Efficient particle labeling in atomistic simulations.
The authors develop an efficient particle labeling procedure based on a linked cell algorithm which is shown to reduce the computing time for a molecular dynamics simulation by a factor of 3. They prove that the improvement of performance is due to the efficient fulfillment of both spatial and temporal locality principles, as implemented by the contiguity of labels corresponding to interacting atoms. Finally, they show that the present label reordering procedure can be used to devise an efficient parallel one-dimensional domain decomposition molecular dynamics scheme.
Meloni
Simone
S
Consorzio per le Applicazioni del Supercalcolo Per Università e Ricerca, Via dei Tizii 6/b, Rome, Italy. meloni@caspur.it
Rosati
Mario
M
Colombo
Luciano
L