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

Owing to its low excitation energy and long radiative lifetime, the first excited isomeric state of thorium-229, 229mTh, can be optically controlled by a laser1,2 and is an ideal candidate for the creation of a nuclear optical clock3, which is expected to complement and outperform current electronic-shell-based atomic clocks4. A nuclear clock will have various applications—such as in relativistic geodesy5, dark matter research6 and the observation of potential temporal variations of fundamental constants7—but its development has so far been impeded by the imprecise knowledge of the energy of 229mTh. Here we report a direct measurement of the transition energy of this isomeric state to the ground state with an uncertainty of 0.17 electronvolts (one standard deviation) using spectroscopy of the internal conversion electrons emitted in flight during the decay of neutral 229mTh atoms. The energy of the transition between the ground state and the first excited state corresponds to a wavelength of 149.7 ± 3.1 nanometres, which is accessible by laser spectroscopy through high-harmonic generation. Our method combines nuclear and atomic physics measurements to advance precision metrology, and our findings are expected to facilitate the application of high-resolution laser spectroscopy on nuclei and to enable the development of a nuclear optical clock of unprecedented accuracy. The transition energy of the first excited state of 229Th to the ground state is determined through the measurement of internal conversion electrons to correspond to a wavelength of 149.7 ± 3.1 nanometres.

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Energy of the 229 Th nuclear clock transition

Received January 7, 2011; Revised April 19, 2011 The Bilbao Crystallographic Server is a web site with crystallographic databases and programs available online (www.cryst.ehu.es). It has been operating for more than ten years and new applications are being added regularly. The programs available on the server do not need a local installation and can be used free of charge. The server gives access to general information related to crystallographic symmetry groups (generators, general and special positions, maximal subgroups, Brillouin zones, etc.). Apart from the simple tools for retrieving the stored data, there are programs for the analysis of group-subgroup relations between space groups. There are also software package studying specific problems of solid-state physics, structural chemistry and crystallography.

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Crystallography online by the Bilbao Crystallographic Server

https://iopscience.iop.org/article/10.3367/UFNe.2016.02.037729/pdf

Discrete breathers in crystals

Strong metal–support interactions (SMSIs) are crucial for the preparation of supported metal catalysts. A prevailing view is that the redox feature of the metal oxide support is the driving force behind SMSI construction. Herein we demonstrate CO2-induced SMSIs between irreducible oxide MgO and noble gold nanoparticles, presenting electronic and geometric features that are similar to those of classical SMSIs. The key to these interactions is activating the oxide surface by a reversible reaction, MgO + CO2 ⇆ MgCO3, which leads to migration of the support onto the gold nanoparticles to form thin overlayers. The overlayer is permeable to the reactant molecules, stable under the oxidation conditions and even water tolerant, resulting in sinter-resistant gold nanoparticle catalysts. This investigation provides an approach for the rational design and optimization of supported metal catalysts based on irreducible oxides, and deepens our understanding of the mechanism of SMSI formation. The strong metal–support interaction is an important phenomenon for the modulation of a catalyst´s performance but is traditionally restricted to reducible oxide supports. Here, a CO2-induced strong metal–support interaction is reported for gold nanoparticles supported on non-reducible MgO to yield a superior oxidation catalyst.

Strong metal–support interactions on gold nanoparticle catalysts achieved through Le Chatelier’s principle

Materials properties of magnesium and calcium hydroxides from first-principles calculations

Based on the combination of density functional theory and theory-group methods, we performed systematic modeling of γ-CuI structural design at the atomistic level. Being started from the metallic copper lattice, we treated a crystal assembly as a stepwise iodination process characterized in terms of a sequence of intermediate lattice geometries. These geometries were selected and validated via screening of possible structural transformations. The genesis of chemical bonding was studied for three structural transformations by analyzing the relevant changes in the topology of valence electron densities. We determined structural trends driven by metal-ligand coupling. This allowed us to suggest the improved scenario of chemical bonding in γ-CuI. In particular, the unconventional effect of spatial separation of metallic and covalent interactions was found to be very important with respect to the preferred arrangements of valence electrons in the iodination process. We rigorously showed that useful electronic and optical properties of γ-CuI originate from the combination of two separated bonding patterns-strong covalency established in I-Cu tetrahedral connections and noncovalent interactions of copper cores is caused by the 3d10 closed-shell electron configurations. The other finding of ours is that the self-consistency of the GW calculations is crucial for correctly determining the dynamic electronic correlations in γ-CuI. Detail reinvestigation of the quasi-particle energy structure by means of the self-consistent GW approach allowed us to explain how p-type electrical conductivity can be engineered in the material.

/pdf/structure-property-relationships-in-cubic-cuprous-iodide-a-1gv6pqbqwv.pdf

Structure-property relationships in cubic cuprous iodide: A novel view on stability, chemical bonding, and electronic properties

Role of oxygen in materials properties of yttrium trihydride

MD simulations of recoil processes, following the scattering of X-rays or neutrons are performed. At small energies (

Modeling of self-localized vibrations and defect formation in solids

The synthesis of stable yttrium oxyhydride-type compounds raised a principal question regarding the key factors that may be responsible for formation routes and structural features of these attractive materials. For solving this challenge, the interplay between chemical composition and crystalline architectures has been theoretically explored via modeling structural transformations caused by the gradual oxidation of the host metal hydride system. The close combination of group-theory methods, mixed-anion chemistry arguments, and relevant density functional theory calculations provided us with the opportunity to suggest and characterize the candidate models for most probable stoichiometric versions of yttrium oxyhydrides. The predicted chemical compositions along with the crystallization results have been summarized in the phase diagram. It is shown that the cation–ligand interaction governs the structural stability which is achieved by matching favorable crystallographic positions of the oxygen and hydrog...

Aleksandr Pishtshev

Papers

Materials properties of magnesium and calcium hydroxides from first-principles calculations

Structure-property relationships in cubic cuprous iodide: A novel view on stability, chemical bonding, and electronic properties

Role of oxygen in materials properties of yttrium trihydride

Modeling of self-localized vibrations and defect formation in solids

Conceptual Design of Yttrium Oxyhydrides: Phase Diagram, Structure, and Properties