Reactive molecular dynamics: numerical methods and algorithmic techniques. ..In this paper, we present implementation details of sPuReMD (serial Purdue reactive molecular dynamics program), a unique reactive classical MD code. We describe various data structures, and the charge equilibration solver at the core of the simulation engine. This Krylov subspace solver relies on a preconditioner based on incomplete LU factorization with thresholds (ILUT), specially targeted to our application. We comprehensively validate the performance and accuracy of sPuReMD on a variety of hydrocarbon systems. In particular, we show excellent per-time-step time, linear time scaling in system size, and a low memory footprint. sPuReMD is a freely distributed software with GPL and is currently being used to model diverse systems ranging from oxidative stress in biomembranes to strain relaxation in Si-Ge nanorods.
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References in zbMATH (referenced in 3 articles , 1 standard article )
Showing results 1 to 3 of 3.
- Kylasa, S.B.; Aktulga, H.M.; Grama, A.Y.: PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs (2014)
- Aktulga, Hasan Metin; Pandit, Sagar A.; Van Duin, Adri C.T.; Grama, Ananth Y.: Reactive molecular dynamics: numerical methods and algorithmic techniques (2012)
- Aktulga, H.M.; Fogarty, J.C.; Pandit, S.A.; Grama, A.Y.: Parallel reactive molecular dynamics: numerical methods and algorithmic techniques (2012)