A. Omeltchenko et al., Scalable I/O of large-scale molecular dynamics simulations: A data-compression algorithm, COMP PHYS C, 131(1-2), 2000, pp. 78-85
Disk space, input/output (I/O) speed, and data-transfer bandwidth present a
major bottleneck in large-scale molecular dynamics simulations, which requ
ire storing positions and velocities of multimillion atoms. A data compress
ion 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 coordinat
es and using an adaptive, variable-length encoding to handle exceptional va
lues, the I/O size is reduced by an order-of-magnitude with user-controlled
error bound. (C) 2000 Elsevier Science B.V. All rights reserved.