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J Chem Theory Comput. 2015 Oct 13;11(10):4644-54. doi: 10.1021/acs.jctc.5b00552. Epub 2015 Sep 29.

Efficient parallel linear scaling construction of the density matrix for Born-Oppenheimer molecular dynamics.

Author information

1
Computer, Computational, and Statistical Sciences Division and ‡Theoretical Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States.

Abstract

We present an algorithm for the calculation of the density matrix that for insulators scales linearly with system size and parallelizes efficiently on multicore, shared memory platforms with small and controllable numerical errors. The algorithm is based on an implementation of the second-order spectral projection (SP2) algorithm [ Niklasson, A. M. N. Phys. Rev. B 2002 , 66 , 155115 ] in sparse matrix algebra with the ELLPACK-R data format. We illustrate the performance of the algorithm within self-consistent tight binding theory by total energy calculations of gas phase poly(ethylene) molecules and periodic liquid water systems containing up to 15,000 atoms on up to 16 CPU cores. We consider algorithm-specific performance aspects, such as local vs nonlocal memory access and the degree of matrix sparsity. Comparisons to sparse matrix algebra implementations using off-the-shelf libraries on multicore CPUs, graphics processing units (GPUs), and the Intel many integrated core (MIC) architecture are also presented. The accuracy and stability of the algorithm are illustrated with long duration Born-Oppenheimer molecular dynamics simulations of 1000 water molecules and a 303 atom Trp cage protein solvated by 2682 water molecules.

PMID:
26574255
DOI:
10.1021/acs.jctc.5b00552

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