Data parallel large-scale molecular dynamics for liquids
- Royal Institute of Technology, Stockholm (Sweden)
- Stockholm Univ. (Sweden)
An efficient data parallel computational scheme is presented for large-scale molecular dynamics (MD) simulations of liquids with short-range interactions. The method is based on decomposition of the simulation cell into equally sized subcells, with the shortest side length equal to the cutoff radius. Inter- and intracell interactions are calculated in a coarse-grained manner. A geometric sorting procedure, based on particle distances to subcell boundaries, is used to minimize the overall computations and the nonproductive communications. Using only nearest-neighbor communications, an efficient scheme is developed for periodic updates of the contents of subcells due to the migration of particles. Special [open quotes]null-particles[close quotes] are introduced, which act as buffers during the periodic updates and allow for a globally uniform algorithm during the calculations. Communication cost is about 7% of the total CPU time. The method is found to be linearly scalable with the number of particles, performing better as the ratio of virtual to physical processors increases. The MD code is written in Fortran 90 and implemented on a CM-200. The overall speed is approximately 5.0 [mu]s per MD step and per particle for 1 million particles and 5.5 [mu]s for 5 million particles. The method should be easily transferred to other massively parallel computers of SIMD and MIMD type. 3 tabs.
- OSTI ID:
- 6138162
- Journal Information:
- International Journal of Quantum Chemistry; (United States), Vol. 46:1; ISSN 0020-7608
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
SUPERCONDUCTIVITY AND SUPERFLUIDITY
LIQUIDS
COMPUTERIZED SIMULATION
ALGORITHMS
DECOMPOSITION
DYNAMICS
FORTRAN
INTERACTIONS
PARALLEL PROCESSING
PARTICLES
CHEMICAL REACTIONS
FLUIDS
MATHEMATICAL LOGIC
MECHANICS
PROGRAMMING
PROGRAMMING LANGUAGES
SIMULATION
665000* - Physics of Condensed Matter- (1992-)