Reactive Molecular Dynamics: Algorithms, Software, and Applications.

Modeling atomic and molecular systems requires computation-intensive
quantum mechanical methods such as, but not limited to, density
functional theory (DFT). These methods have been successful in
predicting various properties of chemical systems at atomistic
detail, albeit at significant computational cost. Classical molecular
dynamics techniques, on the other hand, lack essential chemical
properties such as reactivity and charge transfer. Recently proposed
reactive force fields such as ReaxFF try to achieve essential quantum
properties, while retaining computational simplicity of classical
molecular dynamics.

Implementation of reactive force fields, however, presents
significant algorithmic challenges, including scalable solvers and
specialized preconditioners. In this talk, we present the design
of PuReMD (Purdue Reactive Molecular Dynamics), a unique parallel
reactive molecular dynamics code. We describe various data structures,
the charge equilibration solver at the core of the simulation engine,
and the associated parallel formulations on messaging, single-GPU, and
GPU Cluster platforms. We comprehensively validate the performance
and accuracy of PuReMD on a variety of physical systems and
compute platforms. We show excellent per-timestep time, linear
time scaling in system size, and a low memory footprint. We also
show excellent scaling properties up to thousands of computational cores
and tens of GPUs. PuReMD is available over the public domain and is
currently being used to model diverse systems ranging from
oxidative stress in bio-membranes to strain relaxation in Si-Ge
nanorods.




Speaker Biography:

Ananth Grama is the Director of the Computational Science and Engineering
program and Professor of Computer Science at Purdue University. He also
serves as the Associate Director of the Center for Science of Information.
Ananth received his B. Engg from Indian Institute of Technology, Roorkee (1989),
his M.S. from Wayne State University (1990), and Ph.D. from the University of
Minnesota (1996). His research interests lie in parallel and distributed systems,
numerical methods, large-scale data analysis, and their applications. Ananth
is a recipient of the National Science Foundation CAREER award (1998),
University Faculty Scholar Award (2002-07), and is a Fellow of the American
Association for the Advancement of Sciences (2013).

