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Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

Authors: Lipparini, Filippo; Lagardère, Louis; Stamm, Benjamin; Cancès, Eric; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; +1 Authors

Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

Abstract

In this paper, we investigate various numerical strategies to compute the direct space polarization energy and associated forces in the context of the point dipole approximation (including damping) used in polarizable molecular dynamics. We present a careful mathematical analysis of the algorithms that have been implemented in popular production packages and applied to large test systems. We show that the classical Jacobi Over-Relaxation method (JOR) should not be used as its convergence requires a proper value of the relaxation parameter, whereas other strategies should be preferred. On a single node, Preconditioned Conjugate Gradient methods (PCG) and Jacobi algorithm coupled with the Direct Inversion in the Iterative Subspace (JI/DIIS) provide reliable stability/convergence and are roughly twice as fast as JOR. Moreover, both algorithms are suitable for massively parallel implementations. The lower requirements in terms of processes communications make JI/DIIS the method of choice for MPI and hybrid Op...

Keywords

[CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry, [CHIM] Chemical Sciences, Computer Science Applications1707 Computer Vision and Pattern Recognition; Physical and Theoretical Chemistry

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
74
Top 10%
Top 10%
Top 1%
bronze