Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

Eric J. Bylaska, Jonathan Weare, John H. Weare

Research output: Contribution to journalArticle

Abstract

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t i (trajectory positions and velocities xi = (r i, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0..tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H 2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

Original languageEnglish (US)
Article number074114
JournalJournal of Chemical Physics
Volume139
Issue number7
DOIs
StatePublished - Aug 21 2013

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Quantum chemistry
quantum chemistry
Molecular dynamics
molecular dynamics
simulation
Computer simulation
costs
newton
Trajectories
trajectories
Transmission control protocol
Costs
Internet protocols
Distributed computer systems
Coarsening
integrators
Electronic structure
entry
dynamic models
Dynamic models

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Extending molecular simulation time scales : Parallel in time integrations for high-level quantum chemistry and complex force representations. / Bylaska, Eric J.; Weare, Jonathan; Weare, John H.

In: Journal of Chemical Physics, Vol. 139, No. 7, 074114, 21.08.2013.

Research output: Contribution to journalArticle

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