Data Compression for Optimization of a Molecular Dynamics System: Preserving Basins of Attraction
Loading...
Author/Creator
Author/Creator ORCID
Date
2019-06-08
Department
Program
Citation of Original Publication
Retzlaff, Michael; Munson, Todd; Di, Zichao (Wendy); Data Compression for Optimization of a Molecular Dynamics System: Preserving Basins of Attraction; Computational Science – ICCS 2019. ICCS 2019. Lecture Notes in Computer Science, vol 11538. Springer, Cham; https://doi.org/10.1007/978-3-030-22744-9_36
Rights
This item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.
Access to this item will begin on 2020-06-08
Access to this item will begin on 2020-06-08
Abstract
Understanding the evolution of atomistic systems is essential in various fields such as materials science, biology, and chemistry. The gold standard for these calculations is molecular dynamics, which simulates the dynamical interaction between pairs of molecules. The main challenge of such simulation is the numerical complexity, given a vast number of atoms over a long time scale. Furthermore, such systems often contain exponentially many optimal states, and the simulation tends to get trapped in local configurations. Recent developments leverage the existing temporal evolution of the system to improve the stability and
scalability of the method; however, they suffer from large data storage requirements. To efficiently compress the data while retaining the basins of attraction, we have developed a framework to determine the acceptable level of compression for an optimization method by application of a Kantorovich-type theorem, using binary digit rounding as our compression technique. Choosing the Lennard-Jones potential function as a model problem, we present a method for determining the local Lipschitz
constant of the Hessian with low computational cost, thus allowing the use of our technique in real-time computation.