A special purpose computer for molecular dynamics calculations

Abstract We have constructed a computer facility for interactive study of atomic systems, with fast turnaround between simulation runs. The computer includes a large external memory which is shared by up to 16 parallel processor boards. Each processor board contains four fast floating point chip sets, also operating in parallel. A host computer running the UNIX' operating system is used to assemble and download instructions to the processor boards and to transfer atomic coordinates to the memory. A machine with eight processor boards has a theoretical speed of 182 Mflops, and runs molecular dynmics code 30–100% faster than the in-house supercomputer. The architecture was chosen specifically for applications involving molecular dynamics code, using a new implementation of the algorithm, but it has also been programmed for finite difference calculations. In general, it should be effective for simulations of physical systems that can be subdivided into cells, such that the material of a cell is influenced only by local interactions.

[1]  J. Tersoff,et al.  New empirical approach for the structure and energy of covalent systems. , 1988, Physical review. B, Condensed matter.

[2]  Biswas,et al.  Interatomic potentials for silicon structural energies. , 1985, Physical review letters.

[3]  John R. Ray,et al.  Pulsed laser melting of silicon: A molecular dynamics study , 1987 .

[4]  Aneesur Rahman,et al.  Correlations in the Motion of Atoms in Liquid Argon , 1964 .

[5]  J. Tersoff,et al.  New empirical model for the structural properties of silicon. , 1986, Physical review letters.

[6]  A. F. Bakker,et al.  Molecular dynamics of 16000 Lennard-Jones particles , 1982 .

[7]  Biswas,et al.  Molecular-dynamics simulation of cluster and atom deposition on silicon (111). , 1988, Physical review. B, Condensed matter.

[8]  Broughton,et al.  Pulsed melting of silicon (111) and (100) surfaces simulated by molecular dynamics. , 1986, Physical review letters.

[9]  Robert E. Benner,et al.  Development of Parallel Methods for a $1024$-Processor Hypercube , 1988 .

[10]  George H. Gilmer,et al.  Modeling of epitaxial growth , 1990 .

[11]  R W Hockney,et al.  Computer Simulation Using Particles , 1966 .

[12]  Schuller,et al.  Epitaxial growth of silicon: A molecular-dynamics simulation. , 1987, Physical review. B, Condensed matter.

[13]  Wolfgang J. Paul,et al.  A special purpose parallel computer for molecular dynamics: motivation, design, implementation, and application , 1987 .

[14]  Weber,et al.  Computer simulation of local order in condensed phases of silicon. , 1985, Physical review. B, Condensed matter.

[15]  M. Baskes,et al.  Application of the embedded-atom method to covalent materials: A semiempirical potential for silicon. , 1987, Physical review letters.

[16]  S. Patankar.  Numerical Heat Transfer and Fluid Flow , 2018, Lecture Notes in Mechanical Engineering.

[17]  Jan Kroon,et al.  Molecular-dynamics simulations of β-d-ribose and β-d-deoxyribose solutions , 1989 .