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

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net
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/pdf/avogadro-an-advanced-semantic-chemical-editor-visualization-2imnj3h9vl.pdf

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

/pdf/lanthanide-single-molecule-magnets-efv9mucvem.pdf

Lanthanide single-molecule magnets.

Physical Review B

Synthesis of 3d metallic single-molecule magnets

Boron in MgB2 forms stacks of honeycomb layers with magnesium as a space filler. Band structure calculations indicate that Mg is substantially ionized, and the bands at the Fermi level derive mainly from B orbitals. Strong bonding with an ionic component and considerable metallic density of states yield a sizable electron-phonon coupling. Together with high phonon frequencies, which we estimate via zone-center frozen phonon calculations to be between 300 and 700 cm(-1), this produces a high critical temperature, consistent with recent experiments. Thus MgB2 can be viewed as an analog of the long sought, but still hypothetical, superconducting metallic hydrogen.

/pdf/superconductivity-of-metallic-boron-in-mgb2-hzk6d6rm3a.pdf

Superconductivity of metallic boron in MgB2.

Density-functional calculations of the phonon spectrum and electron-phonon coupling in $\mathrm{MgB}{}_{2}$ are presented The ${E}_{2g}$ phonons, which involve in-plane B displacements, couple strongly to the ${p}_{x,y}$ electronic bands The isotropic electron-phonon coupling constant is calculated to be about 08 Allowing for different order parameters in different bands, the superconducting $\ensuremath{\lambda}$ in the clean limit is calculated to be significantly larger The ${E}_{2g}$ phonons are strongly anharmonic, and the nonlinear contribution to the coupling between the ${E}_{2g}$ modes and the ${p}_{x,y}$ bands is significant

Beyond Eliashberg Superconductivity in MgB 2 : Anharmonicity, Two-Phonon Scattering, and Multiple Gaps

Beyond Eliashberg Superconductivity in MgB2

A large number of experimental facts and theoretical arguments favor a two-gap model for superconductivity in MgB2 However, this model predicts strong suppression of the critical temperature by interband impurity scattering and, presumably, a strong correlation between the critical temperature and the residual resistivity No such correlation has been observed We argue that this fact can be understood if the band disparity of the electronic structure is taken into account, not only in the superconducting state, but also in normal transport

/pdf/superconductivity-in-mgb2-clean-or-dirty-5fptbpun5s.pdf

Superconductivity in MgB2: clean or dirty?

A theoretical model for quasiparticle and Josephson tunneling in multiband superconductors is developed and applied to MgB2-based junctions. The gap functions in different bands in MgB2 are obtained from an extended Eliashberg formalism, using the results of band structure calculations. The temperature and angle dependencies of MgB2 tunneling spectra and the Josephson critical current are calculated. The conditions for observing one or two gaps are given. We argue that the model may help to settle the current debate concerning two-band superconductivity in MgB2.

/pdf/multiband-model-for-tunneling-in-mgb2-junctions-3isu1g5ysl.pdf

Jens Kortus

Papers

Superconductivity of metallic boron in MgB2.

Beyond Eliashberg Superconductivity in MgB 2 : Anharmonicity, Two-Phonon Scattering, and Multiple Gaps

Beyond Eliashberg Superconductivity in MgB2

Superconductivity in MgB2: clean or dirty?

Multiband model for tunneling in MgB2 junctions