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

Note: Times Cited: 875 Reference EPFL-ARTICLE-206025doi:10.1021/cr0501846View record in Web of Science URL: ://WOS:000249839900009 Record created on 2015-03-03, modified on 2017-05-12

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Zn-doped CdS nanoarchitectures with different Zn content are synthesized by a simple hydrothermal method with water as the only solvent. The prepared samples are characterized by X-ray powder diffr...

Zn-Doped CdS Nanoarchitectures Prepared by Hydrothermal Synthesis: Mechanism for Enhanced Photocatalytic Activity and Stability under Visible Light

We have investigated, by means of ab initio calculations, the electronic and magnetic structures of zigzag edge phosphorene nanoribbons (ZPNRs) with various widths. The stable magnetic state was found in pristine ZPNRs by allowing the systems to be spin-polarized. The ground state of pristine ZPNRs prefers ferromagnetic order in the same edge but antiferromagnetic order between two opposite edges. The magnetism arises from the dangling bond states as well as edge localized π-orbital states. The presence of a dangling bond is crucial to the formation of the magnetism of ZPNRs. The hydrogenated ZPNRs get nonmagnetic semiconductors with a direct band gap. While, the O-saturated ZPNRs show magnetic ground states due to the weak P-O bond in the ribbon plane between the pz-orbitals of the edge O and P atoms.

Magnetism of zigzag edge phosphorene nanoribbons

The control of thermal expansion of solid compounds is intriguing but remains challenging. The effect of guests on the thermal expansion of open-framework structures was investigated. Notably, the presence of guest ions (K+) and molecules (H2O) can substantially switch thermal expansion of YFe(CN)6 from negative (αv=−33.67×10−6 K−1) to positive (αv=+42.72×10−6 K−1)—a range that covers the thermal expansion of most inorganic compounds. The mechanism of such substantial thermal expansion switching is revealed by joint studies with synchrotron X-ray diffraction, X-ray absorption fine structure, neutron powder diffraction, and density functional theory calculations. The presence of guest ions or molecules plays a critical damping effect on transverse vibrations, thus inhibiting negative thermal expansion. An effective method is demonstrated to control the thermal expansion in open-framework materials by adjusting the presence of guests.

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Switching Between Giant Positive and Negative Thermal Expansions of a YFe(CN)6‐based Prussian Blue Analogue Induced by Guest Species

Exploring isotropic negative thermal expansion (NTE) compounds is interesting, but remains challenging. Here, a new concept of "average atomic volume" is proposed to find new NTE open-framework materials. According to this guidance, two NTE compounds, AgB(CN)4 and CuB(CN)4, have been discovered, of which AgB(CN)4 exhibits a large NTE over a wide temperature range (αv = -40 × 10-6 K-1, 100-600 K). The analysis by extended X-ray absorption fine structure spectroscopy and first-principles calculation indicate that (i) the NTE driving force comes from the transverse vibrations of bridge chain atoms of C and N, corresponding to the low-frequency phonon modes; and (ii) the same transverse vibration direction of C and N atoms is a key factor for the occurrence of strong NTE in AgB(CN)4. The present concept of "average atomic volume" can be a simple parameter to explore new NTE compounds especially in those open-framework materials.

Discovering Large Isotropic Negative Thermal Expansion in Framework Compound AgB(CN)4 via the Concept of Average Atomic Volume.

The effects of mono-doping of 4f lanthanides with and without oxygen vacancy defect on the electronic structures of anatase TiO2 have been studied by first-principles calculations with DFT+U (DFT with Hubbard U correction) to treat the strong correlation of Ti 3d electrons and lanthanides 4f electrons. Our results revealed that dopant Ce is easy to incorporate into the TiO2 host by substituting Ti due to its lower substitutional energy (∼−2.0 eV), but the band gap of the system almost keeps intact after doping. The Ce 4f states are located at the bottom of conduction band, which mainly originates from Ti 3d states. The magnetic moment of doped Ce disappears due to electron transfer from Ce to the nearest O atoms. For Pr and Gd doping, their substitutional energies are similar and close to zero, indicating that both of them may also incorporate into the TiO2 host. For Pr doping, some 4f spin-down states are located next to the bottom of the conduction band and narrow the band gap of the doping system. However, for Gd doping, the 4f states are located in deep valence band and there is no intermediate band in the band gap. The magnetic moment of dopant Gd is close to the value of isolated Gd atom (∼7 μB), indicating no overlapping between Gd 4f with other orbitals. For Eu, it is hard to incorporate into the TiO2 host due to its very higher substitutional energy. The results also indicated that oxygen vacancy defect may enhance the adsorption of the visible light in Ln-doped TiO2 system.

Qiang Sun

Papers

Zn-Doped CdS Nanoarchitectures Prepared by Hydrothermal Synthesis: Mechanism for Enhanced Photocatalytic Activity and Stability under Visible Light

Magnetism of zigzag edge phosphorene nanoribbons

Switching Between Giant Positive and Negative Thermal Expansions of a YFe(CN)6‐based Prussian Blue Analogue Induced by Guest Species

Discovering Large Isotropic Negative Thermal Expansion in Framework Compound AgB(CN)4 via the Concept of Average Atomic Volume.

Electronic properties of anatase TiO2 doped by lanthanides: A DFT+U study