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 6 articles , 1 standard article )
Showing results 1 to 6 of 6.
- O’Hearn, Kurt A.; Alperen, Abdullah; Aktulga, Hasan Metin: Fast solvers for charge distribution models on shared memory platforms (2020)
- Chen, Qiang; Sun, Yu; Wang, Guannan; Pindera, Marek-Jerzy: Finite-volume homogenization and localization of nanoporous materials with cylindrical voids. II: New results (2019)
- Polyakov, S. V.; Podryga, V. O.; Puzyrkov, D. V.: High performance computing in multiscale problems of gas dynamics (2018)
- 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) ioport