Shuji Ogata

Hybrid finite-element/molecular-dynamics/electronic-density-functional approach to materials simulations on parallel computers

A hybrid simulation approach is developed to study chemical reactions coupled with long-range mechanical phenomena in materials. The finite-element method for continuum mechanics is coupled with the molecular dynamics method for an atomic system that embeds a cluster of atoms described quantum-mechanically with the electronic density-functional method based on real-space multigrids. The hybrid simulation approach is implemented on parallel computers using both task and spatial decompositions. Additive hybridization and unified finite-element/molecular-dynamics schemes allow scalable parallel implementation and rapid code development, respectively. A hybrid simulation of oxidation of Si(111) surface demonstrates seamless coupling of the continuum region with the classical and the quantum atomic regions.

Multiscale simulation of nanosystems

The authors describe simulation approaches that seamlessly combine continuum mechanics with atomistic simulations and quantum mechanics. They also discuss computational and visualization issues associated with these simulations on massively parallel computers. Scientists are combining continuum mechanics and atomistic simulations through integrated multidisciplinary efforts so that a single simulation couples diverse length scales. However, the complexity of these hybrid schemes poses an unprecedented challenge, and developments in scalable parallel algorithms as well as interactive and immersive visualization are crucial for their success. This article describes such multiscale simulation approaches and associated computational issues using recent work as an example.

Scalable and portable implementation of the fast multipole method on parallel computers

A scalable and portable Fortran code is developed to calculate Coulomb interaction potentials of charged particles on parallel computers, based on the fast multipole method. The code has a unique feature to calculate microscopic stress tensors due to the Coulomb interactions, which is useful in constant-pressure simulations and local stress analyses. The code is applicable to various boundary conditions, including periodic boundary conditions in two and three dimensions, corresponding to slab and bulk systems, respectively. Numerical accuracy of the code is tested through comparison of its results with those obtained by the Ewald summation method and by direct calculations. Scalability tests show the parallel efficiency of 0.98 for 512 million charged particles on 512 IBM SP3 processors. The timing results on IBM SP3 are also compared with those on IBM SP4.

Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids

A hybrid quantum mechanical/molecular dynamics simulation scheme is developed, in which a quantum mechanical system described by the density functional theory on real-space multigrids is embedded in a classical system of atoms interacting via an empirical interatomic potential. Handshake atoms coupling the quantum and the classical systems are treated by a novel scaled position method. The scheme is implemented on parallel computers using both task and spatial decompositions. An application to oxidation of Si (100) surface demonstrates seamless coupling of the quantum and the classical systems.

Variable-charge interatomic potentials for molecular-dynamics simulations of TiO2

An interatomic potential model has been developed for molecular-dynamics simulations of TiO2 (rutile) based on the formalism of Streitz and Mintmire [J. Adhes. Sci. Technol. 8, 853 (1994)], in which atomic charges vary dynamically according to the generalized electronegativity equalization principle. The present model potential reproduces the vibrational density of states, the pressure-dependent static dielectric constants, the melting temperature, and the surface relaxation of the rutile crystal, as well as the cohesive energy, the lattice constants, and the elastic moduli. We find the physical properties of rutile are significantly affected by dynamic charge transfer between Ti and O atoms. The potential allows us to perform atomistic simulations on nanostructured TiO2 with various kinds of interfaces (surfaces, grain boundaries, dislocations, etc.).

Sustainable adaptive grid supercomputing: multiscale simulation of semiconductor processing across the pacific

We propose a reservation-based sustainable adaptive grid supercomputing paradigm to enable tightly coupled computations of considerable scale (involving over 1,000 processors) and duration (over tens of continuous days) on a grid of geographically distributed parallel supercomputers. The paradigm is demonstrated for an adaptive multiscale simulation application, in which accurate but compute-intensive quantum mechanical (QM) simulations are embedded within a classical molecular dynamics (MD) simulation only when and where high fidelity is required. Key technical innovations include: 1) an embedded divide-and-conquer algorithmic framework to maximally expose data and computation localities for enhanced scalability; 2) a buffered-cluster hybridization scheme to adaptively adjust MD/QM boundaries to maintain the model accuracy; and 3) a hybrid grid remote procedure call (GridRPC) + message passing interface (MPI) grid application framework to combine flexibility (adaptive resource allocation and migration), fault tolerance (automated fault recovery), and efficiency (scalable management of large computing resources). We have achieved an automated execution of multiscale MD/QM simulation on a Grid consisting of 6 supercomputer centers in Japan and the US (in total of 150 thousand processor hours) for the dynamic simulation of implanted oxygen atoms in a silicon substrate, in which the number of processors changes dynamically on demand and resources are allocated and migrated dynamically according to both reservations and unexpected faults. The simulation results reveal a strong dependence of the oxygen penetration depth on the incident oxygen-beam position, which is useful information to further advance SIMOX (separation by implanted oxygen) technique to fabricate high speed and low power-consumption semiconductor devices

Environmental effects of H2O on fracture initiation in silicon: A hybrid electronic-density-functional/molecular-dynamics study

A hybrid quantum-mechanical/molecular-dynamics simulation is performed to study the effects of environmental molecules on fracture initiation in silicon. A (110) crack under tension (mode-I opening) is simulated with multiple H2O molecules around the crack front. Electronic structure near the crack front is calculated with density functional theory. To accurately model the long-range stress field, the quantum-mechanical description is embedded in a large classical molecular-dynamics simulation. The hybrid simulation results show that the reaction of H2O molecules at a silicon crack tip is sensitive to the stress intensity factor K. For K=0.4 MPa⋅m, an H2O molecule either decomposes and adheres to dangling-bond sites on the crack surface or oxidizes Si, resulting in the formation of a Si–O–Si structure. For a higher K value of 0.5 MPa⋅m, an H2O molecule either oxidizes or breaks a Si–Si bond.

Scalable Atomistic Simulation Algorithms for Materials Research

A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD) simulations and quantum-mechanical (QM) calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. The production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

Nuclear reaction rates in dense carbon-oxygen mixtures

New, first principles calculations of nuclear reaction rates in dense carbon-oxygen mixtures appropriate to Type I supernova progenitors are presented for both fluid and bcc crystalline-solid phases, based on accurate Monte Carlo evaluations of the screening potentials and a correct treatment of the quantum-statistical effects. A blocking effect of oxygen is discovered in the pycnonuclear reaction of carbon. The results are compared with the existing theories in the limit of one-component plasma cases, both for the screening potentials and for the reaction rates. Examples of the carbon ignition curve are shown. 25 refs.

Molecular dynamics and Monte Carlo hybrid simulation for fuzzy tungsten nanostructure formation

For the purposes of long-term use of tungsten divertor walls, the formation process of the fuzzy tungsten nanostructure induced by exposure to the helium plasma was studied. In the present paper, the fuzzy nanostructures formation has been successfully reproduced by the new hybrid simulation method in which the deformation of the tungsten material due to pressure of the helium bubbles was simulated by the molecular dynamics and the diffusion of the helium atoms was simulated by the random walk based on the Monte Carlo method. By the simulation results, the surface height of the fuzzy nanostructure increased only when helium retention was under the steady state. It was proven that the growth of the fuzzy nanostructure was brought about by bursting of the helium bubbles. Moreover, we suggest the following key formation mechanisms of the fuzzy nanostructure: (1) lifting in which the surface lifted up by the helium bubble changes into a convexity, (2) bursting by which the region of the helium bubble changes into a concavity, and (3) the difference of the probability of helium retention by which the helium bubbles tend to appear under the concavity. Consequently, the convex-concave surface structure was enhanced and grew to create the fuzzy nanostructure.