Idempotent permutations

Together with a characteristic function, idempotent permutations uniquely determine idempotent maps, as well as their linearly ordered arrangement simultaneously. Furthermore, in-place linear time transformations are possible between them. Hence, they may be important for succinct data structures, information storing, sorting and searching. In this study, their combinatorial interpretation is given and their application on sorting is examined. Given an array of n integer keys each in [1,n], if it is allowed to modify the keys in the range [-n,n], idempotent permutations make it possible to obtain linearly ordered arrangement of the keys in O(n) time using only 4log(n) bits, setting the theoretical lower bound of time and space complexity of sorting. If it is not allowed to modify the keys out of the range [1,n], then n+4log(n) bits are required where n of them is used to tag some of the keys.Comment: 32 page

Improved neighbor list algorithm in molecular simulations using cell decomposition and data sorting method

An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition approach to accelerate the neighbor list construction speed, and data sorting method to lower the CPU data cache miss rate, as well as partial updating method to minimize the unnecessary reconstruction of the neighbor list. Both serial and parallel performance of molecular dynamics simulation are evaluated using the proposed algorithm and compared with those using conventional Verlet table and cell linked list algorithms. Results show that the new algorithm outperforms the conventional algorithms by a factor of 2~3 in cases of both small and large number of atoms.Comment: 14 pages, 7 figures. Submitted to Computer Physics Communication

Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatial-decomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.Comment: 33 pages, 19 figures, add references and figures are revise