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

To predict the structures, properties, and chemistry of materials involving silicon and silicon oxides; interfaces between these materials; and hydrolysis of such systems, we have developed the ReaxFFSiO, reactive force field. The parameters for this force field were obtained from fitting to the results of quantum chemical (QC) calculations on the structures and energy barriers for a number of silicon oxide clusters and on the equations of state for condensed phases of Si and SiO2 from QC. We expect that ReaxFFSiO will allow accurate dynamical simulations of bond breaking processes in large silicon and silicon oxide systems. ReaxFFSiO is based closely on the potential functions of the ReaxFFCH reactive force field for hydrocarbons, so that it should also be useful for describing reactions of organics with Si and SiO2 systems.

ReaxFFSiO Reactive Force Field for Silicon and Silicon Oxide Systems

This review is about understanding and controlling organic molecular adsorption on silicon. The goal is to provide a microscopic picture of structure and bonding in covalently attached molecule-silicon surface systems. The bias here is that an unprecedented, detailed understanding of adsorbate-surface structures is required in order to gain the control necessary to incorporate organic function into existing technologies or, eventually, to make new molecule-scale devices. A discussion of recent studies of adsorbate structure is presented. This includes simple alkenes, polyenes, benzene, and carene adsorbed on Si(100). Also included is a discussion of wet chemical procedures for forming alkyl and alkoxy covalently functionalized silicon. These discussions are presented together with comments on the related issues of adsorption dynamics and nano-scale manipulation in an effort to point the way toward principles and procedures that will allow the hybrid properties of organic molecules and surfaces to be harnessed.

Controlled molecular adsorption on silicon: laying a foundation for molecular devices.

Recent investigations have shown that cycloaddition reactions, widely used in organic chemistry to form ring compounds, can also be applied to link organic molecules to the (001) surfaces of crystalline silicon, germanium, and diamond. While these surfaces are comprised of SiSi, GeGe, and CC structural units that resemble the CC bonds of organic alkenes, the rates and mechanisms of the surface reactions show some distinct differences from those of their organic counterparts This article reviews recent studies of [2 + 2], [4 + 2] Diels−Alder, and other cycloaddition reactions of organic molecules with semiconductor surfaces and summarizes the current understanding of the reaction pathways.

Cycloaddition chemistry of organic molecules with semiconductor surfaces.

Toward systematic understanding of diversity of electronic properties in low-dimensional molecular solids.

Interface structures of ${\mathrm{SiO}}_{2}/\mathrm{Si}(001)$ are studied by using the first-principles molecular-dynamics method. Three crystalline phases of the ${\mathrm{SiO}}_{2},$ cristobalite, quartz, and tridymite, are stacked on the Si(001) substrate and are fully relaxed. When the ${\mathrm{SiO}}_{2}$ layer is very thin (\ensuremath{\sim}7 \AA{}), the lowest-energy structure is the tridymite, followed by the quartz phase. As the ${\mathrm{SiO}}_{2}$ layer becomes thicker (\ensuremath{\sim}15 \AA{}), the quartz phase has lower energy than the tridymite phase. The cristobalite phase on Si(001) is unstable due to large lattice mismatch, and transforms into a different crystal structure. No defects appear at the interface after the successive bond breaking and rebonding, but the energy of the resulting structure is the highest irrespective of the thickness. Calculations of the local density of states show that the band-gap change occurs on the ${\mathrm{SiO}}_{2}$ side, resulting in an effective decrease of the oxide thickness by 2--5 \AA{}.

Geometric and electronic structures of Si O 2 / Si ( 001 ) interfaces

First-principles molecular dynamics study of acetylene adsorption on the Si(001) surface

More than 100 oxygen-adsorbed configurations with oxygen coverage of up to two monolayers (ML) were studied through first-principles calculations It was found that oxidation proceeds almost laterally When the coverage exceeds 125 ML, oxygen atoms introduced between the second and third layers are captured at a bridging site in the second layer, generating twofold-coordinated Si atoms Emission of such twofold-coordinated Si atoms leaves weakly bonded Si pairs in the fourth layer When such pairs happen to be generated close to each other, they transform into a chain of Si trimers with one P(b0) center at each end

Takahiro Yamasaki

Papers

Geometric and electronic structures of Si O 2 / Si ( 001 ) interfaces

First-principles molecular dynamics study of acetylene adsorption on the Si(001) surface

Oxidation of the Si(001) surface: lateral growth and formation of P(b0) centers.

First-principles theoretical study of metallic states of DCNQI-(Cu,Ag) systems: Simplicity and variety in complex systems.

Structure and electronic property of Si(100)/SiO 2 interface