Patent ID: 7885796
Filing Date: 2011-02-08
Classification: G06F

Abstract:
1. A parallel computing method for executing calculation of the Hartree-Fock method in a molecular orbital method for a target molecule of a biological material, comprising the steps of: using a computer cluster made up of a plurality of computers and a communication device coupled to said plurality of computers, each of said plurality of computers comprising a matrix storage having a memory capacity which is insufficient to store whole matrices used in Hartree-Fock calculation; dividing a density matrix, which is defined by molecular orbital coefficients of the target molecule, into multiple density submatrixes and distributing the multiple density submatrixes to the multiple computers and storing the distributed multiple density matrixes in the respective matrix storages; executing, in parallel in the plurality of the computers, calculation processes including two-electron integrations on the density submatrixes stored in the matrix storages of the respective computers to update the stored density submatrixes based on the result of the two-election integration; and in each of the computers sequentially transferring the density submatrixes stored in the matrix storage to one of other computers according to order of transfer via said communication device, and storing the density submatrixes, which are transferred thereto via said communication device, in the matrix storage, wherein the executing and transferring steps are repeated at the number of times which corresponds to the number of the computers to subject all of the density submatrixes to the calculation processes by sequentially transferring the density submatrixes between the computers, and a Fock matrix of the target molecule is obtained by adding an H-core matrix to the combination of resultant submatrixes stored in said matrix storages of said plurality of computers.