Timothy J. Campbell

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.

Immersive and interactive exploration of billion atom systems

We have developed a visualization system, namedAtomsviewer, to render a billion atoms from the results of a molecular dynamics simulation. This system uses a hierarchical view frustum culling algorithm based on the octree data structure to efficiently remove atoms that are outside of the field of view. A novel occlusion culling algorithm, using a probability function, then selects atoms with a high probability of being visible. These selected atoms are further tested with a traditional occlusion culling algorithm before being rendered as spheres at varying levels of detail. To achieve scalability, Atomsviewer is distributed over a cluster of PCs that execute a parallelized version of the hierarchical view frustum culling and the probabilistic occlusion culling, and a graphics workstation that renders the atoms. We have used Atomsviewer to render a billion-atom data set on a dual processor SGI Onyx2 with an InfiniteReality2 graphics pipeline connected to a four-node PC cluster.

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.

Scalable I/O of large-scale molecular dynamics simulations: A data-compression algorithm

Disk space, input/output (I/O) speed, and data-transfer bandwidth present a major bottleneck in large-scale molecular dynamics simulations, which require storing positions and velocities of multimillion atoms. A data compression algorithm is designed for scalable I/O of molecular dynamics data. The algorithm uses octree indexing and sorts atoms accordingly on the resulting space-filling curve. By storing differences of successive atomic coordinates and using an adaptive, variable-length encoding to handle exceptional values, the I/O size is reduced by an order-of-magnitude with user-controlled error bound.

An adaptive curvilinear-coordinate approach to dynamic load balancing of parallel multiresolution molecular dynamics

Abstract We present a practical experience in adding a dynamic-load-balancing capability to an existing large parallel application — multiresolution molecular dynamics (MRMD) — which is based on uniform mesh decomposition. The new load-balancing scheme uses adaptive curvilinear coordinates to represent partition boundaries. Workloads are partitioned with a uniform 3-dimensional mesh in the curvilinear coordinate system. Simulated annealing is used to determine the optimal coordinate system which minimizes load imbalance and communication costs. The number of messages for performing simulations is minimal because of the underlying regular mesh topology. Periodic boundary conditions are naturally incorporated in the new scheme. Performance of the MRMD algorithm with the new load balancer has been tested for nonuniform multimillion-atom systems.

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%. 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.

Atomistic simulation of nanostructured materials

Materials and devices with microstructures on the nanometer scale are revolutionizing technology, but until recently simulation at this scale has been problematic. The paper considers how developments in parallel computing are now allowing atomistic simulation using multiresolution algorithms, such as fast multipole methods. With these algorithms, researchers may soon be able to simulate applications up to one billion atoms.The International Conference on Computer Design encompasses technical presentations in all fields of the design and implementation of computer systems and their components. ICCDs strength lies in its multidisciplinary character, covering practical and theoretical issues in systems and computer architecture, verification and testing, design and technology, and tools and methodologies. In contrast to most conferences that are specialized in a certain field, ICCD provides an ideal environment for researchers, developers, and students to receive leading-edge information on a wide range of topics related to their own work.

Multimillion atom simulation of materials on parallel computers : nanopixel, interfacial fracture, nanoindentation, and oxidation

We have developed scalable space-time multiresolution algorithms to enable molecular dynamics simulations involving up to a billion atoms on massively parallel computers. Large-scale molecular dynamics simulations have been used to study stress domains and interfacial fracture in semiconductor/dielectric nanopixels, nanoindentation, and oxidation of metallic nanoparticles.

Large-scale atomistic modeling of nanoelectronic structures

Large-scale molecular-dynamics simulations are performed on parallel computers to study critical issues on ultrathin dielectric films and device reliability in next-decade semiconductor devices. New interatomic-potential models based on many-body, reactive, and quantum-mechanical schemes are used to study various atomic-scale effects: growth of oxide layers; dielectric properties of high-permittivity oxides; dislocation activities at semiconductor/dielectric interfaces; effects of amorphous layers and pixellation on atomic-level stresses in lattice-mismatched nanopixels; and nanoindentation testing of thin films. Enabling technologies for 10 to 100 million-atom simulations of nanoelectronic structures are discussed, which include multiresolution algorithms for molecular dynamics, load balancing, and data management. In ten years, this scalable software infrastructure will enable trillion-atom simulations of realistic device structures with sizes well beyond /spl mu/m on petaflop computers.