

Multiple-scattering calculations of x-ray-absorption spectra

Theoretical X-ray Absorption Fine Structure Standards

High-order multiple-scattering calculations of x-ray-absorption fine structure.